From yjiang at asu.edu Wed Aug 3 14:40:59 2005 From: yjiang at asu.edu (Yong Jiang) Date: Wed, 03 Aug 2005 05:40:59 -0700 (MST) Subject: [Pw_forum] restart from an interrupted phonon run In-Reply-To: <23886D71-91EC-4C9D-BE6C-943125166BEF@sissa.it> References: <42E595F6.0000A0.10598@m0201.mail.163.com> <23886D71-91EC-4C9D-BE6C-943125166BEF@sissa.it> Message-ID: <1123072859.42f0bb5bc061b@webmail.asu.edu> Dear PWscf fellows, I notice that pw.x has a input tag of "restart_mode='restart'" which allows users to continue previous interrupted run. Is there a similar tag for ph.x, to restart an interrupted ph.x run? In many cases, ph.x takes a real long time. Looking forwards to your reply. Thanks very much! Sincerely, Yong From maheshp at hamsadvani.serc.iisc.ernet.in Wed Aug 3 15:02:55 2005 From: maheshp at hamsadvani.serc.iisc.ernet.in (Maheshwara Reddy P.) Date: Wed, 3 Aug 2005 18:32:55 +0530 (IST) Subject: [Pw_forum] i am having a problem in compaqs machines Message-ID: hi, i am running a single job on compaq machine it is giving the following error. Previously i cound run the jobs more than 200 jobs runed but today it si giving problem. please immediately any one can help me "forrtl: Connection timed out forrtl: severe (38): error during write, unit 195, file /global/utemp/chevhrao/kumaran5/gem05/dis.txt 0: __FINI_00_remove_gp_range [0x3ff81a6c7c4] 1: __FINI_00_remove_gp_range [0x3ff81a6cd44] 2: __FINI_00_remove_gp_range [0x3ff81aab7ac] 3: hsmd_f90_ [sh.f90: 677, 0x1200038b4] 4: main [for_main.c: 203, 0x120001bec] 5: __start [0x120001b68] " thanks mahesh From giannozz at nest.sns.it Wed Aug 3 15:28:07 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 3 Aug 2005 15:28:07 +0200 Subject: [Pw_forum] restart from an interrupted phonon run In-Reply-To: <1123072859.42f0bb5bc061b@webmail.asu.edu> References: <42E595F6.0000A0.10598@m0201.mail.163.com> <23886D71-91EC-4C9D-BE6C-943125166BEF@sissa.it> <1123072859.42f0bb5bc061b@webmail.asu.edu> Message-ID: <200508031528.07377.giannozz@nest.sns.it> On Wednesday 03 August 2005 14:40, Yong Jiang wrote: > I notice that pw.x has a input tag of "restart_mode='restart'" > which allows users to continue previous interrupted run. Is there > a similar tag for ph.x, to restart an interrupted ph.x run? ph.x should automatically restart from an interrupted run, if it detects the presence of scratch files written by a previous run. This is by the way a source of trouble more often than not, so in the newer version you will have to explicitly specify that you want to restart from a previous run. Note however that 1) restarting is a mess, because files are often corrupted 2) in parallel execution, restarting is a mess multiplied by 1024: you need to run on the same number of processors, with the same number of 'pools', and each processor must see all files produced by all other processors Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From baroni at sissa.it Wed Aug 3 17:23:08 2005 From: baroni at sissa.it (Stefano Baroni) Date: Wed, 3 Aug 2005 17:23:08 +0200 Subject: [Pw_forum] restart from an interrupted phonon run In-Reply-To: <200508031528.07377.giannozz@nest.sns.it> References: <42E595F6.0000A0.10598@m0201.mail.163.com> <23886D71-91EC-4C9D-BE6C-943125166BEF@sissa.it> <1123072859.42f0bb5bc061b@webmail.asu.edu> <200508031528.07377.giannozz@nest.sns.it> Message-ID: <371CCB49-BFBD-4577-811E-4AA58D23B6B6@sissa.it> On Aug 3, 2005, at 3:28 PM, Paolo Giannozzi wrote: > On Wednesday 03 August 2005 14:40, Yong Jiang wrote: > > >> I notice that pw.x has a input tag of "restart_mode='restart'" >> which allows users to continue previous interrupted run. Is there >> a similar tag for ph.x, to restart an interrupted ph.x run? >> > > ph.x should automatically restart from an interrupted run, if it > detects the presence of scratch files written by a previous run. > This is by the way a source of trouble more often than not, so > in the newer version you will have to explicitly specify that you > want to restart from a previous run. > > Note however that > 1) restarting is a mess, because files are often corrupted > 2) in parallel execution, restarting is a mess multiplied by 1024: > you need to run on the same number of processors, with the same > number of 'pools', and each processor must see all files produced > by all other processors ma questo problema non era stato rimosso dal restart centralizzato ??? S. > > Paolo > > -- > Paolo Giannozzi e-mail: giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 > Piazza dei Cavalieri 7 I-56126 Pisa, Italy > _______________________________________________ > 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 [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20050803/14610d2c/attachment.htm From giannozz at nest.sns.it Wed Aug 3 19:19:30 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 3 Aug 2005 19:19:30 +0200 Subject: [Pw_forum] restart from an interrupted phonon run In-Reply-To: <371CCB49-BFBD-4577-811E-4AA58D23B6B6@sissa.it> References: <42E595F6.0000A0.10598@m0201.mail.163.com> <200508031528.07377.giannozz@nest.sns.it> <371CCB49-BFBD-4577-811E-4AA58D23B6B6@sissa.it> Message-ID: <200508031919.30435.giannozz@nest.sns.it> On Wednesday 03 August 2005 17:23, Stefano Baroni wrote: > > Note however that > > 1) restarting is a mess, because files are often corrupted > > 2) in parallel execution, restarting is a mess multiplied by 1024: > > you need to run on the same number of processors, with the same > > number of 'pools', and each processor must see all files produced > > by all other processors > > ma questo problema non era stato rimosso dal restart centralizzato ??? if I remember correctly the phonon code doesn't (yet) store the intermediate results needed to restart into a single file For those of you not especially fluent in Italian, the question (which was intended to me and not to the forum, of course) was whether the 'centralisation' of restart files into a single file hadn't already solved this problem of restarting in parallel Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From swblelia at sw.ehu.es Wed Aug 3 19:38:06 2005 From: swblelia at sw.ehu.es (Aritz Leonardo) Date: Wed, 03 Aug 2005 19:38:06 +0200 Subject: [Pw_forum] double delta Message-ID: <42F100FE.7020001@sw.ehu.es> Hello could anyone tell me what is exactly de meaning of the double_delta in e-ph calculation? thanks! From eyvaz_isaev at yahoo.com Wed Aug 3 22:52:14 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 3 Aug 2005 13:52:14 -0700 (PDT) Subject: [Pw_forum] double delta In-Reply-To: <42F100FE.7020001@sw.ehu.es> Message-ID: <20050803205214.96981.qmail@web60323.mail.yahoo.com> Dear Aritz, Please have a look at the next definitions: 1) \gamma_{qj} = 2\pi\omega_{qj} \sum_{k,n,n'}{|g_{k+q,n';kn}^{qj}|^2 \delta (e_{nk}-e_F)\delta (e_{n'`,k+q}-e_F) This is so called the phonon linewidth which relates two electrons with different wave vectros (k, and k+q) at the Fermi surface. |g|^2 is the square of the electron-phonon matrix element 2) --- Aritz Leonardo wrote: > Hello > > could anyone tell me what is exactly de meaning of > the double_delta in > e-ph calculation? > > thanks! > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From eyvaz_isaev at yahoo.com Wed Aug 3 23:02:53 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 3 Aug 2005 14:02:53 -0700 (PDT) Subject: [Pw_forum] double delta In-Reply-To: <42F100FE.7020001@sw.ehu.es> Message-ID: <20050803210253.92534.qmail@web60312.mail.yahoo.com> Dear Aritz, Please have a look at the next definitions: 1) \gamma_{qj} = 2\pi\omega_{qj} \sum_{k,n,n'}{|g_{k+q,n';kn}^{qj}|^2 \delta (e_{nk}-e_F)\delta (e_{n'`,k+q}-e_F) This is so called the phonon linewidth which relates two electrons with different wave vectros (k, and k+q) at the Fermi surface. |g|^2 is the square of the electron-phonon matrix element. 2) \lambda_{nq} = \gamma_{nq}/(\pi N(e_F) \omega_{nq}^2) I.e. \gamma_{nq} which contains a production of two \delta - functions is among main ingridients of the electron phonon coupling constant \lambda. Bests, Eyvaz. P.S. My apologies for the previous mail which was sent accidently. --- Aritz Leonardo wrote: > Hello > > could anyone tell me what is exactly de meaning of > the double_delta in > e-ph calculation? > > thanks! > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ____________________________________________________ Start your day with Yahoo! - make it your home page http://www.yahoo.com/r/hs From eyvaz_isaev at yahoo.com Wed Aug 3 23:21:33 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 3 Aug 2005 14:21:33 -0700 (PDT) Subject: [Pw_forum] double delta In-Reply-To: <20050803210253.92534.qmail@web60312.mail.yahoo.com> Message-ID: <20050803212133.51575.qmail@web60322.mail.yahoo.com> Sorry, but there is a typos: 2) \lambda_{nq} = \gamma_{nq}/(\pi N(e_F) \omega_{nq}^2) according to the first definition (see previous mail) \lambda_{nq} \to \lambda{qj}, \gamma_{nk} \to \gamma{qj}, and \omega_{nq} \to \omega_{qj}. q stands for a wave vector and j is a phonon mode. Bests, Eyvaz. --- Eyvaz Isaev wrote: > Dear Aritz, > > Please have a look at the next definitions: > > 1) \gamma_{qj} = 2\pi\omega_{qj} > \sum_{k,n,n'}{|g_{k+q,n';kn}^{qj}|^2 \delta > (e_{nk}-e_F)\delta (e_{n'`,k+q}-e_F) > > This is so called the phonon linewidth which relates > two electrons with different wave vectros (k, and > k+q) at the Fermi surface. > |g|^2 is the square of the electron-phonon matrix > element. > > 2) \lambda_{nq} = \gamma_{nq}/(\pi N(e_F) > \omega_{nq}^2) > > I.e. \gamma_{nq} which contains a production of two > \delta - functions is among main ingridients of the > electron phonon coupling constant \lambda. > > > Bests, > Eyvaz. > P.S. My apologies for the previous mail which was > sent > accidently. > > --- Aritz Leonardo wrote: > > > Hello > > > > could anyone tell me what is exactly de meaning of > > the double_delta in > > e-ph calculation? > > > > thanks! > > _______________________________________________ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > ____________________________________________________ > Start your day with Yahoo! - make it your home page > http://www.yahoo.com/r/hs > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ____________________________________________________ Start your day with Yahoo! - make it your home page http://www.yahoo.com/r/hs From swblelia at sw.ehu.es Wed Aug 3 23:35:00 2005 From: swblelia at sw.ehu.es (Aritz Leonardo) Date: Wed, 03 Aug 2005 23:35:00 +0200 Subject: [Pw_forum] double delta In-Reply-To: <20050803212133.51575.qmail@web60322.mail.yahoo.com> References: <20050803212133.51575.qmail@web60322.mail.yahoo.com> Message-ID: <42F13884.4050000@sw.ehu.es> thanks a lot for the reply! Eyvaz Isaev escribi?: >Sorry, but there is a typos: > >2) \lambda_{nq} = \gamma_{nq}/(\pi N(e_F) > \omega_{nq}^2) > >according to the first definition (see previous mail) >\lambda_{nq} \to \lambda{qj}, \gamma_{nk} \to >\gamma{qj}, and \omega_{nq} \to \omega_{qj}. > >q stands for a wave vector and j is a phonon mode. > >Bests, >Eyvaz. > >--- Eyvaz Isaev wrote: > > > >>Dear Aritz, >> >>Please have a look at the next definitions: >> >>1) \gamma_{qj} = 2\pi\omega_{qj} >>\sum_{k,n,n'}{|g_{k+q,n';kn}^{qj}|^2 \delta >>(e_{nk}-e_F)\delta (e_{n'`,k+q}-e_F) >> >>This is so called the phonon linewidth which relates >>two electrons with different wave vectros (k, and >>k+q) at the Fermi surface. >>|g|^2 is the square of the electron-phonon matrix >>element. >> >>2) \lambda_{nq} = \gamma_{nq}/(\pi N(e_F) >>\omega_{nq}^2) >> >>I.e. \gamma_{nq} which contains a production of two >>\delta - functions is among main ingridients of the >>electron phonon coupling constant \lambda. >> >> >>Bests, >>Eyvaz. >>P.S. My apologies for the previous mail which was >>sent >>accidently. >> >>--- Aritz Leonardo wrote: >> >> >> >>>Hello >>> >>>could anyone tell me what is exactly de meaning of >>>the double_delta in >>>e-ph calculation? >>> >>>thanks! >>>_______________________________________________ >>>Pw_forum mailing list >>>Pw_forum at pwscf.org >>>http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> >>> >> >> >>____________________________________________________ >>Start your day with Yahoo! - make it your home page >>http://www.yahoo.com/r/hs >> >>_______________________________________________ >>Pw_forum mailing list >>Pw_forum at pwscf.org >>http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> > > > > >____________________________________________________ >Start your day with Yahoo! - make it your home page >http://www.yahoo.com/r/hs > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > > From triangleman at fastmail.us Thu Aug 4 18:02:56 2005 From: triangleman at fastmail.us (Stephen Daunheimer) Date: Thu, 04 Aug 2005 12:02:56 -0400 Subject: [Pw_forum] Using multiple s shells Message-ID: <42F23C30.8000006@fastmail.us> Dear Users, I am trying to make an ultrasoft pseudopotential for neutral K and I would like to include the 3s, 3p and 4s shells in the valence. I saw that the US pseudopotential for K the pwscf website was made this way. I keep getting an error though that says "too many beta functions" and I am assuming that this has to do with having two s shells. I have tried setting lloc to -1 thinking that it might help but it did not. This is what my input file looks like: &input title='K', zed=19.0, rel=1, beta=0.5, xmin=-7, lsd=0, rlderiv=2.5, eminld=-20.0, emaxld=20.0, isic=0, config='[Ar] 4s1', nld=2, iswitch=3, file_logderae='K.PZ.AELOG', dft='PZ', / &test pseudotype=2, nconf=1, file_wavefunctionsps='K.PZ.PP', configts(1)='3s2 3p6 4s1', / &inputp lloc=-1, rho0=1d-2, file_pseudopw='K.US.PZ.RRKJ3', file_logderps='K.PZ.PPLOG', zval=9.d0, / 6 3S 1 0 2.00 0.00 1.0800 1.2000 3S 1 0 0.00 2.30 1.0800 1.2000 3P 2 1 6.00 0.00 1.2800 1.3500 3P 2 1 0.00 1.50 1.2800 1.3500 4S 3 0 1.00 0.00 3.9800 4.2000 4S 3 0 0.00 0.50 3.9800 4.2000 Thanks for any help. Best, Stephen Daunheimer From giannozz at nest.sns.it Fri Aug 5 09:32:21 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 5 Aug 2005 09:32:21 +0200 Subject: [Pw_forum] i am having a problem in compaqs machines In-Reply-To: References: Message-ID: <200508050932.21561.giannozz@nest.sns.it> On Wednesday 03 August 2005 15:02, Maheshwara Reddy P. wrote: > i am running a single job on compaq machine it is giving the > following error [...] > "forrtl: Connection timed out [...] a parallel machine? it looks like a network problem, not related to the code itself Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Fri Aug 5 10:32:28 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 5 Aug 2005 10:32:28 +0200 Subject: [Pw_forum] Using multiple s shells In-Reply-To: <42F23C30.8000006@fastmail.us> References: <42F23C30.8000006@fastmail.us> Message-ID: <200508051032.28273.giannozz@nest.sns.it> On Thursday 04 August 2005 18:02, Stephen Daunheimer wrote: > eminld=-20.0, > emaxld=20.0, that's a lot: remember that energies here are in Rydberg > 3S 1 0 2.00 0.00 1.0800 1.2000 > 3S 1 0 0.00 2.30 1.0800 1.2000 > 3P 2 1 6.00 0.00 1.2800 1.3500 > 3P 2 1 0.00 1.50 1.2800 1.3500 > 4S 3 0 1.00 0.00 3.9800 4.2000 > 4S 3 0 0.00 0.50 3.9800 4.2000 maybe you should try to use just 2 channels for S states. The simplest choice would be to use the 3S and 4S bound states, but I think this is not (yet) implemented: you should use the 3S state and an unbound state at an energy not too far away from that of 3S, I think, because pseudo-orbitals with nodes are not supported Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From maheshp at hamsadvani.serc.iisc.ernet.in Mon Aug 8 12:33:04 2005 From: maheshp at hamsadvani.serc.iisc.ernet.in (Maheshwara Reddy P.) Date: Mon, 8 Aug 2005 16:03:04 +0530 (IST) Subject: [Pw_forum] booting problem in compaq xp1000 Message-ID: hi to all, i got the following error when i restarted the compaq machine please help me to sort out the problem. (boot dkb0.0.0.12.0 -flags A failed to open dkb 0.0.0.12.0 accoding to me that is boot problem. i donot know exactly that is disk problem or OS problem. please tell me whether reinstall only works or disk change is needed thanks mahe From chaohao2002 at 163.com Wed Aug 10 08:09:07 2005 From: chaohao2002 at 163.com (=?gb2312?B?Q2hhb2hhbyBIdQ==?=) Date: Wed, 10 Aug 2005 14:09:07 +0800 (CST) Subject: [Pw_forum] =?gb2312?B?QSBxdWVzdGlvbiBhYm91dCBWaXN1YWxpemluZyBzdHJ1Y3R1cmUgdWk=?= =?gb2312?B?bmcgWENyeVNEZW4=?= Message-ID: <42F99A03.00001A.07119@bj163app53.163.com> Dear Sir, I want to use XCrySDen to visualize LaNi5 (Hexagonal, I=P6/mmm-191). I wrote a PW input file which is described as below, but it can not be shown as a right crystal structre. While I wrote some other input files which is about FCC or BCC structure, it runs very well. Why? ========== &control calculation = 'scf' restart_mode='from_scratch', prefix='lani5', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 4, celldm(1) =9.477, celldm(3) =0.7944, nat= 6, ntyp= 2, ecutwfc =26.0, ecutrho = 260.0 / &electrons conv_thr = 1.0d-8 / ATOMIC_SPECIES La 138.91 La.Pw91.UPF Ni 58.69 Ni.pw91.UPF ATOMIC_POSITIONS La 0.00 0.00 0.00 Ni 0.50 0.50 0.50 Ni 0.50 0.00 0.50 Ni 0.00 0.50 0.50 Ni 0.6667 0.3333 0.00 Ni 0.3333 0.6667 0.00 K_POINTS {automatic} 6 6 4 1 1 1 ======== -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20050810/a4d6a687/attachment.htm From degironc at sissa.it Wed Aug 10 09:12:43 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Wed, 10 Aug 2005 09:12:43 +0200 Subject: [Pw_forum] A question about Visualizing structure uing XCrySDen References: <42F99A03.00001A.07119@bj163app53.163.com> Message-ID: <42F9A8EB.8020607@sissa.it> Chaohao Hu wrote: > Dear Sir, > I want to use XCrySDen to visualize LaNi5 (Hexagonal, I=P6/mmm-191). I > wrote a PW input file which is described as below, but it can not be > shown as a right crystal structre. While I wrote some other input > files which is about FCC or BCC structure, it runs very well. Why? If the structure looks wrong by visualizing it with XCrysSDen is probably because it is wrong. I guess your atomic coordinates are ment to be cystal coordinates. If this is the case you should specify ATOMIC_POSITIONS crystal in the input Please, specify coordinates with at least 6-7 digits ... or do not complain if symmetry analysis is not what you expect Stefano de Gironcoli > > ========== > &control > calculation = 'scf' > restart_mode='from_scratch', > prefix='lani5', > pseudo_dir = '$PSEUDO_DIR/', > outdir='$TMP_DIR/' > / > &system > ibrav= 4, celldm(1) =9.477, celldm(3) =0.7944, nat= 6, ntyp= 2, > ecutwfc =26.0, ecutrho = 260.0 > / > &electrons > conv_thr = 1.0d-8 > / > ATOMIC_SPECIES > La 138.91 La.Pw91.UPF > Ni 58.69 Ni.pw91.UPF > ATOMIC_POSITIONS > La 0.00 0.00 0.00 > Ni 0.50 0.50 0.50 > Ni 0.50 0.00 0.50 > Ni 0.00 0.50 0.50 > Ni 0.6667 0.3333 0.00 > Ni 0.3333 0.6667 0.00 > K_POINTS {automatic} > 6 6 4 1 1 1 > > ======== > From tim_teatro at rogers.com Fri Aug 12 06:11:48 2005 From: tim_teatro at rogers.com (Timothy A.V. Teatro) Date: Fri, 12 Aug 2005 00:11:48 -0400 Subject: [Pw_forum] Compile and Configure Issue In-Reply-To: <20050806053641.22493.44266.Mailman@democritos.sissa.it> References: <20050806053641.22493.44266.Mailman@democritos.sissa.it> Message-ID: <42FC2184.1020500@rogers.com> Hello Everyone. I'm afraid I have a configuration question. I'm trying to put espresso on a reasonably new cluster. It uses the Portland Group compilers, but it seems that the configure script has a few problems with it. The cluster is of HP make with 193 Opteron CPUs. It's running Fedora Core 3. The compiler version is 5.2-4 When I run the configure script, I get the following: -bash-2.05b$ ./configure checking build system type... x86_64-unknown-linux-gnu checking architecture... x86_64 configure: WARNING: unsupported architecture checking for f90... no checking for Fortran 77 compiler default output file name... configure: error: Fortran 77 compiler cannot create executables See `config.log' for more details. The contents of the config.log file: This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by ESPRESSO configure 2.1, which was generated by GNU Autoconf 2.59. Invocation command line was $ ./configure ## --------- ## ## Platform. ## ## --------- ## hostname = node1 uname -m = x86_64 uname -r = 2.6.11.11 uname -s = Linux uname -v = #22 SMP Tue Jun 28 16:33:54 EDT 2005 /usr/bin/uname -p = unknown /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /home/timtro/bin/x86_64 PATH: /home/timtro/bin PATH: /opt/pgi/linux86-64/5.2/bin PATH: /usr/kerberos/bin PATH: /opt/pathscale/bin PATH: /usr/local/bin PATH: /bin PATH: /usr/bin PATH: /usr/X11R6/bin PATH: /opt/pathscale/bin PATH: /opt/sq/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:1377: checking build system type configure:1395: result: x86_64-unknown-linux-gnu configure:1493: WARNING: unsupported architecture configure:1559: checking for f90 configure:1588: result: no configure:1600: checking for Fortran 77 compiler version configure:1603: --version &5 ./configure: line 1: --version: command not found configure:1606: $? = 127 configure:1608: -v &5 ./configure: line 1: -v: command not found configure:1611: $? = 127 configure:1613: -V &5 ./configure: line 1: -V: command not found configure:1616: $? = 127 configure:1630: checking for Fortran 77 compiler default output file name configure:1633: conftest.f >&5 ./configure: line 1: conftest.f: command not found configure:1636: $? = 127 configure: failed program was: | program main | | end configure:1675: error: Fortran 77 compiler cannot create executables See `config.log' for more details. ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_build=x86_64-unknown-linux-gnu ac_cv_build_alias=x86_64-unknown-linux-gnu ac_cv_env_CC_set= ac_cv_env_CC_value= ac_cv_env_CFLAGS_set= ac_cv_env_CFLAGS_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CPP_set= ac_cv_env_CPP_value= ac_cv_env_F77_set= ac_cv_env_F77_value= ac_cv_env_FFLAGS_set= ac_cv_env_FFLAGS_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ## ----------------- ## ## Output variables. ## ## ----------------- ## CC='' CFLAGS='' CPP='' CPPFLAGS='' DEFS='' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='' EXEEXT='' F77='' FFLAGS='' LDFLAGS='' LIBOBJS='' LIBS='' LTLIBOBJS='' OBJEXT='' PACKAGE_BUGREPORT='' PACKAGE_NAME='ESPRESSO' PACKAGE_STRING='ESPRESSO 2.1' PACKAGE_TARNAME='espresso' PACKAGE_VERSION='2.1' PATH_SEPARATOR=':' SET_MAKE='' SHELL='/bin/sh' ac_ct_CC='' ac_ct_F77='' ar='' arflags='' bindir='${exec_prefix}/bin' build='x86_64-unknown-linux-gnu' build_alias='' build_cpu='x86_64' build_os='linux-gnu' build_vendor='unknown' cc='' cflags='' cpp='' cppflags='' datadir='${prefix}/share' dflags='' exec_prefix='NONE' f77='' f90=' f90' f90flags='' f90flags_noopt='' f90rule='' fdflags='' fflags='' fflags_noopt='' host_alias='' ifftw='' imodule='' includedir='${prefix}/include' infodir='${prefix}/info' ld='' ldflags='' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' libs='' localstatedir='${prefix}/var' mandir='${prefix}/man' mylib='' oldincludedir='/usr/include' pre_fdflags='' prefix='NONE' program_transform_name='s,x,x,' ranlib='' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## #define PACKAGE_BUGREPORT "" #define PACKAGE_NAME "ESPRESSO" #define PACKAGE_STRING "ESPRESSO 2.1" #define PACKAGE_TARNAME "espresso" #define PACKAGE_VERSION "2.1" configure: exit 77 I've tried modifying the script, but most of what goes on in that script is a little over my head. I've tried forcing it to check only for the PGI compilers, but that didn't change anything. Any help would be greatly appreciated! -- Timothy A.V. Teatro University of Ontario Institute of Technology w: 905.721.3111.ext.2930 c: 905.924.0020 e-mail: timtro at gmail.com From yay451 at mail.usask.ca Fri Aug 12 15:07:52 2005 From: yay451 at mail.usask.ca (Yansun Yao) Date: Fri, 12 Aug 2005 07:07:52 -0600 Subject: [Pw_forum] DOS calculation Message-ID: <1123852072.42fc9f289df1b@webmail.usask.ca> Dear PWscf users, It might be a silly question. I got confused by the output of the DOS calculation in example08. Is the DOS in file .dos should be equivenlent to the total projected DOS in file .pdos_total, or the sum of all projected DOS? I found that the larger the energy is , the more apparent the discrepancy is. Why? Thank you in advance! Yansun Yao From proffess at yandex.ru Fri Aug 12 15:34:04 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Fri, 12 Aug 2005 17:34:04 +0400 (MSD) Subject: [Pw_forum] Compile and Configure Issue In-Reply-To: <42FC2184.1020500@rogers.com> References: <20050806053641.22493.44266.Mailman@democritos.sissa.it> <42FC2184.1020500@rogers.com> Message-ID: <42FCA54C.000003.12513@ariel.yandex.ru> Hi, Try to use the next options: ./configure F90=mpif90 F77=mpif77 be sure that mpif90 (mpif77) invokes the pgf90 (pgf77). Good luck, Sergey From degironc at sissa.it Fri Aug 12 15:14:08 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 12 Aug 2005 15:14:08 +0200 Subject: [Pw_forum] DOS calculation References: <1123852072.42fc9f289df1b@webmail.usask.ca> Message-ID: <42FCA0A0.1040606@sissa.it> the file ni.dos in example08 contains four columns; they are: # E (eV) dosup(E) dosdw(E) Int dos(E) and are computed according to the tetrahedron method the file ni.pdos_tot contains 5 columns, they are # E (eV) dosup(E) dosdw(E) pdosup(E) pdosdw(E) and are computed by Gaussian broadening (read from input): ngauss,degauss= 1 0.020000 dosup/dw in the two files should be the same except for the different way they are computed. Tetrahedra give nicer plot, broadening gives more wiggly courves unless very many k-points are used (not the case in the example) but basic features are the same. pdosup/dw are the sum of atomic-wfc projected dos. they agree with dosup/dw for energy where the atomic wfcs are a good approximate basis set (tipically low lying states), they start to disagree at higher energies (usually somewhere above Fermi energy) stefano de Gironcoli Yansun Yao wrote: >Dear PWscf users > It might be a silly question. I got confused by the output of the DOS >calculation in example08. Is the DOS in file .dos should be equivenlent to the >total projected DOS in file .pdos_total, or the sum of all projected DOS? I >found that the larger the energy is , the more apparent the discrepancy is. >Why? > Thank you in advance! > Yansun Yao > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From shaposh at isp.nsc.ru Sat Aug 13 13:35:55 2005 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Sat, 13 Aug 2005 18:35:55 +0700 Subject: [Pw_forum] Fpmd 2.1.5 /example 21 crash. Message-ID: <1123932955.8110.20.camel@m00> Hellow, On my dual Xeon CPU PC , OS is Fedora Core4 x86, with Intel icc and ifort 8.1 compilers Fpmd-2.1.5 in Espresso-2.1.5 crashes then trying to run example 21. No problems with fpmd-2.1.3 in Espresso-2.1.4 package, compiled with all the same options. Trying to run example 21 with 32 H2O mol. crashes with the following output: /////////////////////////////////////////////////////////////////////// cleaning /home/alex/tmp... done running the calculation with 32 H2O molecules...*** glibc detected *** /home/alex/programs/espresso-2.1.5/bin/fpmd.x: free(): invalid next size (normal): 0x1d906d40 *** ======= Backtrace: ========= /lib/libc.so.6[0x175424] /lib/libc.so.6(__libc_free+0x77)[0x17595f] /home/alex/programs/espresso-2.1.5/bin/fpmd.x[0x8494006] /home/alex/programs/espresso-2.1.5/bin/fpmd.x[0x849406d] /home/alex/programs/espresso-2.1.5/bin/fpmd.x[0x810b05b] /home/alex/programs/espresso-2.1.5/bin/fpmd.x[0x810e929] /home/alex/programs/espresso-2.1.5/bin/fpmd.x[0x809c741] /home/alex/programs/espresso-2.1.5/bin/fpmd.x[0x809a3aa] /home/alex/programs/espresso-2.1.5/bin/fpmd.x[0x804c3e0] /home/alex/programs/espresso-2.1.5/bin/fpmd.x[0x804c0a8] /home/alex/programs/espresso-2.1.5/bin/fpmd.x[0x804befd] /lib/libc.so.6(__libc_start_main+0xc6)[0x126de6] /home/alex/programs/espresso-2.1.5/bin/fpmd.x(xdr_u_long +0x59)[0x804bd91] ======= Memory map: ======== 00111000-00112000 rwxp 00111000 00:00 0 00112000-00236000 r-xp 00000000 03:06 587113 /lib/libc-2.3.5.so 00236000-00238000 r-xp 00124000 03:06 587113 /lib/libc-2.3.5.so 00238000-0023a000 rwxp 00126000 03:06 587113 /lib/libc-2.3.5.so 0023a000-0023e000 rwxp 0023a000 00:00 0 0023e000-00247000 r-xp 00000000 03:06 585845 /lib/libnss_files-2.3.5.so 00247000-00248000 r-xp 00008000 03:06 585845 /lib/libnss_files-2.3.5.so 00248000-00249000 rwxp 00009000 03:06 585845 /lib/libnss_files-2.3.5.so 00282000-002a0000 r-xp 00000000 03:06 200183 /opt/intel_fc_80/lib/libcxa.so.5 002a0000-002a9000 rwxp 0001d000 03:06 200183 /opt/intel_fc_80/lib/libcxa.so.5 002a9000-00300000 rwxp 002a9000 00:00 0 00654000-00655000 rwxp 00654000 00:00 0 00934000-0093c000 r-xp 00000000 03:06 587126 /lib/librt-2.3.5.so 0093c000-0093d000 r-xp 00007000 03:06 587126 /lib/librt-2.3.5.so 0093d000-0093e000 rwxp 00008000 03:06 587126 /lib/librt-2.3.5.so 0093e000-00948000 rwxp 0093e000 00:00 0 00a34000-00a4e000 r-xp 00000000 03:06 587112 /lib/ld-2.3.5.so 00a4e000-00a4f000 r-xp 00019000 03:06 587112 /lib/ld-2.3.5.so 00a4f000-00a50000 rwxp 0001a000 03:06 587112 /lib/ld-2.3.5.so 00a59000-00a7d000 r-xp 00000000 03:06 200210 /opt/intel_fc_80/lib/libsvml.so 00a7d000-00aac000 rwxp 00023000 03:06 200210 /opt/intel_fc_80/lib/libsvml.so 00b7e000-00ba0000 r-xp 00000000 03:06 587114 /lib/libm-2.3.5.so 00ba0000-00ba1000 r-xp 00021000 03:06 587114 /lib/libm-2.3.5.so 00ba1000-00ba2000 rwxp 00022000 03:06 587114 /lib/libm-2.3.5.so 00ba4000-00ba6000 r-xp 00000000 03:06 587115 /lib/libdl-2.3.5.so 00ba6000-00ba7000 r-xp 00001000 03:06 587115 /lib/libdl-2.3.5.so 00ba7000-00ba8000 rwxp 00002000 03:06 587115 /lib/libdl-2.3.5.so 00ba9000-00bae000 r-xp 00000000 03:06 200213 /opt/intel_fc_80/lib/libunwind.so.5 00bae000-00baf000 rwxp 00004000 03:06 200213 /opt/intel_fc_80/lib/libunwind.so.5 00cec000-00d0e000 r-xp 00000000 03:06 489405 /opt/intel/mkl721/lib/32/libguide.so 00d0e000-00d13000 rwxp 00021000 03:06 489405 /opt/intel/mkl721/lib/32/libguide.so 00d13000-00d18000 rwxp 00d13000 00:00 0 00d31000-00d3f000 r-xp 00000000 03:06 587116 /lib/libpthread-2.3.5.so 00d3f000-00d40000 r-xp 0000d000 03:06 587116 /lib/libpthread-2.3.5.so 00d40000-00d41000 rwxp 0000e000 03:06 587116 /lib/libpthread-2.3.5.so 00d41000-00d43000 rwxp 00d41000 00:00 0 00dbc000-00dc5000 r-xp 00000000 03:06 587117 /lib/libgcc_s-4.0.0-20050520.so.1 00dc5000-00dc6000 rwxp 00009000 03:06 587117 /lib/libgcc_s-4.0.0-20050520.so.1 00dfc000-00e7e000 rwxp 00dfc000 00:00 0 00e95000-00e96000 r-xp 00e95000 00:00 0 00e96000-06e96000 rwxs 00000000 00:08 983041 /SYSV00000000 (deleted) 08048000-08528000 r-xp 00000000 03:07 1557240 /home/alex/programs/espresso-2.1.5/FPMD/fpmd.x 08528000-08583000 rwxp 004df000 03:07 1557240 /home/alex/programs/espresso-2.1.5/FPMD/fpmd.x 08583000-1beed000 rwxp 08583000 00:00 0 1d8f5000-1d938000 rwxp 1d8f5000 00:00 0 [heap] b7e00000-b7e21000 rwxp b7e00000 00:00 0 b7e21000-b7f00000 --xp b7e21000 00:00 0 bfde3000-bfdf9000 rwxp bfde3000 00:00 0 [stack] forrtl: error (76): IOT trap signal ./run_example: line 247: 22427 Killed $FPMD_COMMAND h2o-32.out done //////////////////////////////////////////////////////////////////////// From yanmingma at sohu.com Sat Aug 13 16:17:03 2005 From: yanmingma at sohu.com (yanmingma at sohu.com) Date: Sat, 13 Aug 2005 22:17:03 +0800 (CST) Subject: [Pw_forum] Further discussion on electronic DOS calculation Message-ID: <8039617.1123942623397.JavaMail.postfix@mx21.mail.sohu.com> Dear Stefano de Gironcoli and all users

As I understand, the electronic DOS calculation in pwscf as illustrated in example8 is ok for the semiconductor.

However, to deal with metals, we might meet some problems. In this case, we need very accurate description of the Fermi energy for metals.

In the SCF calculation, we usually use a Gaussian broadening method to obtain the Fermi energy.

Then in the DOS calcualtion, we use a more accurate tetrahedral technique to get the DOS curve.

But problems come due to the somewhat mismatch in the two steps, particular when one is seeking for the accuate electronic DOS at Fermi energy (N(0)). In principle, if we integrate the DOS below Fermi energy, then the integration should be equal to the total valence electron numbers. Unfortunately, in most cases I tested, the two numbers are different due to the obvious mismatch in the two steps. So I can not very trust the results of N(0) by the above procedure, even I know the N(0) is very close to the real.

Then I tried to do the following.

(1)I use a Gaussian broadening method to obtain the Fermi energy. then I use Gaussian broadening method to obtain the DOS curve. In this case, the integration get a very good agreement with the total electrons. However, due to the limitation in calculation of DOS in Gaussian broadening method, the calculated N(0) is not very trustable.

(2)I tried to use tetrahedral method to find the Fermi energy in SCF step. But I failed to get a reasonable Fermi energy if I remember correctly.

So, in a metal, how to get the very accurate N(0) is quite bothered me using PWSCF. Could anyone describe me how to do this?

I will highly appreciate your answer.

Regards

Yanming

-------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20050813/2d9770fe/attachment.htm From vranjan at uark.edu Mon Aug 15 21:54:45 2005 From: vranjan at uark.edu (Vivek Ranjan) Date: Mon, 15 Aug 2005 15:54:45 -0400 Subject: [Pw_forum] magnetic system Message-ID: <1bd0c01baafa.1baafa1bd0c0@uark.edu> Dear users, I am doing a calucation for a magnetic semiconductor. I would like to calculate Born effective charges for this system. However, the LSDA calculation does not seem feasible without smearing function. This precludes calucation of Born effective charges even though the system is a dielectric. The problem as we understand is that once we use smearing function, the system is taken as metallic and Born effective charges are not calculated. Is it possible to perform an LSDA calculation without smearing function ? or calculate Born effective chages even when smearing function is used in LSDA calculation ? Thank you, Vivek -------------- next part -------------- A non-text attachment was scrubbed... Name: vranjan.vcf Type: text/x-vcard Size: 374 bytes Desc: Card for Vivek Ranjan Url : /pipermail/attachments/20050815/4284002c/attachment.vcf From degironc at sissa.it Tue Aug 16 07:38:40 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 16 Aug 2005 07:38:40 +0200 Subject: [Pw_forum] magnetic system References: <1bd0c01baafa.1baafa1bd0c0@uark.edu> Message-ID: <43017BE0.6020209@sissa.it> In the present implementatio it is not possible. There is no fundamental problem in defining Z* for a magnetic insulator, however the way the code deals with magnetic system assumes it to be a metal (thus Z* is not defined). It will be fixed in future releases, but for the time being it is not possible. stefano Vivek Ranjan wrote: >Dear users, > >I am doing a calucation for a magnetic semiconductor. I would like to calculate Born effective charges for this system. However, the LSDA calculation does not seem feasible without smearing function. This precludes calucation of Born effective charges even though the system is a dielectric. The problem as we understand is that once we use smearing function, the system is taken as metallic and Born effective charges are not calculated. Is it possible to perform an LSDA calculation without smearing function ? or calculate Born effective chages even when smearing function is used in LSDA calculation ? > >Thank you, >Vivek > > > > > From yay451 at mail.usask.ca Thu Aug 18 03:55:36 2005 From: yay451 at mail.usask.ca (Yansun Yao) Date: Wed, 17 Aug 2005 19:55:36 -0600 Subject: [Pw_forum] Projected phonon DOS Message-ID: <1124330136.4303ea984c9ef@webmail.usask.ca> Dear Pwscf users, I am going to calculate the partial phonon DOS (phonon DOS contribution of a choosen atom). I guess that I should use tetrahedra method and modify matdyn.f90. But after reading matdyn.f90 and dost.f90, I am not very clear how to do it. My guess is the following: At first,one needs to extract the contribution of a choosen atom for every phonon frequency w(q). Then use this "partial" phonon frequency to calculate "partial" phonon DOS in the subroutine dos_t. Is it right? If it is, I have no clue know how to extract the "partial" frequency. Specifically, I don't know how frequencies square w2() is calculated in matdyn.f90. I am new to this area so maybe my guess is totally wrong. Could you give me some hints? Could anybody help me? Thanks in advance! Yansun Yao University of Saskatchewan From chaohao2002 at 163.com Thu Aug 18 09:04:59 2005 From: chaohao2002 at 163.com (Chaohao Hu) Date: Thu, 18 Aug 2005 15:04:59 +0800 Subject: [Pw_forum] phonon calculation of h2 molecule Message-ID: <20050818070233.3A4471127AE@democritos.sissa.it> Dear sir, I want to calculate the zero point energy of H2 molecule using pw.x and ph.x. Although I modify my input file many times, the same error information always in the 'h2.phG.out'output file appears. Some contents in it are described as following: =================================== Reading file h2.save ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_file : error # 1 problem reading file /home/hchfox/tmp0-1/h2.save %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... =================================== Here is a part of my input script file, ================================================= &control calculation='scf' restart_mode='from_scratch' prefix='h2' pseudo_dir ='$PSEUDO_DIR/' outdir='$TMP_DIR/' / &system ibrav=1, celldm(1)=18.0, nat=2, ntyp=1, ecutwfc = 24.0, ecutrho = 100.0 / &electrons conv_thr = 1.0d-8 / ATOMIC_SPECIES H 1.0079 H.pw91-van_ak.UPF ATOMIC_POSITITONS {crystal} H 0.489400961 0.50000000 0.50000000 H 0.410590389 0.50000000 0.50000000 K_POINTS automatic 1 1 1 0 0 0 phonon of H2 at Gamma point &inputph tr2_ph=1.0d-12, prefix='h2', epsil=.true., amass(1)=1.0079, outdir='$TMP_DIR/', fildyn='h2.dynG' / 0.0 0.0 0.0 ===================================================== Please help me analysis it. Thanks in advance. Best regards, Chaohao From chaohao2002 at 163.com Thu Aug 18 09:34:21 2005 From: chaohao2002 at 163.com (Chaohao Hu) Date: Thu, 18 Aug 2005 15:34:21 +0800 Subject: [Pw_forum] phonon calculation of h2 molecule Message-ID: <20050818073152.6CEF91127AE@democritos.sissa.it> Sorry??here is new error infromation shown in my terminal. ============================================ running the phonon calculation at Gamma .../run_h2_zero line 127: 23128 block error ============================================ And here is my the end of h2.phG.out file. ============================================ ...... Representaion 3 2 modes - To be done Representaion 4 2 modes - To be done PHONON : 5.76 CPU time Alpha used in Ewald sum = 1.2000 Electric Fields Calculation iter # 1 total cput ieme : 12.4 secs av.it.: 5.0 thresh= 0.100E-01 alpha_mix = 0.700 ddv_scf 2 = 0.480E_07 ============================================ Please help me! Thanks. Best regards, Chaohao ============================================================ Dr.Ch.H.Hu Institute of Metal Research,Chinese Academy of Sciences--IMR Wenhua Road, 72 110016, Shenyang, Liaoning (China) Phone: +086-024-23971641 Email: chhu at imr.ac.cn From eyvaz_isaev at yahoo.com Thu Aug 18 12:47:20 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 18 Aug 2005 03:47:20 -0700 (PDT) Subject: [Pw_forum] phonon calculation of h2 molecule In-Reply-To: <20050818070233.3A4471127AE@democritos.sissa.it> Message-ID: <20050818104720.65530.qmail@web60312.mail.yahoo.com> Hi, More likely, your scf-calculations failed, because > ATOMIC_POSITITONS {crystal} is wrong. It should be "ATOMIC_POSITIONS". I did it sucessfully using your corrected input file and met no problem. You will be surprized getting imaginary frequencies which presumabely is due to H2 molecule which has additional rotational degree of freedom. Bests, Eyvaz. ____________________________________________________ Start your day with Yahoo! - make it your home page http://www.yahoo.com/r/hs From eyvaz_isaev at yahoo.com Thu Aug 18 14:38:25 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 18 Aug 2005 05:38:25 -0700 (PDT) Subject: [Pw_forum] phonon calculation of h2 molecule In-Reply-To: <20050818073152.6CEF91127AE@democritos.sissa.it> Message-ID: <20050818123825.26918.qmail@web60324.mail.yahoo.com> Hi again, I would like just to add that I tested your input file on a single CPU PC. You can try start it using just one CPU, if you are using a parallel computer. If there is no problem the error is due to your network. Bests, Eyvaz. --- Chaohao Hu wrote: > Sorry??here is new error infromation shown in my > terminal. > ============================================ > running the phonon calculation at Gamma > .../run_h2_zero line 127: 23128 block error > ============================================ > > And here is my the end of h2.phG.out file. > ============================================ > ...... > Representaion 3 2 modes - To be done > Representaion 4 2 modes - To be done > PHONON : 5.76 CPU time > > Alpha used in Ewald sum = 1.2000 > > Electric Fields Calculation > > iter # 1 total cput ieme : 12.4 secs > av.it.: 5.0 > thresh= 0.100E-01 alpha_mix = 0.700 ddv_scf > 2 = 0.480E_07 > ============================================ > Please help me! > Thanks. > Best regards, > Chaohao > > > ============================================================ > Dr.Ch.H.Hu > Institute of Metal Research,Chinese Academy of > Sciences--IMR > Wenhua Road, 72 > 110016, Shenyang, Liaoning (China) > Phone: +086-024-23971641 > Email: chhu at imr.ac.cn > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From eyvaz_isaev at yahoo.com Thu Aug 18 19:57:34 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 18 Aug 2005 10:57:34 -0700 (PDT) Subject: [Pw_forum] Fermi Surface construction In-Reply-To: <1123932955.8110.20.camel@m00> Message-ID: <20050818175735.81610.qmail@web60321.mail.yahoo.com> Dear PWSCF and XCrySDen users, Finally, I submit a script and auxialiary files to plot the Fermi Surface. I tested it on a single CPU PC with Intel Fortran 8.1, and on a parallel IBM/SP computer. You have to copy bands_FS.f and kvecs_FS.f files into ./pwtools directory. Makefile in /pwtools should be replaced by the Makefile provided. You can compile additional files typing "make tools" in your Espresso source directory (or go to /pwtools and just type "make"). Then copy Fermi_Surface.sh into your working directory and edit it according to your purpose. I would like also ask Paolo to submit it into /examples directory in order to be included to Espresso distribution. I can do it for myself but I have no account for CVS. Hopefully I will be able to integrate a script for bands structure calculations, soon. Bests, Eyvaz. ____________________________________________________ Start your day with Yahoo! - make it your home page http://www.yahoo.com/r/hs -------------- next part -------------- A non-text attachment was scrubbed... Name: FS_final.tar.gz Type: application/x-gzip Size: 5028 bytes Desc: 3503087434-FS_final.tar.gz Url : /pipermail/attachments/20050818/7c2a981a/attachment.bin From proffess at yandex.ru Thu Aug 18 23:58:46 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Fri, 19 Aug 2005 01:58:46 +0400 (MSD) Subject: [Pw_forum] Definition of PsP in LDA+U Message-ID: <43050496.000001.10005@ariel.yandex.ru> Dear Pwscf users and authors, I look at input file of example 25 of espresso distribution and see: ..... ATOMIC_SPECIES O1 1. O.LDA.US.RRKJ3.UPF Fe1 1. Fe.pz-nd-rrkjus.UPF Fe2 1. Fe.pz-nd-rrkjus.UPF ........ Why all masses of PsP are equal to 1? Does it affect to calculations? Thanks, Sergey From marzari at MIT.EDU Fri Aug 19 00:26:27 2005 From: marzari at MIT.EDU (Nicola Marzari) Date: Thu, 18 Aug 2005 18:26:27 -0400 Subject: [Pw_forum] Definition of PsP in LDA+U + rotational freuqncies of molecules In-Reply-To: <43050496.000001.10005@ariel.yandex.ru> References: <43050496.000001.10005@ariel.yandex.ru> Message-ID: <43050B13.3000604@mit.edu> Dear Sergey, The masses of the atoms are only relevant in the case of a phonon or a molecular dynamics calculation. For the case of phonons, note that the interatomic force constants are independent of the masses, but the phonon frequencies are not (although they depend trivially on them via an inverse square root) Note also that in a molecular dynamics simulation with classical nuclei and boltzmann statistics (as it happens for pwscf, fpmd, and cp) the dynamical properties (e.g. diffusion coefficient) will depend on the masses, but the thermodynamical ones (e.g. the temperature of a phase transition) will not (the kinetic energy integral factors out in the expectation value of observables that do not depend on momenta). Quantum effects change this, usually mildly (e.g. the freezing temperatre of heavy water differs by only 4K from that of regular water). On a different matter, a post yesterday was mentioning vibrational frequencies for H_2 . A new, hopefully improved set of acoustic sum rules has been recently implemented in Pwscf by Nicolas Mounet, from our group. This should take care of all the zero-frequency modes for isolated systems. Best, nicola Sergey Lisenkov wrote: > Dear Pwscf users and authors, > > I look at input file of example 25 of espresso distribution and see: > > ..... > ATOMIC_SPECIES > O1 1. O.LDA.US.RRKJ3.UPF > Fe1 1. Fe.pz-nd-rrkjus.UPF > Fe2 1. Fe.pz-nd-rrkjus.UPF > ........ > > Why all masses of PsP are equal to 1? Does it affect to calculations? > > Thanks, > Sergey > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 617.2586534 marzari at mit.edu http://nnn.mit.edu From chaohao2002 at 163.com Fri Aug 19 02:58:53 2005 From: chaohao2002 at 163.com (Chaohao Hu) Date: Fri, 19 Aug 2005 08:58:53 +0800 Subject: [Pw_forum] phonon calculation of h2 molecule Message-ID: <20050819005620.16F74112733@democritos.sissa.it> Dear Mr. Eyvaz, Sorry,I modify "ATOMIC_POSITIONS" in my input file, the SCF calculation runs very well. My Espresso program is serial,but I can not run it on a single PC CPU. Can you provide me your input file? I will use it to test in my PC. Thanks in advance. Best regards, Chaohao ============================================================ Dr.Ch.H.Hu Institute of Metal Research,Chinese Academy of Sciences--IMR Wenhua Road, 72 110016, Shenyang, Liaoning (China) Phone: +086-024-23971641 Email: chhu at imr.ac.cn From hushujun at mail.sdu.edu.cn Mon Aug 22 05:36:12 2005 From: hushujun at mail.sdu.edu.cn (Shujun Hu) Date: Mon, 22 Aug 2005 11:36:12 +0800 Subject: [Pw_forum] 'etot_conv_thr' and 'forc_conv_thr' in the vc-relax calculation Message-ID: <324681772.10010@mail.sdu.edu.cn> Dear Drs, I have some questions about the vc-relax calculation. I donnt know what is mean by 'etot_conv_thr' and 'forc_conv_thr' in the &CONTROL block of input file. Does "forc_conv_thr" represent the force acting on the ions , or the "Total force"? After a vc-relax calculation of ZnO, i found that "forc_conv_thr" has been achieved in the middle of the calculation, but not the last 'it' (iteration). Also the "etot_conv_thr", does it mean "! total energy" in the general scf calculation or the "Etot" appearing in the process of reconstruction the new structure? And i found that these two values are different. Why? Following is the output information during the calculation where i think 'forc_conv_thr' has been achieved ('etot_conv_thr' may be not. Because i do not know what is mean.) and the input file. Best wishes Shujun Hu &&&&&&&&&&&&&&&&&&fragment of the outfiel&&&&&&&&&&&&&&&&&&&&& iteration # 3 ecut= 40.00 ryd beta=0.70 Davidson diagonalization (with overlap) ethr = 2.97E-09, avg # of iterations = 3.0 total cpu time spent up to now is 987.67 secs End of self-consistent calculation ! total energy = -317.10170234 ryd estimated scf accuracy < 0.00000002 ryd convergence has been achieved Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000020 -0.00000044 -0.00010795 atom 2 type 2 force = 0.00000028 0.00000022 -0.00002781 atom 3 type 1 force = -0.00000068 0.00000033 0.00010481 atom 4 type 2 force = 0.00000020 -0.00000011 0.00003096 Total force = 0.000156 Total SCF correction = 0.000710 entering subroutine stress ... total stress (ryd/bohr**3) (kbar) P= -0.64 -0.00001783 -0.00000002 0.00000000 -2.62 0.00 0.00 -0.00000002 -0.00001778 -0.00000001 0.00 -2.62 0.00 0.00000000 -0.00000001 0.00002266 0.00 0.00 3.33 kinetic stress (kbar) 13774.50 0.00 0.00 0.00 13774.50 0.00 0.00 0.00 13795.05 local stress (kbar) 646.00 -0.13 0.03 -0.13 645.85 0.11 0.03 0.11 -1492.82 nonloc. stress (kbar) 7199.63 0.00 0.00 0.00 7199.64 0.00 0.00 0.00 7192.88 hartree stress (kbar) 17494.88 0.05 -0.01 0.05 17494.94 -0.04 -0.01 -0.04 18496.33 exc-cor stress (kbar) -7171.72 0.00 0.00 0.00 -7171.72 0.00 0.00 0.00 -7171.97 corecor stress (kbar) 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ewald stress (kbar) -31945.92 0.08 -0.02 0.08 -31945.82 -0.07 -0.02 -0.07 -30816.14 hubbard stress (kbar) 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 Entering Dynamics; it = 11 time = 0.04840 pico-seconds new lattice vectors (alat unit) : 0.999930641 0.000000053 -0.000000029 -0.499965100 0.865964990 -0.000000011 -0.000000046 -0.000000054 1.603075493 new unit-cell volume = 333.8823 (a.u.)^3 new positions in cryst coord Zn 0.999979033 0.999979308 1.000277987 O 0.333311334 0.666643783 0.880471939 Zn 0.333323184 0.666651530 0.500187584 O 0.999989077 0.999984074 0.380882269 new positions in cart coord (alat unit) Zn 0.499954876 0.865947070 1.603521087 O -0.000010450 0.577290146 1.411462971 Zn -0.000002457 0.577296876 0.801838442 O 0.499962564 0.865951231 0.610582992 Ekin = 0.00000146 Ryd T = 0.2 K Etot = -317.10170088 &&&&&&&&&&&&&&&&&&fragment of the outfiel&&&&&&&&&&&&&&&&&&&&& &&&&&&&&&&&&&&&&&&&&&&&&input file&&&&&&&&&&&&&&&&&&&&&&&& &CONTROL title = zno , calculation = 'vc-relax' , restart_mode = 'from_scratch' , outdir = '/home/disk2/work/4.19/calculate_u/zno/new/temp/' , pseudo_dir = '/home/disk2/work/bin/PSEUDOPOTENTIAL/' , prefix = zno , disk_io = 'minimal' , verbosity = 'high' , nstep = 100 , tstress = .true. , tprnfor = .true. , dt = 100 , tefield = .false. , / &SYSTEM ibrav = 4, celldm(1) = 6.219036059, celldm(3) = 1.602891754, nat = 4, ntyp = 2, ecutwfc = 40 , nosym = .true. , nbnd = 25, occupations = 'tetrahedra' , degauss = 0.005 , smearing = 'methfessel-paxton' , nspin = 1 , lda_plus_u = .false. , / &ELECTRONS electron_maxstep = 500, startingpot = 'atomic' , startingwfc = 'atomic' , mixing_mode = 'plain' , mixing_ndim = 20, diago_thr_init = 1.0E-7 , / &IONS ion_dynamics = 'damp' , / &CELL cell_dynamics = 'damp-w' , / ATOMIC_SPECIES Zn 65.38000 Zn.pbe-van.UPF O 15.99900 O.pbe-rrkjus.UPF ATOMIC_POSITIONS angstrom Zn 1.645450787 2.850004902 5.274845672 O -0.000000677 1.900003430 4.650981508 Zn 0.000000241 1.900002591 2.637001887 O 1.645451454 2.850004118 2.015462269 K_POINTS automatic 4 4 4 0 0 0 &&&&&&&&&&&&&&&&&&&&&&&&input file&&&&&&&&&&&&&&&&&&&&&&&& From sbraccia at sissa.it Mon Aug 22 13:28:21 2005 From: sbraccia at sissa.it (carlo sbraccia) Date: Mon, 22 Aug 2005 07:28:21 -0400 Subject: [Pw_forum] 'etot_conv_thr' and 'forc_conv_thr' in the vc-relax calculation In-Reply-To: <324681772.10010@mail.sdu.edu.cn> References: <324681772.10010@mail.sdu.edu.cn> Message-ID: <4309B6D5.90302@sissa.it> Dear Shujun Hu, from the file Doc/INPUT_PW (where all the input keywords are documented): etot_conv_thr REAL ( default = 1.0D-4 ) convergence threshold on total energy (a.u) for ionic minimization: the convergence criterion is satisfied when the total energy changes less than etot_conv_thr between two consecutive scf steps. See also forc_conv_thr - both criteria must be satisfied forc_conv_thr REAL ( default = 1.0D-3 ) convergence threshold on forces (a.u) for ionic minimization: the convergence criterion is satisfied when all components of all forces are smaller than forc_conv_thr. See also etot_conv_thr - both criteria must be satisfied carlo From giannozz at nest.sns.it Mon Aug 22 15:14:35 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 22 Aug 2005 15:14:35 +0200 Subject: [Pw_forum] Compile and Configure Issue In-Reply-To: <42FC2184.1020500@rogers.com> References: <20050806053641.22493.44266.Mailman@democritos.sissa.it> <42FC2184.1020500@rogers.com> Message-ID: <200508221514.35728.giannozz@nest.sns.it> On Friday 12 August 2005 06:11, Timothy A.V. Teatro wrote: > I'm afraid I have a configuration question. I'm trying to put espresso > on a reasonably new cluster. you should use a reasonably new configure as well: the version you are using does not seem to recognize your architecture, but recent versions should Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Mon Aug 22 16:56:21 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 22 Aug 2005 16:56:21 +0200 Subject: [Pw_forum] Fpmd 2.1.5 /example 21 crash. In-Reply-To: <1123932955.8110.20.camel@m00> References: <1123932955.8110.20.camel@m00> Message-ID: <200508221656.21620.giannozz@nest.sns.it> On Saturday 13 August 2005 13:35, Alexander Shaposhnikov wrote: > On my dual Xeon CPU PC , OS is Fedora Core4 x86, with Intel icc and > ifort 8.1 compilers > > Fpmd-2.1.5 in Espresso-2.1.5 crashes then trying to run example 21. > No problems with fpmd-2.1.3 in Espresso-2.1.4 package, compiled > with all the same options. > > Trying to run example 21 with 32 H2O mol. crashes with the following > output [...] it is almost impossible to locate the origin of a crash when it occurs in a library call. It might be a bug somewhere in the code leading to an out-of-bound error, but who knows. On my PC it works. If you have more info on this, please let us know Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Mon Aug 22 17:09:38 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 22 Aug 2005 17:09:38 +0200 Subject: [Pw_forum] Projected phonon DOS In-Reply-To: <1124330136.4303ea984c9ef@webmail.usask.ca> References: <1124330136.4303ea984c9ef@webmail.usask.ca> Message-ID: <200508221709.38618.giannozz@nest.sns.it> On Thursday 18 August 2005 03:55, Yansun Yao wrote: > I am going to calculate the partial phonon DOS (phonon DOS > contribution of a choosen atom) see: http://www.democritos.it/pipermail/pw_forum/2005-April/002354.html http://www.democritos.it/pipermail/pw_forum/2004-August/001203.html Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From hushujun at mail.sdu.edu.cn Mon Aug 22 17:56:12 2005 From: hushujun at mail.sdu.edu.cn (Shujun Hu) Date: Mon, 22 Aug 2005 23:56:12 +0800 Subject: [Pw_forum] 'etot_conv_thr' and 'forc_conv_thr' in the vc-relax calculation Message-ID: <324726172.07771@mail.sdu.edu.cn> Dear Sbraccia, Thanks for your reply. I have checked the output file. But something confused me. At the end of the mail there is the fragment of the output file. At it=4 and the following iteration i found that criteria for the force has been satisfied (Default values of etot_conv_thr and forc_conv_thr are used,1.0D-4 and 1.0D-3 respectively, see the input file in the previous mail please). And the total energy change between it=4 and it=5, about 3.0D-6, is also less than etot_conv_thr, 1.0D-4. But calculation had not stopped. I do not know why. I would be appreciating with any reply. Best wishes Shujun Hu ! total energy = -317.10168983 ryd estimated scf accuracy < 0.00000049 ryd convergence has been achieved Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000300 0.00000196 0.00074762 atom 2 type 2 force = -0.00000279 -0.00000316 -0.00072266 atom 3 type 1 force = -0.00000387 -0.00000137 0.00078596 atom 4 type 2 force = 0.00000366 0.00000257 -0.00081093 Total force = 0.001535 Total SCF correction = 0.003535 entering subroutine stress ... total stress (ryd/bohr**3) (kbar) P= 0.38 -0.00000309 0.00000004 0.00000000 -0.45 0.01 0.00 0.00000004 -0.00000314 0.00000000 0.01 -0.46 0.00 0.00000000 0.00000000 0.00001406 0.00 0.00 2.07 kinetic stress (kbar) 13772.77 -0.01 0.00 -0.01 13772.78 0.00 0.00 0.00 13798.59 local stress (kbar) 528.38 -0.82 0.02 -0.82 529.25 0.06 0.02 0.06 -1259.78 nonloc. stress (kbar) 7200.80 0.00 0.00 0.00 7200.80 0.00 0.00 0.00 7191.89 hartree stress (kbar) 17537.79 0.31 -0.01 0.31 17537.46 -0.02 -0.01 -0.02 18411.82 exc-cor stress (kbar) -7171.55 0.00 0.00 0.00 -7171.55 0.00 0.00 0.00 -7172.26 corecor stress (kbar) 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ewald stress (kbar) -31868.64 0.52 -0.01 0.52 -31869.20 -0.04 -0.01 -0.04 -30968.19 hubbard stress (kbar) 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 Entering Dynamics; it = 4 time = 0.01452 pico-seconds new lattice vectors (alat unit) : 0.999996051 0.000000090 -0.000000001 -0.499997948 0.866021846 0.000000000 -0.000000001 -0.000000001 1.602899272 new unit-cell volume = 333.8894 (a.u.)^3 new positions in cryst coord Zn 0.999981148 0.999980324 1.000155166 O 0.333316157 0.666646051 0.880705428 Zn 0.333324345 0.666651729 0.500100426 O 0.999986986 0.999982887 0.381427318 new positions in cart coord (alat unit) Zn 0.499989088 0.866004895 1.603147987 O -0.000006818 0.577330073 1.411682088 Zn -0.000001469 0.577334991 0.801610609 O 0.499993645 0.866007115 0.611389569 Ekin = 0.00001553 Ryd T = 0.2 K Etot = -317.10167430 NEW-OLD atomic charge density approx. for the potential NEW K-POINTS 0.0000000 0.0000000 0.0000000 0.0312500 0.0000000 0.0000000 0.1559674 0.0625000 0.0000000 0.0000000 -0.3119348 0.0312500 0.0000000 0.2886763 0.0000000 0.0625000 0.0000000 0.2886763 0.1559674 0.0625000 0.0000000 0.2886763 -0.3119348 0.0625000 0.0000000 0.2886763 -0.1559674 0.0625000 0.0000001 -0.5773526 0.0000000 0.0312500 0.0000001 -0.5773526 0.1559674 0.0625000 0.0000001 -0.5773526 -0.3119348 0.0312500 0.2500010 0.1443381 0.0000000 0.0625000 0.2500010 0.1443381 0.1559674 0.0625000 0.2500010 0.1443381 -0.3119348 0.0625000 0.2500010 0.1443381 -0.1559674 0.0625000 0.2500009 0.4330144 0.0000000 0.0625000 0.2500009 0.4330144 0.1559674 0.0625000 0.2500009 0.4330144 -0.3119348 0.0625000 0.2500009 0.4330144 -0.1559674 0.0625000 0.2500010 -0.4330145 0.0000000 0.0625000 0.2500010 -0.4330145 0.1559674 0.0625000 0.2500010 -0.4330145 -0.3119348 0.0625000 0.2500010 -0.4330145 -0.1559674 0.0625000 0.2500010 -0.1443382 0.0000000 0.0625000 0.2500010 -0.1443382 0.1559674 0.0625000 0.2500010 -0.1443382 -0.3119348 0.0625000 0.2500010 -0.1443382 -0.1559674 0.0625000 -0.5000019 -0.2886763 0.0000000 0.0312500 -0.5000019 -0.2886763 0.1559674 0.0625000 -0.5000019 -0.2886763 -0.3119348 0.0312500 -0.5000020 0.0000000 0.0000000 0.0625000 -0.5000020 0.0000000 0.1559674 0.0625000 -0.5000020 0.0000000 -0.3119348 0.0625000 -0.5000020 0.0000000 -0.1559674 0.0625000 -0.5000019 -0.8660289 0.0000000 0.0312500 -0.5000019 -0.8660289 0.1559674 0.0625000 -0.5000019 -0.8660289 -0.3119348 0.0312500 extrapolated charge = 36.00001 extrapolated charge renormalised to 36.00000 total cpu time spent up to now is 399.75 secs Self-consistent Calculation iteration # 1 ecut= 40.00 ryd beta=0.70 Davidson diagonalization (with overlap) ethr = 1.00E-05, avg # of iterations = 2.0 Threshold (ethr) on eigenvalues was too large: Diagonalizing with lowered threshold Davidson diagonalization (with overlap) ethr = 3.36E-07, avg # of iterations = 1.3 total cpu time spent up to now is 432.02 secs total energy = -317.10168813 ryd estimated scf accuracy < 0.00001202 ryd iteration # 2 ecut= 40.00 ryd beta=0.70 Davidson diagonalization (with overlap) ethr = 3.34E-08, avg # of iterations = 3.0 total cpu time spent up to now is 453.72 secs total energy = -317.10167292 ryd estimated scf accuracy < 0.00003539 ryd iteration # 3 ecut= 40.00 ryd beta=0.70 Davidson diagonalization (with overlap) ethr = 3.34E-08, avg # of iterations = 3.3 total cpu time spent up to now is 473.92 secs End of self-consistent calculation ! total energy = -317.10169632 ryd estimated scf accuracy < 0.00000022 ryd convergence has been achieved Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000192 0.00000061 0.00050028 atom 2 type 2 force = -0.00000183 -0.00000065 -0.00013547 atom 3 type 1 force = -0.00000185 -0.00000067 0.00040804 atom 4 type 2 force = 0.00000176 0.00000072 -0.00077286 Total force = 0.001016 Total SCF correction = 0.003270 entering subroutine stress ... total stress (ryd/bohr**3) (kbar) P= 0.08 -0.00000935 0.00000001 0.00000000 -1.37 0.00 0.00 0.00000001 -0.00000934 -0.00000001 0.00 -1.37 0.00 0.00000000 -0.00000001 0.00002027 0.00 0.00 2.98 kinetic stress (kbar) 13773.45 -0.01 0.00 -0.01 13773.46 0.00 0.00 0.00 13797.15 local stress (kbar) 580.94 -0.44 0.03 -0.44 581.17 0.12 0.03 0.12 -1364.20 nonloc. stress (kbar) 7200.16 0.00 0.00 0.00 7200.16 0.00 0.00 0.00 7192.33 hartree stress (kbar) 17518.70 0.17 -0.01 0.17 17518.61 -0.04 -0.01 -0.04 18449.76 exc-cor stress (kbar) -7171.62 0.00 0.00 0.00 -7171.62 0.00 0.00 0.00 -7172.13 corecor stress (kbar) 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ewald stress (kbar) -31903.00 0.28 -0.02 0.28 -31903.15 -0.08 -0.02 -0.08 -30899.93 hubbard stress (kbar) 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 Entering Dynamics; it = 5 time = 0.01936 pico-seconds new lattice vectors (alat unit) : 0.999993079 0.000000125 -0.000000001 -0.499996431 0.866019221 -0.000000001 -0.000000002 -0.000000003 1.602908228 new unit-cell volume = 333.8893 (a.u.)^3 new positions in cryst coord Zn 0.999981747 0.999980505 1.000238139 O 0.333306320 0.666642723 0.880334185 Zn 0.333323608 0.666651475 0.500184628 O 0.999988338 0.999983382 0.381115449 new positions in cart coord (alat unit) Zn 0.499988141 0.866002459 1.603289941 O -0.000014971 0.577325450 1.411094908 Zn -0.000002058 0.577333031 0.801750055 O 0.499993294 0.866004954 0.610893087 Ekin = 0.00001990 Ryd T = 0.2 K Etot = -317.10167642 NEW-OLD atomic charge density approx. for the potential NEW K-POINTS 0.0000000 0.0000000 0.0000000 0.0312500 0.0000000 0.0000000 0.1559665 0.0625000 0.0000000 0.0000000 -0.3119330 0.0312500 0.0000000 0.2886772 0.0000000 0.0625000 0.0000000 0.2886772 0.1559665 0.0625000 0.0000000 0.2886772 -0.3119330 0.0625000 0.0000000 0.2886772 -0.1559665 0.0625000 0.0000001 -0.5773543 0.0000000 0.0312500 0.0000001 -0.5773543 0.1559665 0.0625000 0.0000001 -0.5773543 -0.3119330 0.0312500 0.2500017 0.1443386 0.0000000 0.0625000 0.2500017 0.1443386 0.1559665 0.0625000 0.2500017 0.1443386 -0.3119330 0.0625000 0.2500017 0.1443386 -0.1559665 0.0625000 0.2500017 0.4330157 0.0000000 0.0625000 0.2500017 0.4330157 0.1559665 0.0625000 0.2500017 0.4330157 -0.3119330 0.0625000 0.2500017 0.4330157 -0.1559665 0.0625000 0.2500018 -0.4330158 0.0000000 0.0625000 0.2500018 -0.4330158 0.1559665 0.0625000 0.2500018 -0.4330158 -0.3119330 0.0625000 0.2500018 -0.4330158 -0.1559665 0.0625000 0.2500017 -0.1443386 0.0000000 0.0625000 0.2500017 -0.1443386 0.1559665 0.0625000 0.2500017 -0.1443386 -0.3119330 0.0625000 0.2500017 -0.1443386 -0.1559665 0.0625000 -0.5000034 -0.2886771 0.0000000 0.0312500 -0.5000034 -0.2886771 0.1559665 0.0625000 -0.5000034 -0.2886771 -0.3119330 0.0312500 -0.5000035 0.0000001 0.0000000 0.0625000 -0.5000035 0.0000001 0.1559665 0.0625000 -0.5000035 0.0000001 -0.3119330 0.0625000 -0.5000035 0.0000001 -0.1559665 0.0625000 -0.5000034 -0.8660315 0.0000000 0.0312500 -0.5000034 -0.8660315 0.1559665 0.0625000 -0.5000034 -0.8660315 -0.3119330 0.0312500 extrapolated charge = 35.99999 extrapolated charge renormalised to 36.00000 total cpu time spent up to now is 487.62 secs Self-consistent Calculation iteration # 1 ecut= 40.00 ryd beta=0.70 Davidson diagonalization (with overlap) ethr = 1.00E-05, avg # of iterations = 2.0 ------------------------------ -- Shujun Hu e-mail: hushujun at 163.com Shandong university Phone: +86/0531-88375097 Jinan, Shandong Province, China, 250100 From sbraccia at sissa.it Mon Aug 22 17:40:09 2005 From: sbraccia at sissa.it (carlo sbraccia) Date: Mon, 22 Aug 2005 11:40:09 -0400 Subject: [Pw_forum] 'etot_conv_thr' and 'forc_conv_thr' in the vc-relax calculation In-Reply-To: <324726172.07771@mail.sdu.edu.cn> References: <324726172.07771@mail.sdu.edu.cn> Message-ID: <4309F1D9.2010100@sissa.it> Dear Shujun Hu, in the case of variable cell relaxations, a third criterion has to be satisfied: all the components of the stress tensor must be smaller than 0.5 kbar (this cannot be set in the input file). In your case the some components are still larger than this threshold. If you want to change this threshold look for the variable epsp in the PW/vcsmd.f90 file and recompile. carlo From chaohao2002 at 163.com Tue Aug 23 06:40:15 2005 From: chaohao2002 at 163.com (Chaohao Hu) Date: Tue, 23 Aug 2005 12:40:15 +0800 Subject: [Pw_forum] phonon calculation of h2 molecule Message-ID: <20050823043741.94F32112793@democritos.sissa.it> Dear Sir?? I can now calculate the zero point energy of hydrogen molecule. In my phonon input file, I must modify the value of epsil from '.true.' to '.false.'. Why? Who can help me explain more details about this problem? The final value of vibrational frequency of hydrogen is about 4300 cm-1 and reseanoble in some extent. Thanks. >Hi again, > >I would like just to add that I tested your input file >on a single CPU PC. >You can try start it using just one CPU, if you are >using a parallel computer. If there is no problem the >error is due to your network. > >Bests, >Eyvaz. > > >--- Chaohao Hu wrote: > >> Sorry??here is new error infromation shown in my >> terminal. >> ============================================ >> running the phonon calculation at Gamma >> .../run_h2_zero line 127: 23128 block error >> ============================================ >> >> And here is my the end of h2.phG.out file. >> ============================================ >> ...... >> Representaion 3 2 modes - To be done >> Representaion 4 2 modes - To be done >> PHONON : 5.76 CPU time >> >> Alpha used in Ewald sum = 1.2000 >> >> Electric Fields Calculation >> >> iter # 1 total cput ieme : 12.4 secs >> av.it.: 5.0 >> thresh= 0.100E-01 alpha_mix = 0.700 ddv_scf >> 2 = 0.480E_07 >> ============================================ >> Please help me! >> Thanks. >> Best regards, >> Chaohao >> >> >> >============================================================ >> Dr.Ch.H.Hu >> Institute of Metal Research,Chinese Academy of >> Sciences--IMR >> Wenhua Road, 72 >> 110016, Shenyang, Liaoning (China) >> Phone: +086-024-23971641 >> Email: chhu at imr.ac.cn >> >> >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > Thanks in advance. Best regards, Chaohao ============================================================ Dr.Ch.H.Hu Institute of Metal Research,Chinese Academy of Sciences--IMR Wenhua Road, 72 110016, Shenyang, Liaoning (China) Phone: +086-024-23971641 Email: chhu at imr.ac.cn From giannozz at nest.sns.it Tue Aug 23 11:45:30 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Aug 2005 11:45:30 +0200 Subject: [Pw_forum] phonon calculation of h2 molecule In-Reply-To: <20050823043741.94F32112793@democritos.sissa.it> References: <20050823043741.94F32112793@democritos.sissa.it> Message-ID: <200508231145.30462.giannozz@nest.sns.it> On Tuesday 23 August 2005 06:40, Chaohao Hu wrote: > I can now calculate the zero point energy of hydrogen molecule. > In my phonon input file, I must modify the value of epsil from > '.true.' to '.false.'. Why? are you using pseudopotentials with the local part only for H? This is a special case that has been fixed and broken several times. Maybe it is broken again in the calculation of dielectric properties. For the H2 molecule you do not need effective charges anyway. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From eyvaz_isaev at yahoo.com Tue Aug 23 13:18:34 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 23 Aug 2005 04:18:34 -0700 (PDT) Subject: [Pw_forum] phonon calculation of h2 molecule In-Reply-To: <200508231145.30462.giannozz@nest.sns.it> Message-ID: <20050823111834.80872.qmail@web60322.mail.yahoo.com> Dear Paolo, I tested this job before on my PC (Opteron/SuSe9.2/IFC8.1) using HUSPBE.RRKJ3 pseudopotential and PWSCF v.2.1.5 and met no problem with epsil=.true. or .false. options. Sure, for H2 there is no reason using epsil=.true. Even used with epsil=.true. the code results in almost zero charges. Bests, Eyvaz. --- Paolo Giannozzi wrote: > On Tuesday 23 August 2005 06:40, Chaohao Hu wrote: > > > I can now calculate the zero point energy of > hydrogen molecule. > > In my phonon input file, I must modify the value > of epsil from > > '.true.' to '.false.'. Why? > > are you using pseudopotentials with the local part > only for H? > This is a special case that has been fixed and > broken several > times. Maybe it is broken again in the calculation > of dielectric > properties. For the H2 molecule you do not need > effective > charges anyway. > > Paolo > > -- > Paolo Giannozzi e-mail: > giannozz at nest.sns.it > Scuola Normale Superiore Phone: +39/050-509876, > Fax:-563513 > Piazza dei Cavalieri 7 I-56126 Pisa, Italy > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________ Yahoo! Mail for Mobile Take Yahoo! Mail with you! Check email on your mobile phone. http://mobile.yahoo.com/learn/mail From alcantar at phys.ksu.edu Tue Aug 23 17:43:06 2005 From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol) Date: Tue, 23 Aug 2005 10:43:06 -0500 Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. Message-ID: Dear all, I've been running a phonon calculation (54 modes). Everything was OK but suddenly things went wrong at mode 22; it cannot converge. I do not what happened, do I have to restart from the very beginning? Is everything lost? I'd appreciate your commments. Below I show the input and output files. --------------------input--------------- Phonons of COCu atX &inputph tr2_ph=1.0d-16, prefix = 'co_cu100' epsil=.false., alpha_mix(1) = 0.1 amass(1)=63.546, amass(2)=15.9994 amass(3)=12.0107 time_max= 85500 outdir='/home/ac/stolbov/scratch/tmpcoculdaphX/', fildyn='co_cu100_.dynX' / 0.5 0.0 0.0 ---------------------output-------------------- Program PHONON v.2.1.3 starts ... Today is 23Aug2005 at 2: 4:46 Parallel version (MPI) Number of processors in use: 16 R & G space division: nprocp = 16 Ultrasoft (Vanderbilt) Pseudopotentials Reading file co_cu100.save ... read complete Reading file co_cu100.save ... read complete Planes per process (thick) : nr3 =432 npp = 27 ncplane = 2916 Planes per process (smooth): nr3s=243 npps= 16 ncplanes= 1024 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 27 134 37464 16 45 7215 15 1329 2 27 134 37464 16 45 7221 15 1329 3 27 135 37487 16 45 7225 15 1329 4 27 134 37454 15 45 7229 15 1329 5 27 134 37468 15 45 7225 15 1329 6 27 134 37468 15 45 7225 14 1316 7 27 134 37464 15 45 7211 14 1316 8 27 134 37464 15 44 7202 15 1321 9 27 134 37464 15 44 7210 15 1317 10 27 134 37464 15 44 7190 14 1322 11 27 134 37464 15 45 7211 15 1321 12 27 134 37462 15 45 7215 14 1322 13 27 134 37462 15 45 7217 14 1322 14 27 134 37462 15 45 7215 14 1322 15 27 134 37462 15 45 7213 14 1320 16 27 134 37462 15 45 7229 15 1325 0 432 2145 599435 243 717 115453 233 21169 nbndx = 104 nbnd = 104 natomwfc = 100 npwx = 1013 nelec = 174.00 nkb = 214 ngl = 6742 starting from an old run Doing now the calculation for q point nr 1 Restart from Iteration # 2 of Representation # 22 Phonons of COCu atX crystal is bravais-lattice index = 6 lattice parameter (a_0) = 6.7096 a.u. unit-cell volume = 2416.4615 (a.u.)^3 number of atoms/cell = 18 number of atomic types = 3 kinetic-energy cut-off = 50.0000 Ry charge density cut-off = 600.0000 Ry convergence threshold = 1.0E-16 beta = 0.1000 number of iterations used = 4 celldm(1)= 6.70960 celldm(2)= 0.00000 celldm(3)= 8.00000 celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.0000 0.0000 0.0000 ) a(2) = ( 0.0000 1.0000 0.0000 ) a(3) = ( 0.0000 0.0000 8.0000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.0000 0.0000 0.0000 ) b(2) = ( 0.0000 1.0000 0.0000 ) b(3) = ( 0.0000 0.0000 0.1250 ) Atoms inside the unit cell: Cartesian axes site n. atom mass positions (a_0 units) 1 O 15.9994 tau( 1) = ( 0.00000 0.50000 2.33471 ) 2 C 12.0107 tau( 2) = ( 0.00000 0.50000 2.01237 ) 3 Cu 63.5460 tau( 3) = ( 0.00000 0.50000 1.49940 ) 4 Cu 63.5460 tau( 4) = ( 0.50000 0.00000 1.48473 ) 5 Cu 63.5460 tau( 5) = ( 0.50000 0.50000 0.99696 ) 6 Cu 63.5460 tau( 6) = ( 0.00000 0.00000 0.99695 ) 7 Cu 63.5460 tau( 7) = ( 0.00000 0.50000 0.49791 ) 8 Cu 63.5460 tau( 8) = ( 0.50000 0.00000 0.49377 ) 9 Cu 63.5460 tau( 9) = ( 0.00000 0.00000 0.00000 ) 10 Cu 63.5460 tau(10) = ( 0.50000 0.50000 0.00000 ) 11 Cu 63.5460 tau(11) = ( 0.50000 0.00000 -0.49377 ) 12 Cu 63.5460 tau(12) = ( 0.00000 0.50000 -0.49791 ) 13 Cu 63.5460 tau(13) = ( 0.00000 0.00000 -0.99695 ) 14 Cu 63.5460 tau(14) = ( 0.50000 0.50000 -0.99696 ) 15 Cu 63.5460 tau(15) = ( 0.50000 0.00000 -1.48473 ) 16 Cu 63.5460 tau(16) = ( 0.00000 0.50000 -1.49940 ) 17 C 12.0107 tau(17) = ( 0.00000 0.50000 -2.01237 ) 18 O 15.9994 tau(18) = ( 0.00000 0.50000 -2.33471 ) Computing dynamical matrix for q = ( 0.50000 0.00000 0.00000 ) 9 Sym.Ops. (with q -> -q+G ) G cutoff = 684.2027 ( 37464 G-vectors) FFT grid: ( 54, 54,432) G cutoff = 228.0676 ( 7215 G-vectors) smooth grid: ( 32, 32,243) number of k points= 72 gaussian broad. (ryd)= 0.0147 ngauss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0200000 k( 2) = ( 0.5000000 0.0000000 0.0000000), wk = 0.0000000 k( 3) = ( 0.0000000 0.1000000 0.0000000), wk = 0.0400000 k( 4) = ( 0.5000000 0.1000000 0.0000000), wk = 0.0000000 k( 5) = ( 0.0000000 0.2000000 0.0000000), wk = 0.0400000 k( 6) = ( 0.5000000 0.2000000 0.0000000), wk = 0.0000000 k( 7) = ( 0.0000000 0.3000000 0.0000000), wk = 0.0400000 k( 8) = ( 0.5000000 0.3000000 0.0000000), wk = 0.0000000 k( 9) = ( 0.0000000 0.4000000 0.0000000), wk = 0.0400000 k( 10) = ( 0.5000000 0.4000000 0.0000000), wk = 0.0000000 k( 11) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.0200000 k( 12) = ( 0.5000000 -0.5000000 0.0000000), wk = 0.0000000 k( 13) = ( 0.1000000 0.1000000 0.0000000), wk = 0.0800000 k( 14) = ( 0.6000000 0.1000000 0.0000000), wk = 0.0000000 k( 15) = ( 0.1000000 0.2000000 0.0000000), wk = 0.0800000 k( 16) = ( 0.6000000 0.2000000 0.0000000), wk = 0.0000000 k( 17) = ( 0.1000000 0.3000000 0.0000000), wk = 0.0800000 k( 18) = ( 0.6000000 0.3000000 0.0000000), wk = 0.0000000 k( 19) = ( 0.1000000 0.4000000 0.0000000), wk = 0.0800000 k( 20) = ( 0.6000000 0.4000000 0.0000000), wk = 0.0000000 k( 21) = ( 0.1000000 -0.5000000 0.0000000), wk = 0.0400000 k( 22) = ( 0.6000000 -0.5000000 0.0000000), wk = 0.0000000 k( 23) = ( 0.2000000 0.2000000 0.0000000), wk = 0.0800000 k( 24) = ( 0.7000000 0.2000000 0.0000000), wk = 0.0000000 k( 25) = ( 0.2000000 0.3000000 0.0000000), wk = 0.0800000 k( 26) = ( 0.7000000 0.3000000 0.0000000), wk = 0.0000000 k( 27) = ( 0.2000000 0.4000000 0.0000000), wk = 0.0800000 k( 28) = ( 0.7000000 0.4000000 0.0000000), wk = 0.0000000 k( 29) = ( 0.2000000 -0.5000000 0.0000000), wk = 0.0400000 k( 30) = ( 0.7000000 -0.5000000 0.0000000), wk = 0.0000000 k( 31) = ( 0.3000000 0.3000000 0.0000000), wk = 0.0800000 k( 32) = ( 0.8000000 0.3000000 0.0000000), wk = 0.0000000 k( 33) = ( 0.3000000 0.4000000 0.0000000), wk = 0.0800000 k( 34) = ( 0.8000000 0.4000000 0.0000000), wk = 0.0000000 k( 35) = ( 0.3000000 -0.5000000 0.0000000), wk = 0.0400000 k( 36) = ( 0.8000000 -0.5000000 0.0000000), wk = 0.0000000 k( 37) = ( 0.4000000 0.4000000 0.0000000), wk = 0.0800000 k( 38) = ( 0.9000000 0.4000000 0.0000000), wk = 0.0000000 k( 39) = ( 0.4000000 -0.5000000 0.0000000), wk = 0.0400000 k( 40) = ( 0.9000000 -0.5000000 0.0000000), wk = 0.0000000 k( 41) = ( -0.5000000 -0.5000000 0.0000000), wk = 0.0200000 k( 42) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.0000000 k( 43) = ( 0.1000000 0.0000000 0.0000000), wk = 0.0400000 k( 44) = ( 0.6000000 0.0000000 0.0000000), wk = 0.0000000 k( 45) = ( 0.2000000 0.0000000 0.0000000), wk = 0.0400000 k( 46) = ( 0.7000000 0.0000000 0.0000000), wk = 0.0000000 k( 47) = ( 0.3000000 0.0000000 0.0000000), wk = 0.0400000 k( 48) = ( 0.8000000 0.0000000 0.0000000), wk = 0.0000000 k( 49) = ( 0.4000000 0.0000000 0.0000000), wk = 0.0400000 k( 50) = ( 0.9000000 0.0000000 0.0000000), wk = 0.0000000 k( 51) = ( -0.5000000 0.0000000 0.0000000), wk = 0.0200000 k( 52) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0000000 k( 53) = ( 0.2000000 0.1000000 0.0000000), wk = 0.0800000 k( 54) = ( 0.7000000 0.1000000 0.0000000), wk = 0.0000000 k( 55) = ( 0.3000000 0.1000000 0.0000000), wk = 0.0800000 k( 56) = ( 0.8000000 0.1000000 0.0000000), wk = 0.0000000 k( 57) = ( 0.4000000 0.1000000 0.0000000), wk = 0.0800000 k( 58) = ( 0.9000000 0.1000000 0.0000000), wk = 0.0000000 k( 59) = ( -0.5000000 0.1000000 0.0000000), wk = 0.0400000 k( 60) = ( 0.0000000 0.1000000 0.0000000), wk = 0.0000000 k( 61) = ( 0.3000000 0.2000000 0.0000000), wk = 0.0800000 k( 62) = ( 0.8000000 0.2000000 0.0000000), wk = 0.0000000 k( 63) = ( 0.4000000 0.2000000 0.0000000), wk = 0.0800000 k( 64) = ( 0.9000000 0.2000000 0.0000000), wk = 0.0000000 k( 65) = ( -0.5000000 0.2000000 0.0000000), wk = 0.0400000 k( 66) = ( 0.0000000 0.2000000 0.0000000), wk = 0.0000000 k( 67) = ( 0.4000000 0.3000000 0.0000000), wk = 0.0800000 k( 68) = ( 0.9000000 0.3000000 0.0000000), wk = 0.0000000 k( 69) = ( -0.5000000 0.3000000 0.0000000), wk = 0.0400000 k( 70) = ( 0.0000000 0.3000000 0.0000000), wk = 0.0000000 k( 71) = ( -0.5000000 0.4000000 0.0000000), wk = 0.0400000 k( 72) = ( 0.0000000 0.4000000 0.0000000), wk = 0.0000000 pseudo 1 is Cu (US) zval = 11.0 lmax= 2 lloc= 0 Version 0 0 0 of US pseudo code Using log mesh of 899 points The pseudopotential has 3 beta functions with: l(1) = 2 l(2) = 2 l(3) = 1 Q(r) pseudized with 0 coefficients, rinner = 0.000 0.000 0.000 0.000 0.000 pseudo 2 is O (US) zval = 6.0 lmax= 2 lloc= 0 Version 0 0 0 of US pseudo code Using log mesh of 1269 points The pseudopotential has 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 0 coefficients, rinner = 0.000 0.000 0.000 0.000 0.000 pseudo 3 is C (US) zval = 4.0 lmax= 2 lloc= 0 Version 0 0 0 of US pseudo code Using log mesh of 1425 points The pseudopotential has 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 0 coefficients, rinner = 0.000 0.000 0.000 0.000 0.000 Atomic displacements: There are 54 irreducible representations Representation 1 1 modes - Done Representation 2 1 modes - Done Representation 3 1 modes - Done Representation 4 1 modes - Done Representation 5 1 modes - Done Representation 6 1 modes - Done Representation 7 1 modes - Done Representation 8 1 modes - Done Representation 9 1 modes - Done Representation 10 1 modes - Done Representation 11 1 modes - Done Representation 12 1 modes - Done Representation 13 1 modes - Done Representation 14 1 modes - Done Representation 15 1 modes - Done Representation 16 1 modes - Done Representation 17 1 modes - Done Representation 18 1 modes - Done Representation 19 1 modes - Done Representation 20 1 modes - Done Representation 21 1 modes - Done Representation 22 1 modes - To be done Representation 23 1 modes - To be done Representation 24 1 modes - To be done Representation 25 1 modes - To be done Representation 26 1 modes - To be done Representation 27 1 modes - To be done Representation 28 1 modes - To be done Representation 29 1 modes - To be done Representation 30 1 modes - To be done Representation 31 1 modes - To be done Representation 32 1 modes - To be done Representation 33 1 modes - To be done Representation 34 1 modes - To be done Representation 35 1 modes - To be done Representation 36 1 modes - To be done Representation 37 1 modes - To be done Representation 38 1 modes - To be done Representation 39 1 modes - To be done Representation 40 1 modes - To be done Representation 41 1 modes - To be done Representation 42 1 modes - To be done Representation 43 1 modes - To be done Representation 44 1 modes - To be done Representation 45 1 modes - To be done Representation 46 1 modes - To be done Representation 47 1 modes - To be done Representation 48 1 modes - To be done Representation 49 1 modes - To be done Representation 50 1 modes - To be done Representation 51 1 modes - To be done Representation 52 1 modes - To be done Representation 53 1 modes - To be done Representation 54 1 modes - To be done PHONON : 42.45s CPU time Representation # 22 mode # 22 Self-consistent Calculation iter # 2 total cpu time : 505.7 secs av.it.: 14.7 thresh= 0.151E-03 alpha_mix = 0.100 |ddv_scf|^2 = 0.437E-06 iter # 3 total cpu time : 986.8 secs av.it.: 15.7 thresh= 0.661E-04 alpha_mix = 0.100 |ddv_scf|^2 = 0.532E-07 kpoint 1 ibnd 87 linter: root not converged NaN kpoint 2 ibnd 87 linter: root not converged NaN kpoint 3 ibnd 88 linter: root not converged NaN kpoint 4 ibnd 89 linter: root not converged NaN kpoint 5 ibnd 90 linter: root not converged NaN kpoint 6 ibnd 90 linter: root not converged NaN kpoint 7 ibnd 87 linter: root not converged NaN kpoint 8 ibnd 88 linter: root not converged NaN kpoint 9 ibnd 89 linter: root not converged NaN kpoint 10 ibnd 90 linter: root not converged NaN kpoint 11 ibnd 90 linter: root not converged NaN kpoint 12 ibnd 87 linter: root not converged NaN kpoint 13 ibnd 89 linter: root not converged NaN kpoint 14 ibnd 90 linter: root not converged NaN kpoint 15 ibnd 90 linter: root not converged NaN kpoint 16 ibnd 91 linter: root not converged NaN kpoint 17 ibnd 90 linter: root not converged NaN kpoint 18 ibnd 90 linter: root not converged NaN kpoint 19 ibnd 93 linter: root not converged NaN kpoint 20 ibnd 95 linter: root not converged NaN kpoint 21 ibnd 95 linter: root not converged NaN kpoint 22 ibnd 87 linter: root not converged NaN kpoint 23 ibnd 88 linter: root not converged NaN kpoint 24 ibnd 89 linter: root not converged NaN kpoint 25 ibnd 90 linter: root not converged NaN kpoint 26 ibnd 90 linter: root not converged NaN kpoint 27 ibnd 88 linter: root not converged NaN kpoint 28 ibnd 89 linter: root not converged NaN kpoint 29 ibnd 90 linter: root not converged NaN kpoint 30 ibnd 90 linter: root not converged NaN kpoint 31 ibnd 89 linter: root not converged NaN kpoint 32 ibnd 90 linter: root not converged NaN kpoint 33 ibnd 90 linter: root not converged NaN kpoint 34 ibnd 90 linter: root not converged NaN kpoint 35 ibnd 90 linter: root not converged NaN kpoint 36 ibnd 95 linter: root not converged NaN %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%% from broyden : error # 1 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%% stopping ... ------------------------------------------------------------------------ --------------- From giannozz at nest.sns.it Tue Aug 23 17:56:28 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Aug 2005 17:56:28 +0200 Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. In-Reply-To: References: Message-ID: <200508231756.28818.giannozz@nest.sns.it> On Tuesday 23 August 2005 17:43, Alcantara Ortigoza, Marisol wrote: > I've been running a phonon calculation (54 modes). > Everything was OK but suddenly things went wrong at mode 22 what you are showing is the output of a run that is restarting from mode 22. Did things go wrong in the preceding run as well? Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From alcantar at phys.ksu.edu Tue Aug 23 18:00:14 2005 From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol) Date: Tue, 23 Aug 2005 11:00:14 -0500 Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. Message-ID: Thanks for replying. No. Before everything went OK; convergence was achieved after 15 iterations or so. It is just now. Marisol -----Original Message----- From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Tuesday, August 23, 2005 10:56 AM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] CO/Cu(100) phonon calculation problem. On Tuesday 23 August 2005 17:43, Alcantara Ortigoza, Marisol wrote: > I've been running a phonon calculation (54 modes). > Everything was OK but suddenly things went wrong at mode 22 what you are showing is the output of a run that is restarting from mode 22. Did things go wrong in the preceding run as well? Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at nest.sns.it Tue Aug 23 18:10:59 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 23 Aug 2005 18:10:59 +0200 Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. In-Reply-To: References: Message-ID: <200508231810.59711.giannozz@nest.sns.it> On Tuesday 23 August 2005 18:00, Alcantara Ortigoza, Marisol wrote: > No. Before everything went OK; convergence was achieved after 15 > iterations or so. It is just now. "before" what event ? The output you sent is not the output of a run performing a calculation from the beginnning, i.e. from mode 1 to mode 3*N atoms; it is the output of a run restarting from a previous run that was interrupted in mode 22. Is this what you intended to do? Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From alcantar at phys.ksu.edu Tue Aug 23 20:41:19 2005 From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol) Date: Tue, 23 Aug 2005 13:41:19 -0500 Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. Message-ID: Sorry for the delay. I've been waiting for the approval of the forum since the files are too large, but it is taking too long. Yes. The run was interrupted because the available time, specified by the time_max variable, was over. I have to run the calcualtion in several steps because we are not allowed to run things for more than 24 hours. Even these jobs (24 hours) are taking now up to 3 days to start so I have to run the calculation for 4 horus or so and restart, etc. Below, you'll find the first and the last two output files. I cut some parts that are repeated in each file to make it smaller. Thanks . Marisol ----------output 1------------- Program PHONON v.2.1.3 starts ... Today is 18Aug2005 at 13:32:17 Parallel version (MPI) Number of processors in use: 16 R & G space division: nprocp = 16 Ultrasoft (Vanderbilt) Pseudopotentials Reading file co_cu100.save ... read complete Reading file co_cu100.save ... read complete Planes per process (thick) : nr3 =432 npp = 27 ncplane = 2916 Planes per process (smooth): nr3s=243 npps= 16 ncplanes= 1024 Proc/ planes cols G planes cols G columns G Pool (dense grid) (smooth grid) (wavefct grid) 1 27 134 37464 16 45 7215 15 1329 2 27 134 37464 16 45 7221 15 1329 3 27 135 37487 16 45 7225 15 1329 4 27 134 37454 15 45 7229 15 1329 5 27 134 37468 15 45 7225 15 1329 6 27 134 37468 15 45 7225 14 1316 7 27 134 37464 15 45 7211 14 1316 8 27 134 37464 15 44 7202 15 1321 9 27 134 37464 15 44 7210 15 1317 10 27 134 37464 15 44 7190 14 1322 11 27 134 37464 15 45 7211 15 1321 12 27 134 37462 15 45 7215 14 1322 13 27 134 37462 15 45 7217 14 1322 14 27 134 37462 15 45 7215 14 1322 15 27 134 37462 15 45 7213 14 1320 16 27 134 37462 15 45 7229 15 1325 0 432 2145 599435 243 717 115453 233 21169 nbndx = 104 nbnd = 104 natomwfc = 100 npwx = 1013 nelec = 174.00 nkb = 214 ngl = 6742 Phonons of COCu atX crystal is bravais-lattice index = 6 lattice parameter (a_0) = 6.7096 a.u. unit-cell volume = 2416.4615 (a.u.)^3 number of atoms/cell = 18 number of atomic types = 3 kinetic-energy cut-off = 50.0000 Ry charge density cut-off = 600.0000 Ry convergence threshold = 1.0E-16 beta = 0.1000 number of iterations used = 4 celldm(1)= 6.70960 celldm(2)= 0.00000 celldm(3)= 8.00000 celldm(4)= 0.00000 celldm(5)= 0.00000 celldm(6)= 0.00000 crystal axes: (cart. coord. in units of a_0) a(1) = ( 1.0000 0.0000 0.0000 ) a(2) = ( 0.0000 1.0000 0.0000 ) a(3) = ( 0.0000 0.0000 8.0000 ) reciprocal axes: (cart. coord. in units 2 pi/a_0) b(1) = ( 1.0000 0.0000 0.0000 ) b(2) = ( 0.0000 1.0000 0.0000 ) b(3) = ( 0.0000 0.0000 0.1250 ) Atoms inside the unit cell: Cartesian axes site n. atom mass positions (a_0 units) 1 O 15.9994 tau( 1) = ( 0.00000 0.50000 2.33471 ) 2 C 12.0107 tau( 2) = ( 0.00000 0.50000 2.01237 ) 3 Cu 63.5460 tau( 3) = ( 0.00000 0.50000 1.49940 ) 4 Cu 63.5460 tau( 4) = ( 0.50000 0.00000 1.48473 ) 5 Cu 63.5460 tau( 5) = ( 0.50000 0.50000 0.99696 ) 6 Cu 63.5460 tau( 6) = ( 0.00000 0.00000 0.99695 ) 7 Cu 63.5460 tau( 7) = ( 0.00000 0.50000 0.49791 ) 8 Cu 63.5460 tau( 8) = ( 0.50000 0.00000 0.49377 ) 9 Cu 63.5460 tau( 9) = ( 0.00000 0.00000 0.00000 ) 10 Cu 63.5460 tau(10) = ( 0.50000 0.50000 0.00000 ) 11 Cu 63.5460 tau(11) = ( 0.50000 0.00000 -0.49377 ) 12 Cu 63.5460 tau(12) = ( 0.00000 0.50000 -0.49791 ) 13 Cu 63.5460 tau(13) = ( 0.00000 0.00000 -0.99695 ) 14 Cu 63.5460 tau(14) = ( 0.50000 0.50000 -0.99696 ) 15 Cu 63.5460 tau(15) = ( 0.50000 0.00000 -1.48473 ) 16 Cu 63.5460 tau(16) = ( 0.00000 0.50000 -1.49940 ) 17 C 12.0107 tau(17) = ( 0.00000 0.50000 -2.01237 ) 18 O 15.9994 tau(18) = ( 0.00000 0.50000 -2.33471 ) Computing dynamical matrix for q = ( 0.50000 0.00000 0.00000 ) 9 Sym.Ops. (with q -> -q+G ) G cutoff = 684.2027 ( 37464 G-vectors) FFT grid: ( 54, 54,432) G cutoff = 228.0676 ( 7215 G-vectors) smooth grid: ( 32, 32,243) number of k points= 72 gaussian broad. (ryd)= 0.0147 ngauss = 1 cart. coord. in units 2pi/a_0 k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0200000 k( 2) = ( 0.5000000 0.0000000 0.0000000), wk = 0.0000000 k( 3) = ( 0.0000000 0.1000000 0.0000000), wk = 0.0400000 k( 4) = ( 0.5000000 0.1000000 0.0000000), wk = 0.0000000 k( 5) = ( 0.0000000 0.2000000 0.0000000), wk = 0.0400000 k( 6) = ( 0.5000000 0.2000000 0.0000000), wk = 0.0000000 k( 7) = ( 0.0000000 0.3000000 0.0000000), wk = 0.0400000 k( 8) = ( 0.5000000 0.3000000 0.0000000), wk = 0.0000000 k( 9) = ( 0.0000000 0.4000000 0.0000000), wk = 0.0400000 k( 10) = ( 0.5000000 0.4000000 0.0000000), wk = 0.0000000 k( 11) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.0200000 k( 12) = ( 0.5000000 -0.5000000 0.0000000), wk = 0.0000000 k( 13) = ( 0.1000000 0.1000000 0.0000000), wk = 0.0800000 k( 14) = ( 0.6000000 0.1000000 0.0000000), wk = 0.0000000 k( 15) = ( 0.1000000 0.2000000 0.0000000), wk = 0.0800000 k( 16) = ( 0.6000000 0.2000000 0.0000000), wk = 0.0000000 k( 17) = ( 0.1000000 0.3000000 0.0000000), wk = 0.0800000 k( 18) = ( 0.6000000 0.3000000 0.0000000), wk = 0.0000000 k( 19) = ( 0.1000000 0.4000000 0.0000000), wk = 0.0800000 k( 20) = ( 0.6000000 0.4000000 0.0000000), wk = 0.0000000 k( 21) = ( 0.1000000 -0.5000000 0.0000000), wk = 0.0400000 k( 22) = ( 0.6000000 -0.5000000 0.0000000), wk = 0.0000000 k( 23) = ( 0.2000000 0.2000000 0.0000000), wk = 0.0800000 k( 24) = ( 0.7000000 0.2000000 0.0000000), wk = 0.0000000 k( 25) = ( 0.2000000 0.3000000 0.0000000), wk = 0.0800000 k( 26) = ( 0.7000000 0.3000000 0.0000000), wk = 0.0000000 k( 27) = ( 0.2000000 0.4000000 0.0000000), wk = 0.0800000 k( 28) = ( 0.7000000 0.4000000 0.0000000), wk = 0.0000000 k( 29) = ( 0.2000000 -0.5000000 0.0000000), wk = 0.0400000 k( 30) = ( 0.7000000 -0.5000000 0.0000000), wk = 0.0000000 k( 31) = ( 0.3000000 0.3000000 0.0000000), wk = 0.0800000 k( 32) = ( 0.8000000 0.3000000 0.0000000), wk = 0.0000000 k( 33) = ( 0.3000000 0.4000000 0.0000000), wk = 0.0800000 k( 34) = ( 0.8000000 0.4000000 0.0000000), wk = 0.0000000 k( 35) = ( 0.3000000 -0.5000000 0.0000000), wk = 0.0400000 k( 36) = ( 0.8000000 -0.5000000 0.0000000), wk = 0.0000000 k( 37) = ( 0.4000000 0.4000000 0.0000000), wk = 0.0800000 k( 38) = ( 0.9000000 0.4000000 0.0000000), wk = 0.0000000 k( 39) = ( 0.4000000 -0.5000000 0.0000000), wk = 0.0400000 k( 40) = ( 0.9000000 -0.5000000 0.0000000), wk = 0.0000000 k( 41) = ( -0.5000000 -0.5000000 0.0000000), wk = 0.0200000 k( 42) = ( 0.0000000 -0.5000000 0.0000000), wk = 0.0000000 k( 43) = ( 0.1000000 0.0000000 0.0000000), wk = 0.0400000 k( 44) = ( 0.6000000 0.0000000 0.0000000), wk = 0.0000000 k( 45) = ( 0.2000000 0.0000000 0.0000000), wk = 0.0400000 k( 46) = ( 0.7000000 0.0000000 0.0000000), wk = 0.0000000 k( 47) = ( 0.3000000 0.0000000 0.0000000), wk = 0.0400000 k( 48) = ( 0.8000000 0.0000000 0.0000000), wk = 0.0000000 k( 49) = ( 0.4000000 0.0000000 0.0000000), wk = 0.0400000 k( 50) = ( 0.9000000 0.0000000 0.0000000), wk = 0.0000000 k( 51) = ( -0.5000000 0.0000000 0.0000000), wk = 0.0200000 k( 52) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0000000 k( 53) = ( 0.2000000 0.1000000 0.0000000), wk = 0.0800000 k( 54) = ( 0.7000000 0.1000000 0.0000000), wk = 0.0000000 k( 55) = ( 0.3000000 0.1000000 0.0000000), wk = 0.0800000 k( 56) = ( 0.8000000 0.1000000 0.0000000), wk = 0.0000000 k( 57) = ( 0.4000000 0.1000000 0.0000000), wk = 0.0800000 k( 58) = ( 0.9000000 0.1000000 0.0000000), wk = 0.0000000 k( 59) = ( -0.5000000 0.1000000 0.0000000), wk = 0.0400000 k( 60) = ( 0.0000000 0.1000000 0.0000000), wk = 0.0000000 k( 61) = ( 0.3000000 0.2000000 0.0000000), wk = 0.0800000 k( 62) = ( 0.8000000 0.2000000 0.0000000), wk = 0.0000000 k( 63) = ( 0.4000000 0.2000000 0.0000000), wk = 0.0800000 k( 64) = ( 0.9000000 0.2000000 0.0000000), wk = 0.0000000 k( 65) = ( -0.5000000 0.2000000 0.0000000), wk = 0.0400000 k( 66) = ( 0.0000000 0.2000000 0.0000000), wk = 0.0000000 k( 67) = ( 0.4000000 0.3000000 0.0000000), wk = 0.0800000 k( 68) = ( 0.9000000 0.3000000 0.0000000), wk = 0.0000000 k( 69) = ( -0.5000000 0.3000000 0.0000000), wk = 0.0400000 k( 70) = ( 0.0000000 0.3000000 0.0000000), wk = 0.0000000 k( 71) = ( -0.5000000 0.4000000 0.0000000), wk = 0.0400000 k( 72) = ( 0.0000000 0.4000000 0.0000000), wk = 0.0000000 pseudo 1 is Cu (US) zval = 11.0 lmax= 2 lloc= 0 Version 0 0 0 of US pseudo code Using log mesh of 899 points The pseudopotential has 3 beta functions with: l(1) = 2 l(2) = 2 l(3) = 1 Q(r) pseudized with 0 coefficients, rinner = 0.000 0.000 0.000 0.000 0.000 pseudo 2 is O (US) zval = 6.0 lmax= 2 lloc= 0 Version 0 0 0 of US pseudo code Using log mesh of 1425 points The pseudopotential has 4 beta functions with: l(1) = 0 l(2) = 0 l(3) = 1 l(4) = 1 Q(r) pseudized with 0 coefficients, rinner = 0.000 0.000 0.000 0.000 0.000 Atomic displacements: There are 54 irreducible representations Representation 1 1 modes - To be done Representation 2 1 modes - To be done Representation 3 1 modes - To be done Representation 4 1 modes - To be done Representation 5 1 modes - To be done Representation 6 1 modes - To be done Representation 7 1 modes - To be done Representation 8 1 modes - To be done Representation 9 1 modes - To be done Representation 10 1 modes - To be done Representation 11 1 modes - To be done Representation 12 1 modes - To be done Representation 13 1 modes - To be done Representation 14 1 modes - To be done Representation 15 1 modes - To be done Representation 16 1 modes - To be done Representation 17 1 modes - To be done Representation 18 1 modes - To be done Representation 19 1 modes - To be done Representation 20 1 modes - To be done Representation 21 1 modes - To be done Representation 22 1 modes - To be done Representation 23 1 modes - To be done Representation 24 1 modes - To be done Representation 25 1 modes - To be done Representation 26 1 modes - To be done Representation 27 1 modes - To be done Representation 28 1 modes - To be done Representation 29 1 modes - To be done Representation 30 1 modes - To be done Representation 31 1 modes - To be done Representation 32 1 modes - To be done Representation 33 1 modes - To be done Representation 34 1 modes - To be done Representation 35 1 modes - To be done Representation 36 1 modes - To be done Representation 37 1 modes - To be done Representation 38 1 modes - To be done Representation 39 1 modes - To be done Representation 40 1 modes - To be done Representation 41 1 modes - To be done Representation 42 1 modes - To be done Representation 43 1 modes - To be done Representation 44 1 modes - To be done Representation 45 1 modes - To be done Representation 46 1 modes - To be done Representation 47 1 modes - To be done Representation 48 1 modes - To be done Representation 49 1 modes - To be done Representation 50 1 modes - To be done Representation 51 1 modes - To be done Representation 52 1 modes - To be done Representation 53 1 modes - To be done Representation 54 1 modes - To be done PHONON : 13m48.64s CPU time Alpha used in Ewald sum = 2.8000 Representation # 1 mode # 1 Self-consistent Calculation iter # 1 total cpu time : 1090.4 secs av.it.: 8.8 thresh= 0.100E-01 alpha_mix = 0.100 |ddv_scf|^2 = 0.414E-05 iter # 2 total cpu time : 1469.4 secs av.it.: 15.8 thresh= 0.203E-03 alpha_mix = 0.100 |ddv_scf|^2 = 0.482E-06 iter # 3 total cpu time : 1875.0 secs av.it.: 16.5 thresh= 0.694E-04 alpha_mix = 0.100 |ddv_scf|^2 = 0.623E-07 iter # 4 total cpu time : 2288.5 secs av.it.: 17.4 thresh= 0.250E-04 alpha_mix = 0.100 |ddv_scf|^2 = 0.155E-07 iter # 5 total cpu time : 2731.3 secs av.it.: 19.0 thresh= 0.125E-04 alpha_mix = 0.100 |ddv_scf|^2 = 0.219E-08 iter # 6 total cpu time : 3153.0 secs av.it.: 18.0 thresh= 0.468E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.522E-09 iter # 7 total cpu time : 3559.3 secs av.it.: 17.0 thresh= 0.229E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.307E-09 iter # 8 total cpu time : 4010.7 secs av.it.: 19.2 thresh= 0.175E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.276E-10 iter # 9 total cpu time : 4431.1 secs av.it.: 17.8 thresh= 0.525E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.841E-11 iter # 10 total cpu time : 4841.0 secs av.it.: 17.4 thresh= 0.290E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.337E-11 iter # 11 total cpu time : 5267.8 secs av.it.: 18.3 thresh= 0.184E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.103E-11 iter # 12 total cpu time : 5688.8 secs av.it.: 17.8 thresh= 0.102E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.475E-12 iter # 13 total cpu time : 6110.9 secs av.it.: 18.0 thresh= 0.689E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.198E-12 iter # 14 total cpu time : 6498.3 secs av.it.: 16.3 thresh= 0.445E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.116E-12 iter # 15 total cpu time : 6926.3 secs av.it.: 18.4 thresh= 0.340E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.518E-14 iter # 16 total cpu time : 7334.0 secs av.it.: 17.3 thresh= 0.720E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.235E-14 iter # 17 total cpu time : 7744.1 secs av.it.: 17.2 thresh= 0.485E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.119E-14 iter # 18 total cpu time : 8158.9 secs av.it.: 17.8 thresh= 0.345E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.387E-15 iter # 19 total cpu time : 8579.0 secs av.it.: 18.0 thresh= 0.197E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.125E-15 iter # 20 total cpu time : 8990.4 secs av.it.: 17.5 thresh= 0.112E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.640E-16 End of self-consistent calculation Convergence has been achieved Representation # 2 mode # 2 Self-consistent Calculation iter # 1 total cpu time : 9191.8 secs av.it.: 6.4 thresh= 0.100E-01 alpha_mix = 0.100 |ddv_scf|^2 = 0.133E-06 iter # 2 total cpu time : 9543.6 secs av.it.: 14.8 thresh= 0.365E-04 alpha_mix = 0.100 |ddv_scf|^2 = 0.876E-07 iter # 3 total cpu time : 9969.0 secs av.it.: 18.3 thresh= 0.296E-04 alpha_mix = 0.100 |ddv_scf|^2 = 0.968E-09 iter # 4 total cpu time : 10379.0 secs av.it.: 17.2 thresh= 0.311E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.190E-09 iter # 5 total cpu time : 10798.7 secs av.it.: 17.8 thresh= 0.138E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.462E-10 iter # 6 total cpu time : 11224.9 secs av.it.: 18.2 thresh= 0.680E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.906E-12 iter # 7 total cpu time : 11581.8 secs av.it.: 14.9 thresh= 0.952E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.607E-12 iter # 8 total cpu time : 11998.7 secs av.it.: 18.0 thresh= 0.779E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.380E-13 iter # 9 total cpu time : 12412.4 secs av.it.: 17.6 thresh= 0.195E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.129E-13 ------------------------- ... -------------------output 6---------------------------------- Program PHONON v.2.1.3 starts ... Today is 22Aug2005 at 18:11:39 ... starting from an old run Doing now the calculation for q point nr 1 Restart from Iteration # 4 of Representation # 19 Phonons of COCu atX crystal is ... There are 54 irreducible representations Representation 1 1 modes - Done Representation 2 1 modes - Done Representation 3 1 modes - Done Representation 4 1 modes - Done Representation 5 1 modes - Done Representation 6 1 modes - Done Representation 7 1 modes - Done Representation 8 1 modes - Done Representation 9 1 modes - Done Representation 10 1 modes - Done Representation 11 1 modes - Done Representation 12 1 modes - Done Representation 13 1 modes - Done Representation 14 1 modes - Done Representation 15 1 modes - Done Representation 16 1 modes - Done Representation 17 1 modes - Done Representation 18 1 modes - Done Representation 19 1 modes - To be done Representation 20 1 modes - To be done Representation 21 1 modes - To be done Representation 22 1 modes - To be done Representation 23 1 modes - To be done Representation 24 1 modes - To be done Representation 25 1 modes - To be done Representation 26 1 modes - To be done Representation 27 1 modes - To be done Representation 28 1 modes - To be done Representation 29 1 modes - To be done Representation 30 1 modes - To be done Representation 31 1 modes - To be done Representation 32 1 modes - To be done Representation 33 1 modes - To be done Representation 34 1 modes - To be done Representation 35 1 modes - To be done Representation 36 1 modes - To be done Representation 37 1 modes - To be done Representation 38 1 modes - To be done Representation 39 1 modes - To be done Representation 40 1 modes - To be done Representation 41 1 modes - To be done Representation 42 1 modes - To be done Representation 43 1 modes - To be done Representation 44 1 modes - To be done Representation 45 1 modes - To be done Representation 46 1 modes - To be done Representation 47 1 modes - To be done Representation 48 1 modes - To be done Representation 49 1 modes - To be done Representation 50 1 modes - To be done Representation 51 1 modes - To be done Representation 52 1 modes - To be done Representation 53 1 modes - To be done Representation 54 1 modes - To be done PHONON : 34.94s CPU time Representation # 19 mode # 19 Self-consistent Calculation iter # 4 total cpu time : 428.7 secs av.it.: 15.8 thresh= 0.191E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.212E-09 iter # 5 total cpu time : 827.6 secs av.it.: 16.8 thresh= 0.146E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.244E-10 iter # 6 total cpu time : 1373.7 secs av.it.: 14.6 thresh= 0.494E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.119E-10 iter # 7 total cpu time : 1914.1 secs av.it.: 17.4 thresh= 0.345E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.103E-12 iter # 8 total cpu time : 2339.4 secs av.it.: 18.2 thresh= 0.320E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.113E-13 iter # 9 total cpu time : 2774.6 secs av.it.: 18.7 thresh= 0.106E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.153E-14 iter # 10 total cpu time : 3236.2 secs av.it.: 18.9 thresh= 0.391E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.131E-15 iter # 11 total cpu time : 3615.2 secs av.it.: 15.9 thresh= 0.114E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.918E-16 End of self-consistent calculation Convergence has been achieved Representation # 20 mode # 20 Self-consistent Calculation iter # 1 total cpu time : 3799.0 secs av.it.: 5.4 thresh= 0.100E-01 alpha_mix = 0.100 |ddv_scf|^2 = 0.129E-06 iter # 2 total cpu time : 4129.3 secs av.it.: 13.4 thresh= 0.359E-04 alpha_mix = 0.100 |ddv_scf|^2 = 0.850E-07 iter # 3 total cpu time : 4529.3 secs av.it.: 16.8 thresh= 0.291E-04 alpha_mix = 0.100 |ddv_scf|^2 = 0.108E-08 iter # 4 total cpu time : 4928.7 secs av.it.: 16.9 thresh= 0.328E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.134E-09 iter # 5 total cpu time : 5335.0 secs av.it.: 17.1 thresh= 0.116E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.411E-10 iter # 6 total cpu time : 5748.3 secs av.it.: 17.4 thresh= 0.641E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.108E-11 iter # 7 total cpu time : 6104.6 secs av.it.: 14.7 thresh= 0.104E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.703E-12 iter # 8 total cpu time : 6535.1 secs av.it.: 18.1 thresh= 0.839E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.345E-13 iter # 9 total cpu time : 6907.8 secs av.it.: 14.7 thresh= 0.186E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.256E-13 iter # 10 total cpu time : 7325.9 secs av.it.: 17.6 thresh= 0.160E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.828E-14 iter # 11 total cpu time : 7686.1 secs av.it.: 14.9 thresh= 0.910E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.575E-14 iter # 12 total cpu time : 8100.6 secs av.it.: 17.5 thresh= 0.758E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.609E-15 iter # 13 total cpu time : 8465.3 secs av.it.: 15.1 thresh= 0.247E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.450E-15 iter # 14 total cpu time : 8871.0 secs av.it.: 17.0 thresh= 0.212E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.240E-15 iter # 15 total cpu time : 9292.0 secs av.it.: 17.8 thresh= 0.155E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.653E-16 End of self-consistent calculation Convergence has been achieved Representation # 21 mode # 21 Self-consistent Calculation iter # 1 total cpu time : 9458.9 secs av.it.: 4.4 thresh= 0.100E-01 alpha_mix = 0.100 |ddv_scf|^2 = 0.583E-08 iter # 2 total cpu time : 9847.0 secs av.it.: 16.2 thresh= 0.764E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.398E-08 iter # 3 total cpu time : 10279.2 secs av.it.: 17.5 thresh= 0.631E-05 alpha_mix = 0.100 |ddv_scf|^2 = 0.252E-10 iter # 4 total cpu time : 10626.9 secs av.it.: 14.2 thresh= 0.502E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.184E-10 iter # 5 total cpu time : 11052.5 secs av.it.: 18.1 thresh= 0.429E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.134E-11 iter # 6 total cpu time : 11472.9 secs av.it.: 17.7 thresh= 0.116E-06 alpha_mix = 0.100 |ddv_scf|^2 = 0.495E-13 iter # 7 total cpu time : 11868.8 secs av.it.: 16.6 thresh= 0.222E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.260E-13 iter # 8 total cpu time : 12303.6 secs av.it.: 18.6 thresh= 0.161E-07 alpha_mix = 0.100 |ddv_scf|^2 = 0.577E-15 iter # 9 total cpu time : 12667.7 secs av.it.: 15.2 thresh= 0.240E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.408E-15 iter # 10 total cpu time : 13087.0 secs av.it.: 17.7 thresh= 0.202E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.123E-15 iter # 11 total cpu time : 13468.2 secs av.it.: 16.0 thresh= 0.111E-08 alpha_mix = 0.100 |ddv_scf|^2 = 0.787E-16 End of self-consistent calculation Convergence has been achieved Representation # 22 mode # 22 Self-consistent Calculation iter # 1 total cpu time : 13699.2 secs av.it.: 7.4 thresh= 0.100E-01 alpha_mix = 0.100 |ddv_scf|^2 = 0.228E-05 Stopping for time limit 13699. 13400. -----------------------output 7 -------------------------------- Program PHONON v.2.1.3 starts ... Today is 23Aug2005 at 2: 4:46 ... starting from an old run Doing now the calculation for q point nr 1 Restart from Iteration # 2 of Representation # 22 Phonons of COCu atX crystal is ... There are 54 irreducible representations Representation 1 1 modes - Done Representation 2 1 modes - Done Representation 3 1 modes - Done Representation 4 1 modes - Done Representation 5 1 modes - Done Representation 6 1 modes - Done Representation 7 1 modes - Done Representation 8 1 modes - Done Representation 9 1 modes - Done Representation 10 1 modes - Done Representation 11 1 modes - Done Representation 12 1 modes - Done Representation 13 1 modes - Done Representation 14 1 modes - Done Representation 15 1 modes - Done Representation 16 1 modes - Done Representation 17 1 modes - Done Representation 18 1 modes - Done Representation 19 1 modes - Done Representation 20 1 modes - Done Representation 21 1 modes - Done Representation 22 1 modes - To be done Representation 23 1 modes - To be done Representation 24 1 modes - To be done Representation 25 1 modes - To be done Representation 26 1 modes - To be done Representation 27 1 modes - To be done Representation 28 1 modes - To be done Representation 29 1 modes - To be done Representation 30 1 modes - To be done Representation 31 1 modes - To be done Representation 32 1 modes - To be done Representation 33 1 modes - To be done Representation 34 1 modes - To be done Representation 35 1 modes - To be done Representation 36 1 modes - To be done Representation 37 1 modes - To be done Representation 38 1 modes - To be done Representation 39 1 modes - To be done Representation 40 1 modes - To be done Representation 41 1 modes - To be done Representation 42 1 modes - To be done Representation 43 1 modes - To be done Representation 44 1 modes - To be done Representation 45 1 modes - To be done Representation 46 1 modes - To be done Representation 47 1 modes - To be done Representation 48 1 modes - To be done Representation 49 1 modes - To be done Representation 50 1 modes - To be done Representation 51 1 modes - To be done Representation 52 1 modes - To be done Representation 53 1 modes - To be done Representation 54 1 modes - To be done PHONON : 42.45s CPU time Representation # 22 mode # 22 Self-consistent Calculation iter # 2 total cpu time : 505.7 secs av.it.: 14.7 thresh= 0.151E-03 alpha_mix = 0.100 |ddv_scf|^2 = 0.437E-06 iter # 3 total cpu time : 986.8 secs av.it.: 15.7 thresh= 0.661E-04 alpha_mix = 0.100 |ddv_scf|^2 = 0.532E-07 kpoint 1 ibnd 87 linter: root not converged NaN kpoint 2 ibnd 87 linter: root not converged NaN kpoint 3 ibnd 88 linter: root not converged NaN kpoint 4 ibnd 89 linter: root not converged NaN kpoint 5 ibnd 90 linter: root not converged NaN kpoint 6 ibnd 90 linter: root not converged NaN kpoint 7 ibnd 87 linter: root not converged NaN kpoint 8 ibnd 88 linter: root not converged NaN kpoint 9 ibnd 89 linter: root not converged NaN kpoint 10 ibnd 90 linter: root not converged NaN kpoint 11 ibnd 90 linter: root not converged NaN kpoint 12 ibnd 87 linter: root not converged NaN kpoint 13 ibnd 89 linter: root not converged NaN kpoint 14 ibnd 90 linter: root not converged NaN kpoint 15 ibnd 90 linter: root not converged NaN kpoint 16 ibnd 91 linter: root not converged NaN kpoint 17 ibnd 90 linter: root not converged NaN kpoint 18 ibnd 90 linter: root not converged NaN kpoint 19 ibnd 93 linter: root not converged NaN kpoint 20 ibnd 95 linter: root not converged NaN kpoint 21 ibnd 95 linter: root not converged NaN kpoint 22 ibnd 87 linter: root not converged NaN kpoint 23 ibnd 88 linter: root not converged NaN kpoint 24 ibnd 89 linter: root not converged NaN kpoint 25 ibnd 90 linter: root not converged NaN kpoint 26 ibnd 90 linter: root not converged NaN kpoint 27 ibnd 88 linter: root not converged NaN kpoint 28 ibnd 89 linter: root not converged NaN kpoint 29 ibnd 90 linter: root not converged NaN kpoint 30 ibnd 90 linter: root not converged NaN kpoint 31 ibnd 89 linter: root not converged NaN kpoint 32 ibnd 90 linter: root not converged NaN kpoint 33 ibnd 90 linter: root not converged NaN kpoint 34 ibnd 90 linter: root not converged NaN kpoint 35 ibnd 90 linter: root not converged NaN kpoint 36 ibnd 95 linter: root not converged NaN %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%% from broyden : error # 1 factorization %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%% stopping ... ------------------------------------------------------------------------ --------------- On Tuesday 23 August 2005 18:00, Alcantara Ortigoza, Marisol wrote: > No. Before everything went OK; convergence was achieved after 15 > iterations or so. It is just now. "before" what event ? The output you sent is not the output of a run performing a calculation from the beginnning, i.e. from mode 1 to mode 3*N atoms; it is the output of a run restarting from a previous run that was interrupted in mode 22. Is this what you intended to do? Paolo From eyvaz_isaev at yahoo.com Tue Aug 23 21:25:29 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 23 Aug 2005 12:25:29 -0700 (PDT) Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. In-Reply-To: Message-ID: <20050823192530.54407.qmail@web60320.mail.yahoo.com> Hi, Sorry for interfiering. Presumably Paolo has some strong arguments against my suggetion, but in my experience phonon calculations were never succesfull from restart. So, it is much safer to wait in a queue rather than getting unpredicetable results from restart. Bests, Eyvaz. --- "Alcantara Ortigoza, Marisol" wrote: > Sorry for the delay. I've been waiting for the > approval of the forum > since the files are too large, but it is taking too > long. > Yes. The run was interrupted because the available > time, specified by > the time_max variable, was over. I have to run the > calcualtion in > several steps because we are not allowed to run > things for more than 24 > hours. Even these jobs (24 hours) are taking now up > to 3 days to start > so I have to run the calculation for 4 horus or so > and restart, etc. > Below, you'll find the first and the last two output > files. I cut some > parts that are repeated in each file to make it > smaller. > > Thanks . Marisol > > ----------output 1------------- > > Program PHONON v.2.1.3 starts ... > Today is 18Aug2005 at 13:32:17 > > Parallel version (MPI) > > Number of processors in use: 16 > R & G space division: nprocp = 16 > > Ultrasoft (Vanderbilt) Pseudopotentials > > Reading file co_cu100.save ... > read complete > > Reading file co_cu100.save ... > read complete > > Planes per process (thick) : nr3 =432 npp = 27 > ncplane = 2916 > > Planes per process (smooth): nr3s=243 npps= 16 > ncplanes= 1024 > > Proc/ planes cols G planes cols G > columns G > Pool (dense grid) (smooth grid) > (wavefct grid) > 1 27 134 37464 16 45 7215 15 > 1329 > 2 27 134 37464 16 45 7221 15 > 1329 > 3 27 135 37487 16 45 7225 15 > 1329 > 4 27 134 37454 15 45 7229 15 > 1329 > 5 27 134 37468 15 45 7225 15 > 1329 > 6 27 134 37468 15 45 7225 14 > 1316 > 7 27 134 37464 15 45 7211 14 > 1316 > 8 27 134 37464 15 44 7202 15 > 1321 > 9 27 134 37464 15 44 7210 15 > 1317 > 10 27 134 37464 15 44 7190 14 > 1322 > 11 27 134 37464 15 45 7211 15 > 1321 > 12 27 134 37462 15 45 7215 14 > 1322 > 13 27 134 37462 15 45 7217 14 > 1322 > 14 27 134 37462 15 45 7215 14 > 1322 > 15 27 134 37462 15 45 7213 14 > 1320 > 16 27 134 37462 15 45 7229 15 > 1325 > 0 432 2145 599435 243 717 115453 233 > 21169 > > > nbndx = 104 nbnd = 104 natomwfc = > 100 npwx = 1013 > nelec = 174.00 nkb = 214 ngl = > 6742 > > Phonons of COCu atX > > crystal is > > bravais-lattice index = 6 > lattice parameter (a_0) = 6.7096 a.u. > unit-cell volume = 2416.4615 > (a.u.)^3 > number of atoms/cell = 18 > number of atomic types = 3 > kinetic-energy cut-off = 50.0000 Ry > charge density cut-off = 600.0000 Ry > convergence threshold = 1.0E-16 > beta = 0.1000 > number of iterations used = 4 > > celldm(1)= 6.70960 celldm(2)= 0.00000 > celldm(3)= 8.00000 > celldm(4)= 0.00000 celldm(5)= 0.00000 > celldm(6)= 0.00000 > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 1.0000 0.0000 0.0000 ) > a(2) = ( 0.0000 1.0000 0.0000 ) > a(3) = ( 0.0000 0.0000 8.0000 ) > > reciprocal axes: (cart. coord. in units 2 > pi/a_0) > b(1) = ( 1.0000 0.0000 0.0000 ) > b(2) = ( 0.0000 1.0000 0.0000 ) > b(3) = ( 0.0000 0.0000 0.1250 ) > > > Atoms inside the unit cell: > > Cartesian axes > > site n. atom mass positions > (a_0 units) > 1 O 15.9994 tau( 1) = ( > 0.00000 0.50000 > 2.33471 ) > 2 C 12.0107 tau( 2) = ( > 0.00000 0.50000 > 2.01237 ) > 3 Cu 63.5460 tau( 3) = ( > 0.00000 0.50000 > 1.49940 ) > 4 Cu 63.5460 tau( 4) = ( > 0.50000 0.00000 > 1.48473 ) > 5 Cu 63.5460 tau( 5) = ( > 0.50000 0.50000 > 0.99696 ) > 6 Cu 63.5460 tau( 6) = ( > 0.00000 0.00000 > 0.99695 ) > 7 Cu 63.5460 tau( 7) = ( > 0.00000 0.50000 > 0.49791 ) > 8 Cu 63.5460 tau( 8) = ( > 0.50000 0.00000 > 0.49377 ) > 9 Cu 63.5460 tau( 9) = ( > 0.00000 0.00000 > 0.00000 ) > 10 Cu 63.5460 tau(10) = ( > 0.50000 0.50000 > 0.00000 ) > 11 Cu 63.5460 tau(11) = ( > 0.50000 0.00000 > -0.49377 ) > 12 Cu 63.5460 tau(12) = ( > 0.00000 0.50000 > -0.49791 ) > 13 Cu 63.5460 tau(13) = ( > 0.00000 0.00000 > -0.99695 ) > 14 Cu 63.5460 tau(14) = ( > 0.50000 0.50000 > -0.99696 ) > 15 Cu 63.5460 tau(15) = ( > 0.50000 0.00000 > -1.48473 ) > 16 Cu 63.5460 tau(16) = ( > 0.00000 0.50000 > -1.49940 ) > 17 C 12.0107 tau(17) = ( > 0.00000 0.50000 > -2.01237 ) > 18 O 15.9994 tau(18) = ( > 0.00000 0.50000 > -2.33471 ) > > Computing dynamical matrix for > q = ( 0.50000 0.00000 > 0.00000 ) > > 9 Sym.Ops. (with q -> -q+G ) > > > G cutoff = 684.2027 ( 37464 G-vectors) > FFT grid: ( 54, > 54,432) > G cutoff = 228.0676 ( 7215 G-vectors) > smooth grid: ( 32, > 32,243) > number of k points= 72 gaussian broad. > (ryd)= 0.0147 ngauss > = 1 > cart. coord. in units 2pi/a_0 > === message truncated === __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From alcantar at phys.ksu.edu Tue Aug 23 22:44:01 2005 From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol) Date: Tue, 23 Aug 2005 15:44:01 -0500 Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. Message-ID: Thanks for replying. Well, then I'm hopeless because we are not allowed to run jobs for more than 24 hours and this one takes about 115 hours... Thanks. -----Original Message----- From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On Behalf Of Eyvaz Isaev Sent: Tuesday, August 23, 2005 2:25 PM To: pw_forum at pwscf.org Subject: RE: [Pw_forum] CO/Cu(100) phonon calculation problem. Hi, Sorry for interfiering. Presumably Paolo has some strong arguments against my suggetion, but in my experience phonon calculations were never succesfull from restart. So, it is much safer to wait in a queue rather than getting unpredicetable results from restart. Bests, Eyvaz. --- "Alcantara Ortigoza, Marisol" wrote: > Sorry for the delay. I've been waiting for the > approval of the forum > since the files are too large, but it is taking too > long. > Yes. The run was interrupted because the available > time, specified by > the time_max variable, was over. I have to run the > calcualtion in > several steps because we are not allowed to run > things for more than 24 > hours. Even these jobs (24 hours) are taking now up > to 3 days to start > so I have to run the calculation for 4 horus or so > and restart, etc. > Below, you'll find the first and the last two output > files. I cut some > parts that are repeated in each file to make it > smaller. > > Thanks . Marisol > > ----------output 1------------- > > Program PHONON v.2.1.3 starts ... > Today is 18Aug2005 at 13:32:17 > > Parallel version (MPI) > > Number of processors in use: 16 > R & G space division: nprocp = 16 > > Ultrasoft (Vanderbilt) Pseudopotentials > > Reading file co_cu100.save ... > read complete > > Reading file co_cu100.save ... > read complete > > Planes per process (thick) : nr3 =432 npp = 27 > ncplane = 2916 > > Planes per process (smooth): nr3s=243 npps= 16 ncplanes= 1024 > > Proc/ planes cols G planes cols G > columns G > Pool (dense grid) (smooth grid) > (wavefct grid) > 1 27 134 37464 16 45 7215 15 > 1329 > 2 27 134 37464 16 45 7221 15 > 1329 > 3 27 135 37487 16 45 7225 15 > 1329 > 4 27 134 37454 15 45 7229 15 > 1329 > 5 27 134 37468 15 45 7225 15 > 1329 > 6 27 134 37468 15 45 7225 14 > 1316 > 7 27 134 37464 15 45 7211 14 > 1316 > 8 27 134 37464 15 44 7202 15 > 1321 > 9 27 134 37464 15 44 7210 15 > 1317 > 10 27 134 37464 15 44 7190 14 > 1322 > 11 27 134 37464 15 45 7211 15 > 1321 > 12 27 134 37462 15 45 7215 14 > 1322 > 13 27 134 37462 15 45 7217 14 > 1322 > 14 27 134 37462 15 45 7215 14 > 1322 > 15 27 134 37462 15 45 7213 14 > 1320 > 16 27 134 37462 15 45 7229 15 > 1325 > 0 432 2145 599435 243 717 115453 233 > 21169 > > > nbndx = 104 nbnd = 104 natomwfc = > 100 npwx = 1013 > nelec = 174.00 nkb = 214 ngl = > 6742 > > Phonons of COCu atX > > crystal is > > bravais-lattice index = 6 > lattice parameter (a_0) = 6.7096 a.u. > unit-cell volume = 2416.4615 > (a.u.)^3 > number of atoms/cell = 18 > number of atomic types = 3 > kinetic-energy cut-off = 50.0000 Ry > charge density cut-off = 600.0000 Ry > convergence threshold = 1.0E-16 > beta = 0.1000 > number of iterations used = 4 > > celldm(1)= 6.70960 celldm(2)= 0.00000 > celldm(3)= 8.00000 > celldm(4)= 0.00000 celldm(5)= 0.00000 > celldm(6)= 0.00000 > > crystal axes: (cart. coord. in units of a_0) > a(1) = ( 1.0000 0.0000 0.0000 ) > a(2) = ( 0.0000 1.0000 0.0000 ) > a(3) = ( 0.0000 0.0000 8.0000 ) > > reciprocal axes: (cart. coord. in units 2 > pi/a_0) > b(1) = ( 1.0000 0.0000 0.0000 ) > b(2) = ( 0.0000 1.0000 0.0000 ) > b(3) = ( 0.0000 0.0000 0.1250 ) > > > Atoms inside the unit cell: > > Cartesian axes > > site n. atom mass positions > (a_0 units) > 1 O 15.9994 tau( 1) = ( > 0.00000 0.50000 > 2.33471 ) > 2 C 12.0107 tau( 2) = ( > 0.00000 0.50000 > 2.01237 ) > 3 Cu 63.5460 tau( 3) = ( > 0.00000 0.50000 > 1.49940 ) > 4 Cu 63.5460 tau( 4) = ( > 0.50000 0.00000 > 1.48473 ) > 5 Cu 63.5460 tau( 5) = ( > 0.50000 0.50000 > 0.99696 ) > 6 Cu 63.5460 tau( 6) = ( > 0.00000 0.00000 > 0.99695 ) > 7 Cu 63.5460 tau( 7) = ( > 0.00000 0.50000 > 0.49791 ) > 8 Cu 63.5460 tau( 8) = ( > 0.50000 0.00000 > 0.49377 ) > 9 Cu 63.5460 tau( 9) = ( > 0.00000 0.00000 > 0.00000 ) > 10 Cu 63.5460 tau(10) = ( > 0.50000 0.50000 > 0.00000 ) > 11 Cu 63.5460 tau(11) = ( > 0.50000 0.00000 > -0.49377 ) > 12 Cu 63.5460 tau(12) = ( > 0.00000 0.50000 > -0.49791 ) > 13 Cu 63.5460 tau(13) = ( > 0.00000 0.00000 > -0.99695 ) > 14 Cu 63.5460 tau(14) = ( > 0.50000 0.50000 > -0.99696 ) > 15 Cu 63.5460 tau(15) = ( > 0.50000 0.00000 > -1.48473 ) > 16 Cu 63.5460 tau(16) = ( > 0.00000 0.50000 > -1.49940 ) > 17 C 12.0107 tau(17) = ( > 0.00000 0.50000 > -2.01237 ) > 18 O 15.9994 tau(18) = ( > 0.00000 0.50000 > -2.33471 ) > > Computing dynamical matrix for > q = ( 0.50000 0.00000 > 0.00000 ) > > 9 Sym.Ops. (with q -> -q+G ) > > > G cutoff = 684.2027 ( 37464 G-vectors) > FFT grid: ( 54, > 54,432) > G cutoff = 228.0676 ( 7215 G-vectors) > smooth grid: ( 32, > 32,243) > number of k points= 72 gaussian broad. > (ryd)= 0.0147 ngauss > = 1 > cart. coord. in units 2pi/a_0 > === message truncated === __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From eyvaz_isaev at yahoo.com Tue Aug 23 23:04:58 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 23 Aug 2005 14:04:58 -0700 (PDT) Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. In-Reply-To: Message-ID: <20050823210459.57799.qmail@web60312.mail.yahoo.com> But you can take more CPUs. Though it depends on your computer facilities, and in this case there is a dilemma: more CPU (and time) ==> more time in queue. Bests, Eyvaz --- "Alcantara Ortigoza, Marisol" wrote: > Thanks for replying. Well, then I'm hopeless because > we are not allowed > to run jobs for more than 24 hours and this one > takes about 115 hours... > Thanks. > > -----Original Message----- > From: pw_forum-admin at pwscf.org > [mailto:pw_forum-admin at pwscf.org] On > Behalf Of Eyvaz Isaev > Sent: Tuesday, August 23, 2005 2:25 PM > To: pw_forum at pwscf.org > Subject: RE: [Pw_forum] CO/Cu(100) phonon > calculation problem. > > > Hi, > > Sorry for interfiering. Presumably Paolo has some > strong arguments against my suggetion, but in my > experience phonon calculations were never succesfull > from restart. > > So, it is much safer to wait in a queue rather than > getting unpredicetable results from restart. > > Bests, > Eyvaz. > > --- "Alcantara Ortigoza, Marisol" > wrote: > > > Sorry for the delay. I've been waiting for the > > approval of the forum > > since the files are too large, but it is taking > too > > long. > > Yes. The run was interrupted because the available > > time, specified by > > the time_max variable, was over. I have to run the > > calcualtion in > > several steps because we are not allowed to run > > things for more than 24 > > hours. Even these jobs (24 hours) are taking now > up > > to 3 days to start > > so I have to run the calculation for 4 horus or so > > and restart, etc. > > Below, you'll find the first and the last two > output > > files. I cut some > > parts that are repeated in each file to make it > > smaller. > > > > Thanks . Marisol > > > > ----------output 1------------- > > > > Program PHONON v.2.1.3 starts ... > > Today is 18Aug2005 at 13:32:17 > > > > Parallel version (MPI) > > > > Number of processors in use: 16 > > R & G space division: nprocp = 16 > > > > Ultrasoft (Vanderbilt) Pseudopotentials > > > > Reading file co_cu100.save ... > > read complete > > > > Reading file co_cu100.save ... > > read complete > > > > Planes per process (thick) : nr3 =432 npp = > 27 > > ncplane = 2916 > > > > Planes per process (smooth): nr3s=243 npps= > 16 ncplanes= 1024 > > > > Proc/ planes cols G planes cols G > > columns G > > Pool (dense grid) (smooth grid) > > (wavefct grid) > > 1 27 134 37464 16 45 7215 15 > > 1329 > > 2 27 134 37464 16 45 7221 15 > > 1329 > > 3 27 135 37487 16 45 7225 15 > > 1329 > > 4 27 134 37454 15 45 7229 15 > > 1329 > > 5 27 134 37468 15 45 7225 15 > > 1329 > > 6 27 134 37468 15 45 7225 14 > > 1316 > > 7 27 134 37464 15 45 7211 14 > > 1316 > > 8 27 134 37464 15 44 7202 15 > > 1321 > > 9 27 134 37464 15 44 7210 15 > > 1317 > > 10 27 134 37464 15 44 7190 14 > > 1322 > > 11 27 134 37464 15 45 7211 15 > > 1321 > > 12 27 134 37462 15 45 7215 14 > > 1322 > > 13 27 134 37462 15 45 7217 14 > > 1322 > > 14 27 134 37462 15 45 7215 14 > > 1322 > > 15 27 134 37462 15 45 7213 14 > > 1320 > > 16 27 134 37462 15 45 7229 15 > > 1325 > > 0 432 2145 599435 243 717 115453 233 > > 21169 > > > > > > nbndx = 104 nbnd = 104 natomwfc = > > 100 npwx = 1013 > > nelec = 174.00 nkb = 214 ngl = > > 6742 > > > > Phonons of COCu atX > > > > crystal is > > > > bravais-lattice index = 6 > > lattice parameter (a_0) = 6.7096 > a.u. > > unit-cell volume = 2416.4615 > > (a.u.)^3 > > number of atoms/cell = 18 > > number of atomic types = 3 > > kinetic-energy cut-off = 50.0000 Ry > > charge density cut-off = 600.0000 Ry > > convergence threshold = 1.0E-16 > > beta = 0.1000 > > number of iterations used = 4 > > > > celldm(1)= 6.70960 celldm(2)= 0.00000 > > celldm(3)= 8.00000 > > celldm(4)= 0.00000 celldm(5)= 0.00000 > > celldm(6)= 0.00000 > > > > crystal axes: (cart. coord. in units of a_0) > > a(1) = ( 1.0000 0.0000 0.0000 ) > > a(2) = ( 0.0000 1.0000 0.0000 ) > > a(3) = ( 0.0000 0.0000 8.0000 ) > > > > reciprocal axes: (cart. coord. in units 2 > > pi/a_0) > > b(1) = ( 1.0000 0.0000 0.0000 ) > > b(2) = ( 0.0000 1.0000 0.0000 ) > > b(3) = ( 0.0000 0.0000 0.1250 ) > > > > > > Atoms inside the unit cell: > > > > Cartesian axes > > > > site n. atom mass positions > > (a_0 units) > > 1 O 15.9994 tau( 1) = ( > > 0.00000 0.50000 > > 2.33471 ) > > 2 C 12.0107 tau( 2) = ( > > 0.00000 0.50000 > > 2.01237 ) > > 3 Cu 63.5460 tau( 3) = ( > > 0.00000 0.50000 > > 1.49940 ) > > 4 Cu 63.5460 tau( 4) = ( > > 0.50000 0.00000 > > 1.48473 ) > > 5 Cu 63.5460 tau( 5) = ( > > 0.50000 0.50000 > > 0.99696 ) > > 6 Cu 63.5460 tau( 6) = ( > > 0.00000 0.00000 > > 0.99695 ) > > 7 Cu 63.5460 tau( 7) = ( > > 0.00000 0.50000 > > 0.49791 ) > > 8 Cu 63.5460 tau( 8) = ( > > 0.50000 0.00000 > > 0.49377 ) > > 9 Cu 63.5460 tau( 9) = ( > > 0.00000 0.00000 > > 0.00000 ) > > 10 Cu 63.5460 tau(10) = ( > > 0.50000 0.50000 > > 0.00000 ) > > 11 Cu 63.5460 tau(11) = ( > > 0.50000 0.00000 > > -0.49377 ) > > 12 Cu 63.5460 tau(12) = ( > > 0.00000 0.50000 > === message truncated === __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From giannozz at nest.sns.it Wed Aug 24 14:46:04 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 24 Aug 2005 14:46:04 +0200 Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. In-Reply-To: <20050823192530.54407.qmail@web60320.mail.yahoo.com> References: <20050823192530.54407.qmail@web60320.mail.yahoo.com> Message-ID: <200508241446.04444.giannozz@nest.sns.it> On Tuesday 23 August 2005 21:25, Eyvaz Isaev wrote: > Sorry for interfiering. Presumably Paolo has some > strong arguments against my suggetion, but in my > experience phonon calculations were never succesfull > from restart. if one restarts from a run that was stopped because of cpu time limit or machine crash or whatever unexpected reason, the probability that something goes wrong (i.e. that files are corrupted) is very high. If however the run is cleanly stopped, i.e. by the code itself and not by external factors, one should be able to restart without any problem. It is however prudent to save a copy of the temporary files before restarting a new job. It is hard to say what happened in this specific case, since it is not clear whether the problem occurs due to restarting or independently of it. In the former case, it should be possible to find cases in which the restart reproducibly fails. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From alcantar at phys.ksu.edu Wed Aug 24 19:09:31 2005 From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol) Date: Wed, 24 Aug 2005 12:09:31 -0500 Subject: [Pw_forum] CO/Cu(100) phonon calculation problem. Message-ID: Paolo Giannozzi wrote: >if one restarts from a run that was stopped because of cpu >time limit or machine crash or whatever unexpected reason, >the probability that something goes wrong (i.e. that files are >corrupted) is very high. If however the run is cleanly stopped, >i.e. by the code itself and not by external factors, one should >be able to restart without any problem. It is however prudent >to save a copy of the temporary files before restarting a new >job. >It is hard to say what happened in this specific case, since it >is not clear whether the problem occurs due to restarting or independently of it. In the >former case, it should be possible >to find cases in which the restart reproducibly fails. Then, it is clear to me that the problem was not because of restarting issues. First, the run stopped cleanly. At the end the last 'correct' output file shows "Stopping for time limit 13699. 13400.". Second, the next run - where the problem arose - started properly. It still performed two iterations without any problem. Therefore, it couldn't be a restarting problem. What then? Is it possible to recover anything? Thanks. Marisol. -----Original Message----- From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Wednesday, August 24, 2005 7:46 AM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] CO/Cu(100) phonon calculation problem. On Tuesday 23 August 2005 21:25, Eyvaz Isaev wrote: > Sorry for interfiering. Presumably Paolo has some > strong arguments against my suggetion, but in my > experience phonon calculations were never succesfull > from restart. if one restarts from a run that was stopped because of cpu time limit or machine crash or whatever unexpected reason, the probability that something goes wrong (i.e. that files are corrupted) is very high. If however the run is cleanly stopped, i.e. by the code itself and not by external factors, one should be able to restart without any problem. It is however prudent to save a copy of the temporary files before restarting a new job. It is hard to say what happened in this specific case, since it is not clear whether the problem occurs due to restarting or independently of it. In the former case, it should be possible to find cases in which the restart reproducibly fails. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From jasonsun98 at hotmail.com Thu Aug 25 17:30:06 2005 From: jasonsun98 at hotmail.com (sun jason) Date: Thu, 25 Aug 2005 15:30:06 +0000 Subject: [Pw_forum] how to write the q-points in a uniform grid in the irreducible Brillouin Zone? In-Reply-To: <20050825053640.21145.84056.Mailman@democritos.sissa.it> Message-ID: Dear all, I want to calculate the phonon and the interatomic force constants of some particular material, its bravais lattice is primitive orthorhombic. follow example06, I should make a phonon calculation for a uniform grid of q-points, such as 444 grid, but I don't know how to write these q-points for orthorhombic lattice. does anyone know how to write these q-points? not only for orthorhombic lattice, but also for all the other bravais lattice. any suggestions would be appreciated. jason sun From eyvaz_isaev at yahoo.com Thu Aug 25 19:34:41 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Thu, 25 Aug 2005 10:34:41 -0700 (PDT) Subject: [Pw_forum] how to write the q-points in a uniform grid in the irreducible Brillouin Zone? In-Reply-To: Message-ID: <20050825173441.40794.qmail@web60315.mail.yahoo.com> Hi, Use kpoints.x from /pwtools directory. Bests, Eyvaz. --- sun jason wrote: > Dear all, > > I want to calculate the phonon and the interatomic > force constants of some > particular material, its bravais lattice is > primitive orthorhombic. > > follow example06, I should make a phonon calculation > for a uniform grid of > q-points, such as 444 grid, but I don't know how to > write these q-points > for orthorhombic lattice. > > does anyone know how to write these q-points? not > only for orthorhombic > lattice, but also for all the other bravais lattice. > > any suggestions would be appreciated. > > > jason sun > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From konstantin_kudin at yahoo.com Fri Aug 26 22:03:51 2005 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Fri, 26 Aug 2005 13:03:51 -0700 (PDT) Subject: [Pw_forum] mpich2 and Espresso Message-ID: <20050826200351.66129.qmail@web52015.mail.yahoo.com> Did anyone manage to get Espresso working with mpich2 ? If so, could you share your config files for mpich2 ? I could compile a recent CVS with mpich2, and then run it. The version of mpiexec comes from OSC. However, the CP code with mpich2 hangs at random places while consuming CPU cycles. At the same time with mpich things work correctly on the same cluster. Kostya ____________________________________________________ Start your day with Yahoo! - make it your home page http://www.yahoo.com/r/hs From xhongjun at mail.ustc.edu.cn Sat Aug 27 15:21:33 2005 From: xhongjun at mail.ustc.edu.cn (xianghjun) Date: Sat, 27 Aug 2005 21:21:33 +0800 Subject: [Pw_forum] About maximally localized wannier function Message-ID: <431068DD.6030006@mail.ustc.edu.cn> Dear all, I am trying to get MLWF for some systems and want to know if MLWF has been implemented in PWSCF. Thanks in advance. Best regards, xianghjun ============================================================= H. J. Xiang Ph.D. Candidate, Hefei National Laboratory For Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China Tel.: 86-551-3606428 Fax.: 86-551-3602969 E-mail: xhongjun at mail.ustc.edu.cn ============================================================= From eyvaz_isaev at yahoo.com Sat Aug 27 16:17:53 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Sat, 27 Aug 2005 07:17:53 -0700 (PDT) Subject: [Pw_forum] About maximally localized wannier function In-Reply-To: <431068DD.6030006@mail.ustc.edu.cn> Message-ID: <20050827141753.56713.qmail@web60311.mail.yahoo.com> Hi, Please see www.wannier.org. There is an interface between PWSCF and WanT packages (see /PP directory in PWSCF). Sure, Nikola Marzari konws much more about the package. Bests, Eyvaz. --- xianghjun wrote: > Dear all, > I am trying to get MLWF for some systems and want > to know if MLWF has > been implemented in PWSCF. > Thanks in advance. > > Best regards, > xianghjun > > ============================================================= > H. J. Xiang > Ph.D. Candidate, > Hefei National Laboratory For Physical Sciences at > Microscale, > University of Science and Technology of China, > Hefei, Anhui, 230026, > People's Republic of China > Tel.: 86-551-3606428 > Fax.: 86-551-3602969 > E-mail: xhongjun at mail.ustc.edu.cn > ============================================================= > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ____________________________________________________ Start your day with Yahoo! - make it your home page http://www.yahoo.com/r/hs From marzari at MIT.EDU Sat Aug 27 16:46:49 2005 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 27 Aug 2005 10:46:49 -0400 Subject: [Pw_forum] About maximally localized wannier function In-Reply-To: <431068DD.6030006@mail.ustc.edu.cn> References: <431068DD.6030006@mail.ustc.edu.cn> Message-ID: <43107CD9.7070803@mit.edu> Dear Xinaghjun, the version that Ivo Souza and myself have been using and developing is at www.wannier.org . I've uploaded there the latest files (wannier_0.9b) that contain the graphics output for Xcrysden (courtesy of Michel Posternak) and the interface with PWscf and the new makefiles (both courtesy of Jonathan Yates). Arrigo Calzolari has in www.wannier-transport.org a transport/wannier code interfaced with pwscf, where the wannier part is similar to the above. Note that also, inside quantum-Espresso, the Car-Parrinello, Gamma-sampling code CP has its own Wannier subroutines available. Best, nicola xianghjun wrote: > Dear all, > I am trying to get MLWF for some systems and want to know if MLWF has > been implemented in PWSCF. > Thanks in advance. > > Best regards, > xianghjun > > ============================================================= > H. J. Xiang > Ph.D. Candidate, > Hefei National Laboratory For Physical Sciences at Microscale, > University of Science and Technology of China, > Hefei, Anhui, 230026, > People's Republic of China > Tel.: 86-551-3606428 > Fax.: 86-551-3602969 > E-mail: xhongjun at mail.ustc.edu.cn > ============================================================= > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum -- --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 617.2586534 marzari at mit.edu http://nnn.mit.edu From xhongjun at mail.ustc.edu.cn Sat Aug 27 16:52:13 2005 From: xhongjun at mail.ustc.edu.cn (xianghjun) Date: Sat, 27 Aug 2005 22:52:13 +0800 Subject: [Pw_forum] About maximally localized wannier function In-Reply-To: <325152336.15652@ustc.edu.cn> References: <325152336.15652@ustc.edu.cn> Message-ID: <43107E1D.8040200@mail.ustc.edu.cn> Dear Eyvaz, Thanks a lot for your helpful suggestion. Eyvaz Isaev wrote: >Hi, > >Please see www.wannier.org. >There is an interface between PWSCF and WanT packages >(see /PP directory in PWSCF). >Sure, Nikola Marzari konws much more about the >package. > >Bests, >Eyvaz. > > >--- xianghjun wrote: > > > >>Dear all, >> I am trying to get MLWF for some systems and want >>to know if MLWF has >>been implemented in PWSCF. >>Thanks in advance. >> >>Best regards, >>xianghjun >> >> >> >> >============================================================= > > >> H. J. Xiang >> Ph.D. Candidate, >> Hefei National Laboratory For Physical Sciences at >>Microscale, >> University of Science and Technology of China, >> Hefei, Anhui, 230026, >> People's Republic of China >> Tel.: 86-551-3606428 >> Fax.: 86-551-3602969 >> E-mail: xhongjun at mail.ustc.edu.cn >> >> >> >============================================================= > > >>_______________________________________________ >>Pw_forum mailing list >>Pw_forum at pwscf.org >>http://www.democritos.it/mailman/listinfo/pw_forum >> >> >> > > > > >____________________________________________________ >Start your day with Yahoo! - make it your home page >http://www.yahoo.com/r/hs > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > > -- Best regards, xianghjun ============================================================= H. J. Xiang Ph.D. Candidate, Hefei National Laboratory For Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China Tel.: 86-551-3606428 Fax.: 86-551-3602969 E-mail: xhongjun at mail.ustc.edu.cn ============================================================= From xhongjun at mail.ustc.edu.cn Sat Aug 27 17:05:05 2005 From: xhongjun at mail.ustc.edu.cn (xianghjun) Date: Sat, 27 Aug 2005 23:05:05 +0800 Subject: [Pw_forum] About maximally localized wannier function In-Reply-To: <325154126.20670@ustc.edu.cn> References: <431068DD.6030006@mail.ustc.edu.cn> <325154126.20670@ustc.edu.cn> Message-ID: <43108121.7070307@mail.ustc.edu.cn> Dear Prof. Marzari, Thank you very much for your valuable reply. I will use the excellent wannier and PWSCF codes to calculate the MLWF. Nicola Marzari wrote: > > > Dear Xinaghjun, > > > the version that Ivo Souza and myself have been using and > developing is at www.wannier.org . I've uploaded there the > latest files (wannier_0.9b) that contain the graphics output > for Xcrysden (courtesy of Michel Posternak) and the interface > with PWscf and the new makefiles (both courtesy of Jonathan Yates). > > Arrigo Calzolari has in www.wannier-transport.org a transport/wannier > code interfaced with pwscf, where the wannier part is similar to the > above. > > Note that also, inside quantum-Espresso, the Car-Parrinello, > Gamma-sampling code CP has its own Wannier subroutines available. > > Best, > > nicola > > > xianghjun wrote: > >> Dear all, >> I am trying to get MLWF for some systems and want to know if MLWF >> has been implemented in PWSCF. >> Thanks in advance. >> >> Best regards, >> xianghjun >> >> ============================================================= >> H. J. Xiang >> Ph.D. Candidate, >> Hefei National Laboratory For Physical Sciences at Microscale, >> University of Science and Technology of China, >> Hefei, Anhui, 230026, >> People's Republic of China >> Tel.: 86-551-3606428 >> Fax.: 86-551-3602969 >> E-mail: xhongjun at mail.ustc.edu.cn >> ============================================================= >> >> _______________________________________________ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > -- Best regards, xianghjun ============================================================= H. J. Xiang Ph.D. Candidate, Hefei National Laboratory For Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China Tel.: 86-551-3606428 Fax.: 86-551-3602969 E-mail: xhongjun at mail.ustc.edu.cn ============================================================= From silviu at Princeton.EDU Sat Aug 27 17:03:51 2005 From: silviu at Princeton.EDU (Silviu Zilberman) Date: Sat, 27 Aug 2005 11:03:51 -0400 Subject: [Pw_forum] About maximally localized wannier function In-Reply-To: <431068DD.6030006@mail.ustc.edu.cn> References: <431068DD.6030006@mail.ustc.edu.cn> Message-ID: <431080D7.8090000@Princeton.EDU> Dear Xianghjun, MLWF are implemented in the CP code. I believe that the latest cvs version has compatible restart files, which means you could use any PWSCF calculation result as an input to a CP Wannier calculation. This compatibility has only been introduced recently, and it may still be unstable. You could also take the geometry from your PW calculation and start a CP calculation from scratch and minimize the wavefunction using Wannier dynamics. Look at the INPUT_CP file for more details, as well as example #23. Silviu. xianghjun wrote: > Dear all, > I am trying to get MLWF for some systems and want to know if MLWF has > been implemented in PWSCF. > Thanks in advance. > > Best regards, > xianghjun > > ============================================================= > H. J. Xiang > Ph.D. Candidate, > Hefei National Laboratory For Physical Sciences at Microscale, > University of Science and Technology of China, > Hefei, Anhui, 230026, > People's Republic of China > Tel.: 86-551-3606428 > Fax.: 86-551-3602969 > E-mail: xhongjun at mail.ustc.edu.cn > ============================================================= > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum From marzari at MIT.EDU Sat Aug 27 17:17:09 2005 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 27 Aug 2005 11:17:09 -0400 Subject: [Pw_forum] About maximally localized wannier function In-Reply-To: <431080D7.8090000@Princeton.EDU> References: <431068DD.6030006@mail.ustc.edu.cn> <431080D7.8090000@Princeton.EDU> Message-ID: <431083F5.9070501@mit.edu> Dear Silviu, this is an interesting suggestion. The good thing about the Gamma-sampling CP code algorithm is that it will always lead to the true minimum of the localization functional, as long as a cubic/tetragonal/orthorombic cells are used (i.e. derivatives are calculated with 3 orthogonal G vectors). Depending on your application, this could be very important or irrelevant - the more the system is large and disordered, the more it becomes useful/essential. Another advantage is that the CP/Wannier subroutines work with ultrasoft pseudopotentials, although this capability is forthcoming in wannier-transport.org and wannier.org . The regular k-point wannier codes use instead trial projection orbitals (very straightforward ones - usually one specifies the center of a gaussian, and the l,m of a spherical harmonics) to start the minimization already in the right basin of attraction. This approach works again very well in most cases - to the point that some groups just use these projections, without localization, to get localized WFs (I think, e.g., Pickett's group). As a last note - if you use CP, your sampling can be "poor" if you have a smallish unit cell. On the other hand, if you use PWSCF to feed CP, you can make your charge density as good as you want it, sampling-wise. Then, the only finite-size errors remaining will be on the calculation of the MLWFs themselves, that, using CP, will only combine states obtained at Gamma, instead of using all the Brillouin zone. nicola Silviu Zilberman wrote: > Dear Xianghjun, > > MLWF are implemented in the CP code. I believe that the latest cvs > version has compatible restart files, which means you could use any > PWSCF calculation result as an input to a CP Wannier calculation. This > compatibility has only been introduced recently, and it may still be > unstable. You could also take the geometry from your PW calculation and > start a CP calculation from scratch and minimize the wavefunction using > Wannier dynamics. Look at the INPUT_CP file for more details, as well as > example #23. > > Silviu. > > xianghjun wrote: > >> Dear all, >> I am trying to get MLWF for some systems and want to know if MLWF has >> been implemented in PWSCF. >> Thanks in advance. >> >> Best regards, >> xianghjun >> >> ============================================================= >> H. J. Xiang >> Ph.D. Candidate, >> Hefei National Laboratory For Physical Sciences at Microscale, >> University of Science and Technology of China, >> Hefei, Anhui, 230026, >> People's Republic of China >> Tel.: 86-551-3606428 >> Fax.: 86-551-3602969 >> E-mail: xhongjun at mail.ustc.edu.cn >> ============================================================= >> >> _______________________________________________ >> 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 Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 617.2586534 marzari at mit.edu http://nnn.mit.edu From jasonsun98 at hotmail.com Sat Aug 27 17:38:57 2005 From: jasonsun98 at hotmail.com (sun jason) Date: Sat, 27 Aug 2005 15:38:57 +0000 Subject: [Pw_forum] cann't get the LO-TO spliting using dynmat.x In-Reply-To: <20050827053633.25550.42392.Mailman@democritos.sissa.it> Message-ID: Dear all, follw example06, I calculate the phonon frequency of BN, I can get LO/TO spliting using q2r.x + matdyn.x , the result at gamma point is like that: ============================================================ 0.0000 0.0000 0.0001 1055.3982 1055.3982 1294.1370 ============================================================ but I cann't get the LO mode when I use dynmat.x, the result is like this: ============================================================ 0.0000 0.0000 0.0001 1055.3982 1055.3982 1055.3982 ============================================================ my input file for dynmat.x is like that: ===================================================== phonons of cubic BN at 0.0000000,0.0000000,0.0000000 &input amass(1)=10.81100, amass(2)=14.00674, asr=.true., fildyn='bn.dynG', filout='bn.out', filmol='bn.molden' &end 0.0000000,0.0000000,0.0000000 ===================================================== but someone had told me that both this two methods can be use to get LO/TO spliting. is it right? why I cann't get the LO mode just use dynmat.x ? any comment would be appreciated. best regards, ============================================== Jian Sun Physics Dept. of Nanjing University National Lab. of Solid State Microstructures 22 Hankou Road, Gulou District Nanjing, Jiangsu Province 210093 China ============================================== From silviu at Princeton.EDU Sat Aug 27 17:40:31 2005 From: silviu at Princeton.EDU (Silviu Zilberman) Date: Sat, 27 Aug 2005 11:40:31 -0400 Subject: [Pw_forum] About maximally localized wannier function In-Reply-To: <431083F5.9070501@mit.edu> References: <431068DD.6030006@mail.ustc.edu.cn> <431080D7.8090000@Princeton.EDU> <431083F5.9070501@mit.edu> Message-ID: <4310896F.3000005@Princeton.EDU> Dear Nicola, Thank you for your detailed explanation. Following on your last point, suppose you do the best k-point sampling with PW, to obtain the total charge density. One could impose this charge density in the CP calculation, at every step, to get MLWF at the gamma-point that are consistent with this charge density. Wouldn't it implicitly be equivalent to the MLWF obtained in the full k-points optimization? Thanks, Silviu. Nicola Marzari wrote: > > > Dear Silviu, > > this is an interesting suggestion. The good thing about the > Gamma-sampling CP code algorithm is that it will always lead to > the true minimum of the localization functional, as long as a > cubic/tetragonal/orthorombic cells are used (i.e. derivatives are > calculated with 3 orthogonal G vectors). Depending on your application, > this could be very important or irrelevant - the more the system is > large and disordered, the more it becomes useful/essential. > Another advantage is that the CP/Wannier subroutines work with ultrasoft > pseudopotentials, although this capability is forthcoming in > wannier-transport.org and wannier.org . > > The regular k-point wannier codes use instead trial projection orbitals > (very straightforward ones - usually one specifies the center of a > gaussian, and the l,m of a spherical harmonics) to start the > minimization already in the right basin of attraction. This > approach works again very well in most cases - to the point that some > groups just use these projections, without localization, to get > localized WFs (I think, e.g., Pickett's group). > > As a last note - if you use CP, your sampling can be "poor" if you have > a smallish unit cell. On the other hand, if you use PWSCF to feed CP, > you can make your charge density as good as you want it, sampling-wise. > Then, the only finite-size errors remaining will be on the calculation > of the MLWFs themselves, that, using CP, will only combine states > obtained at Gamma, instead of using all the Brillouin zone. > > nicola > > > Silviu Zilberman wrote: > >> Dear Xianghjun, >> >> MLWF are implemented in the CP code. I believe that the latest cvs >> version has compatible restart files, which means you could use any >> PWSCF calculation result as an input to a CP Wannier calculation. >> This compatibility has only been introduced recently, and it may >> still be unstable. You could also take the geometry from your PW >> calculation and start a CP calculation from scratch and minimize the >> wavefunction using Wannier dynamics. Look at the INPUT_CP file for >> more details, as well as example #23. >> >> Silviu. >> >> xianghjun wrote: >> >>> Dear all, >>> I am trying to get MLWF for some systems and want to know if MLWF >>> has been implemented in PWSCF. >>> Thanks in advance. >>> >>> Best regards, >>> xianghjun >>> >>> ============================================================= >>> H. J. Xiang >>> Ph.D. Candidate, >>> Hefei National Laboratory For Physical Sciences at Microscale, >>> University of Science and Technology of China, >>> Hefei, Anhui, 230026, >>> People's Republic of China >>> Tel.: 86-551-3606428 >>> Fax.: 86-551-3602969 >>> E-mail: xhongjun at mail.ustc.edu.cn >>> ============================================================= >>> >>> _______________________________________________ >>> 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 > > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu 213 Frick Laboratory, Department of Chemistry Princeton University Princeton, NJ 08544 phone: 609-258-1834 fax: 609-258-6746 silviu at Princeton.EDU %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -------------- next part -------------- A non-text attachment was scrubbed... Name: silviu.vcf Type: text/x-vcard Size: 272 bytes Desc: not available Url : /pipermail/attachments/20050827/5e5a60dc/attachment.vcf From silviu at Princeton.EDU Sat Aug 27 17:46:40 2005 From: silviu at Princeton.EDU (Silviu Zilberman) Date: Sat, 27 Aug 2005 11:46:40 -0400 Subject: [Pw_forum] About maximally localized wannier function In-Reply-To: <4310896F.3000005@Princeton.EDU> References: <431068DD.6030006@mail.ustc.edu.cn> <431080D7.8090000@Princeton.EDU> <431083F5.9070501@mit.edu> <4310896F.3000005@Princeton.EDU> Message-ID: <43108AE0.1010107@Princeton.EDU> Sorry, after reading again your email I reallized that you did answer my question. Thanks, Silviu. Silviu Zilberman wrote: > Dear Nicola, > > Thank you for your detailed explanation. Following on your last point, > suppose you do the best k-point sampling with PW, to obtain the total > charge density. One could impose this charge density in the CP > calculation, at every step, to get MLWF at the gamma-point that are > consistent with this charge density. Wouldn't it implicitly be > equivalent to the MLWF obtained in the full k-points optimization? > > Thanks, Silviu. > > Nicola Marzari wrote: > >> >> >> Dear Silviu, >> >> this is an interesting suggestion. The good thing about the >> Gamma-sampling CP code algorithm is that it will always lead to >> the true minimum of the localization functional, as long as a >> cubic/tetragonal/orthorombic cells are used (i.e. derivatives are >> calculated with 3 orthogonal G vectors). Depending on your application, >> this could be very important or irrelevant - the more the system is >> large and disordered, the more it becomes useful/essential. >> Another advantage is that the CP/Wannier subroutines work with ultrasoft >> pseudopotentials, although this capability is forthcoming in >> wannier-transport.org and wannier.org . >> >> The regular k-point wannier codes use instead trial projection orbitals >> (very straightforward ones - usually one specifies the center of a >> gaussian, and the l,m of a spherical harmonics) to start the >> minimization already in the right basin of attraction. This >> approach works again very well in most cases - to the point that some >> groups just use these projections, without localization, to get >> localized WFs (I think, e.g., Pickett's group). >> >> As a last note - if you use CP, your sampling can be "poor" if you have >> a smallish unit cell. On the other hand, if you use PWSCF to feed CP, >> you can make your charge density as good as you want it, sampling-wise. >> Then, the only finite-size errors remaining will be on the calculation >> of the MLWFs themselves, that, using CP, will only combine states >> obtained at Gamma, instead of using all the Brillouin zone. >> >> nicola >> >> >> Silviu Zilberman wrote: >> >>> Dear Xianghjun, >>> >>> MLWF are implemented in the CP code. I believe that the latest cvs >>> version has compatible restart files, which means you could use any >>> PWSCF calculation result as an input to a CP Wannier calculation. >>> This compatibility has only been introduced recently, and it may >>> still be unstable. You could also take the geometry from your PW >>> calculation and start a CP calculation from scratch and minimize the >>> wavefunction using Wannier dynamics. Look at the INPUT_CP file for >>> more details, as well as example #23. >>> >>> Silviu. >>> >>> xianghjun wrote: >>> >>>> Dear all, >>>> I am trying to get MLWF for some systems and want to know if MLWF >>>> has been implemented in PWSCF. >>>> Thanks in advance. >>>> >>>> Best regards, >>>> xianghjun >>>> >>>> ============================================================= >>>> H. J. Xiang >>>> Ph.D. Candidate, >>>> Hefei National Laboratory For Physical Sciences at Microscale, >>>> University of Science and Technology of China, >>>> Hefei, Anhui, 230026, >>>> People's Republic of China >>>> Tel.: 86-551-3606428 >>>> Fax.: 86-551-3602969 >>>> E-mail: xhongjun at mail.ustc.edu.cn >>>> ============================================================= >>>> >>>> _______________________________________________ >>>> 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 >> >> >> > > -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu 213 Frick Laboratory, Department of Chemistry Princeton University Princeton, NJ 08544 phone: 609-258-1834 fax: 609-258-6746 silviu at Princeton.EDU %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -------------- next part -------------- A non-text attachment was scrubbed... Name: silviu.vcf Type: text/x-vcard Size: 272 bytes Desc: not available Url : /pipermail/attachments/20050827/22d99736/attachment.vcf From jasonsun98 at hotmail.com Sat Aug 27 17:49:07 2005 From: jasonsun98 at hotmail.com (sun jason) Date: Sat, 27 Aug 2005 15:49:07 +0000 Subject: [Pw_forum] how to start a new task based on the optimized structure automatically? In-Reply-To: <20050827053633.25550.42392.Mailman@democritos.sissa.it> Message-ID: Dear all, we want to calculate phonon or other properties after optimizing one structure sometimes. I'm a little lazy and want to write a scriptfile to combine the pw.x(vc-relax)+pw.x(scf)+ph.x together, is it possible? and how to write it? ============================================== Jian Sun Physics Dept. of Nanjing University National Lab. of Solid State Microstructures 22 Hankou Road, Gulou District Nanjing, Jiangsu Province 210093 China ============================================== From marzari at MIT.EDU Sat Aug 27 17:51:51 2005 From: marzari at MIT.EDU (Nicola Marzari) Date: Sat, 27 Aug 2005 11:51:51 -0400 Subject: [Pw_forum] About maximally localized wannier function In-Reply-To: <4310896F.3000005@Princeton.EDU> References: <431068DD.6030006@mail.ustc.edu.cn> <431080D7.8090000@Princeton.EDU> <431083F5.9070501@mit.edu> <4310896F.3000005@Princeton.EDU> Message-ID: <43108C17.1070804@mit.edu> Silviu, I had already written this out, so I still post it for clarification. Apologies for the bandwidth. Suppose in PWSCF you use infinite k-points. This allows you to calculate the perfectly converged charge density with respect to k-point sampling. This perfect charge density is then read by CP, and it allows it to construct the perfect Hamiltonian, and perfectly diagonalize it at Gamma (but nowhere else !). If your unit cell is (very) small, these Gamma eigenstates will be different than those that would have been calculated self-consistently by CP (you are using the perfect charge density). (Of course, you shouldn't use CP to do small calculations where you need BZ sampling finer than Gamma). But now the issue is that, with the perfect Gamma-orbitals, CP will allow you to construct localized wavefunctions using only Gamma, while in principle you should use all states at all k-points. So your CP MLWFs will not be equivalent to the PWSCF MLWFs, even if the Hamiltonian is the same. In particular, the CP MLWFs, since they use only the Bloch orbitals at Gamma, will have the same periodicity of your unit cell, while the PSCF MLWFs, calculated from a nk X nk X nk Monkhorst-Pack mesh, while be periodic with the periodicity of a nk X nk X nk supercell. Best, nicola --------------------------------------------------------------------- Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 617.2586534 marzari at mit.edu http://nnn.mit.edu From jasonsun98 at hotmail.com Sat Aug 27 18:12:30 2005 From: jasonsun98 at hotmail.com (sun jason) Date: Sat, 27 Aug 2005 16:12:30 +0000 Subject: [Pw_forum] how to read lattice constant from the output file of vc-relax In-Reply-To: <20050827053633.25550.42392.Mailman@democritos.sissa.it> Message-ID: Dear all, I execute a vc-relax calculation, the output file is like this: ================================================================================ End of self-consistent calculation ! total energy = -26.26021699 ryd estimated scf accuracy < 2.4E-10 ryd convergence has been achieved Forces acting on atoms (Ry/au): atom 1 type 1 force = 0.00000000 0.00000000 0.00000000 atom 2 type 2 force = 0.00000000 0.00000000 0.00000000 Total force = 0.000000 Total SCF correction = 0.000000 entering subroutine stress ... total stress (ryd/bohr**3) (kbar) P= -0.20 -0.00000138 0.00000000 0.00000000 -0.20 0.00 0.00 0.00000000 -0.00000138 0.00000000 0.00 -0.20 0.00 0.00000000 0.00000000 -0.00000138 0.00 0.00 -0.20 Wentzcovitch Damped Dynamics: convergence achieved, Efinal= -26.26021699 ------------------------------------------------------------------------ Final estimate of lattice vectors (input alat units) -0.500982241 0.000000000 0.500982241 0.000000000 0.500982241 0.500982241 -0.500982241 0.500982241 0.000000000 final unit-cell volume = 80.2290 (a.u.)^3 input alat = 6.8330 (a.u.) CELL_PARAMETERS (alat) -0.500982241 0.000000000 0.500982241 0.000000000 0.500982241 0.500982241 -0.500982241 0.500982241 0.000000000 ATOMIC_POSITIONS (crystal) B 0.000000000 0.000000000 0.000000000 N 0.250000000 0.250000000 0.250000000 Writing file bn.save for program phonon ======================================================================================== does it mean that the lattice constant is changed to (0.500982241/0.5)*3.615=3.6221 angstrom? if it is right, the lattice constant optimized by GGA pseudopotential using pwscf code is large than the experimental value, but the GGA result by CASTEP code is small than the experimental value. which one is reasonable? any help would be appreciated. best regards, ============================================== Jian Sun Physics Dept. of Nanjing University National Lab. of Solid State Microstructures 22 Hankou Road, Gulou District Nanjing, Jiangsu Province 210093 China ============================================== From giannozz at nest.sns.it Mon Aug 29 11:29:10 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 29 Aug 2005 11:29:10 +0200 Subject: [Pw_forum] cann't get the LO-TO spliting using dynmat.x In-Reply-To: References: Message-ID: <200508291129.10790.giannozz@nest.sns.it> On Saturday 27 August 2005 17:38, sun jason wrote: > I can't get the LO mode when I use dynmat.x, the result is like this: > ============================================================ > 0.0000 0.0000 0.0001 1055.3982 1055.3982 1055.3982 > ============================================================ > my input file for dynmat.x is like that: > ===================================================== > phonons of cubic BN at 0.0000000,0.0000000,0.0000000 > &input > amass(1)=10.81100, > amass(2)=14.00674, > asr=.true., > fildyn='bn.dynG', > filout='bn.out', > filmol='bn.molden' > &end > 0.0000000,0.0000000,0.0000000 > ===================================================== From the header of pwtools/dynmat.f90: ! Input data (namelist "input") ! q(3) real calculate LO modes (add nonanalytic terms) along ! the direction q (default: q=(0,0,0) ) so q(i) must be specified inside the namelist as q(1)=..., q(2)=..., q(3)=... If you do not specify anything, or specify 0, the non-analytical part will not be added. For BN any direction will yield the same TO-LO splitting. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Mon Aug 29 11:37:13 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 29 Aug 2005 11:37:13 +0200 Subject: [Pw_forum] how to read lattice constant from the output file of vc-relax In-Reply-To: References: Message-ID: <200508291137.13670.giannozz@nest.sns.it> On Saturday 27 August 2005 18:12, sun jason wrote: > I execute a vc-relax calculation, the output file is like this: > [...[ > does it mean that the lattice constant is changed to > (0.500982241/0.5)*3.615=3.6221 angstrom? if it is right, the > lattice constant optimized by GGA pseudopotential using pwscf > code is large than the experimental value, but the GGA result > by CASTEP code is small than the experimental value. which > one is reasonable? variable-cell calculations locate the lattice constant at which the pressure vanishes. This method is typically much slower to converge wrt the kinetic energy cutoff than the good old method of fitting the E(V) curve to an equation of state. GGA lattice parameters are often slightly larger than the experimental results. In any event, if you compare calculations performed under the same assumptions, you should find only minor differences between pwscf and castep. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From leoant21 at hotmail.com Mon Aug 29 11:40:11 2005 From: leoant21 at hotmail.com (=?gb2312?B?1cUguumx8g==?=) Date: Mon, 29 Aug 2005 09:40:11 +0000 Subject: [Pw_forum] Questions on supercell calculation of MgB2 In-Reply-To: <20050828053635.26142.98697.Mailman@democritos.sissa.it> Message-ID: Dear All: Now I am trying to do some calculation about properties of MgB2 using supercell method, however, there are some problems which I don't understand: I have done a calculation to check the convergence of supercell method by calculating a 3*3*1 supercell without atom loss, but the band energy is very different with those of original unit cell, where parameters are the same except nat=27,nband=108, results are shown below: for /gamma points only k = 0.0000 0.0000 0.0000 band energies (ev): -12.0174 -10.2019 -10.2018 -10.2018 -10.2018 -10.2018 -10.2018 -7.2039 -7.2039 -7.2039 -7.2039 -4.7605 -4.7605 -4.7605 -4.7605 -4.7605 -4.7605 -4.7511 -4.7511 -1.1770 -1.1769 -1.1769 -1.1769 -1.1769 -1.1769 0.7865 0.7865 4.2776 4.2776 4.2776 4.2776 4.2776 4.2776 4.6061 5.5116 6.7205 6.7205 6.7205 6.7206 6.7206 6.7206 7.4459 7.4459 7.4459 7.4459 7.4999 7.4999 9.9779 9.9779 9.9779 9.9779 9.9779 9.9779 11.0717 11.0717 11.1852 13.0561 13.0561 13.0561 13.0561 13.0561 13.0561 13.4153 13.4153 13.4153 13.4153 13.4153 13.4153 14.4582 14.4582 14.4582 14.4582 14.9112 16.4510 16.4510 16.5120 16.5120 16.5120 16.5120 17.2677 17.2677 17.2677 17.2677 17.2677 17.2677 18.5590 18.5590 18.5590 18.5591 18.5591 18.5591 19.5087 19.5087 19.5730 19.5730 19.5730 19.5730 19.5730 19.5731 20.6149 20.6149 20.6149 20.6149 20.6149 20.6149 21.1872 24.7356 24.7356 while for orignal unit cell, those energy value are: k = 0.0000 0.0000 0.0000 band energies (ev): -4.9799 4.4905 8.0545 8.0548 9.3576 13.7607 13.7610 15.5855 17.5768 20.6496 25.7276 26.3962 Further more, when I want to plot the band structure using bands.x to get the .dat file, there is an error like: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from punch_band : error # 5 increase maxdeg %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... And at the beggining of the scf calculation procedure, there are "additional transition found" in the output window of Pwgui, does this means the space group has been changed? Since I didn't omit any atom in the structure, why or why not? Thank you very much for any comments. Hongbin Zhang _________________________________________________________________ ???? MSN Explorer: http://explorer.msn.com/lccn/ From ferretti.andrea at unimore.it Mon Aug 29 12:09:33 2005 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Mon, 29 Aug 2005 12:09:33 +0200 (CEST) Subject: [Pw_forum] About maximally localized wannier function Message-ID: thanks to Nicola for citing the "WanT" code (http://wannier-transport.org) for the calculation maximally localized wannier functions (and transport properties within them). > > Another advantage is that the CP/Wannier subroutines work with ultrasoft > pseudopotentials, although this capability is forthcoming in > wannier-transport.org and wannier.org . > I would like just to add a note: since a new release of the code is scheduled for the end of September, those who might be interested can directly write to me (or to the other contacts in the web site) to have a pre-release version (part of the manual is still missing but upgraded interfacing to Espresso, performance issues and the task of ultrasoft PP have been included) cheers Andrea -- Andrea Ferretti INFM National Research Center on nanoStructures and bioSystems at Surfaces (S3) Dipartimento di Fisica, Universita' di Modena e Reggio Emilia Via Campi 213/A I-41100 Modena, Italy Tel: +39 059 2055283 Fax: +39 059 374794 E-mail: ferretti.andrea at unimore.it URL: http://www.nanoscience.unimo.it From proffess at yandex.ru Mon Aug 29 22:42:33 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Tue, 30 Aug 2005 00:42:33 +0400 (MSD) Subject: [Pw_forum] Error during restart Message-ID: <43137339.000003.12610@camay.yandex.ru> From proffess at yandex.ru Mon Aug 29 22:47:24 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Tue, 30 Aug 2005 00:47:24 +0400 (MSD) Subject: [Pw_forum] Error during restart Message-ID: <4313745C.000004.28470@pantene.yandex.ru> Dear PWscf users and authors, I got an error when restart calculations The initial density is read from file b.rho Starting wfc from file %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from efermit : error # 1 unexpected error %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I looked at archive and found the similar problem (for version 2.1.2!): http://www.democritos.it/pipermail/pw_forum/2005-February/002023.html On Wednesday 09 February 2005 16:19, Ben Hope wrote: > from efermit : error # 1 > unexpected error and also something like "Only input k-points are used (inequivalent points not generated)" at the beginning of the run? it is a bug. For the time being, change in routine PW/setup.f90 the line ltest = ( nks /= input_nks ) .AND. & ( .NOT. lscf ) .AND. ( .NOT. ( lphonon .OR. lraman ) ) into ltest = ( nks /= input_nks ) .AND. ( .NOT. ( ltetra ) .AND. & ( .NOT. lscf ) .AND. ( .NOT. ( lphonon .OR. lraman ) ) Gaussian smearing with an automatic k-point grid may have the same problem, by the way Paolo I made the changes of the file PW/setup.f90 but it did not helps. Any idea? Thanks, Sergey From dxs571 at mail.ustc.edu.cn Tue Aug 30 09:32:43 2005 From: dxs571 at mail.ustc.edu.cn (XiaoSong Du) Date: Tue, 30 Aug 2005 15:32:43 +0800 Subject: [Pw_forum] (no subject) Message-ID: <325387163.07602@ustc.edu.cn> Hello From giannozz at nest.sns.it Tue Aug 30 09:35:11 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 30 Aug 2005 09:35:11 +0200 Subject: [Pw_forum] Error during restart In-Reply-To: <4313745C.000004.28470@pantene.yandex.ru> References: <4313745C.000004.28470@pantene.yandex.ru> Message-ID: <200508300935.11323.giannozz@nest.sns.it> On Monday 29 August 2005 22:47, Sergey Lisenkov wrote: > I got an error when restart calculations > [...] > from efermit : error # 1 > unexpected error > [...] this is something that may happen under some circumstances, typically very few k-points > I looked at archive and found the similar problem (for version 2.1.2!): it was a different problem that has been fixed. Please provide a case in which this behavior is observed Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From dxs571 at mail.ustc.edu.cn Tue Aug 30 10:15:03 2005 From: dxs571 at mail.ustc.edu.cn (XiaoSong Du) Date: Tue, 30 Aug 2005 16:15:03 +0800 Subject: [Pw_forum] (no subject) Message-ID: <325389703.00766@ustc.edu.cn> Recently, I have a problem running the tests in pwscf. To test the phonon frequency in Gamma of Si, I get the following wrong message Incorrectly built binary which accesses errno, h_errno or _res directly. Needs to be fixed. Program PHONON v.1.3.0 starts ... Today is 15Aug2003 at 11:30:45 Ultrasoft (Vanderbilt) Pseudopotentials %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from phq_readin : error # 146 reading inputph namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... The title problem and the final interrupting is unknown to me till now The following is the Si scf caculation input file and the phonon part,by the way i haven't seen the way to reply a post in the forum ,anyone can tell me? Si Silicon &control calculation='scf', restart_mode='from_scratch', prefix='si' pseudo_dir = '/public/soft/PWSCF/pseudo//', outdir='/public/achen/scratch//' / &system ibrav = 2, celldm(1) =10.20, nat= 2, ntyp= 1, ecutwfc = 18.0 / &electrons mixing_beta = 0.7 conv_thr = 1.0d-8 / ATOMIC_SPECIES Si 28.086 Si.vbc.UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 K_POINTS 10 0.1250000 0.1250000 0.1250000 1.00 0.1250000 0.1250000 0.3750000 3.00 0.1250000 0.1250000 0.6250000 3.00 0.1250000 0.1250000 0.8750000 3.00 0.1250000 0.3750000 0.3750000 3.00 0.1250000 0.3750000 0.6250000 6.00 0.1250000 0.3750000 0.8750000 6.00 0.1250000 0.6250000 0.6250000 3.00 0.3750000 0.3750000 0.3750000 1.00 0.3750000 0.3750000 0.6250000 3.00 phonons of si at Gamma &inputph tr2_ph=1.0d-14, prefix='si', epsil=.true., amass(1)=28.08, tmp_dir='/home/scratch/', fildyn='si.dynG', / 0.0 0.0 0.0 From chaohao2002 at 163.com Tue Aug 30 12:10:52 2005 From: chaohao2002 at 163.com (Chaohao Hu) Date: Tue, 30 Aug 2005 18:10:52 +0800 Subject: [Pw_forum] A question about Gamma-point calculation Message-ID: <20050830100753.83A091127DD@democritos.sissa.it> I am trying to do phonon calculation about lanthanum hydride. For a small cell only containing 6 atoms (LaNi5), I can obtain good results of scf and phonon calculations. But for a larger supercell (LaNi5-xMx and its hydrides), this task will stop when calculating the fifth or sixth irreducible representations. Why??? Can you give me some hints about this problem? How to resolve it? In my *.phG.out file, some informations are described as following, ==================================================== ...... Representation 33 2 modes - To be done Representation 34 2 modes - To be done Representation 35 1 modes - To be done Representation 36 1 modes - To be done PHONON : 53m35.87s CPU time ...... Representation # 5 modes # 5 6 Self-consistent Calculation Pert. # 1: Fermi energy shift (Ryd) = 0.0000 0.0000 Pert. # 2: Fermi energy shift (Ryd) = 0.0000 0.0000 iter # 1 total cpu time : 10373.3 secs av.it.: 7.5 thresh= 0.100E-01 alpha_mix = 0.700 |ddv_scf|^2 = 0.162E-05 ==================================================== Thanks in advance. Best regards, Chaohao ============================================================ Dr.Ch.H.Hu Institute of Metal Research,Chinese Academy of Sciences--IMR Wenhua Road, 72 110016, Shenyang, Liaoning (China) Phone: +086-024-23971641 Email: chhu at imr.ac.cn From eyvaz_isaev at yahoo.com Tue Aug 30 13:02:33 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 30 Aug 2005 04:02:33 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: <325389703.00766@ustc.edu.cn> Message-ID: <20050830110233.26858.qmail@web60321.mail.yahoo.com> Hi, > > Incorrectly built binary which accesses errno, > h_errno or _res directly. Needs to > be fixed. This means that PWSCF was compiled and run on different computers with a different compatible CPU, say Athlon and Pentium. It is just a warning, and according to my experience it will not in > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from phq_readin : error # 146 > reading inputph namelist > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > stopping ... > > restart_mode='from_scratch', > prefix='si' > pseudo_dir = '/public/soft/PWSCF/pseudo//', > outdir='/public/achen/scratch//' > phonons of si at Gamma > &inputph > tr2_ph=1.0d-14, > prefix='si', > epsil=.true., > amass(1)=28.08, > tmp_dir='/home/scratch/', You have wrong definition for temporary directroy in phonons. It should be outdir='temp_dir_name'. Apparantly, the definition of temporary directory is different for scf and phonons calculations. Bests, Eyvaz. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From giannozz at nest.sns.it Tue Aug 30 15:21:30 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 30 Aug 2005 15:21:30 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <20050830110233.26858.qmail@web60321.mail.yahoo.com> References: <20050830110233.26858.qmail@web60321.mail.yahoo.com> Message-ID: <200508301521.30270.giannozz@nest.sns.it> On Tuesday 30 August 2005 13:02, Eyvaz Isaev wrote: > > Incorrectly built binary which accesses errno, > > h_errno or _res directly. Needs to be fixed. > > This means that PWSCF was compiled and run on > different computers with a different compatible CPU, > say Athlon and Pentium. it looks to me more like an installation problem, involving the compiler or some library > > &inputph > > tr2_ph=1.0d-14, > > prefix='si', > > epsil=.true., > > amass(1)=28.08, > > tmp_dir='/home/scratch/', > > You have wrong definition for temporary directory in > phonons. It should be outdir='temp_dir_name'. in recent versions; he is using an old version of the phonon code, which might accept the old variable name "tmp_dir" Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From eyvaz_isaev at yahoo.com Tue Aug 30 17:05:44 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Tue, 30 Aug 2005 08:05:44 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: <200508301521.30270.giannozz@nest.sns.it> Message-ID: <20050830150544.70386.qmail@web60315.mail.yahoo.com> Hi again, --- Paolo Giannozzi wrote: > On Tuesday 30 August 2005 13:02, Eyvaz Isaev wrote: > > > > Incorrectly built binary which accesses errno, > > > h_errno or _res directly. Needs to be fixed. > > > > This means that PWSCF was compiled and run on > > different computers with a different compatible > CPU, > > say Athlon and Pentium. > > it looks to me more like an installation problem, > involving > the compiler or some library > In fact, some time ago I compiled PWSCF on Athlon-based PC, and then migrated to Pentium-based PC. There was the same messages but everything worked fine. > > > &inputph > > > tr2_ph=1.0d-14, > > > prefix='si', > > > epsil=.true., > > > amass(1)=28.08, > > > tmp_dir='/home/scratch/', > > > > You have wrong definition for temporary directory > in > > phonons. It should be outdir='temp_dir_name'. > > in recent versions; he is using an old version of > the phonon > code, which might accept the old variable name > "tmp_dir" > Yes, I am agree with your comment, but it seems strange to me use different versions of pw.x and ph.x. Are output files are compatible in this case? Bests, Eyvaz. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From giannozz at nest.sns.it Tue Aug 30 17:28:27 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 30 Aug 2005 17:28:27 +0200 Subject: [Pw_forum] (no subject) In-Reply-To: <20050830150544.70386.qmail@web60315.mail.yahoo.com> References: <20050830150544.70386.qmail@web60315.mail.yahoo.com> Message-ID: <200508301728.27689.giannozz@nest.sns.it> On Tuesday 30 August 2005 17:05, Eyvaz Isaev wrote: > Yes, I am agree with your comment, but it seems > strange to me use different versions of pw.x and ph.x. > Are output files are compatible in this case? typically they aren't at all ! This is hopefully going to change in the future - the new file format should be extensible, so that minor changes will not break everything as it happens now. In this specific case, the error arises while reading the namelist, well before data files are read. Actually your suggestion was good: even that version of the phonon code uses "outdir", not "tmp_dir", to point to the scratch directory P. -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From giannozz at nest.sns.it Tue Aug 30 17:31:36 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 30 Aug 2005 17:31:36 +0200 Subject: [Pw_forum] A question about Gamma-point calculation In-Reply-To: <20050830100753.83A091127DD@democritos.sissa.it> References: <20050830100753.83A091127DD@democritos.sissa.it> Message-ID: <200508301731.36919.giannozz@nest.sns.it> On Tuesday 30 August 2005 12:10, Chaohao Hu wrote: > [...] for a larger supercell (LaNi5-xMx and its hydrides), this task > will stop when calculating the fifth or sixth irreducible representations. > Why??? why, nobody can tell for sure on the basis of available information! Likely explanations: - not enough memory - not enough disk space - cpu time limit P. -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From proffess at yandex.ru Tue Aug 30 20:40:51 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Tue, 30 Aug 2005 22:40:51 +0400 (MSD) Subject: [Pw_forum] Error during restart In-Reply-To: <200508300935.11323.giannozz@nest.sns.it> References: <4313745C.000004.28470@pantene.yandex.ru> <200508300935.11323.giannozz@nest.sns.it> Message-ID: <4314A833.000001.16537@mfront7.yandex.ru> Dear Paolo, Thanks for the reply. >this is something that may happen under some circumstances, >typically very few k-points I used 8 8 8 k-point mesh without shifting. Because this is LSDA calculations, number of k points= 180 (tetrahedron method). >it was a different problem that has been fixed. Please provide a >case in which this behavior is observed This is a huge demand calculations, so I don't know how you will reproduce this error. Sergey From chaohao2002 at 163.com Wed Aug 31 03:34:56 2005 From: chaohao2002 at 163.com (Chaohao Hu) Date: Wed, 31 Aug 2005 09:34:56 +0800 Subject: [Pw_forum] A question about Gamma-point calculation Message-ID: <20050831013212.7225F11272D@democritos.sissa.it> Dear Mr Paolo, Sorry, more details about my input file for LaNi4Al scf and phonon calculation in my script file is listed as below. For scf: ================================== &control calculation='scf' restart_mode='from_scratch', tstress = .true. tprnfor = .true. prefix='lani4al', pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' / &system ibrav= 4, celldm(1) =16.4146, celldm(3) =0.4587, nat= 18, ntyp= 3, ecutwfc = 24.0, ecutrho = 240.0, occupations='smearing', smearing='methfessel-paxton', degauss=0.02 / &electrons conv_thr = 1.0d-8 mixing_beta = 0.7 / ATOMIC_SPECIES La 138.91 La.pbe-nsp-van.UPF Ni 58.69 Ni.pbe-nd-rrkjus.UPF Al 26.98 Al.pbe-rrkjus.UPF ATOMIC_POSITIONS {crystal} La 0.0000000 0.0000000 0.0000000 ... ... K_POINTS {automatic} 4 4 2 1 1 1 ================================ For phonon: ================================ &inputph tr2_ph=1.0d-12, prefix='lani4al', epsil=.false., amass(1)=138.91, amass(2)=58.69, amass(3)=26.98, outdir='$TMP_DIR/', fildyn='lani4al.dynG', / 0.0 0.0 0.0 ================================ Finally, some error informtion shows in my bash terminal: ================================ cleaning /home/hchfox/tmp0-1... done running the scf calculation... done running the phonon calculation at Gamma..../run_lani4al_gamma: line 151: 4032 block error $PH_COMMAND lani4al.phG.out done ================================ What's wrong with it? >why, nobody can tell for sure on the basis of available information! >Likely explanations: >- not enough memory My computer memory is 2 Gb >- not enough disk space I just intall my linux system and leave about 25 Gb space >- cpu time limit Maybe it is a reason. But my supercell only contains 18 atoms. If it is, how to resolve it? Thanks in advance. Best regards, Chaohao ============================================================ Dr.Ch.H.Hu Institute of Metal Research,Chinese Academy of Sciences--IMR Wenhua Road, 72 110016, Shenyang, Liaoning (China) Phone: +086-024-23971641 Email: chhu at imr.ac.cn From whzhang at ustc.edu Wed Aug 31 09:29:56 2005 From: whzhang at ustc.edu (whzhang) Date: Wed, 31 Aug 2005 15:29:56 +0800 Subject: [Pw_forum] (no subject) Message-ID: <20050831072123.59C321127BB@democritos.sissa.it> hi,all Below is my input file &CONTROL title = 'sur' , calculation = 'scf' , outdir = '/para/whzhang/pwscf/surface/' , pseudo_dir = '/para/whzhang/pwscf/surface/' , prefix = 'sur' , nstep = 500 , tstress = .false. , tprnfor = .true. , tefield = .false. , / &SYSTEM ibrav = 8, A = 9.27 , B = 9.27 , C = 25.23 , cosAB = 0.5 , cosAC = 0.0 , cosBC = 0.0 , nat = 45, ntyp = 3, ecutwfc = 25 , ecutrho = 100 , occupations = 'smearing' , degauss = 0.005 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = 0, starting_magnetization(2) = 1, starting_magnetization(3) = 0, / &ELECTRONS electron_maxstep = 200, conv_thr = 1D-6 , mixing_mode = 'plain' , mixing_beta = 0.7 , mixing_ndim = 8, mixing_fixed_ns = 20, / ATOMIC_SPECIES Pt 195.07800 Pt.UPF Fe 55.84500 Fe.UPF O 15.99940 O.UPF ATOMIC_POSITIONS crystal . . . K_POINTS automatic 2 2 1 1 1 1 but the program stops as soon as it begins and I get the information that warning: negative or imaginary core charge -0.000001 0.000000 Initial potential from superposition of free atoms npt with |zeta| > 1: 24174, npt tot 576000, 4.20 % npt with rhoup < 0: 125496, npt tot 576000, 21.79 % npt with rhodw < 0: 131535, npt tot 576000, 22.84 % starting charge = 463.49586 Starting wfc are atomic total cpu time spent up to now is 602.28 secs iteration # 1 ecut= 25.00 ryd beta=0.70 Davidson diagonalization (with overlap) p0_9430: p4_error: interrupt SIGSEGV: 11 so what's the problem with my input file? Can anybody help me? thanks a lot ????????whzhang ????????whzhang at ustc.edu ??????????2005-08-31 From eyvaz_isaev at yahoo.com Wed Aug 31 15:20:42 2005 From: eyvaz_isaev at yahoo.com (Eyvaz Isaev) Date: Wed, 31 Aug 2005 06:20:42 -0700 (PDT) Subject: [Pw_forum] (no subject) In-Reply-To: <20050831072123.59C321127BB@democritos.sissa.it> Message-ID: <20050831132042.90886.qmail@web60320.mail.yahoo.com> Hi, >p0_9430: p4_error: interrupt SIGSEGV: 11 >so what's the problem with my input file? Can anybody >help me? Based on p4_error message I assume that the error is due to your network configuration rather than input file. May be your network is slow. Bests, Eyvaz. --- whzhang wrote: > hi,all > Below is my input file > &CONTROL > title = 'sur' , > calculation = 'scf' , > outdir = > '/para/whzhang/pwscf/surface/' , > pseudo_dir = > '/para/whzhang/pwscf/surface/' , > prefix = 'sur' , > nstep = 500 , > tstress = .false. , > tprnfor = .true. , > tefield = .false. , > / > &SYSTEM > ibrav = 8, > A = 9.27 , > B = 9.27 , > C = 25.23 , > cosAB = 0.5 , > cosAC = 0.0 , > cosBC = 0.0 , > nat = 45, > ntyp = 3, > ecutwfc = 25 , > ecutrho = 100 , > occupations = 'smearing' , > degauss = 0.005 , > smearing = 'gaussian' , > nspin = 2 , > starting_magnetization(1) = 0, > starting_magnetization(2) = 1, > starting_magnetization(3) = 0, > / > &ELECTRONS > electron_maxstep = 200, > conv_thr = 1D-6 , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > mixing_ndim = 8, > mixing_fixed_ns = 20, > / > ATOMIC_SPECIES > Pt 195.07800 Pt.UPF > Fe 55.84500 Fe.UPF > O 15.99940 O.UPF > ATOMIC_POSITIONS crystal > . > . > . > K_POINTS automatic > 2 2 1 1 1 1 > > but the program stops as soon as it begins and I get > the information that > > > > > warning: negative or imaginary core charge > -0.000001 0.000000 > > Initial potential from superposition of free > atoms > > npt with |zeta| > 1: 24174, npt tot > 576000, 4.20 % > > npt with rhoup < 0: 125496, npt tot 576000, > 21.79 % > > npt with rhodw < 0: 131535, npt tot 576000, > 22.84 % > > starting charge = 463.49586 > Starting wfc are atomic > > total cpu time spent up to now is 602.28 > secs > > iteration # 1 ecut= 25.00 ryd > beta=0.70 > Davidson diagonalization (with overlap) > p0_9430: p4_error: interrupt SIGSEGV: 11 > > > so what's the problem with my input file? Can > anybody help me? > > > thanks a lot > > > ????????????????whzhang > ????????????????whzhang at ustc.edu > ????????????????????2005-08-31 > ?????j)b? b???~????,q?+?m????^??+??,???j)fj???b??????? __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From dxs571 at mail.ustc.edu.cn Wed Aug 31 15:46:59 2005 From: dxs571 at mail.ustc.edu.cn (XiaoSong Du) Date: Wed, 31 Aug 2005 21:46:59 +0800 Subject: [Pw_forum] other explanatory script for *.x? Message-ID: <325496019.07021@ustc.edu.cn> If i want to see the usage of other *.x such as q2r.x ,how can i get that kind of information except to see the fortran source code of the file, e.g q2r.f90? From giannozz at nest.sns.it Wed Aug 31 16:22:07 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 31 Aug 2005 16:22:07 +0200 Subject: [Pw_forum] other explanatory script for *.x? In-Reply-To: <325496019.07021@ustc.edu.cn> References: <325496019.07021@ustc.edu.cn> Message-ID: <200508311622.07860.giannozz@nest.sns.it> On Wednesday 31 August 2005 15:46, XiaoSong Du wrote: > If i want to see the usage of other *.x such as q2r.x , > how can i get that kind of information except to see > the fortran source code of the file, e.g q2r.f90? all available documentation is contained in directory Doc/, in the examples, and sometimes in the header of the source code. Paolo -- Paolo Giannozzi e-mail: giannozz at nest.sns.it Scuola Normale Superiore Phone: +39/050-509876, Fax:-563513 Piazza dei Cavalieri 7 I-56126 Pisa, Italy From dxs571 at mail.ustc.edu.cn Wed Aug 31 17:25:52 2005 From: dxs571 at mail.ustc.edu.cn (Xiaosong Du) Date: Wed, 31 Aug 2005 23:25:52 +0800 Subject: [Pw_forum] (no subject) Message-ID: <200508311516.j7VFGKR22953@mx1.ustc.edu.cn> In a test of GaAs phonon frequency caculation, at a k-point e.g. (-0.25000 -0.25000 0.25000 ),the outfile has such result as follows, what i can't understand is the meaning of the 4 q-points in the star. Number of q in the star = 4 List of q in the star: 1 -0.250000000 -0.250000000 0.250000000 2 0.250000000 0.250000000 0.250000000 3 0.250000000 -0.250000000 -0.250000000 4 -0.250000000 0.250000000 -0.250000000 In addition there is the -q list: 1 0.250000000 0.250000000-0.250000000 2-0.250000000-0.250000000-0.250000000 3-0.250000000 0.250000000 0.250000000 4 0.250000000-0.250000000 0.250000000 And i find the inputfile of non-scf and phonon caculation describing k-space sampling is wrong ,which should be a 444 M_P sampling instead of the 2 point.Am I right? ????????Xiaosong Du ????????dxs571 at mail.ustc.edu.cn ??????????2005-08-31 From yay451 at mail.usask.ca Wed Aug 31 19:03:10 2005 From: yay451 at mail.usask.ca (Yansun Yao) Date: Wed, 31 Aug 2005 11:03:10 -0600 Subject: [Pw_forum] Projected phonon DOS, done In-Reply-To: <1123852072.42fc9f289df1b@webmail.usask.ca> References: <1123852072.42fc9f289df1b@webmail.usask.ca> Message-ID: <1125507790.4315e2ceb370d@webmail.usask.ca> Hello Pwscf developers, A couple of weeks ago I wanted to calculate the projected phonon DOS and posted my questions here. Mr. Paolo Giannozzi gave me some hints. Now I have made a subroutine to do it by tetrahedron method. It works well. I am just wondering whether the developers want to include it in the next version. Thank you! Yansun Yao University of Saskatchewan