From bdslipun at gmail.com  Mon Jan  2 05:51:36 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Mon, 2 Jan 2012 10:21:36 +0530
Subject: [Pw_forum] Fwd: beta tin structure
In-Reply-To: <CAJVAAvD=rcTA2+85vM3yL5ODqP7h_ztqS-RNbZSK-=XWtsd09A@mail.gmail.com>
References: <CAJVAAvD=rcTA2+85vM3yL5ODqP7h_ztqS-RNbZSK-=XWtsd09A@mail.gmail.com>
Message-ID: <CAJVAAvCA5bKCMceWRWt-K+QGXTHf4Jo8VFtejaJnF2NNuJmvWQ@mail.gmail.com>

---------- Forwarded message ----------
From: bhabya sahoo <bdslipun at gmail.com>
Date: Thu, Dec 29, 2011 at 11:04 AM
Subject: beta tin structure
To: PWSCF Forum <pw_forum at pwscf.org>


i want the phonon dispersion curve for beta tin structure
so i gave the positions of atoms as primitive tetragonal structure having
coordinates
0 0 0,
.5 0 .25 ,
.5 .5 .5,
 0 .5 .75
like 4a whychoff positions (c/a=.546)
so no of atoms is 4 in the unit cell so in phonon there will be 12 branches
but i have seen 6 branches so how can i put my primitive tetragonal
structure having two atoms in unitcell
or in other way how can i give the input for beta tin structure






b d sahoo
reserch scholar
mumbai
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From eiklm at mail.ru  Mon Jan  2 09:40:17 2012
From: eiklm at mail.ru (=?UTF-8?B?0JPRgNC40YjQsCDQk9C+0L3Rh9Cw0YDQvtCy0YHQutC40Lk=?=)
Date: Mon, 02 Jan 2012 12:40:17 +0400
Subject: [Pw_forum] =?utf-8?q?Negative_phonon_frequencies_in_SiO=5F2?=
Message-ID: <E1RhdRK-0008RQ-00.eiklm-mail-ru@f202.mail.ru>

Dear QE users,

I attempt to calculate phonon dispersion in alpha-quartz and keep getting the wrong result. Optical branches look rather plausible, but acoustic branches include some negative frequencies, moreover, one branch seems to be negative in the whole Brillouin zone. I tried to use different pseudopotentials, to select different q-grids, ecutwfc and ecutrho values, but result remains the same.
My scf input:

&control
    calculation='scf',
    restart_mode='from_scratch',
    prefix='sio2',
    pseudo_dir = '/home/grysha/espresso/pseudo/',
    outdir='/home/grysha/espresso/tmp/'
 /
 &system
    ibrav=4,
    celldm(1)=9.289897331,
    celldm(3)=1.099552482,
    nat=  9, ntyp= 2,
    ecutwfc = 20.0
    ecutrho = 150.0
 /
 &electrons
    electron_maxstep=1000
    mixing_mode = 'plain'
    mixing_beta = 0.7
    conv_thr =  1.0d-8
 /
ATOMIC_SPECIES
 Si  28.086  Si.pz-vbc.UPF
 O   15.999  O.pz-rrkjus.UPF
ATOMIC_POSITIONS crystal
 Si   0.46990000   0.00000000   0.66666667
 Si   0.00000000   0.46990000   0.33333333
 Si  -0.46990000  -0.46990000   0.00000000
 O    0.41410000   0.26810000   0.78540000
 O   -0.26810000   0.14600000   0.45206667
 O   -0.14600000  -0.41410000   0.11873333
 O    0.26810000   0.41410000  -0.78540000
 O   -0.41410000  -0.14600000  -0.11873333
 O    0.14600000  -0.26810000  -0.45206667
K_POINTS automatic
4 4 4 0 0 0

Phonon input:

phonons of SiO_2
 &inputph
  tr2_ph=1.0d-12,
  prefix='sio2',
  ldisp=.true.,
  nq1=4, nq2=4, nq3=4
  amass(1)=28.086,
  amass(2)=15.999,
  outdir='/home/grysha/espresso/tmp',
  fildyn='sio2.dynFull',
 /

q2r input:

&input
   fildyn='sio2.dynFull', zasr='simple', flfrc='sio2444.fc'
 /


Trying to calculate dispersion e.g. along the Gamma --- A line with such input

&input
    asr='simple',  amass(1)=28.086, amass(2)=15.999,
    flfrc='sio2444.fc', flfrq='sio2.freq'
 /
 11
  0.0 0.0 0.000000  0.0
  0.0 0.0 0.0866025  0.0
  0.0 0.0 0.173205  0.0
  0.0 0.0 0.259808  0.0
  0.0 0.0 0.346410  0.0
  0.0 0.0 0.433013  0.0
  0.0 0.0 0.519615  0.0
  0.0 0.0 0.606218  0.0
  0.0 0.0 0.692820  0.0
  0.0 0.0 0.779423  0.0
  0.0 0.0 0.866025  0.0

I obtain in the sio2.freq file

&plot nbnd=  27, nks=  11 /
            0.000000  0.000000  0.000000
   -3.9029   -1.6909   -0.9482   55.4410   58.8549  184.0277
  232.6261  232.8523  328.4843  362.4152  372.6477  373.7721
  424.6636  425.2693  446.6598  518.9579  681.4918  682.2090
  775.2395  775.6317  778.7409 1081.8532 1082.0740 1096.3594
 1172.6020 1172.7318 1231.8798
            0.000000  0.000000  0.086602
  -27.8791  -24.0601   34.3374   57.7231   79.0905  185.5367
  222.9925  242.2063  317.0109  365.2996  371.2517  382.6987
  418.6292  430.0279  445.5397  521.3980  655.6902  706.8253
  771.8412  778.2792  779.1211 1079.7256 1084.3283 1096.2590
 1161.7487 1183.7450 1233.8392
            0.000000  0.000000  0.173205
  -42.4501   -9.1280   61.2822   73.4236  100.4741  191.4075
  214.2298  250.4044  293.9354  359.5278  385.7910  392.7004
  412.1738  433.0018  442.8980  527.3652  629.0604  729.1692
  768.1371  779.8632  780.1202 1077.7929 1086.6829 1095.9627
 1152.2769 1193.5893 1237.5794
            0.000000  0.000000  0.259808
  -52.8832   51.6657   77.3462   97.0335  116.7849  202.2120
  207.1785  255.6953  266.4743  356.9882  398.4107  401.5138
  405.7037  434.3569  440.0324  534.6626  602.8471  747.0288
  764.9138  780.6564  780.8533 1076.3172 1088.9413 1095.4574
 1144.7947 1202.0362 1238.6139
            0.000000  0.000000  0.346410
  -58.6717   74.3589   85.0705  128.2999  130.9468  201.2035
  208.4521  243.0812  255.8998  358.7639  398.8673  406.8712
  407.6452  435.0435  437.8321  542.7959  579.1644  758.8697
  762.7038  780.9131  781.1744 1075.3784 1091.0091 1094.6777
 1139.5788 1210.4478 1234.1293
            0.000000  0.000000  0.433013
  -60.8276   83.9302   87.2635  134.9317  167.8644  185.4667
  197.4218  245.0537  249.7366  362.0234  393.8809  410.1527
  410.7431  435.4336  436.7230  553.4463  560.5617  761.4133
  764.3324  781.0491  781.1413 1074.9821 1092.7449 1093.5520
 1137.1544 1220.0745 1225.2006
            0.000000  0.000000  0.519615
  -60.1379   80.5518   86.7839  132.6697  149.3933  198.7177
  200.3888  241.4125  253.5269  360.6371  395.7978  409.1896
  409.5822  435.2824  437.1175  547.6607  569.0894  761.4928
  762.8666  780.9771  781.1909 1075.1131 1091.9347 1094.1553
 1137.9753 1215.1177 1230.0095
            0.000000  0.000000  0.606218
  -56.3113   65.0439   82.0152  112.8013  123.3145  204.0657
  207.4619  252.7666  256.6986  357.3738  402.2872  403.2411
  404.9860  434.7431  438.8123  538.5747  590.4774  753.7985
  763.6404  780.8314  781.0603 1075.7777 1090.0095 1095.1065
 1141.8689 1206.1496 1237.0771
            0.000000  0.000000  0.692820
  -48.3077   33.4208   70.6393   84.0546  109.2574  196.4080
  210.5025  253.5698  280.4439  357.7446  392.5521  397.3795
  408.9672  433.8191  441.4193  530.9458  615.7606  738.7961
  766.4268  780.3237  780.5636 1076.9885 1087.8329 1095.7382
 1148.2613 1197.9403 1238.6959
            0.000000  0.000000  0.779423
  -35.4182  -25.8479   49.1690   64.6900   90.4259  187.7989
  218.3935  246.5521  306.2412  362.0995  378.5373  387.7484
  415.3698  431.7777  444.3207  524.1062  642.3589  718.4768
  769.9587  779.2468  779.5653 1078.7078 1085.5161 1096.1347
 1156.7679 1188.8888 1235.7641
            0.000000  0.000000  0.866025
  -17.2456  -13.7809   17.5251   53.9027   67.3275  184.3786
  227.8145  237.5840  325.1353  365.1032  368.9991  377.8392
  421.8521  427.7529  446.3640  519.5984  668.8173  694.5999
  773.6796  776.9999  778.8399 1080.8109 1083.1472 1096.3340
 1167.0735 1178.3041 1232.4106

Single-phonon calculation at the A point also gives some negative frequencies:

     omega(  1 -  1) =        -96.6  [cm-1]   --> A                  
     omega(  2 -  2) =        -69.9  [cm-1]   --> A                  
     omega(  3 -  3) =        -52.9  [cm-1]   --> A                  
     omega(  4 -  4) =        -25.6  [cm-1]   --> A                  
     omega(  5 -  5) =        -13.8  [cm-1]   --> A                  
     omega(  6 -  6) =        169.3  [cm-1]   --> A                  
     omega(  7 -  7) =        218.6  [cm-1]   --> A                  
     omega(  8 -  8) =        227.9  [cm-1]   --> A                  
     omega(  9 -  9) =        318.1  [cm-1]   --> A                  
     omega( 10 - 10) =        360.1  [cm-1]   --> A                  
     omega( 11 - 11) =        362.7  [cm-1]   --> A                  
     omega( 12 - 12) =        371.0  [cm-1]   --> A                  
     omega( 13 - 13) =        412.5  [cm-1]   --> A                  
     omega( 14 - 14) =        419.1  [cm-1]   --> A                  
     omega( 15 - 15) =        441.1  [cm-1]   --> A                  
     omega( 16 - 16) =        524.0  [cm-1]   --> A                  
     omega( 17 - 17) =        668.1  [cm-1]   --> A                  
     omega( 18 - 18) =        694.6  [cm-1]   --> A                  
     omega( 19 - 19) =        773.0  [cm-1]   --> A                  
     omega( 20 - 20) =        776.0  [cm-1]   --> A                  
     omega( 21 - 21) =        779.8  [cm-1]   --> A                  
     omega( 22 - 22) =       1078.2  [cm-1]   --> A                  
     omega( 23 - 23) =       1080.8  [cm-1]   --> A                  
     omega( 24 - 24) =       1094.3  [cm-1]   --> A                  
     omega( 25 - 25) =       1165.6  [cm-1]   --> A                  
     omega( 26 - 26) =       1175.8  [cm-1]   --> A                  
     omega( 27 - 27) =       1244.2  [cm-1]   --> A       

but I wonder that positive frequencies in these two cases are not significantly different.
Where should I dig to avoid instability? I would be grateful for any suggestion!

Regards

Mikhail Goncharovski

From iyad.ne at gmail.com  Mon Jan  2 16:33:02 2012
From: iyad.ne at gmail.com (IYAD AL-QASIR)
Date: Mon, 2 Jan 2012 10:33:02 -0500
Subject: [Pw_forum] Negative phonon frequencies in SiO_2
In-Reply-To: <E1RhdRK-0008RQ-00.eiklm-mail-ru@f202.mail.ru>
References: <E1RhdRK-0008RQ-00.eiklm-mail-ru@f202.mail.ru>
Message-ID: <CAJMDj42PUr+qkqwLr_ysSKatyM5mUF39AKytC9gQKUeDOt=ang@mail.gmail.com>

Hello,
I have a suggestion that might help, since we experienced this problem
before.
Try to relax the structure, and especially the* atomic positions* before
you start phonon calculations.
Based on your optimization results also you will have better idea about
your PP choices.

Good Luck
IYAD

2012/1/2 ????? ???????????? <eiklm at mail.ru>

> Dear QE users,
>
> I attempt to calculate phonon dispersion in alpha-quartz and keep getting
> the wrong result. Optical branches look rather plausible, but acoustic
> branches include some negative frequencies, moreover, one branch seems to
> be negative in the whole Brillouin zone. I tried to use different
> pseudopotentials, to select different q-grids, ecutwfc and ecutrho values,
> but result remains the same.
> My scf input:
>
> &control
>    calculation='scf',
>    restart_mode='from_scratch',
>    prefix='sio2',
>    pseudo_dir = '/home/grysha/espresso/pseudo/',
>    outdir='/home/grysha/espresso/tmp/'
>  /
>  &system
>    ibrav=4,
>    celldm(1)=9.289897331,
>    celldm(3)=1.099552482,
>    nat=  9, ntyp= 2,
>    ecutwfc = 20.0
>    ecutrho = 150.0
>  /
>  &electrons
>    electron_maxstep=1000
>    mixing_mode = 'plain'
>    mixing_beta = 0.7
>    conv_thr =  1.0d-8
>  /
> ATOMIC_SPECIES
>  Si  28.086  Si.pz-vbc.UPF
>  O   15.999  O.pz-rrkjus.UPF
> ATOMIC_POSITIONS crystal
>  Si   0.46990000   0.00000000   0.66666667
>  Si   0.00000000   0.46990000   0.33333333
>  Si  -0.46990000  -0.46990000   0.00000000
>  O    0.41410000   0.26810000   0.78540000
>  O   -0.26810000   0.14600000   0.45206667
>  O   -0.14600000  -0.41410000   0.11873333
>  O    0.26810000   0.41410000  -0.78540000
>  O   -0.41410000  -0.14600000  -0.11873333
>  O    0.14600000  -0.26810000  -0.45206667
> K_POINTS automatic
> 4 4 4 0 0 0
>
> Phonon input:
>
> phonons of SiO_2
>  &inputph
>  tr2_ph=1.0d-12,
>  prefix='sio2',
>  ldisp=.true.,
>  nq1=4, nq2=4, nq3=4
>  amass(1)=28.086,
>  amass(2)=15.999,
>  outdir='/home/grysha/espresso/tmp',
>  fildyn='sio2.dynFull',
>  /
>
> q2r input:
>
> &input
>   fildyn='sio2.dynFull', zasr='simple', flfrc='sio2444.fc'
>  /
>
>
> Trying to calculate dispersion e.g. along the Gamma --- A line with such
> input
>
> &input
>    asr='simple',  amass(1)=28.086, amass(2)=15.999,
>    flfrc='sio2444.fc', flfrq='sio2.freq'
>  /
>  11
>  0.0 0.0 0.000000  0.0
>  0.0 0.0 0.0866025  0.0
>  0.0 0.0 0.173205  0.0
>  0.0 0.0 0.259808  0.0
>  0.0 0.0 0.346410  0.0
>  0.0 0.0 0.433013  0.0
>  0.0 0.0 0.519615  0.0
>  0.0 0.0 0.606218  0.0
>  0.0 0.0 0.692820  0.0
>  0.0 0.0 0.779423  0.0
>  0.0 0.0 0.866025  0.0
>
> I obtain in the sio2.freq file
>
> &plot nbnd=  27, nks=  11 /
>            0.000000  0.000000  0.000000
>   -3.9029   -1.6909   -0.9482   55.4410   58.8549  184.0277
>  232.6261  232.8523  328.4843  362.4152  372.6477  373.7721
>  424.6636  425.2693  446.6598  518.9579  681.4918  682.2090
>  775.2395  775.6317  778.7409 1081.8532 1082.0740 1096.3594
>  1172.6020 1172.7318 1231.8798
>            0.000000  0.000000  0.086602
>  -27.8791  -24.0601   34.3374   57.7231   79.0905  185.5367
>  222.9925  242.2063  317.0109  365.2996  371.2517  382.6987
>  418.6292  430.0279  445.5397  521.3980  655.6902  706.8253
>  771.8412  778.2792  779.1211 1079.7256 1084.3283 1096.2590
>  1161.7487 1183.7450 1233.8392
>            0.000000  0.000000  0.173205
>  -42.4501   -9.1280   61.2822   73.4236  100.4741  191.4075
>  214.2298  250.4044  293.9354  359.5278  385.7910  392.7004
>  412.1738  433.0018  442.8980  527.3652  629.0604  729.1692
>  768.1371  779.8632  780.1202 1077.7929 1086.6829 1095.9627
>  1152.2769 1193.5893 1237.5794
>            0.000000  0.000000  0.259808
>  -52.8832   51.6657   77.3462   97.0335  116.7849  202.2120
>  207.1785  255.6953  266.4743  356.9882  398.4107  401.5138
>  405.7037  434.3569  440.0324  534.6626  602.8471  747.0288
>  764.9138  780.6564  780.8533 1076.3172 1088.9413 1095.4574
>  1144.7947 1202.0362 1238.6139
>            0.000000  0.000000  0.346410
>  -58.6717   74.3589   85.0705  128.2999  130.9468  201.2035
>  208.4521  243.0812  255.8998  358.7639  398.8673  406.8712
>  407.6452  435.0435  437.8321  542.7959  579.1644  758.8697
>  762.7038  780.9131  781.1744 1075.3784 1091.0091 1094.6777
>  1139.5788 1210.4478 1234.1293
>            0.000000  0.000000  0.433013
>  -60.8276   83.9302   87.2635  134.9317  167.8644  185.4667
>  197.4218  245.0537  249.7366  362.0234  393.8809  410.1527
>  410.7431  435.4336  436.7230  553.4463  560.5617  761.4133
>  764.3324  781.0491  781.1413 1074.9821 1092.7449 1093.5520
>  1137.1544 1220.0745 1225.2006
>            0.000000  0.000000  0.519615
>  -60.1379   80.5518   86.7839  132.6697  149.3933  198.7177
>  200.3888  241.4125  253.5269  360.6371  395.7978  409.1896
>  409.5822  435.2824  437.1175  547.6607  569.0894  761.4928
>  762.8666  780.9771  781.1909 1075.1131 1091.9347 1094.1553
>  1137.9753 1215.1177 1230.0095
>            0.000000  0.000000  0.606218
>  -56.3113   65.0439   82.0152  112.8013  123.3145  204.0657
>  207.4619  252.7666  256.6986  357.3738  402.2872  403.2411
>  404.9860  434.7431  438.8123  538.5747  590.4774  753.7985
>  763.6404  780.8314  781.0603 1075.7777 1090.0095 1095.1065
>  1141.8689 1206.1496 1237.0771
>            0.000000  0.000000  0.692820
>  -48.3077   33.4208   70.6393   84.0546  109.2574  196.4080
>  210.5025  253.5698  280.4439  357.7446  392.5521  397.3795
>  408.9672  433.8191  441.4193  530.9458  615.7606  738.7961
>  766.4268  780.3237  780.5636 1076.9885 1087.8329 1095.7382
>  1148.2613 1197.9403 1238.6959
>            0.000000  0.000000  0.779423
>  -35.4182  -25.8479   49.1690   64.6900   90.4259  187.7989
>  218.3935  246.5521  306.2412  362.0995  378.5373  387.7484
>  415.3698  431.7777  444.3207  524.1062  642.3589  718.4768
>  769.9587  779.2468  779.5653 1078.7078 1085.5161 1096.1347
>  1156.7679 1188.8888 1235.7641
>            0.000000  0.000000  0.866025
>  -17.2456  -13.7809   17.5251   53.9027   67.3275  184.3786
>  227.8145  237.5840  325.1353  365.1032  368.9991  377.8392
>  421.8521  427.7529  446.3640  519.5984  668.8173  694.5999
>  773.6796  776.9999  778.8399 1080.8109 1083.1472 1096.3340
>  1167.0735 1178.3041 1232.4106
>
> Single-phonon calculation at the A point also gives some negative
> frequencies:
>
>     omega(  1 -  1) =        -96.6  [cm-1]   --> A
>     omega(  2 -  2) =        -69.9  [cm-1]   --> A
>     omega(  3 -  3) =        -52.9  [cm-1]   --> A
>     omega(  4 -  4) =        -25.6  [cm-1]   --> A
>     omega(  5 -  5) =        -13.8  [cm-1]   --> A
>     omega(  6 -  6) =        169.3  [cm-1]   --> A
>     omega(  7 -  7) =        218.6  [cm-1]   --> A
>     omega(  8 -  8) =        227.9  [cm-1]   --> A
>     omega(  9 -  9) =        318.1  [cm-1]   --> A
>     omega( 10 - 10) =        360.1  [cm-1]   --> A
>     omega( 11 - 11) =        362.7  [cm-1]   --> A
>     omega( 12 - 12) =        371.0  [cm-1]   --> A
>     omega( 13 - 13) =        412.5  [cm-1]   --> A
>     omega( 14 - 14) =        419.1  [cm-1]   --> A
>     omega( 15 - 15) =        441.1  [cm-1]   --> A
>     omega( 16 - 16) =        524.0  [cm-1]   --> A
>     omega( 17 - 17) =        668.1  [cm-1]   --> A
>     omega( 18 - 18) =        694.6  [cm-1]   --> A
>     omega( 19 - 19) =        773.0  [cm-1]   --> A
>     omega( 20 - 20) =        776.0  [cm-1]   --> A
>     omega( 21 - 21) =        779.8  [cm-1]   --> A
>     omega( 22 - 22) =       1078.2  [cm-1]   --> A
>     omega( 23 - 23) =       1080.8  [cm-1]   --> A
>     omega( 24 - 24) =       1094.3  [cm-1]   --> A
>     omega( 25 - 25) =       1165.6  [cm-1]   --> A
>     omega( 26 - 26) =       1175.8  [cm-1]   --> A
>     omega( 27 - 27) =       1244.2  [cm-1]   --> A
>
> but I wonder that positive frequencies in these two cases are not
> significantly different.
> Where should I dig to avoid instability? I would be grateful for any
> suggestion!
>
> Regards
>
> Mikhail Goncharovski
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
_______________________________
IYAD I. AL-QASIR, PhD
Research Associate

Department of Nuclear Engineering
North Carolina State University
Campus Box 7909
2500 Stinson Dr.
Raleigh, NC 27695-7909
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From jun.physics at gmail.com  Tue Jan  3 18:42:52 2012
From: jun.physics at gmail.com (Jun Liu)
Date: Tue, 3 Jan 2012 11:42:52 -0600
Subject: [Pw_forum] how to treat free electron gas,
	especially how to setup input file
Message-ID: <CA+1PuT9ps1t350_642je9DNNytNVBN7zqRmu5NaZCMKCzYG6ew@mail.gmail.com>

Dear All,

Let me wish all of you a Happy New Year first.

Maybe this is a very fundamental problem, but I cannot google any hint
online, so here I am. I would like to work out a free electron gas problem
with QE. I know total number of charges, and the size of the box the
electrons move in and probably periodic b.c. applied to it. Now how can I
possibly set up the input file for it? It seems many fundamentional
properties of a lattice do not come with free electron gas. The code itself
should be well-defined for a lattice system, so how is the code adapted to
the free electron problem?

Thank you very much,

Sincerely,
Jun Liu
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From samolyuk at gmail.com  Tue Jan  3 20:10:41 2012
From: samolyuk at gmail.com (German Samolyuk)
Date: Tue, 3 Jan 2012 14:10:41 -0500
Subject: [Pw_forum] pwscf: constrained total magnetic moment
Message-ID: <CAGGYvC0f=kRzAQ=6s0U_EO67L8waSPowi3ZbR3K5kjqUUz+=cg@mail.gmail.com>

Dear all,

I do self-consistent calculation of supercell with 135 Fe atoms with
constrained magnetization.

nspin = 2,
fixed_magnetization(3) = 360.0,
constrained_magnetization = 'total' ,

The output value of magnetic field:

   Magnetic field            =   0.0785401 Ry


In order to make a rough estimation of corresponding magnetic field in
Tesla I should divide this value by mu_B and difference between
total magnetic moments of system with constrain and without it?

Thank you

German Samolyuk
Oak Rigde National Laboratory

From trambui at u.boisestate.edu  Tue Jan  3 22:51:25 2012
From: trambui at u.boisestate.edu (Tram Bui)
Date: Tue, 3 Jan 2012 14:51:25 -0700
Subject: [Pw_forum] error on the pseudo wavefunction
Message-ID: <CANzxBn9x6OzUhQMkdYr12nD70x_7W0AdoAXjd3PK6X0uvAnJcA@mail.gmail.com>

Dear Everyone,
     I ran a ld1.x calculation with the following input file. And for the
output, the ld1ps.wfc file, I got a similar results for both the 5s and 6s
pseudo wavefunction which is not correct.  Would anyone please give me a
suggestion on what might have been the reason? here is the input file I
used:

 &input
     title='Cs',
     zed=55.0,
     iswitch=3,
     rel=1,
     dft='PBE',
     config='[Kr] 4d10 5s2 5p6 6s1 ',

     rlderiv=4.30,
     eminld=-8.0,
     emaxld=3.0,
     deld=0.01d0,
     nld=3,
/
 &inputp
     lloc=0,
     pseudotype=3,
     rho0=0.01,
     file_pseudopw='Cs.uspp-tb.UPF'
/
4
6S 1 0 1.00 0.00 4.30 4.50
6S 1 0 0.00 0.10 4.00 4.50
5P 2 1 6.00 0.00 1.60 1.60
5S 1 0 2.00 0.00 1.40 1.40

Regards,

Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From Ari.P.Seitsonen at iki.fi  Tue Jan  3 23:09:19 2012
From: Ari.P.Seitsonen at iki.fi (Ari P Seitsonen)
Date: Tue, 3 Jan 2012 23:09:19 +0100 (CET)
Subject: [Pw_forum] error on the pseudo wavefunction
In-Reply-To: <CANzxBn9x6OzUhQMkdYr12nD70x_7W0AdoAXjd3PK6X0uvAnJcA@mail.gmail.com>
References: <CANzxBn9x6OzUhQMkdYr12nD70x_7W0AdoAXjd3PK6X0uvAnJcA@mail.gmail.com>
Message-ID: <alpine.LNX.2.00.1201032303580.17286@pcihpc19.uzh.ch>


Dear Tram Bui,

   Shouldn't you increase the value of 'nns' for the wave functions that 
you want to become 6s-like? This is what I have understood:

  6S 2 0 1.00 0.00 4.30 4.50
  6S 2 0 0.00 0.10 4.00 4.50
  5P 2 1 6.00 0.00 1.60 1.60
  5S 1 0 2.00 0.00 1.40 1.40

The first column is "just" a label, the second one the principal quantum 
number of the _pseudo_ atom: "1 0" in the second and third column means 
node-less s wave function (like 1s of hydrogen), "2 0" has one node (like 
2s of Li), "2 1" is the node-less p wave function (like 2p of oxygen), 
etc.

   Hopefully this helps.

     Greetings from Zurich (and Happy New Year to every one),

        apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
   Physikalisch-Chemisches Institut der Universitaet Zuerich
   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935


On Tue, 3 Jan 2012, Tram Bui wrote:

> Dear Everyone,
> ???? I ran a ld1.x calculation with the following input file. And for the
> output, the ld1ps.wfc file, I got a similar results for both the 5s and 6s
> pseudo wavefunction which is not correct.? Would anyone please give me a
> suggestion on what might have been the reason? here is the input file I
> used:
> ???
> ?&input
> ???? title='Cs',
> ???? zed=55.0,
> ???? iswitch=3,
> ???? rel=1,
> ???? dft='PBE',
> ???? config='[Kr] 4d10 5s2 5p6 6s1 ',
> 
> ???? rlderiv=4.30,
> ???? eminld=-8.0,
> ???? emaxld=3.0,
> ???? deld=0.01d0,
> ???? nld=3,
> /
> ?&inputp
> ???? lloc=0,
> ???? pseudotype=3,
> ???? rho0=0.01,
> ???? file_pseudopw='Cs.uspp-tb.UPF'
> /
> 4
> 6S 1 0 1.00 0.00 4.30 4.50
> 6S 1 0 0.00 0.10 4.00 4.50
> 5P 2 1 6.00 0.00 1.60 1.60
> 5S 1 0 2.00 0.00 1.40 1.40
> 
> Regards,
> ?
> Tram Bui
> 
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>

From trambui at u.boisestate.edu  Tue Jan  3 23:33:48 2012
From: trambui at u.boisestate.edu (Tram Bui)
Date: Tue, 3 Jan 2012 15:33:48 -0700
Subject: [Pw_forum] error on the pseudo wavefunction
In-Reply-To: <alpine.LNX.2.00.1201032303580.17286@pcihpc19.uzh.ch>
References: <CANzxBn9x6OzUhQMkdYr12nD70x_7W0AdoAXjd3PK6X0uvAnJcA@mail.gmail.com>
	<alpine.LNX.2.00.1201032303580.17286@pcihpc19.uzh.ch>
Message-ID: <CANzxBn_CziSS4zizqG8yJeEUHWijpr6QFEDGU0Vp7-BfgdQfvQ@mail.gmail.com>

Dear Zurich,
    Thank you very much for your respond. I tried the configuration you
suggested and it gave me an error saying :
from run_pseudo : error #         1
     Errors in PS-KS equation
 I think it should be 1 for "nns" of the 6s states. But I actually don't
have much background on the whole pseudo potential thing, so I don't know
what cause the 6s and 5s pseudo wavefunction turned out to be the same on
my ld1ps.wfc output file. Would it be something else in my input file?

I really appreciate all the helps,
Tram
On Tue, Jan 3, 2012 at 3:09 PM, Ari P Seitsonen <Ari.P.Seitsonen at iki.fi>wrote:

>
> Dear Tram Bui,
>
>  Shouldn't you increase the value of 'nns' for the wave functions that you
> want to become 6s-like? This is what I have understood:
>
>
>  6S 2 0 1.00 0.00 4.30 4.50
>  6S 2 0 0.00 0.10 4.00 4.50
>  5P 2 1 6.00 0.00 1.60 1.60
>  5S 1 0 2.00 0.00 1.40 1.40
>
> The first column is "just" a label, the second one the principal quantum
> number of the _pseudo_ atom: "1 0" in the second and third column means
> node-less s wave function (like 1s of hydrogen), "2 0" has one node (like
> 2s of Li), "2 1" is the node-less p wave function (like 2p of oxygen), etc.
>
>  Hopefully this helps.
>
>    Greetings from Zurich (and Happy New Year to every one),
>
>       apsi
>
> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=***=-=*=-=*=-=*=-=*=-=*=-=*=-=*=**
> -=*=-=*=-=*=-=*=-
>  Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
>  Physikalisch-Chemisches Institut der Universitaet Zuerich
>  Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935
>
>
>
> On Tue, 3 Jan 2012, Tram Bui wrote:
>
>  Dear Everyone,
>>      I ran a ld1.x calculation with the following input file. And for the
>> output, the ld1ps.wfc file, I got a similar results for both the 5s and 6s
>> pseudo wavefunction which is not correct.  Would anyone please give me a
>> suggestion on what might have been the reason? here is the input file I
>> used:
>>
>>  &input
>>      title='Cs',
>>      zed=55.0,
>>      iswitch=3,
>>      rel=1,
>>      dft='PBE',
>>      config='[Kr] 4d10 5s2 5p6 6s1 ',
>>
>>      rlderiv=4.30,
>>      eminld=-8.0,
>>      emaxld=3.0,
>>      deld=0.01d0,
>>      nld=3,
>> /
>>  &inputp
>>      lloc=0,
>>      pseudotype=3,
>>      rho0=0.01,
>>      file_pseudopw='Cs.uspp-tb.UPF'
>> /
>> 4
>> 6S 1 0 1.00 0.00 4.30 4.50
>> 6S 1 0 0.00 0.10 4.00 4.50
>> 5P 2 1 6.00 0.00 1.60 1.60
>> 5S 1 0 2.00 0.00 1.40 1.40
>>
>> Regards,
>>
>> Tram Bui
>>
>> M.S. Materials Science & Engineering
>> trambui at u.boisestate.edu
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Tram Bui

M.S. Materials Science & Engineering
trambui at u.boisestate.edu
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From baroni at sissa.it  Wed Jan  4 09:16:34 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 4 Jan 2012 09:16:34 +0100
Subject: [Pw_forum] how to treat free electron gas,
	especially how to setup input file
In-Reply-To: <CA+1PuT9ps1t350_642je9DNNytNVBN7zqRmu5NaZCMKCzYG6ew@mail.gmail.com>
References: <CA+1PuT9ps1t350_642je9DNNytNVBN7zqRmu5NaZCMKCzYG6ew@mail.gmail.com>
Message-ID: <18E5109A-639A-43DC-9FBE-FC8308CFEF79@sissa.it>

Hem, what a weird request!
Why not doing the exercise with pencil-and-paper?
If you insist using a very sophisticated code to do that, you have two options, I believe, both of which will require somewhat more work than the simple pencil-and-paper exercise.
dig into the code where the the hamiltonian*wavefunctions operations are performed (the routine used to be called "h_psi", and simply have the the multiplication times the external potential skipped, which will set the electrons "free" ...
build a fake pseudo-potential which is simply null, and feed it into the computer ...
HTH - Stefano B


On Jan 3, 2012, at 6:42 PM, Jun Liu wrote:

> Dear All,
> 
> Let me wish all of you a Happy New Year first.
> 
> Maybe this is a very fundamental problem, but I cannot google any hint online, so here I am. I would like to work out a free electron gas problem with QE. I know total number of charges, and the size of the box the electrons move in and probably periodic b.c. applied to it. Now how can I possibly set up the input file for it? It seems many fundamentional properties of a lattice do not come with free electron gas. The code itself should be well-defined for a lattice system, so how is the code adapted to the free electron problem?
> 
> Thank you very much,
>  
> Sincerely,
> Jun Liu
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From bdslipun at gmail.com  Wed Jan  4 09:48:12 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Wed, 4 Jan 2012 14:18:12 +0530
Subject: [Pw_forum] Fwd: beta tin structure
In-Reply-To: <CAJVAAvD=rcTA2+85vM3yL5ODqP7h_ztqS-RNbZSK-=XWtsd09A@mail.gmail.com>
References: <CAJVAAvD=rcTA2+85vM3yL5ODqP7h_ztqS-RNbZSK-=XWtsd09A@mail.gmail.com>
Message-ID: <CAJVAAvDsaxXTtKD2+LbU0WqRx+D__JDmTRti4GoqfWW5P_KMeA@mail.gmail.com>

---------- Forwarded message ----------
From: bhabya sahoo <bdslipun at gmail.com>
Date: Thu, Dec 29, 2011 at 11:04 AM
Subject: beta tin structure
To: PWSCF Forum <pw_forum at pwscf.org>


i want the phonon dispersion curve for beta tin structure
so i gave the positions of atoms as primitive tetragonal structure having
coordinates
0 0 0, .5 0 .25 , .5 .5 .5, 0 .5 .75 like 4a whychoff positions (c/a=.546)
so no of atoms is 4 in the unit cell so in phonon there will be 12 branches
but i have seen 6 branches so how can i put my primitive tetragonal
structure having two atoms in unitcell
or in other way how can i give the input for beta tin structure






b d sahoo
reserch scholar
mumbai
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From Lorenzo.Paulatto at impmc.upmc.fr  Wed Jan  4 11:17:51 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Wed, 04 Jan 2012 11:17:51 +0100
Subject: [Pw_forum] how to treat free electron gas,
 especially how to setup input file
In-Reply-To: <CA+1PuT9ps1t350_642je9DNNytNVBN7zqRmu5NaZCMKCzYG6ew@mail.gmail.com>
References: <CA+1PuT9ps1t350_642je9DNNytNVBN7zqRmu5NaZCMKCzYG6ew@mail.gmail.com>
Message-ID: <op.v7j1j1dwxuur8c@vanoxite>

On Tue, 03 Jan 2012 18:42:52 +0100, Jun Liu <jun.physics at gmail.com> wrote:
> Let me wish all of you a Happy New Year first.

Thnak you, a happy new too you as well.

> The code itself
> should be well-defined for a lattice system, so how is the code adapted  
> to the free electron problem?

In principle, if you set ntyp=0, nat=0 and nelec>0 and  
input_dft='whatever' the code will perform a calculation for a free  
electron gas in the unit cell you specify with the functional you  
selected. It will of course assume a positive-charged background to keep  
the total charge neutral. For a large enough unit cell, this should tend  
to an actual free-electron gas.

However, keep in mind that this feature is very rarely used, so you could  
incur in some unknown bug. Take care to test it for consistency on  
simple/well known cases before.

best regards


-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From Michael.Mehl at nrl.navy.mil  Wed Jan  4 14:55:29 2012
From: Michael.Mehl at nrl.navy.mil (Mike Mehl)
Date: Wed, 04 Jan 2012 08:55:29 -0500
Subject: [Pw_forum] Fwd: beta tin structure
In-Reply-To: <CAJVAAvDsaxXTtKD2+LbU0WqRx+D__JDmTRti4GoqfWW5P_KMeA@mail.gmail.com>
References: <CAJVAAvD=rcTA2+85vM3yL5ODqP7h_ztqS-RNbZSK-=XWtsd09A@mail.gmail.com>
	<CAJVAAvDsaxXTtKD2+LbU0WqRx+D__JDmTRti4GoqfWW5P_KMeA@mail.gmail.com>
Message-ID: <4F045A51.5090708@nrl.navy.mil>

All right, the fourth time is a charm:

The full tetragonal unit cell of beta-tin has four atoms in it.

However, the primitive body-centered unit cell as two atoms in it.

You may want to look up the beta-tin structure, e.g.

http://cst-www.nrl.navy.mil/lattice/struk/a5.html

and see how you can construct the full tetragonal cell with four atoms 
from the primitive body-centered tetragonal unit cell containing two atoms.

Understand this and you'll understand the origin of your 6/12 problem.

On 01/04/2012 03:48 AM, bhabya sahoo wrote:

> i want the phonon dispersion curve for beta tin structure
> so i gave the positions of atoms as primitive tetragonal structure
> having coordinates
> 0 0 0, .5 0 .25 , .5 .5 .5, 0 .5 .75 like 4a whychoff positions (c/a=.546)
> so no of atoms is 4 in the unit cell so in phonon there will be 12 branches
> but i have seen 6 branches so how can i put my primitive tetragonal
> structure having two atoms in unitcell
> or in other way how can i give the input for beta tin structure

-- 
Michael J. Mehl
Head, Center for Computational Materials Science
Naval Research Laboratory Code 6390
Washington DC

From bdslipun at gmail.com  Wed Jan  4 16:28:19 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Wed, 4 Jan 2012 20:58:19 +0530
Subject: [Pw_forum] beta tin structure
Message-ID: <CAJVAAvBgq7Yada2X2OHk6dfhqRBhOPot1mG-xvS9qBN3nFG0ng@mail.gmail.com>

i give the input as bct containing
two atoms having position
0, 0, 0
.5 ,0 ,.25
but the structure doesnot looks like beta tin structure
in pwscf why? is it coorect or not?






bd sahoo
reserch scholar
mumbai
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From jun.physics at gmail.com  Wed Jan  4 18:08:44 2012
From: jun.physics at gmail.com (Jun Liu)
Date: Wed, 4 Jan 2012 11:08:44 -0600
Subject: [Pw_forum] Pw_forum Digest, Vol 55, Issue 4
In-Reply-To: <mailman.12.1325665002.9401.pw_forum@pwscf.org>
References: <mailman.12.1325665002.9401.pw_forum@pwscf.org>
Message-ID: <CA+1PuT_vmd3Q47JijV1322r1U1qVMJB3-wf14CwL-yOKYt1eeQ@mail.gmail.com>

Dear Dr. Baroni and other forum members,

Thanks for your kind and patient response on my question. I am glad to know
that there is a way to cheat QE to do a free electron gas calculation by
giving a null pseudo-potential. I guess this "null" means replacing every
number in the pp file with zero. If the case, then I might ask a bit
further on my question.

With a free electron gas system, plane wave expansion would be enough. But
what if I want to replace the plane wave basis with the plane wave + some
local orbital basis and do the calculation. Although a weird request, this
should be able to be done in principle. But the issue is how to introduce
the local orbits into the problem. Can I do something like this? Choose
some pp giving the local orbitals to be included in the calculation, and
set in the input pp file the local/nonlocal potential and the pseudo/AE
core charge to vanish, to mimic the fact that there is no ion existing in
the system. Then what is left in the pp file might render QE to do some
type of plane wave+local orbital calculation. Please let me know whether
this idea works and whether these modifications are sufficient for the
purpose.

I might here ask a very fundamental question. The reason we choose the
sophisticated PAW treatment by introducing projector/pseudo/AE wavefunction
directly relies on the non-smoothness nature of the valence orbital itself,
but not on a specific ion to be treated. That is to say, we don't need to
know what is behind the scene when deciding whether PAW treatment is needed
given a specific valence orbital in the pp file. Am I right?

Thanks,

Sincerely,
Jun Liu



> Message: 6
> Date: Wed, 4 Jan 2012 09:16:34 +0100
> From: Stefano Baroni <baroni at sissa.it>
> Subject: Re: [Pw_forum] how to treat free electron gas, especially how
>        to setup input file
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <18E5109A-639A-43DC-9FBE-FC8308CFEF79 at sissa.it>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hem, what a weird request!
> Why not doing the exercise with pencil-and-paper?
> If you insist using a very sophisticated code to do that, you have two
> options, I believe, both of which will require somewhat more work than the
> simple pencil-and-paper exercise.
> dig into the code where the the hamiltonian*wavefunctions operations are
> performed (the routine used to be called "h_psi", and simply have the the
> multiplication times the external potential skipped, which will set the
> electrons "free" ...
> build a fake pseudo-potential which is simply null, and feed it into the
> computer ...
> HTH - Stefano B
>
>
> On Jan 3, 2012, at 6:42 PM, Jun Liu wrote:
>
> > Dear All,
> >
> > Let me wish all of you a Happy New Year first.
> >
> > Maybe this is a very fundamental problem, but I cannot google any hint
> online, so here I am. I would like to work out a free electron gas problem
> with QE. I know total number of charges, and the size of the box the
> electrons move in and probably periodic b.c. applied to it. Now how can I
> possibly set up the input file for it? It seems many fundamentional
> properties of a lattice do not come with free electron gas. The code itself
> should be well-defined for a lattice system, so how is the code adapted to
> the free electron problem?
> >
> > Thank you very much,
> >
> > Sincerely,
> > Jun Liu
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> ---
> Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
> http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) /
> stefanobaroni (skype)
>
> La morale est une logique de l'action comme la logique est une morale de
> la pens?e - Jean Piaget
>
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> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
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-- 
Sincerely,
Jun
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From bdslipun at gmail.com  Wed Jan  4 18:57:01 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Wed, 4 Jan 2012 23:27:01 +0530
Subject: [Pw_forum] phonons in espresso
Message-ID: <CAJVAAvAijvnr8fQ3AcTimrmswObF+YgHdsMWiTv5hOiBF1xGYw@mail.gmail.com>

i am using espresso
can i find the phonon dispersion curve of beta-tin from this phon code
because here bct is not implimented
so how can  can produce the dispersion curve from this















b sahoo
mumbai
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From Michael.Mehl at nrl.navy.mil  Wed Jan  4 19:58:11 2012
From: Michael.Mehl at nrl.navy.mil (Mike Mehl)
Date: Wed, 04 Jan 2012 13:58:11 -0500
Subject: [Pw_forum] beta tin structure
In-Reply-To: <CAJVAAvBgq7Yada2X2OHk6dfhqRBhOPot1mG-xvS9qBN3nFG0ng@mail.gmail.com>
References: <CAJVAAvBgq7Yada2X2OHk6dfhqRBhOPot1mG-xvS9qBN3nFG0ng@mail.gmail.com>
Message-ID: <4F04A143.60007@nrl.navy.mil>

Again, look up the difference between

1) the tetragonal lattice

and

2) the body-centered tetragonal lattice

Until you understand that, you will not understand your problem.

On 01/04/2012 10:28 AM, bhabya sahoo wrote:
> i give the input as bct containing
> two atoms having position
> 0, 0, 0
> .5 ,0 ,.25
> but the structure doesnot looks like beta tin structure
> in pwscf why? is it coorect or not?
>


-- 
Michael J. Mehl
Head, Center for Computational Materials Science
Naval Research Laboratory Code 6390
Washington DC

From baroni at sissa.it  Wed Jan  4 20:09:33 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Wed, 4 Jan 2012 20:09:33 +0100
Subject: [Pw_forum] Pw_forum Digest, Vol 55, Issue 4
In-Reply-To: <CA+1PuT_vmd3Q47JijV1322r1U1qVMJB3-wf14CwL-yOKYt1eeQ@mail.gmail.com>
References: <mailman.12.1325665002.9401.pw_forum@pwscf.org>
	<CA+1PuT_vmd3Q47JijV1322r1U1qVMJB3-wf14CwL-yOKYt1eeQ@mail.gmail.com>
Message-ID: <50EBFAE1-22EE-4043-B071-731B574961BB@sissa.it>


On Jan 4, 2012, at 6:08 PM, Jun Liu wrote:

> Dear Dr. Baroni and other forum members,
> 
> Thanks for your kind and patient response on my question. I am glad to know that there is a way to cheat QE to do a free electron gas calculation by giving a null pseudo-potential. I guess this "null" means replacing every number in the pp file with zero. If the case, then I might ask a bit further on my question.

well, you have to understand what the various "zeroes" mean, and be sure that what you do makes sense. for this, I am afraid, you will need to dig a bit into the UPF format. not sure the effort would be worth the result. I would rather suggest to try first what Lorenzo Paulatto suggested, and then, if anything else fails, it may be simpler to modify the code than to fudge the .upf files ...

> With a free electron gas system, plane wave expansion would be enough. But what if I want to replace the plane wave basis with the plane wave + some local orbital basis and do the calculation.

not sure I understand why with the zillions of interesting physics problems to solve that exist out there you want to solve a trivial problem with a very complicated method ... in any case, mixed basis sets are not implemented in any of the QE codes ...

> Although a weird request, this should be able to be done in principle. But the issue is how to introduce the local orbits into the problem. Can I do something like this?

yes, but not with QE

> Choose some pp giving the local orbitals to be included in the calculation, and set in the input pp file the local/nonlocal potential and the pseudo/AE core charge to vanish, to mimic the fact that there is no ion existing in the system. Then what is left in the pp file might render QE to do some type of plane wave+local orbital calculation. Please let me know whether this idea works and whether these modifications are sufficient for the purpose. 

I do not understand what the idea is. I am afraid you are confusing the localized nature of *some* basis sets (including, e.g., gaussians, or atomic orbitals) with the atomic wavefunctions that come with the .upf file and that are *NOT* used as basis functions. be sure you understand what US PP, PAW, and the like work ...

> I might here ask a very fundamental question. The reason we choose the sophisticated PAW treatment by introducing projector/pseudo/AE wavefunction directly relies on the non-smoothness nature of the valence orbital itself, but not on a specific ion to be treated. That is to say, we don't need to know what is behind the scene when deciding whether PAW treatment is needed given a specific valence orbital in the pp file. Am I right?

you always need to know "what is behind the scene": that's exactly the purpose of Science ...

Stefano B

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From gabriele.sclauzero at epfl.ch  Thu Jan  5 11:50:50 2012
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Thu, 5 Jan 2012 11:50:50 +0100
Subject: [Pw_forum] pwscf: constrained total magnetic moment
In-Reply-To: <CAGGYvC0f=kRzAQ=6s0U_EO67L8waSPowi3ZbR3K5kjqUUz+=cg@mail.gmail.com>
References: <CAGGYvC0f=kRzAQ=6s0U_EO67L8waSPowi3ZbR3K5kjqUUz+=cg@mail.gmail.com>
Message-ID: <8A46AB04-62AB-4586-93AF-FEED76E4A0A6@epfl.ch>

Dear German,

    have you checked the manuals? In the input description of PWscf I've found:

                   'total':
                            total magnetization is constrained by
                            adding a penalty functional to the total energy:
                   
                            LAMBDA * SUM_{i} ( magnetization(i) - fixed_magnetization(i) )**2
                   
                            where the sum over i runs over the three components of
                            the magnetization. Lambda is a real number (see below).
                            Noncolinear case only. Use "tot_magnetization" for LSDA

I think that, in order to fix the total magnetization in LSDA calculations (nspin=2), you should simply set the tot_magnetization parameter (two-Fermi-energies method) and not specify the constrained_magnetization keyword. Which version of QE are you using?


HTH

GS


Il giorno 03/gen/2012, alle ore 20.10, German Samolyuk ha scritto:

> Dear all,
> 
> I do self-consistent calculation of supercell with 135 Fe atoms with
> constrained magnetization.
> 
> nspin = 2,
> fixed_magnetization(3) = 360.0,
> constrained_magnetization = 'total' ,
> 
> The output value of magnetic field:
> 
>   Magnetic field            =   0.0785401 Ry
> 
> 
> In order to make a rough estimation of corresponding magnetic field in
> Tesla I should divide this value by mu_B and difference between
> total magnetic moments of system with constrain and without it?
> 
> Thank you
> 
> German Samolyuk
> Oak Rigde National Laboratory
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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From gabriele.sclauzero at epfl.ch  Thu Jan  5 12:01:22 2012
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Thu, 5 Jan 2012 12:01:22 +0100
Subject: [Pw_forum] pwcond diff leads with some shift in space
In-Reply-To: <1324723668.26823.YahooMailClassic@web112404.mail.gq1.yahoo.com>
References: <1324723668.26823.YahooMailClassic@web112404.mail.gq1.yahoo.com>
Message-ID: <5232490B-6B6F-4AEC-8472-431EC16A742E@epfl.ch>

Dear M. Sanaee,

    there are two ways to specify the regions of the leads, depending if you do a single scf calculation for the whole structure (left lead+scattering region+right lead) or separate calculations for these three regions. In the latter case, you don't need bds bdr and bdl, but you have to specify prefixl, prefixs, and prefixr.
If you have a unique calculation (just one prefix), then it's a bit more tricky... Alexander has some notes on his webpage
http://people.sissa.it/~smogunov/
(under PWCOND, at the bottom of the page). Essentially, you have to tell the code at which point (z coordinate) the left lead ends (the scattering regions starts there) and where the scattering region ends (the right lead starts there).

HTH

GS

P.S.: please specify your academic afiliation

Il giorno 24/dic/2011, alle ore 11.47, mary bababarghi ha scritto:

> I want to simulate the transport of a scattering region which is between two identical contacts , but these contacts have a little shift in space.
> In other words, the right lead at y-direction is 7Angestrum upper than left lead.
> I have read the pwcond_input help but couldn't understand some items.
> Would you please help us?
> 
>  How should I define the 'bds', 'bdr' and 'bdl' in cond.in input file?
> 
> Thank you in advance
> Looking forward to your help.
> M. Sanaee
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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From bdslipun at gmail.com  Thu Jan  5 12:55:28 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Thu, 5 Jan 2012 17:25:28 +0530
Subject: [Pw_forum] bct
Message-ID: <CAJVAAvBCzQh5nJs=PXS35eo0PL07XEG3WkVARnTBMw20j5FFdw@mail.gmail.com>

can any one suggest triinp file for bct cell
i have  (c/a=.89)
how can i find the vertex of tetrahedron


can phonon dispersion curve of bct cell














bdsahoo
mumbai
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From giannozz at democritos.it  Thu Jan  5 13:31:08 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 5 Jan 2012 13:31:08 +0100
Subject: [Pw_forum] how to treat free electron gas,
	especially how to setup input file
In-Reply-To: <op.v7j1j1dwxuur8c@vanoxite>
References: <CA+1PuT9ps1t350_642je9DNNytNVBN7zqRmu5NaZCMKCzYG6ew@mail.gmail.com>
	<op.v7j1j1dwxuur8c@vanoxite>
Message-ID: <EB1C4765-19C9-4A55-8DB9-A7D562EF004E@democritos.it>


On Jan 4, 2012, at 11:17 , Lorenzo Paulatto wrote:

> In principle, if you set ntyp=0, nat=0 and nelec>0

tot_charge: nelec is obsolete. The number of bands nbnd is also needed.

> and  input_dft='whatever' the code will perform a calculation for a  
> free electron
> gas in the unit cell you specify with the functional you selected.  
> [...] keep in mind
> that this feature is very rarely used, so you could incur in some  
> unknown bug.

in fact it isn't working any longer, since a long time

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Thu Jan  5 16:15:54 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 05 Jan 2012 16:15:54 +0100
Subject: [Pw_forum] orthogonality of phonon eigenvectors?
In-Reply-To: <CALN9FpTkp+OLHP95m5zggrXkn4F0O+0skpDx60MV=bXc-bGw=w@mail.gmail.com>
References: <CAHePdfDrJ50p7A4mPf6nZu8chtRocg-HbTBwhqShq2NGe1VsCg@mail.gmail.com>
	<EE0FD22B-BBC5-4205-896D-1474B0179B04@sissa.it>
	<CALN9FpTkp+OLHP95m5zggrXkn4F0O+0skpDx60MV=bXc-bGw=w@mail.gmail.com>
Message-ID: <1325776554.5202.3.camel@fe12lx.fisica.uniud.it>

On Fri, 2011-12-30 at 14:41 +0100, Suza W wrote:

> Since eigen displacements are more useful than phonon eigenvectors,
>  it would be better if QE rather prints eigen-displacements

IIRC the phonon code, and all other auxiliary codes, always print
displacement patterns, not phonon eigenvectors

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From samolyuk at gmail.com  Thu Jan  5 19:41:17 2012
From: samolyuk at gmail.com (German Samolyuk)
Date: Thu, 5 Jan 2012 13:41:17 -0500
Subject: [Pw_forum] pwscf: constrained total magnetic moment
In-Reply-To: <8A46AB04-62AB-4586-93AF-FEED76E4A0A6@epfl.ch>
References: <CAGGYvC0f=kRzAQ=6s0U_EO67L8waSPowi3ZbR3K5kjqUUz+=cg@mail.gmail.com>
	<8A46AB04-62AB-4586-93AF-FEED76E4A0A6@epfl.ch>
Message-ID: <CAGGYvC3uRsoHK_FrdTHYMzEV9S0GNAPps8W6dNjTZ+9TGzWzoQ@mail.gmail.com>

Dear Gabriele,

Thank you for your answer.
I use version 4.2.1 and the input I used works for this version. For
the 4.3.2 vesion the input should be as you mentioned
tot_magnetization = some_number;. The results obtained with both
version are the same.

The output from 4.2.1 version has value of "corresponding" magnetic
field which according to text is defined as (e_f_up-e_f_dn)/2 in
Rydbergs.
My question was if there is any way to estimate corresponding external
magnetic field?

 Thank you,

German


On Thu, Jan 5, 2012 at 5:50 AM, Gabriele Sclauzero
<gabriele.sclauzero at epfl.ch> wrote:
> Dear German,
>
> ? ? have you checked the manuals? In the input description of PWscf I've
> found:
>
> ? ? ? ? ? ? ? ? ? ?'total':
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? total magnetization is constrained by
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? adding a penalty functional to the total energy:
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? LAMBDA * SUM_{i} ( magnetization(i) -
> fixed_magnetization(i) )**2
>
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? where the sum over i runs over the three
> components of
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? the magnetization. Lambda is a real number (see
> below).
> ? ? ? ? ? ? ? ? ? ? ? ? ? ? Noncolinear case only. Use "tot_magnetization"
> for LSDA
>
> I think that, in order to fix the total magnetization in LSDA calculations
> (nspin=2), you should simply set the tot_magnetization parameter
> (two-Fermi-energies method) and not specify the constrained_magnetization
> keyword. Which version of QE are you using?
>
>
> HTH
>
> GS
>
>
> Il giorno 03/gen/2012, alle ore 20.10, German Samolyuk ha scritto:
>
> Dear all,
>
> I do self-consistent calculation of supercell with 135 Fe atoms with
> constrained magnetization.
>
> nspin = 2,
> fixed_magnetization(3) = 360.0,
> constrained_magnetization = 'total' ,
>
> The output value of magnetic field:
>
> ??Magnetic field ???????????= ??0.0785401 Ry
>
>
> In order to make a rough estimation of corresponding magnetic field in
> Tesla I should divide this value by mu_B and difference between
> total magnetic moments of system with constrain and without it?
>
> Thank you
>
> German Samolyuk
> Oak Rigde National Laboratory
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> ? Gabriele Sclauzero,?EPFL SB ITP CSEA
> ?? PH H2 462, Station 3,?CH-1015 Lausanne
>
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From suza.rri at gmail.com  Thu Jan  5 21:58:26 2012
From: suza.rri at gmail.com (Suza W)
Date: Thu, 5 Jan 2012 21:58:26 +0100
Subject: [Pw_forum] orthogonality of phonon eigenvectors?
In-Reply-To: <1325776554.5202.3.camel@fe12lx.fisica.uniud.it>
References: <CAHePdfDrJ50p7A4mPf6nZu8chtRocg-HbTBwhqShq2NGe1VsCg@mail.gmail.com>
	<EE0FD22B-BBC5-4205-896D-1474B0179B04@sissa.it>
	<CALN9FpTkp+OLHP95m5zggrXkn4F0O+0skpDx60MV=bXc-bGw=w@mail.gmail.com>
	<1325776554.5202.3.camel@fe12lx.fisica.uniud.it>
Message-ID: <CALN9FpR_bbaUCvQcyDNRdHgyaTTyFCvaxarM+Beg3rFEXXssoQ@mail.gmail.com>

 Dear All ,


> > IIRC the phonon code, and all other auxiliary codes, always print
> > displacement patterns, not phonon eigenvectors
>
>   Not always, perhaps. In case of a homo-atomic system, the phonon
eigen-vectots (v)
  can directly be  presented as atomic displacements (u) . However, for a
hetero-
  atomic system, it is not so straight-forward. We need  some more algebra,
because

 u = v / sqrt (M)   and  SUM_i  ( u_i . u_i . M_i )  = constant  .

 After that one can obtain correct atomic displacement  from the
eigen-vectors in case of a
 hetero-atomic system.

 Now I am going to ask here a different question.
 In the PWFORUM, I have found some discussions about Dario Alfe's PHON
code.
 Is here anybody who has used this code to obtain the full phonon
dispersion for BaTiO3 ?
 In the example directory of the PHON code, I find  Al, and MgO  as the
test cases.
 Please do share the files for BaTiO3 as well, if available.

 Thanking you all,

 Yours sincerely,
 Suza
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From payam.norouzzadeh at gmail.com  Thu Jan  5 22:00:15 2012
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Thu, 5 Jan 2012 15:00:15 -0600
Subject: [Pw_forum] Space groups
Message-ID: <CAND4gJF9LynR=BwSZcRWWnzWQUo7E81q4sS7n28d0E78zutt3w@mail.gmail.com>

Hello QE users

I'm interested to know if QE can recognize the space groups of structures
or not?
If yes then how can I see it (for example space group number) in output
file and if no how the structural symmetries of crystals are kept during
relaxation procedure?
Is it possible that relaxation process change the space group number?

Best regards,Payam Norouzzadeh
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From giannozz at democritos.it  Thu Jan  5 22:15:03 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 5 Jan 2012 22:15:03 +0100
Subject: [Pw_forum] Space groups
In-Reply-To: <CAND4gJF9LynR=BwSZcRWWnzWQUo7E81q4sS7n28d0E78zutt3w@mail.gmail.com>
References: <CAND4gJF9LynR=BwSZcRWWnzWQUo7E81q4sS7n28d0E78zutt3w@mail.gmail.com>
Message-ID: <8497D948-4736-4EA3-903B-784D2FDB01F2@democritos.it>


On Jan 5, 2012, at 22:00 , Payam Norouzzadeh wrote:

> I'm interested to know if QE can recognize the space groups of  
> structures or not?

it recognizes the symmetry (if present) but it doesn't associate it to a
specific space group

> if no how the structural symmetries of crystals are kept during  
> relaxation procedure?
> Is it possible that relaxation process change the space group number?

structural optimization using forces doesn't break symmetry,
by construction (except for numerical noise)

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From germaneau at gucas.ac.cn  Fri Jan  6 17:21:30 2012
From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=)
Date: Fri, 06 Jan 2012 11:21:30 -0500
Subject: [Pw_forum] phonon dispersion issue
Message-ID: <4F071F8A.4080707@gucas.ac.cn>

Dear all,

I was running a phonon dispersion calculation along a 36 points path.
During the point number 30 the calculation crashed with the message

    from ph_setup : error #         1
          problem with modes file

What does that mean?
Why does that happen at this stage and not before?
Is there a way to restart the run at this point?

Thank you,

                            ?ric.

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau 
<http://www.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>

Graduate University of Chinese Academy of Sciences
College of Physical Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

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From giannozz at democritos.it  Fri Jan  6 14:21:22 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 6 Jan 2012 14:21:22 +0100
Subject: [Pw_forum] phonon dispersion issue
In-Reply-To: <4F071F8A.4080707@gucas.ac.cn>
References: <4F071F8A.4080707@gucas.ac.cn>
Message-ID: <AC98FAD0-8CB4-42C5-B967-44D5F07BE892@democritos.it>


On Jan 6, 2012, at 17:21 , ?ric Germaneau wrote:

> During the point number 30 the calculation crashed with the message
>      from ph_setup : error #         1
>      problem with modes file

this error arises only if you are restarting from a previous run.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From germaneau at gucas.ac.cn  Sat Jan  7 06:03:15 2012
From: germaneau at gucas.ac.cn (=?ISO-8859-1?Q?=C9ric_Germaneau?=)
Date: Sat, 07 Jan 2012 00:03:15 -0500
Subject: [Pw_forum] phonon dispersion issue
In-Reply-To: <525853443.19885@gscas.net.cn>
References: <4F071F8A.4080707@gucas.ac.cn> <525853443.19885@gscas.net.cn>
Message-ID: <4F07D213.7070308@gucas.ac.cn>

Thank you Professor Giannozzi.
So it seems to be a hardware issue because I did not restart the job.
I'm going to resubmit from scratch and see.

On 01/06/2012 08:21 AM, Paolo Giannozzi wrote:
> On Jan 6, 2012, at 17:21 , ?ric Germaneau wrote:
>
>> During the point number 30 the calculation crashed with the message
>>       from ph_setup : error #         1
>>       problem with modes file
> this error arises only if you are restarting from a previous run.
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

-- 
/Be the change you wish to see in the world
/ --- Mahatma Gandhi ---

Dr. ?ric Germaneau 
<http://www.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986>

Graduate University of Chinese Academy of Sciences
College of Physical Sciences
Yuquan Road 19A
Beijing 100049
China

/Please, if possible, don't send me MS Word or PowerPoint attachments
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/

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From chenhanghuipwscf at gmail.com  Fri Jan  6 21:01:25 2012
From: chenhanghuipwscf at gmail.com (Hanghui Chen)
Date: Fri, 6 Jan 2012 15:01:25 -0500
Subject: [Pw_forum] d orbital order
Message-ID: <CAOE2MOy0T36DXgmmvgb=C7smVDLCyCSvsUigT_VQ=94YueF3TA@mail.gmail.com>

Dear PWscf developers,
     I have a simple question. I know that in the post-processing, the
atomic projection of d-orbital has the following order: dz^2, dxz, dyz,
dx^2-y^2 and dxy. However, when I turn on the Hubbard U on d orbitals,
there is an 'occupations' matrix which is calculated based on atomic
d-orbital. Does any one know the order of d-orbital basis? Is it the same
as the orbital order of atomic projection in the post processing?
     Thank you very much.

Hanghui Chen
Department of Physics
Yale University
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From flux_ray12 at 163.com  Sat Jan  7 02:35:22 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sat, 7 Jan 2012 09:35:22 +0800 (CST)
Subject: [Pw_forum] Can ph.x use 'cg' diagonalization?
Message-ID: <69a70bcd.1683.134b5ce4811.Coremail.flux_ray12@163.com>

Dear QE developer and users:
I am using ph.x to calculate phonon dispersion. But I met a problem during my computation.
My structure needs 12 dynamic matrics files. But after 3 *.dyn file were calculated, the error occurred during band structure calculation:
Band Structure Calculation
Davidson diagonalizaion with overlap
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  from cdiaghg:  error #            126
  diagonalization  (ZHEGV*)  failed
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Therefore, I changed to diagonalization='cg' in scf calculation and recalculate it, the problem remained. It seemed no matter which diag method I used in scf calculation, only Davidson algorithm is used in ph.x.
Is it possible to use conjugate gradient in ph.x ?
Thanks a lot.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 
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From giannozz at democritos.it  Sat Jan  7 10:10:47 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 7 Jan 2012 10:10:47 +0100
Subject: [Pw_forum] Can ph.x use 'cg' diagonalization?
In-Reply-To: <69a70bcd.1683.134b5ce4811.Coremail.flux_ray12@163.com>
References: <69a70bcd.1683.134b5ce4811.Coremail.flux_ray12@163.com>
Message-ID: <7590BCB0-7564-4A50-B0E6-9D56455F9EBD@democritos.it>


On Jan 7, 2012, at 2:35 , GAO Zhe wrote:

> Is it possible to use conjugate gradient in ph.x ?

edit routine "set_defaults_pw.f90", change "isolve=0" to
"isolve=1", recompile

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From matteo at umn.edu  Sat Jan  7 10:16:32 2012
From: matteo at umn.edu (Matteo Cococcioni)
Date: Sat, 7 Jan 2012 03:16:32 -0600
Subject: [Pw_forum] d orbital order
In-Reply-To: <CAOE2MOy0T36DXgmmvgb=C7smVDLCyCSvsUigT_VQ=94YueF3TA@mail.gmail.com>
References: <CAOE2MOy0T36DXgmmvgb=C7smVDLCyCSvsUigT_VQ=94YueF3TA@mail.gmail.com>
Message-ID: <CAMZASgF9FSOXTRR5V3dwK6kc3yK7_U4bwWJ_S+58Da6PXFBSVg@mail.gmail.com>

Dear Hanghui,

yes the order of the d states is the same when the occupation matrix is
constructed.

regards,

Matteo

On Fri, Jan 6, 2012 at 2:01 PM, Hanghui Chen <chenhanghuipwscf at gmail.com>wrote:

> Dear PWscf developers,
>      I have a simple question. I know that in the post-processing, the
> atomic projection of d-orbital has the following order: dz^2, dxz, dyz,
> dx^2-y^2 and dxy. However, when I turn on the Hubbard U on d orbitals,
> there is an 'occupations' matrix which is calculated based on atomic
> d-orbital. Does any one know the order of d-orbital basis? Is it the same
> as the orbital order of atomic projection in the post processing?
>      Thank you very much.
>
> Hanghui Chen
> Department of Physics
> Yale University
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056    Fax +1 612 626 7246
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From flux_ray12 at 163.com  Sat Jan  7 14:43:20 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Sat, 7 Jan 2012 21:43:20 +0800 (CST)
Subject: [Pw_forum] Can ph.x use 'cg' diagonalization?
In-Reply-To: <7590BCB0-7564-4A50-B0E6-9D56455F9EBD@democritos.it>
References: <7590BCB0-7564-4A50-B0E6-9D56455F9EBD@democritos.it>
	<69a70bcd.1683.134b5ce4811.Coremail.flux_ray12@163.com>
Message-ID: <e8528ce.a1e3.134b868c2d8.Coremail.flux_ray12@163.com>

Prof. GIannozzi, thank you very much. It is really helpful to me.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 
At 2012-01-07 17:11:01,"Paolo Giannozzi" <giannozz at democritos.it> wrote:

>
>On Jan 7, 2012, at 2:35 , GAO Zhe wrote:
>
>> Is it possible to use conjugate gradient in ph.x ?
>
>edit routine "set_defaults_pw.f90", change "isolve=0" to
>"isolve=1", recompile
>
>P.
>---
>Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From funsopaul at yahoo.com  Sat Jan  7 20:47:07 2012
From: funsopaul at yahoo.com (Paul Funso)
Date: Sat, 7 Jan 2012 11:47:07 -0800 (PST)
Subject: [Pw_forum] Atomic position for Ni-Al alloy with BCC structure
Message-ID: <1325965627.10399.YahooMailNeo@web121104.mail.ne1.yahoo.com>

Dear All,
?I am working on BCC NI-Al alloy, which has a CsCl structure with ibrav = 3 and atomic position 0 0 0 for Ni atom and? 0.5 0.5 0.5 for Al atom. I am using xcrysden to view the structure, I only see Ni atoms and with no Al atom in the matrix. Can anybody please tell me where I am going wrong. I have my input file below.

?&control
??? calculation='scf'
??? restart_mode='from_scratch',
??? pseudo_dir = '/home/adebambo/espresso-4.2.1/pseudo/',
??? outdir='./'
??? prefix='Ni-Al'
??? tstress = .true.
??? tprnfor = .true.
?/
?&system
??? ibrav = 3, celldm(1) =5.44 nat= 2, ntyp= 2,
??? ecutwfc = 15, ecutrho = 300.0
??? occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05
?/
?&electrons
??? diagonalization='cg'
??? mixing_beta = 0.7
?/
ATOMIC_SPECIES
?Ni 58.69? Ni.pz-nd-rrkjus.UPF
?Al 26.98? Al.pz-vbc.UPF

ATOMIC_POSITIONS
?Ni? 0.00? 0.00? 0.00
?Al? 0.50? 0.50? 0.50
K_POINTS (automatic)
?4 4 4? 0 0 0


Thanks.

Adebambo Paul Olufunso? PhD student,
Department of Physics,
University of Agriculture Abeokuta,
Nigeria.
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From rcjhawk at gmail.com  Sat Jan  7 21:02:15 2012
From: rcjhawk at gmail.com (Michael Mehl)
Date: Sat, 07 Jan 2012 15:02:15 -0500
Subject: [Pw_forum] Atomic position for Ni-Al alloy with BCC structure
In-Reply-To: <1325965627.10399.YahooMailNeo@web121104.mail.ne1.yahoo.com>
References: <1325965627.10399.YahooMailNeo@web121104.mail.ne1.yahoo.com>
Message-ID: <4F08A4C7.5010603@gmail.com>

CsCl has the simple cubic structure, so ibrav=1.

It's only called "BCC" because the atoms are on the sites of the BCC 
lattice, so if you replace Al by Ni you'd get a BCC Ni structure.

On 01/07/2012 02:47 PM, Paul Funso wrote:
> Dear All,
>   I am working on BCC NI-Al alloy, which has a CsCl structure with ibrav
> = 3 and atomic position 0 0 0 for Ni atom and  0.5 0.5 0.5 for Al atom.
> I am using xcrysden to view the structure, I only see Ni atoms and with
> no Al atom in the matrix. Can anybody please tell me where I am going
> wrong. I have my input file below.
>


-- 
Michael Mehl
Naval Research Laboratory
Washington DC


From bamideleibrahim at yahoo.com  Sun Jan  8 05:38:31 2012
From: bamideleibrahim at yahoo.com (bamidele ibrahim)
Date: Sat, 7 Jan 2012 20:38:31 -0800 (PST)
Subject: [Pw_forum] Atomic position for Ni-Al alloy with BCC structure
In-Reply-To: <1325965627.10399.YahooMailNeo@web121104.mail.ne1.yahoo.com>
References: <1325965627.10399.YahooMailNeo@web121104.mail.ne1.yahoo.com>
Message-ID: <1325997511.1846.YahooMailNeo@web39405.mail.mud.yahoo.com>

Dear Paul, 

? I think one of your pseudopotential need to be change for conformity. I try to run pw.x for your input file
and noticed that there is overlapping between the two atoms. This the program complained. It is as 

a result of this that you are only seeing one atom in the matrix. ? 

?
Adetunji Bamidele Ibrahim
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.


________________________________
 From: Paul Funso <funsopaul at yahoo.com>
To: "pw_forum at pwscf.org" <pw_forum at pwscf.org> 
Sent: Saturday, January 7, 2012 8:47 PM
Subject: [Pw_forum] Atomic position for Ni-Al alloy with BCC structure
 

Dear All,
?I am working on BCC NI-Al alloy, which has a CsCl structure with ibrav = 3 and atomic position 0 0 0 for Ni atom and? 0.5 0.5 0.5 for Al atom. I am using xcrysden to view the structure, I only see Ni atoms and with no Al atom in the matrix. Can anybody please tell me where I am going wrong. I have my input file below.

?&control
??? calculation='scf'
??? restart_mode='from_scratch',
??? pseudo_dir = '/home/adebambo/espresso-4.2.1/pseudo/',
??? outdir='./'
??? prefix='Ni-Al'
??? tstress = .true.
??? tprnfor = .true.
?/
?&system
??? ibrav = 3, celldm(1) =5.44 nat= 2, ntyp= 2,
??? ecutwfc = 15,
 ecutrho = 300.0
??? occupations='smearing', smearing='marzari-vanderbilt', degauss=0.05
?/
?&electrons
??? diagonalization='cg'
??? mixing_beta = 0.7
?/
ATOMIC_SPECIES
?Ni 58.69? Ni.pz-nd-rrkjus.UPF
?Al 26.98? Al.pz-vbc.UPF

ATOMIC_POSITIONS
?Ni? 0.00? 0.00? 0.00
?Al? 0.50? 0.50? 0.50
K_POINTS (automatic)
?4 4 4? 0 0 0


Thanks.

Adebambo Paul Olufunso? PhD student,
Department of Physics,
University of Agriculture Abeokuta,
Nigeria.

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From spmmal at gmail.com  Sun Jan  8 17:43:12 2012
From: spmmal at gmail.com (Caloma Trumica)
Date: Sun, 8 Jan 2012 11:43:12 -0500
Subject: [Pw_forum] What is the difference between Q points mesh and k
	points mesh
Message-ID: <CAM0egYbi=NzpJM9K6HDAcy6+RhFSrYM1km=E2jWPDN=FT+gpxA@mail.gmail.com>

Dear All,

I have a quick question:

When doing phonon calculation for a unit cell, we need to set up a qpoints
mesh. This mesh is built also based on M-K scheme, so the resulting
coordinates and weight should be exactly the same as those for k points if
the input grid is the same? say 5*5*5 for a cubic cell.

Is my understanding correct? If so, why do we need to have such an
additional setting of q points rather than just using k points mesh for
both?

Thanks.

Caloma Ditrica

PhD student from Penn State University
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From giannozz at democritos.it  Sun Jan  8 18:51:34 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 8 Jan 2012 18:51:34 +0100
Subject: [Pw_forum] What is the difference between Q points mesh and k
	points mesh
In-Reply-To: <CAM0egYbi=NzpJM9K6HDAcy6+RhFSrYM1km=E2jWPDN=FT+gpxA@mail.gmail.com>
References: <CAM0egYbi=NzpJM9K6HDAcy6+RhFSrYM1km=E2jWPDN=FT+gpxA@mail.gmail.com>
Message-ID: <CA1C49F7-3136-4D07-AA58-89826C6C953A@democritos.it>


On Jan 8, 2012, at 17:43 , Caloma Trumica wrote:

> why do we need to have such an additional setting of q points
> rather than just using k points mesh for both?

because they refer to different quantities and have different
convergence criteria. The "k-point" grid is used to perform the
integral over the Brillouin Zone; the "q-point" grid is used to
perform integrals over phonon wave vectors, or to obtain
Interatomic Force Constants in real space.

P.
---
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

"Nothing is impossible for the man who doesn't have to do it himself"




From baroni at sissa.it  Sun Jan  8 21:18:22 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 8 Jan 2012 21:18:22 +0100
Subject: [Pw_forum] What is the difference between Q points mesh and k
	points mesh
In-Reply-To: <CA1C49F7-3136-4D07-AA58-89826C6C953A@democritos.it>
References: <CAM0egYbi=NzpJM9K6HDAcy6+RhFSrYM1km=E2jWPDN=FT+gpxA@mail.gmail.com>
	<CA1C49F7-3136-4D07-AA58-89826C6C953A@democritos.it>
Message-ID: <BB266271-76CA-4531-858B-B2953D20B803@sissa.it>

On Jan 8, 2012, at 6:51 PM, Paolo Giannozzi wrote:

just a few more more words

> On Jan 8, 2012, at 17:43 , Caloma Trumica wrote:
> 
>> why do we need to have such an additional setting of q points
>> rather than just using k points mesh for both?
> 
> because they refer to different quantities and have different
> convergence criteria. The "k-point" grid is used to perform the
> integral over the Brillouin Zone;

... for electronic properties (squared Bloch states -> charge density, 1-electron energies -> sum thereof, etc.)

> the "q-point" grid is used to
> perform integrals over phonon wave vectors,

... which is also a sum over the Brillouin zone, but of quantities belonging to a different class of properties, which usually display different convergence properties (as pointed out by Paolo)

> or to obtain
> Interatomic Force Constants in real space.

as above ...

Also, q-point meshes usually include the gamma point (both because technically they often appear as differences between "k-points" q=k2-k1, hence if k2 and k1 both belong to a same mesh, q can be equal to zero; and also because one is often interested in zone-center phonons per se); k-points, instead, are often offset from the origin, because the sum over points of a regular grid of a periodic function converges slightly better as a function of the number of points if the grid is offset (this the somewhat obscure logics behind the construction of the Monkhorst-Pack sets of "special points").

SB

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From cwandtj at gmail.com  Sun Jan  8 23:03:24 2012
From: cwandtj at gmail.com (Chan-Woo Lee)
Date: Sun, 8 Jan 2012 17:03:24 -0500
Subject: [Pw_forum] Understanding Co psp (by Dr. Andrea Dal Corso) from QE
	website
Message-ID: <002201ccce51$58367ae0$08a370a0$@gmail.com>

Dear all,

First of all, happy new year!

I am trying to understand the details of Co psp from QE
(http://www.quantum-espresso.org/pseudo/1.3/html/Co.html). In specific, I
have interests in following psps:

Co.rel-pz-n-rrkjus.UPF
(http://www.quantum-espresso.org/pseudo/1.3/UPF/Co.rel-pz-n-rrkjus.UPF) 
Co.pbe-nd-rrkjus.UPF
(http://www.quantum-espresso.org/pseudo/1.3/UPF/Co.pbe-nd-rrkjus.UPF)

In their <PP_INFO>, can anyone explain me why we have multiple lines 4s, 4p,
and 3d sometimes identical occ but sometimes different occ (see below (after
++++) for more details)? I expect that these are related to nonlinear core
correction, I am not so sure
 Your help will ?truly? be appreciated. 

Sincerely,

Chan-Woo

+++++++++++++++++++++++++++

For Co.rel-pz-n-rrkjus.UPF,

nl pn  l   occ               Rcut            Rcut US             E pseu
4S  1  0  1.00      2.20000000000      2.50000000000     -0.33855297011
4S  1  0  0.00      2.20000000000      2.50000000000     -0.06831336257
4P  2  1  0.00      2.40000000000      2.60000000000     -0.06564055631
4P  2  1  0.00      2.40000000000      2.60000000000     -0.33727583802
4P  2  1  0.00      2.40000000000      2.60000000000     -0.32443820910
4P  2  1  0.00      2.40000000000      2.60000000000      0.10000000000
3D  3  2  4.00      1.50000000000      2.10000000000     -0.33733396598
3D  3  2  0.00      1.50000000000      2.10000000000     -0.43000000000
3D  3  2  4.00      1.50000000000      2.10000000000     -0.32449570554
3D  3  2  0.00      1.50000000000      2.10000000000     -0.43000000000


For Co.pbe-nd-rrkjus.UPF, 

nl pn  l   occ               Rcut            Rcut US             E pseu
4S  1  0  1.00      2.20000000000      2.50000000000      0.00000000000
4S  1  0  0.00      2.20000000000      2.50000000000      0.00000000000
4P  2  1  0.00      2.40000000000      2.60000000000      0.00000000000
4P  2  1  0.00      2.40000000000      2.60000000000      0.00000000000
3D  3  2  8.00      1.50000000000      2.10000000000      0.00000000000
3D  3  2  0.00      1.50000000000      2.10000000000      0.00000000000




-------
Chan-Woo Lee,?Ph.D.
Postdoctoral Research Associate

Room 265
Department of Chemistry
University of Pennsylvania
231 South 34th Street
Philadelphia, PA 19104-6323 
Phone: 1-215-898-3564 (Office)
Email: leechanw at sas.upenn.edu / cwandtj at gmail.com






From eiklm at mail.ru  Sun Jan  8 23:13:27 2012
From: eiklm at mail.ru (=?UTF-8?B?0JPRgNC40YjQsCDQk9C+0L3Rh9Cw0YDQvtCy0YHQutC40Lk=?=)
Date: Mon, 09 Jan 2012 02:13:27 +0400
Subject: [Pw_forum] =?utf-8?q?Too_low_speed_of_sound_in_quartz?=
Message-ID: <E1Rk0zX-0007r3-00.eiklm-mail-ru@f169.mail.ru>

Dear QE developers and users,

I've calculated phonon dispersion for alpha-quartz. It gives for acoustic branches at Gamma --- A direction:

q (2*pi/a_0) ? ? ? omega_1 ? omega_2 ? omega_3 (cm^(-1))
------------------------------------------------------------------
0.00000000 ? ? ? -1.1614 ? ? ?-0.8602 ? ? ? -0.7608
0.045470455 ? ? ?9.2277 ? ? ?18.1443 ? ? 24.0697
0.09094091 ? ? ? 21.8192 ? ? 34.5505 ? ? 47.4024
. . .Differentiating these dispersion relations I found that the speed of the "fastest" sound waves is about 1000 m/sec, while the simple mechanical calculation (as well as reference data) gives at least a five times larger value.

My scf input:

&control
 calculation='scf',
 restart_mode='from_scratch',
 prefix='sio2',
 pseudo_dir = '/home/user/espresso/pseudo',
 outdir='/home/user/espresso/tmp'
 /
 &system
 ibrav=4,
 celldm(1)=9.289897331,
 celldm(3)=1.099552482,
 nat= 9, ntyp= 2,
 ecutwfc = 20.0
 ecutrho = 150.0
 /
 &electrons
 electron_maxstep=1000
 mixing_mode = 'plain'
 mixing_beta = 0.7
 conv_thr = 1.0d-8
 /
ATOMIC_SPECIES
 Si 28.086 Si.pw91-n-van.UPF
 O 15.999 O.pw91-van_ak.UPF
ATOMIC_POSITIONS crystal
Si 0.465976452 0.000000000 0.000000000
Si -0.000045477 0.465778133 0.666710600
Si -0.465823610 -0.465778133 0.333289400
O 0.410406470 0.274336629 0.112688982
O -0.274215479 0.135800008 0.779283047
O -0.136110820 -0.409868933 0.446516439
O 0.273758113 0.409868933 0.553483561
O -0.410015489 -0.135800008 0.220716953
O 0.136069841 -0.274336629 -0.112688982
K_POINTS automatic
4 4 4 0 0 0


Phonon input:
phonons of SiO_2
 &inputph
 tr2_ph=1.0d-12,
 prefix='sio2',
 ldisp=.true.,
 nq1=2, nq2=2, nq3=2
 amass(1)=28.086,
 amass(2)=15.999,
 outdir='/home/user/espresso/tmp',
 fildyn='sio2.dyn',
 /

Does anyone know the origin of such?discrepancy??Regards,
Mikhail Goncharovskii,
postgraduate student, Omsk State University, Russia


-------------------------------------------------------------------------------------------------------------------
Please, if possible, don't send me MS Word or PowerPoint attachments.
Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
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From baroni at sissa.it  Mon Jan  9 07:39:42 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Mon, 9 Jan 2012 07:39:42 +0100
Subject: [Pw_forum] Too low speed of sound in quartz
In-Reply-To: <E1Rk0zX-0007r3-00.eiklm-mail-ru@f169.mail.ru>
References: <E1Rk0zX-0007r3-00.eiklm-mail-ru@f169.mail.ru>
Message-ID: <AACDF637-3312-4D87-8293-54E34053F0FA@sissa.it>

Dear Mikhail,

I have only faint memories of things done long ago, but I kind of remember that making elastic constants (EC) calculated from sound velocities match with those obtained by "frozen strain" calculations is a far-from-trivial task. The reason is, when you try to convert one expression into the other, you realize that ECs can actually be expressed as some moments (don't remember exactly which one) of the interatomic force constants (IFC). This means that the former are very sensitive to the long-range behavior of the latter. This imply, in turn, that in order to have good ECs you have to have many (and accurate) IFCs, which can only be obtained from a correspondingly fine grid of wave-vectors at which the phonon frequencies are sampled.

The factor of five that you find in the difference between the two calculations seems to me a bit too large to be explained by the above arguments, and you may want to cross-check all of your algebra, but once you are sure that the algebra is OK, the above considerations are worth considering and understanding in somewhat more detail than I have given. Before proceeding you may want to give your mastering of the whole subject a final check by calculating the elastic constants of, say, bulk silicon, which is a case you can treat with arbitrary accuracy on any laptop ...

HTH - good luck!
SB

On Jan 8, 2012, at 11:13 PM, ????? ???????????? wrote:

> Dear QE developers and users,
> 
> I've calculated phonon dispersion for alpha-quartz. It gives for acoustic branches at Gamma --- A direction:
> 
> q (2*pi/a_0)       omega_1   omega_2   omega_3 (cm^(-1))
> ------------------------------------------------------------------
> 0.00000000       -1.1614      -0.8602       -0.7608
> 0.045470455      9.2277      18.1443     24.0697
> 0.09094091       21.8192     34.5505     47.4024
> . . .
> 
> Differentiating these dispersion relations I found that the speed of the "fastest" sound waves is about 1000 m/sec, while the simple mechanical calculation (as well as reference data) gives at least a five times larger value.
> 
> My scf input:
> 
> &control
> calculation='scf',
> restart_mode='from_scratch',
> prefix='sio2',
> pseudo_dir = '/home/user/espresso/pseudo',
> outdir='/home/user/espresso/tmp'
> /
> &system
> ibrav=4,
> celldm(1)=9.289897331,
> celldm(3)=1.099552482,
> nat= 9, ntyp= 2,
> ecutwfc = 20.0
> ecutrho = 150.0
> /
> &electrons
> electron_maxstep=1000
> mixing_mode = 'plain'
> mixing_beta = 0.7
> conv_thr = 1.0d-8
> /
> ATOMIC_SPECIES
> Si 28.086 Si.pw91-n-van.UPF
> O 15.999 O.pw91-van_ak.UPF
> ATOMIC_POSITIONS crystal
> Si 0.465976452 0.000000000 0.000000000
> Si -0.000045477 0.465778133 0.666710600
> Si -0.465823610 -0.465778133 0.333289400
> O 0.410406470 0.274336629 0.112688982
> O -0.274215479 0.135800008 0.779283047
> O -0.136110820 -0.409868933 0.446516439
> O 0.273758113 0.409868933 0.553483561
> O -0.410015489 -0.135800008 0.220716953
> O 0.136069841 -0.274336629 -0.112688982
> K_POINTS automatic
> 4 4 4 0 0 0
> 
> 
> Phonon input:
> 
> phonons of SiO_2
> &inputph
> tr2_ph=1.0d-12,
> prefix='sio2',
> ldisp=.true.,
> nq1=2, nq2=2, nq3=2
> amass(1)=28.086,
> amass(2)=15.999,
> outdir='/home/user/espresso/tmp',
> fildyn='sio2.dyn',
> /
> 
> 
> Does anyone know the origin of such discrepancy? 
> 
> Regards,
> Mikhail Goncharovskii,
> postgraduate student, Omsk State University, Russia
> 
> 
> -------------------------------------------------------------------------------------------------------------------
> Please, if possible, don't send me MS Word or PowerPoint attachments.
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From hicpalm at gmail.com  Mon Jan  9 11:11:46 2012
From: hicpalm at gmail.com (hichem bouderba)
Date: Mon, 9 Jan 2012 10:11:46 +0000
Subject: [Pw_forum] phonon frenquecies convergences
Message-ID: <CADnCFAPtpRRxYVXuLvzRZpbojnihKESJtt8w6br=T5W++tMRQw@mail.gmail.com>

Dear all,

1) It is a question about convergence study of phonon frequencies.
Suppose that one performs a convergence study for just one q-point  (say
Gamma for example),
is it reasonable to expect that results will be reliable for other q-points
?

2)
this is a comment about the input card "dos" in the matdyn.f90 file:

 !     dos       if .true. calculate phonon Density of States (DOS)
 !               using tetrahedra and a uniform q-point grid (see below)
 !               NB: may not work properly in noncubic materials

Does the last line mean :
(a) Do not use it with non cubic symmetries.
(b) One may use it, but results should be carrefuly checked for eventual
problems. In this case, wath kind of problems one may expect.

thank you for comments and suggestions.
regards.

-- 
Hichem Bouderba
d?partement de physique
Universit? de Batna
Alg?rie
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From giannozz at democritos.it  Mon Jan  9 11:21:04 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 09 Jan 2012 11:21:04 +0100
Subject: [Pw_forum] Understanding Co psp (by Dr. Andrea Dal Corso)
	from	QE website
In-Reply-To: <002201ccce51$58367ae0$08a370a0$@gmail.com>
References: <002201ccce51$58367ae0$08a370a0$@gmail.com>
Message-ID: <1326104464.11811.9.camel@fe12lx.fisica.uniud.it>

On Sun, 2012-01-08 at 17:03 -0500, Chan-Woo Lee wrote:

> can anyone explain me why we have multiple lines 4s, 4p,
> and 3d sometimes identical occ but sometimes different occ (..)?

> For Co.rel-pz-n-rrkjus.UPF,

rel = with spin orbit

> nl pn  l   occ               Rcut            Rcut US             E pseu
> 4S  1  0  1.00      2.20000000000      2.50000000000     -0.33855297011
> 4S  1  0  0.00      2.20000000000      2.50000000000     -0.06831336257

two L=0 projectors: one generated starting from a bound 4S state at its
energy, the other from an unbound state at an energy given in input

> 4P  2  1  0.00      2.40000000000      2.60000000000     -0.06564055631
> 4P  2  1  0.00      2.40000000000      2.60000000000     -0.33727583802
> 4P  2  1  0.00      2.40000000000      2.60000000000     -0.32443820910
> 4P  2  1  0.00      2.40000000000      2.60000000000      0.10000000000

As above for L=1, but now there are J=1/2 and J=3/2 projectors

> 3D  3  2  4.00      1.50000000000      2.10000000000     -0.33733396598
> 3D  3  2  0.00      1.50000000000      2.10000000000     -0.43000000000
> 3D  3  2  4.00      1.50000000000      2.10000000000     -0.32449570554
> 3D  3  2  0.00      1.50000000000      2.10000000000     -0.43000000000

As above for L=2 (occupations of reference state: 4 electrons om J=3/2,
4 electrons in J=5/2 states)

> For Co.pbe-nd-rrkjus.UPF, 

no spin orbit

> nl pn  l   occ               Rcut            Rcut US             E pseu
> 4S  1  0  1.00      2.20000000000      2.50000000000      0.00000000000
> 4S  1  0  0.00      2.20000000000      2.50000000000      0.00000000000
> 4P  2  1  0.00      2.40000000000      2.60000000000      0.00000000000
> 4P  2  1  0.00      2.40000000000      2.60000000000      0.00000000000
> 3D  3  2  8.00      1.50000000000      2.10000000000      0.00000000000
> 3D  3  2  0.00      1.50000000000      2.10000000000      0.00000000000

two L=0, two L=1, two L=2 projectors. Typically, one is the bound
state, the other is for some suitably chosen energy

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From mourad_fsm at yahoo.fr  Mon Jan  9 11:23:39 2012
From: mourad_fsm at yahoo.fr (debbichi mourad)
Date: Mon, 9 Jan 2012 10:23:39 +0000 (GMT)
Subject: [Pw_forum] (no subject)
In-Reply-To: <mailman.1.1323419672.18984.pw_forum@pwscf.org>
References: <mailman.1.1323419672.18984.pw_forum@pwscf.org>
Message-ID: <1326104619.15056.YahooMailNeo@web29504.mail.ird.yahoo.com>

Dear pwscf users
I would like to do some calculations with LDA+U.
I would like to know the interval of the validity of potential U. 

Thanks in advance,

Sincerely
?Mourad


DEBBICHI Mourad
Unit? de Recherche Physique des Solides,99/UR/13-19,
D?partement de Physique, Facult? des Science de Monastir,
Avenue de l'Environnement 5019, Monastir Tunisie.
t?l:+21697487042
mourad_fsm at yahoo.fr


________________________________
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From sufeer03 at gmail.com  Mon Jan  9 12:01:22 2012
From: sufeer03 at gmail.com (sufyan)
Date: Mon, 9 Jan 2012 11:01:22 +0000
Subject: [Pw_forum] problem of installation make: *** [libiotk] Error 2
Message-ID: <CAOMC65ji2e2DSCunRSgi-uLsgd0S_OajyN7PFf3w5935iTByhA@mail.gmail.com>

Dears users,
i am new user in pw community  and i need your help ,i use  the version
espresso-4.3 on (opensuse, INTEL I5 64, ifort ,mkl) first i use the steps
in the user guide

./configure

 .but when i run make all  i have this in the end :

mpif90 -O3 -g -x f95-cpp-input -D__GFORTRAN -D__STD_F95 -D__FFTW3
-I../include  -c iotk_print_kinds.f90
make loclib_only
make[3]: Entering directory `/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src'
make[3]: Nothing to be done for `loclib_only'.
make[3]: Leaving directory `/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src'
mpif90 -g -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a
/usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:
cannot find -lmpi_f90
collect2: ld returned 1 exit status
make[2]: *** [iotk_print_kinds.x] Error 1
make[2]: Leaving directory `/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src'
make[1]: *** [libiotk] Error 2
make[1]: Leaving directory `/home/sufyan2020/qs/espresso-4.3/extlibs'
make: *** [libiotk] Error 2

thanks
sufyan naji
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From giannozz at democritos.it  Mon Jan  9 12:13:07 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 09 Jan 2012 12:13:07 +0100
Subject: [Pw_forum] problem of installation make: *** [libiotk] Error 2
In-Reply-To: <CAOMC65ji2e2DSCunRSgi-uLsgd0S_OajyN7PFf3w5935iTByhA@mail.gmail.com>
References: <CAOMC65ji2e2DSCunRSgi-uLsgd0S_OajyN7PFf3w5935iTByhA@mail.gmail.com>
Message-ID: <1326107587.14089.2.camel@fe12lx.fisica.uniud.it>

On Mon, 2012-01-09 at 11:01 +0000, sufyan wrote:

> mpif90 -g -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a
> /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld: cannot find -lmpi_f90

apparently you have a parallel compiler that looks good enough to be
accepted by configure, but it is not properly installed, or in any
event, it doesn't work properly for fortran 90. Use 
"./configure --disable-parallel"

P.

-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From giannozz at democritos.it  Mon Jan  9 12:17:18 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 09 Jan 2012 12:17:18 +0100
Subject: [Pw_forum] phonon frenquecies convergences
In-Reply-To: <CADnCFAPtpRRxYVXuLvzRZpbojnihKESJtt8w6br=T5W++tMRQw@mail.gmail.com>
References: <CADnCFAPtpRRxYVXuLvzRZpbojnihKESJtt8w6br=T5W++tMRQw@mail.gmail.com>
Message-ID: <1326107838.14089.7.camel@fe12lx.fisica.uniud.it>

On Mon, 2012-01-09 at 10:11 +0000, hichem bouderba wrote:

> Suppose that one performs a convergence study for just one q-point
> (say Gamma for example), is it reasonable to expect that results will
> be reliable for other q-points ?

if you check convergence wrt cutoff, or wrt k-points in insulators, 
I would say it is reliable. Convergence wrt k-points may be very 
tricky in metals, though, due to the presence of Kohn anomalies.

> Does the last line mean :
> (a) Do not use it with non cubic symmetries.
> (b) One may use it, but results should be carefully checked for
> eventual problems. In this case, wath kind of problems one may expect.

no major problems, I think: the DOS close to Gamma may be inaccurate

P.

-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From sufeer03 at gmail.com  Mon Jan  9 12:19:08 2012
From: sufeer03 at gmail.com (sufyan)
Date: Mon, 9 Jan 2012 11:19:08 +0000
Subject: [Pw_forum] problem of installation make: *** [libiotk] Error 2
In-Reply-To: <1326107587.14089.2.camel@fe12lx.fisica.uniud.it>
References: <CAOMC65ji2e2DSCunRSgi-uLsgd0S_OajyN7PFf3w5935iTByhA@mail.gmail.com>
	<1326107587.14089.2.camel@fe12lx.fisica.uniud.it>
Message-ID: <CAOMC65gQvUMswuAp1M7BuBqpr6W9ch8dr1MnLey6e4eDG44btw@mail.gmail.com>

Dear  Paolo Giannozzi
thank you for time ,i have ifort
but when i do this i have
home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:141: undefined
reference to `_gfortran_st_write'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:141: undefined
reference to `_gfortran_transfer_real'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:141: undefined
reference to `_gfortran_st_write_done'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_adjustl'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_string_trim'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_concat_string'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_os_error'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_runtime_error'
make[2]: *** [iotk_print_kinds.x] Error 1
make[2]: Leaving directory `/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src'
make[1]: *** [libiotk] Error 2
make[1]: Leaving directory `/home/sufyan2020/qs/espresso-4.3/extlibs'
make: *** [libiotk] Error 2


2012/1/9 Paolo Giannozzi <giannozz at democritos.it>

> On Mon, 2012-01-09 at 11:01 +0000, sufyan wrote:
>
> > mpif90 -g -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a
> >
> /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:
> cannot find -lmpi_f90
>
> apparently you have a parallel compiler that looks good enough to be
> accepted by configure, but it is not properly installed, or in any
> event, it doesn't work properly for fortran 90. Use
> "./configure --disable-parallel"
>
> P.
>
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From giannozz at democritos.it  Mon Jan  9 12:24:15 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 09 Jan 2012 12:24:15 +0100
Subject: [Pw_forum] problem of installation make: *** [libiotk] Error 2
In-Reply-To: <CAOMC65gQvUMswuAp1M7BuBqpr6W9ch8dr1MnLey6e4eDG44btw@mail.gmail.com>
References: <CAOMC65ji2e2DSCunRSgi-uLsgd0S_OajyN7PFf3w5935iTByhA@mail.gmail.com>
	<1326107587.14089.2.camel@fe12lx.fisica.uniud.it>
	<CAOMC65gQvUMswuAp1M7BuBqpr6W9ch8dr1MnLey6e4eDG44btw@mail.gmail.com>
Message-ID: <1326108255.14089.10.camel@fe12lx.fisica.uniud.it>

On Mon, 2012-01-09 at 11:19 +0000, sufyan wrote:

> thank you for time ,i have ifort
> but when i do this i have
> home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:141: undefined reference to `_gfortran_st_write'

make clean
./configure --disable-parallel

P.

-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From sufeer03 at gmail.com  Mon Jan  9 12:25:45 2012
From: sufeer03 at gmail.com (sufyan)
Date: Mon, 9 Jan 2012 11:25:45 +0000
Subject: [Pw_forum] problem of installation make: *** [libiotk] Error 2
In-Reply-To: <CAOMC65gQvUMswuAp1M7BuBqpr6W9ch8dr1MnLey6e4eDG44btw@mail.gmail.com>
References: <CAOMC65ji2e2DSCunRSgi-uLsgd0S_OajyN7PFf3w5935iTByhA@mail.gmail.com>
	<1326107587.14089.2.camel@fe12lx.fisica.uniud.it>
	<CAOMC65gQvUMswuAp1M7BuBqpr6W9ch8dr1MnLey6e4eDG44btw@mail.gmail.com>
Message-ID: <CAOMC65jeXDHJ3rNjApDShJv7Oc02FWzfLtp=UCFEqU=UJkfRqA@mail.gmail.com>

Dear  Paolo Giannozzi
thank you for time ,i have ifort
but when i do this ./configure --disable-parallel
i have this
home/sufyan2020/qs/espresso-4.
3/S3DE/iotk/src/iotk_attr.spp:141: undefined reference to
`_gfortran_st_write'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:141: undefined
reference to `_gfortran_transfer_real'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:141: undefined
reference to `_gfortran_st_write_done'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_adjustl'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_string_trim'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_concat_string'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_os_error'
/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146: undefined
reference to `_gfortran_runtime_error'

make[2]: *** [iotk_print_kinds.x] Error 1
make[2]: Leaving directory `/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src'
make[1]: *** [libiotk] Error 2
make[1]: Leaving directory `/home/sufyan2020/qs/espresso-4.3/extlibs'
make: *** [libiotk] Error 2
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From giannozz at democritos.it  Mon Jan  9 12:31:58 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 09 Jan 2012 12:31:58 +0100
Subject: [Pw_forum] problem of installation make: *** [libiotk] Error 2
In-Reply-To: <CAOMC65jeXDHJ3rNjApDShJv7Oc02FWzfLtp=UCFEqU=UJkfRqA@mail.gmail.com>
References: <CAOMC65ji2e2DSCunRSgi-uLsgd0S_OajyN7PFf3w5935iTByhA@mail.gmail.com>
	<1326107587.14089.2.camel@fe12lx.fisica.uniud.it>
	<CAOMC65gQvUMswuAp1M7BuBqpr6W9ch8dr1MnLey6e4eDG44btw@mail.gmail.com>
	<CAOMC65jeXDHJ3rNjApDShJv7Oc02FWzfLtp=UCFEqU=UJkfRqA@mail.gmail.com>
Message-ID: <1326108718.14089.17.camel@fe12lx.fisica.uniud.it>

remove all *.o *.a *.mod files in iotk/src/
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From sufeer03 at gmail.com  Mon Jan  9 12:42:37 2012
From: sufeer03 at gmail.com (sufyan)
Date: Mon, 9 Jan 2012 11:42:37 +0000
Subject: [Pw_forum] problem of installation make: *** [libiotk] Error 2
In-Reply-To: <CAOMC65gQvUMswuAp1M7BuBqpr6W9ch8dr1MnLey6e4eDG44btw@mail.gmail.com>
References: <CAOMC65ji2e2DSCunRSgi-uLsgd0S_OajyN7PFf3w5935iTByhA@mail.gmail.com>
	<1326107587.14089.2.camel@fe12lx.fisica.uniud.it>
	<CAOMC65gQvUMswuAp1M7BuBqpr6W9ch8dr1MnLey6e4eDG44btw@mail.gmail.com>
Message-ID: <CAOMC65jOg8JZeifMtux9gVGTm74=R3D5O-A1af0igQMOL2A32g@mail.gmail.com>

thanks it install without any problem
2012/1/9 sufyan <sufeer03 at gmail.com>

> Dear  Paolo Giannozzi
> thank you for time ,i have ifort
> but when i do this i have
> home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:141: undefined
> reference to `_gfortran_st_write'
> /home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:141:
> undefined reference to `_gfortran_transfer_real'
> /home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:141:
> undefined reference to `_gfortran_st_write_done'
> /home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146:
> undefined reference to `_gfortran_adjustl'
> /home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146:
> undefined reference to `_gfortran_string_trim'
> /home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146:
> undefined reference to `_gfortran_concat_string'
> /home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146:
> undefined reference to `_gfortran_os_error'
> /home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src/iotk_attr.spp:146:
> undefined reference to `_gfortran_runtime_error'
>
> make[2]: *** [iotk_print_kinds.x] Error 1
> make[2]: Leaving directory `/home/sufyan2020/qs/espresso-4.3/S3DE/iotk/src'
> make[1]: *** [libiotk] Error 2
> make[1]: Leaving directory `/home/sufyan2020/qs/espresso-4.3/extlibs'
> make: *** [libiotk] Error 2
>
>
> 2012/1/9 Paolo Giannozzi <giannozz at democritos.it>
>
>> On Mon, 2012-01-09 at 11:01 +0000, sufyan wrote:
>>
>> > mpif90 -g -o iotk_print_kinds.x iotk_print_kinds.o libiotk.a
>> >
>> /usr/lib64/gcc/x86_64-suse-linux/4.4/../../../../x86_64-suse-linux/bin/ld:
>> cannot find -lmpi_f90
>>
>> apparently you have a parallel compiler that looks good enough to be
>> accepted by configure, but it is not properly installed, or in any
>> event, it doesn't work properly for fortran 90. Use
>> "./configure --disable-parallel"
>>
>> P.
>>
>> --
>> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>
>
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From faccin.giovani at gmail.com  Mon Jan  9 13:49:47 2012
From: faccin.giovani at gmail.com (Giovani Faccin)
Date: Mon, 9 Jan 2012 08:49:47 -0400
Subject: [Pw_forum] Relation between cell magnetization and atomic
 magnetization in the non-collinear calculation
Message-ID: <CAK-VqZAeKYt6WjiLWYWHrUbuFwxvfxdn=bzzxOzb=dpvntLL9A@mail.gmail.com>

Dear PW-Users,

While performing a test calculation for a non-collinear Fe2 dimer without
spin-orbit, I get the following results (just printing the relevant part):


==============================================================================
     atom number    1 relative position :    0.1234   0.0000   0.0000
     charge :     5.500331
     magnetization :          0.000000    0.000000    2.549039
     magnetization/charge:    0.000000    0.000000    0.463434
     polar coord.: r, theta, phi [deg] :     2.549039    0.000000
360.000000

 ==============================================================================

 ==============================================================================
     atom number    2 relative position :    0.0001   0.0000   0.0000
     charge :     5.500187
     magnetization :          0.000000    0.000000    2.548980
     magnetization/charge:    0.000000    0.000000    0.463435
     polar coord.: r, theta, phi [deg] :     2.548980    0.000000
360.000000

 ==============================================================================

(little more output here, then)

    total magnetization       =     0.00     0.00     6.00 Bohr mag/cell
     absolute magnetization    =     6.36 Bohr mag/cell


The cell magnetization prints 6.0 Bohr/cell, which is the expected result.
However, the atomic magnetization prints 2.549039 + 2.548980 ~ 5.10 mB.

I'm wondering: why is not the atomic magnetization sum equal (or very close
to) the cell magnetization? If needed, the input file is attached.

Thanks in advance.

Giovani Faccin
UFMS / Brazil








Giovani
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 &CONTROL
                 calculation = 'relax' ,
                restart_mode = 'from_scratch' ,
                  wf_collect = .true. ,
                      outdir = './output' ,
                  pseudo_dir = './pseudo/' ,
                      prefix = 'fe2' ,
               etot_conv_thr = 1.0D-6 ,
               forc_conv_thr = 1.0D-4 ,
                     tstress = .false. ,
                     tprnfor = .true. ,
 /
 &SYSTEM
                       ibrav = 1,
                   celldm(1) = 30,
                         nat = 2,
                        ntyp = 2,
                     ecutwfc = 100 ,
                     ecutrho = 1200 ,
                        nbnd = 50,
                 occupations = 'smearing' ,
                     degauss = 0.0005 ,
                    smearing = 'methfessel-paxton' ,
   starting_magnetization(1) = 0.7,
                  lda_plus_u = .false. ,
                Hubbard_U(1) = 1.0d-9,
		Hubbard_U(2) = 1.0d-9,
             assume_isolated = 'none' ,
                    noncolin = .TRUE.,
                   angle1(1) = 0,
                   angle2(1) = 0,
 /
 &ELECTRONS
            electron_maxstep = 2500,
                    conv_thr = 1.0e-8 ,
                 mixing_beta = 0.4 ,
             diagonalization = 'david' ,
 /
 &IONS
 /
ATOMIC_SPECIES
   Fe   55.845  Fe.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS angstrom 
Fe      1.96       0.000000000    0.000000000    
Fe      0.000000000    0.000000000    0.000000000
K_POINTS {automatic}
1 1 1 1 1 1






           

From hicpalm at gmail.com  Mon Jan  9 13:51:58 2012
From: hicpalm at gmail.com (hichem bouderba)
Date: Mon, 9 Jan 2012 13:51:58 +0100
Subject: [Pw_forum] phonon frenquecies convergences
In-Reply-To: <1326107838.14089.7.camel@fe12lx.fisica.uniud.it>
References: <CADnCFAPtpRRxYVXuLvzRZpbojnihKESJtt8w6br=T5W++tMRQw@mail.gmail.com>
	<1326107838.14089.7.camel@fe12lx.fisica.uniud.it>
Message-ID: <CADnCFAP8TphhtO9=FtFJzkNTYTFMme-NPwP-GQroeZNZjMsBHg@mail.gmail.com>

thank you.

On 1/9/12, Paolo Giannozzi <giannozz at democritos.it> wrote:
> On Mon, 2012-01-09 at 10:11 +0000, hichem bouderba wrote:
>
>> Suppose that one performs a convergence study for just one q-point
>> (say Gamma for example), is it reasonable to expect that results will
>> be reliable for other q-points ?
>
> if you check convergence wrt cutoff, or wrt k-points in insulators,
> I would say it is reliable. Convergence wrt k-points may be very
> tricky in metals, though, due to the presence of Kohn anomalies.
>
>> Does the last line mean :
>> (a) Do not use it with non cubic symmetries.
>> (b) One may use it, but results should be carefully checked for
>> eventual problems. In this case, wath kind of problems one may expect.
>
> no major problems, I think: the DOS close to Gamma may be inaccurate
>
> P.
>
> --
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


-- 
Mr. Hichem Bouderba
d?partement de physique
Universit? de Batna
Alg?rie

From bdslipun at gmail.com  Mon Jan  9 14:01:13 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Mon, 9 Jan 2012 18:31:13 +0530
Subject: [Pw_forum] bct_cell
Message-ID: <CAJVAAvDcyRYBhU74_z4TK+qpu7USw5Ji1g99isRpoz5wsN5pHA@mail.gmail.com>

i want to find the vibrational energy of a bct_cell
so i need tetra hedra file my c/a=.9
for this how can i find the vertex of cordinates






i have seen in the tetrahedra in put of bct cell in QHA code given
so how i can calculate my triinp_bct  file
 my question is how can i find the vertex by xcrysden
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From fratesi at mater.unimib.it  Mon Jan  9 15:08:49 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Mon, 09 Jan 2012 15:08:49 +0100
Subject: [Pw_forum] Relation between cell magnetization and atomic
 magnetization in the non-collinear calculation
In-Reply-To: <CAK-VqZAeKYt6WjiLWYWHrUbuFwxvfxdn=bzzxOzb=dpvntLL9A@mail.gmail.com>
References: <CAK-VqZAeKYt6WjiLWYWHrUbuFwxvfxdn=bzzxOzb=dpvntLL9A@mail.gmail.com>
Message-ID: <4F0AF4F1.1050403@mater.unimib.it>

Dear Giovani,

the unit cell is not 100% filled by the atom-centered spheres where the 
quantities of your interest are computed. Notice that also the sum of 
the atomic charges (11) is different than the cell one (16?).

For information about such spheres, you might want to have a look in the 
output file to something like:

      Generating pointlists ...
      new r_m :   0.3457 (alat units)  1.8649 (a.u.) for type    1

and the subroutine in PW/make_pointlists.f90. From that file:

   ! This initialization is needed in order to integrate charge (or
   ! magnetic moment) in a sphere around the atomic positions.
   ! This can be used to simply monitor these quantities during the scf
   ! cycles or in order to calculate constrains on these quantities.
   !
   ! If the integration radius r_m is not provided in input, it is
   ! calculated here. The integration is a sum over all points in real
   ! space with the weight 1, if they are closer than r_m to an atom
   ! and 1 - (distance-r_m)/(0.2*r_m) if r_m<distance<1.2*r_m

HTH,
Guido

Il 01/09/2012 01:49 PM, Giovani Faccin ha scritto:
> Dear PW-Users,
>
> While performing a test calculation for a non-collinear Fe2 dimer
> without spin-orbit, I get the following results (just printing the
> relevant part):
>
>
> ==============================================================================
>       atom number    1 relative position :    0.1234   0.0000   0.0000
>       charge :     5.500331
>       magnetization :          0.000000    0.000000    2.549039
>       magnetization/charge:    0.000000    0.000000    0.463434
>       polar coord.: r, theta, phi [deg] :     2.549039    0.000000
> 360.000000
>
>   ==============================================================================
>
>   ==============================================================================
>       atom number    2 relative position :    0.0001   0.0000   0.0000
>       charge :     5.500187
>       magnetization :          0.000000    0.000000    2.548980
>       magnetization/charge:    0.000000    0.000000    0.463435
>       polar coord.: r, theta, phi [deg] :     2.548980    0.000000
> 360.000000
>
>   ==============================================================================
>
> (little more output here, then)
>
>      total magnetization       =     0.00     0.00     6.00 Bohr mag/cell
>       absolute magnetization    =     6.36 Bohr mag/cell
>
>
> The cell magnetization prints 6.0 Bohr/cell, which is the expected
> result. However, the atomic magnetization prints 2.549039 + 2.548980 ~
> 5.10 mB.
>
> I'm wondering: why is not the atomic magnetization sum equal (or very
> close to) the cell magnetization? If needed, the input file is attached.
>
> Thanks in advance.
>
> Giovani Faccin
> UFMS / Brazil
>
>
>
>
>
>
>
>
> Giovani
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy

From jean-roch.huntzinger at univ-montp2.fr  Mon Jan  9 15:53:54 2012
From: jean-roch.huntzinger at univ-montp2.fr (Jean-Roch Huntzinger)
Date: Mon, 9 Jan 2012 15:53:54 +0100
Subject: [Pw_forum] md calculation and constraints in 4.3.2
Message-ID: <201201091553.54410.jean-roch.huntzinger@univ-montp2.fr>

Dear all,

Are 'md' calculations compatible with constraints in 4.3.2 ?

The following error occurs :
"constraints only with damped dynamics and fixed cell"
(in acetylene.out attached)
with qe-4.3.2, following the nice hands-on tutorial, relaxation part, at
http://www.fisica.uniud.it/~giannozz/QE-Tutorial/
using the modified input acetylene-SHAKE_mod.in (attached)
(modified because the format seems to have changed a little since 
the writing of the tutorial)


But the INPUT_PW.html says that
CONSTRAINTS is an
"Optional card, used for constrained dynamics or constrained optimisations 
(only if ion_dynamics='damp' or 'verlet', variable-cell excepted)"
This is also supported by
CASE ( calculation = 'md' )
    'verlet' : (default)   use Verlet algorithm to integrate
                           Newton's equation. For constrained
                           dynamics, see CONSTRAINTS card

So constraints should work with md and verlet ?

but in PW/input.f90 there is, line 1436 :
  IF ( lconstrain ) THEN
     IF ( .NOT. ldamped .OR. lmovecell ) CALL errore( 'iosys', &
              'constraints only with damped dynamics and fixed cell', 1 )

which seems to forbid constraints with verlet ?
(This has been introduced in Revision 7099 )

Note: changing 'verlet' to 'langevin' yields the same error, 
And actually ldamped is not defined for 'md' calculations 
(ibid, lines 372-393)



Should 'md' calculations really work with constraints or not ?
Or am I missing anything ?


Best regards,
Jean-Roch Huntzinger

-- 
L2C/SMC UMR 5221 - Universit? Montpellier 2, CNRS
case courrier 074
34095 Montpellier cedex 5
tel: 04 67 14 41 38
fax: 04 67 14 37 60
-------------- next part --------------
 &CONTROL
                 calculation = 'md' ,
                restart_mode = 'restart' ,
                  pseudo_dir = './' ,
                       nstep = 50 ,
                          dt = 10.D0 ,
 /
 &SYSTEM
                       ibrav = 1,
                   celldm(1) = 10.D0,
                         nat = 4,
                        ntyp = 2,
                     ecutwfc = 24.0D0 ,
                     ecutrho = 144.0D0 ,
                       nosym = .true. ,
                 occupations = 'smearing' ,
                     degauss = 0.01D0 ,
                    smearing = 'gaussian' ,
 /
 &ELECTRONS
                    conv_thr = 1.D-7 ,
                 mixing_beta = 0.5D0 ,
 /
 &IONS
                ion_dynamics = 'verlet' ,
           pot_extrapolation = 'second_order' ,
           wfc_extrapolation = 'second_order' ,
 /
ATOMIC_SPECIES
    H    1.00000  H.US_PBE.RRKJ3.UPF 
    C   12.00000  C.US_PBE.RRKJ3.UPF 
ATOMIC_POSITIONS bohr 
    C      0.000000000    0.000000000    0.000000000    0  0  0 
    C      2.100000000    0.000000000    0.000000000    
    H     -1.600000000    0.400000000    0.000000000    
    H      3.600000000   -0.400000000    0.000000000    
K_POINTS gamma 
CONSTRAINTS
  3 1e-8 
  'planar_angle'       1 2 4
  'distance'      1 3 
  'distance'      2 4 

-------------- next part --------------

     Program PWSCF v.4.3.2      starts on  8Jan2012 at  2:15:46 

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org", 
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Reading input from stdin
     Reading   3 constraints; tolerance:    0.000000
         1) planar angle between atoms:   1  2  4
         2) distance between atoms:   1  3
         3) distance between atoms:   2  4
               file H.US_PBE.RRKJ3.UPF: wavefunction(s)  1S renormalized
               file C.US_PBE.RRKJ3.UPF: wavefunction(s)  2S 2P renormalized

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from iosys : error #         1
     constraints only with damped dynamics and fixed cell
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...

From giannozz at democritos.it  Mon Jan  9 16:25:41 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 09 Jan 2012 16:25:41 +0100
Subject: [Pw_forum] md calculation and constraints in 4.3.2
In-Reply-To: <201201091553.54410.jean-roch.huntzinger@univ-montp2.fr>
References: <201201091553.54410.jean-roch.huntzinger@univ-montp2.fr>
Message-ID: <1326122741.15779.14.camel@fe12lx.fisica.uniud.it>

On Mon, 2012-01-09 at 15:53 +0100, Jean-Roch Huntzinger wrote:

> in PW/input.f90 there is, line 1436 :
>   IF ( lconstrain ) THEN
>      IF ( .NOT. ldamped .OR. lmovecell ) CALL errore( 'iosys', &
>               'constraints only with damped dynamics and fixed cell', 1 )
> 
> which seems to forbid constraints with verlet ?

may I suggest experiment instead of theory? replace the above check 
with a weaker one

     IF ( lbfgs .OR. lmovecell ) CALL errore( 'iosys', &
                'constraints only with fixed-cell dynamics', 1 )

and please report if it works or not.

> Note: changing 'verlet' to 'langevin' yields the same error, 

"langevin" is a poorly documented unmaintained option

> And actually ldamped is not defined for 'md' calculations 

because it is used for minimization, not MD. There are two algorithms
for minimization, BFGS (no constraints) and damped Verlet (constraints
implemented)

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From faccin.giovani at gmail.com  Mon Jan  9 17:42:25 2012
From: faccin.giovani at gmail.com (Giovani Faccin)
Date: Mon, 9 Jan 2012 12:42:25 -0400
Subject: [Pw_forum] Relation between cell magnetization and atomic
 magnetization in the non-collinear calculation
In-Reply-To: <4F0AF4F1.1050403@mater.unimib.it>
References: <CAK-VqZAeKYt6WjiLWYWHrUbuFwxvfxdn=bzzxOzb=dpvntLL9A@mail.gmail.com>
	<4F0AF4F1.1050403@mater.unimib.it>
Message-ID: <CAK-VqZCMGX6RdzukoN3_tOkuv_B70j_5XG4=eNSPbGvOA7D1UA@mail.gmail.com>

Dear Guido,

Thank you very much!

Giovani


2012/1/9 Guido Fratesi <fratesi at mater.unimib.it>

> Dear Giovani,
>
> the unit cell is not 100% filled by the atom-centered spheres where the
> quantities of your interest are computed. Notice that also the sum of
> the atomic charges (11) is different than the cell one (16?).
>
> For information about such spheres, you might want to have a look in the
> output file to something like:
>
>      Generating pointlists ...
>      new r_m :   0.3457 (alat units)  1.8649 (a.u.) for type    1
>
> and the subroutine in PW/make_pointlists.f90. From that file:
>
>   ! This initialization is needed in order to integrate charge (or
>   ! magnetic moment) in a sphere around the atomic positions.
>   ! This can be used to simply monitor these quantities during the scf
>   ! cycles or in order to calculate constrains on these quantities.
>   !
>   ! If the integration radius r_m is not provided in input, it is
>   ! calculated here. The integration is a sum over all points in real
>   ! space with the weight 1, if they are closer than r_m to an atom
>   ! and 1 - (distance-r_m)/(0.2*r_m) if r_m<distance<1.2*r_m
>
> HTH,
> Guido
>
> Il 01/09/2012 01:49 PM, Giovani Faccin ha scritto:
> > Dear PW-Users,
> >
> > While performing a test calculation for a non-collinear Fe2 dimer
> > without spin-orbit, I get the following results (just printing the
> > relevant part):
> >
> >
> >
> ==============================================================================
> >       atom number    1 relative position :    0.1234   0.0000   0.0000
> >       charge :     5.500331
> >       magnetization :          0.000000    0.000000    2.549039
> >       magnetization/charge:    0.000000    0.000000    0.463434
> >       polar coord.: r, theta, phi [deg] :     2.549039    0.000000
> > 360.000000
> >
> >
> ==============================================================================
> >
> >
> ==============================================================================
> >       atom number    2 relative position :    0.0001   0.0000   0.0000
> >       charge :     5.500187
> >       magnetization :          0.000000    0.000000    2.548980
> >       magnetization/charge:    0.000000    0.000000    0.463435
> >       polar coord.: r, theta, phi [deg] :     2.548980    0.000000
> > 360.000000
> >
> >
> ==============================================================================
> >
> > (little more output here, then)
> >
> >      total magnetization       =     0.00     0.00     6.00 Bohr mag/cell
> >       absolute magnetization    =     6.36 Bohr mag/cell
> >
> >
> > The cell magnetization prints 6.0 Bohr/cell, which is the expected
> > result. However, the atomic magnetization prints 2.549039 + 2.548980 ~
> > 5.10 mB.
> >
> > I'm wondering: why is not the atomic magnetization sum equal (or very
> > close to) the cell magnetization? If needed, the input file is attached.
> >
> > Thanks in advance.
> >
> > Giovani Faccin
> > UFMS / Brazil
> >
> >
> >
> >
> >
> >
> >
> >
> > Giovani
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
> --
> Guido Fratesi
>
> Dipartimento di Scienza dei Materiali
> Universita` degli Studi di Milano-Bicocca
> via Cozzi 53, 20125 Milano, Italy
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From cwandtj at gmail.com  Mon Jan  9 17:50:44 2012
From: cwandtj at gmail.com (Chan-Woo Lee)
Date: Mon, 9 Jan 2012 11:50:44 -0500
Subject: [Pw_forum] Understanding Co psp (by Dr. Andrea Dal Corso)
	from	QE website
In-Reply-To: <1326104464.11811.9.camel@fe12lx.fisica.uniud.it>
References: <002201ccce51$58367ae0$08a370a0$@gmail.com>
	<1326104464.11811.9.camel@fe12lx.fisica.uniud.it>
Message-ID: <003401ccceee$d56cfe10$8046fa30$@gmail.com>

Thank you for your reply, Prof. Giannozzi.

I will only focus on non-spin-orbit psp for now. While you explained that
for two projectors,"typically",  one is the bound state, the other is for
some suitably chosen energy. My question is that E_pseu are identical for
each L projector. 
For instance, two 4p projectors are identical. Also, two 3d projectors are
identical except their different occupations (8.00 and 0.0 respectively). Is
this normal? Two projectors with same E level? 

nl pn  l   occ               Rcut            Rcut US            E pseu
4S  1  0  1.00      2.20000000000      2.50000000000      0.00000000000
4S  1  0  0.00      2.20000000000      2.50000000000      0.00000000000
4P  2  1  0.00      2.40000000000      2.60000000000      0.00000000000
4P  2  1  0.00      2.40000000000      2.60000000000      0.00000000000
3D  3  2  8.00      1.50000000000      2.10000000000      0.00000000000
3D  3  2  0.00      1.50000000000      2.10000000000      0.00000000000

Thank you for your help in advance. 

Chan-Woo

-------
Chan-Woo Lee, Ph.D.
Postdoctoral Research Associate

Room 265
Department of Chemistry
University of Pennsylvania
231 South 34th Street
Philadelphia, PA 19104-6323 
Phone: 1-215-898-3564 (Office)
Email: leechanw at sas.upenn.edu / cwandtj at gmail.com



-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Paolo Giannozzi
Sent: Monday, January 09, 2012 5:21 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] Understanding Co psp (by Dr. Andrea Dal Corso) from
QE website

On Sun, 2012-01-08 at 17:03 -0500, Chan-Woo Lee wrote:

> can anyone explain me why we have multiple lines 4s, 4p, and 3d 
> sometimes identical occ but sometimes different occ (..)?

> For Co.rel-pz-n-rrkjus.UPF,

rel = with spin orbit

> nl pn  l   occ               Rcut            Rcut US             E pseu
> 4S  1  0  1.00      2.20000000000      2.50000000000     -0.33855297011
> 4S  1  0  0.00      2.20000000000      2.50000000000     -0.06831336257

two L=0 projectors: one generated starting from a bound 4S state at its
energy, the other from an unbound state at an energy given in input

> 4P  2  1  0.00      2.40000000000      2.60000000000     -0.06564055631
> 4P  2  1  0.00      2.40000000000      2.60000000000     -0.33727583802
> 4P  2  1  0.00      2.40000000000      2.60000000000     -0.32443820910
> 4P  2  1  0.00      2.40000000000      2.60000000000      0.10000000000

As above for L=1, but now there are J=1/2 and J=3/2 projectors

> 3D  3  2  4.00      1.50000000000      2.10000000000     -0.33733396598
> 3D  3  2  0.00      1.50000000000      2.10000000000     -0.43000000000
> 3D  3  2  4.00      1.50000000000      2.10000000000     -0.32449570554
> 3D  3  2  0.00      1.50000000000      2.10000000000     -0.43000000000

As above for L=2 (occupations of reference state: 4 electrons om J=3/2,
4 electrons in J=5/2 states)

> For Co.pbe-nd-rrkjus.UPF,

no spin orbit

> nl pn  l   occ               Rcut            Rcut US             E pseu
> 4S  1  0  1.00      2.20000000000      2.50000000000      0.00000000000
> 4S  1  0  0.00      2.20000000000      2.50000000000      0.00000000000
> 4P  2  1  0.00      2.40000000000      2.60000000000      0.00000000000
> 4P  2  1  0.00      2.40000000000      2.60000000000      0.00000000000
> 3D  3  2  8.00      1.50000000000      2.10000000000      0.00000000000
> 3D  3  2  0.00      1.50000000000      2.10000000000      0.00000000000

two L=0, two L=1, two L=2 projectors. Typically, one is the bound state, the
other is for some suitably chosen energy

P.
--
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


From jean-roch.huntzinger at univ-montp2.fr  Mon Jan  9 17:57:45 2012
From: jean-roch.huntzinger at univ-montp2.fr (Jean-Roch Huntzinger)
Date: Mon, 9 Jan 2012 17:57:45 +0100
Subject: [Pw_forum] md calculation and constraints in 4.3.2
In-Reply-To: <1326122741.15779.14.camel@fe12lx.fisica.uniud.it>
References: <201201091553.54410.jean-roch.huntzinger@univ-montp2.fr>
	<1326122741.15779.14.camel@fe12lx.fisica.uniud.it>
Message-ID: <201201091757.45499.jean-roch.huntzinger@univ-montp2.fr>

On Monday, January 09, 2012 16:25:41 Paolo Giannozzi wrote:
> may I suggest experiment instead of theory? 

Sure !

> replace the above check
> with a weaker one
> 
>      IF ( lbfgs .OR. lmovecell ) CALL errore( 'iosys', &
>                 'constraints only with fixed-cell dynamics', 1 )
> 
> and please report if it works or not.

It works (patch attached for convenience). 
And with xcrysden animation,
at first sight the constraints seem fulfilled,
thank you !

Should I file a bug report ? 
 
And thank you also for the additional explanations.

Best regards,
Jean-Roch Huntzinger

-- 
L2C/SMC UMR 5221 - Universit? Montpellier 2, CNRS
case courrier 074
34095 Montpellier cedex 5
tel: 04 67 14 41 38
fax: 04 67 14 37 60
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From giannozz at democritos.it  Mon Jan  9 18:14:07 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 09 Jan 2012 18:14:07 +0100
Subject: [Pw_forum] Understanding Co psp (by Dr. Andrea Dal
	Corso)	from	QE website
In-Reply-To: <003401ccceee$d56cfe10$8046fa30$@gmail.com>
References: <002201ccce51$58367ae0$08a370a0$@gmail.com>
	<1326104464.11811.9.camel@fe12lx.fisica.uniud.it>
	<003401ccceee$d56cfe10$8046fa30$@gmail.com>
Message-ID: <1326129247.17580.1.camel@fe12lx.fisica.uniud.it>

On Mon, 2012-01-09 at 11:50 -0500, Chan-Woo Lee wrote:

> My question is that E_pseu are identical for each L projector. 

they aren't. Most likely the file was written by an old version of
the tomic code that didn't save all the needed info

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From giannozz at democritos.it  Mon Jan  9 18:31:26 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 09 Jan 2012 18:31:26 +0100
Subject: [Pw_forum] md calculation and constraints in 4.3.2
In-Reply-To: <201201091757.45499.jean-roch.huntzinger@univ-montp2.fr>
References: <201201091553.54410.jean-roch.huntzinger@univ-montp2.fr>
	<1326122741.15779.14.camel@fe12lx.fisica.uniud.it>
	<201201091757.45499.jean-roch.huntzinger@univ-montp2.fr>
Message-ID: <1326130286.17580.3.camel@fe12lx.fisica.uniud.it>

On Mon, 2012-01-09 at 17:57 +0100, Jean-Roch Huntzinger wrote:

> It works (patch attached for convenience). 
> [...] Should I file a bug report ? 

I can fix it. Than you

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From rahen29 at yahoo.com  Mon Jan  9 18:55:49 2012
From: rahen29 at yahoo.com (Rahen Badsha)
Date: Mon, 9 Jan 2012 09:55:49 -0800 (PST)
Subject: [Pw_forum] k-point
Message-ID: <1326131749.88634.YahooMailNeo@web44704.mail.sp1.yahoo.com>

Dear All,
I am a new user of QE. I have a question.

What is meant by k-points in pwscf?


Regards,
Md. Rahen Badsha (Raihan)

A Post Graguate Thesis Student of Rajshahi University, Bangladesh.
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From rahen29 at yahoo.com  Mon Jan  9 18:55:49 2012
From: rahen29 at yahoo.com (Rahen Badsha)
Date: Mon, 9 Jan 2012 09:55:49 -0800 (PST)
Subject: [Pw_forum] k-point
Message-ID: <1326131749.88634.YahooMailNeo@web44704.mail.sp1.yahoo.com>

Dear All,
I am a new user of QE. I have a question.

What is meant by k-points in pwscf?


Regards,
Md. Rahen Badsha (Raihan)

A Post Graguate Thesis Student of Rajshahi University, Bangladesh.
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From avallabh at purdue.edu  Tue Jan 10 00:38:14 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Mon, 9 Jan 2012 18:38:14 -0500 (EST)
Subject: [Pw_forum] query on k-points with MP
In-Reply-To: <1068884647.254737.1326151643282.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <1429284447.254758.1326152293970.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear users,

           I am doing some scf calculations with K-points specified by the Monkhorst-Pack grid scheme. In the output file,  only the k-points in the IBZ are shown. Is there any way i can see all the K-points in the entire BZ? I just want to make sure certain K points are included. 


Thanks
Ajit 

From yunpengwang at live.com  Tue Jan 10 05:33:32 2012
From: yunpengwang at live.com (Peter Wang)
Date: Tue, 10 Jan 2012 12:33:32 +0800
Subject: [Pw_forum] query on k-points with MP
In-Reply-To: <1429284447.254758.1326152293970.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <1429284447.254758.1326152293970.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <SNT108-DS221E195CDD432059061F1CC2990@phx.gbl>

You can give k-points in input file explicitly, that is, you write them one 
by one. I think this may work.

Yun-Peng

-----????----- 
From: Ajit Vallabhaneni
Sent: Tuesday, January 10, 2012 7:38 AM
To: PWSCF Forum
Subject: [Pw_forum] query on k-points with MP

Dear users,

           I am doing some scf calculations with K-points specified by the 
Monkhorst-Pack grid scheme. In the output file,  only the k-points in the 
IBZ are shown. Is there any way i can see all the K-points in the entire BZ? 
I just want to make sure certain K points are included.


Thanks
Ajit
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 


From yunpengwang at live.com  Tue Jan 10 05:37:08 2012
From: yunpengwang at live.com (Peter Wang)
Date: Tue, 10 Jan 2012 12:37:08 +0800
Subject: [Pw_forum] k-point
In-Reply-To: <1326131749.88634.YahooMailNeo@web44704.mail.sp1.yahoo.com>
References: <1326131749.88634.YahooMailNeo@web44704.mail.sp1.yahoo.com>
Message-ID: <SNT108-DS163B7004745862B6829BD8C2990@phx.gbl>

k-points are used for integration over BZ which is described in any DFT book.

Yun-Peng

From: Rahen Badsha 
Sent: Tuesday, January 10, 2012 1:55 AM
To: pw_forum at pwscf.org 
Cc: pw_forum at pwscf.org 
Subject: [Pw_forum] k-point

Dear All,
I am a new user of QE. I have a question.

What is meant by k-points in pwscf?


Regards,
Md. Rahen Badsha (Raihan)

A Post Graguate Thesis Student of Rajshahi University, Bangladesh.



--------------------------------------------------------------------------------
_______________________________________________
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Pw_forum at pwscf.org
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From baroni at sissa.it  Tue Jan 10 07:43:38 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 10 Jan 2012 07:43:38 +0100
Subject: [Pw_forum] phonon frenquecies convergences
In-Reply-To: <1326107838.14089.7.camel@fe12lx.fisica.uniud.it>
References: <CADnCFAPtpRRxYVXuLvzRZpbojnihKESJtt8w6br=T5W++tMRQw@mail.gmail.com>
	<1326107838.14089.7.camel@fe12lx.fisica.uniud.it>
Message-ID: <CB13980B-CFFB-409B-B5D6-F8B96A769882@sissa.it>


On Jan 9, 2012, at 12:17 PM, Paolo Giannozzi wrote:

> On Mon, 2012-01-09 at 10:11 +0000, hichem bouderba wrote:
> 
>> Suppose that one performs a convergence study for just one q-point
>> (say Gamma for example), is it reasonable to expect that results will
>> be reliable for other q-points ?
> 
> if you check convergence wrt cutoff, or wrt k-points in insulators, 
> I would say it is reliable. Convergence wrt k-points may be very 
> tricky in metals, though, due to the presence of Kohn anomalies.

One more word of caution. You should understand what convergence stems from. If you think about it, you will realize that phonon frequencies depend critically on electronic screening. The latter, in turn, is expressed in terms of the independent-electron susceptibility, whose expression contains differences between empty and conduction energies at the denominator. That's the technical reason for Kohn anomalies. I do not have examples handy, but I could imagine cases where E_c(k+q)-E_v(k) may depend sensitively on q (typically, in a semi-metal), for which the convergence of phonon frequencies on q may be not so obvious. Again, I think that Paolo's answer is correct as a rule of thumb, but you better make sure you understand why ...

SB


---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From baroni at sissa.it  Tue Jan 10 07:52:20 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 10 Jan 2012 07:52:20 +0100
Subject: [Pw_forum] query on k-points with MP
In-Reply-To: <SNT108-DS221E195CDD432059061F1CC2990@phx.gbl>
References: <1429284447.254758.1326152293970.JavaMail.root@mailhub016.itcs.purdue.edu>
	<SNT108-DS221E195CDD432059061F1CC2990@phx.gbl>
Message-ID: <767FA7FF-8A54-45BB-964F-F44CC74BE157@sissa.it>

> -----????----- 
> From: Ajit Vallabhaneni
> Sent: Tuesday, January 10, 2012 7:38 AM
> To: PWSCF Forum
> Subject: [Pw_forum] query on k-points with MP
> 
> Dear users,
> 
>           I am doing some scf calculations with K-points specified by the 
> Monkhorst-Pack grid scheme. In the output file,  only the k-points in the 
> IBZ are shown. Is there any way i can see all the K-points in the entire BZ? 
> I just want to make sure certain K points are included.

They are not. Only points in the IBZ are actually used, and the sums of the IBZ are then symmetrized with respect to the point group of the system.

On Jan 10, 2012, at 5:33 AM, Peter Wang wrote:

> You can give k-points in input file explicitly, that is, you write them one 
> by one. I think this may work.

It will. If you want just to make sure that the code work as you expect (it does, if your expectations are correct), you may want to compare the results produced by k-pt sampling in the IBZ, with those produced by feeding the computer with k-pts over the entire BZ, as Peter Wang suggest ...

SB
 

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From tavana.ali at gmail.com  Tue Jan 10 08:22:31 2012
From: tavana.ali at gmail.com (Ali Tavana)
Date: Tue, 10 Jan 2012 10:52:31 +0330
Subject: [Pw_forum] (no subject)
Message-ID: <CALvVrfBLYVe9HD5j+wpxe8iuzv=dyBQ6jjKBAVQ0JjeN8ius_g@mail.gmail.com>

Dear QE Users,

I am looking for the reference paper for the VCA implementation in QE (i.e.
virtual.x code).
I will be grateful if any body can guide me.

Ali Tavana, PhD.,
Assistant Prof.,
Department of Physics,
University of Mohaghegh Ardabili,
Ardabil, Iran.

TEL: +98 451 5512081 (2430)
FAX: +98 451 5514701
EMAIL: a_tavana at alum.sharif.edu, tavana at uma.ac.ir
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From farzad_c81 at yahoo.com  Tue Jan 10 08:49:08 2012
From: farzad_c81 at yahoo.com (Farzad Molani)
Date: Mon, 9 Jan 2012 23:49:08 -0800 (PST)
Subject: [Pw_forum] problem with kband and kpoint in pp.x
Message-ID: <1326181748.7441.YahooMailClassic@web125902.mail.ne1.yahoo.com>

Hello pwscf users,
I want to study |psi|^2 by pp.x, but I don't know how can I choose?good numbers for kpoint and kband? please help me.
with the best regards?

Farzad Molani,
Ph.D Student,
Department of Theoretical Physical Chemistry,
K. N. Toosi University of Technology,
Tehran, Iran.
Tel.: 009891 4442 3308
Tel.: 009821 2306 4280 
Fax: 009821 2285 3650 
Web: http://www.chem.kntu.ac.ir/~sjalili:/
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From flux_ray12 at 163.com  Tue Jan 10 11:39:47 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Tue, 10 Jan 2012 18:39:47 +0800 (CST)
Subject: [Pw_forum] problem with kband and kpoint in pp.x
In-Reply-To: <1326181748.7441.YahooMailClassic@web125902.mail.ne1.yahoo.com>
References: <1326181748.7441.YahooMailClassic@web125902.mail.ne1.yahoo.com>
Message-ID: <5e98130a.22ad4.134c733cb35.Coremail.flux_ray12@163.com>

Definitely, you have to determine which |psi|^2 you wanna to check. This idea normaly comes from the band structure analysis. In other words, you should know which part you'd like to study, then such a part can be described as band and k-points index.
There is a good example for |psi|^2 application in paper, even though it is a little bit old one: http://www.nature.com/nature/journal/v399/n6732/full/399132a0.html.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-01-10 15:49:48,"Farzad Molani" <farzad_c81 at yahoo.com> wrote:

|
Hello pwscf users,
I want to study |psi|^2 by pp.x, but I don't know how can I choose good numbers for kpoint and kband? please help me.
with the best regards 

Farzad Molani,
Ph.D Student,
Department of Theoretical Physical Chemistry,
K. N. Toosi University of Technology,
Tehran, Iran.
Tel.: 009891 4442 3308
Tel.: 009821 2306 4280
Fax: 009821 2285 3650
Web: http://www.chem.kntu.ac.ir/~sjalili:/
|
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From eariel99 at gmail.com  Tue Jan 10 12:50:38 2012
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 10 Jan 2012 12:50:38 +0100
Subject: [Pw_forum] scaling of turbo_lanczos.x
Message-ID: <CAM5Vcw_UhaMuS3nvgwDSFrp6iFU8rTV5epho+7KJoi5w7Azy9w@mail.gmail.com>

Hi
I am calculating optical spectra of a carbon nanotube with turbo-TDDFPT. I
would like to know how scales the cost and the needed parameters with the
size of the unit cell. As only the gamma point is allowed I need to
replicate the unit cell. for example, if I duplicate the unit cell, how
scales

a) the itermax parameter to achieve an equivalent resolution of the
spectrum (is the same or must be scaled)
b) RAM, CPU time for fixed itermax

Is there any advice to use efficiently multiple CPU systems that may differ
from the advices to use pw.x ? Are task groups implemented (-ntg or
similar) ?

Thank you
Eduardo
-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en
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From hicpalm at gmail.com  Tue Jan 10 13:51:02 2012
From: hicpalm at gmail.com (hichem bouderba)
Date: Tue, 10 Jan 2012 12:51:02 +0000
Subject: [Pw_forum] phonon frenquecies convergences
In-Reply-To: <CB13980B-CFFB-409B-B5D6-F8B96A769882@sissa.it>
References: <CADnCFAPtpRRxYVXuLvzRZpbojnihKESJtt8w6br=T5W++tMRQw@mail.gmail.com>
	<1326107838.14089.7.camel@fe12lx.fisica.uniud.it>
	<CB13980B-CFFB-409B-B5D6-F8B96A769882@sissa.it>
Message-ID: <CADnCFAPWZWK50uaJyHbV4nvXbq+eh2=5G1nSJW2AyzKz_CZx3A@mail.gmail.com>

> One more word of caution. You should understand what convergence stems from.
> If you think about it, you will realize that phonon frequencies depend
> critically on electronic screening. The latter, in turn, is expressed in
> terms of the independent-electron susceptibility, whose expression contains
> differences between empty and conduction energies at the denominator. That's
> the technical reason for Kohn anomalies. I do not have examples handy, but I
> could imagine cases where E_c(k+q)-E_v(k) may depend sensitively on q
> (typically, in a semi-metal), for which the convergence of phonon
> frequencies on q may be not so obvious. Again, I think that Paolo's answer
> is correct as a rule of thumb, but you better make sure you understand why

thank you for the valuable explanation !  I will take the time for
thinking about it !

-- 
Mr. Hichem Bouderba
d?partement de physique
Universit? de Batna
Alg?rie

From kissi at uni-mainz.de  Tue Jan 10 14:38:49 2012
From: kissi at uni-mainz.de (Kiss, Ioan)
Date: Tue, 10 Jan 2012 13:38:49 +0000
Subject: [Pw_forum] charge-density.dat file missing after SCF calculations
Message-ID: <C2A03FEA95390F46839DC92BB46F57742672DC6A@e14mdb-03.zdv.Uni-Mainz.DE>

Dear PWSCF users and developers,

I would like to perform a series of geometry optimizations and band-structure
calculations for a slab (hexagonal surface slab model with 30 atoms in the unit cell)
and during my testing I have encountered a strange issue with espresso 4.3.2.
Namely, the SCF calculations and NSCF calculations end without any problem
and pw.x exits properly.
However, after the NSCF calculation is finished there is no charge-density.dat
file present in the prefix.save directory. All other files are there, including the
K000** directories, the UPF files, the data-file.xml, and the gvectors.dat.
Inside the gvectors.dat there is clearly and entry:
<CHARGE-DENSITY iotk_link="./charge-density.dat">
but the charge-density.dat is missing. When I intend to reuse this
.save directory for obtaining the band-structure, the bands.x executable
will of course crash with the error message:

 from read_rho_xml : error #        10
     searching for ./prefix.save/charge-density.xml

For the NSCF calculation I use k-point parallelisation over 4 pools of CPUs
and in the G-space over 8-to-16 CPU cores with the following options:
&CONTROL
      calculation = 'nscf' ,
           outdir = './' ,
           wfcdir = './',
       wf_collect = .true.
       pseudo_dir = './' ,
           wfcdir = './',
           prefix = '30Atom_BAND',
        verbosity = 'high'
            nstep = 3000
      max_seconds = 335600
/
&SYSTEM
   ibrav=  4, celldm(1) =7.788236356893399213, celldm(3)=21.28350100219813388,
    nat=  30, ntyp= 2, ecutwfc = 32.0, ecutrho =450.0,
 noncolin=.true. ,
 lspinorb=.true. ,
 starting_magnetization=0.0,
 occupations='smearing', smearing='methfessel-paxton', degauss=0.00735d0


I have the abovementioned issue both on a Xeon based Linux cluster running LSF with OpenMPI
and on a completely different IBM Power6 architecture with AIX, Loadleveler and MPI.
If I slightly change the cell parameters (expand about 1% along a and c) than I get a charge-density.dat.
In some other case if I use 16 instead of 8 CPUs for the R and G-space parallelisation
there will be also a charge-density.dat file generated without any issues.
Could you please give me a hint whether I have overlooked something very simple,
or if not, what could I do to be able to calculate the band structure for my system?

Best regards,
Janos Kiss.

==========================================
  Dr. Janos Kiss      e-mail: kissi at uni-mainz.de
  Johannes Gutenberg-Universitaet
  Institut f. Anorg. u. Analyt. Chemie
  AK Prof. Dr. Claudia Felser
  Staudinger Weg 9 / Raum 01-230
  55128 Mainz/ Germany
  Phone: +49-(0)6131-39-22703
  Fax:     +49-(0)6131-39-26267
  Web:     http://www.superconductivity.de/
 =========================================

From habdslam at yahoo.fr  Tue Jan 10 15:32:52 2012
From: habdslam at yahoo.fr (Abdeslam Houari)
Date: Tue, 10 Jan 2012 14:32:52 +0000 (GMT)
Subject: [Pw_forum] MD calculation, and Conjugate Gradient?
In-Reply-To: <1326122741.15779.14.camel@fe12lx.fisica.uniud.it>
Message-ID: <1326205972.21620.YahooMailClassic@web27402.mail.ukl.yahoo.com>

Dear QE developers and users; 
I'm using QE-4.3.2 and I wanna do Molecular Dynamics calculations, with Conjugate Gradient scheme... When looking to PWscf documentation (INPUT_PW) I find only the "verlet" and "langevin" algorithm for "calculation=md" !! I wanna be sure if the conjugate gradient is included (possible) or not? 

Thanks in advance
Best regards? ? 

=======================================
Abdesalem HOUARI
-------------------------------------------------------------------------------------------
Department of physics, Theoretical Physics Laboratory
University of Bejaia-06000. Algeria.
E-mail:?abdeslam.houari at univ-bejaia.dz & habdslam at yahoo.fr
https://sites.google.com/site/houariabdeslam/homepage
Phone: +213 34 21 53 04
Fax: +213 34 21 59 86
Cell phone: +213 551 36 29 01 (emergency only !!)
========================================
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From yunpengwang at live.com  Tue Jan 10 15:37:05 2012
From: yunpengwang at live.com (Yunpeng Wang)
Date: Tue, 10 Jan 2012 09:37:05 -0500
Subject: [Pw_forum] MD calculation, and Conjugate Gradient?
In-Reply-To: <1326205972.21620.YahooMailClassic@web27402.mail.ukl.yahoo.com>
References: <1326122741.15779.14.camel@fe12lx.fisica.uniud.it>,
	<1326205972.21620.YahooMailClassic@web27402.mail.ukl.yahoo.com>
Message-ID: <SNT108-W524504C2295A61CAFF73F3C2990@phx.gbl>


Meaning of MD is to follow the Newton equation with the total energy (kinetic energy plus interaction energy). However, the CG method is used to find the minimum interaction energy and kinetic energy makes no sense in CG method.

YP

Date: Tue, 10 Jan 2012 14:32:52 +0000
From: habdslam at yahoo.fr
To: pw_forum at pwscf.org
Subject: [Pw_forum] MD calculation, and Conjugate Gradient?

Dear QE developers and users; 
I'm using QE-4.3.2 and I wanna do Molecular Dynamics calculations, with Conjugate Gradient scheme... When looking to PWscf documentation (INPUT_PW) I find only the "verlet" and "langevin" algorithm for "calculation=md" !! I wanna be sure if the conjugate gradient is included (possible) or not? 

Thanks in advance
Best regards    

=======================================Abdesalem HOUARI-------------------------------------------------------------------------------------------Department of physics, Theoretical Physics LaboratoryUniversity of Bejaia-06000. Algeria.E-mail: abdeslam.houari at univ-bejaia.dz & habdslam at yahoo.frhttps://sites.google.com/site/houariabdeslam/homepagePhone: +213 34 21 53 04Fax: +213 34 21 59 86Cell phone: +213 551 36 29 01 (emergency only !!)========================================

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		  
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From habdslam at yahoo.fr  Tue Jan 10 17:48:30 2012
From: habdslam at yahoo.fr (Abdeslam Houari)
Date: Tue, 10 Jan 2012 16:48:30 +0000 (GMT)
Subject: [Pw_forum] MD calculation, and Conjugate Gradient?
In-Reply-To: <SNT108-W524504C2295A61CAFF73F3C2990@phx.gbl>
Message-ID: <1326214110.91893.YahooMailClassic@web27402.mail.ukl.yahoo.com>

I understand ... may be I was deceived by another ab inito code (without citing the name) where they specify "conjugate gradient" as a type of run of the molecular dynamics !!!? 
Thanks a lot Y.P

--- En date de?: Mar 10.1.12, Yunpeng Wang <yunpengwang at live.com> a ?crit?:

De: Yunpeng Wang <yunpengwang at live.com>
Objet: Re: [Pw_forum] MD calculation, and Conjugate Gradient?
?: pw_forum at pwscf.org
Date: Mardi 10 janvier 2012, 15h37





Meaning of MD is to follow the Newton equation with the total energy (kinetic energy plus interaction energy). However, the CG method is used to find the minimum interaction energy and kinetic energy makes no sense in CG method.

YP

Date: Tue, 10 Jan 2012 14:32:52 +0000
From: habdslam at yahoo.fr
To: pw_forum at pwscf.org
Subject: [Pw_forum] MD calculation, and Conjugate Gradient?

Dear QE developers and users; 
I'm using QE-4.3.2 and I wanna do Molecular Dynamics calculations, with Conjugate Gradient scheme... When looking to PWscf documentation (INPUT_PW) I find only the "verlet" and "langevin" algorithm for "calculation=md" !! I wanna be sure if the conjugate gradient is included (possible) or not? 

Thanks in advance
Best regards? ? 

=======================================
Abdesalem HOUARI
-------------------------------------------------------------------------------------------
Department of physics, Theoretical Physics Laboratory
University of Bejaia-06000. Algeria.
E-mail:?abdeslam.houari at univ-bejaia.dz & habdslam at yahoo.fr
https://sites.google.com/site/houariabdeslam/homepage
Phone: +213 34 21 53 04
Fax: +213 34 21 59 86
Cell phone: +213 551 36 29 01 (emergency only !!)
========================================

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		  

-----La pi?ce jointe associ?e suit-----

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
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From giannozz at democritos.it  Tue Jan 10 18:31:52 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 10 Jan 2012 18:31:52 +0100
Subject: [Pw_forum] VCA (was: no subject)
In-Reply-To: <CALvVrfBLYVe9HD5j+wpxe8iuzv=dyBQ6jjKBAVQ0JjeN8ius_g@mail.gmail.com>
References: <CALvVrfBLYVe9HD5j+wpxe8iuzv=dyBQ6jjKBAVQ0JjeN8ius_g@mail.gmail.com>
Message-ID: <0EF6524A-68CC-468A-8D8A-B25CF4473734@democritos.it>


On Jan 10, 2012, at 8:22 , Ali Tavana wrote:

> I am looking for the reference paper for the VCA implementation
> in QE (i.e. virtual.x code).

there is no such paper. This is the VCA implementation in QE,
if I remember correctly:
    V^{(vca)} = V_{loc)^{(vca)} + V_{nl}^{(vca)}
where
    V_{loc)^{(vca)} = x V_{loc}^{(1)} + (1-x) V_{loc}^{(2)}
and
    V_{nl)^{(vca)} = \sum_{ij} |\beta^{(1)}_i> x D^{(1)}_{ij} <\beta^ 
{(1)}_j|
                      +  \sum_{ij} |\beta^{(2)}_i> (1-x) D^{(2)}_{ij}  
<\beta^{(2)}_j|
where
  V_{loc}^{(n)}(r) is the local part of PP n ;
  \beta^{{n)}_i(r) are the projectors for PP n ;
  D^{(n))_{ij} are the (bare) components of matrix D for PP n

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Tue Jan 10 18:49:33 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 10 Jan 2012 18:49:33 +0100
Subject: [Pw_forum] MD calculation, and Conjugate Gradient?
In-Reply-To: <1326214110.91893.YahooMailClassic@web27402.mail.ukl.yahoo.com>
References: <1326214110.91893.YahooMailClassic@web27402.mail.ukl.yahoo.com>
Message-ID: <637B6B27-1302-4B0E-833D-031B397AE9F6@democritos.it>


On Jan 10, 2012, at 17:48 , Abdeslam Houari wrote:

> [...] they specify "conjugate gradient" as a type of run of the  
> molecular dynamics !!!

you can perform molecular dynamics, using a conjugate-gradient  
algorithm to
solve the electronic problem at each step. The CP code can also do  
this, by
the way, in addition to Car-Parrinello dynamics (which is a different  
kind of
dynamics)

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From giannozz at democritos.it  Tue Jan 10 18:55:13 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 10 Jan 2012 18:55:13 +0100
Subject: [Pw_forum] charge-density.dat file missing after SCF
	calculations
In-Reply-To: <C2A03FEA95390F46839DC92BB46F57742672DC6A@e14mdb-03.zdv.Uni-Mainz.DE>
References: <C2A03FEA95390F46839DC92BB46F57742672DC6A@e14mdb-03.zdv.Uni-Mainz.DE>
Message-ID: <DFABCDF6-69ED-4D1B-AB64-071010E2183F@democritos.it>


On Jan 10, 2012, at 14:38 , Kiss, Ioan wrote:

> However, after the NSCF calculation is finished there is no
> charge-density.dat file present in the prefix.save directory


this sounds hard to believe to me. The non-scf calculation
doesn't destroy the charge density file.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From bdslipun at gmail.com  Tue Jan 10 20:52:15 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Wed, 11 Jan 2012 01:22:15 +0530
Subject: [Pw_forum] sn calculation
Message-ID: <CAJVAAvBWmMK_0-o-xdip_n0xaReLggghwevJgWSvT72G4p20SQ@mail.gmail.com>

i am a new user of quantum espresso
i want study the alpha-beta transition of tin(Sn)
i found the phonon dispersion of alpha(diamond) structure
but for beta structure how can  find the phonon dispersion and vibrational
energy


because i calculated the static calculation of beta tin having tetragonal
cell (c/a=,546)
and 4 atoms having position 0 0 0 , .5.5.5, 0.5.75,.5 0 .25


for phonon calculation what should my position of atoms so that i can get
the vibrational energy from linear response theory
if i used the above i am getting 12 phonon branches  is it correct?
suggestions may help to know more about it
thanks














bd sahoo
barc
mumbai
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From tavana.ali at gmail.com  Wed Jan 11 03:58:58 2012
From: tavana.ali at gmail.com (Ali Tavana)
Date: Wed, 11 Jan 2012 06:28:58 +0330
Subject: [Pw_forum] VCA (was: no subject)
In-Reply-To: <0EF6524A-68CC-468A-8D8A-B25CF4473734@democritos.it>
References: <CALvVrfBLYVe9HD5j+wpxe8iuzv=dyBQ6jjKBAVQ0JjeN8ius_g@mail.gmail.com>
	<0EF6524A-68CC-468A-8D8A-B25CF4473734@democritos.it>
Message-ID: <CALvVrfDGizFEx-mcz=GQ+Xx1-fSBBVPAd+mDyUunf-XLL66s=Q@mail.gmail.com>

Thank you very much.


Ali Tavana, PhD.,
Assistant Prof.,
Department of Physics,
University of Mohaghegh Ardabili,
Ardabil, Iran.

TEL: +98 451 5512081 (2430)
FAX: +98 451 5514701
EMAIL: a_tavana at alum.sharif.edu, tavana at uma.ac.ir




On Tue, Jan 10, 2012 at 9:01 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Jan 10, 2012, at 8:22 , Ali Tavana wrote:
>
> > I am looking for the reference paper for the VCA implementation
> > in QE (i.e. virtual.x code).
>
> there is no such paper. This is the VCA implementation in QE,
> if I remember correctly:
>    V^{(vca)} = V_{loc)^{(vca)} + V_{nl}^{(vca)}
> where
>    V_{loc)^{(vca)} = x V_{loc}^{(1)} + (1-x) V_{loc}^{(2)}
> and
>    V_{nl)^{(vca)} = \sum_{ij} |\beta^{(1)}_i> x D^{(1)}_{ij} <\beta^
> {(1)}_j|
>                      +  \sum_{ij} |\beta^{(2)}_i> (1-x) D^{(2)}_{ij}
> <\beta^{(2)}_j|
> where
>  V_{loc}^{(n)}(r) is the local part of PP n ;
>  \beta^{{n)}_i(r) are the projectors for PP n ;
>  D^{(n))_{ij} are the (bare) components of matrix D for PP n
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From bdslipun at gmail.com  Wed Jan 11 06:13:40 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Tue, 10 Jan 2012 21:13:40 -0800
Subject: [Pw_forum] Fwd: sn calculation
In-Reply-To: <CAJVAAvBWmMK_0-o-xdip_n0xaReLggghwevJgWSvT72G4p20SQ@mail.gmail.com>
References: <CAJVAAvBWmMK_0-o-xdip_n0xaReLggghwevJgWSvT72G4p20SQ@mail.gmail.com>
Message-ID: <CAJVAAvBmeW3MvkfrZ+5B6H8RxDH-Xg7RuKrd0Pt8JKNWoHFm0A@mail.gmail.com>

---------- Forwarded message ----------
From: bhabya sahoo <bdslipun at gmail.com>
Date: Tue, Jan 10, 2012 at 11:52 AM
Subject: sn calculation
To: PWSCF Forum <pw_forum at pwscf.org>


i am a new user of quantum espresso
i want study the alpha-beta transition of tin(Sn)
i found the phonon dispersion of alpha(diamond) structure
but for beta structure how can  find the phonon dispersion and vibrational
energy


because i calculated the static calculation of beta tin having tetragonal
cell (c/a=,546)
and 4 atoms having position 0 0 0 , .5.5.5, 0.5.75,.5 0 .25


for phonon calculation what should my position of atoms so that i can get
the vibrational energy from linear response theory
if i used the above i am getting 12 phonon branches  is it correct?
suggestions may help to know more about it
thanks














bd sahoo
barc
mumbai
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From yunpengwang at live.com  Wed Jan 11 11:33:50 2012
From: yunpengwang at live.com (Yunpeng Wang)
Date: Wed, 11 Jan 2012 05:33:50 -0500
Subject: [Pw_forum] RPA by PWscf
In-Reply-To: <CAJVAAvBmeW3MvkfrZ+5B6H8RxDH-Xg7RuKrd0Pt8JKNWoHFm0A@mail.gmail.com>
References: <CAJVAAvBWmMK_0-o-xdip_n0xaReLggghwevJgWSvT72G4p20SQ@mail.gmail.com>,
	<CAJVAAvBmeW3MvkfrZ+5B6H8RxDH-Xg7RuKrd0Pt8JKNWoHFm0A@mail.gmail.com>
Message-ID: <SNT108-W12DA31A090FF05007871D9C29E0@phx.gbl>




Date: Tue, 10 Jan 2012 21:13:40 -0800
From: bdslipun at gmail.com
To: pw_forum at pwscf.org
Subject: [Pw_forum] Fwd: sn calculation



---------- Forwarded message ----------
From: bhabya sahoo <bdslipun at gmail.com>
Date: Tue, Jan 10, 2012 at 11:52 AM

Subject: sn calculation
To: PWSCF Forum <pw_forum at pwscf.org>


i am a new user of quantum espressoi want study the alpha-beta transition of tin(Sn)
i found the phonon dispersion of alpha(diamond) structurebut for beta structure how can  find the phonon dispersion and vibrational energy


because i calculated the static calculation of beta tin having tetragonal cell (c/a=,546)and 4 atoms having position 0 0 0 , .5.5.5, 0.5.75,.5 0 .25



for phonon calculation what should my position of atoms so that i can get the vibrational energy from linear response theoryif i used the above i am getting 12 phonon branches  is it correct?

suggestions may help to know more about it   thanks















bd sahoobarc mumbai



_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		  
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From yunpengwang at live.com  Wed Jan 11 11:36:55 2012
From: yunpengwang at live.com (Yunpeng Wang)
Date: Wed, 11 Jan 2012 05:36:55 -0500
Subject: [Pw_forum] RPA by PWscf
Message-ID: <SNT108-W49E52E40ACE82246E41B29C29E0@phx.gbl>


Hi all:

I want to calculate the RPA/EXX exchange-correlation energies. I have seen in some papers RPA/EXX total energy has been implemented in PWscf. However, I can not find any example or explanation. Could you please teach me how to do that or use some examples to illustrate the calculation?

best wishes,
Yun-Peng
 		 	   		  
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From habdslam at yahoo.fr  Wed Jan 11 11:48:53 2012
From: habdslam at yahoo.fr (Abdeslam Houari)
Date: Wed, 11 Jan 2012 10:48:53 +0000 (GMT)
Subject: [Pw_forum] MD calculation, and Conjugate Gradient?
In-Reply-To: <637B6B27-1302-4B0E-833D-031B397AE9F6@democritos.it>
Message-ID: <1326278933.13395.YahooMailClassic@web27407.mail.ukl.yahoo.com>


> --- En date de?: Mar 10.1.12, Paolo Giannozzi <giannozz at democritos.it> a ?crit?:

>> On Jan 10, 2012, at 17:48 , Abdeslam Houari wrote:

>> [...] they specify "conjugate gradient" as a type of run of the? 
>> molecular dynamics !!!

>you can perform molecular dynamics, using a conjugate-gradient? 
>algorithm to
>solve the electronic problem at each step. 

Dear Paolo;

How to do it in PW-scf (QE-4.3.2) ? I didn't find it in the INPUT-PW or somewhere else !

>The CP code can also do? this, by
>the way, in addition to Car-Parrinello dynamics (which is a different? 
>kind of
>dynamics)

Best regards and thanks in advance

ASH

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From giannozz at democritos.it  Wed Jan 11 11:55:10 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 11 Jan 2012 11:55:10 +0100
Subject: [Pw_forum] MD calculation, and Conjugate Gradient?
In-Reply-To: <1326278933.13395.YahooMailClassic@web27407.mail.ukl.yahoo.com>
References: <1326278933.13395.YahooMailClassic@web27407.mail.ukl.yahoo.com>
Message-ID: <1326279310.26182.1.camel@fe12lx.fisica.uniud.it>

On Wed, 2012-01-11 at 10:48 +0000, Abdeslam Houari wrote:


> How to do it in PW-scf (QE-4.3.2) ? I didn't find it in the INPUT-PW
> or somewhere else !


you cannot do it with PWscf. You can do it with CP.

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From messadleila at yahoo.fr  Wed Jan 11 12:25:22 2012
From: messadleila at yahoo.fr (leila messad)
Date: Wed, 11 Jan 2012 11:25:22 +0000 (GMT)
Subject: [Pw_forum] help
In-Reply-To: <mailman.142.1326258822.9401.pw_forum@pwscf.org>
Message-ID: <1326281122.20828.YahooMailClassic@web26304.mail.ukl.yahoo.com>

i am a new user of quantum espresso
i want to study the phonon dispersion of CoPt (tetragonal

cell (c/a=,95)) structure,with 2 atoms having position 0 0 0 , .5.5.5, 


?how can? find the phonon dispersion and vibrational
energy


because i used the ph.x code to calculate the phonon dispersion at q = 0,

i found six branches with:
???? omega( 1) =????? -0.316230 [THz] =???? -10.548352 [cm-1]
???? omega( 2) =?????? 1.110175 [THz] =????? 37.031704 [cm-1]
???? omega( 3) =?????? 1.110175 [THz] =????? 37.031704 [cm-1]
???? omega( 4) =?????? 4.301130 [THz] =???? 143.471216 [cm-1]
???? omega( 5) =?????? 4.301130 [THz] =???? 143.471216 [cm-1]
???? omega( 6) =?????? 5.145640 [THz] =???? 171.641221 [cm-1]
is it correct?

thanks


for phonon calculation what should my position of atoms so that i can get
the vibrational energy from linear response theory
if i used the above i am getting 12 phonon branches? is it correct?
suggestions may help to know more about it
thanks


--- En date de?: Mer 11.1.12, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> a ?crit?:

De: pw_forum-request at pwscf.org <pw_forum-request at pwscf.org>
Objet: Pw_forum Digest, Vol 55, Issue 18
?: pw_forum at pwscf.org
Date: Mercredi 11 janvier 2012, 6h13

Send Pw_forum mailing list submissions to
??? pw_forum at pwscf.org

To subscribe or unsubscribe via the World Wide Web, visit
??? http://www.democritos.it/mailman/listinfo/pw_forum
or, via email, send a message with subject or body 'help' to
??? pw_forum-request at pwscf.org

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??? pw_forum-owner at pwscf.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Pw_forum digest..."


Today's Topics:

???1. Re: MD calculation, and Conjugate Gradient? (Abdeslam Houari)
???2. Re: VCA (was: no subject) (Paolo Giannozzi)
???3. Re: MD calculation, and Conjugate Gradient? (Paolo Giannozzi)
???4. Re: charge-density.dat file missing after SCF??? calculations
? ? ? (Paolo Giannozzi)
???5. sn calculation (bhabya sahoo)
???6. Re: VCA (was: no subject) (Ali Tavana)
???7. Fwd: sn calculation (bhabya sahoo)


----------------------------------------------------------------------

Message: 1
Date: Tue, 10 Jan 2012 16:48:30 +0000 (GMT)
From: Abdeslam Houari <habdslam at yahoo.fr>
Subject: Re: [Pw_forum] MD calculation, and Conjugate Gradient?
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
??? <1326214110.91893.YahooMailClassic at web27402.mail.ukl.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"

I understand ... may be I was deceived by another ab inito code (without citing the name) where they specify "conjugate gradient" as a type of run of the molecular dynamics !!!? 
Thanks a lot Y.P

--- En date de?: Mar 10.1.12, Yunpeng Wang <yunpengwang at live.com> a ?crit?:

De: Yunpeng Wang <yunpengwang at live.com>
Objet: Re: [Pw_forum] MD calculation, and Conjugate Gradient?
?: pw_forum at pwscf.org
Date: Mardi 10 janvier 2012, 15h37





Meaning of MD is to follow the Newton equation with the total energy (kinetic energy plus interaction energy). However, the CG method is used to find the minimum interaction energy and kinetic energy makes no sense in CG method.

YP

Date: Tue, 10 Jan 2012 14:32:52 +0000
From: habdslam at yahoo.fr
To: pw_forum at pwscf.org
Subject: [Pw_forum] MD calculation, and Conjugate Gradient?

Dear QE developers and users; 
I'm using QE-4.3.2 and I wanna do Molecular Dynamics calculations, with Conjugate Gradient scheme... When looking to PWscf documentation (INPUT_PW) I find only the "verlet" and "langevin" algorithm for "calculation=md" !! I wanna be sure if the conjugate gradient is included (possible) or not? 

Thanks in advance
Best regards? ? 

=======================================
Abdesalem HOUARI
-------------------------------------------------------------------------------------------
Department of physics, Theoretical Physics Laboratory
University of Bejaia-06000. Algeria.
E-mail:?abdeslam.houari at univ-bejaia.dz & habdslam at yahoo.fr
https://sites.google.com/site/houariabdeslam/homepage
Phone: +213 34 21 53 04
Fax: +213 34 21 59 86
Cell phone: +213 551 36 29 01 (emergency only !!)
========================================

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum ??? ???????? ?????? ??? ? 

-----La pi?ce jointe associ?e suit-----

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Message: 2
Date: Tue, 10 Jan 2012 18:31:52 +0100
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] VCA (was: no subject)
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <0EF6524A-68CC-468A-8D8A-B25CF4473734 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed


On Jan 10, 2012, at 8:22 , Ali Tavana wrote:

> I am looking for the reference paper for the VCA implementation
> in QE (i.e. virtual.x code).

there is no such paper. This is the VCA implementation in QE,
if I remember correctly:
? ? V^{(vca)} = V_{loc)^{(vca)} + V_{nl}^{(vca)}
where
? ? V_{loc)^{(vca)} = x V_{loc}^{(1)} + (1-x) V_{loc}^{(2)}
and
? ? V_{nl)^{(vca)} = \sum_{ij} |\beta^{(1)}_i> x D^{(1)}_{ij} <\beta^ 
{(1)}_j|
? ? ? ? ? ? ? ? ? ? ? +? \sum_{ij} |\beta^{(2)}_i> (1-x) D^{(2)}_{ij}? 
<\beta^{(2)}_j|
where
? V_{loc}^{(n)}(r) is the local part of PP n ;
? \beta^{{n)}_i(r) are the projectors for PP n ;
? D^{(n))_{ij} are the (bare) components of matrix D for PP n

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222






------------------------------

Message: 3
Date: Tue, 10 Jan 2012 18:49:33 +0100
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] MD calculation, and Conjugate Gradient?
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <637B6B27-1302-4B0E-833D-031B397AE9F6 at democritos.it>
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed


On Jan 10, 2012, at 17:48 , Abdeslam Houari wrote:

> [...] they specify "conjugate gradient" as a type of run of the? 
> molecular dynamics !!!

you can perform molecular dynamics, using a conjugate-gradient? 
algorithm to
solve the electronic problem at each step. The CP code can also do? 
this, by
the way, in addition to Car-Parrinello dynamics (which is a different? 
kind of
dynamics)

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222






------------------------------

Message: 4
Date: Tue, 10 Jan 2012 18:55:13 +0100
From: Paolo Giannozzi <giannozz at democritos.it>
Subject: Re: [Pw_forum] charge-density.dat file missing after SCF
??? calculations
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID: <DFABCDF6-69ED-4D1B-AB64-071010E2183F at democritos.it>
Content-Type: text/plain; charset=US-ASCII; format=flowed


On Jan 10, 2012, at 14:38 , Kiss, Ioan wrote:

> However, after the NSCF calculation is finished there is no
> charge-density.dat file present in the prefix.save directory


this sounds hard to believe to me. The non-scf calculation
doesn't destroy the charge density file.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222






------------------------------

Message: 5
Date: Wed, 11 Jan 2012 01:22:15 +0530
From: bhabya sahoo <bdslipun at gmail.com>
Subject: [Pw_forum] sn calculation
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
??? <CAJVAAvBWmMK_0-o-xdip_n0xaReLggghwevJgWSvT72G4p20SQ at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

i am a new user of quantum espresso
i want study the alpha-beta transition of tin(Sn)
i found the phonon dispersion of alpha(diamond) structure
but for beta structure how can? find the phonon dispersion and vibrational
energy


because i calculated the static calculation of beta tin having tetragonal
cell (c/a=,546)
and 4 atoms having position 0 0 0 , .5.5.5, 0.5.75,.5 0 .25


for phonon calculation what should my position of atoms so that i can get
the vibrational energy from linear response theory
if i used the above i am getting 12 phonon branches? is it correct?
suggestions may help to know more about it
thanks














bd sahoo
barc
mumbai
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Message: 6
Date: Wed, 11 Jan 2012 06:28:58 +0330
From: Ali Tavana <tavana.ali at gmail.com>
Subject: Re: [Pw_forum] VCA (was: no subject)
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
??? <CALvVrfDGizFEx-mcz=GQ+Xx1-fSBBVPAd+mDyUunf-XLL66s=Q at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Thank you very much.


Ali Tavana, PhD.,
Assistant Prof.,
Department of Physics,
University of Mohaghegh Ardabili,
Ardabil, Iran.

TEL: +98 451 5512081 (2430)
FAX: +98 451 5514701
EMAIL: a_tavana at alum.sharif.edu, tavana at uma.ac.ir




On Tue, Jan 10, 2012 at 9:01 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Jan 10, 2012, at 8:22 , Ali Tavana wrote:
>
> > I am looking for the reference paper for the VCA implementation
> > in QE (i.e. virtual.x code).
>
> there is no such paper. This is the VCA implementation in QE,
> if I remember correctly:
>? ? V^{(vca)} = V_{loc)^{(vca)} + V_{nl}^{(vca)}
> where
>? ? V_{loc)^{(vca)} = x V_{loc}^{(1)} + (1-x) V_{loc}^{(2)}
> and
>? ? V_{nl)^{(vca)} = \sum_{ij} |\beta^{(1)}_i> x D^{(1)}_{ij} <\beta^
> {(1)}_j|
>? ? ? ? ? ? ? ? ? ? ? +? \sum_{ij} |\beta^{(2)}_i> (1-x) D^{(2)}_{ij}
> <\beta^{(2)}_j|
> where
>? V_{loc}^{(n)}(r) is the local part of PP n ;
>? \beta^{{n)}_i(r) are the projectors for PP n ;
>? D^{(n))_{ij} are the (bare) components of matrix D for PP n
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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------------------------------

Message: 7
Date: Tue, 10 Jan 2012 21:13:40 -0800
From: bhabya sahoo <bdslipun at gmail.com>
Subject: [Pw_forum] Fwd: sn calculation
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
??? <CAJVAAvBmeW3MvkfrZ+5B6H8RxDH-Xg7RuKrd0Pt8JKNWoHFm0A at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

---------- Forwarded message ----------
From: bhabya sahoo <bdslipun at gmail.com>
Date: Tue, Jan 10, 2012 at 11:52 AM
Subject: sn calculation
To: PWSCF Forum <pw_forum at pwscf.org>


i am a new user of quantum espresso
i want study the alpha-beta transition of tin(Sn)
i found the phonon dispersion of alpha(diamond) structure
but for beta structure how can? find the phonon dispersion and vibrational
energy


because i calculated the static calculation of beta tin having tetragonal
cell (c/a=,546)
and 4 atoms having position 0 0 0 , .5.5.5, 0.5.75,.5 0 .25


for phonon calculation what should my position of atoms so that i can get
the vibrational energy from linear response theory
if i used the above i am getting 12 phonon branches? is it correct?
suggestions may help to know more about it
thanks














bd sahoo
barc
mumbai
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------------------------------

_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


End of Pw_forum Digest, Vol 55, Issue 18
****************************************
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From gbilalbegovic at gmail.com  Wed Jan 11 13:23:42 2012
From: gbilalbegovic at gmail.com (Goranka Bilalbegovic)
Date: Wed, 11 Jan 2012 13:23:42 +0100
Subject: [Pw_forum] example09 segfault - ramtns used but not allocated
	in dynmatrix.f90
In-Reply-To: <1323686999.21852.39.camel@fe12lx.fisica.uniud.it>
References: <201112121002.27711.jean-roch.huntzinger@univ-montp2.fr>
	<1323686999.21852.39.camel@fe12lx.fisica.uniud.it>
Message-ID: <CALj7P9vT70k7ikPM1FP-UVdk+PsPNbz6g1KGcqdpjXep2UQBkg@mail.gmail.com>

On Mon, Dec 12, 2011 at 11:49 AM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> On Mon, 2011-12-12 at 10:02 +0100, Jean-Roch Huntzinger wrote:
>
> > The attached patch solves a segfault in example09
> > [...] Should I file a bug report ?
>
> too late: it was fixed a few days ago. Thank you anyway!
>
> http://qe-forge.org/scm/viewvc.php?view=rev&root=q-e&sortby=date&revision=8244
>
>
Hello,

I have applied this correction in:
http://qe-forge.org/scm/viewvc.php?view=rev&root=q-e&sortby=date&revision=8244
I  also replaced the  routine set_asr in dynmat.f90 (attached in:
http://www.democritos.it/pipermail/pw_forum/2011-December/022706.html)

However, the CH4 part of example 9 from 4.3.2, compiled with ifort 11.1, on
the Linux cluster, still does not work (both with asr ='simple' and
'zero-dim').

Error is:
----------
0 - MPI_BARRIER : Null communicator
Exit code -3 signaled from (host)
Killing remote processes...[0] [] Aborting Program!
Abort signaled by rank 0:  Aborting program !
forrtl: error (69): process interrupted (SIGINT)
Image              PC                Routine            Line        Source

libpthread.so.0    00002ADEFF3158FB  Unknown               Unknown  Unknown
libmpich.so.1.0    00002ADEFEA615A0  Unknown               Unknown  Unknown
libmpich.so.1.0    00002ADEFEA60E36  Unknown               Unknown  Unknown
libmpich.so.1.0    00002ADEFEA56371  Unknown               Unknown  Unknown
libmpich.so.1.0    00002ADEFEA55B40  Unknown               Unknown  Unknown
libmpich.so.1.0    00002ADEFEA55718  Unknown               Unknown  Unknown
libmpich.so.1.0    00002ADEFEA10AE4  Unknown               Unknown  Unknown
libmpich.so.1.0    00002ADEFEA109DC  Unknown               Unknown  Unknown
dynmat.x           000000000042E993  mp_synchronize_            37
 mp_base.f90
dynmat.x           000000000042EA12  bcast_integer_            112
 mp_base.f90
dynmat.x           000000000041B307  mp_mp_mp_bcast_i1         295  mp.f90
dynmat.x           0000000000415BC5  io_dyn_mat_mp_rea         259
 io_dyn_mat.f90
dynmat.x           0000000000407691  MAIN__                    129
 dynmat.f90
dynmat.x           0000000000406A0C  Unknown               Unknown  Unknown
libc.so.6          00002ADEFF9CD994  Unknown               Unknown  Unknown
dynmat.x           0000000000406919  Unknown               Unknown  Unknown
MPI process terminated unexpectedly
error: executing task of job 220258 failed: execution daemon on host ...
didn't accept task
DONE
----------------

In *.out there is only:   Reading Dynamical Matrix from file ch4.dyn.xml
Therefore it stops before writing:  Acoustic Sum Rule: || Z*(ASR) -
Z*(orig)|| = ...

Thank you for any help.
-- 
Goranka Bilalbegovic,
Department of Physics, Faculty of Science,
University of Zagreb, Croatia
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From giannozz at democritos.it  Wed Jan 11 14:50:02 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 11 Jan 2012 14:50:02 +0100
Subject: [Pw_forum] example09 segfault - ramtns used but not
	allocated	in dynmatrix.f90
In-Reply-To: <CALj7P9vT70k7ikPM1FP-UVdk+PsPNbz6g1KGcqdpjXep2UQBkg@mail.gmail.com>
References: <201112121002.27711.jean-roch.huntzinger@univ-montp2.fr>
	<1323686999.21852.39.camel@fe12lx.fisica.uniud.it>
	<CALj7P9vT70k7ikPM1FP-UVdk+PsPNbz6g1KGcqdpjXep2UQBkg@mail.gmail.com>
Message-ID: <1326289802.26182.16.camel@fe12lx.fisica.uniud.it>

On Wed, 2012-01-11 at 13:23 +0100, Goranka Bilalbegovic wrote:

> However, the CH4 part of example 9 from 4.3.2, compiled with ifort
> 11.1, on the Linux cluster, still does not work

do not run "dynmat.x" in parallel. It is a serial code that should
be run on a single processor. It used to work even if launched by
"mpirun -np N" with N > 1, just in case, but some new pieces of code
reading the dynamical matrix in xml format do not work in that case

P. 

-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From gbilalbegovic at gmail.com  Wed Jan 11 15:09:29 2012
From: gbilalbegovic at gmail.com (Goranka Bilalbegovic)
Date: Wed, 11 Jan 2012 15:09:29 +0100
Subject: [Pw_forum] example09 segfault - ramtns used but not allocated
	in dynmatrix.f90
In-Reply-To: <1326289802.26182.16.camel@fe12lx.fisica.uniud.it>
References: <201112121002.27711.jean-roch.huntzinger@univ-montp2.fr>
	<1323686999.21852.39.camel@fe12lx.fisica.uniud.it>
	<CALj7P9vT70k7ikPM1FP-UVdk+PsPNbz6g1KGcqdpjXep2UQBkg@mail.gmail.com>
	<1326289802.26182.16.camel@fe12lx.fisica.uniud.it>
Message-ID: <CALj7P9v3Z-2fhFshzmwo9xO2QL83XZRjtCmbiD92J13uw7jsaw@mail.gmail.com>

On Wed, Jan 11, 2012 at 2:50 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> On Wed, 2012-01-11 at 13:23 +0100, Goranka Bilalbegovic wrote:
>
> > However, the CH4 part of example 9 from 4.3.2, compiled with ifort
> > 11.1, on the Linux cluster, still does not work
>
> do not run "dynmat.x" in parallel. It is a serial code that should
> be run on a single processor. It used to work even if launched by
> "mpirun -np N" with N > 1, just in case, but some new pieces of code
> reading the dynamical matrix in xml format do not work in that case
>
>
>
I do not run dynmat.x for N >1, but for N=1. However, I have to use
mpirun in *.sge script, because there is no other options on this cluster.

Thanks for your answer.
Best regards,

-- 
Goranka Bilalbegovic,
Department of Physics, Faculty of Science,
University of Zagreb, Croatia
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From giannozz at democritos.it  Wed Jan 11 15:46:41 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 11 Jan 2012 15:46:41 +0100
Subject: [Pw_forum] example09 segfault - ramtns used but not
	allocated	in dynmatrix.f90
In-Reply-To: <CALj7P9v3Z-2fhFshzmwo9xO2QL83XZRjtCmbiD92J13uw7jsaw@mail.gmail.com>
References: <201112121002.27711.jean-roch.huntzinger@univ-montp2.fr>
	<1323686999.21852.39.camel@fe12lx.fisica.uniud.it>
	<CALj7P9vT70k7ikPM1FP-UVdk+PsPNbz6g1KGcqdpjXep2UQBkg@mail.gmail.com>
	<1326289802.26182.16.camel@fe12lx.fisica.uniud.it>
	<CALj7P9v3Z-2fhFshzmwo9xO2QL83XZRjtCmbiD92J13uw7jsaw@mail.gmail.com>
Message-ID: <1326293201.27523.1.camel@fe12lx.fisica.uniud.it>

On Wed, 2012-01-11 at 15:09 +0100, Goranka Bilalbegovic wrote:

> I do not run dynmat.x for N >1, but for N=1. 

if you run in parallel on 1 processor, it works

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From spmmal at gmail.com  Thu Jan 12 02:56:23 2012
From: spmmal at gmail.com (Caloma Trumica)
Date: Wed, 11 Jan 2012 20:56:23 -0500
Subject: [Pw_forum] Which subroutine is related to the atomic displacement
	in DFPT
Message-ID: <CAM0egYbcJV_++x=07zf81ZoaCwSE5Lq-i31gEvYSPnasArP5DQ@mail.gmail.com>

Dear All,

I could not find the name of the subroutine, which applies a pattern of
atomic displacements in order to get the wavefunction perturbation in any q
vector? Could you please help me out? It is supposed to be hidden somewhere
in "PH" folder.

Thanks.

Andy Lau  Postgraduate student from HKUST, China
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From kalamaillist at gmail.com  Thu Jan 12 05:58:41 2012
From: kalamaillist at gmail.com (WF)
Date: Thu, 12 Jan 2012 12:58:41 +0800
Subject: [Pw_forum] SCF Convergence problem in all-electron calculation of
	ld1.x
Message-ID: <000501ccd0e6$dd077250$971656f0$@gmail.com>

Dear everyone,
	I would like to verify the validity of a norm-conserving pp of
carbon by use some different configurations as what documentation says.
However, I cannot complete all-electron calculation of C with configuration
"[He] 2s2 2p3", in which ld1.x shows "warning: convergence not achieved".
The convergence cannot be achieved by adjusting beta and maximum iteration
count from what I have tried. What can make it converge or should I just
skip this step ?  Thanks very much.
	
------------------------------------------------------------
Wu Feng,
Chemistry and Molecular Engineering, Peking University
------------------------------------------------------------


From giannozz at democritos.it  Thu Jan 12 08:30:50 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 12 Jan 2012 08:30:50 +0100
Subject: [Pw_forum] SCF Convergence problem in all-electron calculation
	of ld1.x
In-Reply-To: <000501ccd0e6$dd077250$971656f0$@gmail.com>
References: <000501ccd0e6$dd077250$971656f0$@gmail.com>
Message-ID: <9EEF29D5-95C2-4702-B340-839D6CF6EE9E@democritos.it>


On Jan 12, 2012, at 5:58 , WF wrote:

> I cannot complete all-electron calculation of C with configuration
> "[He] 2s2 2p3"

negative ions are not bound in DFT

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From bdslipun at gmail.com  Thu Jan 12 10:08:59 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Thu, 12 Jan 2012 01:08:59 -0800
Subject: [Pw_forum] pressure
Message-ID: <CAJVAAvB-tNsnDAxnD1np8emfnUde6Cb_6ojrkysGnXcUPDEvrA@mail.gmail.com>

how one can claculate the pressure in pwscf
by giving only a single volume













sahu
reserch scholar
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From Lorenzo.Paulatto at impmc.upmc.fr  Thu Jan 12 11:00:23 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 12 Jan 2012 11:00:23 +0100
Subject: [Pw_forum] pressure
In-Reply-To: <CAJVAAvB-tNsnDAxnD1np8emfnUde6Cb_6ojrkysGnXcUPDEvrA@mail.gmail.com>
References: <CAJVAAvB-tNsnDAxnD1np8emfnUde6Cb_6ojrkysGnXcUPDEvrA@mail.gmail.com>
Message-ID: <op.v7yt2xhzxuur8c@vanoxite>

On Thu, 12 Jan 2012 10:08:59 +0100, bhabya sahoo <bdslipun at gmail.com>  
wrote:
> how one can claculate the pressure in pwscf
> by giving only a single volume



 From Doc/INPUT_PW.txt:
    +--------------------------------------------------------------------
    Variable:       tstress

    Type:           LOGICAL
    Default:        .false.
    Description:    calculate stress. It is set to .TRUE. automatically if
                    calculation='vc-md' or 'vc-relax'
    +--------------------------------------------------------------------

best regards



-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From lmartinsamos at gmail.com  Thu Jan 12 11:50:50 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Thu, 12 Jan 2012 11:50:50 +0100
Subject: [Pw_forum] Fwd: postdoc position at Nova Gorica
Message-ID: <CAGCSmJQLAzi-RSLWm6HwvNW9vx4W7WXxd64fG-ioKNLD6MMPHQ@mail.gmail.com>

Dear all, the University of Nova Gorica has an open position for a
computational theoretician. I forward the proposal for your information.

bests

Layla


---------- Forwarded message ----------
From: Matjaz Valant <matjaz.valant at ung.si>
Date: 2012/1/11
Subject: Job add
To: Layla Martin-Samos <lmartinsamos at gmail.com>



-- 

prof. dr. Matjaz Valant
Head of Materials Research Laboratory
Dean of School of Environmental Sciences
University of Nova Gorica
Vipavska 11c, 5270 Ajdovscina, Slovenia
Phone: +386 5 3653502
http://www.ung.si/~mvalant
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From eariel99 at gmail.com  Thu Jan 12 12:28:53 2012
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Thu, 12 Jan 2012 12:28:53 +0100
Subject: [Pw_forum] scaling of turbo_lanczos.x
Message-ID: <CAM5Vcw-u2NMhEN23y+u1RmSA3F4Kc1H0-tQjgXaFQrdTR-WHDA@mail.gmail.com>

I have one more question ? What is nipol ? The manual reads

        nipol           1 if ipol < 4; 3 if ipol=4
                Determines the number of zeta coefficients to be calculated
for
                 a given polarization direction.
I think this z is the $^{m}z_{ij}$ present in Eqs. 33, 34-36 of the article
included in the Doc directory. What parameter in the Eq. correspond to
nipol ?


------------------------------

Hi
I am calculating optical spectra of a carbon nanotube with turbo-TDDFPT. I
would like to know how scales the cost and the needed parameters with the
size of the unit cell. As only the gamma point is allowed I need to
replicate the unit cell. for example, if I duplicate the unit cell, how
scales

a) the itermax parameter to achieve an equivalent resolution of the
spectrum (is the same or must be scaled)
b) RAM, CPU time for fixed itermax

Is there any advice to use efficiently multiple CPU systems that may differ
from the advices to use pw.x ? Are task groups implemented (-ntg or
similar) ?

Thank you
Eduardo
-- 


-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en
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From bdslipun at gmail.com  Thu Jan 12 12:56:23 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Thu, 12 Jan 2012 03:56:23 -0800
Subject: [Pw_forum] pressure
In-Reply-To: <op.v7yt2xhzxuur8c@vanoxite>
References: <CAJVAAvB-tNsnDAxnD1np8emfnUde6Cb_6ojrkysGnXcUPDEvrA@mail.gmail.com>
	<op.v7yt2xhzxuur8c@vanoxite>
Message-ID: <CAJVAAvCuHa4K4aFDvG198BUgM9EWJFe4Pba1V5Z_tDCshbgF2g@mail.gmail.com>

i know this how the program calculates?

On Thu, Jan 12, 2012 at 2:00 AM, Lorenzo Paulatto <
Lorenzo.Paulatto at impmc.upmc.fr> wrote:

> On Thu, 12 Jan 2012 10:08:59 +0100, bhabya sahoo <bdslipun at gmail.com>
> wrote:
> > how one can claculate the pressure in pwscf
> > by giving only a single volume
>
>
>
>  From Doc/INPUT_PW.txt:
>    +--------------------------------------------------------------------
>    Variable:       tstress
>
>    Type:           LOGICAL
>    Default:        .false.
>    Description:    calculate stress. It is set to .TRUE. automatically if
>                    calculation='vc-md' or 'vc-relax'
>    +--------------------------------------------------------------------
>
> best regards
>
>
>
> --
> Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From yunpengwang at live.com  Thu Jan 12 13:44:16 2012
From: yunpengwang at live.com (Peter Wang)
Date: Thu, 12 Jan 2012 20:44:16 +0800
Subject: [Pw_forum] RPA+EXX in PWscf
Message-ID: <SNT108-DS19272E7DFB6F1147A0B2F5C29F0@phx.gbl>

Hi:

I found RPA+EXX has been implemented in QE, see this paper: H. Nguyen, et al., Phys. Rev. B 79, 205114 (2009). However, I found nothing related to RPA+EXX in manual or examples. My question is, does the RPA+EXX implementation been released? Which version? Any manual? Any example?

best wishes,
Yun-Peng
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From akohlmey at gmail.com  Thu Jan 12 15:41:22 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 12 Jan 2012 09:41:22 -0500
Subject: [Pw_forum] Which subroutine is related to the atomic
 displacement in DFPT
In-Reply-To: <CAM0egYbcJV_++x=07zf81ZoaCwSE5Lq-i31gEvYSPnasArP5DQ@mail.gmail.com>
References: <CAM0egYbcJV_++x=07zf81ZoaCwSE5Lq-i31gEvYSPnasArP5DQ@mail.gmail.com>
Message-ID: <CADTmJ6GJACeJh1jUkbb=C_RV3J3D_ROZrX=pkdydtrtOMxzPRQ@mail.gmail.com>

On Wed, Jan 11, 2012 at 8:56 PM, Caloma Trumica <spmmal at gmail.com> wrote:
> Dear All,
>
> I could not find the name of the subroutine, which applies a pattern of
> atomic displacements in order to get the wavefunction perturbation in any q
> vector? Could you please help me out? It is supposed to be hidden somewhere
> in "PH" folder.

if you compute perturbations,
there are no displacements.
that is the whole point.

axel.


>
> Thanks.
>
> Andy Lau? Postgraduate student from HKUST, China
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From akohlmey at gmail.com  Thu Jan 12 15:43:45 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 12 Jan 2012 09:43:45 -0500
Subject: [Pw_forum] pressure
In-Reply-To: <CAJVAAvB-tNsnDAxnD1np8emfnUde6Cb_6ojrkysGnXcUPDEvrA@mail.gmail.com>
References: <CAJVAAvB-tNsnDAxnD1np8emfnUde6Cb_6ojrkysGnXcUPDEvrA@mail.gmail.com>
Message-ID: <CADTmJ6Gu1g+-CmPS2jBfD=8iMTtkhqJqwg2bZzCMrDoT2zZYyA@mail.gmail.com>

On Thu, Jan 12, 2012 at 4:08 AM, bhabya sahoo <bdslipun at gmail.com> wrote:
> how one can claculate the pressure in pwscf
> by giving only a single volume

why would you need more than one?

axel.


>
>
>
>
>
>
>
>
>
>
>
>
>
> sahu
> reserch scholar
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From akohlmey at gmail.com  Thu Jan 12 15:44:53 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 12 Jan 2012 09:44:53 -0500
Subject: [Pw_forum] RPA+EXX in PWscf
In-Reply-To: <SNT108-DS19272E7DFB6F1147A0B2F5C29F0@phx.gbl>
References: <SNT108-DS19272E7DFB6F1147A0B2F5C29F0@phx.gbl>
Message-ID: <CADTmJ6G6EoDgvZKAHD7ZX=g4SAPQwHoJVu0jHMEVfRqR-vyvDQ@mail.gmail.com>

2012/1/12 Peter Wang <yunpengwang at live.com>:
> Hi:
>
> I found RPA+EXX has been implemented in QE, see this paper: H. Nguyen, et
> al., Phys. Rev. B 79, 205114 (2009). However, I found nothing related to
> RPA+EXX in manual or examples. My question is, does the RPA+EXX
> implementation been released? Which version? Any manual? Any example?

you should direct this kind of questions first
to the (corresponding) author of the paper,
don't you think?

axel.


>
> best wishes,
> Yun-Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From spmmal at gmail.com  Thu Jan 12 15:47:06 2012
From: spmmal at gmail.com (Caloma Trumica)
Date: Thu, 12 Jan 2012 09:47:06 -0500
Subject: [Pw_forum] Which subroutine is related to the atomic
 displacement in DFPT
In-Reply-To: <CADTmJ6GJACeJh1jUkbb=C_RV3J3D_ROZrX=pkdydtrtOMxzPRQ@mail.gmail.com>
References: <CAM0egYbcJV_++x=07zf81ZoaCwSE5Lq-i31gEvYSPnasArP5DQ@mail.gmail.com>
	<CADTmJ6GJACeJh1jUkbb=C_RV3J3D_ROZrX=pkdydtrtOMxzPRQ@mail.gmail.com>
Message-ID: <CAM0egYbGnQbzz4buQzrsGfwfHo9QGMv+15POpzHOPXaRT-t7_g@mail.gmail.com>

Thanks.Axel.

I was wondering how to make perturbations for the ground state
wavefunctions in the Phonon code.

Isn't it either by atomic displacement or electric field?

On Thu, Jan 12, 2012 at 9:41 AM, Axel Kohlmeyer <akohlmey at gmail.com> wrote:

> On Wed, Jan 11, 2012 at 8:56 PM, Caloma Trumica <spmmal at gmail.com> wrote:
> > Dear All,
> >
> > I could not find the name of the subroutine, which applies a pattern of
> > atomic displacements in order to get the wavefunction perturbation in
> any q
> > vector? Could you please help me out? It is supposed to be hidden
> somewhere
> > in "PH" folder.
>
> if you compute perturbations,
> there are no displacements.
> that is the whole point.
>
> axel.
>
>
> >
> > Thanks.
> >
> > Andy Lau  Postgraduate student from HKUST, China
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey at gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From yunpengwang at live.com  Thu Jan 12 15:47:37 2012
From: yunpengwang at live.com (Peter Wang)
Date: Thu, 12 Jan 2012 22:47:37 +0800
Subject: [Pw_forum] RPA+EXX in PWscf
In-Reply-To: <CADTmJ6G6EoDgvZKAHD7ZX=g4SAPQwHoJVu0jHMEVfRqR-vyvDQ@mail.gmail.com>
References: <SNT108-DS19272E7DFB6F1147A0B2F5C29F0@phx.gbl>
	<CADTmJ6G6EoDgvZKAHD7ZX=g4SAPQwHoJVu0jHMEVfRqR-vyvDQ@mail.gmail.com>
Message-ID: <SNT108-DS1467EE5D478C172B8FF5C2C29F0@phx.gbl>

thanks! once I have response, I will told you and all the members here.

Yun-Peng

-----????----- 
From: Axel Kohlmeyer
Sent: Thursday, January 12, 2012 10:44 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] RPA+EXX in PWscf

2012/1/12 Peter Wang <yunpengwang at live.com>:
> Hi:
>
> I found RPA+EXX has been implemented in QE, see this paper: H. Nguyen, et
> al., Phys. Rev. B 79, 205114 (2009). However, I found nothing related to
> RPA+EXX in manual or examples. My question is, does the RPA+EXX
> implementation been released? Which version? Any manual? Any example?

you should direct this kind of questions first
to the (corresponding) author of the paper,
don't you think?

axel.


>
> best wishes,
> Yun-Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com  http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 


From Lorenzo.Paulatto at impmc.upmc.fr  Thu Jan 12 15:55:46 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 12 Jan 2012 15:55:46 +0100
Subject: [Pw_forum] pressure
In-Reply-To: <CAJVAAvCuHa4K4aFDvG198BUgM9EWJFe4Pba1V5Z_tDCshbgF2g@mail.gmail.com>
References: <CAJVAAvB-tNsnDAxnD1np8emfnUde6Cb_6ojrkysGnXcUPDEvrA@mail.gmail.com>
	<op.v7yt2xhzxuur8c@vanoxite>
	<CAJVAAvCuHa4K4aFDvG198BUgM9EWJFe4Pba1V5Z_tDCshbgF2g@mail.gmail.com>
Message-ID: <op.v7y7q8daxuur8c@vanoxite>

On Thu, 12 Jan 2012 12:56:23 +0100, bhabya sahoo <bdslipun at gmail.com>  
wrote:
> i know this how the program calculates?

It would be way too long to explain here; you can check it on electronic  
structure books, i.e.
R.M. Martin, Electronic Structure, chapter 3.3 and appendix G

In the code, various terms (e.g. contributions from ultrasoft,  
core-correction, local potential...) are computed in the following  
subroutines:
./PW/addusstress.f90
./PW/stres_cc.f90
./PW/stres_loc.f90
./PW/stres_ewa.f90
./PW/stres_gradcorr.f90
./PW/stres_knl.f90
./PW/stres_us.f90
./PW/stress.f90
./PW/stres_hub.f90
./PW/forces_bp_efield.f90
./PW/stres_har.f90


bests


-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From Lorenzo.Paulatto at impmc.upmc.fr  Thu Jan 12 16:06:04 2012
From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto)
Date: Thu, 12 Jan 2012 16:06:04 +0100
Subject: [Pw_forum] Which subroutine is related to the atomic
 displacement in DFPT
In-Reply-To: <CAM0egYbGnQbzz4buQzrsGfwfHo9QGMv+15POpzHOPXaRT-t7_g@mail.gmail.com>
References: <CAM0egYbcJV_++x=07zf81ZoaCwSE5Lq-i31gEvYSPnasArP5DQ@mail.gmail.com>
	<CADTmJ6GJACeJh1jUkbb=C_RV3J3D_ROZrX=pkdydtrtOMxzPRQ@mail.gmail.com>
	<CAM0egYbGnQbzz4buQzrsGfwfHo9QGMv+15POpzHOPXaRT-t7_g@mail.gmail.com>
Message-ID: <op.v7y78ensxuur8c@vanoxite>

On Thu, 12 Jan 2012 15:47:06 +0100, Caloma Trumica <spmmal at gmail.com>  
wrote:
> Isn't it either by atomic displacement or electric field?

It's done by density functional perturbation theory (DFPT). If you have  
never heard it before, you can start with these slides by Stefano baroni  
(http://stefano.baroni.me/presentations_files/lecture-ictp-Jan2011.pdf)  
and/or from chapter 19.3 in R.M. Martin's book (Electronic Structure,  
2004) and follow the references to go in depth.

bests

-- 
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

From giannozz at democritos.it  Thu Jan 12 16:14:18 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 12 Jan 2012 16:14:18 +0100
Subject: [Pw_forum] RPA+EXX in PWscf
In-Reply-To: <SNT108-DS19272E7DFB6F1147A0B2F5C29F0@phx.gbl>
References: <SNT108-DS19272E7DFB6F1147A0B2F5C29F0@phx.gbl>
Message-ID: <B919C865-A707-4F9A-89F1-BA2229739AF1@democritos.it>


On Jan 12, 2012, at 13:44 , Peter Wang wrote:

> My question is, does the RPA+EXX implementation been released?

not yet. See: http://qe-forge.org/projects/qe-acfdt/

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From payam.norouzzadeh at gmail.com  Thu Jan 12 16:48:13 2012
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Thu, 12 Jan 2012 09:48:13 -0600
Subject: [Pw_forum] atom positions in terms of alat
Message-ID: <CAND4gJFyoRt2wvN=rb1_spr2LofMTKmM5uAa=+o8irKefUZDDw@mail.gmail.com>

Dear Q.E users
I have a simple question: atom coordinates in terms of alat and after
relaxation  should be the same for different lattice constants.
Regardless of the lattice constant the atom position for atom number 1 in a
system should not change.
For example, for lattice constants 10 or 12 angstroms it should be 0. 0.5
0.25.It must be scaled.Is that correct?
Best regards,Nima Pirouzmand
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From habdslam at yahoo.fr  Thu Jan 12 16:58:09 2012
From: habdslam at yahoo.fr (Abdeslam Houari)
Date: Thu, 12 Jan 2012 15:58:09 +0000 (GMT)
Subject: [Pw_forum] RPA+EXX in PWscf
In-Reply-To: <SNT108-DS1467EE5D478C172B8FF5C2C29F0@phx.gbl>
Message-ID: <1326383889.7064.YahooMailClassic@web27407.mail.ukl.yahoo.com>

Hi;
In the QE-4.3.2, that I'm using, and according to EXX-Example, there are only: HF, PBE0, B3LYP and HSE-EXX which are implemented. 
We wish eally to know if the the RPA-EXX has been or not ?!! 

=======================================
Abdesalem HOUARI
-------------------------------------------------------------------------------------------
Department of physics, Theoretical Physics Laboratory
University of Bejaia-06000. Algeria.
E-mail:?abdeslam.houari at univ-bejaia.dz & habdslam at yahoo.fr
https://sites.google.com/site/houariabdeslam/homepage
Phone: +213 34 21 53 04
Fax: +213 34 21 59 86
Cell phone: +213 551 36 29 01 (emergency only !!)
========================================


--- En date de?: Jeu 12.1.12, Peter Wang <yunpengwang at live.com> a ?crit?:

De: Peter Wang <yunpengwang at live.com>
Objet: Re: [Pw_forum] RPA+EXX in PWscf
?: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Jeudi 12 janvier 2012, 15h47

thanks! once I have response, I will told you and all the members here.

Yun-Peng

-----????----- 
From: Axel Kohlmeyer
Sent: Thursday, January 12, 2012 10:44 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] RPA+EXX in PWscf

2012/1/12 Peter Wang <yunpengwang at live.com>:
> Hi:
>
> I found RPA+EXX has been implemented in QE, see this paper: H. Nguyen, et
> al., Phys. Rev. B 79, 205114 (2009). However, I found nothing related to
> RPA+EXX in manual or examples. My question is, does the RPA+EXX
> implementation been released? Which version? Any manual? Any example?

you should direct this kind of questions first
to the (corresponding) author of the paper,
don't you think?

axel.


>
> best wishes,
> Yun-Peng
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com? http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 

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From yunpengwang at live.com  Thu Jan 12 16:58:53 2012
From: yunpengwang at live.com (Peter Wang)
Date: Thu, 12 Jan 2012 23:58:53 +0800
Subject: [Pw_forum] atom positions in terms of alat
In-Reply-To: <CAND4gJFyoRt2wvN=rb1_spr2LofMTKmM5uAa=+o8irKefUZDDw@mail.gmail.com>
References: <CAND4gJFyoRt2wvN=rb1_spr2LofMTKmM5uAa=+o8irKefUZDDw@mail.gmail.com>
Message-ID: <SNT108-DS235C7DC87405ED9158DB80C29F0@phx.gbl>

I am not sure I understand your question clearly. In relax calculation, lattice is not changed and positions of atoms also change unless you explicitly make them fixed.

Yun-Peng

From: Payam Norouzzadeh 
Sent: Thursday, January 12, 2012 11:48 PM
To: pw_forum at pwscf.org 
Subject: [Pw_forum] atom positions in terms of alat

Dear Q.E users
I have a simple question: atom coordinates in terms of alat and after relaxation  should be the same for different lattice constants.
Regardless of the lattice constant the atom position for atom number 1 in a system should not change.
For example, for lattice constants 10 or 12 angstroms it should be 0. 0.5 0.25.It must be scaled.Is that correct?
Best regards,Nima Pirouzmand



--------------------------------------------------------------------------------
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From spmmal at gmail.com  Thu Jan 12 17:20:43 2012
From: spmmal at gmail.com (Caloma Trumica)
Date: Thu, 12 Jan 2012 11:20:43 -0500
Subject: [Pw_forum] Which subroutine is related to the atomic
 displacement in DFPT
In-Reply-To: <op.v7y78ensxuur8c@vanoxite>
References: <CAM0egYbcJV_++x=07zf81ZoaCwSE5Lq-i31gEvYSPnasArP5DQ@mail.gmail.com>
	<CADTmJ6GJACeJh1jUkbb=C_RV3J3D_ROZrX=pkdydtrtOMxzPRQ@mail.gmail.com>
	<CAM0egYbGnQbzz4buQzrsGfwfHo9QGMv+15POpzHOPXaRT-t7_g@mail.gmail.com>
	<op.v7y78ensxuur8c@vanoxite>
Message-ID: <CAM0egYZtyL4ftOUvOp-CnGXDscVcYdue6N9m4Dc9wS7bN_6Ovw@mail.gmail.com>

Hi Professor,

Can you comment on this thread.

Question again, how to induce the perturbation in PWSCF?

Many Thanks.

On Thu, Jan 12, 2012 at 10:06 AM, Lorenzo Paulatto <
Lorenzo.Paulatto at impmc.upmc.fr> wrote:

> On Thu, 12 Jan 2012 15:47:06 +0100, Caloma Trumica <spmmal at gmail.com>
> wrote:
> > Isn't it either by atomic displacement or electric field?
>
> It's done by density functional perturbation theory (DFPT). If you have
> never heard it before, you can start with these slides by Stefano baroni
> (http://stefano.baroni.me/presentations_files/lecture-ictp-Jan2011.pdf)
> and/or from chapter 19.3 in R.M. Martin's book (Electronic Structure,
> 2004) and follow the references to go in depth.
>
> bests
>
> --
> Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
> phone: +33 (0)1 44275 084 / skype: paulatz
> www:   http://www-int.impmc.upmc.fr/~paulatto/
> mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From flux_ray12 at 163.com  Thu Jan 12 18:33:55 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Fri, 13 Jan 2012 01:33:55 +0800 (CST)
Subject: [Pw_forum] Which subroutine is related to the atomic
 displacement in DFPT
In-Reply-To: <CAM0egYZtyL4ftOUvOp-CnGXDscVcYdue6N9m4Dc9wS7bN_6Ovw@mail.gmail.com>
References: <CAM0egYZtyL4ftOUvOp-CnGXDscVcYdue6N9m4Dc9wS7bN_6Ovw@mail.gmail.com>
	<CAM0egYbcJV_++x=07zf81ZoaCwSE5Lq-i31gEvYSPnasArP5DQ@mail.gmail.com>
	<CADTmJ6GJACeJh1jUkbb=C_RV3J3D_ROZrX=pkdydtrtOMxzPRQ@mail.gmail.com>
	<CAM0egYbGnQbzz4buQzrsGfwfHo9QGMv+15POpzHOPXaRT-t7_g@mail.gmail.com>
	<op.v7y78ensxuur8c@vanoxite>
Message-ID: <45d9a778.3e5.134d2fbab27.Coremail.flux_ray12@163.com>

Do you mean the displacement modes in DFPT, as:
     Atomic displacements:
     "There are",  i3, "irreducible representations"
May the code mode_group.f90 be able to give you some idea~


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-01-13 00:20:57,"Caloma Trumica" <spmmal at gmail.com> wrote:
Hi Professor,

Can you comment on this thread.

Question again, how to induce the perturbation in PWSCF?

Many Thanks.


On Thu, Jan 12, 2012 at 10:06 AM, Lorenzo Paulatto <Lorenzo.Paulatto at impmc.upmc.fr> wrote:
On Thu, 12 Jan 2012 15:47:06 +0100, Caloma Trumica <spmmal at gmail.com>
wrote:

> Isn't it either by atomic displacement or electric field?


It's done by density functional perturbation theory (DFPT). If you have
never heard it before, you can start with these slides by Stefano baroni
(http://stefano.baroni.me/presentations_files/lecture-ictp-Jan2011.pdf)
and/or from chapter 19.3 in R.M. Martin's book (Electronic Structure,
2004) and follow the references to go in depth.

bests

--
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05

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From degironc at sissa.it  Thu Jan 12 19:43:10 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 12 Jan 2012 19:43:10 +0100
Subject: [Pw_forum] RPA+EXX in PWscf
In-Reply-To: <1326383889.7064.YahooMailClassic@web27407.mail.ukl.yahoo.com>
References: <1326383889.7064.YahooMailClassic@web27407.mail.ukl.yahoo.com>
Message-ID: <4F0F29BE.2040106@sissa.it>

Dear Yun-Peng Wang, Abdesalem HOUARI, dear All,

    EXX+RPA is a quite interesting approach to be explored but it very 
far from being released publicly, because  there are a number of 
important issues to be addressed before it can be used by anyone as a 
black box, in particular we are working on the calculation of the scf 
RPA potential. It is yet to be explored the quality of the approximation 
in critical systems and how important the self consistency is. A number 
of things have to be understood before we can release it publicly.
    So:
    If you are interested in applying it to some applications, forget it 
for the next 5-10 yrs (I'm possibly exaggerating, some bright young 
people will join the effort later this year).
    If you are interested in working on its development and you have a 
strong background in electronic structure and/or scientific coding... 
let's talk about.
    If you are interested to systems with significant vdW interaction 
you should try to use vdw-DF functionals and keep an eye on future 
developments.

Stefano de Gironcoli

On 01/12/2012 04:58 PM, Abdeslam Houari wrote:
> Hi;
> In the QE-4.3.2, that I'm using, and according to EXX-Example, there are only: HF, PBE0, B3LYP and HSE-EXX which are implemented.
> We wish eally to know if the the RPA-EXX has been or not ?!!
>
> =======================================
> Abdesalem HOUARI
> -------------------------------------------------------------------------------------------
> Department of physics, Theoretical Physics Laboratory
> University of Bejaia-06000. Algeria.
> E-mail: abdeslam.houari at univ-bejaia.dz&  habdslam at yahoo.fr
> https://sites.google.com/site/houariabdeslam/homepage
> Phone: +213 34 21 53 04
> Fax: +213 34 21 59 86
> Cell phone: +213 551 36 29 01 (emergency only !!)
> ========================================
>
>
> --- En date de : Jeu 12.1.12, Peter Wang<yunpengwang at live.com>  a ?crit :
>
> De: Peter Wang<yunpengwang at live.com>
> Objet: Re: [Pw_forum] RPA+EXX in PWscf
> ?: "PWSCF Forum"<pw_forum at pwscf.org>
> Date: Jeudi 12 janvier 2012, 15h47
>
> thanks! once I have response, I will told you and all the members here.
>
> Yun-Peng
>
> -----????-----
> From: Axel Kohlmeyer
> Sent: Thursday, January 12, 2012 10:44 PM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] RPA+EXX in PWscf
>
> 2012/1/12 Peter Wang<yunpengwang at live.com>:
>> Hi:
>>
>> I found RPA+EXX has been implemented in QE, see this paper: H. Nguyen, et
>> al., Phys. Rev. B 79, 205114 (2009). However, I found nothing related to
>> RPA+EXX in manual or examples. My question is, does the RPA+EXX
>> implementation been released? Which version? Any manual? Any example?
> you should direct this kind of questions first
> to the (corresponding) author of the paper,
> don't you think?
>
> axel.
>
>


From somayehfotohi at yahoo.com  Thu Jan 12 20:06:04 2012
From: somayehfotohi at yahoo.com (somayeh fotohi)
Date: Thu, 12 Jan 2012 11:06:04 -0800 (PST)
Subject: [Pw_forum] quantum espresso
In-Reply-To: <1326181748.7441.YahooMailClassic@web125902.mail.ne1.yahoo.com>
Message-ID: <1326395164.78144.YahooMailClassic@web161404.mail.bf1.yahoo.com>

hi,

I am a new user of quantum espresso. I found your address from your mail to pw_forum at pwscf.org. 
I want to relax a structure with 32 atoms carbon and topological defect.Now, the program is running and 24 step of relaxation calculation has done but the structure hasn?t relax.
Is it correct that I stop running ?the program and change the position of atoms ?
thanks.
somayeh fotoohi
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From luleon13 at gmail.com  Thu Jan 12 20:13:38 2012
From: luleon13 at gmail.com (Luis Antonio Leon Martinez)
Date: Thu, 12 Jan 2012 14:13:38 -0500
Subject: [Pw_forum] quantum espresso
In-Reply-To: <1326395164.78144.YahooMailClassic@web161404.mail.bf1.yahoo.com>
References: <1326181748.7441.YahooMailClassic@web125902.mail.ne1.yahoo.com>
	<1326395164.78144.YahooMailClassic@web161404.mail.bf1.yahoo.com>
Message-ID: <CAC3yZuGQcUaGSbbY7Zr05O=W_tsX3FE3i7yMzoDrP90gMENE=g@mail.gmail.com>

Hi Somayeh.
I think that there is no problem with stop the calculation. But, how long
it takes to be running? Relaxation calculations are delayed.

Best regards,

Luis A. Leon.
Chemist, M.Sc.


On Thu, Jan 12, 2012 at 2:06 PM, somayeh fotohi <somayehfotohi at yahoo.com>wrote:

>   hi,
>
> I am a new user of quantum espresso. I found your address from your mail
> to pw_forum at pwscf.org.
> I want to relax a structure with 32 atoms carbon and topological
> defect.Now, the program is running and 24 step of relaxation calculation
> has done but the structure hasn?t relax.******
>
> Is it correct that I stop running  the program and change the position of
> atoms ?
>
> thanks.
>
> somayeh fotoohi
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From gbilalbegovic at gmail.com  Thu Jan 12 20:58:46 2012
From: gbilalbegovic at gmail.com (Goranka Bilalbegovic)
Date: Thu, 12 Jan 2012 20:58:46 +0100
Subject: [Pw_forum] example09 segfault - ramtns used but not allocated
	in dynmatrix.f90
In-Reply-To: <1326293201.27523.1.camel@fe12lx.fisica.uniud.it>
References: <201112121002.27711.jean-roch.huntzinger@univ-montp2.fr>
	<1323686999.21852.39.camel@fe12lx.fisica.uniud.it>
	<CALj7P9vT70k7ikPM1FP-UVdk+PsPNbz6g1KGcqdpjXep2UQBkg@mail.gmail.com>
	<1326289802.26182.16.camel@fe12lx.fisica.uniud.it>
	<CALj7P9v3Z-2fhFshzmwo9xO2QL83XZRjtCmbiD92J13uw7jsaw@mail.gmail.com>
	<1326293201.27523.1.camel@fe12lx.fisica.uniud.it>
Message-ID: <CALj7P9svLM+eKCDdL2kaMszFeq1B_=+8Oirs3_0XTuC7e=Pa8A@mail.gmail.com>

On Wed, Jan 11, 2012 at 3:46 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

> On Wed, 2012-01-11 at 15:09 +0100, Goranka Bilalbegovic wrote:
>
> > I do not run dynmat.x for N >1, but for N=1.
>
> if you run in parallel on 1 processor, it works
>
>
Not on the cluster I am using. However, system managers told me how to
write *.sge script and submit a dynmat job without mpirun. I have also
compiled a special "dynmat" version of QE using --enable-parallel=no, and
now dynmat.x works.

Thank you very much for a help.
Best regards,

-- 
Goranka Bilalbegovic,
Department of Physics, Faculty of Science,
University of Zagreb, Croatia
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From giannozz at democritos.it  Thu Jan 12 22:34:27 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Thu, 12 Jan 2012 22:34:27 +0100
Subject: [Pw_forum] Which subroutine is related to the atomic
	displacement in DFPT
In-Reply-To: <CAM0egYZtyL4ftOUvOp-CnGXDscVcYdue6N9m4Dc9wS7bN_6Ovw@mail.gmail.com>
References: <CAM0egYbcJV_++x=07zf81ZoaCwSE5Lq-i31gEvYSPnasArP5DQ@mail.gmail.com>
	<CADTmJ6GJACeJh1jUkbb=C_RV3J3D_ROZrX=pkdydtrtOMxzPRQ@mail.gmail.com>
	<CAM0egYbGnQbzz4buQzrsGfwfHo9QGMv+15POpzHOPXaRT-t7_g@mail.gmail.com>
	<op.v7y78ensxuur8c@vanoxite>
	<CAM0egYZtyL4ftOUvOp-CnGXDscVcYdue6N9m4Dc9wS7bN_6Ovw@mail.gmail.com>
Message-ID: <ECE09CD1-78C2-4732-ACB7-9DF520ADAD66@democritos.it>


On Jan 12, 2012, at 17:20 , Caloma Trumica wrote:

> Can you comment on this thread.

there is nothing to comment. The phonon code is very complex
(36000 specific lines, plus many thousands more from PW and
from libraries). I would say it is the most complex in the QE
distribution. Without a clear idea of how the theory works, or
even WITH a clear idea, it is hard to understand how the code
works. The only way is to delve into the code and figure out
what the different pieces do; then, locate the piece that performs
the operations you are interested in.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From daijiayu at nudt.edu.cn  Fri Jan 13 14:49:59 2012
From: daijiayu at nudt.edu.cn (jiayudai)
Date: Fri, 13 Jan 2012 21:49:59 +0800
Subject: [Pw_forum] Ewald and Coulomb
In-Reply-To: <526403438.06189@eyou.net>
References: <526403438.06189@eyou.net>
Message-ID: <120113214959bbfde8bebdfe6219d8828a5fa8949b6b@nudt.edu.cn>


Dear users and developers,

Happy new year!

I have a confusion about the calculations of ion-ion interactions. We know, we usually use Ewald scheme to represent the real Coulomb potentials in a periodic cell. Generally, it is correct for a neutral system or one electron taken out (or into ) system. However, if the system is constructed with partially charged ions, that is to say, there are more positive charges than negative charges, the Ewald scheme should be not right. Although this system is not stable, but there should be some properties deserved to study.

So, how can we calculate the true Coulomb potentials in DFT? That is to say, we do not use Ewald, but only use th 1/r type. I know it can be realized in classical calculations, but i did not find the path to get it in QE.

Thanks a lot.

Jiayu


----------------
-------------------------------------------
Jiayu Dai
Department of PhysicsNational University of Defense Technology, 
Changsha, 410073, P R China
-----------------------------------------

 
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From yunpengwang at live.com  Fri Jan 13 15:22:54 2012
From: yunpengwang at live.com (Yunpeng Wang)
Date: Fri, 13 Jan 2012 09:22:54 -0500
Subject: [Pw_forum] Ewald and Coulomb
In-Reply-To: <120113214959bbfde8bebdfe6219d8828a5fa8949b6b@nudt.edu.cn>
References: <526403438.06189@eyou.net>,
	<120113214959bbfde8bebdfe6219d8828a5fa8949b6b@nudt.edu.cn>
Message-ID: <SNT108-W3AAC6555AC333E1012243C29C0@phx.gbl>


what do you mean by "true Coulomb potential"? Based on density functional theory, adding an uniform potential to the system make no difference. In fact, the ion-ion interaction energy is an infinite value because of 1/r type of Coulomb potential. However, if an uniform charge density which makes total charge zero, hence uniform Coulomb potential is added to the system, the electrostatic energy as well as potential is finite, at the same time, physics keep unchanged.
best wishes,Yun-Peng

Date: Fri, 13 Jan 2012 21:49:59 +0800
From: daijiayu at nudt.edu.cn
To: pw_forum at pwscf.org
Subject: [Pw_forum] Ewald and Coulomb


	Dear users and developers,

	

	Happy new year!

	

	I have a confusion about the calculations of ion-ion interactions. We know, we usually use Ewald scheme to represent the real Coulomb potentials in a periodic cell. Generally, it is correct for a neutral system or one electron taken out (or into ) system. However, if the system is constructed with partially charged ions, that is to say, there are more positive charges than negative charges, the Ewald scheme should be not right. Although this system is not stable, but there should be some properties deserved to study.

	

	So, how can we calculate the true Coulomb potentials in DFT? That is to say, we do not use Ewald, but only use th 1/r type. I know it can be realized in classical calculations, but i did not find the path to get it in QE.

	

	Thanks a lot.

	

	Jiayu






----------------


	-------------------------------------------

	Jiayu Dai

	Department of PhysicsNational University of Defense Technology, 

	Changsha, 410073, P R China

	-----------------------------------------

	

	 



_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 		 	   		  
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From giannozz at democritos.it  Fri Jan 13 16:50:16 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 13 Jan 2012 16:50:16 +0100
Subject: [Pw_forum] scaling of turbo_lanczos.x
In-Reply-To: <CAM5Vcw_UhaMuS3nvgwDSFrp6iFU8rTV5epho+7KJoi5w7Azy9w@mail.gmail.com>
References: <CAM5Vcw_UhaMuS3nvgwDSFrp6iFU8rTV5epho+7KJoi5w7Azy9w@mail.gmail.com>
Message-ID: <1326469816.24688.6.camel@fe12lx.fisica.uniud.it>

On Tue, 2012-01-10 at 12:50 +0100, Eduardo Ariel Menendez Proupin wrote:

> Is there any advice to use efficiently multiple CPU systems
>  that may differ from the advices to use pw.x ? 
> Are task groups implemented (-ntg or similar) ?

I don't think they are

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From sbinnie at sissa.it  Fri Jan 13 17:38:46 2012
From: sbinnie at sissa.it (Simon Binnie)
Date: Fri, 13 Jan 2012 17:38:46 +0100
Subject: [Pw_forum] scaling of turbo_lanczos.x
In-Reply-To: <1243EB51-388D-4B27-BC76-AEF86E9D5080@sissa.it>
References: <1326449636.19575.35.camel@fe12lx.fisica.uniud.it>
	<1243EB51-388D-4B27-BC76-AEF86E9D5080@sissa.it>
Message-ID: <op.v7066wmgb4z88i@mugon.cm.sissa.it>

Hello Eduardo,

The relevant Equation is Eq. 33 and the definition of \alpha_{ij}(\omega)
at the start of Section 2. 'ipol' refers to the axis long which the
perturbing electric field is polarized for the calculation. If only one
direction is considered (1 =< ipol =< 3) then only the appropriate
diagonal part of \alpha_{ij}(\omega) is calculated, so you get
\alpha_{ipol,ipol}(\omega). Since this only depends on ^{m}z_{ipol ipol}
the off diagonal parts, ^{m}z_{i ipol} (for i \= ipol) are not calculated.

In the case where ipol=4 the programme runs three times with ipol=1,2,3.
In this case the off-diagonal parts of \alpha_{ij}(\omega) are also
calculated which in turn require the off-diagonal components of z, leading
to three z components at each step (^{m}z_{i ipol} for i = 1,2 3).

Brgrds,

Simon

>> From: Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
>> Date: January 12, 2012 12:28:53 PM GMT+01:00
>> To: pw_forum at pwscf.org
>> Subject: Re: [Pw_forum] scaling of turbo_lanczos.x
>> Reply-To: PWSCF Forum <pw_forum at pwscf.org>
>>
>>
>> I have one more question ? What is nipol ? The manual reads
>>
>>         nipol           1 if ipol < 4; 3 if ipol=4
>>                 Determines the number of zeta coefficients to be  
>> calculated for
>>                  a given polarization direction.
>> I think this z is the $^{m}z_{ij}$ present in Eqs. 33, 34-36 of the  
>> article included in the Doc directory. What parameter in the Eq.  
>> correspond to nipol ?
>>

-- 
Simon Binnie | Post Doc, Condensed Matter Sector
Scuola Internazionale di Studi Avanzati (SISSA)
Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it

From avallabh at purdue.edu  Sat Jan 14 08:32:52 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Sat, 14 Jan 2012 02:32:52 -0500 (EST)
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <1207216877.269512.1326525818751.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <534814102.269514.1326526372215.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear users,

          1.  I was wondering how to calculate the absolute value of fermi energy for graphene single layer. By varying the size of the super cell in the out of plane direction, i observed that the total energy is constant indicating no  interactions in the out of plane direction, but the fermi energy is varying with increasing distance. I think it is the relative fermi energy which is output after the scf calculation. I want to know the absolute value. 

             
           2.  Another question i have is regarding the e-ph calculation. For a give set of q and k points, what is the best way to ensure that all k+q points are available to avoid the message " q is not a vector in the dense grid" in the calculations"? I observed that using a dense grid is not enough sometimes. Do we have to check it outside of the quantum espresso before the calculation begins? 


Thanks
Ajit

From w2agz at w2agz.com  Sat Jan 14 07:59:49 2012
From: w2agz at w2agz.com (W2AGZ)
Date: Fri, 13 Jan 2012 22:59:49 -0800
Subject: [Pw_forum] ph.x, q2r.x and low symmetries
Message-ID: <021801ccd28a$1c8fd5d0$55af8170$@w2agz.com>

To The Community:

 

A question/issue(maybe) re interaction between electron-phonon calculation
output from ph.x and subsequent following calculation of force constants
using q2r.x for low symmetry lattices.  I'm attempting an e-p exercise on a
low symmetry, two light element, crystal (ibrav=12, monoclinic) targeting
eventually appropriate Eliashberg-McMillan  parameters for this system.  I'm
still testing, but I'm getting (8 parallel processors) errors after the ph.x
step from q2r.x to wit:

"nc already filled: wrong q grid or wrong nr"
and, yes, nq = 2 and there is no xq.
A 100 years ago, (well, 2005, actually), there was a similar post,
http://www.democritos.it/pipermail/pw_forum/2005-December.txt
for ibrav=0, which was "fixed" in the next CVS release.  Was it for all
nasty symmetries?
 
-Paul Grant
www.w2agz.com
JPL-CalTech

 

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From yunpengwang at live.com  Sat Jan 14 10:26:07 2012
From: yunpengwang at live.com (Peter Wang)
Date: Sat, 14 Jan 2012 17:26:07 +0800
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <534814102.269514.1326526372215.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <534814102.269514.1326526372215.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <SNT108-DS17F4C4F02858103E20ABBCC29D0@phx.gbl>

for the first question, there is no absolute Fermi energy. The only absolute 
energy is that substracting vacuum energy level from it.

best
Yun-Peng

-----????----- 
From: Ajit Vallabhaneni
Sent: Saturday, January 14, 2012 3:32 PM
To: PWSCF Forum
Subject: [Pw_forum] query on fermi energy

Dear users,

          1.  I was wondering how to calculate the absolute value of fermi 
energy for graphene single layer. By varying the size of the super cell in 
the out of plane direction, i observed that the total energy is constant 
indicating no  interactions in the out of plane direction, but the fermi 
energy is varying with increasing distance. I think it is the relative fermi 
energy which is output after the scf calculation. I want to know the 
absolute value.


           2.  Another question i have is regarding the e-ph calculation. 
For a give set of q and k points, what is the best way to ensure that all 
k+q points are available to avoid the message " q is not a vector in the 
dense grid" in the calculations"? I observed that using a dense grid is not 
enough sometimes. Do we have to check it outside of the quantum espresso 
before the calculation begins?


Thanks
Ajit
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 


From daijiayu at nudt.edu.cn  Sat Jan 14 15:17:51 2012
From: daijiayu at nudt.edu.cn (jiayudai)
Date: Sat, 14 Jan 2012 22:17:51 +0800
Subject: [Pw_forum] Ewald and Coulomb
In-Reply-To: <526529701.03430@eyou.net>
References: <526529701.03430@eyou.net>
Message-ID: <1201142217515531d5359710debc14cad65776dda9fe@nudt.edu.cn>


Dear Yun-Peng,

Thanks for your explanation. In fact, what i mean is that how to treat the ion-ion interactions with some charges. For example, sometimes we want to take out one or more electrons out of the system, thus the tot_charge in the system is not zero. In an extreme case, all electrons are ionized and taken out, there are only positive ions in the system. In this case, the Ewald potential should not be right but the real Coulomb potential should be correct. Since Ewald scheme considers the screnning by the electrons. Thus, i want to use the exact 1/r potential to represent the Ewald scheme. So, how can we reach this goal?

Best wishes.

Jiayu


>>>>>>>>>>>>>>>>>>>
what do you mean by "true Coulomb potential"? Based on density functional theory, adding an uniform potential to the system make no difference. In fact, the ion-ion interaction energy is an infinite value because of 1/r type of Coulomb potential. However, if an uniform charge density which makes total charge zero, hence uniform Coulomb potential is added to the system, the electrostatic energy as well as potential is finite, at the same time, physics keep unchanged.
best wishes,Yun-Peng
Date: Fri, 13 Jan 2012 21:49:59 +0800
From: daijiayu at nudt.edu.cn
To: pw_forum at pwscf.org
Subject: [Pw_forum] Ewald and Coulomb

Dear users and developers,
Happy new year!
 
I have a confusion about the calculations of ion-ion interactions. We know, we usually use Ewald scheme to represent the real Coulomb potentials in a periodic cell. Generally, it is correct for a neutral system or one electron taken out (or into ) system. However, if the system is constructed with partially charged ions, that is to say, there are more positive charges than negative charges, the Ewald scheme should be not right. Although this system is not stable, but there should be some properties deserved to study.
So, how can we calculate the true Coulomb potentials in DFT? That is to say, we do not use Ewald, but only use th 1/r type. I know it can be realized in classical calculations, but i did not find the path to get it in QE.
 
Thanks a lot.
 
Jiayu
 
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From yunpengwang at live.com  Sat Jan 14 15:56:00 2012
From: yunpengwang at live.com (Peter Wang)
Date: Sat, 14 Jan 2012 22:56:00 +0800
Subject: [Pw_forum] Ewald and Coulomb
In-Reply-To: <1201142217515531d5359710debc14cad65776dda9fe@nudt.edu.cn>
References: <526529701.03430@eyou.net>
	<1201142217515531d5359710debc14cad65776dda9fe@nudt.edu.cn>
Message-ID: <SNT108-DS22B287C27F9CAD93AF0A21C29D0@phx.gbl>

Let?s consider positive point charges q in one dimensional lattice, that is, at x=a*j, j=-infinity,...,-2,-1,0,1,2,...,+infinity. In order to calculate the electrostatic energy due to Coulomb interaction between the charge at x=0 and all the other charges, one should calculate the summation: 1/a * sum_j q^2/j. However, the summation is not converged and is positive infinite. In summary, electrostatic interaction energy for charged system is infinite and one needs some other technique to calculate it.

Yun-Peng

From: jiayudai 
Sent: Saturday, January 14, 2012 10:17 PM
To: pw_forum at pwscf.org 
Subject: Re: [Pw_forum] Ewald and Coulomb

Dear Yun-Peng,

Thanks for your explanation. In fact, what i mean is that how to treat the ion-ion interactions with some charges. For example, sometimes we want to take out one or more electrons out of the system, thus the tot_charge in the system is not zero. In an extreme case, all electrons are ionized and taken out, there are only positive ions in the system. In this case, the Ewald potential should not be right but the real Coulomb potential should be correct. Since Ewald scheme considers the screnning by the electrons. Thus, i want to use the exact 1/r potential to represent the Ewald scheme. So, how can we reach this goal?

Best wishes.

Jiayu


>>>>>>>>>>>>>>>>>>>
what do you mean by "true Coulomb potential"? Based on density functional theory, adding an uniform potential to the system make no difference. In fact, the ion-ion interaction energy is an infinite value because of 1/r type of Coulomb potential. However, if an uniform charge density which makes total charge zero, hence uniform Coulomb potential is added to the system, the electrostatic energy as well as potential is finite, at the same time, physics keep unchanged.
best wishes,Yun-Peng

Date: Fri, 13 Jan 2012 21:49:59 +0800
From: daijiayu at nudt.edu.cn
To: pw_forum at pwscf.org
Subject: [Pw_forum] Ewald and Coulomb


Dear users and developers,

Happy new year!



I have a confusion about the calculations of ion-ion interactions. We know, we usually use Ewald scheme to represent the real Coulomb potentials in a periodic cell. Generally, it is correct for a neutral system or one electron taken out (or into ) system. However, if the system is constructed with partially charged ions, that is to say, there are more positive charges than negative charges, the Ewald scheme should be not right. Although this system is not stable, but there should be some properties deserved to study.

So, how can we calculate the true Coulomb potentials in DFT? That is to say, we do not use Ewald, but only use th 1/r type. I know it can be realized in classical calculations, but i did not find the path to get it in QE.



Thanks a lot.



Jiayu
 



--------------------------------------------------------------------------------
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From giannozz at democritos.it  Sat Jan 14 16:47:22 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sat, 14 Jan 2012 16:47:22 +0100
Subject: [Pw_forum] ph.x, q2r.x and low symmetries
In-Reply-To: <021801ccd28a$1c8fd5d0$55af8170$@w2agz.com>
References: <021801ccd28a$1c8fd5d0$55af8170$@w2agz.com>
Message-ID: <6A42AE7F-6CFA-4052-A3A0-9EF2B7FD4330@democritos.it>


On Jan 14, 2012, at 7:59 , W2AGZ wrote:
> I?m getting (...) errors after the ph.x step from q2r.x to wit: ?nc  
> already filled: wrong q grid or wrong nr?and, yes, nq = 2 and there  
> is no xq.
>

no way to say anyrthing sensible without a (simple!) example

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From avallabh at purdue.edu  Sat Jan 14 18:06:18 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Sat, 14 Jan 2012 12:06:18 -0500 (EST)
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <SNT108-DS17F4C4F02858103E20ABBCC29D0@phx.gbl>
Message-ID: <1411025427.269847.1326560778944.JavaMail.root@mailhub016.itcs.purdue.edu>

Yun-peng,

         Thanks for your response. Is it possible to know what the vaccum energy level is ? I read in the FAQ that it cannot be calculated from the a bulk calculation alone. 


Thanks
Ajit

From yunpengwang at live.com  Sat Jan 14 18:14:00 2012
From: yunpengwang at live.com (Peter Wang)
Date: Sun, 15 Jan 2012 01:14:00 +0800
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <1411025427.269847.1326560778944.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <1411025427.269847.1326560778944.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <SNT108-DS15CED8C06D5F150E6FB753C29D0@phx.gbl>

if we do a bulk calculation, vacuum energy level can not be calculated, 
because in bulk, there is no vacuum. To calculate vacuum energy level and 
the relative energies in bulk with respect to vacuum energy level, a slab 
calculation should be done. In a slab calculation, several layer of 
materials as well as a vacuum with sufficient thinkness should be included 
in one unit cell.

YP

-----????----- 
From: Ajit Vallabhaneni
Sent: Sunday, January 15, 2012 1:06 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] query on fermi energy

Yun-peng,

         Thanks for your response. Is it possible to know what the vaccum 
energy level is ? I read in the FAQ that it cannot be calculated from the a 
bulk calculation alone.


Thanks
Ajit
_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum 


From akohlmey at gmail.com  Sat Jan 14 20:10:17 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Sat, 14 Jan 2012 14:10:17 -0500
Subject: [Pw_forum] Ewald and Coulomb
In-Reply-To: <1201142217515531d5359710debc14cad65776dda9fe@nudt.edu.cn>
References: <526529701.03430@eyou.net>
	<1201142217515531d5359710debc14cad65776dda9fe@nudt.edu.cn>
Message-ID: <CADTmJ6H_qwNpHMVSk1EO2UD_N0PQ93Jo9b=UD5+qDoVHe_Gc2A@mail.gmail.com>

2012/1/14 jiayudai <daijiayu at nudt.edu.cn>:
> Dear Yun-Peng,
>
> Thanks for your explanation. In fact, what i mean is that how to treat the
> ion-ion interactions with some charges. For example, sometimes we want to
> take out one or more electrons out of the system, thus the tot_charge in the
> system is not zero. In an extreme case, all electrons are ionized and taken
> out, there are only positive ions in the system. In this case, the Ewald
> potential should not be right but the real Coulomb potential should be
> correct. Since Ewald scheme considers the screnning by the electrons. Thus,
> i want to use the exact 1/r potential to represent the Ewald scheme. So, how
> can we reach this goal?

if you want to look at things at this level,
then you have to accept the fact that you
cannot remove electrons from an infinite
system. only from a finite system.

you can still do the calculation with a
periodic system, if you ignore the divergent
term that stems from the total charge of
your unit cell. if you do ewald summation
with conducting boundary conditions, the
forces will not be affected (at least not for
the classical system), but the energy is
- of course - wrong.

either this approach is good enough to you,
or you have to use a real space DFT code
instead, where you don't have to worry about
periodicity by construction (but have some
other issues...).

axel.


>
> Best wishes.
>
> Jiayu
>
>
>
>
>>>>>>>>>>>>>>>>>>>>
> what do you mean by "true Coulomb potential"? Based on density functional
> theory, adding an uniform potential to the system make no difference. In
> fact, the ion-ion interaction energy is an infinite value because of 1/r
> type of Coulomb potential. However, if an uniform charge density which makes
> total charge zero, hence uniform Coulomb potential is added to the system,
> the electrostatic energy as well as potential is finite, at the same time,
> physics keep unchanged.
> best wishes,Yun-Peng
>
> Date: Fri, 13 Jan 2012 21:49:59 +0800
>
>
> From: daijiayu at nudt.edu.cn
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] Ewald and Coulomb
>
>
> Dear users and developers,
>
> Happy new year!
>
>
>
> I have a confusion about the calculations of ion-ion interactions. We know,
> we usually use Ewald scheme to represent the real Coulomb potentials in a
> periodic cell. Generally, it is correct for a neutral system or one electron
> taken out (or into ) system. However, if the system is constructed with
> partially charged ions, that is to say, there are more positive charges than
> negative charges, the Ewald scheme should be not right. Although this system
> is not stable, but there should be some properties deserved to study.
>
> So, how can we calculate the true Coulomb potentials in DFT? That is to say,
> we do not use Ewald, but only use th 1/r type. I know it can be realized in
> classical calculations, but i did not find the path to get it in QE.
>
>
>
> Thanks a lot.
>
>
>
> Jiayu
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From w2agz at w2agz.com  Sat Jan 14 20:26:38 2012
From: w2agz at w2agz.com (W2AGZ)
Date: Sat, 14 Jan 2012 11:26:38 -0800
Subject: [Pw_forum] ph.x, q2r.x and low symmetries
In-Reply-To: <6A42AE7F-6CFA-4052-A3A0-9EF2B7FD4330@democritos.it>
References: <021801ccd28a$1c8fd5d0$55af8170$@w2agz.com>
	<6A42AE7F-6CFA-4052-A3A0-9EF2B7FD4330@democritos.it>
Message-ID: <025e01ccd2f2$7114d110$533e7330$@w2agz.com>

Still working on this issue to make sure (well, as best I can) that I've
made no egregiously stupid blunders.  The e-p run is quite long...24
IRs...about a day on 8 processors.  Should the problem persist, would it be
useful to post the input files to ph.x and q2r.x?  About 30 lines total?

-Paul

-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Paolo Giannozzi
Sent: Saturday, January 14, 2012 7:47 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] ph.x, q2r.x and low symmetries


On Jan 14, 2012, at 7:59 , W2AGZ wrote:
> I'm getting (...) errors after the ph.x step from q2r.x to wit: "nc 
> already filled: wrong q grid or wrong nr"and, yes, nq = 2 and there is 
> no xq.
>

no way to say anyrthing sensible without a (simple!) example

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via
delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax
+39-0432-558222




_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum



From roccad at gmail.com  Sat Jan 14 22:28:50 2012
From: roccad at gmail.com (dario rocca)
Date: Sat, 14 Jan 2012 13:28:50 -0800
Subject: [Pw_forum] scaling of turbo_lanczos.x
In-Reply-To: <CAM5Vcw_UhaMuS3nvgwDSFrp6iFU8rTV5epho+7KJoi5w7Azy9w@mail.gmail.com>
References: <CAM5Vcw_UhaMuS3nvgwDSFrp6iFU8rTV5epho+7KJoi5w7Azy9w@mail.gmail.com>
Message-ID: <CAAEv5EV=nnzo1vNWcOV483JrPngJ8RJnOK08T1pgpm0e_QZeqg@mail.gmail.com>

2012/1/10 Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
>
>
> a) the itermax parameter to achieve an equivalent resolution of the
> spectrum (is the same or must be scaled)
>
>
The itermax depends on the cutoff but not on the number of electrons. If
for example in a calculation you use a single or 8 repeated units the total
number of iterations to converge is basically the same (but of course the
convergence should always be tested in each case).
Dario
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From w2agz at w2agz.com  Sun Jan 15 06:18:46 2012
From: w2agz at w2agz.com (W2AGZ)
Date: Sat, 14 Jan 2012 21:18:46 -0800
Subject: [Pw_forum] ph.x, q2r.x and low symmetries
In-Reply-To: <025e01ccd2f2$7114d110$533e7330$@w2agz.com>
References: <021801ccd28a$1c8fd5d0$55af8170$@w2agz.com>	<6A42AE7F-6CFA-4052-A3A0-9EF2B7FD4330@democritos.it>
	<025e01ccd2f2$7114d110$533e7330$@w2agz.com>
Message-ID: <028201ccd345$295b1160$7c113420$@w2agz.com>

Mea Culpa (that's Italian...hmm...actually Latin).  It appears that some
"leftovers" in temp files persisted between ph.x runs employing "qx"
wavevector bases and  subsequent "nq" input.  As Dick Feynman reportedly
observed, " The first principle is that you must not fool yourself, and you
are the easiest person to fool."  Erase the past...and least what's
temporary!

-Paul

-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of W2AGZ
Sent: Saturday, January 14, 2012 11:27 AM
To: 'PWSCF Forum'
Subject: Re: [Pw_forum] ph.x, q2r.x and low symmetries

Still working on this issue to make sure (well, as best I can) that I've
made no egregiously stupid blunders.  The e-p run is quite long...24
IRs...about a day on 8 processors.  Should the problem persist, would it be
useful to post the input files to ph.x and q2r.x?  About 30 lines total?

-Paul

-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Paolo Giannozzi
Sent: Saturday, January 14, 2012 7:47 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] ph.x, q2r.x and low symmetries


On Jan 14, 2012, at 7:59 , W2AGZ wrote:
> I'm getting (...) errors after the ph.x step from q2r.x to wit: "nc 
> already filled: wrong q grid or wrong nr"and, yes, nq = 2 and there is 
> no xq.
>

no way to say anyrthing sensible without a (simple!) example

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via
delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax
+39-0432-558222




_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum


_______________________________________________
Pw_forum mailing list
Pw_forum at pwscf.org
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From nicola.marzari at epfl.ch  Sun Jan 15 11:41:17 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Sun, 15 Jan 2012 11:41:17 +0100
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <SNT108-DS15CED8C06D5F150E6FB753C29D0@phx.gbl>
References: <1411025427.269847.1326560778944.JavaMail.root@mailhub016.itcs.purdue.edu>
	<SNT108-DS15CED8C06D5F150E6FB753C29D0@phx.gbl>
Message-ID: <4F12AD4D.3040300@epfl.ch>



Dear Peter,

also, there is an example in the qe distribution on how to calculate 
fermi energies via slab calculations - and there is extensive literature 
- e.g. the PhD thesis of Caspar Fall
http://library.epfl.ch/en/theses/?nr=1955 , or
Phys. Rev. B 80, 235407 (2009).


			nicola


On 1/14/12 6:14 PM, Peter Wang wrote:
> if we do a bulk calculation, vacuum energy level can not be calculated,
> because in bulk, there is no vacuum. To calculate vacuum energy level and
> the relative energies in bulk with respect to vacuum energy level, a slab
> calculation should be done. In a slab calculation, several layer of
> materials as well as a vacuum with sufficient thinkness should be included
> in one unit cell.
>
> YP
>
> -----????-----
> From: Ajit Vallabhaneni
> Sent: Sunday, January 15, 2012 1:06 AM
> To: PWSCF Forum
> Subject: Re: [Pw_forum] query on fermi energy
>
> Yun-peng,
>
>           Thanks for your response. Is it possible to know what the vaccum
> energy level is ? I read in the FAQ that it cannot be calculated from the a
> bulk calculation alone.
>
>
> Thanks
> Ajit
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From avallabh at purdue.edu  Sun Jan 15 12:50:30 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Sun, 15 Jan 2012 06:50:30 -0500 (EST)
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <1411025427.269847.1326560778944.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <1062311597.270734.1326628230787.JavaMail.root@mailhub016.itcs.purdue.edu>



       Any thoughts on my second question  regarding the e-ph calculation. 
For a give set of q and k points, what is the best way to ensure that all 
k+q points are available to avoid the message " q is not a vector in the 
dense grid" in the calculations"? I observed that using a dense grid is not 
enough sometimes. Do we have to check it outside of the quantum espresso 
before the calculation begins?
 
Thanks
Ajit

From daijiayu at nudt.edu.cn  Sun Jan 15 13:58:17 2012
From: daijiayu at nudt.edu.cn (jiayudai)
Date: Sun, 15 Jan 2012 20:58:17 +0800
Subject: [Pw_forum] Ewald and Coulomb
In-Reply-To: <526567564.00770@eyou.net>
References: <526567564.00770@eyou.net>
Message-ID: <120115205817c0058460c3643c133f3d4842948f2f57@nudt.edu.cn>


Dear Axel and Yun-Peng,

Thanks for your physial translation. Now, i think i can understand the physical figures in this problem. As axel said, the forces can be correct, but the energies are wrong. However, what i want to get is the pressure from positive ions. Thus, i should need the correct energies at first. For the treatment of Coulomb interations, we usually do the summation within a cutoff of a distance if we only use the formation of 1/r. This is an approach but it can solve the problem of divergence. Therefore, i think we can change the ewald formula in DFT using 1/r (with a cutoff). Is it?

Message: 7
Date: Sat, 14 Jan 2012 14:10:17 -0500
From: Axel Kohlmeyer <akohlmey at gmail.com>
Subject: Re: [Pw_forum] Ewald and Coulomb
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
<CADTmJ6H_qwNpHMVSk1EO2UD_N0PQ93Jo9b=UD5+qDoVHe_Gc2A at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
2012/1/14 jiayudai <daijiayu at nudt.edu.cn>:
> Dear Yun-Peng,
>
> Thanks for your explanation. In fact, what i mean is that how to treat the
> ion-ion interactions with some charges. For example, sometimes we want to
> take out one or more electrons out of the system, thus the tot_charge in the
> system is not zero. In an extreme case, all electrons are ionized and taken
> out, there are only positive ions in the system. In this case, the Ewald
> potential should not be right but the real Coulomb potential should be
> correct. Since Ewald scheme considers the screnning by the electrons. Thus,
> i want to use the exact 1/r potential to represent the Ewald scheme. So, how
> can we reach this goal?
if you want to look at things at this level,
then you have to accept the fact that you
cannot remove electrons from an infinite
system. only from a finite system.
you can still do the calculation with a
periodic system, if you ignore the divergent
term that stems from the total charge of
your unit cell. if you do ewald summation
with conducting boundary conditions, the
forces will not be affected (at least not for
the classical system), but the energy is
- of course - wrong.
either this approach is good enough to you,
or you have to use a real space DFT code
instead, where you don't have to worry about
periodicity by construction (but have some
other issues...).
axel.

>
> Best wishes.
>
> Jiayu
>
>
>
>
>>>>>>>>>>>>>>>>>>>>
> what do you mean by "true Coulomb potential"? Based on density functional
> theory, adding an uniform potential to the system make no difference. In
> fact, the ion-ion interaction energy is an infinite value because of 1/r
> type of Coulomb potential. However, if an uniform charge density which makes
> total charge zero, hence uniform Coulomb potential is added to the system,
> the electrostatic energy as well as potential is finite, at the same time,
> physics keep unchanged.
> best wishes,Yun-Peng
>
> Date: Fri, 13 Jan 2012 21:49:59 +0800
>
>
> From: daijiayu at nudt.edu.cn
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] Ewald and Coulomb
>
>
> Dear users and developers,
>
> Happy new year!
>
>
>
> I have a confusion about the calculations of ion-ion interactions. We know,
> we usually use Ewald scheme to represent the real Coulomb potentials in a
> periodic cell. Generally, it is correct for a neutral system or one electron
> taken out (or into ) system. However, if the system is constructed with
> partially charged ions, that is to say, there are more positive charges than
> negative charges, the Ewald scheme should be not right. Although this system
> is not stable, but there should be some properties deserved to study.
>
> So, how can we calculate the true Coulomb potentials in DFT? That is to say,
> we do not use Ewald, but only use th 1/r type. I know it can be realized in
> classical calculations, but i did not find the path to get it in QE.
>
>
>
> Thanks a lot.
>
>
>
> Jiayu
>
>
>  
The pressure of positive ions confused me for a long time, i think it can be obtained using the 1/r interactions, but i can not make sure. Is there some other physics in it?

Thanks.

Jiayu

Message: 7
Date: Sat, 14 Jan 2012 14:10:17 -0500
From: Axel Kohlmeyer <akohlmey at gmail.com>
Subject: Re: [Pw_forum] Ewald and Coulomb
To: PWSCF Forum <pw_forum at pwscf.org>
Message-ID:
<CADTmJ6H_qwNpHMVSk1EO2UD_N0PQ93Jo9b=UD5+qDoVHe_Gc2A at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
2012/1/14 jiayudai <daijiayu at nudt.edu.cn>:
> Dear Yun-Peng,
>
> Thanks for your explanation. In fact, what i mean is that how to treat the
> ion-ion interactions with some charges. For example, sometimes we want to
> take out one or more electrons out of the system, thus the tot_charge in the
> system is not zero. In an extreme case, all electrons are ionized and taken
> out, there are only positive ions in the system. In this case, the Ewald
> potential should not be right but the real Coulomb potential should be
> correct. Since Ewald scheme considers the screnning by the electrons. Thus,
> i want to use the exact 1/r potential to represent the Ewald scheme. So, how
> can we reach this goal?
if you want to look at things at this level,
then you have to accept the fact that you
cannot remove electrons from an infinite
system. only from a finite system.
you can still do the calculation with a
periodic system, if you ignore the divergent
term that stems from the total charge of
your unit cell. if you do ewald summation
with conducting boundary conditions, the
forces will not be affected (at least not for
the classical system), but the energy is
- of course - wrong.
either this approach is good enough to you,
or you have to use a real space DFT code
instead, where you don't have to worry about
periodicity by construction (but have some
other issues...).
axel.

>
> Best wishes.
>
> Jiayu
>
>
>
>
>>>>>>>>>>>>>>>>>>>>
> what do you mean by "true Coulomb potential"? Based on density functional
> theory, adding an uniform potential to the system make no difference. In
> fact, the ion-ion interaction energy is an infinite value because of 1/r
> type of Coulomb potential. However, if an uniform charge density which makes
> total charge zero, hence uniform Coulomb potential is added to the system,
> the electrostatic energy as well as potential is finite, at the same time,
> physics keep unchanged.
> best wishes,Yun-Peng
>
> Date: Fri, 13 Jan 2012 21:49:59 +0800
>
>
> From: daijiayu at nudt.edu.cn
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] Ewald and Coulomb
>
>
> Dear users and developers,
>
> Happy new year!
>
>
>
> I have a confusion about the calculations of ion-ion interactions. We know,
> we usually use Ewald scheme to represent the real Coulomb potentials in a
> periodic cell. Generally, it is correct for a neutral system or one electron
> taken out (or into ) system. However, if the system is constructed with
> partially charged ions, that is to say, there are more positive charges than
> negative charges, the Ewald scheme should be not right. Although this system
> is not stable, but there should be some properties deserved to study.
>
> So, how can we calculate the true Coulomb potentials in DFT? That is to say,
> we do not use Ewald, but only use th 1/r type. I know it can be realized in
> classical calculations, but i did not find the path to get it in QE.
>
>
>
> Thanks a lot.
>
>
>
> Jiayu
>
>
>
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From akohlmey at gmail.com  Mon Jan 16 00:49:03 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Sun, 15 Jan 2012 18:49:03 -0500
Subject: [Pw_forum] Ewald and Coulomb
In-Reply-To: <120115205817c0058460c3643c133f3d4842948f2f57@nudt.edu.cn>
References: <526567564.00770@eyou.net>
	<120115205817c0058460c3643c133f3d4842948f2f57@nudt.edu.cn>
Message-ID: <CADTmJ6GCgKxCqs1hns1bMsLQya0APPo4Eajf6BWRBw=66Xsh8Q@mail.gmail.com>

2012/1/15 jiayudai <daijiayu at nudt.edu.cn>:
>
> Dear Axel and Yun-Peng,
>
> Thanks for your physial translation. Now, i think i can understand the
> physical figures in this problem. As axel said, the forces can be correct,
> but the energies are wrong. However, what i want to get is the pressure from
> positive ions. Thus, i should need the correct energies at first. For the
> treatment of Coulomb interations, we usually do the summation within a
> cutoff of a distance if we only use the formation of 1/r. This is an
> approach but it can solve the problem of divergence. Therefore, i think we

this is not *solving* the problem, it is *ignoring* it.
and much worse. since coulomb interactions are
so very long-range, a cutoff will induce *massive*
fluctuations of properties like pressure relative
to the choice of cutoff (and what kind of cutoff,
spherical? or use the minimum image cell?)
and that already for a neutral system.

i suggest you set up a classical simple test
case with a simle rocksalt like crystal structure
and check out how much the pressure depends
on the choice of cutoff with and without ewald
summation. i am certain, this will change your
mind and you will be shocked.

axel.



> can change the ewald formula in DFT using 1/r (with a cutoff). Is it?
>

-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From mahdi_fn109 at yahoo.com  Mon Jan 16 06:08:32 2012
From: mahdi_fn109 at yahoo.com (Mahdi Faghih nasiri)
Date: Sun, 15 Jan 2012 21:08:32 -0800 (PST)
Subject: [Pw_forum] distinguish between the isotopes of an element
Message-ID: <1326690512.40276.YahooMailNeo@web43139.mail.sp1.yahoo.com>

Dear all,
How can we distinguish between the isotopes of an elementin pwscf?
?
Mahdi Faghih nasiri
MSC,
Guilan University,
Rasht, Iran.
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From mohnish.iitk at gmail.com  Mon Jan 16 07:04:41 2012
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Mon, 16 Jan 2012 11:34:41 +0530
Subject: [Pw_forum] distinguish between the isotopes of an element
In-Reply-To: <1326690512.40276.YahooMailNeo@web43139.mail.sp1.yahoo.com>
References: <1326690512.40276.YahooMailNeo@web43139.mail.sp1.yahoo.com>
Message-ID: <CAMhNW-dv871gRZkem5RcJHc1+=G3Mm8vGY2TmUu6bWy+xAZAPQ@mail.gmail.com>

You have to calculate the energies of the two isotopes to compare their
stability and there is no automatic way to distinguish between isotopes.

On Mon, Jan 16, 2012 at 10:38 AM, Mahdi Faghih nasiri <mahdi_fn109 at yahoo.com
> wrote:

> Dear all,
> How can we distinguish between the isotopes of an element in pwscf?
>
> Mahdi Faghih nasiri
> MSC,
> Guilan University,
> Rasht, Iran.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
BTech-Mtech, IIT Kanpur
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From giannozz at democritos.it  Mon Jan 16 09:35:14 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 16 Jan 2012 09:35:14 +0100
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <1062311597.270734.1326628230787.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <1062311597.270734.1326628230787.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <CF7144E6-76BA-43B9-9B11-D8CED8E69B41@democritos.it>


On Jan 15, 2012, at 12:50 , Ajit Vallabhaneni wrote:

> I observed that using a dense grid is not enough sometimes

you observed in which case?

P.
---
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

"Nothing is impossible for the man who doesn't have to do it himself"




From giannozz at democritos.it  Mon Jan 16 09:38:00 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 16 Jan 2012 09:38:00 +0100
Subject: [Pw_forum] distinguish between the isotopes of an element
In-Reply-To: <1326690512.40276.YahooMailNeo@web43139.mail.sp1.yahoo.com>
References: <1326690512.40276.YahooMailNeo@web43139.mail.sp1.yahoo.com>
Message-ID: <0316E378-515E-451E-8537-A8779888E751@democritos.it>


On Jan 16, 2012, at 6:08 , Mahdi Faghih nasiri wrote:

> How can we distinguish between the isotopes of an element in pwscf?


set the correct atomic mass. Note however that the electronic properties
do not depend upon the mass

P.
---
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy

"Nothing is impossible for the man who doesn't have to do it himself"




From mourad_fsm at yahoo.fr  Mon Jan 16 09:52:40 2012
From: mourad_fsm at yahoo.fr (debbichi mourad)
Date: Mon, 16 Jan 2012 08:52:40 +0000 (GMT)
Subject: [Pw_forum] LDA+U.
In-Reply-To: <1326104619.15056.YahooMailNeo@web29504.mail.ird.yahoo.com>
References: <mailman.1.1323419672.18984.pw_forum@pwscf.org>
	<1326104619.15056.YahooMailNeo@web29504.mail.ird.yahoo.com>
Message-ID: <1326703960.20738.YahooMailNeo@web29502.mail.ird.yahoo.com>

Dear pwscf users

I would like to do some calculations with LDA+U.
I would like to know the interval of the validity of the potential U. 

Thanks in advance,

Sincerely
?Mourad


DEBBICHI Mourad
Unit? de Recherche Physique des Solides,99/UR/13-19,
D?partement de Physique, Facult? des Science de Monastir,
Avenue de l'Environnement 5019, Monastir Tunisie.
t?l:+21697487042
mourad_fsm at yahoo.fr


________________________________
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From degironc at sissa.it  Mon Jan 16 14:04:41 2012
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 16 Jan 2012 14:04:41 +0100
Subject: [Pw_forum] distinguish between the isotopes of an element
In-Reply-To: <1326690512.40276.YahooMailNeo@web43139.mail.sp1.yahoo.com>
References: <1326690512.40276.YahooMailNeo@web43139.mail.sp1.yahoo.com>
Message-ID: <4F142069.3060908@sissa.it>

from the electronic point of view, all isotopes are the same.
what is different for different isotopes is their mass, which enters in 
the vibrational contribution to the free energy.

stefano

On 01/16/2012 06:08 AM, Mahdi Faghih nasiri wrote:
> Dear all,
> How can we distinguish between the isotopes of an elementin pwscf?
>   
> Mahdi Faghih nasiri
> MSC,
> Guilan University,
> Rasht, Iran.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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From giuseppe.mattioli at mlib.ism.cnr.it  Mon Jan 16 14:22:01 2012
From: giuseppe.mattioli at mlib.ism.cnr.it (Giuseppe Mattioli)
Date: Mon, 16 Jan 2012 14:22:01 +0100
Subject: [Pw_forum] LDA+U.
In-Reply-To: <1326703960.20738.YahooMailNeo@web29502.mail.ird.yahoo.com>
References: <mailman.1.1323419672.18984.pw_forum@pwscf.org>
	<1326104619.15056.YahooMailNeo@web29504.mail.ird.yahoo.com>
	<1326703960.20738.YahooMailNeo@web29502.mail.ird.yahoo.com>
Message-ID: <201201161422.01516.giuseppe.mattioli@mlib.ism.cnr.it>


Dear Mourad
What do you mean by "validity"? You can set a given U value without any restriction, but if you mean 
a "meaningful U value" it depends on the physical properties of your system.
HTH
Giuseppe

On Monday 16 January 2012 09:52:40 debbichi mourad wrote:
> Dear pwscf users
>
> I would like to do some calculations with LDA+U.
> I would like to know the interval of the validity of the potential U.
>
> Thanks in advance,
>
> Sincerely
> ?Mourad
>
>
> DEBBICHI Mourad
> Unit? de Recherche Physique des Solides,99/UR/13-19,
> D?partement de Physique, Facult? des Science de Monastir,
> Avenue de l'Environnement 5019, Monastir Tunisie.
> t?l:+21697487042
> mourad_fsm at yahoo.fr
>
>
> ________________________________



-- 
********************************************************
- Article premier - Les hommes naissent et demeurent
libres et ?gaux en droits. Les distinctions sociales
ne peuvent ?tre fond?es que sur l'utilit? commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et 
imprescriptibles de l'homme. Ces droits sont la libert?,
la propri?t?, la s?ret? et la r?sistance ? l'oppression.
********************************************************

? ?Giuseppe Mattioli ? ? ? ? ? ? ? ? ? ? ? ? ? ?
? ?CNR - ISTITUTO DI STRUTTURA DELLA MATERIA ? 
? ?v. Salaria Km 29,300 - C.P. 10 ? ? ? ? ? ? ? ?
? ?I 00015 - Monterotondo Stazione (RM) ? ? ? ? ?
? ?Tel + 39 06 90672836 - Fax +39 06 90672316 ? ?
? ?E-mail: <giuseppe.mattioli at ism.cnr.it>

From avallabh at purdue.edu  Mon Jan 16 15:19:03 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Mon, 16 Jan 2012 09:19:03 -0500 (EST)
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <CF7144E6-76BA-43B9-9B11-D8CED8E69B41@democritos.it>
Message-ID: <480318836.272189.1326723543618.JavaMail.root@mailhub016.itcs.purdue.edu>

Dr. Paolo,

         Like in graphene, i used 60x60 mesh, but for some q-points it terminates with the message that "it is not a part of dense grid".
Should i increase the grid size even more? It is very expensive computationally though.

Thanks
Ajit

From giannozz at democritos.it  Mon Jan 16 15:24:49 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 16 Jan 2012 15:24:49 +0100
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <480318836.272189.1326723543618.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <480318836.272189.1326723543618.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <77C4ECFF-A212-4E64-A825-59D742A2D71D@democritos.it>


On Jan 16, 2012, at 15:19 , Ajit Vallabhaneni wrote:

> Like in graphene, i used 60x60 mesh, but for some q-points
> it terminates with the message that "it is not a part of dense
> grid".

..and have you any evidence of the opposite?

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From mohnish.iitk at gmail.com  Mon Jan 16 16:51:34 2012
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Mon, 16 Jan 2012 21:21:34 +0530
Subject: [Pw_forum] distinguish between the isotopes of an element
In-Reply-To: <4F142069.3060908@sissa.it>
References: <1326690512.40276.YahooMailNeo@web43139.mail.sp1.yahoo.com>
	<4F142069.3060908@sissa.it>
Message-ID: <CAMhNW-fKh-5LHDkt16R_g_dcQpJZOzaEVegWUdrZpoPE9CLznQ@mail.gmail.com>

Sorry I mistook isotopes as allotropes.

On Mon, Jan 16, 2012 at 6:34 PM, Stefano de Gironcoli <degironc at sissa.it>wrote:

> **
> from the electronic point of view, all isotopes are the same.
> what is different for different isotopes is their mass, which enters in
> the vibrational contribution to the free energy.
>
> stefano
>
>
> On 01/16/2012 06:08 AM, Mahdi Faghih nasiri wrote:
>
> Dear all,
> How can we distinguish between the isotopes of an elementin pwscf?
>
> Mahdi Faghih nasiri
> MSC,
> Guilan University,
> Rasht, Iran.
>
>
> _______________________________________________
> Pw_forum mailing listPw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
BTech-Mtech, IIT Kanpur
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From mrahimi93 at gmail.com  Mon Jan 16 17:57:58 2012
From: mrahimi93 at gmail.com (Mojtaba Rahimi)
Date: Mon, 16 Jan 2012 20:27:58 +0330
Subject: [Pw_forum] LDA+U.
In-Reply-To: <201201161422.01516.giuseppe.mattioli@mlib.ism.cnr.it>
References: <mailman.1.1323419672.18984.pw_forum@pwscf.org>
	<1326104619.15056.YahooMailNeo@web29504.mail.ird.yahoo.com>
	<1326703960.20738.YahooMailNeo@web29502.mail.ird.yahoo.com>
	<201201161422.01516.giuseppe.mattioli@mlib.ism.cnr.it>
Message-ID: <CADVDPCniqgA6qRG0ja1osGDK9RK+QuMSWa9PrNS9qsiitSiHOQ@mail.gmail.com>

dear Mourad

as Mr. Giuseppe has said the interval of U depends on matter and condition
that you have. the best answer for you is, of course i think, at first you
should calculate U by some approach such as RPA,cRPA or perturbation and
than exert it on your calculation.

Best regards

2012/1/16 Giuseppe Mattioli <giuseppe.mattioli at mlib.ism.cnr.it>

>
> Dear Mourad
> What do you mean by "validity"? You can set a given U value without any
> restriction, but if you mean
> a "meaningful U value" it depends on the physical properties of your
> system.
> HTH
> Giuseppe
>
> On Monday 16 January 2012 09:52:40 debbichi mourad wrote:
> > Dear pwscf users
> >
> > I would like to do some calculations with LDA+U.
> > I would like to know the interval of the validity of the potential U.
> >
> > Thanks in advance,
> >
> > Sincerely
> >  Mourad
> >
> >
> > DEBBICHI Mourad
> > Unit? de Recherche Physique des Solides,99/UR/13-19,
> > D?partement de Physique, Facult? des Science de Monastir,
> > Avenue de l'Environnement 5019, Monastir Tunisie.
> > t?l:+21697487042
> > mourad_fsm at yahoo.fr
> >
> >
> > ________________________________
>
>
>
> --
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et ?gaux en droits. Les distinctions sociales
> ne peuvent ?tre fond?es que sur l'utilit? commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et
> imprescriptibles de l'homme. Ces droits sont la libert?,
> la propri?t?, la s?ret? et la r?sistance ? l'oppression.
> ********************************************************
>
>    Giuseppe Mattioli
>    CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>    v. Salaria Km 29,300 - C.P. 10
>    I 00015 - Monterotondo Stazione (RM)
>    Tel + 39 06 90672836 - Fax +39 06 90672316
>    E-mail: <giuseppe.mattioli at ism.cnr.it>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
-----
Mojtaba Rahimi (Mr.)
Master of science -condensed matter,

Email: mrahimi93 at gmail.com
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From avallabh at purdue.edu  Mon Jan 16 19:06:15 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Mon, 16 Jan 2012 13:06:15 -0500 (EST)
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <77C4ECFF-A212-4E64-A825-59D742A2D71D@democritos.it>
Message-ID: <14572444.272716.1326737175479.JavaMail.root@mailhub016.itcs.purdue.edu>

Dr.Paolo,

         Sorry i didnot understand your question.

Thanks
Ajit

From giannozz at democritos.it  Mon Jan 16 20:20:19 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 16 Jan 2012 20:20:19 +0100
Subject: [Pw_forum] query on fermi energy
In-Reply-To: <14572444.272716.1326737175479.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <14572444.272716.1326737175479.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <892062A9-695A-473A-BFF3-F0475CDFFFFE@democritos.it>


On Jan 16, 2012, at 19:06 , Ajit Vallabhaneni wrote:

>          Sorry i didnot understand your question.

I don' understand why you insist that something is not
working and don't provide any evidence.

---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From torstein.fjermestad at kjemi.uio.no  Mon Jan 16 20:11:12 2012
From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad)
Date: Mon, 16 Jan 2012 20:11:12 +0100
Subject: [Pw_forum] NEB in QE 4.3: NaN values of some of the initially
	generated images
Message-ID: <82f95d4fe22509183285949879e861e0@ulrik.uio.no>

 Dear all,

 I have recently made several attempts to submit a NEB calculation using 
 Quantum Espresso version 4.3.
 Unfortunately, every attempt fails with the program printing NaN values 
 instead of the Cartesian coordinates for some of the initial images. For 
 instance, in the .path file corresponding to the attached input file, 
 image 3 and 4 (num_of_images=5) consists entirely of NaN values instead 
 of real Cartesian coordinates. Of cause, if some of the initial images 
 consist only of NaN values the calculation has no chance of continuing.

 There have been significant changes in the way to submit a NEB 
 calculation between version 4.2.1 and version 4.3, and to test whether 
 the same behavior would occur in version 4.2.1, I submitted a NEB 
 calculation with QE version 4.2.1 with exactly the same input 
 structures. In that case the program had no problem in generating the 
 initial images. Because of this I think we can exclude the possibility 
 of the error being caused by the input coordinates themselves.
 
 In the script I used to submit the calculation, the line to run the 
 neb.x executable is the following:

 mpirun -np 16 -npernode 8 neb.x -inp neb_11.inp > neb_11.out


 Have any of you come across a similar problem before?
 Does anyone have suggestions on how to prevent the NaN values from 
 appearing?

 Thanks in advance.

 Yours sincerely

 Torstein Fjermestad
 University of Oslo,
 Norway.

 




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From baroni at sissa.it  Tue Jan 17 07:35:00 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 17 Jan 2012 07:35:00 +0100
Subject: [Pw_forum] distinguish between the isotopes of an element
In-Reply-To: <CAMhNW-fKh-5LHDkt16R_g_dcQpJZOzaEVegWUdrZpoPE9CLznQ@mail.gmail.com>
References: <1326690512.40276.YahooMailNeo@web43139.mail.sp1.yahoo.com>
	<4F142069.3060908@sissa.it>
	<CAMhNW-fKh-5LHDkt16R_g_dcQpJZOzaEVegWUdrZpoPE9CLznQ@mail.gmail.com>
Message-ID: <58334B56-7D98-40E9-A40F-13001F25D80C@sissa.it>

not sure I understand the question either: different allotropes have different structures. just feed the computer with the appropriate structure. what else? am I missing something of your question? are you sure you understand what "allotrope" means and what pwscf (or any other electronic-strucyure code, for that matter) is designed to do? SB

On Jan 16, 2012, at 4:51 PM, mohnish pandey wrote:

> Sorry I mistook isotopes as allotropes. 
> 
> On Mon, Jan 16, 2012 at 6:34 PM, Stefano de Gironcoli <degironc at sissa.it> wrote:
> from the electronic point of view, all isotopes are the same.
> what is different for different isotopes is their mass, which enters in the vibrational contribution to the free energy.
> 
> stefano
> 
> 
> On 01/16/2012 06:08 AM, Mahdi Faghih nasiri wrote:
>> Dear all,
>> How can we distinguish between the isotopes of an elementin pwscf?
>>  
>> Mahdi Faghih nasiri
>> MSC,
>> Guilan University,
>> Rasht, Iran.
>> 
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> 
> 
> -- 
> Regards,
> MOHNISH,
> -----------------------------------------------------------------
> Mohnish Pandey
> BTech-Mtech, IIT Kanpur
> Senior Project Associate,
> Department of Chemical Engineering,
> IIT KANPUR, UP, INDIA
> -----------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From lmartinsamos at gmail.com  Tue Jan 17 15:18:25 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Tue, 17 Jan 2012 15:18:25 +0100
Subject: [Pw_forum] NEB in QE 4.3: NaN values of some of the initially
 generated images
In-Reply-To: <82f95d4fe22509183285949879e861e0@ulrik.uio.no>
References: <82f95d4fe22509183285949879e861e0@ulrik.uio.no>
Message-ID: <CAGCSmJR7bvXkmwkv93EvwA1vv_qfxQ+G7-r0FM0PO5SPDWdWow@mail.gmail.com>

Dear Torstein, nstep_path=0 produces a "strange behavior" as NEB starts
counting at 1. So if you just set nstep_path=1 it should work.

bests

Layla

2012/1/16 Torstein Fjermestad <torstein.fjermestad at kjemi.uio.no>

> Dear all,
>
> I have recently made several attempts to submit a NEB calculation using
> Quantum Espresso version 4.3.
> Unfortunately, every attempt fails with the program printing NaN values
> instead of the Cartesian coordinates for some of the initial images. For
> instance, in the .path file corresponding to the attached input file, image
> 3 and 4 (num_of_images=5) consists entirely of NaN values instead of real
> Cartesian coordinates. Of cause, if some of the initial images consist only
> of NaN values the calculation has no chance of continuing.
>
> There have been significant changes in the way to submit a NEB calculation
> between version 4.2.1 and version 4.3, and to test whether the same
> behavior would occur in version 4.2.1, I submitted a NEB calculation with
> QE version 4.2.1 with exactly the same input structures. In that case the
> program had no problem in generating the initial images. Because of this I
> think we can exclude the possibility of the error being caused by the input
> coordinates themselves.
>
> In the script I used to submit the calculation, the line to run the neb.x
> executable is the following:
>
> mpirun -np 16 -npernode 8 neb.x -inp neb_11.inp > neb_11.out
>
>
> Have any of you come across a similar problem before?
> Does anyone have suggestions on how to prevent the NaN values from
> appearing?
>
> Thanks in advance.
>
> Yours sincerely
>
> Torstein Fjermestad
> University of Oslo,
> Norway.
>
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From bdslipun at gmail.com  Tue Jan 17 16:04:34 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Tue, 17 Jan 2012 20:34:34 +0530
Subject: [Pw_forum] vibrational energy
Message-ID: <CAJVAAvCUk01XeQKgjjHe10L2qgU9QG5ri_+1teb2_fGTHeTXSg@mail.gmail.com>

i am using espresso
i am calculating vibrational energy of hcp and bcc phase
by QHA code
i have got for both the phases. when i am comparing gibbs free energy for
both phases
i have to add cold energy of the respective phases
so weather the vibrational energy obtained from code for hcp phase will be
added or half of the vibrational energy
will be added for hcp phase?


i am given 0 0 0 for bcc
.33333334,,66666667,.-25
.6666667,.333333334,.75 for hcp phase
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From bdslipun at gmail.com  Tue Jan 17 16:07:50 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Tue, 17 Jan 2012 20:37:50 +0530
Subject: [Pw_forum] vibrational energy
In-Reply-To: <CAJVAAvCUk01XeQKgjjHe10L2qgU9QG5ri_+1teb2_fGTHeTXSg@mail.gmail.com>
References: <CAJVAAvCUk01XeQKgjjHe10L2qgU9QG5ri_+1teb2_fGTHeTXSg@mail.gmail.com>
Message-ID: <CAJVAAvCsSuexcCedsKfph8zMn+7JdgHOpWe+5dDi=YauoPpxxA@mail.gmail.com>

On Tue, Jan 17, 2012 at 8:34 PM, bhabya sahoo <bdslipun at gmail.com> wrote:

> i am using espresso
> i am calculating vibrational energy of hcp and bcc phase
> by QHA code
> i have got for both the phases. when i am comparing gibbs free energy for
> both phases
> i have to add cold energy of the respective phases
> so weather the vibrational energy obtained from code for hcp phase will be
> added or half of the vibrational energy
> will be added for hcp phase?
>
>
> i am given 0 0 0 for bcc
> .33333334,,66666667,.-25
> .6666667,.333333334,.75 for hcp phase
>






sahoo B
 reserch scholar
mumbai

>
>
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From annetindele at yahoo.fr  Tue Jan 17 17:23:52 2012
From: annetindele at yahoo.fr (anne etindele)
Date: Tue, 17 Jan 2012 16:23:52 +0000 (GMT)
Subject: [Pw_forum] Dynamic polarizability of C60
In-Reply-To: <1326796829.17888.YahooMailNeo@web29601.mail.ird.yahoo.com>
References: <1324962092.423.YahooMailNeo@web29602.mail.ird.yahoo.com>
	<1324962402.39622.YahooMailNeo@web29602.mail.ird.yahoo.com>
	<1326796829.17888.YahooMailNeo@web29601.mail.ird.yahoo.com>
Message-ID: <1326817432.85566.YahooMailNeo@web29606.mail.ird.yahoo.com>

Dear all


I am a new user of Quantum espresso (espresso-4.3.1), and I have found that it is possible, 

as it is done in example 33, to calculate dynamic polarizability of molecules using pw.x 

and ph.x.

I am interested on the description of properties of C60 complex. I tried to modify the script of example 33
in order to get its dynamic polarizability but I couldn't even run self consistent calculation as the code signals "MPI abort..".

I would like to know if:

	* it is possible to get dynamic polarizability or photoionization cross section of C60 using this method or with any other code
	* it can run on normal desktop or laptop (Dual Core CPU with 4GB of RAM and 2.8 GHz) of frequency?

	* there is an input file of C60 available in case if my in put file may be the problem


The sample in put file I modified and used is joined to this mail.


Kind regards

Anne J. ETINDELE
PhD Student
Laboratoire de Physique Fondamentale
Universit? de Douala, Cameroun
Assistant Lecturer 
Ecole Normale Sup?rieure 
Universit? de Yaound?, Cameroun
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From akohlmey at gmail.com  Tue Jan 17 17:41:50 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Tue, 17 Jan 2012 11:41:50 -0500
Subject: [Pw_forum] Dynamic polarizability of C60
In-Reply-To: <1326817432.85566.YahooMailNeo@web29606.mail.ird.yahoo.com>
References: <1324962092.423.YahooMailNeo@web29602.mail.ird.yahoo.com>
	<1324962402.39622.YahooMailNeo@web29602.mail.ird.yahoo.com>
	<1326796829.17888.YahooMailNeo@web29601.mail.ird.yahoo.com>
	<1326817432.85566.YahooMailNeo@web29606.mail.ird.yahoo.com>
Message-ID: <CADTmJ6GWcJqRiu+zpRRY8x9=5B0EHNL6Q2pyTfyQaWb9OH=zdw@mail.gmail.com>

On Tue, Jan 17, 2012 at 11:23 AM, anne etindele <annetindele at yahoo.fr> wrote:
> Dear all
>
> I am a new user of Quantum espresso (espresso-4.3.1), and I have found that
> it is possible,
> as it is done in example 33, to calculate dynamic polarizability of
> molecules using pw.x
> and ph.x.
>
> I am interested on the description of properties of C60 complex. I tried to
> modify the script of example 33
> in order to get its dynamic polarizability but I couldn't even run self
> consistent calculation as the code signals "MPI abort..".
>
> I would like to know if:
>
> it is possible to get dynamic polarizability or photoionization cross
> section of C60 using this method or with any other code
> it can run on normal desktop or laptop (Dual Core CPU with 4GB of RAM and
> 2.8 GHz) of frequency?

anne,

a C60 system is pretty large for a DFT calculation,
particularly, since you need to leave enough vacuum
space around it, to get the result for the isolated object.

this kind of calculation would require more than just a
laptop to be completed before the next ice age. you have
to factor in, that plane wave DFT calculations are not
scaling linearly with the system size (and not at all
with the number of electrons).

perhaps you should do your first independent calculations
with a less ambitious project. ;-)

salut,
    axel.

> there is an input file of C60 available in case if my in put file may be the
> problem
>
>
> The sample in put file I modified and used is joined to this mail.
>
> Kind regards
>
> Anne J. ETINDELE
> PhD Student
> Laboratoire de Physique Fondamentale
> Universit? de Douala, Cameroun
> Assistant Lecturer
> Ecole Normale Sup?rieure
> Universit? de Yaound?, Cameroun
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From torstein.fjermestad at kjemi.uio.no  Tue Jan 17 18:51:40 2012
From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad)
Date: Tue, 17 Jan 2012 18:51:40 +0100
Subject: [Pw_forum]
 =?utf-8?q?NEB_in_QE_4=2E3=3A_NaN_values_of_some_of_the?=
 =?utf-8?q?_initially_generated_images?=
In-Reply-To: <CAGCSmJR7bvXkmwkv93EvwA1vv_qfxQ+G7-r0FM0PO5SPDWdWow@mail.gmail.com>
References: <82f95d4fe22509183285949879e861e0@ulrik.uio.no>
	<CAGCSmJR7bvXkmwkv93EvwA1vv_qfxQ+G7-r0FM0PO5SPDWdWow@mail.gmail.com>
Message-ID: <d25f4a8d67e79d40208f0244f0a13271@ulrik.uio.no>

 Dear Layla,

 thanks for your suggestion.

 Unfortunately setting nstep_path=1 did not solve the problem. Image 3 
 and 4 of the .path file contained the NaN values just as before.

 In the output file of the calculation it says nearly at the top:

      initial path length           =     NaN bohr
      initial inter-image distance  =     NaN bohr

 To me this result seems fairly obvious. Because two of the initial 
 images contain NaN values, there is no way in which the program can 
 calculate the initial path length.
 

 Some lines further down it says:

        ------------------------------ iteration   1 
 ------------------------------

      tcpu =      3.0    self-consistency for image   1
      tcpu =    129.3    self-consistency for image   2

  
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from coset : error #         1
      nsym == 0
  
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

      stopping ...


 The way I interpret this information is that the program manages to 
 finish the SCF cycle for image 1 and 2, but when it comes to image 3 it 
 fails because that structure consists only of NaN values.

 The origin of the problem seems to lay in the generation of the initial 
 images.
 Does anyone have further suggestions on how to solve this problem?

 Thank you very much in advance.

 Yours sincerely

 Torstein Fjermestad

 


 On Tue, 17 Jan 2012 15:18:25 +0100, Layla Martin-Samos 
 <lmartinsamos at gmail.com> wrote:
> Dear Torstein, nstep_path=0 produces a "strange behavior" as NEB
> starts counting at 1. So if you just set nstep_path=1 it should work.
>
> bests
>
> Layla
>
> 2012/1/16 Torstein Fjermestad
>  Dear all,
>
>  I have recently made several attempts to submit a NEB calculation
> using Quantum Espresso version 4.3.
>  Unfortunately, every attempt fails with the program printing NaN
> values instead of the Cartesian coordinates for some of the initial
> images. For instance, in the .path file corresponding to the attached
> input file, image 3 and 4 (num_of_images=5) consists entirely of NaN
> values instead of real Cartesian coordinates. Of cause, if some of 
> the
> initial images consist only of NaN values the calculation has no
> chance of continuing.
>
>  There have been significant changes in the way to submit a NEB
> calculation between version 4.2.1 and version 4.3, and to test 
> whether
> the same behavior would occur in version 4.2.1, I submitted a NEB
> calculation with QE version 4.2.1 with exactly the same input
> structures. In that case the program had no problem in generating the
> initial images. Because of this I think we can exclude the 
> possibility
> of the error being caused by the input coordinates themselves.
>
>  In the script I used to submit the calculation, the line to run the
> neb.x executable is the following:
>
>  mpirun -np 16 -npernode 8 neb.x -inp neb_11.inp > neb_11.out
>
>  Have any of you come across a similar problem before?
>  Does anyone have suggestions on how to prevent the NaN values from
> appearing?
>
>  Thanks in advance.
>
>  Yours sincerely
>
>  Torstein Fjermestad
>  University of Oslo,
>  Norway.
>
> _______________________________________________
>  Pw_forum mailing list
>  Pw_forum at pwscf.org [2]
>  http://www.democritos.it/mailman/listinfo/pw_forum [3]
>
>
>
> Links:
> ------
> [1] mailto:torstein.fjermestad at kjemi.uio.no
> [2] mailto:Pw_forum at pwscf.org
> [3] http://www.democritos.it/mailman/listinfo/pw_forum


From giannozz at democritos.it  Tue Jan 17 19:17:52 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 17 Jan 2012 19:17:52 +0100
Subject: [Pw_forum] NEB in QE 4.3: NaN values of some of the initially
	generated images
In-Reply-To: <d25f4a8d67e79d40208f0244f0a13271@ulrik.uio.no>
References: <82f95d4fe22509183285949879e861e0@ulrik.uio.no>
	<CAGCSmJR7bvXkmwkv93EvwA1vv_qfxQ+G7-r0FM0PO5SPDWdWow@mail.gmail.com>
	<d25f4a8d67e79d40208f0244f0a13271@ulrik.uio.no>
Message-ID: <3F570C0F-A3BB-48C1-8A30-379A47A2DFFF@democritos.it>


On Jan 17, 2012, at 18:51 , Torstein Fjermestad wrote:

>   Does anyone have further suggestions on how to solve this problem?

first of all, please try v.4.3.2; it contains a few fixes for NEB wrt  
v.4.3
=== Doc/release-notes
Fixed in 4.3.2 version
[...]
    * NEB: possible problem in parallel execution (if command-line  
arguments
      are not available to all processors) avoided by broadcasting  
arguments
[...]
Fixed in 4.3.1 version
[...]
    * NEB + nonlocal exchange (DF-vdW) or hybrid functionals wasn't  
working
    * NEB: incorrect parsing of intermediate images fixed
===

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From eariel99 at gmail.com  Tue Jan 17 22:04:12 2012
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 17 Jan 2012 22:04:12 +0100
Subject: [Pw_forum] Dynamic polarizability of C60
Message-ID: <CAM5Vcw8PDav6xQ0Kp0L73Uab-cXt+4KyhA-nHx1TJkiC1tdpjw@mail.gmail.com>

What is exactly this dynamical polarizability? Does it include  the
electronic , phonon or both contributions?

What are the frequency units (THz, eV? ) in the example 33.

&inputph
  tr2_ph=1.0d-14,
  prefix='ch4',
  epsil=.true.,
  trans=.false.,
  fpol=.true.,
  amass(1)=12.0107,
  amass(2)=1.00794,
  outdir='/home/giannozz/tmp/',
  fildyn='ch4.dynG',
 /
0.0 0.0 0.0

FREQUENCIES
 2
 0.0d0
 1.5d0

Best regards
eduardo


---------- Mensaje reenviado ----------
From: anne etindele <annetindele at yahoo.fr>
To: "pw_forum at pwscf.org" <pw_forum at pwscf.org>
Cc:
Date: Tue, 17 Jan 2012 16:23:52 +0000 (GMT)
Subject: [Pw_forum] Dynamic polarizability of C60
Dear all

I am a new user of Quantum espresso (espresso-4.3.1), and I have found that
it is possible,
as it is done in example 33, to calculate dynamic polarizability of
molecules using pw.x
and ph.x.

I am interested on the description of properties of C60 complex. I tried to
modify the script of example 33
in order to get its dynamic polarizability but I couldn't even run self
consistent calculation as the code signals "MPI abort..".


-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez
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From bdslipun at gmail.com  Wed Jan 18 06:23:51 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Wed, 18 Jan 2012 10:53:51 +0530
Subject: [Pw_forum] Fwd: vibrational energy
In-Reply-To: <CAJVAAvCsSuexcCedsKfph8zMn+7JdgHOpWe+5dDi=YauoPpxxA@mail.gmail.com>
References: <CAJVAAvCUk01XeQKgjjHe10L2qgU9QG5ri_+1teb2_fGTHeTXSg@mail.gmail.com>
	<CAJVAAvCsSuexcCedsKfph8zMn+7JdgHOpWe+5dDi=YauoPpxxA@mail.gmail.com>
Message-ID: <CAJVAAvDOELbSuSoR4qsimbjVvS6DEQr908VVhyQHSj1JX0xEGA@mail.gmail.com>

---------- Forwarded message ----------
From: bhabya sahoo <bdslipun at gmail.com>
Date: Tue, Jan 17, 2012 at 8:37 PM
Subject: Re: vibrational energy
To: PWSCF Forum <pw_forum at pwscf.org>




On Tue, Jan 17, 2012 at 8:34 PM, bhabya sahoo <bdslipun at gmail.com> wrote:

> i am using espresso
> i am calculating vibrational energy of hcp and bcc phase
> by QHA code
> i have got for both the phases. when i am comparing gibbs free energy for
> both phases
> i have to add cold energy of the respective phases
> so weather the vibrational energy obtained from code for hcp phase will be
> added or half of the vibrational energy
> will be added for hcp phase?
>
>
> i am given 0 0 0 for bcc
> .33333334,,66666667,.-25
> .6666667,.333333334,.75 for hcp phase
>






sahoo B
 reserch scholar
mumbai

>
>
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From antonio.aliano at polito.it  Wed Jan 18 10:18:10 2012
From: antonio.aliano at polito.it (Antonio Aliano)
Date: Wed, 18 Jan 2012 10:18:10 +0100
Subject: [Pw_forum] potential units
Message-ID: <0E0A2FA8-ED7D-476C-9E01-02C562A9F72B@polito.it>


Dear all,

I am calculating the potential using the post processing program of QE  
(setting in the input file plot_num=1 or 11). I am note sure about the  
unit of measurements of the results. Are the Rydberg?

Thank you

AA


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From antonio.aliano at polito.it  Wed Jan 18 11:33:15 2012
From: antonio.aliano at polito.it (Antonio Aliano)
Date: Wed, 18 Jan 2012 11:33:15 +0100
Subject: [Pw_forum] potential units
In-Reply-To: <0E0A2FA8-ED7D-476C-9E01-02C562A9F72B@polito.it>
References: <0E0A2FA8-ED7D-476C-9E01-02C562A9F72B@polito.it>
Message-ID: <8460E4C0-83AF-43B1-BB8D-773A7C35F9DA@polito.it>

Of course Ry is a unit for energy... The question rest unchanged: what  
is the unit of measurements for potential data obtained by the post  
processing program in QE?

Thank you

AA

On 18 Jan 2012, at 10:18, Antonio Aliano wrote:

>
> Dear all,
>
> I am calculating the potential using the post processing program of  
> QE (setting in the input file plot_num=1 or 11). I am note sure  
> about the unit of measurements of the results. Are the Rydberg?
>
> Thank you
>
> AA
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

------------------------------------------------------------
Antonio Aliano, PhD, Department of Physics
Politecnico di Torino
C.so Duca degli Abruzzi 24, 10129 Torino Italy
Tel +39 011 090 4659
Fax +39 011 090 4699








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From giannozz at democritos.it  Wed Jan 18 13:19:57 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Jan 2012 13:19:57 +0100
Subject: [Pw_forum] potential units
In-Reply-To: <8460E4C0-83AF-43B1-BB8D-773A7C35F9DA@polito.it>
References: <0E0A2FA8-ED7D-476C-9E01-02C562A9F72B@polito.it>
	<8460E4C0-83AF-43B1-BB8D-773A7C35F9DA@polito.it>
Message-ID: <1326889197.3439.9.camel@fe12lx.fisica.uniud.it>

On Wed, 2012-01-18 at 11:33 +0100, Antonio Aliano wrote:

> Of course Ry is a unit for energy... 

potentials are always multiplied by e, so they are in energy units
(Ry unless otherwise specified, Ha for CP)

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From antonio.aliano at polito.it  Wed Jan 18 16:46:38 2012
From: antonio.aliano at polito.it (Antonio Aliano)
Date: Wed, 18 Jan 2012 16:46:38 +0100
Subject: [Pw_forum] potential units
In-Reply-To: <1326889197.3439.9.camel@fe12lx.fisica.uniud.it>
References: <0E0A2FA8-ED7D-476C-9E01-02C562A9F72B@polito.it>
	<8460E4C0-83AF-43B1-BB8D-773A7C35F9DA@polito.it>
	<1326889197.3439.9.camel@fe12lx.fisica.uniud.it>
Message-ID: <B76EBFFC-C78E-4AE0-8E1E-E5808335A307@polito.it>

Thanks

On 18 Jan 2012, at 13:19, Paolo Giannozzi wrote:

> On Wed, 2012-01-18 at 11:33 +0100, Antonio Aliano wrote:
>
>> Of course Ry is a unit for energy...
>
> potentials are always multiplied by e, so they are in energy units
> (Ry unless otherwise specified, Ha for CP)
>
> P.
> -- 
> Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

------------------------------------------------------------
Antonio Aliano, PhD, Department of Physics
Politecnico di Torino
C.so Duca degli Abruzzi 24, 10129 Torino Italy
Tel +39 011 090 4659
Fax +39 011 090 4699








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From nicola.marzari at epfl.ch  Wed Jan 18 16:50:55 2012
From: nicola.marzari at epfl.ch (Nicola Marzari)
Date: Wed, 18 Jan 2012 16:50:55 +0100
Subject: [Pw_forum] minimizing traffic on the pw_forum list
In-Reply-To: <B76EBFFC-C78E-4AE0-8E1E-E5808335A307@polito.it>
References: <0E0A2FA8-ED7D-476C-9E01-02C562A9F72B@polito.it>
	<8460E4C0-83AF-43B1-BB8D-773A7C35F9DA@polito.it>
	<1326889197.3439.9.camel@fe12lx.fisica.uniud.it>
	<B76EBFFC-C78E-4AE0-8E1E-E5808335A307@polito.it>
Message-ID: <4F16EA5F.9020306@epfl.ch>



Dear All,


let's make an effort in minimizing traffic on this
mailing list to communications that are only relevant to
a question posed, or a question answered - if you want
to thank someone, or make a private comment, use a direct
email. I have sinned in the past, and even this email is a sin,
but well...

Can the reply_to field go directly to the poster, so that we force
someone to include pw_forum explicitly if they wish to do so?


			nicola

----------------------------------------------------------------------
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

From giannozz at democritos.it  Wed Jan 18 17:17:33 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Wed, 18 Jan 2012 17:17:33 +0100
Subject: [Pw_forum] minimizing traffic on the pw_forum list
In-Reply-To: <4F16EA5F.9020306@epfl.ch>
References: <0E0A2FA8-ED7D-476C-9E01-02C562A9F72B@polito.it>
	<8460E4C0-83AF-43B1-BB8D-773A7C35F9DA@polito.it>
	<1326889197.3439.9.camel@fe12lx.fisica.uniud.it>
	<B76EBFFC-C78E-4AE0-8E1E-E5808335A307@polito.it>
	<4F16EA5F.9020306@epfl.ch>
Message-ID: <1326903453.6004.18.camel@fe12lx.fisica.uniud.it>

On Wed, 2012-01-18 at 16:50 +0100, Nicola Marzari wrote:

> Can the reply_to field go directly to the poster, so that we force
> someone to include pw_forum explicitly if they wish to do so?

it is a configuration option of the mailing list. Most people think
that the reply_to field should point to the poster and not to the
mailing list:
- http://www.unicom.com/pw/reply-to-harmful.html
Others disagree:
- http://www.metasystema.net/essays/reply-to.mhtml
I personally prefer that people answer to the mailing list
whenever they have more than 0 bits of information. Anyway, 
I just changed that option. Let's see how it works.

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From iyad.ne at gmail.com  Fri Jan 20 05:44:35 2012
From: iyad.ne at gmail.com (IYAD AL-QASIR)
Date: Thu, 19 Jan 2012 23:44:35 -0500
Subject: [Pw_forum] electron-phonon calculation with spin-polarization
Message-ID: <CAJMDj41ezNgnSqhsj-BDQ6tjt-F6L3-xHZr6d3EKFvNEJ3RouA@mail.gmail.com>

Hello,
I am interested in the getting the electron-phonon transition matrix
elements. However, I am wondering if the electron-phonon modules of QE
support  the inclusion of spin-polarization calculations.


Kindest Regards,
_______________________________
IYAD I. AL-QASIR, PhD
Research Associate

Department of Nuclear Engineering
North Carolina State University
Campus Box 7909
2500 Stinson Dr.
Raleigh, NC 27695-7909
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From vsk.physics at gmail.com  Fri Jan 20 10:16:34 2012
From: vsk.physics at gmail.com (sampath kumar)
Date: Fri, 20 Jan 2012 14:46:34 +0530
Subject: [Pw_forum] PWgui
Message-ID: <CALWRKzdY75sqgqs0imn+=9qrqTaxeeQr3hMT-N7nm7C+Te1Z=w@mail.gmail.com>

Dear all
I am using PWgui stand alone vesion  unable to open pw.x inputfile to edit
. The error showing like this
ERROR: failed to locate object from identifier path_inter_nimages

ERROR: failed to locate object from identifier path_inter_nimages

    while executing
"error $::tclu::error(errMsg) $::tclu::error(info) $::tclu::error(code)"
    ("uplevel" body line 2)
    invoked from within
"uplevel 1 {
    error $::tclu::error(errMsg) $::tclu::error(info) $::tclu::error(code)
    }"
    (procedure "::tclu::ERROR" line 20)
    invoked from within
"::tclu::ERROR "failed to locate object from identifier $varIdent""
    (object "::guib::PWmoduleObj2" method
"::guib::moduleObj::valueToTextvalue" body line 11)
    invoked from within
"valueToTextvalue $ident $value"
    (object "::guib::PWmoduleObj2" method "::guib::moduleObj::varset" body
line 4)
    invoked from within
"$moduleObj varset path_inter_nimages -value $ni"
    (procedure "::pwscf::pwReadFilter" line 59)
    invoked from within
"$readFilter $this $fileChannel"
    (object "::guib::PWmoduleObj2" method "::guib::moduleObj::readFile"
body line 8)
    invoked from within
"::guib::PWmoduleObj2 readFile file6"
    (in namespace eval "::guib" script line 1)
    invoked from within
"namespace eval ::guib [list $obj readFile $fileChannel]"
    (object "::gUI0" method "::guib::GUI::_openInput" body line 27)
    invoked from within
"::gUI0 _openInput pw PW.X
/home/sampath/PWscf/pwgui/lib/app-pwgui/modules/pw/pw.tcl"
    (in namespace inscope "::guib::GUI" script line 1)
    invoked from within
"namespace inscope ::guib::GUI {::gUI0 _openInput pw PW.X
/home/sampath/PWscf/pwgui/lib/app-pwgui/modules/pw/pw.tcl}"
    invoked from within
".gui0.shellchildsite.menubar.menubar.file.menu.openinp invoke active"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke active]"
    (procedure "tk::MenuInvoke" line 50)
    invoked from within
"tk::MenuInvoke .gui0.shellchildsite.menubar.menubar.file.menu.openinp 1"
    (command bound to event)

plese help me how to fix the problem.



Thank you......
*Sampath Kumar. V
Research scholor
Department of Physics
Indian Institute of Technology Hyderabad
Ph: 91+9490122237*
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From iurii.timrov at polytechnique.edu  Fri Jan 20 12:30:11 2012
From: iurii.timrov at polytechnique.edu (Iurii TIMROV)
Date: Fri, 20 Jan 2012 12:30:11 +0100
Subject: [Pw_forum] Transformation of a tensor from the crystal basis to the
 cartesian basis and viceversa
Message-ID: <590842b6b5d760ebdd388a294d1dc34a.squirrel@theory.polytechnique.fr>

Dear All,

I would appreciate if someone can help me to understand what crystal basis
we deal with (composed from direct or reciprocal vectors) in the routines
PH/trntnsc.f90 and PW/trntns.f90.

In the routine PH/trntnsc.f90 there is a comment that it does a
transformation of a complex tensor (like the dynamical matrix) from
crystal to cartesian axes or viceversa. I have a question: Which crystal
axes we are dealing with, the crystal basis of direct vectors
(at(i),i=1,2,3) or the crystal basis of reciprocal vectors
(bg(i),i=1,2,3)?

Crystal -> Cartesian : D_cart  = B * D_cryst * B^T ,
Crystal <- Cartesian : D_cryst = A^T * D_cart * A ,

where D_cryst, D_cart are the tensors of the dynamical matrix in the
crystal and cartesian basis respectively, A is the matrix composed from
the direct lattice vectors (at(i),i=1,2,3), B is the matrix composed from
the reciprocal lattice vectors (bg(i),i=1,2,3), the symbol * stands for
the matrix multiplication, and "T" stands for the transposition of the
matrix.

It seems to me that in these routines (PH/trntnsc.f90 and PW/trntns.f90)
we are dealing with the crystal basis of reciprocal vectors, not sure.

And I think that if one wants to do a transformation from the cartesian
basis to the crystal basis of direct vectors then the equations would
read:

Crystal(direct vectors) -> Cartesian : W_cart  = A * W_cryst * A^T ,
Crystal(direct vectors) <- Cartesian : W_cryst = B^T * W_cart * B ,

here W is some tensor.

Is it true?

Yours faithfully,
Iurii Timrov


Iurii TIMROV
Doctorant (PhD student)
Laboratoire des Solides Irradies
Ecole Polytechnique
F-91128 Palaiseau
+33 1 69 33 45 08
timrov at theory.polytechnique.fr


From bdslipun at gmail.com  Fri Jan 20 14:14:22 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Fri, 20 Jan 2012 18:44:22 +0530
Subject: [Pw_forum] optimisation
Message-ID: <CAJVAAvB+Tk+6XbRgmuKGzTbaz0x6TfoHU+D4uRuTnPaissiBwQ@mail.gmail.com>

i am a new user of espresso
i want to optimise my structure (orthorombhic pnma )
but the optimisation takes 30 steps still it is not relaxed
material=PtAl2
what should i look into?







sahu b
resrch scholar
mumbai
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From giannozz at democritos.it  Fri Jan 20 14:28:59 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 20 Jan 2012 14:28:59 +0100
Subject: [Pw_forum] Transformation of a tensor from the crystal basis	to
	the cartesian basis and viceversa
In-Reply-To: <590842b6b5d760ebdd388a294d1dc34a.squirrel@theory.polytechnique.fr>
References: <590842b6b5d760ebdd388a294d1dc34a.squirrel@theory.polytechnique.fr>
Message-ID: <1327066139.16626.2.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-01-20 at 12:30 +0100, Iurii TIMROV wrote:

> I have a question: Which crystal axes we are dealing with,
>  the crystal basis of direct vectors (at(i),i=1,2,3)

yes. The "crystal basis" is formed by three vectors,
   v_1 = at(:,1), v_2 = at(:,2), v_3 = at(:,3)
(in units of the lattice parameter a)

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From cwandtj at gmail.com  Fri Jan 20 14:30:29 2012
From: cwandtj at gmail.com (Chan-Woo Lee)
Date: Fri, 20 Jan 2012 08:30:29 -0500
Subject: [Pw_forum] optimisation
In-Reply-To: <CAJVAAvB+Tk+6XbRgmuKGzTbaz0x6TfoHU+D4uRuTnPaissiBwQ@mail.gmail.com>
References: <CAJVAAvB+Tk+6XbRgmuKGzTbaz0x6TfoHU+D4uRuTnPaissiBwQ@mail.gmail.com>
Message-ID: <008001ccd777$ae007f50$0a017df0$@gmail.com>

 

 

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of bhabya sahoo
Sent: Friday, January 20, 2012 8:14 AM
To: PWSCF Forum
Subject: [Pw_forum] optimisation

 

i am a new user of espresso

i want to optimise my structure (orthorombhic pnma )

but the optimisation takes 30 steps still it is not relaxed

material=PtAl2

what should i look into?

 

1) Your initial atomic structure. See what is force for each atomic element
as well as force for entire system. If they are large, then, check your
structure. 

2) Your input criteria. Compare yours with those from QE manual. This can be
roughly checked by tracking your total DFT energy. If they are fluctuating,
your input "may" be problematic.

 

Any additional suggestions from other QE users?

 

 

-------

Chan-Woo Lee, Ph.D.

Postdoctoral Research Associate

 

Department of Chemistry

University of Pennsylvania

231 South 34th Street

Philadelphia, PA 19104-6323 

 

 

 

 

 

 

 

 

 

sahu b

resrch scholar

mumbai

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From jean-roch.huntzinger at univ-montp2.fr  Fri Jan 20 15:35:21 2012
From: jean-roch.huntzinger at univ-montp2.fr (Jean-Roch Huntzinger)
Date: Fri, 20 Jan 2012 15:35:21 +0100
Subject: [Pw_forum] PWgui
In-Reply-To: <CALWRKzdY75sqgqs0imn+=9qrqTaxeeQr3hMT-N7nm7C+Te1Z=w@mail.gmail.com>
References: <CALWRKzdY75sqgqs0imn+=9qrqTaxeeQr3hMT-N7nm7C+Te1Z=w@mail.gmail.com>
Message-ID: <201201201535.21603.jean-roch.huntzinger@univ-montp2.fr>

On Friday, January 20, 2012 10:16:34 sampath kumar wrote:
> Dear all
> I am using PWgui stand alone vesion  unable to open pw.x inputfile to edit
> . The error showing like this
> ERROR: failed to locate object from identifier path_inter_nimages
> 


Is this patch working for you also ?

Best regards,
Jean-Roch Huntzinger

-- 
L2C/SMC UMR 5221 - Universit? Montpellier 2, CNRS
case courrier 074
34095 Montpellier cedex 5
tel: 04 67 14 41 38
fax: 04 67 14 37 60
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From tone.kokalj at ijs.si  Fri Jan 20 16:19:23 2012
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 20 Jan 2012 16:19:23 +0100
Subject: [Pw_forum] PWgui
In-Reply-To: <CALWRKzdY75sqgqs0imn+=9qrqTaxeeQr3hMT-N7nm7C+Te1Z=w@mail.gmail.com>
References: <CALWRKzdY75sqgqs0imn+=9qrqTaxeeQr3hMT-N7nm7C+Te1Z=w@mail.gmail.com>
Message-ID: <1327072763.3152.50.camel@catalyst.ijs.si>

On Fri, 2012-01-20 at 14:46 +0530, sampath kumar wrote:
> Dear all 
> I am using PWgui stand alone vesion  unable to open pw.x inputfile to
> edit . The error showing like this
> ERROR: failed to locate object from identifier path_inter_nimages

This error has been fixed. You may re-download pwgui from:

http://www-k3.ijs.si/kokalj/pwgui/download.html

There the version 4.3 is corrected for this error.

Best regards,
-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html


From elie.moujaes at hotmail.co.uk  Sun Jan 22 20:23:48 2012
From: elie.moujaes at hotmail.co.uk (Elie M)
Date: Sun, 22 Jan 2012 19:23:48 +0000
Subject: [Pw_forum] quantum espresso on SLURM
Message-ID: <DUB110-W6619690EC4CD3C542F8562D3850@phx.gbl>


Dear all,
I am trying to do parallel computing on a SLURM interface..Can anyone tell me what is the script form that i need to employ to run the job there (with examples if possible).
Thanks
Elie MoujaesUniversity of NottinghamNG7 2RDUK

 		 	   		  
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From giannozz at democritos.it  Sun Jan 22 20:45:53 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 22 Jan 2012 20:45:53 +0100
Subject: [Pw_forum] quantum espresso on SLURM
In-Reply-To: <DUB110-W6619690EC4CD3C542F8562D3850@phx.gbl>
References: <DUB110-W6619690EC4CD3C542F8562D3850@phx.gbl>
Message-ID: <B6909908-0A6E-4FE0-83DB-EDFE898B6152@democritos.it>


On Jan 22, 2012, at 20:23 , Elie M wrote:

> I am trying to do parallel computing on a SLURM interface. Can anyone
> tell me what is the script form that i need to employ to run the  
> job there

the same that you need to run any parallel job using MPI ...

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From konda.physics at gmail.com  Mon Jan 23 11:15:23 2012
From: konda.physics at gmail.com (Kondaiah Samudrala)
Date: Mon, 23 Jan 2012 15:45:23 +0530
Subject: [Pw_forum] Regarding raman spectra
Message-ID: <CAKjMXpZWjUUtKf_-HRtQgaP862qbO7Xr1fijX9RpctsiXJmmsA@mail.gmail.com>

   Dear all,
   I get the result of cross section of Raman and IR. The results are:

#  mode   [cm-1]     [THz]      IR           Raman     depol
    1      0.00   -0.0001    0.0000         0.0000    0.7298
    2      0.00    0.0000    0.0000         0.0000    0.4596
    3      0.00    0.0000    0.0000         0.0000    0.3769
    4     72.48    2.1728    0.2093         0.0000    0.7221
    5    181.80    5.4503    0.0000      1725.7832    0.7500
    6    216.89    6.5023    0.0000      2083.4500    0.7500
    7    363.65   10.9021    0.0000     91729.5039    0.2795
    8    396.95   11.9001    0.0000    104976.3780    0.7500
    9    420.27   12.5992    0.0000         0.0000    0.6389
   10    425.05   12.7427    0.0000      1248.5419    0.7500
   11    451.38   13.5321    0.0000    329620.4654    0.3306
   12    460.15   13.7949    0.1942         0.0000    0.3225

   The result of raman data are very well compared with the experimental
result. But I am not able to plot Raman spectrum with this o/p using
XMGRACE.

   Please give me suggetion for plot raman spectra. Here with i attached
direct plot of my trail with xmgrace (2 and 5th colums) .

   What is the meaning of cross section in this calculation?

   Please provide norm conserving pseudopotential for phosphorus using GGA
(PBE or PW91) XC-functional ( Using LDA-CAPZ is already in website).

   Finally, for structural properties semiemperical correction of Vdw
interactions plays very importent role. But, Is there any  influence of
semiemperical  correction  to Vdw interaction on vibrational properties????
.

  I appreciate to all your instructions.

  with regards
  S.Appalakondaiah
  Research Schloar
  University of hyderabad
  Hyderabad
  India
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From vv0210 at gmail.com  Mon Jan 23 17:09:45 2012
From: vv0210 at gmail.com (Vikas Varshney)
Date: Mon, 23 Jan 2012 11:09:45 -0500
Subject: [Pw_forum] Help with atomic relaxation (Issue with convergence)
Message-ID: <CAHvkJPMeFDL_eN_M78tTqtgcKcHVmR2aEXFgfS5e=S6gBQo4aw@mail.gmail.com>

Dear Users,

I want to relax (not vc-relax) the combined system of Al2O3 slab with 2 or
3 layers of Ni-atoms on the top of it. Before this combined study, I have
successfully relax the Al2O3 slab and Ni layers seperately. When I combine
them together, I dont know (in advance) the seperation at which I should
keep the Ni layers on the top of Al2O3 slab. So, I keep it ~2 Angs apart
and was hoping that with relax, I should get a relaxed geometry.

The issue I am having is that the electronic relaxation is not converging
(1e-8) even after 500 steps (electron_maxstep = 500).
 I tried 1000 steps also. It ran through few iterations of atom relaxations
but then got crashed after few iterative steps (at a certain step).

So, I wanted to ask how I can make is equilibrate faster? Would a lower
value of conv_thr (1e-4 oe 1e-5)  at the initial stages help (to relax
atomic coordinates) for frequently. Once, I know the approximate good
positions for Ni, atoms, I could increase the conv_thr then.

Please guide, any other suggestions are also highly welcomed

Best Regards,
Vikas

Computational Reseacher,
Wright Patterson Air Force Base,
Dayton, OH.
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From giuseppe.mattioli at mlib.ism.cnr.it  Mon Jan 23 17:25:51 2012
From: giuseppe.mattioli at mlib.ism.cnr.it (giuseppe.mattioli at mlib.ism.cnr.it)
Date: Mon, 23 Jan 2012 17:25:51 +0100
Subject: [Pw_forum] Help with atomic relaxation (Issue with	convergence)
Message-ID: <20120123172551.pb563vaikg8wkwg8@webmail.sic.rm.cnr.it>


Dear Vikas
Hard to say without looking at your input file...

> So, I wanted to ask how I can make is equilibrate faster? Would a lower
> value of conv_thr (1e-4 oe 1e-5)

Maybe, but you are going to calculate poorly converged forces on
ions... Dangerous!

I suppose that you are running a nspin=2 calculation; open shell
systems are sometimes very nasty. You may try to:

lower your mixing_beta parameter, maybe down to 0.05 or 0.02;
perform a (slower) diagonalization="cg" calculation;
increase the smearing value (but check the results at the end of the
calculation with the lowest value which allows you to converge)

HTH but it may turn out not to be enough...

Giuseppe

Giuseppe Mattioli
ISM-CNR
ITALY

Quoting Vikas Varshney <vv0210 at gmail.com>:

> Dear Users,
>
> I want to relax (not vc-relax) the combined system of Al2O3 slab with 2 or
> 3 layers of Ni-atoms on the top of it. Before this combined study, I have
> successfully relax the Al2O3 slab and Ni layers seperately. When I combine
> them together, I dont know (in advance) the seperation at which I should
> keep the Ni layers on the top of Al2O3 slab. So, I keep it ~2 Angs apart
> and was hoping that with relax, I should get a relaxed geometry.
>
> The issue I am having is that the electronic relaxation is not converging
> (1e-8) even after 500 steps (electron_maxstep = 500).
>  I tried 1000 steps also. It ran through few iterations of atom relaxations
> but then got crashed after few iterative steps (at a certain step).
>
> So, I wanted to ask how I can make is equilibrate faster? Would a lower
> value of conv_thr (1e-4 oe 1e-5)  at the initial stages help (to relax
> atomic coordinates) for frequently. Once, I know the approximate good
> positions for Ni, atoms, I could increase the conv_thr then.
>
> Please guide, any other suggestions are also highly welcomed
>
> Best Regards,
> Vikas
>
> Computational Reseacher,
> Wright Patterson Air Force Base,
> Dayton, OH.
>





----- End forwarded message -----




From giannozz at democritos.it  Mon Jan 23 18:29:50 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 23 Jan 2012 18:29:50 +0100
Subject: [Pw_forum] Help with atomic relaxation (Issue with	convergence)
In-Reply-To: <20120123172551.pb563vaikg8wkwg8@webmail.sic.rm.cnr.it>
References: <20120123172551.pb563vaikg8wkwg8@webmail.sic.rm.cnr.it>
Message-ID: <EB81D8BA-FBC3-4DB8-8F49-4ADE2621C641@democritos.it>


On Jan 23, 2012, at 17:25 , giuseppe.mattioli at mlib.ism.cnr.it wrote:

>> So, I wanted to ask how I can make is equilibrate faster? Would a  
>> lower
>> value of conv_thr (1e-4 oe 1e-5)
>
> Maybe, but you are going to calculate poorly converged forces on  
> ions...

note however that as the structural optimization goes on, the  
convergence
threshold for self-consistency is automatically reduced (by up to a  
factor
"upscale" that can be specified in input; default=100). So starting  
with a
relatively large conv_thr (although I would not recommand anything >  
1e-5)
may not be that bad after all

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From vv0210 at gmail.com  Mon Jan 23 18:51:00 2012
From: vv0210 at gmail.com (Vikas Varshney)
Date: Mon, 23 Jan 2012 12:51:00 -0500
Subject: [Pw_forum] Help with atomic relaxation (Issue with convergence)
In-Reply-To: <EB81D8BA-FBC3-4DB8-8F49-4ADE2621C641@democritos.it>
References: <20120123172551.pb563vaikg8wkwg8@webmail.sic.rm.cnr.it>
	<EB81D8BA-FBC3-4DB8-8F49-4ADE2621C641@democritos.it>
Message-ID: <CAHvkJPP0Qyaj8S34kxaeWRtEeNZJR_L9rSOckywWJjkihU4OUQ@mail.gmail.com>

Dear Paolo, Giuseppe,

Thank you for all your comments. I will try to run simulations as you
suggested. In any case, this is how my input file looks if you have further
suggestions.

 &CONTROL
                 calculation = 'relax' ,
                restart_mode = 'from_scratch' ,
                  wf_collect = .true. ,
                      outdir = './' ,
                  pseudo_dir = '/lustre/app2/espresso/pseudo/' ,
                     disk_io = 'default' ,
                   verbosity = 'high' ,
 /
 &SYSTEM
                       ibrav = 0,
                    celldm(1)=   9.050787,
                         nat = 34,
                        ntyp = 3,
                     ecutwfc = 55 ,
                     ecutrho = 550 ,
                 occupations = 'smearing' ,
                     degauss = 0.01 ,
                    smearing = 'methfessel-paxton' ,
                nosym   = .true. ,
                nosym_evc = .true. ,
 /
 &ELECTRONS
                    conv_thr = 1.0D-4 ,
             diagonalization = 'david' ,
                 mixing_mode = 'local-TF' ,
                 mixing_beta = 0.1 ,
        electron_maxstep = 500 ,
 /
 &IONS
                ion_dynamics = 'bfgs' ,
               ion_positions = 'from_input' ,
 /
CELL_PARAMETERS hexagonal
     1.000000000    0.000000000    0.000000000
     0.500000000    0.866025000    0.000000000
     0.000000000    0.000000000    10.824313000
ATOMIC_SPECIES
    O   15.99940  O.pbe-van_ak.UPF
   Al   26.98154  Al.pbe-n-van.UPF
   Ni   58.69340  Ni.pbe-nd-rrkjus.UPF
ATOMIC_POSITIONS angstrom
O        1.473346033   0.017326072   3.218609176
O        3.863581042   1.378379317   7.574956508
O        1.513480866   2.829876285  11.933514340
O       -0.751677351   1.267293591   3.218609163
O        1.663968734   2.656771683   7.574956486
O       -0.812749430   4.043578468  11.933514157
O        1.673065193   2.863185205   3.218609361
O        1.656654190   0.112656124   7.574956554
O       -0.700731568   1.422153909  11.933514350
O        3.298048338   0.005706615   9.773211485
O        0.927961928   1.382600916   1.089494747    0   0   0
O       -1.464820834   2.766734881   5.396064047
O       -1.653964847   2.853342545   9.773211296
O        3.128121670   0.112338146   1.089494747    0   0   0
O        0.731082457   1.495864856   5.396064158
Al      -0.000000812   0.000001493   4.556157709
Al       2.394734647   1.382602298   8.876166342
Al       0.000000000   2.765201880   0.243870515    0   0   0
Al       0.000000000   0.000000000   1.935118618    0   0   0
Al       2.394734540   1.382602230   6.225550857
Al      -0.000000007   2.765202952  10.790402310
Al      -0.000000362   0.000002278   8.430662634
Al       2.394735475   1.382602563  12.021576409
Al      -0.000000581   2.765202130   4.047340256
Al       0.000000075   0.000002190  11.054412333
Al       2.394734840   1.382601177   2.258435418
Al      -0.000000323   2.765202460   6.730673987
  Ni      -0.016734       -0.025515       15.297379
  Ni       1.180634       -2.099417       15.297379
  Ni      -1.214101       -2.099417       15.297379
  Ni      -2.411469       -0.025515       15.297379
K_POINTS automatic
  4 4 1   0 0 0
 Best Regards,
Vikas

Computational Reseacher,
Wright Patterson Air Force Base,
Dayton, OH.



On Mon, Jan 23, 2012 at 12:29 PM, Paolo Giannozzi <giannozz at democritos.it>wrote:

>
> On Jan 23, 2012, at 17:25 , giuseppe.mattioli at mlib.ism.cnr.it wrote:
>
> >> So, I wanted to ask how I can make is equilibrate faster? Would a
> >> lower
> >> value of conv_thr (1e-4 oe 1e-5)
> >
> > Maybe, but you are going to calculate poorly converged forces on
> > ions...
>
> note however that as the structural optimization goes on, the
> convergence
> threshold for self-consistency is automatically reduced (by up to a
> factor
> "upscale" that can be specified in input; default=100). So starting
> with a
> relatively large conv_thr (although I would not recommand anything >
> 1e-5)
> may not be that bad after all
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From shinsha at umich.edu  Tue Jan 24 00:05:14 2012
From: shinsha at umich.edu (Seungha Shin)
Date: Mon, 23 Jan 2012 18:05:14 -0500
Subject: [Pw_forum] Electron phonon coupling coefficient calculations
Message-ID: <038301ccda23$7790a360$66b1ea20$@edu>

Dear all, 


From bogus@does.not.exist.com  Tue Jan  3 18:43:30 2012
From: bogus@does.not.exist.com ()
Date: Tue, 03 Jan 2012 17:43:30 -0000
Subject: No subject
Message-ID: <mailman.0.1327359922.9398.pw_forum@pwscf.org>

calculation of the e-p interaction coefficient in QE is available in metals
only. 

But I also found some papers which used QE package to calculate GaAs, Si,
Ge, Graphene, etc, which are semiconductor or semimetal. 

[PRL, 99, 236405, 2007 - GaAs, GaP,
http://prl.aps.org/abstract/PRL/v99/i23/e236405 

 Phys. of the Solid State, 51 1110 (2009) - Si,
http://www.springerlink.com/content/c0g804860348r072/ 

PRB, 81, 121412(R) (2010), - Graphene,
http://prb.aps.org/abstract/PRB/v81/i12/e121412 

PRB, 84, 035201 (2011) - Ge, http://prb.aps.org/abstract/PRB/v84/i3/e035201
]

To do this calculation (e-p deformation potential for semiconductors), do we
have to go inside the code? 

Or can we calculate those materials (GaAs or Graphene) with the current
version of QE?  

Also, can we expect any possibility for higher order coupling (the second or
higher order coupling, to see multi-phonon absorption or emission)?

Any comment or suggestion would be appreciated. Many Thanks in advance. 

 

Seungha Shin

Heat Transfer Physics Laboratory, Mechanical Engineering

University of Michigan at Ann Arbor

 


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</o:shapelayout></xml><![endif]--></head><body lang=3DEN-US link=3Dblue =
vlink=3Dpurple><div class=3DWordSection1><p class=3DMsoNormal>Dear all, =
<o:p></o:p></p><p class=3DMsoNormal>From the &#8216;user guide&#8217; =
and some previous posts in forum, I see that the calculation of the e-p =
interaction coefficient in QE is available in metals only. =
<o:p></o:p></p><p class=3DMsoNormal>But I also found some papers which =
used QE package to calculate GaAs, Si, Ge, Graphene, etc, which are =
semiconductor or semimetal. <o:p></o:p></p><p class=3DMsoNormal>[PRL, =
99, 236405, 2007 &#8211; GaAs, GaP, <a =
href=3D"http://prl.aps.org/abstract/PRL/v99/i23/e236405">http://prl.aps.o=
rg/abstract/PRL/v99/i23/e236405</a> <o:p></o:p></p><p =
class=3DMsoNormal>&nbsp;Phys. of the Solid State, 51 1110 (2009) &#8211; =
Si, &nbsp;<a =
href=3D"http://www.springerlink.com/content/c0g804860348r072/">http://www=
.springerlink.com/content/c0g804860348r072/</a> <o:p></o:p></p><p =
class=3DMsoNormal>PRB, 81, 121412(R) (2010), - Graphene, <a =
href=3D"http://prb.aps.org/abstract/PRB/v81/i12/e121412">http://prb.aps.o=
rg/abstract/PRB/v81/i12/e121412</a> <o:p></o:p></p><p =
class=3DMsoNormal>PRB, 84, 035201 (2011) &#8211; Ge, <a =
href=3D"http://prb.aps.org/abstract/PRB/v84/i3/e035201">http://prb.aps.or=
g/abstract/PRB/v84/i3/e035201</a> &nbsp;]<o:p></o:p></p><p =
class=3DMsoNormal>To do this calculation (e-p deformation potential for =
semiconductors), do we have to go inside the code? <o:p></o:p></p><p =
class=3DMsoNormal>Or can we calculate those materials (GaAs or Graphene) =
with the current version of QE?&nbsp; <o:p></o:p></p><p =
class=3DMsoNormal>Also, can we expect any possibility for higher order =
coupling (the second or higher order coupling, to see multi-phonon =
absorption or emission)?<o:p></o:p></p><p class=3DMsoNormal>Any comment =
or suggestion would be appreciated. Many Thanks in advance. =
<o:p></o:p></p><p class=3DMsoNormal><o:p>&nbsp;</o:p></p><p =
class=3DMsoNormal>Seungha Shin<o:p></o:p></p><p class=3DMsoNormal>Heat =
Transfer Physics Laboratory, Mechanical Engineering<o:p></o:p></p><p =
class=3DMsoNormal>University of Michigan at Ann Arbor<o:p></o:p></p><p =
class=3DMsoNormal><o:p>&nbsp;</o:p></p></div></body></html>
------=_NextPart_000_0384_01CCD9F9.8EBA9B60--


From joshiniharika20 at yahoo.in  Tue Jan 24 07:19:00 2012
From: joshiniharika20 at yahoo.in (Niharika Joshi)
Date: Tue, 24 Jan 2012 11:49:00 +0530 (IST)
Subject: [Pw_forum] Occupied states in XAS
Message-ID: <1327385940.93549.YahooMailNeo@web95709.mail.in.yahoo.com>

Hello,

In the xspectra calculation, the option 'cut_occ_states=.false.' will include the occupied states in XAS.
Why should one consider occupied states in absorption spectra because the transitions are only to empty states. Or have understood it wrong?
?-Niharika Joshi
(Project student, Indian Institute of Science Education and Research, Pune, India)
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From fratesi at mater.unimib.it  Tue Jan 24 09:46:55 2012
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Tue, 24 Jan 2012 09:46:55 +0100
Subject: [Pw_forum] Help with atomic relaxation (Issue with convergence)
In-Reply-To: <CAHvkJPP0Qyaj8S34kxaeWRtEeNZJR_L9rSOckywWJjkihU4OUQ@mail.gmail.com>
References: <20120123172551.pb563vaikg8wkwg8@webmail.sic.rm.cnr.it>
	<EB81D8BA-FBC3-4DB8-8F49-4ADE2621C641@democritos.it>
	<CAHvkJPP0Qyaj8S34kxaeWRtEeNZJR_L9rSOckywWJjkihU4OUQ@mail.gmail.com>
Message-ID: <4F1E6FFF.1060605@mater.unimib.it>

Have you checked the input is read correctly? Apparently, the number of 
atoms listed (31) does not correspond to "nat" (ii)
Guido

Il 01/23/2012 06:51 PM, Vikas Varshney ha scritto:
> &CONTROL
>                   calculation = 'relax' ,
>                  restart_mode = 'from_scratch' ,
>                    wf_collect = .true. ,
>                        outdir = './' ,
>                    pseudo_dir = '/lustre/app2/espresso/pseudo/' ,
>                       disk_io = 'default' ,
>                     verbosity = 'high' ,
>   /
> &SYSTEM
>                         ibrav = 0,
>                      celldm(1)=   9.050787,
>                           nat = 34,
>                          ntyp = 3,
>                       ecutwfc = 55 ,
>                       ecutrho = 550 ,
>                   occupations = 'smearing' ,
>                       degauss = 0.01 ,
>                      smearing = 'methfessel-paxton' ,
>                  nosym   = .true. ,
>                  nosym_evc = .true. ,
>   /
> &ELECTRONS
>                      conv_thr = 1.0D-4 ,
>               diagonalization = 'david' ,
>                   mixing_mode = 'local-TF' ,
>                   mixing_beta = 0.1 ,
>          electron_maxstep = 500 ,
>   /
> &IONS
>                  ion_dynamics = 'bfgs' ,
>                 ion_positions = 'from_input' ,
>   /
> CELL_PARAMETERS hexagonal
>       1.000000000    0.000000000    0.000000000
>       0.500000000    0.866025000    0.000000000
>       0.000000000    0.000000000    10.824313000
> ATOMIC_SPECIES
>      O   15.99940  O.pbe-van_ak.UPF
>     Al   26.98154  Al.pbe-n-van.UPF
>     Ni   58.69340  Ni.pbe-nd-rrkjus.UPF
> ATOMIC_POSITIONS angstrom
> O        1.473346033   0.017326072   3.218609176
> O        3.863581042   1.378379317   7.574956508
> O        1.513480866   2.829876285  11.933514340
> O       -0.751677351   1.267293591   3.218609163
> O        1.663968734   2.656771683   7.574956486
> O       -0.812749430   4.043578468  11.933514157
> O        1.673065193   2.863185205   3.218609361
> O        1.656654190   0.112656124   7.574956554
> O       -0.700731568   1.422153909  11.933514350
> O        3.298048338   0.005706615   9.773211485
> O        0.927961928   1.382600916   1.089494747    0   0   0
> O       -1.464820834   2.766734881   5.396064047
> O       -1.653964847   2.853342545   9.773211296
> O        3.128121670   0.112338146   1.089494747    0   0   0
> O        0.731082457   1.495864856   5.396064158
> Al      -0.000000812   0.000001493   4.556157709
> Al       2.394734647   1.382602298   8.876166342
> Al       0.000000000   2.765201880   0.243870515    0   0   0
> Al       0.000000000   0.000000000   1.935118618    0   0   0
> Al       2.394734540   1.382602230   6.225550857
> Al      -0.000000007   2.765202952  10.790402310
> Al      -0.000000362   0.000002278   8.430662634
> Al       2.394735475   1.382602563  12.021576409
> Al      -0.000000581   2.765202130   4.047340256
> Al       0.000000075   0.000002190  11.054412333
> Al       2.394734840   1.382601177   2.258435418
> Al      -0.000000323   2.765202460   6.730673987
>    Ni      -0.016734       -0.025515       15.297379
>    Ni       1.180634       -2.099417       15.297379
>    Ni      -1.214101       -2.099417       15.297379
>    Ni      -2.411469       -0.025515       15.297379
> K_POINTS automatic
>    4 4 1   0 0 0

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca
via Cozzi 53, 20125 Milano, Italy

From matteo.calandra at impmc.jussieu.fr  Tue Jan 24 10:37:18 2012
From: matteo.calandra at impmc.jussieu.fr (Matteo Calandra)
Date: Tue, 24 Jan 2012 10:37:18 +0100
Subject: [Pw_forum] (Niharika Joshi)
In-Reply-To: <mailman.1.1327393988.19669.pw_forum@pwscf.org>
References: <mailman.1.1327393988.19669.pw_forum@pwscf.org>
Message-ID: <4F1E7BCE.4060801@impmc.jussieu.fr>

Le 24/01/12 09:33, pw_forum-request at pwscf.org a ?crit :
> ------------------------------
>
> Message: 2
> Date: Tue, 24 Jan 2012 11:49:00 +0530 (IST)
> From: Niharika Joshi<joshiniharika20 at yahoo.in>
> Subject: [Pw_forum] Occupied states in XAS
> To: "pw_forum at pwscf.org"<pw_forum at pwscf.org>
> Message-ID:<1327385940.93549.YahooMailNeo at web95709.mail.in.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> In the xspectra calculation, the option 'cut_occ_states=.false.' will include the occupied states in XAS.
> Why should one consider occupied states in absorption spectra because the transitions are only to empty states. Or have understood it wrong?
> ?-Niharika Joshi

Dear Niharika,

   of course in XAS only empty states are measured. However plotting 
occupied states could
be useful for low energy features (pre-edge region). When for example 
there is not a clear large
gap, it can be difficult to isolate empty from occupied states. This is 
the case in metals or small gap
systems. So it can be useful to look at the full spectrum and see where 
the Fermi level is located.

M.

> (Project student, Indian Institute of Science Education and Research, Pune, India)
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> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 55, Issue 39
> ****************************************


-- 
* * * *
Matteo Calandra, Directeur de Recherche (DR2)
Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris
Universit? Pierre et Marie Curie, tour 23, 3eme etage, case 115
4 Place Jussieu, 75252 Paris Cedex 05 France
Tel: +33-1-44 27 52 16       Fax: +33-1-44 27 37 85
http://www.impmc.jussieu.fr/~calandra


From annetindele at yahoo.fr  Tue Jan 24 11:17:07 2012
From: annetindele at yahoo.fr (anne etindele)
Date: Tue, 24 Jan 2012 10:17:07 +0000 (GMT)
Subject: [Pw_forum] Dynamic polarizability of C60
Message-ID: <1327400227.51803.YahooMailNeo@web29601.mail.ird.yahoo.com>

DearEduardo

You wanted to know What exactly this dynamical polarizability is?

In fact, when a system (atomic, molecule,...) is submitted to an external field, 
its electrons are reorganised according to the frequence of that external field. 
One can then evaluate the aptitude of the system to be subject to that reorganisation
by evaluating the polarizability. Particularly when the phenomenon is time dependent,
one evaluate the dynamical polarizability.
?
?is it include  the electronic , phonon or both contributions?
?
For my case, I want to consider C60 as a dielectric sphere of finite or infinite 
thickness, I don't know exactly if the phonon contribution is relevant, but I am 
mostly evolved in electronic calculations. 

?What are the frequency units (THz, eV? ) in the example 33.

?As I see in output of that example 33 (it is also the case for almost all the other 
input and output files of espresso-4.3.1), the energies and frequencies are in Ry


Kind regard 
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From baroni at sissa.it  Tue Jan 24 12:54:53 2012
From: baroni at sissa.it (Stefano Baroni)
Date: Tue, 24 Jan 2012 12:54:53 +0100
Subject: [Pw_forum] Quantum ESPRESSO developers' meeting
Message-ID: <F8DD4844-6ED8-4CC6-B5AD-D1B2C4817BE9@sissa.it>

Dear All:

this is just to inform (remind) everybody that in this very moment some of the most significant developers in the Quantum ESPRESSO community are discussing the most exciting developments and future perspectives, in the QE annual developers' that is being held in Trieste.

I hope everybody will join me in wishing them the best success and in thanking them for running the best open source quantum simulation software project ever.

Thanks to all of them, and to all of you for rewarding their efforts by using their work for doing top science!

Stefano B

---
Stefano Baroni - SISSA  &  DEMOCRITOS National Simulation Center - Trieste
http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)

La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget

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From eariel99 at gmail.com  Tue Jan 24 16:04:54 2012
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 24 Jan 2012 16:04:54 +0100
Subject: [Pw_forum] Regarding raman spectra
Message-ID: <CAM5Vcw9tsU8yfkg1Yw3YXXX+1DtxQLAODZ-Ar=NTP=jh4uApZg@mail.gmail.com>

Hi,
save the data in a file, let's name it archive.dat

call gnuplot with the command of the same name. Inside the gnuplot
terminal,
plot "archive.dat"  using 2:5  with impulses
or
plot "archive.dat"  u 2:5  w i

that will produce a plot of vertical lines. If you want a continuous curve,
you need to write your own program. I know no utility in Quantum ESRESSO to
do that. Any user of Quantum ESPRESSO and similar non-commercial packages
needs to write, and enjoy doing it :-),  some small programs to analize the
output data.

Yoy have asked for a GGA pseudopotential, but take into account that the
PHONON  code calculates the Raman spectra only for LDA and norm conserving
pseudopotentials.

I guess that vdW interaction is important for soft modes, or at least to
have an apropriate strucuture with minimal energy, otherwise there are
imaginary frequencies. Graphene is a famous case where vdW is important.

best regards
Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706



---------- Mensaje reenviado ----------
From: Kondaiah Samudrala <konda.physics at gmail.com>
To: pw_forum at pwscf.org
Cc:
Date: Mon, 23 Jan 2012 15:45:23 +0530
Subject: [Pw_forum] Regarding raman spectra

   Dear all,
   I get the result of cross section of Raman and IR. The results are:

#  mode   [cm-1]     [THz]      IR           Raman     depol
    1      0.00   -0.0001    0.0000         0.0000    0.7298
    2      0.00    0.0000    0.0000         0.0000    0.4596
    3      0.00    0.0000    0.0000         0.0000    0.3769
    4     72.48    2.1728    0.2093         0.0000    0.7221
    5    181.80    5.4503    0.0000      1725.7832    0.7500
    6    216.89    6.5023    0.0000      2083.4500    0.7500
    7    363.65   10.9021    0.0000     91729.5039    0.2795
    8    396.95   11.9001    0.0000    104976.3780    0.7500
    9    420.27   12.5992    0.0000         0.0000    0.6389
   10    425.05   12.7427    0.0000      1248.5419    0.7500
   11    451.38   13.5321    0.0000    329620.4654    0.3306
   12    460.15   13.7949    0.1942         0.0000    0.3225


   The result of raman data are very well compared with the experimental
result. But I am not able to plot Raman spectrum with this o/p using
XMGRACE.

   Please give me suggetion for plot raman spectra. Here with i attached
direct plot of my trail with xmgrace (2 and 5th colums) .

   What is the meaning of cross section in this calculation?

   Please provide norm conserving pseudopotential for phosphorus using GGA
(PBE or PW91) XC-functional ( Using LDA-CAPZ is already in website).

   Finally, for structural properties semiemperical correction of Vdw
interactions plays very importent role. But, Is there any  influence of
semiemperical  correction  to Vdw interaction on vibrational properties????
.

  I appreciate to all your instructions.

  with regards
  S.Appalakondaiah
  Research Schloar
  University of hyderabad
  Hyderabad
  India

-- 




On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en
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From eariel99 at gmail.com  Tue Jan 24 16:26:54 2012
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Tue, 24 Jan 2012 16:26:54 +0100
Subject: [Pw_forum] Dynamic polarizability of C60
Message-ID: <CAM5Vcw_cmN17s8wPo=nSTc4B-0fAPNgvO5bpUoWuQrDU4P-w2g@mail.gmail.com>

Hi Anne, and everybody,

My question about the dynamical polarizability was more for the developers,
because I don not find it clear in the documentation.
Let me focus my question

The electronic dynamical  polarizability is calculated with the
turbo-TDDFPT code. Then, what dynamic polarizability is calculated with
PHONON ? Knowing some of he applications of the PHONON code, I foresee two
logical answers
a) the polarizabilty due to phonon excitations, plus the electronic
polarizabilty in the static limit, i.e., for energy much smaller than the
electronic transition energies.
b) the same, but with the frequency dependent electronic contributions,
calculated with ground state DFT instead of TDDFT.
and the answer is c)  ...........?

I do not believe that the frequencies in the example 33 are in Ry. They are
too high if the units are Ry, and PHONON is esentially a code to calculate
phonons and derived properties. I would bet for THz.

best regards
Eduardo


DearEduardo You wanted to know What exactly this dynamical polarizability
is? In fact, when a system (atomic, molecule,...) is submitted to an
external field, its electrons are reorganised according to the frequence of
that external field. One can then evaluate the aptitude of the system to be
subject to that reorganisation by evaluating the polarizability.
Particularly when the phenomenon is time dependent, one evaluate the
dynamical polarizability.    is it include the electronic , phonon or both
contributions?   For my case, I want to consider C60 as a dielectric sphere
of finite or infinite thickness, I don't know exactly if the phonon
contribution is relevant, but I am mostly evolved in electronic
calculations.  What are the frequency units (THz, eV? ) in the example 33.
 As I see in output of that example 33 (it is also the case for almost all
the other input and output files of espresso-4.3.1), the energies and
frequencies are in Ry Kind regard
-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en
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From payam.norouzzadeh at gmail.com  Tue Jan 24 17:53:43 2012
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Tue, 24 Jan 2012 10:53:43 -0600
Subject: [Pw_forum] unit-cell volume for bcc crystals
Message-ID: <CAND4gJHZ5DH9scrDCdGjNyV3sbXcUATAdUJoYGTPsJyiwgmHnw@mail.gmail.com>

Hello QE users
What is the unit-cell volume reported by PWSCF for bcc crystals? is that
a^3/2 (primitive unit-cell) or simply a^3 (conventional crystal)?
Best regards,Payam Norouzzadeh
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From chenhanghuipwscf at gmail.com  Tue Jan 24 23:15:34 2012
From: chenhanghuipwscf at gmail.com (Hanghui Chen)
Date: Tue, 24 Jan 2012 17:15:34 -0500
Subject: [Pw_forum] different ways to calculate charges on atoms
Message-ID: <CAOE2MOxWHdCmpYPj1NPU1ny_KcLVwQqRr2+WB7WeznPgYggi_w@mail.gmail.com>

Dear QE developers,
     I have a very naive question. It seems that there are two ways to
calculate the charges on atoms in QE. One is to use the Lowdin orbitals to
do the atomic projection and get the charges on different orbitals. The
other way is to turn on Hubbard U and calculate the occupation on the
localized orbitals. Recently, I tested LaNiO3 and found the two methods
give different results of the charge on Ni d orbitals. I would like to know
whether this is normal and if yes, is that because the Ni d orbitals are
different in the two approaches?
    Thank you very much.

Hanghui Chen
Department of Physics
Yale University
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From zafartariq2003 at yahoo.com  Wed Jan 25 12:34:58 2012
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Wed, 25 Jan 2012 03:34:58 -0800 (PST)
Subject: [Pw_forum] Errors during calculation of thermal properties using QHA
Message-ID: <1327491298.26885.YahooMailClassic@web65410.mail.ac4.yahoo.com>

Dear All I am working on ZnO(hcp structure). I want to calculate thermal properties using QHA.I am using fedora core 9 (gfortran version 4.3.0). for thermal properties following errors occures.
Would any body tell me how I can cover this problem?
[zafar at localhost ZnO]$ ./Run_Me?****** input tetrahedra for BZ-integration ******? ?6 ? 3 ?12? 0.000000 ?0.000000 ?0.000000? 0.000000 ?0.577350 ?0.000000?-0.333330 ?0.577350 ?0.000000? 0.000000 ?0.000000 ?0.803030? 0.000000 ?0.577350 ?0.803030?-0.333330 ?0.577350 ?0.803030****** input tetrahedra for BZ-integration **************************** generate_tetra *********************? NT0= ? ? ? ? ? 3 ?NTETMX= ? ? ? ?1728? ? 0.0000 ? 0.0000 ?-0.3333 ?-0.3333? ? 0.0000 ? 0.5774 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.0000 ? 0.0000 ? 0.8030? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? ? 0.0000 ? 0.0000 ? 0.0000 ?-0.3333? ? 0.0000 ? 0.0000 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.8030 ? 0.8030 ? 0.8030? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? ? 0.0000 ? 0.0000 ?-0.3333 ? 0.0000? ? 0.0000 ? 0.5774 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.8030
 ? 0.8030 ? 0.0000? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? total volume of BZ is = ? 0.0773 ?omg48= ?25.8830****************** end of generate_tetra ******************?Recalculating omega(q) from C(R)STOP Partial_DOS finished?natoms== ? ? ? ? ? 4?irec==== ? ? ? ? 168? 0.75000000000000000 ? ???Zn ?Zn ?It seems you have imaginary frequences.\ ? ? ? ? ? ? ? ? ? ? ? Hopefully you know what you are doing?nstep==== ? ? ? ? 734? 112.0761 ?112.0767 ?136.8345? 120.2794 ?129.5796 ?132.5383? 123.3896 ?128.8859 ?131.0670? 126.1556 ?126.1563 ?131.4016? 123.0497 ?123.8439 ?148.2783? 125.4183 ?128.9576 ?144.2191? 126.6441 ?130.6791 ?142.6102? 126.1474 ?131.6514 ?141.8672? 127.5920 ?134.0565 ?139.4667? 128.0304 ?136.7692 ?136.7699? 116.8975 ?118.1902 ?151.5177?E_min= ? 0.0000000000000000 ? ? ? ? E_max= ? 530.33650000000000 ? ???nstep==== ? ? ?
 ? 734****** input tetrahedra for BZ-integration ******? ?6 ? 3 ?12? 0.000000 ?0.000000 ?0.000000? 0.000000 ?0.577350 ?0.000000?-0.333330 ?0.577350 ?0.000000? 0.000000 ?0.000000 ?0.803030? 0.000000 ?0.577350 ?0.803030?-0.333330 ?0.577350 ?0.803030****** input tetrahedra for BZ-integration **************************** generate_tetra *********************? NT0= ? ? ? ? ? 3 ?NTETMX= ? ? ? ?1728? ? 0.0000 ? 0.0000 ?-0.3333 ?-0.3333? ? 0.0000 ? 0.5774 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.0000 ? 0.0000 ? 0.8030? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? ? 0.0000 ? 0.0000 ? 0.0000 ?-0.3333? ? 0.0000 ? 0.0000 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.8030 ? 0.8030 ? 0.8030? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? ? 0.0000 ? 0.0000 ?-0.3333 ? 0.0000? ? 0.0000 ? 0.5774 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.8030 ? 0.8030 ? 0.0000? ?
 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? total volume of BZ is = ? 0.0773 ?omg48= ?25.8830****************** end of generate_tetra ******************?before integration: ?E_min= ? 0.0000000000000000 ? ? ? ? E_max= ? 530.33650000000000 ? ???Freq,Tot_DOS,DOS== ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ?At line 107 of file Integration.f (unit = 32, file = '')Fortran runtime error: File already opened in another unit?ndiv from file === ? ? ? ? 734?ndiv=== ? ? ? ? ? 1?norm_partial== ? 0.0000000000000000 ? ???ndiv from file === ? ? ? ? 734?ndiv=== ? ? ? ? ? 1?norm_partial== ? 0.0000000000000000 ? ??At line 58 of file Atom_projected_properties.f90 (unit = 9, file = 'projected.DOS')Fortran runtime error: End of fileAt line 71 of file Mean_square_displacement.f90 (unit = 1, file =
 'projected_DOS.O')Fortran runtime error: End of filemv: cannot stat `Displacements': No such file or directoryAt line 58 of file Atom_projected_properties.f90 (unit = 9, file = 'projected.DOS')Fortran runtime error: End of fileAt line 71 of file Mean_square_displacement.f90 (unit = 1, file = 'projected_DOS.O')Fortran runtime error: End of filemv: cannot stat `Displacements': No such file or directory?ndiv from file === ? ? ? ? 734?ndiv=== ? ? ? ? ? 0? ? 0.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 100.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 200.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 300.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 400.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 500.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 600.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ?
 ?0.00000000? 700.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 800.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 900.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1000.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1100.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1200.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1300.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1400.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1500.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1600.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1700.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1800.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1900.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ?
 ?0.00000000?2000.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2100.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2200.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2300.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2400.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2500.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2600.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2700.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2800.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2900.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?3000.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000Phonon DOS and Quasiharmonic calculations have finished.Now you can analyse these data using Gnuplot or xmgrace
Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan
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From bdslipun at gmail.com  Wed Jan 25 13:44:35 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Wed, 25 Jan 2012 18:14:35 +0530
Subject: [Pw_forum] error in relaxation
Message-ID: <CAJVAAvCptKy8jR-Ngd4zyHSmoh19g88QVTqJGS8Z9upm27Pb0A@mail.gmail.com>

i want to use vc-relax in p6/3mmc phase of ptal2
but at end the error looks like this


   2445 !    total energy              =    -228.56236722 Ry
   2446      Harris-Foulkes estimate   =    -228.56236722 Ry
   2447      estimated scf accuracy    <          8.1E-09 Ry
   2448
   2449      The total energy is the sum of the following terms:
   2450
   2451      one-electron contribution =      14.22118625 Ry
   2452      hartree contribution      =      21.19884711 Ry
   2453      xc contribution           =    -137.66928250 Ry
   2454      ewald contribution        =    -126.31282800 Ry
   2455      smearing contrib. (-TS)   =      -0.00029008 Ry
   2456
   2457      convergence has been achieved in   7 iterations
   2458
   2459      Forces acting on atoms (Ry/au):
   2460
   2461      atom   1 type  2   force =     0.00000000    0.00000000
 0.00000000
   2462      atom   2 type  1   force =     0.00000000    0.00000000
 0.00000000
   2463      atom   3 type  2   force =     0.00000000    0.00000000
 0.00000000
   2464      atom   4 type  2   force =     0.00000000    0.00000000
 0.00000000
   2465      atom   5 type  1   force =     0.00000000    0.00000000
 0.00000000
   2466      atom   6 type  2   force =     0.00000000    0.00000000
 0.00000000
   2467
   2468      Total force =     0.000000     Total SCF correction =
0.000000
   2469
   2470
   2471      entering subroutine stress ...
   2472
   2473           total   stress  (Ry/bohr**3)                   (kbar)
P=    0.13
   2474    0.00000208   0.00000000   0.00000000          0.31      0.00
 0.00
   2475    0.00000000   0.00000208   0.00000000          0.00      0.31
 0.00
   2476    0.00000000   0.00000000  -0.00000142          0.00      0.00
-0.21
   2477





   2480      (criteria: energy < 0.10E-03, force < 0.10E-02, cell <
0.50E+00)
   2481
   2482      End of BFGS Geometry Optimization
   2483
   2484      Final enthalpy =    -228.5623672168 Ry
   2485 Begin final coordinates
   2486      new unit-cell volume =    616.53001 a.u.^3 (    91.36032 Ang^3
)
   2487
   2488 CELL_PARAMETERS (alat=  8.07405095)
   2489    1.021263439   0.000000000   0.000000000
   2490   -0.510631719   0.884440082   0.000000000
   2491    0.000000000   0.000000000   1.296801680
   2492
   2493 ATOMIC_POSITIONS (crystal)
   2494 al       0.000000000   0.000000000   0.000000000
   2495 pt       0.333333333   0.666666667   0.250000000
   2496 al       0.333333333   0.666666667   0.750000000
   2497 al       0.000000000   0.000000000   0.500000000
   2498 pt       0.666666667   0.333333333   0.750000000
   2499 al       0.666666667   0.333333333   0.250000000
   2500 End final coordinates
   2501
   2502
   2503
   2504      A final scf calculation at the relaxed structure.
   2505
   2506      The G-vectors are recalculated.
   2507
   2508    Stick Mesh
   2509    ----------
   2510    nst =  2795,  nstw =   313, nsts =  1135
   2511                n.st   n.stw   n.sts    n.g    n.gw   n.gs
   2512    min        2795     313    1135  152759    6087   38757
   2513    max        2795     313    1135  152759    6087   38757
   2514        2795     313    1135  152759    6087   38757
   2515
   2516
   2517
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   2518      from sym_rho_init_shell : error #         3
   2519







SAHOO B
RESERCH SCHOLAR
MUMBAI
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From mohnish.iitk at gmail.com  Wed Jan 25 17:09:16 2012
From: mohnish.iitk at gmail.com (mohnish pandey)
Date: Wed, 25 Jan 2012 21:39:16 +0530
Subject: [Pw_forum] Thanks a lot to QE forum for immense help in my first
	paper
Message-ID: <CAMhNW-c-DNdecmGY2ajU8=0UQagBKVMhyNeDkVUPhiX=2NBSbQ@mail.gmail.com>

Dear QE users,

I thank you all for being so helpful in guiding me in learning QE. I
especially thank Prof. Giannozzi, Prof. Baroni, Prof. Marzari, Dr. Paulatto
for immense help in the beginning. With guidance of you people I got my
first paper accepted in The Journal of Chemical Physics. Below is the title
and link to the paper.

"Stabilization and growth of non-native nanocrystals at low and atmospheric
pressures"
 J. Chem. Phys. *136*, 044703 (2012); doi:10.1063/1.3678181

I thank you all once again for your cooperation.

-- 
Regards,
MOHNISH,
-----------------------------------------------------------------
Mohnish Pandey
BTech-Mtech, IIT Kanpur
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-----------------------------------------------------------------
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From payam.norouzzadeh at gmail.com  Thu Jan 26 01:54:07 2012
From: payam.norouzzadeh at gmail.com (Payam Norouzzadeh)
Date: Wed, 25 Jan 2012 18:54:07 -0600
Subject: [Pw_forum] xsf to pwscf input
Message-ID: <CAND4gJE0ZmOOTBB-pH-JCz784jTeD53+JsPZxpM7fGH-9pEv2g@mail.gmail.com>

Hello QE users
Is there any way,software,.. to convert xsf file formats(readable by
Xcrysden) to input file for PWSCF( just crystal structure and atom
coordinates)?
Best regards,Payam Norouzzadeh
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From faccin.giovani at gmail.com  Thu Jan 26 02:11:01 2012
From: faccin.giovani at gmail.com (Giovani Faccin)
Date: Wed, 25 Jan 2012 21:11:01 -0400
Subject: [Pw_forum] xsf to pwscf input
In-Reply-To: <CAND4gJE0ZmOOTBB-pH-JCz784jTeD53+JsPZxpM7fGH-9pEv2g@mail.gmail.com>
References: <CAND4gJE0ZmOOTBB-pH-JCz784jTeD53+JsPZxpM7fGH-9pEv2g@mail.gmail.com>
Message-ID: <CAK-VqZCQjF-ERhdvU8eaVZQki5c+eMqTo+ik9o8B_fqz6F+USg@mail.gmail.com>

Software I'm not sure. But "a way" would be to open the xsf file in a text
editor and copy/paste the information you need into a pw input file.

The atomic coordinates in the real space are located after the  PRIMCOORD
flag. The primitive cell vectors are after the  PRIMVEC flag. If it's just
a one time thing, maybe you can handle it this way.

Regards,

Giovani Faccin

CPPP/UFMS
Brazil


2012/1/25 Payam Norouzzadeh <payam.norouzzadeh at gmail.com>

> Hello QE users
> Is there any way,software,.. to convert xsf file formats(readable by
> Xcrysden) to input file for PWSCF( just crystal structure and atom
> coordinates)?
> Best regards,Payam Norouzzadeh
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From bdslipun at gmail.com  Thu Jan 26 06:56:37 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Thu, 26 Jan 2012 11:26:37 +0530
Subject: [Pw_forum] Fwd: error in relaxation
In-Reply-To: <CAJVAAvArpDiHTACmZDH5ZNtKuDbC_yTc1V0PDu5by4KY315PFA@mail.gmail.com>
References: <CAJVAAvCptKy8jR-Ngd4zyHSmoh19g88QVTqJGS8Z9upm27Pb0A@mail.gmail.com>
	<CAJVAAvArpDiHTACmZDH5ZNtKuDbC_yTc1V0PDu5by4KY315PFA@mail.gmail.com>
Message-ID: <CAJVAAvDWTVuFVbL1tgpcbKxmFEbVtJL=a8kMgfnK7ZQj=H4eVQ@mail.gmail.com>

---------- Forwarded message ----------
From: bhabya sahoo <bdslipun at gmail.com>
Date: Wed, Jan 25, 2012 at 10:26 PM
Subject: Fwd: error in relaxation
To: pw_forum-request at pwscf.org




---------- Forwarded message ----------
From: bhabya sahoo <bdslipun at gmail.com>
Date: Wed, Jan 25, 2012 at 6:14 PM
Subject: error in relaxation
To: PWSCF Forum <pw_forum at pwscf.org>


i want to use vc-relax in p6/3mmc phase of ptal2
but at end the error looks like this


   2445 !    total energy              =    -228.56236722 Ry
   2446      Harris-Foulkes estimate   =    -228.56236722 Ry
   2447      estimated scf accuracy    <          8.1E-09 Ry
   2448
   2449      The total energy is the sum of the following terms:
   2450
   2451      one-electron contribution =      14.22118625 Ry
   2452      hartree contribution      =      21.19884711 Ry
   2453      xc contribution           =    -137.66928250 Ry
   2454      ewald contribution        =    -126.31282800 Ry
   2455      smearing contrib. (-TS)   =      -0.00029008 Ry
   2456
   2457      convergence has been achieved in   7 iterations
   2458
   2459      Forces acting on atoms (Ry/au):
   2460
   2461      atom   1 type  2   force =     0.00000000    0.00000000
 0.00000000
   2462      atom   2 type  1   force =     0.00000000    0.00000000
 0.00000000
   2463      atom   3 type  2   force =     0.00000000    0.00000000
 0.00000000
   2464      atom   4 type  2   force =     0.00000000    0.00000000
 0.00000000
   2465      atom   5 type  1   force =     0.00000000    0.00000000
 0.00000000
   2466      atom   6 type  2   force =     0.00000000    0.00000000
 0.00000000
   2467
   2468      Total force =     0.000000     Total SCF correction =
0.000000
   2469
   2470
   2471      entering subroutine stress ...
   2472
   2473           total   stress  (Ry/bohr**3)                   (kbar)
P=    0.13
   2474    0.00000208   0.00000000   0.00000000          0.31      0.00
 0.00
   2475    0.00000000   0.00000208   0.00000000          0.00      0.31
 0.00
   2476    0.00000000   0.00000000  -0.00000142          0.00      0.00
-0.21
   2477





   2480      (criteria: energy < 0.10E-03, force < 0.10E-02, cell <
0.50E+00)
   2481
   2482      End of BFGS Geometry Optimization
   2483
   2484      Final enthalpy =    -228.5623672168 Ry
   2485 Begin final coordinates
   2486      new unit-cell volume =    616.53001 a.u.^3 (    91.36032 Ang^3
)
   2487
   2488 CELL_PARAMETERS (alat=  8.07405095)
   2489    1.021263439   0.000000000   0.000000000
   2490   -0.510631719   0.884440082   0.000000000
   2491    0.000000000   0.000000000   1.296801680
   2492
   2493 ATOMIC_POSITIONS (crystal)
   2494 al       0.000000000   0.000000000   0.000000000
   2495 pt       0.333333333   0.666666667   0.250000000
   2496 al       0.333333333   0.666666667   0.750000000
   2497 al       0.000000000   0.000000000   0.500000000
   2498 pt       0.666666667   0.333333333   0.750000000
   2499 al       0.666666667   0.333333333   0.250000000
   2500 End final coordinates
   2501
   2502
   2503
   2504      A final scf calculation at the relaxed structure.
   2505
   2506      The G-vectors are recalculated.
   2507
   2508    Stick Mesh
   2509    ----------
   2510    nst =  2795,  nstw =   313, nsts =  1135
   2511                n.st   n.stw   n.sts    n.g    n.gw   n.gs
   2512    min        2795     313    1135  152759    6087   38757
   2513    max        2795     313    1135  152759    6087   38757
   2514        2795     313    1135  152759    6087   38757
   2515
   2516
   2517
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   2518      from sym_rho_init_shell : error #         3
   2519







SAHOO B
RESERCH SCHOLAR
MUMBAI
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From bdslipun at gmail.com  Thu Jan 26 07:13:01 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Thu, 26 Jan 2012 11:43:01 +0530
Subject: [Pw_forum] (no subject)
Message-ID: <CAJVAAvCs-xJQp7fL_r8BgW2su8w8B9NqxebwTVNvDme6=DPFMw@mail.gmail.com>

is there any space group iimplimentation in espresso?
if no how to handel that problem
















SAHU
MUMBAI
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From bdslipun at gmail.com  Thu Jan 26 09:51:08 2012
From: bdslipun at gmail.com (bhabya sahoo)
Date: Thu, 26 Jan 2012 14:21:08 +0530
Subject: [Pw_forum] (no subject)
In-Reply-To: <CAJVAAvCs-xJQp7fL_r8BgW2su8w8B9NqxebwTVNvDme6=DPFMw@mail.gmail.com>
References: <CAJVAAvCs-xJQp7fL_r8BgW2su8w8B9NqxebwTVNvDme6=DPFMw@mail.gmail.com>
Message-ID: <CAJVAAvADORPwY=4fhwj96tNKLx+LwFt4Omym6GWjKCtabkKHtA@mail.gmail.com>

so always do wwith primitive ok i am doing that but in many completed
system it requires a mind full thorough of crystal structere/or xcrysteden
like software

On Thu, Jan 26, 2012 at 11:43 AM, bhabya sahoo <bdslipun at gmail.com> wrote:

> is there any space group iimplimentation in espresso?
> if no how to handel that problem
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> SAHU
> MUMBAI
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From gabriele.sclauzero at epfl.ch  Thu Jan 26 10:51:41 2012
From: gabriele.sclauzero at epfl.ch (Gabriele Sclauzero)
Date: Thu, 26 Jan 2012 10:51:41 +0100
Subject: [Pw_forum] Fwd:  xsf to pwscf input
References: <2E52F489-4004-40F0-AC93-250BF1C24C6E@epfl.ch>
Message-ID: <B843E112-1329-422F-880C-4C05B6402415@epfl.ch>


Forwarding... (@#!^$%&**?... but it's just my opinion)

Inizio messaggio inoltrato:

> Da: Gabriele Sclauzero <gabriele.sclauzero at epfl.ch>
> Data: 26 gennaio 2012 10.16.53 GMT+01.00
> A: Payam Norouzzadeh <payam.norouzzadeh at gmail.com>
> Oggetto: Re: [Pw_forum] xsf to pwscf input
> 
> Hello Payam,
> 
>     there is something doing that in the PWTK program by Tone Kokalj, see http://pwtk.qe-forge.org/ and search for XSF in the webpage.
> You could search the corresponding code in the script files (should be under pwtk/src/pwi.tcl, see http://qe-forge.org/scm/browser.php?group_id=29) 
> and adapt it to your needs. 
> 
> HTH
> 
> 
> GS
> 
> P.S: please sign including your affiliation too, thanks
> 
> Il giorno 26/gen/2012, alle ore 01.54, Payam Norouzzadeh ha scritto:
> 
>> Hello QE users
>> Is there any way,software,.. to convert xsf file formats(readable by Xcrysden) to input file for PWSCF( just crystal structure and atom coordinates)?
>> Best regards,Payam Norouzzadeh
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
> 
> 
> ? Gabriele Sclauzero, EPFL SB ITP CSEA
>    PH H2 462, Station 3, CH-1015 Lausanne
> 
> 
> 
> 
> 
> 
> 


? Gabriele Sclauzero, EPFL SB ITP CSEA
   PH H2 462, Station 3, CH-1015 Lausanne







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From giacsport at libero.it  Thu Jan 26 11:45:16 2012
From: giacsport at libero.it (giacsport at libero.it)
Date: Thu, 26 Jan 2012 11:45:16 +0100 (CET)
Subject: [Pw_forum] from  read_namelists  : error #        88
Message-ID: <17761526.1581801327574716844.JavaMail.defaultUser@defaultHost>

Excuse me, I forgot to add a title to the email....

G
>----Messaggio originale----
>Da: giacsport at libero.it
>Data: 26/01/2012 11.43
>A: <pw_forum at pwscf.org>
>Ogg: 
>
>Dear All,
>              I have installed the 4.3.2 version of pwscf on the CINECA sp6 
>machine. The compilation was successful. 
>Now I am trying to make some benchmark calculations with some pseudos I 
>previously used and well tested.
>As far as I launch the job whose input you find below, I get the "usual" 
error 
>message regarding the namelist error, i.e.
>
> 
>     Program PWSCF v.4.3.2      starts on 26Jan2012 at 11:22:14
>
>     Parallel version (MPI), running on     8 processors
>     R & G space division:  proc/pool =    8
>
>     Current dimensions of program PWSCF are:
>     Max number of different atomic species (ntypx) = 10
>     Max number of k-points (npk) =  40000
>     Max angular momentum in pseudopotentials (lmaxx) =  3
>     Waiting for input...
>     Reading input from stdin
>
> 

>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     from  read_namelists  : error #        88
>      reading namelist system
> 

>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>     stopping ...
>
>
>Now, I find it quite strange, because exactly same input and pseudos gave no 
>error message in a local cluster (Intel Xeon machine).
>Can you help me?
>Thanks!
>
>Giacomo
>
>
>
>
>&CONTROL
>    calculation = "relax"
>    pseudo_dir = './'
>    outdir='./',
>    restart_mode="from_scratch",
>    prefix='ZnO_WZ',
>    tprnfor     = .true.,
>    tstress     = .true.,
>    wf_collect=.true.,
>/
>&SYSTEM
>    ibrav=  4, celldm(1) =6.13821, celldm(3)=1.6023951, nat=  4, ntyp= 2,
>    ecutwfc =105.0,  nbnd = 100,
>    input_dft='hse', nqx1 = 3, nqx2 = 3, nqx3 = 2,
>    x_gamma_extrapolation = .TRUE.
>/
>&ELECTRONS
>    diagonalization='david'
>    mixing_mode = 'plain'
>    mixing_beta = 0.7
>    conv_thr =  1.0d-8
>/
>&IONS
>    ion_dynamics='bfgs'
>/
>ATOMIC_SPECIES
> Zn  65.38     Zn_pz-12.cpi.UPF
>  O  15.9994   O.pz-mt.UPF
>ATOMIC_POSITIONS (crystal)
>Zn       0.935705        1.62101        0.
>Zn       1.87141         0.             2.5938
>O        0.935705        1.62101        1.98114
>O        1.87141         0.             4.57494
>K_POINTS (automatic)
>9 9 6 0 0 0
>
>
>
>-- 
>Giacomo GIORGI
>
>Department of Chemical System Engineering,
>School of Engineering, The University of Tokyo
>7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
>E-mail: giacomo at tcl.t.u-tokyo.ac.jp
>
>



From giacsport at libero.it  Thu Jan 26 11:43:29 2012
From: giacsport at libero.it (giacsport at libero.it)
Date: Thu, 26 Jan 2012 11:43:29 +0100 (CET)
Subject: [Pw_forum] (no subject)
Message-ID: <13504185.1580231327574609953.JavaMail.defaultUser@defaultHost>

Dear All,
              I have installed the 4.3.2 version of pwscf on the CINECA sp6 
machine. The compilation was successful. 
Now I am trying to make some benchmark calculations with some pseudos I 
previously used and well tested.
As far as I launch the job whose input you find below, I get the "usual" error 
message regarding the namelist error, i.e.

 
     Program PWSCF v.4.3.2      starts on 26Jan2012 at 11:22:14

     Parallel version (MPI), running on     8 processors
     R & G space division:  proc/pool =    8

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Reading input from stdin

 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from  read_namelists  : error #        88
      reading namelist system
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...


Now, I find it quite strange, because exactly same input and pseudos gave no 
error message in a local cluster (Intel Xeon machine).
Can you help me?
Thanks!

Giacomo




&CONTROL
    calculation = "relax"
    pseudo_dir = './'
    outdir='./',
    restart_mode="from_scratch",
    prefix='ZnO_WZ',
    tprnfor     = .true.,
    tstress     = .true.,
    wf_collect=.true.,
/
&SYSTEM
    ibrav=  4, celldm(1) =6.13821, celldm(3)=1.6023951, nat=  4, ntyp= 2,
    ecutwfc =105.0,  nbnd = 100,
    input_dft='hse', nqx1 = 3, nqx2 = 3, nqx3 = 2,
    x_gamma_extrapolation = .TRUE.
/
&ELECTRONS
    diagonalization='david'
    mixing_mode = 'plain'
    mixing_beta = 0.7
    conv_thr =  1.0d-8
/
&IONS
    ion_dynamics='bfgs'
/
ATOMIC_SPECIES
 Zn  65.38     Zn_pz-12.cpi.UPF
  O  15.9994   O.pz-mt.UPF
ATOMIC_POSITIONS (crystal)
Zn       0.935705        1.62101        0.
Zn       1.87141         0.             2.5938
O        0.935705        1.62101        1.98114
O        1.87141         0.             4.57494
K_POINTS (automatic)
9 9 6 0 0 0



-- 
Giacomo GIORGI

Department of Chemical System Engineering,
School of Engineering, The University of Tokyo
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
E-mail: giacomo at tcl.t.u-tokyo.ac.jp



From eariel99 at gmail.com  Thu Jan 26 12:10:33 2012
From: eariel99 at gmail.com (Eduardo Ariel Menendez Proupin)
Date: Thu, 26 Jan 2012 12:10:33 +0100
Subject: [Pw_forum] doubt on TDDFPT output
Message-ID: <CAM5Vcw_5hXWxVg=oLCGcbTfY5S3yiEVnCADOBgynUeJEvNPLwA@mail.gmail.com>

Hi,
I am rather confused with the TDDFPT output. In the turbo_spectrum run I
pretend to obtain the polarizabilty \alpha_{33}, and I set the input as

&lr_input
  prefix='cnt_21',
  outdir='./temp',
  itermax=10000
  itermax0=4000
  extrapolation="osc"
  epsil=0.0073495
  units=1
  start=0.d0
  end=5.0d0
  increment=0.01d0
  start=0.0d0
  ipol=3
  verbosity=1


In the output I get references only to the direction 1, as seen below

     Program TDDFPT_PP v.4.3.1  starts on 11Jan2012 at 12: 6:32
.........
     Parallel version (MPI), running on    56 processors
     R & G space division:  proc/pool =   56

     Reading  10000 Lanczos steps for direction 1
       3500 steps will be considered
.....
     Polarization direction:1
....
    Static dipole polarizability Tensor:
     chi_1_1=  0.523359728355224E+03 + i0.000000000000000E+00


I check that the chi_1_1 values in the output are different the results
when I set ipol=3. Is it a bug of the output or is somehing different to
the \alpha_{33} that I want to obtain ?

Thanks

-- 


Eduardo Menendez Proupin
Departamento de Qu?mica Fisica Aplicada
Facultad de Ciencias
Universidad Aut?noma de Madrid
28049 Madrid, Spain
Phone: +34 91 497 6706

On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de
Chile URL: http://fisica.ciencias.uchile.cl/~emenendez

"*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez
padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices,
pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n
que le es otorgada. Pero la grandeza del hombre est? precisamente en querer
mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay
grandeza que conquistar, puesto que all? todo es jerarqu?a establecida,
inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio,
reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro
de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar
su grandeza, su m?xima medida en el Reino de este Mundo*".
Alejo Carpentier, El reino de este mundo, (1949).

Translate from spanish here
http://translate.google.com/?hl=&ie=UTF-8&text=&sl=es&tl=en
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From zafartariq2003 at yahoo.com  Thu Jan 26 12:21:26 2012
From: zafartariq2003 at yahoo.com (zafar rasheed)
Date: Thu, 26 Jan 2012 03:21:26 -0800 (PST)
Subject: [Pw_forum] errors during calculation of thermal properties of ZnO
	using QHA
Message-ID: <1327576886.10114.YahooMailClassic@web65403.mail.ac4.yahoo.com>

Dear All I am working on ZnO(hcp structure). I want to calculate thermal properties?using QHA.I am using fedora core 9 (gfortran version 4.3.0).?for thermal properties following errors occures.
Would any body tell me how I can cover this problem?[zafar at localhost ZnO]$ ./Run_Me?****** input tetrahedra for BZ-integration ******? ?6 ? 3 ?12? 0.000000 ?0.000000 ?0.000000? 0.000000 ?0.577350 ?0.000000?-0.333330 ?0.577350 ?0.000000? 0.000000 ?0.000000 ?0.803030? 0.000000 ?0.577350 ?0.803030?-0.333330 ?0.577350 ?0.803030****** input tetrahedra for BZ-integration **************************** generate_tetra *********************? NT0= ? ? ? ? ? 3 ?NTETMX= ? ? ? ?1728? ? 0.0000 ? 0.0000 ?-0.3333 ?-0.3333? ? 0.0000 ? 0.5774 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.0000 ? 0.0000 ? 0.8030? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? ? 0.0000 ? 0.0000 ? 0.0000 ?-0.3333? ? 0.0000 ? 0.0000 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.8030 ? 0.8030 ? 0.8030? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? ? 0.0000 ? 0.0000 ?-0.3333 ? 0.0000? ?
 0.0000 ? 0.5774 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.8030 ? 0.8030 ? 0.0000? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? total volume of BZ is = ? 0.0773 ?omg48= ?25.8830****************** end of generate_tetra ******************?Recalculating omega(q) from C(R)STOP Partial_DOS finished?natoms== ? ? ? ? ? 4?irec==== ? ? ? ? 168? 0.75000000000000000 ? ???Zn ?Zn ?It seems you have imaginary frequences.\ ? ? ? ? ? ? ? ? ? ? ??Hopefully you know what you are doing?nstep==== ? ? ? ? 734? 112.0761 ?112.0767 ?136.8345? 120.2794 ?129.5796 ?132.5383? 123.3896 ?128.8859 ?131.0670? 126.1556 ?126.1563 ?131.4016? 123.0497 ?123.8439 ?148.2783? 125.4183 ?128.9576 ?144.2191? 126.6441 ?130.6791 ?142.6102? 126.1474 ?131.6514 ?141.8672? 127.5920 ?134.0565 ?139.4667? 128.0304 ?136.7692 ?136.7699? 116.8975 ?118.1902 ?151.5177?E_min= ? 0.0000000000000000 ? ? ?
 ? E_max= ? 530.33650000000000 ? ???nstep==== ? ? ? ? 734****** input tetrahedra for BZ-integration ******? ?6 ? 3 ?12? 0.000000 ?0.000000 ?0.000000? 0.000000 ?0.577350 ?0.000000?-0.333330 ?0.577350 ?0.000000? 0.000000 ?0.000000 ?0.803030? 0.000000 ?0.577350 ?0.803030?-0.333330 ?0.577350 ?0.803030****** input tetrahedra for BZ-integration **************************** generate_tetra *********************? NT0= ? ? ? ? ? 3 ?NTETMX= ? ? ? ?1728? ? 0.0000 ? 0.0000 ?-0.3333 ?-0.3333? ? 0.0000 ? 0.5774 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.0000 ? 0.0000 ? 0.8030? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? ? 0.0000 ? 0.0000 ? 0.0000 ?-0.3333? ? 0.0000 ? 0.0000 ? 0.5774 ? 0.5774? ? 0.0000 ? 0.8030 ? 0.8030 ? 0.8030? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? ? 0.0000 ? 0.0000 ?-0.3333 ? 0.0000? ? 0.0000 ? 0.5774 ?
 0.5774 ? 0.5774? ? 0.0000 ? 0.8030 ? 0.8030 ? 0.0000? ? 1.0000 ? 1.0000 ? 1.0000 ? 1.0000? volume of tetrahedron = ?0.02576? total volume of BZ is = ? 0.0773 ?omg48= ?25.8830****************** end of generate_tetra ******************?before integration: ?E_min= ? 0.0000000000000000 ? ? ? ? E_max= ? 530.33650000000000 ? ???Freq,Tot_DOS,DOS== ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ? ? 0.000000 ? ?At line 107 of file Integration.f (unit = 32, file = '')Fortran runtime error: File already opened in another unit?ndiv from file === ? ? ? ? 734?ndiv=== ? ? ? ? ? 1?norm_partial== ? 0.0000000000000000 ? ???ndiv from file === ? ? ? ? 734?ndiv=== ? ? ? ? ? 1?norm_partial== ? 0.0000000000000000 ? ??At line 58 of file Atom_projected_properties.f90 (unit = 9, file = 'projected.DOS')Fortran runtime error: End of fileAt line 71 of file
 Mean_square_displacement.f90 (unit = 1, file = 'projected_DOS.O')Fortran runtime error: End of filemv: cannot stat `Displacements': No such file or directoryAt line 58 of file Atom_projected_properties.f90 (unit = 9, file = 'projected.DOS')Fortran runtime error: End of fileAt line 71 of file Mean_square_displacement.f90 (unit = 1, file = 'projected_DOS.O')Fortran runtime error: End of filemv: cannot stat `Displacements': No such file or directory?ndiv from file === ? ? ? ? 734?ndiv=== ? ? ? ? ? 0? ? 0.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 100.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 200.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 300.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 400.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 500.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 600.00 ?
 ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 700.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 800.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000? 900.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1000.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1100.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1200.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1300.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1400.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1500.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1600.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1700.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1800.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?1900.00 ? ?0.00000000 ?
 ?0.00000000 ? ?0.00000000 ? ?0.00000000?2000.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2100.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2200.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2300.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2400.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2500.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2600.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2700.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2800.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?2900.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000?3000.00 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000 ? ?0.00000000Phonon DOS and Quasiharmonic calculations have finished.Now you can analyse these data using Gnuplot or xmgrace

Muhammad Zafar

PhD Scholar

Department of Physics

The Islamia University of Bahawalpur,Pakistan
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From rahen29 at yahoo.com  Thu Jan 26 15:03:11 2012
From: rahen29 at yahoo.com (Rahen Badsha)
Date: Thu, 26 Jan 2012 06:03:11 -0800 (PST)
Subject: [Pw_forum] Input file of graphene
Message-ID: <1327586591.7650.YahooMailNeo@web44711.mail.sp1.yahoo.com>





Dear All,
I am a new user of QE. 

I want to calculate the electronic structure of graphene . So I need the 
input file of graphene.(Hints: scf ,nscf, bands,dos calculation). 

Please send me & help me.? 





Regards,
Md. Rahen Badsha (Raihan)
A? post graduate thesis student,
Rajshahi University, Bangladesh.
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From rahen29 at yahoo.com  Thu Jan 26 15:03:11 2012
From: rahen29 at yahoo.com (Rahen Badsha)
Date: Thu, 26 Jan 2012 06:03:11 -0800 (PST)
Subject: [Pw_forum] Input file of graphene
Message-ID: <1327586591.7650.YahooMailNeo@web44711.mail.sp1.yahoo.com>





Dear All,
I am a new user of QE. 

I want to calculate the electronic structure of graphene . So I need the 
input file of graphene.(Hints: scf ,nscf, bands,dos calculation). 

Please send me & help me.? 





Regards,
Md. Rahen Badsha (Raihan)
A? post graduate thesis student,
Rajshahi University, Bangladesh.
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From lmartinsamos at gmail.com  Thu Jan 26 16:11:23 2012
From: lmartinsamos at gmail.com (Layla Martin-Samos)
Date: Thu, 26 Jan 2012 16:11:23 +0100
Subject: [Pw_forum] (no subject)
In-Reply-To: <13504185.1580231327574609953.JavaMail.defaultUser@defaultHost>
References: <13504185.1580231327574609953.JavaMail.defaultUser@defaultHost>
Message-ID: <CAGCSmJSwZrrbuO8sOrfPG=R=X7-JxPfhjmPkTBw4MUTWkAiSQw@mail.gmail.com>

Dear Giacomo, you are trying to make an EXX calculation did you compile
addig by hand in the make.sys file (DFLAGS and FDFLAGS) the -DEXX flag?

bests

Layla

2012/1/26 giacsport at libero.it <giacsport at libero.it>

> Dear All,
>              I have installed the 4.3.2 version of pwscf on the CINECA sp6
> machine. The compilation was successful.
> Now I am trying to make some benchmark calculations with some pseudos I
> previously used and well tested.
> As far as I launch the job whose input you find below, I get the "usual"
> error
> message regarding the namelist error, i.e.
>
>
>     Program PWSCF v.4.3.2      starts on 26Jan2012 at 11:22:14
>
>     Parallel version (MPI), running on     8 processors
>     R & G space division:  proc/pool =    8
>
>     Current dimensions of program PWSCF are:
>     Max number of different atomic species (ntypx) = 10
>     Max number of k-points (npk) =  40000
>     Max angular momentum in pseudopotentials (lmaxx) =  3
>     Waiting for input...
>     Reading input from stdin
>
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     from  read_namelists  : error #        88
>      reading namelist system
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>     stopping ...
>
>
> Now, I find it quite strange, because exactly same input and pseudos gave
> no
> error message in a local cluster (Intel Xeon machine).
> Can you help me?
> Thanks!
>
> Giacomo
>
>
>
>
> &CONTROL
>    calculation = "relax"
>    pseudo_dir = './'
>    outdir='./',
>    restart_mode="from_scratch",
>    prefix='ZnO_WZ',
>    tprnfor     = .true.,
>    tstress     = .true.,
>    wf_collect=.true.,
> /
> &SYSTEM
>    ibrav=  4, celldm(1) =6.13821, celldm(3)=1.6023951, nat=  4, ntyp= 2,
>    ecutwfc =105.0,  nbnd = 100,
>    input_dft='hse', nqx1 = 3, nqx2 = 3, nqx3 = 2,
>    x_gamma_extrapolation = .TRUE.
> /
> &ELECTRONS
>    diagonalization='david'
>    mixing_mode = 'plain'
>    mixing_beta = 0.7
>    conv_thr =  1.0d-8
> /
> &IONS
>    ion_dynamics='bfgs'
> /
> ATOMIC_SPECIES
>  Zn  65.38     Zn_pz-12.cpi.UPF
>  O  15.9994   O.pz-mt.UPF
> ATOMIC_POSITIONS (crystal)
> Zn       0.935705        1.62101        0.
> Zn       1.87141         0.             2.5938
> O        0.935705        1.62101        1.98114
> O        1.87141         0.             4.57494
> K_POINTS (automatic)
> 9 9 6 0 0 0
>
>
>
> --
> Giacomo GIORGI
>
> Department of Chemical System Engineering,
> School of Engineering, The University of Tokyo
> 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
> E-mail: giacomo at tcl.t.u-tokyo.ac.jp
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
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From pandey.bramha at gmail.com  Thu Jan 26 17:21:53 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Thu, 26 Jan 2012 21:51:53 +0530
Subject: [Pw_forum] problen to run q2r.x code.
Message-ID: <CAC2dNGE_XARSo5Mg-p1Wer9+Wp0NQgJek1FtHaGRsLuCHQnvZg@mail.gmail.com>

Dear QE Users..
good evening.

i got a problem when running the q2r.x code for obtaing the IFC file. I am
using QE-4.3.2 on ubantu 11.10 of 32 bits

the error is shown;;;;

 file /home/espresso-4.2/phcal/si/
dyn.G0 not found
  reading grid info from input


but i have a file of dyn.G not dyn.G0. I have also look in q2r.f90   file.

>>>> nr1,nr2,nr3:  dimensions of the FFT grid formed by the q-point grid
  !     nfile      :  number of files containing C(q_n), n=1,nfile
  !  followed by nfile cards:
  !     filin      :  name of file containing C(q_n)
  !  The name and order of files is not important as long as q=0 is the
first<<<<
I am unable to exploit the meaning of above statement due to my new
entrance in QE.

Thanks in advanced for your valuable time and suggestions.


-- 
Thanks and Regards
Bramha Prasad Pandey
Assistant Professor (Electronics and Communication Engg)
GLA Group of Institutions, Mathura.
Ph. No. 08954143009
email id pandey.bramha at gmail.com
            bpglaitm at yahoo.co.in
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From flux_ray12 at 163.com  Thu Jan 26 17:58:58 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Fri, 27 Jan 2012 00:58:58 +0800 (CST)
Subject: [Pw_forum] problen to run q2r.x code.
In-Reply-To: <CAC2dNGE_XARSo5Mg-p1Wer9+Wp0NQgJek1FtHaGRsLuCHQnvZg@mail.gmail.com>
References: <CAC2dNGE_XARSo5Mg-p1Wer9+Wp0NQgJek1FtHaGRsLuCHQnvZg@mail.gmail.com>
Message-ID: <4c55fcb1.5e0a.1351af4b11a.Coremail.flux_ray12@163.com>

The function of q2r.x is summarizing a series of dynamic matrics and transferring to real space force constants by FFT. Such series dyn files, declaring as fildyn='*' in the input file of q2r.x, are named as *0, *1, *2,..., where *0 contains the dyn files list.
Therefore, when you have only one dyn file, it is not recommanded to form the force constants. Or, if you really want, you can make a file, let's call it dyn.G0, and write such contents in it:
1  1  1
1
0.000000000000000E+00   0.000000000000000E+00   0.000000000000000E+00
Then change the file name of dyn.G to dyn.G1, and using q2r.x by the input:
&input
   zasr = 'simple' ,
   fildyn = 'dyn.G' ,
   flfrc = 'fc' ,
/
I do not guarantee such a method can help you to achieve meaningful result~~~~


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-01-27 00:22:08,"bramha pandey" <pandey.bramha at gmail.com> wrote:
Dear QE Users..
good evening.

i got a problem when running the q2r.x code for obtaing the IFC file. I am using QE-4.3.2 on ubantu 11.10 of 32 bits

the error is shown;;;;

 file /home/espresso-4.2/phcal/si/
dyn.G0 not found
  reading grid info from input


but i have a file of dyn.G not dyn.G0. I have also look in q2r.f90   file.

>>>> nr1,nr2,nr3:  dimensions of the FFT grid formed by the q-point grid
  !     nfile      :  number of files containing C(q_n), n=1,nfile
  !  followed by nfile cards:
  !     filin      :  name of file containing C(q_n)
  !  The name and order of files is not important as long as q=0 is the first<<<<
I am unable to exploit the meaning of above statement due to my new entrance in QE.

Thanks in advanced for your valuable time and suggestions.


--
Thanks and Regards
Bramha Prasad Pandey
Assistant Professor (Electronics and Communication Engg)
GLA Group of Institutions, Mathura.
Ph. No. 08954143009
email id pandey.bramha at gmail.com
            bpglaitm at yahoo.co.in
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From w2agz at w2agz.com  Fri Jan 27 02:19:25 2012
From: w2agz at w2agz.com (W2AGZ)
Date: Thu, 26 Jan 2012 17:19:25 -0800
Subject: [Pw_forum] Mysterious Matdyn Message(s)
Message-ID: <016001ccdc91$b66b3670$2341a350$@w2agz.com>

To Matdyn Users:

 

I'm trying to trace back some matdyn.x messages I've not seen before.  They
start with:

 

Message from routine matdyn:

     Z* not found in file SNx.fc, TO-LO splitting at q=0 will be absent!

     A direction for q was not specified:TO-LO splitting will be absent

 

This I do understand, both the origin and the physics, and the messages
originate from a

call to routine infomsg.

 

However, this is followed by a long list of (several hundred) lines of
format:

     Max |d(i,j)-d*(j,i)| =  0.014209

     Max |d(i,j)-d*(j,i)|/|d(i,j)|:  39.5291%

     Max |d(i,j)-d*(j,i)| =  0.014209

     Max |d(i,j)-d*(j,i)|/|d(i,j)|:  37.8906%

     Max |d(i,j)-d*(j,i)| =  0.014209

     Max |d(i,j)-d*(j,i)|/|d(i,j)|:  34.1814%

 

I am unable to trace this output to source code within matdyn.f90, nor to
various modules linked 

by the USE command.  In fact, the infomsg subroutine is contained within
module error_handler, which

doesn't seem to be linked (at least directly) to matdyn.

 

I suspect the above are error messages related (possibly) to
representation/symmetry inconsistencies, but

can anyone tell me their origin in the PWSCF code first?

 

Thanks, -Paul

 

Paul Grant, W2AGZ Technologies, JPL/CalTech Staff Associate

 

 

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From akohlmey at gmail.com  Fri Jan 27 02:53:08 2012
From: akohlmey at gmail.com (Axel Kohlmeyer)
Date: Thu, 26 Jan 2012 20:53:08 -0500
Subject: [Pw_forum] Mysterious Matdyn Message(s)
In-Reply-To: <016001ccdc91$b66b3670$2341a350$@w2agz.com>
References: <016001ccdc91$b66b3670$2341a350$@w2agz.com>
Message-ID: <CADTmJ6ER6CV7Sx8DUf1cB79L3V+=g5oud+guXxykAoWpts+Hvw@mail.gmail.com>

On Thu, Jan 26, 2012 at 8:19 PM, W2AGZ <w2agz at w2agz.com> wrote:
> To Matdyn Users:
>
>
>
> I?m trying to trace back some matdyn.x messages I?ve not seen before.? They
> start with:
>
>
>
> Message from routine matdyn:
>
> ???? Z* not found in file SNx.fc, TO-LO splitting at q=0 will be absent!
>
> ?? ??A direction for q was not specified:TO-LO splitting will be absent
>
>
>
> This I do understand, both the origin and the physics, and the messages
> originate from a
>
> call to routine infomsg.
>
>
>
> However, this is followed by a long list of (several hundred) lines of
> format:
>
> ???? Max |d(i,j)-d*(j,i)| =? 0.014209
>
> ???? Max |d(i,j)-d*(j,i)|/|d(i,j)|:? 39.5291%
>
> ???? Max |d(i,j)-d*(j,i)| =? 0.014209
>
> ???? Max |d(i,j)-d*(j,i)|/|d(i,j)|:? 37.8906%
>
> ???? Max |d(i,j)-d*(j,i)| =? 0.014209
>
> ???? Max |d(i,j)-d*(j,i)|/|d(i,j)|:? 34.1814%
>
>
>
> I am unable to trace this output to source code within matdyn.f90, nor to
> various modules linked
>
> by the USE command.? In fact, the infomsg subroutine is contained within
> module error_handler, which
>
> doesn?t seem to be linked (at least directly) to matdyn.
>
>
>
> I suspect the above are error messages related (possibly) to
> representation/symmetry inconsistencies, but
>
> can anyone tell me their origin in the PWSCF code first?

[akohlmey at fermi espresso]$ find ./ -name \*.f90 -print | xargs grep -n 'Max |d'
./espresso/PHonon/PH/rigid.f90:272:  if ( diff > 1.d-6 ) write
(6,'(5x,"Max |d(i,j)-d*(j,i)| = ",f9.6,/,5x, &
./espresso/PHonon/PH/rigid.f90:273:       & "Max
|d(i,j)-d*(j,i)|/|d(i,j)|: ",f8.4,"%")') diff, difrel*100

is this what you are looking for?

axel.


>
>
>
> Thanks, -Paul
>
>
>
> Paul Grant, W2AGZ Technologies, JPL/CalTech Staff Associate
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Dr. Axel Kohlmeyer
akohlmey at gmail.com ?http://goo.gl/1wk0

College of Science and Technology
Temple University, Philadelphia PA, USA.

From mourad_fsm at yahoo.fr  Fri Jan 27 09:26:08 2012
From: mourad_fsm at yahoo.fr (debbichi mourad)
Date: Fri, 27 Jan 2012 08:26:08 +0000 (GMT)
Subject: [Pw_forum] Re : Pw_forum Digest, Vol 55, Issue 46
In-Reply-To: <mailman.443.1327627374.9401.pw_forum@pwscf.org>
References: <mailman.443.1327627374.9401.pw_forum@pwscf.org>
Message-ID: <1327652768.14442.YahooMailNeo@web29502.mail.ird.yahoo.com>

Dear Giacomo,
verify if your pseudopotential for Zn it is Norm - Conserving pseudopotential ?

Sincerely
A+


DEBBICHI Mourad
?Unit? de Recherche Physique des Solides,
99/UR/13-19,
D?partement de Physique, 
Facult? des Science de Monastir, 
Avenue de l'Environnement 5019, Monastir Tunisie. 
t?l:+21697487042
mourad_fsm at yahoo.fr


________________________________

------------------------------

Message: 2
Date: Thu, 26 Jan 2012 16:11:23 +0100
From: Layla Martin-Samos <lmartinsamos at gmail.com>
Subject: Re: [Pw_forum] (no subject)
To: "giacsport at libero.it" <giacsport at libero.it>
Cc: pw_forum at pwscf.org
Message-ID:
??? <CAGCSmJSwZrrbuO8sOrfPG=R=X7-JxPfhjmPkTBw4MUTWkAiSQw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Giacomo, you are trying to make an EXX calculation did you compile
addig by hand in the make.sys file (DFLAGS and FDFLAGS) the -DEXX flag?

bests

Layla

2012/1/26 giacsport at libero.it <giacsport at libero.it>

> Dear All,
>? ? ? ? ? ? ? I have installed the 4.3.2 version of pwscf on the CINECA sp6
> machine. The compilation was successful.
> Now I am trying to make some benchmark calculations with some pseudos I
> previously used and well tested.
> As far as I launch the job whose input you find below, I get the "usual"
> error
> message regarding the namelist error, i.e.
>
>
>? ?  Program PWSCF v.4.3.2? ? ? starts on 26Jan2012 at 11:22:14
>
>? ?  Parallel version (MPI), running on? ?  8 processors
>? ?  R & G space division:? proc/pool =? ? 8
>
>? ?  Current dimensions of program PWSCF are:
>? ?  Max number of different atomic species (ntypx) = 10
>? ?  Max number of k-points (npk) =? 40000
>? ?  Max angular momentum in pseudopotentials (lmaxx) =? 3
>? ?  Waiting for input...
>? ?  Reading input from stdin
>
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>? ?  from? read_namelists? : error #? ? ? ? 88
>? ? ? reading namelist system
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>? ?  stopping ...
>
>
> Now, I find it quite strange, because exactly same input and pseudos gave
> no
> error message in a local cluster (Intel Xeon machine).
> Can you help me?
> Thanks!
>
> Giacomo
>
>
>
>
> &CONTROL
>? ? calculation = "relax"
>? ? pseudo_dir = './'
>? ? outdir='./',
>? ? restart_mode="from_scratch",
>? ? prefix='ZnO_WZ',
>? ? tprnfor? ?  = .true.,
>? ? tstress? ?  = .true.,
>? ? wf_collect=.true.,
> /
> &SYSTEM
>? ? ibrav=? 4, celldm(1) =6.13821, celldm(3)=1.6023951, nat=? 4, ntyp= 2,
>? ? ecutwfc =105.0,? nbnd = 100,
>? ? input_dft='hse', nqx1 = 3, nqx2 = 3, nqx3 = 2,
>? ? x_gamma_extrapolation = .TRUE.
> /
> &ELECTRONS
>? ? diagonalization='david'
>? ? mixing_mode = 'plain'
>? ? mixing_beta = 0.7
>? ? conv_thr =? 1.0d-8
> /
> &IONS
>? ? ion_dynamics='bfgs'
> /
> ATOMIC_SPECIES
>? Zn? 65.38? ?  Zn_pz-12.cpi.UPF
>? O? 15.9994?  O.pz-mt.UPF
> ATOMIC_POSITIONS (crystal)
> Zn? ? ?  0.935705? ? ? ? 1.62101? ? ? ? 0.
> Zn? ? ?  1.87141? ? ? ?  0.? ? ? ? ? ?  2.5938
> O? ? ? ? 0.935705? ? ? ? 1.62101? ? ? ? 1.98114
> O? ? ? ? 1.87141? ? ? ?  0.? ? ? ? ? ?  4.57494
> K_POINTS (automatic)
> 9 9 6 0 0 0
>
>
>
> --
> Giacomo GIORGI
>
> Department of Chemical System Engineering,
> School of Engineering, The University of Tokyo
> 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
> E-mail: giacomo at tcl.t.u-tokyo.ac.jp
>
>
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From giannozz at democritos.it  Fri Jan 27 09:38:10 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 27 Jan 2012 09:38:10 +0100
Subject: [Pw_forum] Mysterious Matdyn Message(s)
In-Reply-To: <016001ccdc91$b66b3670$2341a350$@w2agz.com>
References: <016001ccdc91$b66b3670$2341a350$@w2agz.com>
Message-ID: <1327653490.9387.10.camel@fe12lx.fisica.uniud.it>

On Thu, 2012-01-26 at 17:19 -0800, W2AGZ wrote:

>      Max |d(i,j)-d*(j,i)| =  0.014209
>      Max |d(i,j)-d*(j,i)|/|d(i,j)|:  39.5291%

this signals tha the dynamical matrix, as calculated by the
phonon code, is not hermitian. Since hermiticity violation 
for very small elements of the dynamical matrices is not a
problem, both absolute and relative values of the violation 
are printed. In this case, it does not seem to be irrelevant.

The main reason for violation of hermiticity is insufficient
convergence of the phonon self-consistency. 

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From giannozz at democritos.it  Fri Jan 27 10:24:15 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 27 Jan 2012 10:24:15 +0100
Subject: [Pw_forum] problen to run q2r.x code.
In-Reply-To: <CAC2dNGE_XARSo5Mg-p1Wer9+Wp0NQgJek1FtHaGRsLuCHQnvZg@mail.gmail.com>
References: <CAC2dNGE_XARSo5Mg-p1Wer9+Wp0NQgJek1FtHaGRsLuCHQnvZg@mail.gmail.com>
Message-ID: <1327656255.9387.22.camel@fe12lx.fisica.uniud.it>

On Thu, 2012-01-26 at 21:51 +0530, bramha pandey wrote:

> file /home/espresso-4.2/phcal/si/dyn.G0 not found

> but i have a file of dyn.G not dyn.G0

the phonon code produces it if you perform a complete
phonon dispersion calculation. If you don't, or if you 
are running an old version of the ohonon code, you have 
to provide as input variables to q2r.x the information 
contained in file dyn.G0

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From torstein.fjermestad at kjemi.uio.no  Fri Jan 27 10:35:02 2012
From: torstein.fjermestad at kjemi.uio.no (Torstein Fjermestad)
Date: Fri, 27 Jan 2012 10:35:02 +0100
Subject: [Pw_forum]
 =?utf-8?q?NEB_in_QE_4=2E3=3A_NaN_values_of_some_of_the?=
 =?utf-8?q?_initially_generated_images?=
In-Reply-To: <3F570C0F-A3BB-48C1-8A30-379A47A2DFFF@democritos.it>
References: <82f95d4fe22509183285949879e861e0@ulrik.uio.no>
	<CAGCSmJR7bvXkmwkv93EvwA1vv_qfxQ+G7-r0FM0PO5SPDWdWow@mail.gmail.com>
	<d25f4a8d67e79d40208f0244f0a13271@ulrik.uio.no>
	<3F570C0F-A3BB-48C1-8A30-379A47A2DFFF@democritos.it>
Message-ID: <b0e33bc5b01897e277f245071e7dede5@ulrik.uio.no>

 Dear Prof. Giannozzi,

 Thanks for your suggestion.
 Using version 4.3.2 of Quantum Espresso solved the problem I had 
 generating the initial NEB images.
 With this e-mail I do not only want to thank you, but also make people 
 aware of the need to update to v 4.3.2 in case they encounter a similar 
 problem in the future. This is why I send this e-mail to pw_forum.

 Yours sincerely

 Torstein Fjermestad
 University of Oslo
 Norway
 
 

 On Tue, 17 Jan 2012 19:17:52 +0100, Paolo Giannozzi 
 <giannozz at democritos.it> wrote:
> On Jan 17, 2012, at 18:51 , Torstein Fjermestad wrote:
>
>>   Does anyone have further suggestions on how to solve this problem?
>
> first of all, please try v.4.3.2; it contains a few fixes for NEB wrt
> v.4.3
> === Doc/release-notes
> Fixed in 4.3.2 version
> [...]
>     * NEB: possible problem in parallel execution (if command-line
> arguments
>       are not available to all processors) avoided by broadcasting
> arguments
> [...]
> Fixed in 4.3.1 version
> [...]
>     * NEB + nonlocal exchange (DF-vdW) or hybrid functionals wasn't
> working
>     * NEB: incorrect parsing of intermediate images fixed
> ===
>
> P.
> ---
> Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


From giannozz at democritos.it  Fri Jan 27 10:44:52 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 27 Jan 2012 10:44:52 +0100
Subject: [Pw_forum] NEB in QE 4.3: NaN values of some of the
	initially	generated images
In-Reply-To: <b0e33bc5b01897e277f245071e7dede5@ulrik.uio.no>
References: <82f95d4fe22509183285949879e861e0@ulrik.uio.no>
	<CAGCSmJR7bvXkmwkv93EvwA1vv_qfxQ+G7-r0FM0PO5SPDWdWow@mail.gmail.com>
	<d25f4a8d67e79d40208f0244f0a13271@ulrik.uio.no>
	<3F570C0F-A3BB-48C1-8A30-379A47A2DFFF@democritos.it>
	<b0e33bc5b01897e277f245071e7dede5@ulrik.uio.no>
Message-ID: <1327657492.9387.37.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-01-27 at 10:35 +0100, Torstein Fjermestad wrote:

>  With this e-mail I do not only want to thank you, but also make people 
>  aware of the need to update to v 4.3.2 in case they encounter a similar 
>  problem in the future.

Thank you. Not only for a "similar" problem, but for ANY problem, 
should people upgrade to the latest "bugfix" releases (those with
N>0 in X.Y.N).

P./
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From giannozz at democritos.it  Fri Jan 27 10:51:22 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 27 Jan 2012 10:51:22 +0100
Subject: [Pw_forum] (no subject)
In-Reply-To: <CAJVAAvCs-xJQp7fL_r8BgW2su8w8B9NqxebwTVNvDme6=DPFMw@mail.gmail.com>
References: <CAJVAAvCs-xJQp7fL_r8BgW2su8w8B9NqxebwTVNvDme6=DPFMw@mail.gmail.com>
Message-ID: <1327657882.9387.45.camel@fe12lx.fisica.uniud.it>

On Thu, 2012-01-26 at 11:43 +0530, bhabya sahoo wrote:

> is there any space group implementation in espresso?

QE finds and uses the correct crystal symmetry; some
codes also make an attempt to guess what the symmetry 
group is. Currently you cannot specify a space group
and symmetry positions.

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From tone.kokalj at ijs.si  Fri Jan 27 12:17:45 2012
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 27 Jan 2012 12:17:45 +0100
Subject: [Pw_forum] Fwd:  xsf to pwscf input
In-Reply-To: <B843E112-1329-422F-880C-4C05B6402415@epfl.ch>
References: <2E52F489-4004-40F0-AC93-250BF1C24C6E@epfl.ch>
	<B843E112-1329-422F-880C-4C05B6402415@epfl.ch>
Message-ID: <1327663065.3895.15.camel@catalyst.ijs.si>

On Thu, 2012-01-26 at 10:51 +0100, Gabriele Sclauzero wrote:

> > Hello Payam,
> > 
> > 
> >     there is something doing that in the PWTK program by Tone
> > Kokalj, see http://pwtk.qe-forge.org/ and search for XSF in the
> > webpage.
> > You could search the corresponding code in the script files (should
> > be under pwtk/src/pwi.tcl, see
> > http://qe-forge.org/scm/browser.php?group_id=29) 
> > and adapt it to your needs. 

Indeed the pwtk can do it. How, see the attached pwtk's script; 
note that it requires pwtk,
http://qe-forge.org/frs/download.php/64/pwtk-0.99.1.tar.gz


Regards,

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html
-------------- next part --------------
#
# Usage:  pwtk xsf2pwi.pwtk xsfFile [celldm(1)]
#
# Purpose: converts XSF file into pw.x syntax
# 
# celldm(1) parameter is optional, if not given, will be set to 1.0
#

if { [llength $argv] < 2 } {
    puts stderr "Usage: pwtk [lindex $argv 0]  xsfFile  \[celldm(1)\]"
    exit 1
}
if { [llength $argv] == 3 } {
    set celldm1 [lindex $argv 2]
    if { ! [string is double $celldm1] } {
	puts stderr "*** user error: specified celldm(1) is not a number ***"
	exit 1
    }
} else {
    set celldm1 1.0
}
set xsfFile [lindex $argv 1]



#
# do the job
#

SYSTEM " celldm(1) = $celldm1 "
::pwtk::pwi::CELL_PARAMETERS_and_ATOMIC_POSITIONS_fromXSF $xsfFile

puts ""
puts [::pwtk::input::namelistGet SYSTEM]
puts [::pwtk::input::cardGet CELL_PARAMETERS]
puts [::pwtk::input::cardGet ATOMIC_POSITIONS] 

From tone.kokalj at ijs.si  Fri Jan 27 12:28:24 2012
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Fri, 27 Jan 2012 12:28:24 +0100
Subject: [Pw_forum] xsf to pwscf input
In-Reply-To: <CAND4gJE0ZmOOTBB-pH-JCz784jTeD53+JsPZxpM7fGH-9pEv2g@mail.gmail.com>
References: <CAND4gJE0ZmOOTBB-pH-JCz784jTeD53+JsPZxpM7fGH-9pEv2g@mail.gmail.com>
Message-ID: <1327663704.3895.19.camel@catalyst.ijs.si>

On Wed, 2012-01-25 at 18:54 -0600, Payam Norouzzadeh wrote:
> Hello QE users
> Is there any way,software,.. to convert xsf file formats(readable by
> Xcrysden) to input file for PWSCF( just crystal structure and atom
> coordinates)?

I noticed I have a shell script that does the job. Regards, Tone

-- 
Anton Kokalj
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
(tel: +386-1-477-3523 // fax:+386-1-477-3822)

Please, if possible, avoid sending me Word or PowerPoint attachments.
See:  http://www.gnu.org/philosophy/no-word-attachments.html
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From sbinnie at sissa.it  Fri Jan 27 13:47:25 2012
From: sbinnie at sissa.it (Simon Binnie)
Date: Fri, 27 Jan 2012 13:47:25 +0100
Subject: [Pw_forum] doubt on TDDFPT output
In-Reply-To: <CAM5Vcw_5hXWxVg=oLCGcbTfY5S3yiEVnCADOBgynUeJEvNPLwA@mail.gmail.com>
References: <CAM5Vcw_5hXWxVg=oLCGcbTfY5S3yiEVnCADOBgynUeJEvNPLwA@mail.gmail.com>
Message-ID: <op.v8qttbgsb4z88i@mugon.cm.sissa.it>

Hi there,

Yes you are right, this is a bug in the labelling of the output, the  
values printed are indeed the the 3_3 component. This will be fixed in the  
new version of QE.

Brgrds,

Simon

On Thu, 26 Jan 2012 12:10:33 +0100, Eduardo Ariel Menendez Proupin  
<eariel99 at gmail.com> wrote:

> Hi,
> I am rather confused with the TDDFPT output. In the turbo_spectrum run I
> pretend to obtain the polarizabilty \alpha_{33}, and I set the input as
>
> &lr_input
>   prefix='cnt_21',
>   outdir='./temp',
>   itermax=10000
>   itermax0=4000
>   extrapolation="osc"
>   epsil=0.0073495
>   units=1
>   start=0.d0
>   end=5.0d0
>   increment=0.01d0
>   start=0.0d0
>   ipol=3
>   verbosity=1
>
>
> In the output I get references only to the direction 1, as seen below
>
>      Program TDDFPT_PP v.4.3.1  starts on 11Jan2012 at 12: 6:32
> .........
>      Parallel version (MPI), running on    56 processors
>      R & G space division:  proc/pool =   56
>
>      Reading  10000 Lanczos steps for direction 1
>        3500 steps will be considered
> .....
>      Polarization direction:1
> ....
>     Static dipole polarizability Tensor:
>      chi_1_1=  0.523359728355224E+03 + i0.000000000000000E+00
>
>
> I check that the chi_1_1 values in the output are different the results
> when I set ipol=3. Is it a bug of the output or is somehing different to
> the \alpha_{33} that I want to obtain ?
>
> Thanks
>


-- 
Simon Binnie | Post Doc, Condensed Matter Sector
Scuola Internazionale di Studi Avanzati (SISSA)
Via Bonomea 256 | 34100 Trieste | sbinnie at sissa.it

From w2agz at w2agz.com  Fri Jan 27 18:30:54 2012
From: w2agz at w2agz.com (W2AGZ)
Date: Fri, 27 Jan 2012 09:30:54 -0800
Subject: [Pw_forum] Mysterious Matdyn Messages - More
Message-ID: <01f501ccdd19$722e4e60$568aeb20$@w2agz.com>

Thanks, Alex and Paolo,

 

I've tried replying to both of you (Alex, I've replied to separately through
his direct e-mail address) on the Forum through the "reply" feature of
Outlook, but for some reason it's not working.  I suspect it may be that I
have some old PW_Forum registrations littering things up.

 

Paolo, I found the portion of subroutine dyndiag you referred to, and it
should have been obvious to me that a non-hermitian issue is present.  This
may be due to the fact that the system, polysulfur nitride, I'm studying is
"quite" monoclinic, and the nq Monkhorst-Pack grid (2x2x2) I've used does
not sufficiently reflect this low symmetry.  Is there a "rule of thumb" for
setting the MP phonon grid for non-cubic systems?  For calculating band
structures and Fermi surfaces, even for low-symmetry metals, "cubic" grids
seem to work OK in pw.x, whatever the unit cell symmetry may be, and yield
expected results.  

 

-Paul Grant, W2AGZ Technologies, JPL/CalTech

 

 

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From giannozz at democritos.it  Fri Jan 27 18:41:41 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Fri, 27 Jan 2012 18:41:41 +0100
Subject: [Pw_forum] Mysterious Matdyn Messages - More
In-Reply-To: <01f501ccdd19$722e4e60$568aeb20$@w2agz.com>
References: <01f501ccdd19$722e4e60$568aeb20$@w2agz.com>
Message-ID: <1327686101.11042.5.camel@fe12lx.fisica.uniud.it>

On Fri, 2012-01-27 at 09:30 -0800, W2AGZ wrote:

> I found the portion of subroutine dyndiag you referred to, and it
> should have been obvious to me that a non-hermitian issue is present.
> This may be due to the fact that the system, polysulfur nitride, I?m
> studying is ?quite? monoclinic, and the nq Monkhorst-Pack grid (2x2x2)
> I?ve used does not sufficiently reflect this low symmetry.

I don't think this is a problem. The opposite is a source of
problems: when you have a grid that doesn't reflect the
symmetry of your crystal

>   Is there a ?rule of thumb? for setting the MP phonon grid for non-cubic systems? 

the longer the axis, the smaller the MP index, so that the
spacing along the three axis is approximately the same?

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From mrahimi93 at gmail.com  Fri Jan 27 21:50:18 2012
From: mrahimi93 at gmail.com (Mojtaba Rahimi)
Date: Sat, 28 Jan 2012 00:20:18 +0330
Subject: [Pw_forum] hubbard potential
Message-ID: <CADVDPC=gnj+J=FLO729NHr7Omvzf_hafaWyDPpUN0Azm585_+g@mail.gmail.com>

Dear all

I'm using QE to calculate U-hubbard for graphene. I've used 18 atom super
cell which has hexagonal structure, and linear response approach code,
which is written by Dr. cococcioni. I've modified cococcioni's shell
scripts which has been located at training part of QE website for graphene,
but I've confronted to some problem and I have some question about this cod
as well. I hope someone could answer me.

Thanks in advance

I prefer to propose my question at first:

   -

   As you know in graphene pz orbital which is perpendicular to graphene
   plane, and play the most important role in transport and optical
   properties, isn't localized, but that cod is written for localized orbital
   such as d, and f(at least from my knowledge). can I use this cod for
   graphene?
   -

   At atomic position file, the three first line specifies the parameter
   cell. Is it important that parameter cell to be cubic or it doesn't matter
   what it is?
   -

   In this approach we can just determine the on-site hubbard potential. f
   I tended to determine the nearest neighbor and next nearest neighbor
   hubbard potential, how would I do them by this code?

   And my problems are:
   -

   when I calculated the U for super cell dimension n=1-2, I obtained a
   negative U, which i think is wrong because U have to be positive.
   -

   When I changed the super cell dimension to n=3,... I encountered to a
   problem which I mentioned below. How can I over com to this problem. I
   would be grateful if somebody could help me.

*** glibc detected *** ./r.x: free(): invalid next size (normal):
0x09d29018 ***

======= Backtrace: =========

[0x82507db]

[0x825368b]

[0x81f4324]

[0x81f4299]

[0x805181d]

[0x804824a]

[0x823805d]

[0x8048131]

======= Memory map: ========

08048000-082c3000 r-xp 00000000 08:11 77561870
/home/nano2/mojtaba-work/plan/isolated-graphen/U-graphene/Ucalc/r.x

082c3000-082ce000 rwxp 0027b000 08:11 77561870
/home/nano2/mojtaba-work/plan/isolated-graphen/U-graphene/Ucalc/r.x

082ce000-088de000 rwxp 082ce000 00:00 0

09d23000-09d45000 rwxp 09d23000 00:00 0

55555000-556d2000 rwxp 55555000 00:00 0

55700000-55721000 rwxp 55700000 00:00 0

55721000-55800000 ---p 55721000 00:00 0

ffc05000-ffc2a000 rwxp 7ffffffd9000 00:00 0 [stack]

ffffe000-fffff000 r-xp ffffe000 00:00 0

forrtl: error (76): IOT trap signal


-- 
-----
Mojtaba Rahimi (Mr.)
Master of science -condensed matter,

Email: mrahimi93 at gmail.com

Phone:+ 98-9134515197
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From pandey.bramha at gmail.com  Sat Jan 28 15:11:40 2012
From: pandey.bramha at gmail.com (bramha pandey)
Date: Sat, 28 Jan 2012 19:41:40 +0530
Subject: [Pw_forum] help regarding fqha.x
Message-ID: <CAC2dNGGQKO-uaJ1m1orz7hzsmjPRi9=B0iScwFungG=jBGQT-g@mail.gmail.com>

Good evening to all QE users

 I wanted to calculate the thermodynamical property of system using QE.  i
was trying to use fqha.x code which was giving only free energy at each
temperature. but i require other properties of thermodynamic like cv,
internal energy etc. how can i get other properties of thermodynamic using
fqha.x.

Thanks in advanced for your valuable comments.



-- 
Thanks and Regards
Bramha Prasad Pandey
Assistant Professor (Electronics and Communication Engg)
GLA Group of Institutions, Mathura.
Ph. No. 08954143009
email id pandey.bramha at gmail.com
            bpglaitm at yahoo.co.in
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From konda.physics at gmail.com  Sat Jan 28 21:31:55 2012
From: konda.physics at gmail.com (Kondaiah Samudrala)
Date: Sun, 29 Jan 2012 02:01:55 +0530
Subject: [Pw_forum] Requesting for structural details
Message-ID: <CAKjMXpYvXxw8HNE14fZndw9kzJhFKmG8BnNdyuj3=KCrTBk8rw@mail.gmail.com>

Dear All,

I am working on layered type material which crystallizes in rhombohedral
structure with space group 166 ( ibrav =5). In the i/p file for VC-Relax, i
used the lattice parameters and angle as  celldm(1)=7.4870 and
celldm(4)=0.586005.

In the first step of the of the o/p file shows the basis vectors as
0.454970 -0.262677 0.850884
0.000000 0.525354 0.850884
-0.4504970 -0.262677 0.850884

After completing the VC-Relax i got the basis vectors as


CELL-PARAMETERS ( alat=7.4870)
0.441119855 -0.254680667 0.78874941
0.00000000   0.509361335 0.78874941
-0.441119855 -0.254680667 0.78874941

  with this o/p values, how can i calculate lattice vector and angle for my
material ( For orthorhombic and tetragonal structures i calculated lattice
parametrs successfully but i am not able to do this structure ).


i am requesting your favorable reply.

with regards
S.Appalakondaiah
PhD Scholar
University of Hyderabad
Hyderabad
India
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From giacsport at libero.it  Sun Jan 29 06:21:30 2012
From: giacsport at libero.it (giacsport at libero.it)
Date: Sun, 29 Jan 2012 06:21:30 +0100 (CET)
Subject: [Pw_forum] R: Re:  (no subject)
Message-ID: <14074710.7033621327814490912.JavaMail.defaultUser@defaultHost>

Thanks Layla. Got it!
Best,G


----Messaggio originale----

Da: lmartinsamos at gmail.com

Data: 26/01/2012 16.11

A: "giacsport at libero.it"<giacsport at libero.it>

Cc: <pw_forum at pwscf.org>

Ogg: Re: [Pw_forum] (no subject)



Dear Giacomo, you are trying to make an EXX calculation did you compile addig by hand in the make.sys file (DFLAGS and FDFLAGS) the -DEXX flag? 

bests

Layla

2012/1/26 giacsport at libero.it <giacsport at libero.it>

Dear All,

              I have installed the 4.3.2 version of pwscf on the CINECA sp6

machine. The compilation was successful.

Now I am trying to make some benchmark calculations with some pseudos I

previously used and well tested.

As far as I launch the job whose input you find below, I get the "usual" error

message regarding the namelist error, i.e.





     Program PWSCF v.4.3.2      starts on 26Jan2012 at 11:22:14



     Parallel version (MPI), running on     8 processors

     R &amp; G space division:  proc/pool =    8



     Current dimensions of program PWSCF are:

     Max number of different atomic species (ntypx) = 10

     Max number of k-points (npk) =  40000

     Max angular momentum in pseudopotentials (lmaxx) =  3

     Waiting for input...

     Reading input from stdin





%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     from  read_namelists  : error #        88

      reading namelist system



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%



     stopping ...





Now, I find it quite strange, because exactly same input and pseudos gave no

error message in a local cluster (Intel Xeon machine).

Can you help me?

Thanks!



Giacomo









&amp;CONTROL

    calculation = "relax"

    pseudo_dir = './'

    outdir='./',

    restart_mode="from_scratch",

    prefix='ZnO_WZ',

    tprnfor     = .true.,

    tstress     = .true.,

    wf_collect=.true.,

/

&amp;SYSTEM

    ibrav=  4, celldm(1) =6.13821, celldm(3)=1.6023951, nat=  4, ntyp= 2,

    ecutwfc =105.0,  nbnd = 100,

    input_dft='hse', nqx1 = 3, nqx2 = 3, nqx3 = 2,

    x_gamma_extrapolation = .TRUE.

/

&amp;ELECTRONS

    diagonalization='david'

    mixing_mode = 'plain'

    mixing_beta = 0.7

    conv_thr =  1.0d-8

/

&amp;IONS

    ion_dynamics='bfgs'

/

ATOMIC_SPECIES

 Zn  65.38     Zn_pz-12.cpi.UPF

  O  15.9994   O.pz-mt.UPF

ATOMIC_POSITIONS (crystal)

Zn       0.935705        1.62101        0.

Zn       1.87141         0.             2.5938

O        0.935705        1.62101        1.98114

O        1.87141         0.             4.57494

K_POINTS (automatic)

9 9 6 0 0 0







--

Giacomo GIORGI



Department of Chemical System Engineering,

School of Engineering, The University of Tokyo

7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan

E-mail: giacomo at tcl.t.u-tokyo.ac.jp





_______________________________________________

Pw_forum mailing list

Pw_forum at pwscf.org

http://www.democritos.it/mailman/listinfo/pw_forum







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From avallabh at purdue.edu  Sun Jan 29 07:30:36 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Sun, 29 Jan 2012 01:30:36 -0500 (EST)
Subject: [Pw_forum] query on e-ph tutorial
Message-ID: <1850128893.310576.1327818636195.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear users,


            I have a couple of questions regarding the e-ph calculation.
1. Are the e-ph matrix element (g), coefficients lambda and gamma symmetric with respect to the phonon wave vector (q)? I mean will calculating those quantities across the IBZ sufficient to obtain the values thru out the entire BZ? 

2. In the tutorial on for calculating the "Electron-phonon interaction coefficients" on the website of QE (http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_advph.html), in step 3 it was mentioned to perform an nscf calculation to prepare k and k+q wavefunctions with the keyword "calculation='phonon'". I tried to run the same, but it was termintated with the message that calculation "phonon" is not allowed. Are there any typos in this part of the example.

-bash-3.2$ pw.x < al.nscf.in

     Program PWSCF v.4.3.2      starts on 29Jan2012 at  1:21:57

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org",
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO

     Parallel version (MPI), running on     1 processors

     Current dimensions of program PWSCF are:
     Max number of different atomic species (ntypx) = 10
     Max number of k-points (npk) =  40000
     Max angular momentum in pseudopotentials (lmaxx) =  3
     Waiting for input...
     Reading input from stdin

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from  control_checkin     : error #         1
      calculation 'phonon' not allowed
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0



Thanks
Ajit

From matteo at umn.edu  Sun Jan 29 16:32:43 2012
From: matteo at umn.edu (Matteo Cococcioni)
Date: Sun, 29 Jan 2012 09:32:43 -0600
Subject: [Pw_forum] hubbard potential
In-Reply-To: <CADVDPC=gnj+J=FLO729NHr7Omvzf_hafaWyDPpUN0Azm585_+g@mail.gmail.com>
References: <CADVDPC=gnj+J=FLO729NHr7Omvzf_hafaWyDPpUN0Azm585_+g@mail.gmail.com>
Message-ID: <CAMZASgE2_f=OZnuqXAgH3HKOOt0-SOrYe9y=cAX6G3ALOdT2ZQ@mail.gmail.com>

Dear Mojtaba,

I wil try to answer your questions one by one.

On Fri, Jan 27, 2012 at 2:50 PM, Mojtaba Rahimi <mrahimi93 at gmail.com> wrote:
> Dear all
>
> I'm using QE to calculate U-hubbard for graphene. I've used 18 atom super
> cell which has hexagonal structure, and linear response approach code, which
> is written by Dr. cococcioni. I've modified cococcioni's shell scripts which
> has been located at training part of QE website for graphene, but I've
> confronted to some problem and I have some question about this cod as well.
> I hope someone could answer me.
>
> Thanks in advance
>
> I prefer to propose my question at first:
>
> As you know in graphene pz orbital which is perpendicular to graphene plane,
> and play the most important role in transport and optical properties, isn't
> localized, but that cod is written for localized orbital such as d, and f(at
> least from my knowledge). can I use this cod for graphene?

in principle yes. I'm not sure why you want to compute the U for
graphene. have you tried to
see if U has any effect on the actual calculation?

>
> At atomic position file, the three first line specifies the parameter cell.
> Is it important that parameter cell to be cubic or it doesn't matter what it
> is?
>

in principle it is not necessary the cell to be cubic. it should work
with any cell.

> In this approach we can just determine the on-site hubbard potential. f I
> tended to determine the nearest neighbor and next nearest neighbor hubbard
> potential, how would I do them by this code?
>

if you mean intersite interactions those come for free from the
off-diagonal elements of the interaction matrix
(of which U is the diagonal).

> And my problems are:
>
> when I calculated the U for super cell dimension n=1-2, I obtained a
> negative U, which i think is wrong because U have to be positive.
>

yes it should not be the case. but I am not able to tell you what the
problem is.

> When I changed the super cell dimension to n=3,... I encountered to a
> problem which I mentioned below. How can I over com to this problem. I would
> be grateful if somebody could help me.
>

seems like a problem of memory. probably you should increase the size
of some arrays. this is my guess.

hope this helps.

Matteo



> *** glibc detected *** ./r.x: free(): invalid next size (normal): 0x09d29018
> ***
>
> ======= Backtrace: =========
>
> [0x82507db]
>
> [0x825368b]
>
> [0x81f4324]
>
> [0x81f4299]
>
> [0x805181d]
>
> [0x804824a]
>
> [0x823805d]
>
> [0x8048131]
>
> ======= Memory map: ========
>
> 08048000-082c3000 r-xp 00000000 08:11 77561870
> /home/nano2/mojtaba-work/plan/isolated-graphen/U-graphene/Ucalc/r.x
>
> 082c3000-082ce000 rwxp 0027b000 08:11 77561870
> /home/nano2/mojtaba-work/plan/isolated-graphen/U-graphene/Ucalc/r.x
>
> 082ce000-088de000 rwxp 082ce000 00:00 0
>
> 09d23000-09d45000 rwxp 09d23000 00:00 0
>
> 55555000-556d2000 rwxp 55555000 00:00 0
>
> 55700000-55721000 rwxp 55700000 00:00 0
>
> 55721000-55800000 ---p 55721000 00:00 0
>
> ffc05000-ffc2a000 rwxp 7ffffffd9000 00:00 0 [stack]
>
> ffffe000-fffff000 r-xp ffffe000 00:00 0
>
> forrtl: error (76): IOT trap signal
>
>
>
> --
> -----
> Mojtaba Rahimi (Mr.)
> Master of science -condensed matter,
>
> Email: mrahimi93 at gmail.com
>
> Phone:+ 98-9134515197
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Matteo Cococcioni
Department of Chemical Engineering and Materials Science,
University of Minnesota
421 Washington Av. SE
Minneapolis, MN 55455
Tel. +1 612 624 9056 ? ?Fax +1 612 626 7246

From giannozz at democritos.it  Sun Jan 29 19:32:24 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Sun, 29 Jan 2012 19:32:24 +0100
Subject: [Pw_forum] query on e-ph tutorial
In-Reply-To: <1850128893.310576.1327818636195.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <1850128893.310576.1327818636195.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <1E6B6E47-7561-4094-BFF3-1973662D0282@democritos.it>


On Jan 29, 2012, at 7:30 , Ajit Vallabhaneni wrote:

> I mean will calculating those quantities across the IBZ sufficient
> to obtain the values thru out the entire BZ?

I don't think so: at a given q, you can sum over the IBZ of the small
group of q and symmetrize with the small group of q, or else, if you
sum over the IBZ of the symmetry group, you will need the unsymmetrized
quantity for all q vectors in the star of q.

> 2. In the tutorial on for calculating the "Electron-phonon  
> interaction coefficients"
> on the website of QE (http://www.fisica.uniud.it/~giannozz/QE- 
> Tutorial/tutorial_advph.html)

it is not "the website of QE": it is my website, where I keep a copy  
of some
files often used in tutorials. Unfortunately that part is obsolete.  
You should
look at the example 07.

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From flux_ray12 at 163.com  Mon Jan 30 09:04:07 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Mon, 30 Jan 2012 16:04:07 +0800 (CST)
Subject: [Pw_forum] help regarding fqha.x
In-Reply-To: <CAC2dNGGQKO-uaJ1m1orz7hzsmjPRi9=B0iScwFungG=jBGQT-g@mail.gmail.com>
References: <CAC2dNGGQKO-uaJ1m1orz7hzsmjPRi9=B0iScwFungG=jBGQT-g@mail.gmail.com>
Message-ID: <7de5a559.c23d.1352da4778a.Coremail.flux_ray12@163.com>

You can use the QHA module in QE, which gives you more detailed result.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 

At 2012-01-28 22:11:54,"bramha pandey" <pandey.bramha at gmail.com> wrote:

Good evening to all QE users

 I wanted to calculate the thermodynamical property of system using QE.  i was trying to use fqha.x code which was giving only free energy at each temperature. but i require other properties of thermodynamic like cv, internal energy etc. how can i get other properties of thermodynamic using fqha.x.

Thanks in advanced for your valuable comments.



--
Thanks and Regards
Bramha Prasad Pandey
Assistant Professor (Electronics and Communication Engg)
GLA Group of Institutions, Mathura.
Ph. No. 08954143009
email id pandey.bramha at gmail.com
            bpglaitm at yahoo.co.in
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From asei_aefla at yahoo.com  Mon Jan 30 13:07:56 2012
From: asei_aefla at yahoo.com (Asei Aefla)
Date: Mon, 30 Jan 2012 04:07:56 -0800 (PST)
Subject: [Pw_forum] exit status = 129
Message-ID: <1327925276.47617.YahooMailNeo@web113720.mail.gq1.yahoo.com>

Dear QE users,
I successfully performed a scf calculation on a bulk-alloy system or nonperiodic system. But sometimes I took following messages running
phonon calculation. Could you help me about meaning of this exit code?
"Error condition encountered during test: exit status = 129"


Thank you in advance,

Assei Aefla
ITU
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From giannozz at democritos.it  Mon Jan 30 13:12:54 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Mon, 30 Jan 2012 13:12:54 +0100
Subject: [Pw_forum] exit status = 129
In-Reply-To: <1327925276.47617.YahooMailNeo@web113720.mail.gq1.yahoo.com>
References: <1327925276.47617.YahooMailNeo@web113720.mail.gq1.yahoo.com>
Message-ID: <61067C9B-9C5E-40F3-A1F1-75D6581203E2@democritos.it>


On Jan 30, 2012, at 13:07 , Asei Aefla wrote:

> "Error condition encountered during test: exit status = 129"

it means close to nothing: look into the output

P.
---
Paolo Giannozzi, Dept of Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222





From avallabh at purdue.edu  Mon Jan 30 15:47:52 2012
From: avallabh at purdue.edu (Ajit Vallabhaneni)
Date: Mon, 30 Jan 2012 09:47:52 -0500 (EST)
Subject: [Pw_forum] query on e-ph tutorial
In-Reply-To: <1E6B6E47-7561-4094-BFF3-1973662D0282@democritos.it>
Message-ID: <651145446.313230.1327934872664.JavaMail.root@mailhub016.itcs.purdue.edu>

Dear Paolo,

                Sorry for sending my response to your personal email. I didn't see it before.Here is my question.

             I tried example 7 with the same parameters given. But the al.elph.in (with nq1=nq2=nq3=4) was terminated with the following message: 


Band Structure Calculation
     Davidson diagonalization with overlap

 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from cdiaghg : error #        19
     diagonalization (ZHEGV*) failed
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...


        Is this because of the small mesh size (16x16x16)?

Thanks
Ajit

From tribhuwan.physics at gmail.com  Mon Jan 30 16:06:19 2012
From: tribhuwan.physics at gmail.com (Tribhuwan Pandey)
Date: Mon, 30 Jan 2012 20:36:19 +0530
Subject: [Pw_forum] phonon life time
Message-ID: <CACKvTSP3ENJ9WYHhUawWSq9AimiVjGUWF+iDjG3GcKwJjowouA@mail.gmail.com>

Hi all,
          I am calculating phonon life time using D3 code.So i want to know
that whether those life time are in reciprocal space or in real space.



any help in this regard will be appreciated



-- 

Best
Tribhuwan
*IISC


With Regards
Tribhuwan Pandey
Research Scholar
Indian Institute of Science, Bangalore, India



*
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From deyulu at yahoo.com  Mon Jan 30 17:25:42 2012
From: deyulu at yahoo.com (Deyu Lu)
Date: Mon, 30 Jan 2012 08:25:42 -0800 (PST)
Subject: [Pw_forum] multiple-manifold DFT+U on a single atom
Message-ID: <1327940742.66324.YahooMailNeo@web125504.mail.ne1.yahoo.com>

Dear all:
???????? I'm interested in doing DFT+U calculation on a single atom with multiple
manifolds, and I'm wondering whether the code is available in some developmental stage.
To be more specific, I'm looking at small Ce clusters and want to understand how linear 

response U of Ce changes according to the local chemical environment, e.g., valence state
and spin state, etc. If I use only Ce 4f, I found chi0 and chi matrices don't obey sum rule,
and in some cases, an eigenmode of chi0 and chi can be clearly identified corresponding to 

a uniform potential perturbation with a small negative eigenvalue. This means there is an exchange

of the induced charge density between the 4f manifold and the background. 

By looking at PDOS, a non-negligible? 4f-5d and 4f-6s hybridization are found right at LUMO, 

however, the hybridization with nearby O 2p seems to be weaker. In order to eliminate this error 

during the chi0 and chi inversion and
obtain more accurate estimate on U, it makes sense to me to add Ce 5d and 6s. This modification
is not quite obvious in set_hubbard_l.f90 and tabd.f90, since these subroutines assume one channel
per atom type.

???????? Best regards,
???????? Deyu Lu
************************************************
Deyu Lu
Assistant Physicist, Theory & Computation Group
the Center for Functional Nanomaterials
Rm 1002, Building 735, Brookhaven National Lab
Upton, NY, 11973
webpage: http://www.bnl.gov/cfn/people/Deyu_Lu.asp ************************************************
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From himm0013 at umn.edu  Mon Jan 30 22:40:56 2012
From: himm0013 at umn.edu (Burak Himmetoglu)
Date: Mon, 30 Jan 2012 15:40:56 -0600
Subject: [Pw_forum] multiple-manifold DFT+U on a single atom
In-Reply-To: <1327940742.66324.YahooMailNeo@web125504.mail.ne1.yahoo.com>
References: <1327940742.66324.YahooMailNeo@web125504.mail.ne1.yahoo.com>
Message-ID: <CAH55yVS-crmWAo1J3xKhs5C+kYae4w5aNMi0G8RdsP34adKENA@mail.gmail.com>

Hi Deyu,

I have recently implemented a capability in the code that allows for using
Hubbard U on two orbital manifolds per atom (e.g. d and s states of
transition metals). If you are interested I can send you the code.

Regards

Burak Himmetoglu
Post-doctoral associate
Department of Chemical Engineering and Materials Sciecne
University of Minnesota,
421 Washington Av. SE
Minneapolis, MN 55455

On Mon, Jan 30, 2012 at 10:25 AM, Deyu Lu <deyulu at yahoo.com> wrote:

> Dear all:
>          I'm interested in doing DFT+U calculation on a single atom with
> multiple
> manifolds, and I'm wondering whether the code is available in some
> developmental stage.
> To be more specific, I'm looking at small Ce clusters and want to
> understand how linear
> response U of Ce changes according to the local chemical environment,
> e.g., valence state
> and spin state, etc. If I use only Ce 4f, I found chi0 and chi matrices
> don't obey sum rule,
> and in some cases, an eigenmode of chi0 and chi can be clearly identified
> corresponding to
> a uniform potential perturbation with a small negative eigenvalue. This
> means there is an exchange
> of the induced charge density between the 4f manifold and the background.
> By looking at PDOS, a non-negligible  4f-5d and 4f-6s hybridization are
> found right at LUMO,
> however, the hybridization with nearby O 2p seems to be weaker. In order
> to eliminate this error
> during the chi0 and chi inversion and
> obtain more accurate estimate on U, it makes sense to me to add Ce 5d and
> 6s. This modification
> is not quite obvious in set_hubbard_l.f90 and tabd.f90, since these
> subroutines assume one channel
> per atom type.
>
>          Best regards,
>          Deyu Lu
>
> ************************************************
> Deyu Lu
> Assistant Physicist, Theory & Computation Group
> the Center for Functional Nanomaterials
> Rm 1002, Building 735, Brookhaven National Lab
> Upton, NY, 11973
> webpage: http://www.bnl.gov/cfn/people/Deyu_Lu.asp
> ************************************************
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
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From flux_ray12 at 163.com  Tue Jan 31 06:23:36 2012
From: flux_ray12 at 163.com (GAO Zhe)
Date: Tue, 31 Jan 2012 13:23:36 +0800 (CST)
Subject: [Pw_forum] query on e-ph tutorial
In-Reply-To: <651145446.313230.1327934872664.JavaMail.root@mailhub016.itcs.purdue.edu>
References: <651145446.313230.1327934872664.JavaMail.root@mailhub016.itcs.purdue.edu>
Message-ID: <6521c2ce.4291.1353237ddb4.Coremail.flux_ray12@163.com>

This problem happens during diagonalize the matrix. At least there are two methods to solve this problem: Firstly, changing the diagonalization method to CG, which requires to modify the PH code; secondly, increasing empty bands by "nbnd" parameter in the input file of pw.x.


--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
 



At 2012-01-30 22:48:10,"Ajit Vallabhaneni" <avallabh at purdue.edu> wrote:
>Dear Paolo,
>
>                Sorry for sending my response to your personal email. I didn't see it before.Here is my question.
>
>             I tried example 7 with the same parameters given. But the al.elph.in (with nq1=nq2=nq3=4) was terminated with the following message: 
>
>
>Band Structure Calculation
>     Davidson diagonalization with overlap
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     from cdiaghg : error #        19
>     diagonalization (ZHEGV*) failed
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>     stopping ...
>
>
>        Is this because of the small mesh size (16x16x16)?
>
>Thanks
>Ajit
>_______________________________________________
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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From tribhuwan.physics at gmail.com  Tue Jan 31 05:14:45 2012
From: tribhuwan.physics at gmail.com (Tribhuwan Pandey)
Date: Tue, 31 Jan 2012 09:44:45 +0530
Subject: [Pw_forum] phonon life time
In-Reply-To: <80916151-BBE6-437B-B1F2-8C9B0E0B3A9B@sissa.it>
References: <CACKvTSP3ENJ9WYHhUawWSq9AimiVjGUWF+iDjG3GcKwJjowouA@mail.gmail.com>
	<80916151-BBE6-437B-B1F2-8C9B0E0B3A9B@sissa.it>
Message-ID: <CACKvTSNg65RfreS2oChA4MNE_rSHsu10XJqh8x3jVj5NAirrNA@mail.gmail.com>

Dear Professor Baroni

Sorry if my question is so trivial. 
I think Reciprocal space is Fourier transform of the real space so as theIFCs.
When we calculate Harmonic IFCs there is  a command called q2r.x which converts reciprocal space IFCs to real space by taking Fourier Transform .
But in the case of harmonic IFCs this is not the case. For my work i need an-harmonic IFCs  in real space that whys i wanted to know whether Quantum espresso calculates those in real space or reciprocal space. 



Thanks a lot for your response





Regards
Tribhuwan








On Tue, Jan 31, 2012 at 7:02 AM, Stefano Baroni <baroni at sissa.it> wrote:
I beg your pardon? What is the difference between a "real-space" and a "reciprocal-space" lifetime? SB

--
Stefano Baroni, Trieste -- swift message written and sent on the go

On 30/gen/2012, at 16:06, Tribhuwan Pandey <tribhuwan.physics at gmail.com> wrote:

> Hi all,
>           I am calculating phonon life time using D3 code.So i want to know that whether those life time are in reciprocal space or in real space.
> 
> 
> 
> any help in this regard will be appreciated
> 
> 
> 
> -- 
> 
> Best
> Tribhuwan
> IISC 
> 
> 
> With Regards
> Tribhuwan Pandey
> Research Scholar
> Indian Institute of Science, Bangalore, India
> 
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum



-- 

With Regards
Tribhuwan Pandey
Research Scholar
Indian Institute of Science, Bangalore, India




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From saishi at inbox.ru  Tue Jan 31 10:27:43 2012
From: saishi at inbox.ru (=?UTF-8?B?0KHQtdGA0LPQtdC5INCd0LjQutC+0LvQsNC10LI=?=)
Date: Tue, 31 Jan 2012 13:27:43 +0400
Subject: [Pw_forum] =?utf-8?q?BEC_from_DFPT?=
Message-ID: <E1RsA07-0001ul-HD.saishi-inbox-ru@f250.mail.ru>

Dear all,
I am trying to calculate Born effective charges from DFTP for the spin-polarized system. However, these systems must be treated as metallic (scf-calculation with occupations='smearing').
The problem is that ph.x complains about my calculation, but the system has an insulator behavior.
Are there any methods to solve this problem?
 
Sincerely,
Sergey Nikolaev
Department of theoretical physics and applied mathematics
Ural Federal University
Yekaterinburg, Russia

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From vv0210 at gmail.com  Tue Jan 31 15:05:18 2012
From: vv0210 at gmail.com (Vikas Varshney)
Date: Tue, 31 Jan 2012 09:05:18 -0500
Subject: [Pw_forum] Help with atomic relaxation (Issue with convergence)
In-Reply-To: <4F1ED8DD.2010506@mater.unimib.it>
References: <20120123172551.pb563vaikg8wkwg8@webmail.sic.rm.cnr.it>
	<EB81D8BA-FBC3-4DB8-8F49-4ADE2621C641@democritos.it>
	<CAHvkJPP0Qyaj8S34kxaeWRtEeNZJR_L9rSOckywWJjkihU4OUQ@mail.gmail.com>
	<4F1E6FFF.1060605@mater.unimib.it>
	<CAHvkJPNTEd8Hd0x1p2sep=0LCzr323z8MWh1feFS+3Pt5zDjJw@mail.gmail.com>
	<4F1ECFD7.8070406@mater.unimib.it>
	<CAHvkJPP50wSmJQDhOmo5_wqUWm4NHrHNN4nw3r2FkiNHcWvGyA@mail.gmail.com>
	<4F1ED8DD.2010506@mater.unimib.it>
Message-ID: <CAHvkJPOAp0EiE0zJ6AO2cSfs1iC4hcPR3tRatvjO7pcQytUo0g@mail.gmail.com>

Dear Guido, Paolo, Giuseppe
I just wanted to tell you guys (and put this in the forum) that gaussian
smearing with low convergence (1e-5) worked for Ni layer relaxation on
Al2O3 slab as first step (with K meshing of 4 4 1). Later, I increased
the convergence to 1e-8 and the runs finished successfully as well. Thanks
for all your help and guidance.

Best Regards,
Vikas
Getting ready for next set of simulations.
On Tue, Jan 24, 2012 at 11:14 AM, Guido Fratesi <fratesi at mater.unimib.it>wrote:

>  I have not tired gaussian smearing. I will try that as well. I will also
>> reduce the k-mesh style to get to final coordinates quicker.
>> How do I specify larger broadening. Sorry but I am new to QE so please
>> help here.
>>
>
> sorry, it's the parameter called "degauss"
>
>
> Yes you are very true to say that Ni Atoms are a bit closer than their
>> respective positions in crystal. As I wanted to lay down a Ni layer of
>> Al2O3, I started with 1 1 1 plane of Ni (hexagonal symmetry) with to put
>> on top of Al2O3 (hexagonal symmetry). However as you see below, the unit
>> cell of Al2O3 is a little smaller than that of Ni, so, I compressed the
>> Ni atoms a little bit so as to fit them in Al2O3 geometry.
>> Al2O3 a cell dimension = 4.789471
>> Ni a cell dimension (along 1 1 1) plane = 4.951255
>>
>
> well, not that much indeed. Still some buckling could be expected, as you
> say below.
>
>
> I could now very well see that is this could be a source of the problem.
>> In that case, what do you suggest? What about moving 2 of the 4 atoms in
>> z direction so that distance between the atoms becomes similar to ~ what
>> it is in bulk crystal. I had nspin=2 (default) in my calculations.
>>
>
> in the input posted to the forum there was no spin polarization. The
> default is nspin=1.
>
> Regards,
> Guido
>
>  Should I change it to nspin = 1?
>> Thank you very much for the insights.
>> Best Regards,
>> Vikas
>> On Tue, Jan 24, 2012 at 10:35 AM, Guido Fratesi <fratesi at mater.unimib.it
>>  <mailto:fratesi at mater.unimib.**it <fratesi at mater.unimib.it>>> wrote:
>>
>>    Have you tried with gaussian smearing, by chance? In a test I was
>>    making sometimes ago with TiO2 slabs, that was more easy to converge
>>    than the other choices. A larger broadening could also help,
>>    especially to get an initial configuration/charge to be refined
>>    later, and you might want to reduce the kpoint mesh to speed up your
>>    tests. Ni atoms look a bit (not too much) close which could be also
>>    source of problems: is the Ni overlayer compressed with respect to a
>>    free-standing Ni layer in 2D? Finally, I guess you will be
>>    interested in spin-polarized calculations at the end.
>>    I'd be curious about what solves the problem, eventually.
>>    Guido
>>
>>    Il 01/24/2012 03:48 PM, Vikas Varshney ha scritto:
>>
>>        Dear Guido,
>>        Sorry for the confusion, actually when I was copy pasting the
>>        data on
>>        the email from my input file, 3 lines got deleted by error.
>>        Number of
>>        atoms are actually 34. 30 Al203 atoms for a unit cell and 4 Ni
>>        atoms.
>>        THe full positions are below.The bold lines were missing before.
>>        Thanks
>>        for looking into this.
>>        ATOMIC_POSITIONS angstrom
>>        O        1.473346033   0.017326072   3.218609176
>>        O 3.863581042 <tel:3.863581042>   1.378379317 7.574956508
>>        <tel:7.574956508>
>>        O        1.513480866   2.829876285  11.933514340
>>        O       -0.751677351   1.267293591   3.218609163
>>        O        1.663968734   2.656771683   7.574956486
>>        O       -0.812749430   4.043578468  11.933514157
>>        O        1.673065193   2.863185205   3.218609361
>>        O        1.656654190   0.112656124   7.574956554
>>        O       -0.700731568   1.422153909  11.933514350
>>        O        3.298048338   0.005706615   9.773211485
>>        O        0.927961928   1.382600916   1.089494747    0   0   0
>>        O       -1.464820834   2.766734881   5.396064047
>>        O       -1.653964847   2.853342545   9.773211296
>>        O 3.128121670 <tel:3.128121670>   0.112338146   1.089494747    0
>>           0   0
>>        O        0.731082457   1.495864856   5.396064158
>>        *O        0.750650394   1.288758309   9.773211044
>>
>>        O 3.128121627 <tel:3.128121627>   2.652863759   1.089494747    0
>>
>>           0   0
>>        O        0.733736896   4.033006936   5.396064408
>>        *Al      -0.000000812   0.000001493   4.556157709
>>
>>        Al 2.394734647 <tel:2.394734647>   1.382602298   8.876166342
>>        Al       0.000000000   2.765201880   0.243870515    0   0   0
>>        Al       0.000000000   0.000000000   1.935118618    0   0   0
>>        Al 2.394734540 <tel:2.394734540>   1.382602230   6.225550857
>>
>>        Al      -0.000000007   2.765202952  10.790402310
>>        Al      -0.000000362   0.000002278   8.430662634
>>        Al 2.394735475 <tel:2.394735475>   1.382602563  12.021576409
>>
>>        Al      -0.000000581   2.765202130   4.047340256
>>        Al       0.000000075   0.000002190  11.054412333
>>        Al 2.394734840 <tel:2.394734840>   1.382601177 2.258435418
>>        <tel:2.258435418>
>>
>>        Al      -0.000000323   2.765202460   6.730673987
>>           Ni      -0.016734       -0.025515       15.297379
>>           Ni       1.180634       -2.099417       15.297379
>>           Ni      -1.214101       -2.099417       15.297379
>>           Ni      -2.411469       -0.025515       15.297379
>>        Best Regards,
>>        Vikas
>>
>>        On Tue, Jan 24, 2012 at 3:46 AM, Guido Fratesi
>>        <fratesi at mater.unimib.it <mailto:fratesi at mater.unimib.**it<fratesi at mater.unimib.it>
>> >
>>        <mailto:fratesi at mater.unimib._**_it
>>
>>        <mailto:fratesi at mater.unimib.**it <fratesi at mater.unimib.it>>>>
>> wrote:
>>
>>            Have you checked the input is read correctly? Apparently,
>>        the number of
>>            atoms listed (31) does not correspond to "nat" (ii)
>>            Guido
>>
>>            Il 01/23/2012 06:51 PM, Vikas Varshney ha scritto:
>>         > &CONTROL
>>         >                   calculation = 'relax' ,
>>         >                  restart_mode = 'from_scratch' ,
>>         >                    wf_collect = .true. ,
>>         >                        outdir = './' ,
>>         >                    pseudo_dir =
>>        '/lustre/app2/espresso/pseudo/**__' ,
>>
>>         >                       disk_io = 'default' ,
>>         >                     verbosity = 'high' ,
>>         >   /
>>         > &SYSTEM
>>         >                         ibrav = 0,
>>         >                      celldm(1)=   9.050787,
>>         >                           nat = 34,
>>         >                          ntyp = 3,
>>         >                       ecutwfc = 55 ,
>>         >                       ecutrho = 550 ,
>>         >                   occupations = 'smearing' ,
>>         >                       degauss = 0.01 ,
>>         >                      smearing = 'methfessel-paxton' ,
>>         >                  nosym   = .true. ,
>>         >                  nosym_evc = .true. ,
>>         >   /
>>         > &ELECTRONS
>>         >                      conv_thr = 1.0D-4 ,
>>         >               diagonalization = 'david' ,
>>         >                   mixing_mode = 'local-TF' ,
>>         >                   mixing_beta = 0.1 ,
>>         >          electron_maxstep = 500 ,
>>         >   /
>>         > &IONS
>>         >                  ion_dynamics = 'bfgs' ,
>>         >                 ion_positions = 'from_input' ,
>>         >   /
>>         > CELL_PARAMETERS hexagonal
>>         >       1.000000000    0.000000000    0.000000000
>>         >       0.500000000    0.866025000    0.000000000
>>         >       0.000000000    0.000000000    10.824313000
>>         > ATOMIC_SPECIES
>>         >      O   15.99940  O.pbe-van_ak.UPF
>>         >     Al   26.98154  Al.pbe-n-van.UPF
>>         >     Ni   58.69340  Ni.pbe-nd-rrkjus.UPF
>>         > ATOMIC_POSITIONS angstrom
>>         > O        1.473346033   0.017326072   3.218609176
>>         > O 3.863581042 <tel:3.863581042> <tel:3.863581042
>>
>>        <tel:3.863581042>>   1.378379317 7.574956508 <tel:7.574956508>
>>        <tel:7.574956508 <tel:7.574956508>>
>>
>>
>>         > O        1.513480866   2.829876285  11.933514340
>>         > O       -0.751677351   1.267293591   3.218609163
>>         > O        1.663968734   2.656771683   7.574956486
>>         > O       -0.812749430   4.043578468  11.933514157
>>         > O        1.673065193   2.863185205   3.218609361
>>         > O        1.656654190   0.112656124   7.574956554
>>         > O       -0.700731568   1.422153909  11.933514350
>>         > O        3.298048338   0.005706615   9.773211485
>>         > O        0.927961928   1.382600916   1.089494747    0   0   0
>>         > O       -1.464820834   2.766734881   5.396064047
>>         > O       -1.653964847   2.853342545   9.773211296
>>         > O 3.128121670 <tel:3.128121670> <tel:3.128121670
>>
>>        <tel:3.128121670>>   0.112338146   1.089494747    0
>>
>>               0   0
>>         > O        0.731082457   1.495864856   5.396064158
>>         > Al      -0.000000812   0.000001493   4.556157709
>>         > Al 2.394734647 <tel:2.394734647> <tel:2.394734647
>>
>>        <tel:2.394734647>>   1.382602298   8.876166342
>>
>>         > Al       0.000000000   2.765201880   0.243870515    0   0   0
>>         > Al       0.000000000   0.000000000   1.935118618    0   0   0
>>         > Al 2.394734540 <tel:2.394734540>   1.382602230   6.225550857
>>
>>         > Al      -0.000000007   2.765202952  10.790402310
>>         > Al      -0.000000362   0.000002278   8.430662634
>>         > Al 2.394735475 <tel:2.394735475>   1.382602563  12.021576409
>>
>>         > Al      -0.000000581   2.765202130   4.047340256
>>         > Al       0.000000075   0.000002190  11.054412333
>>         > Al 2.394734840 <tel:2.394734840>   1.382601177 2.258435418
>>        <tel:2.258435418>
>>
>>         > Al      -0.000000323   2.765202460   6.730673987
>>         >    Ni      -0.016734       -0.025515       15.297379
>>         >    Ni       1.180634       -2.099417       15.297379
>>         >    Ni      -1.214101       -2.099417       15.297379
>>         >    Ni      -2.411469       -0.025515       15.297379
>>         > K_POINTS automatic
>>         >    4 4 1   0 0 0
>>
>>            --
>>            Guido Fratesi
>>
>>            Dipartimento di Scienza dei Materiali
>>            Universita` degli Studi di Milano-Bicocca
>>            via Cozzi 53, 20125 Milano, Italy
>>            ______________________________**___________________
>>
>>            Pw_forum mailing list
>>        Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>>        <mailto:Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>>
>>        http://www.democritos.it/__**mailman/listinfo/pw_forum<http://www.democritos.it/__mailman/listinfo/pw_forum>
>>
>>        <http://www.democritos.it/**mailman/listinfo/pw_forum<http://www.democritos.it/mailman/listinfo/pw_forum>
>> >
>>
>>
>>
>>    --
>>    Guido Fratesi
>>
>>    Dipartimento di Scienza dei Materiali
>>    Universita` degli Studi di Milano-Bicocca
>>    via Cozzi 53, 20125 Milano, Italy
>>
>>
>>
> --
> Guido Fratesi
>
> Dipartimento di Scienza dei Materiali
> Universita` degli Studi di Milano-Bicocca
> via Cozzi 53, 20125 Milano, Italy
>
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From bahadira at buffalo.edu  Tue Jan 31 16:31:37 2012
From: bahadira at buffalo.edu (Bahadir Altintas)
Date: Tue, 31 Jan 2012 10:31:37 -0500
Subject: [Pw_forum] Negative stress(vacuum) in vc-relax's last scf
Message-ID: <4F280959.9010509@buffalo.edu>

hi,

I am getting negative stress around -500 Kbar for the SCF procedure at the end
for the vc-relax. is it normal or should it be 0.00 Kbar? For bfgs steps, it
converges around 0.01 Kbar but last scf shows -500Kbar  total stress. ewald is
the same for latest bfgs and scf.  I am confused. any explaination?
I use QE 4.3.2 fhi.UPF(converted from abinit LDA_FHI pseudpotentials using
fhi2upf), ecutwfc is 45 Ry and K-mesh is 8 8 8 automatic.
i think convvergence thresholds are enough as D-12 for energy D-8 for forces.

thank you


Bahadir Altintas, PhD
Department of Chemistry(Visiting Scholar)

335 NATURAL SCIENCES COMPLEX
UNIVERSITY AT BUFFALO
STATE UNIVERSITY OF NEW YORK





From giannozz at democritos.it  Tue Jan 31 16:47:09 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 31 Jan 2012 16:47:09 +0100
Subject: [Pw_forum] Negative stress(vacuum) in vc-relax's last scf
In-Reply-To: <4F280959.9010509@buffalo.edu>
References: <4F280959.9010509@buffalo.edu>
Message-ID: <1328024829.2471.3.camel@fe12lx.fisica.uniud.it>

On Tue, 2012-01-31 at 10:31 -0500, Bahadir Altintas wrote:

> For bfgs steps, it converges around 0.01 Kbar
> but last scf shows -500Kbar  total stress

this is the typical observed behavior when the cutoff is very low

P.
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From bahadira at buffalo.edu  Tue Jan 31 17:21:58 2012
From: bahadira at buffalo.edu (Bahadir Altintas)
Date: Tue, 31 Jan 2012 11:21:58 -0500
Subject: [Pw_forum] matdyn input explanation
Message-ID: <4F281526.6080702@buffalo.edu>

I have a question about matdyn input file in elphon calculations. ihow 
to define coordinates in matdyn.in.freq file? are those the coordinates 
along the special points on BZ?

thanks

Bahadir Altintas, PhD
Dept.Chemistry
University at Buffalo
SUNY
USA

From giannozz at democritos.it  Tue Jan 31 18:29:38 2012
From: giannozz at democritos.it (Paolo Giannozzi)
Date: Tue, 31 Jan 2012 18:29:38 +0100
Subject: [Pw_forum] matdyn input explanation
In-Reply-To: <4F281526.6080702@buffalo.edu>
References: <4F281526.6080702@buffalo.edu>
Message-ID: <1328030978.4323.1.camel@fe12lx.fisica.uniud.it>

On Tue, 2012-01-31 at 11:21 -0500, Bahadir Altintas wrote:
> how to define coordinates in matdyn.in.freq file? 
> are those the coordinates along the special points on BZ?

cartesian axis, 2pi/a units

P,
-- 
Paolo Giannozzi, IOM-Democritos and University of Udine, Italy



From bahadira at buffalo.edu  Tue Jan 31 21:31:08 2012
From: bahadira at buffalo.edu (Bahadir Altintas)
Date: Tue, 31 Jan 2012 15:31:08 -0500
Subject: [Pw_forum] NaN values for Tc calculations
Message-ID: <4F284F8C.2050908@buffalo.edu>


I have some problem in calculation of Tc of a system with spacegroup 166 
(LiH_6).

1. By adapting the example07 to my system, I tried to calculate Tc but I 
got NaN values for both omega_log and T_c values in lambda.out also all 
values are NaN in alpha2F.dat

In my calculation: there is no problem with phononDos btu i can not be 
able to get any values for Tc. i am really confused.

P.S: there is no problem for Tc calculations of Li-fcc structure.

thanks if anyone has any suggestions

Bahadir Altintas
SUY Buffalo-USA
Dept. Chem


From berbermohamed at yahoo.fr  Tue Jan 31 22:21:22 2012
From: berbermohamed at yahoo.fr (berber mo)
Date: Tue, 31 Jan 2012 21:21:22 +0000 (GMT)
Subject: [Pw_forum] volume optimization
In-Reply-To: <4F284F8C.2050908@buffalo.edu>
References: <4F284F8C.2050908@buffalo.edu>
Message-ID: <1328044882.27533.YahooMailNeo@web171403.mail.ir2.yahoo.com>




how to optimize the volume of the following system:
a =15.95 A? ? ? ? ? ? ? ? b = 19.53 A????????????????????????????? c =15.95 A?
alpha=90 ???????????????? ? beta =90 ??????????????????????????????? ?? gamma =144.73 ?
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From bogus@does.not.exist.com  Tue Jan  3 18:43:30 2012
From: bogus@does.not.exist.com ()
Date: Tue, 03 Jan 2012 17:43:30 -0000
Subject: No subject
Message-ID: <mailman.2.1334236878.9398.pw_forum@pwscf.org>

---------------------------------------------------------------------------=
----------------
     Subspace diagonalization in iterative solution of the eigenvalue probl=
em:
     parallel, distributed-memory algorithm (size of sub-group:  6*  6 proc=
s)
---------------------------------------------------------------------------=
----------------

I have also attached the input file. Any help would be appreciated.

Many thanks,
Paul Jennings=20

******************************************************
Paul Jennings

Centre for Hydrogen and Fuel Cell Research
PEMFC Research group
School of Chemical Engineering
The University of Birmingham
Edgbaston, Birmingham B15 2TT (U.K.)

E:  PCJ994 at bham.ac.uk
T:  07816644583
W: www.fuelcells.bham.ac.uk

******************************************************=

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--_002_86CAF89B0E5A344E90835C7D6EEFCF47039A75CC8C52mbx5adfbham_--

From bogus@does.not.exist.com  Tue Jan  3 18:43:30 2012
From: bogus@does.not.exist.com ()
Date: Tue, 03 Jan 2012 17:43:30 -0000
Subject: No subject
Message-ID: <mailman.5.1337868992.9398.pw_forum@pwscf.org>

Cu.pbe-n-van.UPF  (hard to say...I dont find it anymore in the database....=
has=20
the database been changed recently?...anyway the header of the pseudo is=20
reported below)

pseudo that is a USPP one.

Do you mean that hybrid calcs can be performed only with Norm Conserving on=
es?=20
:'(

Thanks once more!

Best,
Giacomo


the pseudo header

<PP_INFO>
Generated using Vanderbilt code, version   7  3 =20
4                             =20
Author: unknown    Generation date:    4    3   =20
5                             =20
Automatically converted from original=20
format                                   =20
    1        The Pseudo was generated with a Scalar-Relativistic Calculatio=
n
  2.00000000000E+00    Local Potential cutoff radius
nl pn  l   occ               Rcut            Rcut US             E pseu
3D  3  2  9.50     10.00000000000      2.00000000000     -0.60492460120
4S  4  0  1.00     10.00000000000      2.10000000000     -0.43710222811
4P  4  1  0.50     10.00000000000      2.20000000000     -0.10740671642
</PP_INFO>


<PP_HEADER>
   0                   Version Number
  Cu                   Element
   US                  Ultrasoft pseudopotential
    T                  Nonlinear Core Correction
 SLA  PW   PBE  PBE    PBE  Exchange-Correlation functional
   11.00000000000      Z valence
 -121.01063523375      Total energy
  0.0000000  0.0000000 Suggested cutoff for wfc and rho
    2                  Max angular momentum component
  867                  Number of points in mesh
    3    6             Number of Wavefunctions, Number of Projectors
 Wavefunctions         nl  l   occ
                       3D  2  9.50
                       4S  0  1.00
                       4P  1  0.50
</PP_HEADER>


>----Messaggio originale----
>Da: giuseppe.mattioli at ism.cnr.it
>Data: 24/05/2012 11.27
>A: "giacsport at libero.it"<giacsport at libero.it>, "PWSCF Forum"<pw_forum at pwsc=
f.
org>
>Ogg: Re: [Pw_forum] HSE vs PBE
>
>
>Dear Giacomo
>
>> is it OK? can I do it? I.e., using PBE psudopotential for HSE calculatio=
ns?
>
>A the present time, there is no other way to perform hybrid calculations b=
ut=20
with GGA (norm=20
>conserving) pseudopotentials. In this regard, I suppose that a 95 Ry wfc=
=20
cutoff may be poor for=20
>copper (with semicore 3s and 3p). You should test the convergence of your =
PBE=20
results before=20
>attempting HSE calculations.
>
>> and then use the same for HSE (same pseudopotentials at PBE, taken from =
the
>> PwSCF website)
>
>I'm quite puzzled... There is no NC pseudopotential for copper in the=20
website. Do you mean the=20
>pslibrary?
>
>>     input_dft=3D'hse', nqx1=3D 2, nqx2=3D 2, nqx3=3D 2,
>
>You should check the convergence of your results wrt the blend of k points=
=20
and q points, and this is=20
>the most painful task when using hybrid functionals (and metals are very=
=20
sensitive to k points...).
>In practice, be sure to the convergence of k points in the PBE calculation=
,=20
and starting from
>
>nqx1=3D 1, nqx2=3D 1, nqx3=3D 1,
>
>try to reach convergence (or reach the most bloody-cpu-consuming grid you =
can=20
afford) wrt the q=20
>points.
>
>> nspin=3D2
>
>Copper is nonmagnetic, and you have an even number of atoms. Save (a lot o=
f)=20
time with nspin=3D1.
>
>> nbnd =3D 80
>> occupations=3D'smearing'
>
>The latter provide already a fair number of unoccupied states, you do not=
=20
need to use the former.
>
>HTH
>
>Giuseppe
>
>
>On Thursday 24 May 2012 04:45:14 giacsport at libero.it wrote:
>> Dear All,
>>             I am using the development version of PWscf.
>>=20
>> I would like to ask you this question.
>>=20
>> I want to make HSE hybrid calculations (vc-relax) using pseudopotential =
at
>> PBE level.
>> I want indeed test the impact of the hybrid functional in the lattice
>> parameter (this is the case of Copper)
>>=20
>> I mean is it a correct procedure to optimize the system with such initia=
l
>> settings
>>=20
>> /
>> &system
>>     ibrav=3D  2, celldm(1) =3D 6.830792531
>>     nat=3D  4, ntyp=3D 1, nspin=3D2,
>>     ecutwfc =3D 95.,  nbnd =3D 80, occupations=3D'smearing',
>>     degauss=3D0.01,smearing=3D'gaussian', starting_magnetization(1)=3D1
>> /
>>=20
>> and then use the same for HSE (same pseudopotentials at PBE, taken from =
the
>> PwSCF website)
>>=20
>> /
>> &system
>>     ibrav=3D  2, celldm(1) =3D 6.830792531
>>     nat=3D  4, ntyp=3D 1, nspin=3D2,
>>     ecutwfc =3D 95.,  nbnd =3D 80, occupations=3D'smearing',
>>     degauss=3D0.01,smearing=3D'gaussian', starting_magnetization(1)=3D1
>>     input_dft=3D'hse', nqx1=3D 2, nqx2=3D 2, nqx3=3D 2,
>>     x_gamma_extrapolation =3D .TRUE.
>> /
>>=20
>> is it OK? can I do it? I.e., using PBE psudopotential for HSE calculatio=
ns?
>>=20
>>=20
>> Thanks in advance for any suggestion!
>>=20
>> Best,
>> Giacomo
>
>--=20
>********************************************************
>- Article premier - Les hommes naissent et demeurent
>libres et =C3=A8gaux en droits. Les distinctions sociales
>ne peuvent =C3=AAtre fond=C3=A8es que sur l'utilit=C3=A8 commune
>- Article 2 - Le but de toute association politique
>est la conservation des droits naturels et=20
>imprescriptibles de l'homme. Ces droits sont la libert=C3=A8,
>la propri=C3=A8t=C3=A8, la s=C3=B9ret=C3=A8 et la r=C3=A8sistance =C3=A0 l=
'oppression.
>********************************************************
>
>   Giuseppe Mattioli                           =20
>   CNR - ISTITUTO DI STRUTTURA DELLA MATERIA  =20
>   v. Salaria Km 29,300 - C.P. 10               =20
>   I 00015 - Monterotondo Stazione (RM)         =20
>   Tel + 39 06 90672836 - Fax +39 06 90672316   =20
>   E-mail: <giuseppe.mattioli at ism.cnr.it>
>



From bogus@does.not.exist.com  Tue Jan  3 18:43:30 2012
From: bogus@does.not.exist.com ()
Date: Tue, 03 Jan 2012 17:43:30 -0000
Subject: No subject
Message-ID: <mailman.6.1338759407.9398.pw_forum@pwscf.org>

result will be meaningful, I ought to find some way to test what this
pseudo hydrogen actually is.

bests

P.S: I don't think I misread you, but if you only wanted to generate the
pseudopotential in a slightly ionic configuration, all you have to do is
add a zval variable in the inputp namelist, it's value should be  1.25 or
0.25, I never remember how it is exactly defined.


--=20
Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit=E9 Paris 6
phone: +33 (0)1 44275 084 / skype: paulatz
www:   http://www-int.impmc.upmc.fr/~paulatto/
mail:  23-24/4=E916 Bo=EEte courrier 115, 4 place Jussieu 75252 Paris C=E9d=
ex 05

--e89a8f23532b816e9f04c19836fd
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<div class=3D"gmail_quote">On Sun, Jun 3, 2012 at 9:42 PM, Vic Bermudez <sp=
an dir=3D"ltr">&lt;<a href=3D"mailto:victor.bermudez at nrl.navy.mil" target=
=3D"_blank">victor.bermudez at nrl.navy.mil</a>&gt;</span> wrote:<br><blockquo=
te class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px #ccc so=
lid;padding-left:1ex">
=A0 =A0 =A0 =A0I&#39;ve never tried to generate a pseudopotential before, s=
o this is all very<br>
new to me. I&#39;m trying to construct a PW91 PP for a Z=3D5/4 pseudo hydro=
gen<br>
atom.=A0</blockquote><div><br></div><div>=A0</div></div>Dear Victor,<div>th=
e ld1 code does not allow you to have a non-integer nuclear charge. However=
 the zed variable is indeed a real number, so maybe the functionality is th=
ere but it has never been tested, or not tested for 20 years. If you know w=
hat are doing and how to test it, you can open file atomic/src/ld1_reading.=
f90 and at line ~240 remove all the checks about zed being integer and simi=
lar and recompile the code.</div>
<div><br></div><div>From there on you are on your own. I don&#39;t think an=
ybody knows if the result will be meaningful, I ought to find some way to t=
est what this pseudo hydrogen actually is.</div><div><br></div><div>bests</=
div>
<div><br></div><div>P.S: I don&#39;t think I misread you, but if you only w=
anted to generate the pseudopotential in a slightly ionic configuration, al=
l you have to do is add a zval variable in the inputp namelist, it&#39;s va=
lue should be =A01.25 or 0.25, I never remember how it is exactly defined.<=
/div>
<div><br clear=3D"all"><div><br></div>-- <br><div>Lorenzo Paulatto IdR @ IM=
PMC/CNRS &amp; Universit=E9 Paris 6</div><div>phone: +33 (0)1 44275 084 / s=
kype: paulatz</div><div>www: =A0 <a href=3D"http://www-int.impmc.upmc.fr/~p=
aulatto/" target=3D"_blank">http://www-int.impmc.upmc.fr/~paulatto/</a></di=
v>
<div>mail: =A023-24/4=E916 Bo=EEte courrier 115, 4 place Jussieu 75252 Pari=
s C=E9dex 05</div><br>
</div>

--e89a8f23532b816e9f04c19836fd--

From bogus@does.not.exist.com  Tue Jan  3 18:43:30 2012
From: bogus@does.not.exist.com ()
Date: Tue, 03 Jan 2012 17:43:30 -0000
Subject: No subject
Message-ID: <mailman.8.1341574703.9398.pw_forum@pwscf.org>

>
+-------------------------------------------------------------------- 
> Variable: output_format 
> 
> Type: INTEGER 
> Description: (ignored on 1D plot) 
> 0 format suitable for
gnuplot (1D) 
> 1 format suitable for contour.x (2D) 
> 2
format suitable for plotrho (2D) 
> 3 format suitable for XCRYSDEN
(2D or user-supplied 
> 3D 
> region) 
> 4 format
suitable for gOpenMol (3D) 
> (formatted: convert to unformatted
*.plt) 
> 5 format suitable for XCRYSDEN (3D, using entire FFT 
> grid) 
> 6 format as gaussian cube file (3D) 
>
(can be read by many programs) 
>
+-------------------------------------------------------------------- 
> 
> 
> -- 
> Lorenzo Paulatto IdR @
IMPMC/CNRS & Universit? Paris 6 
> phone: +33 (0)1
44275 084 / skype: paulatz 
> www:
http://www-int.impmc.upmc.fr/~paulatto/ 
> mail: 23-24/4?16
Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 
> 
> -- 
> This message has been scanned for viruses
and 
> dangerous content by MailScanner, and is 
>
believed to be clean. 
> 
>
_______________________________________________ 
> Pw_forum
mailing list 
> Pw_forum at pwscf.org 
>
http://www.democritos.it/mailman/listinfo/pw_forum 
> 


-- 
This message has been scanned for viruses and
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------=_20120706160810_31749
Content-Type: text/html; charset="utf-8"
Content-Transfer-Encoding: 8bit

Dear All,<br />I wish to have a kohn-sham orbitals for different states in
cube format.&nbsp; In&nbsp; pp.x if&nbsp; the output format 6 is chosen
the cube file will be produced but&nbsp; the density is written in cube
format ( header of output: <span lang="EN">Cubfile created from PWScf
calculation, Total SCF Density). How can I obtain the kohen-sham orbitals
in cube file format.<br /></span>Regards<br />Fariba Nazari<br />IASBS<br
/><br /><br /><br /><br />&gt; On Fri, Jun 29, 2012 at 11:14 AM,
&lt;nazari at iasbs.ac.ir&gt; wrote: <br />&gt; <br />&gt;&gt; Dear All, <br
/>&gt;&gt; Would you please let me know if it is possible that the
kohn-Sham <br />&gt;&gt; orbitals is written in cube format. I mean I need
the PSI(r) in cube <br />&gt;&gt; format&nbsp;&nbsp; not density. <br
/>&gt;&gt; regards <br />&gt;&gt; Fariba Nazari <br />&gt;&gt; IASBS&nbsp;
<br />&gt; <br />&gt; <br />From INPUT_PP.txt: <br />&gt;
+-------------------------------------------------------------------- <br
/>&gt; Variable: output_format <br />&gt; <br />&gt; Type: INTEGER <br
/>&gt; Description: (ignored on 1D plot) <br />&gt; 0 format suitable for
gnuplot (1D) <br />&gt; 1 format suitable for contour.x (2D) <br />&gt; 2
format suitable for plotrho (2D) <br />&gt; 3 format suitable for XCRYSDEN
(2D or user-supplied <br />&gt; 3D <br />&gt; region) <br />&gt; 4 format
suitable for gOpenMol (3D) <br />&gt; (formatted: convert to unformatted
*.plt) <br />&gt; 5 format suitable for XCRYSDEN (3D, using entire FFT <br
/>&gt; grid) <br />&gt; 6 format as gaussian cube file (3D) <br />&gt;
(can be read by many programs) <br />&gt;
+-------------------------------------------------------------------- <br
/>&gt; <br />&gt; <br />&gt; -- <br />&gt; Lorenzo Paulatto IdR @
IMPMC/CNRS &amp; Universit&eacute; Paris 6 <br />&gt; phone: +33 (0)1
44275 084 / skype: paulatz <br />&gt; www:
http://www-int.impmc.upmc.fr/~paulatto/ <br />&gt; mail: 23-24/4&eacute;16
Bo&icirc;te courrier 115, 4 place Jussieu 75252 Paris C&eacute;dex 05 <br
/>&gt; <br />&gt; -- <br />&gt; This message has been scanned for viruses
and <br />&gt; dangerous content by MailScanner, and is <br />&gt;
believed to be clean. <br />&gt; <br />&gt;
_______________________________________________ <br />&gt; Pw_forum
mailing list <br />&gt; Pw_forum at pwscf.org <br />&gt;
http://www.democritos.it/mailman/listinfo/pw_forum <br />&gt; <br /><br />-- 
<br />This message has been scanned for viruses and
<br />dangerous content by
<a href="http://www.mailscanner.info/"><b>MailScanner</b></a>, and is
<br />believed to be clean.



------=_20120706160810_31749--