From giannozz at nest.sns.it Thu Dec 1 10:17:40 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 1 Dec 2005 10:17:40 +0100 Subject: [Pw_forum] test of generated pseudopotential In-Reply-To: <20051129085840.60513.qmail@web15607.mail.cnb.yahoo.com> References: <20051129085840.60513.qmail@web15607.mail.cnb.yahoo.com> Message-ID: <200512011017.40649.giannozz@nest.sns.it> On Tuesday 29 November 2005 09:58, li yan wrote: > i want to test the pseudopotential generated by pwscf (version 3.0). > in the output file, i can find out the energy difference between the ps and > the ae about the valence electrons. But which part can embody the equality > of logarithmic derivatives at the reference energy? best regards you have to write the logarithmic derivatives for both the all-electron and the pseudopotential case. Fromnfile: aotmic_fdoc/INPUT_LD1: --- nld = the number of logarithmic derivatives to be calculated rlderiv= radius (a.u.) at which logarithmic derivatives are calculated eminld, emaxld = energy range (min, max energy, in Ry) at which logarithmic derivatives are calculated deld = delta e (Ry) of energy for logarithmic derivatives If the above parameters are not specified, logarithmic derivaties are not calculated --- The output is written in an easily plottable format to files "file_logder" and "file_logderps" listed below: --- Output files written: file_tests "prefix".test results of transferability test and for each testing configuration N: file_wavefunctions "prefix"N.wfc all-electron KS orbitals file_wavefunctionsps "prefix"Nps.wfc pseudo KS orbitals if parameters for logarithmic derivatives are specified: file_logder "prefix"Nps.dlog all-electron logarithmic derivatives file_logderps "prefix"Nps.dlog pseudo logarithmic derivatives "N" is not present if there is just one testing configuration --- 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 Thu Dec 1 10:45:49 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 1 Dec 2005 10:45:49 +0100 Subject: [Pw_forum] Understanding o/p of projwfc.x In-Reply-To: <34978.202.41.111.151.1133370658.squirrel@202.41.111.151> References: <34978.202.41.111.151.1133370658.squirrel@202.41.111.151> Message-ID: <200512011045.49380.giannozz@nest.sns.it> On Wednesday 30 November 2005 18:10, Mousumi Upadhyay Kahaly wrote: > 1. What is Lowdin charges? Modern Quantum Chemistry, A. Szabo and N. Ostlund (Dover, NY 1996) p. 153; P. O. Loewdin, J. Chem. Phys. 18, 365 (1950) > 2. What is the "Spilling Parameter"? from projwfc.f90: ! Sanchez-Portal et al., Sol. State Commun. 95, 685 (1995). ! The spilling parameter measures the ability of the basis provided by ! the pseudo-atomic wfc to represent the PW eigenstates, ! by measuring how much of the subspace of the Hamiltonian ! eigenstates falls outside the subspace spanned by the atomic basis > 3. For each atom, for each 4 states s, p, d, f why only 3 numbers are > given? because there are only s,p,d states; but the person who wrote that part of the code (me) is lazy and didn't bother to write a more accurate output format 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 Thu Dec 1 10:56:18 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 1 Dec 2005 10:56:18 +0100 Subject: [Pw_forum] Error in q2r.x In-Reply-To: References: Message-ID: <200512011056.18418.giannozz@nest.sns.it> On Wednesday 30 November 2005 20:59, Alcantara Ortigoza, Marisol wrote: > > from init : error # 1 > > nc already filled: wrong q grid or wrong nr did you use the manual procedure (i.e. one q at the time) or the "automatic" one (i.e. specifying a q-grid and calculating all q's at the same time)? In the former case, verify if you have correctly passed the grid: 2,2,1, in the input of q2r.x. 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 Thu Dec 1 11:27:53 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 1 Dec 2005 11:27:53 +0100 Subject: [Pw_forum] spin-polarized GGA calculation in pw In-Reply-To: <20051128082447.79933.qmail@web51009.mail.yahoo.com> References: <20051128082447.79933.qmail@web51009.mail.yahoo.com> Message-ID: <200512011127.53181.giannozz@nest.sns.it> On Monday 28 November 2005 09:24, W. YU wrote: > Is it really possible to do spin-polarized GGA calculation > in PW now? of course it is. Not all functionals are implemented, though, but the most important are > I read about the LSDA-functionals.f90 and found only > the LSDA choices for PZ and PW are allowed. this is for the LDA part-only. You can combine these with various gradient corrections. Several popular gradient- corrected functionals are available (Becke86-Perdew88, Perdew-Wang 91, PBE). BLYP with spin polarization is also implemented in 3.0 > By the way, I couldn't find this source file in espresso-3.0. > Where has it gone? part in Modules/functionals.f90, part in flib/functionals.f90, flib/lsda_functionals.f90, flib/more_functionals.f90 . 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 wierzbom at ts.infn.it Thu Dec 1 15:15:52 2005 From: wierzbom at ts.infn.it (Malgorzata Wierzbowska) Date: Thu, 1 Dec 2005 15:15:52 +0100 (CET) Subject: [Pw_forum] Error in q2r.x In-Reply-To: <200512011056.18418.giannozz@nest.sns.it> References: <200512011056.18418.giannozz@nest.sns.it> Message-ID: On Thu, 1 Dec 2005, Paolo Giannozzi wrote: Marisol, Can you send me all your files *dyn* with which you get this q2r error? Thanks, Gosia > On Wednesday 30 November 2005 20:59, Alcantara Ortigoza, Marisol wrote: > >>> from init : error # 1 >>> nc already filled: wrong q grid or wrong nr > > did you use the manual procedure (i.e. one q at the time) or the > "automatic" one (i.e. specifying a q-grid and calculating all q's > at the same time)? In the former case, verify if you have correctly > passed the grid: 2,2,1, in the input of q2r.x. > > Paolo > > From jaita at jncasr.ac.in Fri Dec 2 05:34:42 2005 From: jaita at jncasr.ac.in (Jaita Paul) Date: Fri, 2 Dec 2005 10:04:42 +0530 (IST) Subject: [Pw_forum] Error in running bands.x In-Reply-To: References: <200512011056.18418.giannozz@nest.sns.it> Message-ID: <35886.202.41.111.151.1133498082.squirrel@202.41.111.151> hello everyone. While running the file si.bands.in the followin error msg comes: Program POST-PROC v.2.0.4 starts ... Today is 2Dec2005 at 9:53:41 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from do_bands : error # 1 reading inputpp namelist %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... why is this coming? any help would be greatly appreciated. jaita From alcantar at phys.ksu.edu Fri Dec 2 08:41:50 2005 From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol) Date: Fri, 2 Dec 2005 01:41:50 -0600 Subject: [Pw_forum] Error in q2r.x Message-ID: Thanks for replying. I specified a q-grid: (nr1=2, nr2=2, nr3=1) in the input file of q2r. It was supposed to read the dynamical matices from 3 "dyn" files, one containg q = (0,0,0), other containing q=(0.5,-0.5,0) and q=(0.5,0.5,0) , and the last one containing q=(1,0,0). Thank you. Marisol. -----Original Message----- From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On Behalf Of Paolo Giannozzi Sent: Thursday, December 01, 2005 3:56 AM To: pw_forum at pwscf.org Subject: Re: [Pw_forum] Error in q2r.x On Wednesday 30 November 2005 20:59, Alcantara Ortigoza, Marisol wrote: > > from init : error # 1 > > nc already filled: wrong q grid or wrong nr did you use the manual procedure (i.e. one q at the time) or the "automatic" one (i.e. specifying a q-grid and calculating all q's at the same time)? In the former case, verify if you have correctly passed the grid: 2,2,1, in the input of q2r.x. 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 alcantar at phys.ksu.edu Fri Dec 2 08:50:22 2005 From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol) Date: Fri, 2 Dec 2005 01:50:22 -0600 Subject: [Pw_forum] Error in q2r.x Message-ID: Dear Goshia, The files are too large so they are waiting for moderator approval... . I think the best would be that you give me your email and I will send you the files directly to you email. Thanks. Marisol. -----Original Message----- From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] Sent: Friday, December 02, 2005 1:46 AM To: Alcantara Ortigoza, Marisol Subject: Your message to Pw_forum awaits moderator approval Your mail to 'Pw_forum' with the subject RE: [Pw_forum] Error in q2r.x Is being held until the list moderator can review it for approval. The reason it is being held: Message body is too big: 182627 bytes but there's a limit of 40 KB Either the message will get posted to the list, or you will receive notification of the moderator's decision. From giannozz at nest.sns.it Fri Dec 2 09:24:03 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 2 Dec 2005 09:24:03 +0100 Subject: [Pw_forum] Error in q2r.x In-Reply-To: References: Message-ID: <200512020924.03950.giannozz@nest.sns.it> On Friday 02 December 2005 08:50, Alcantara Ortigoza, Marisol wrote: > The files are too large so they are waiting for moderator approval... forget about "moderator approval": every day the list receives tens of spam messages. All messages "held for moderator approval" are automatically removed after a while. Could you please post your input data (for the entire calculation) instead? 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 Dec 2 09:28:33 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 2 Dec 2005 09:28:33 +0100 Subject: [Pw_forum] Error in running bands.x Message-ID: <200512020928.33223.giannozz@nest.sns.it> On Friday 02 December 2005 05:34, Jaita Paul wrote: > from do_bands : error # 1 > reading inputpp namelist > > why is this coming? because there is a nonexistent (usually misspelled) variable in &inputpp namelist. Yes, there is one, look carefully! 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 mousumi at jncasr.ac.in Fri Dec 2 10:39:09 2005 From: mousumi at jncasr.ac.in (Mousumi Upadhyay Kahaly) Date: Fri, 2 Dec 2005 15:09:09 +0530 (IST) Subject: [Pw_forum] o/p of projwfc.x Message-ID: <54324.202.41.111.151.1133516349.squirrel@202.41.111.151> Hi, I posted this mail two days back but didn't get any reply till now. I want to understand the meaning of "Lowdin charges" and "Spilling Parameter" in the o/p of projwfc.x executable. How can i get the contribution of each atom in the total charge density. Best regards, mousumi. ---------------------------- Original Message ---------------------------- Subject: Understanding o/p of projwfc.x From: mousumi at jncasr.ac.in Date: Wed, November 30, 2005 10:40 pm To: pw_forum at pwscf.org -------------------------------------------------------------------------- Dear All, For Cd_2CH3COO molecule, I want to do band-by-band analysis of the charge densities and understand the contribution of each atom in the total charge density. For that I performed "projwfc.x" run in PWSCF. I didn't understand last lines of the output file of the above mentioned run. My questions are- 1. What is Lowdin charges? 2. What is the "Spilling Parameter"? 3. For each atom, for each 4 states s, p, d, f why only 3 numbers are given? 4. How can I get the total charge density of the system (in .xsf format) & each atom's contribution? I've copied here last few lines of the projwfc output file. Thanks & regards, mousumi. =========================================================================== Lowdin Charges: Atom # 1: total charge = 6.5387, s, p, d, f = 1.7168 4.8219 0.0000 Atom # 2: total charge = 6.5397, s, p, d, f = 1.7169 4.8227 0.0000 Atom # 3: total charge = 3.4229, s, p, d, f = 0.8756 2.5472 0.0000 Atom # 4: total charge = 4.5180, s, p, d, f = 1.0568 3.4613 0.0000 Atom # 5: total charge = 0.7671, s, p, d, f = 0.7671 0.0000 0.0000 Atom # 6: total charge = 0.7607, s, p, d, f = 0.7607 0.0000 0.0000 Atom # 7: total charge = 0.7682, s, p, d, f = 0.7682 0.0000 0.0000 Atom # 8: total charge = 10.6229, s, p, d, f = 0.6518 0.0000 9.9711 Atom # 9: total charge = 3.4228, s, p, d, f = 0.8756 2.5473 0.0000 Atom # 10: total charge = 6.5387, s, p, d, f = 1.7169 4.8218 0.0000 Atom # 11: total charge = 6.5396, s, p, d, f = 1.7168 4.8228 0.0000 Atom # 12: total charge = 4.5181, s, p, d, f = 1.0568 3.4613 0.0000 Atom # 13: total charge = 0.7679, s, p, d, f = 0.7679 0.0000 0.0000 Atom # 14: total charge = 0.7608, s, p, d, f = 0.7608 0.0000 0.0000 Atom # 15: total charge = 0.7674, s, p, d, f = 0.7674 0.0000 0.0000 Spilling Parameter: 0.0129 =========================================================================== From g.ballabio at cineca.it Fri Dec 2 10:49:42 2005 From: g.ballabio at cineca.it (Gerardo Ballabio) Date: Fri, 2 Dec 2005 10:49:42 +0100 (MET) Subject: [Pw_forum] Understanding o/p of projwfc.x In-Reply-To: <200512011045.49380.giannozz@nest.sns.it> (from giannozz@nest.sns.it on Thu Dec 1 10:45:49 2005) References: <34978.202.41.111.151.1133370658.squirrel@202.41.111.151> <200512011045.49380.giannozz@nest.sns.it> Message-ID: <1133516981l.4640l.1l@nb-ballabio.cineca.it> On 12/02/2005 10:39:09 AM, Mousumi Upadhyay Kahaly wrote: > I posted this mail two days back but didn't get any reply till now. Not really, it was answered yesterday by Paolo Giannozzi. You must have lost that email somehow. Gerardo On 12/01/2005 10:45:49 AM, Paolo Giannozzi wrote: > On Wednesday 30 November 2005 18:10, Mousumi Upadhyay Kahaly wrote: > > > 1. What is Lowdin charges? > > Modern Quantum Chemistry, A. Szabo and N. Ostlund (Dover, NY 1996) > p. 153; P. O. Loewdin, J. Chem. Phys. 18, 365 (1950) > > > 2. What is the "Spilling Parameter"? > > from projwfc.f90: > > ! Sanchez-Portal et al., Sol. State Commun. 95, 685 (1995). > ! The spilling parameter measures the ability of the basis > provided by > ! the pseudo-atomic wfc to represent the PW eigenstates, > ! by measuring how much of the subspace of the Hamiltonian > ! eigenstates falls outside the subspace spanned by the atomic > basis > > > 3. For each atom, for each 4 states s, p, d, f why only 3 numbers > are > > given? > > because there are only s,p,d states; but the person who wrote that > part of the code (me) is lazy and didn't bother to write a more > accurate > output format > > 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 degironc at sissa.it Fri Dec 2 10:52:07 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 2 Dec 2005 10:52:07 +0100 (CET) Subject: [Pw_forum] o/p of projwfc.x In-Reply-To: <54324.202.41.111.151.1133516349.squirrel@202.41.111.151> References: <54324.202.41.111.151.1133516349.squirrel@202.41.111.151> Message-ID: On Fri, 2 Dec 2005, Mousumi Upadhyay Kahaly wrote: > Hi, > > I posted this mail two days back but didn't get any reply till now. > I want to understand the meaning of "Lowdin charges" and "Spilling > Parameter" in the o/p of projwfc.x executable. this is not true. please check messages from Paolo Giannozzi (Dec 1st) stefano > > How can i get the contribution of each atom in the total charge density. > > Best regards, mousumi. > > ---------------------------- Original Message ---------------------------- > Subject: Understanding o/p of projwfc.x > From: mousumi at jncasr.ac.in > Date: Wed, November 30, 2005 10:40 pm > To: pw_forum at pwscf.org > -------------------------------------------------------------------------- > > Dear All, > > For Cd_2CH3COO molecule, I want to do band-by-band analysis of the > charge densities and understand the contribution of each atom in > the total charge density. For that I performed "projwfc.x" run in > PWSCF. > > I didn't understand last lines of the output file of the above > mentioned run. My questions are- > 1. What is Lowdin charges? > 2. What is the "Spilling Parameter"? > 3. For each atom, for each 4 states s, p, d, f why only 3 numbers are > given? 4. How can I get the total charge density of the system (in .xsf > format) & each atom's contribution? > > I've copied here last few lines of the projwfc output file. > > Thanks & regards, mousumi. > =========================================================================== > > Lowdin Charges: > > Atom # 1: total charge = 6.5387, s, p, d, f = 1.7168 4.8219 > 0.0000 > Atom # 2: total charge = 6.5397, s, p, d, f = 1.7169 4.8227 > 0.0000 > Atom # 3: total charge = 3.4229, s, p, d, f = 0.8756 2.5472 > 0.0000 > Atom # 4: total charge = 4.5180, s, p, d, f = 1.0568 3.4613 > 0.0000 > Atom # 5: total charge = 0.7671, s, p, d, f = 0.7671 0.0000 > 0.0000 > Atom # 6: total charge = 0.7607, s, p, d, f = 0.7607 0.0000 > 0.0000 > Atom # 7: total charge = 0.7682, s, p, d, f = 0.7682 0.0000 > 0.0000 > Atom # 8: total charge = 10.6229, s, p, d, f = 0.6518 0.0000 > 9.9711 > Atom # 9: total charge = 3.4228, s, p, d, f = 0.8756 2.5473 > 0.0000 > Atom # 10: total charge = 6.5387, s, p, d, f = 1.7169 4.8218 > 0.0000 > Atom # 11: total charge = 6.5396, s, p, d, f = 1.7168 4.8228 > 0.0000 > Atom # 12: total charge = 4.5181, s, p, d, f = 1.0568 3.4613 > 0.0000 > Atom # 13: total charge = 0.7679, s, p, d, f = 0.7679 0.0000 > 0.0000 > Atom # 14: total charge = 0.7608, s, p, d, f = 0.7608 0.0000 > 0.0000 > Atom # 15: total charge = 0.7674, s, p, d, f = 0.7674 0.0000 > 0.0000 > Spilling Parameter: 0.0129 > =========================================================================== > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From degironc at sissa.it Fri Dec 2 10:58:56 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 2 Dec 2005 10:58:56 +0100 (CET) Subject: [Pw_forum] Error in q2r.x In-Reply-To: References: Message-ID: Hi, q2r does not work properly with ibrav=0, actually does not work at all. Somehow, information on lattice_parameters are not written in the dynmat files and then q2r (but probably other codes reading dynmat files) does not work properly with ibrav=0 Thanks for pointing out this problem. We'll fix it. stefano On Fri, 2 Dec 2005, Alcantara Ortigoza, Marisol wrote: > Thanks for replying. I specified a q-grid: (nr1=2, nr2=2, nr3=1) in the > input file of q2r. It was supposed to read the dynamical matices from 3 > "dyn" files, one containg q = (0,0,0), other containing q=(0.5,-0.5,0) > and q=(0.5,0.5,0) , and the last one containing q=(1,0,0). Thank you. > Marisol. > > -----Original Message----- > From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On > Behalf Of Paolo Giannozzi > Sent: Thursday, December 01, 2005 3:56 AM > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Error in q2r.x > > > On Wednesday 30 November 2005 20:59, Alcantara Ortigoza, Marisol wrote: > >>> from init : error # 1 >>> nc already filled: wrong q grid or wrong nr > > did you use the manual procedure (i.e. one q at the time) or the > "automatic" one (i.e. specifying a q-grid and calculating all q's at the > same time)? In the former case, verify if you have correctly passed the > grid: 2,2,1, in the input of q2r.x. > > Paolo > > From degironc at sissa.it Fri Dec 2 16:04:58 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 2 Dec 2005 16:04:58 +0100 (CET) Subject: [Pw_forum] Error in q2r.x In-Reply-To: References: Message-ID: Dear Marisol, I fixed the problem with ibrav=0 in the ph.x -> q2r.x -> matdyn.x chain. I did it in the CVS version. Could you please try it ? Everybody: please report any additional mis-behaviour using ibrav=0 . I think I did not introduce any new bug ... but you never know stefano On Fri, 2 Dec 2005, Stefano de Gironcoli wrote: > Hi, > > q2r does not work properly with ibrav=0, actually does not work at all. > Somehow, information on lattice_parameters are not written in the dynmat > files and then q2r (but probably other codes reading dynmat files) does not > work properly with ibrav=0 > > Thanks for pointing out this problem. We'll fix it. > > stefano > > > On Fri, 2 Dec 2005, Alcantara Ortigoza, Marisol wrote: > >> Thanks for replying. I specified a q-grid: (nr1=2, nr2=2, nr3=1) in the >> input file of q2r. It was supposed to read the dynamical matices from 3 >> "dyn" files, one containg q = (0,0,0), other containing q=(0.5,-0.5,0) >> and q=(0.5,0.5,0) , and the last one containing q=(1,0,0). Thank you. >> Marisol. >> >> -----Original Message----- >> From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On >> Behalf Of Paolo Giannozzi >> Sent: Thursday, December 01, 2005 3:56 AM >> To: pw_forum at pwscf.org >> Subject: Re: [Pw_forum] Error in q2r.x >> >> >> On Wednesday 30 November 2005 20:59, Alcantara Ortigoza, Marisol wrote: >> >>>> from init : error # 1 >>>> nc already filled: wrong q grid or wrong nr >> >> did you use the manual procedure (i.e. one q at the time) or the >> "automatic" one (i.e. specifying a q-grid and calculating all q's at the >> same time)? In the former case, verify if you have correctly passed the >> grid: 2,2,1, in the input of q2r.x. >> >> Paolo >> >> > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From alcantar at phys.ksu.edu Fri Dec 2 22:27:17 2005 From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol) Date: Fri, 2 Dec 2005 15:27:17 -0600 Subject: [Pw_forum] Error in q2r.x Message-ID: Dear Stefano, I'm trying to test the new executable files but now I get errors while reading my "dyn" files : "wrong data read". Does that mean that the format have changed so I have to repeat the whole thing (I mean, the scf, ncsf, and the three q-points phonon calculations)? Thank you very much. Marisol. -----Original Message----- From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On Behalf Of Stefano de Gironcoli Sent: Friday, December 02, 2005 9:05 AM To: pw_forum at pwscf.org Subject: RE: [Pw_forum] Error in q2r.x Dear Marisol, I fixed the problem with ibrav=0 in the ph.x -> q2r.x -> matdyn.x chain. I did it in the CVS version. Could you please try it ? Everybody: please report any additional mis-behaviour using ibrav=0 . I think I did not introduce any new bug ... but you never know stefano On Fri, 2 Dec 2005, Stefano de Gironcoli wrote: > Hi, > > q2r does not work properly with ibrav=0, actually does not work at > all. Somehow, information on lattice_parameters are not written in the dynmat > files and then q2r (but probably other codes reading dynmat files) > does not > work properly with ibrav=0 > > Thanks for pointing out this problem. We'll fix it. > > stefano > > > On Fri, 2 Dec 2005, Alcantara Ortigoza, Marisol wrote: > >> Thanks for replying. I specified a q-grid: (nr1=2, nr2=2, nr3=1) in >> the input file of q2r. It was supposed to read the dynamical matices >> from 3 "dyn" files, one containg q = (0,0,0), other containing >> q=(0.5,-0.5,0) and q=(0.5,0.5,0) , and the last one containing >> q=(1,0,0). Thank you. Marisol. >> >> -----Original Message----- >> From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On >> Behalf Of Paolo Giannozzi >> Sent: Thursday, December 01, 2005 3:56 AM >> To: pw_forum at pwscf.org >> Subject: Re: [Pw_forum] Error in q2r.x >> >> >> On Wednesday 30 November 2005 20:59, Alcantara Ortigoza, Marisol >> wrote: >> >>>> from init : error # 1 >>>> nc already filled: wrong q grid or wrong nr >> >> did you use the manual procedure (i.e. one q at the time) or the >> "automatic" one (i.e. specifying a q-grid and calculating all q's at >> the same time)? In the former case, verify if you have correctly >> passed the >> grid: 2,2,1, in the input of q2r.x. >> >> Paolo >> >> > > _______________________________________________ > 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 From degironc at sissa.it Fri Dec 2 23:26:45 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 2 Dec 2005 23:26:45 +0100 Subject: [Pw_forum] Error in q2r.x In-Reply-To: References: Message-ID: <1133562405.4390ca252c752@webmail.sissa.it> The format has chaged . Information about cell_parameters has been added and in principle you should run nscf+ph again. However you can also manually add the information missing in the "dyn" files. The new files should have after the first line with the title and the second line containing nat ntyp ibrav celldm1 ... celldm6 four more lines containing symm_type at(1,1) at(2,1) at(3,1) at(1,2) at(2,2) at(3,2) at(1,3) at(2,3) at(3,3) followed by the remainder of the file. in practice you should take the CELL_PARAMETERS section of your scf input and put it after the second line of EACH "dyn" file, just removing the label CELL_PARAMETERS stefano Quoting "Alcantara Ortigoza, Marisol" : > Dear Stefano, > > I'm trying to test the new executable files but now I get errors while > reading my "dyn" files : "wrong data read". Does that mean that the > format have changed so I have to repeat the whole thing (I mean, the > scf, ncsf, and the three q-points phonon calculations)? > > Thank you very much. > Marisol. > > -----Original Message----- > From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On > Behalf Of Stefano de Gironcoli > Sent: Friday, December 02, 2005 9:05 AM > To: pw_forum at pwscf.org > Subject: RE: [Pw_forum] Error in q2r.x > > > > Dear Marisol, > > I fixed the problem with ibrav=0 in the ph.x -> q2r.x -> matdyn.x chain. > > I did it in the CVS version. > Could you please try it ? > > Everybody: > please report any additional mis-behaviour using ibrav=0 . > I think I did not introduce any new bug ... but you never know > > stefano > > > On Fri, 2 Dec 2005, Stefano de Gironcoli wrote: > > > Hi, > > > > q2r does not work properly with ibrav=0, actually does not work at > > all. Somehow, information on lattice_parameters are not written in the > dynmat > > files and then q2r (but probably other codes reading dynmat files) > > does not > > work properly with ibrav=0 > > > > Thanks for pointing out this problem. We'll fix it. > > > > stefano > > > > > > On Fri, 2 Dec 2005, Alcantara Ortigoza, Marisol wrote: > > > >> Thanks for replying. I specified a q-grid: (nr1=2, nr2=2, nr3=1) in > >> the input file of q2r. It was supposed to read the dynamical matices > >> from 3 "dyn" files, one containg q = (0,0,0), other containing > >> q=(0.5,-0.5,0) and q=(0.5,0.5,0) , and the last one containing > >> q=(1,0,0). Thank you. Marisol. > >> > >> -----Original Message----- > >> From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On > >> Behalf Of Paolo Giannozzi > >> Sent: Thursday, December 01, 2005 3:56 AM > >> To: pw_forum at pwscf.org > >> Subject: Re: [Pw_forum] Error in q2r.x > >> > >> > >> On Wednesday 30 November 2005 20:59, Alcantara Ortigoza, Marisol > >> wrote: > >> > >>>> from init : error # 1 > >>>> nc already filled: wrong q grid or wrong nr > >> > >> did you use the manual procedure (i.e. one q at the time) or the > >> "automatic" one (i.e. specifying a q-grid and calculating all q's at > >> the same time)? In the former case, verify if you have correctly > >> passed the > >> grid: 2,2,1, in the input of q2r.x. > >> > >> Paolo > >> > >> > > > > _______________________________________________ > > 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 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ From liyanpcl at yahoo.com.cn Sat Dec 3 04:07:39 2005 From: liyanpcl at yahoo.com.cn (li yan) Date: Sat, 3 Dec 2005 11:07:39 +0800 (CST) Subject: [Pw_forum] another two problems about the pseudopotential In-Reply-To: <200512011017.40649.giannozz@nest.sns.it> Message-ID: <20051203030739.13759.qmail@web15606.mail.cnb.yahoo.com> first, i will appreciate to paolo for your help. but i encontered two more problems about the pseudopotential. (1) in the example about the generation of the pseudopotential for Al given by version 3.0. in the pseudo-gen part, the configuration is [Ne] 3s2 3p1 3d-1, while in the pseudo-test part, the configuration is [Ne] 3s2 3p1 3d0, why? "negtive number flags the unbound states" is given by the input_ld1. Is this negtive number related to the local number? (2) The dft is selected as 3 which means the XC potential is PBE, but In the UPF files, there is a line wrie with "SLA PW PBX PBC PBE exchang-correlation function". In fhi98, this line is read as "SLA PW PBE PBE PBE exchang-correlation function". what's the meaning fo PBX PBC? I do some work about AgCl, the pseudopontential of Ag is given by fhi98pp, whie for Cl , i generated the pseudopotential with pwscf. But the scf.out said that DFT is inconsistent. So can I change directly the PBX PBC to PBE PBE in Cl.UPF to achieve the consistent of the DFT for Ag and Cl? thank you for any words about these two questions best ragards --------------------------------- ??????2006????2006? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20051203/7b81e105/attachment.htm From alcantar at phys.ksu.edu Sat Dec 3 08:30:03 2005 From: alcantar at phys.ksu.edu (Alcantara Ortigoza, Marisol) Date: Sat, 3 Dec 2005 01:30:03 -0600 Subject: [Pw_forum] Error in q2r.x Message-ID: Dear Stefano, Both q2r and matdyn codes of the CVS version worked fine. I thank you very much for your time and patience. Marisol. -----Original Message----- From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On Behalf Of Stefano de Gironcoli Sent: Friday, December 02, 2005 4:27 PM To: pw_forum at pwscf.org Subject: RE: [Pw_forum] Error in q2r.x The format has chaged . Information about cell_parameters has been added and in principle you should run nscf+ph again. However you can also manually add the information missing in the "dyn" files. The new files should have after the first line with the title and the second line containing nat ntyp ibrav celldm1 ... celldm6 four more lines containing symm_type at(1,1) at(2,1) at(3,1) at(1,2) at(2,2) at(3,2) at(1,3) at(2,3) at(3,3) followed by the remainder of the file. in practice you should take the CELL_PARAMETERS section of your scf input and put it after the second line of EACH "dyn" file, just removing the label CELL_PARAMETERS stefano Quoting "Alcantara Ortigoza, Marisol" : > Dear Stefano, > > I'm trying to test the new executable files but now I get errors while > reading my "dyn" files : "wrong data read". Does that mean that the > format have changed so I have to repeat the whole thing (I mean, the > scf, ncsf, and the three q-points phonon calculations)? > > Thank you very much. > Marisol. > > -----Original Message----- > From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On > Behalf Of Stefano de Gironcoli > Sent: Friday, December 02, 2005 9:05 AM > To: pw_forum at pwscf.org > Subject: RE: [Pw_forum] Error in q2r.x > > > > Dear Marisol, > > I fixed the problem with ibrav=0 in the ph.x -> q2r.x -> matdyn.x > chain. > > I did it in the CVS version. > Could you please try it ? > > Everybody: > please report any additional mis-behaviour using ibrav=0 . > I think I did not introduce any new bug ... but you never know > > stefano > > > On Fri, 2 Dec 2005, Stefano de Gironcoli wrote: > > > Hi, > > > > q2r does not work properly with ibrav=0, actually does not work at > > all. Somehow, information on lattice_parameters are not written in the > dynmat > > files and then q2r (but probably other codes reading dynmat files) > > does not > > work properly with ibrav=0 > > > > Thanks for pointing out this problem. We'll fix it. > > > > stefano > > > > > > On Fri, 2 Dec 2005, Alcantara Ortigoza, Marisol wrote: > > > >> Thanks for replying. I specified a q-grid: (nr1=2, nr2=2, nr3=1) in > >> the input file of q2r. It was supposed to read the dynamical matices > >> from 3 "dyn" files, one containg q = (0,0,0), other containing > >> q=(0.5,-0.5,0) and q=(0.5,0.5,0) , and the last one containing > >> q=(1,0,0). Thank you. Marisol. > >> > >> -----Original Message----- > >> From: pw_forum-admin at pwscf.org [mailto:pw_forum-admin at pwscf.org] On > >> Behalf Of Paolo Giannozzi > >> Sent: Thursday, December 01, 2005 3:56 AM > >> To: pw_forum at pwscf.org > >> Subject: Re: [Pw_forum] Error in q2r.x > >> > >> > >> On Wednesday 30 November 2005 20:59, Alcantara Ortigoza, Marisol > >> wrote: > >> > >>>> from init : error # 1 > >>>> nc already filled: wrong q grid or wrong nr > >> > >> did you use the manual procedure (i.e. one q at the time) or the > >> "automatic" one (i.e. specifying a q-grid and calculating all q's at > >> the same time)? In the former case, verify if you have correctly > >> passed the > >> grid: 2,2,1, in the input of q2r.x. > >> > >> Paolo > >> > >> > > > > _______________________________________________ > > 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 > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/ _______________________________________________ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum From giannozz at nest.sns.it Sat Dec 3 10:39:13 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 3 Dec 2005 10:39:13 +0100 Subject: [Pw_forum] Help about vc-relax In-Reply-To: References: Message-ID: <200512031039.13324.giannozz@nest.sns.it> On Wednesday 23 November 2005 22:48, You Lin wrote: > I'm trying to do a variable cell relaxation [...] > The code stops at the second step [...] > The error message gives no hint. well, it gives a hint, if you know what it means (which is far from obvious)... > from checkallsym : error # 2 > not orthogonal operation this means that the variable-cell relaxation has broken the original symmetry of the unit cell. Since the number of k-points depends on the symmetry of the cell, the run has to be stopped. Possible solutions: - start with a nonsymmetric cell - use a symmetry-conserving algorithm: the Wentzcovitch algorithm (cell_dynamics='damp-w') shouldn't break the symmetry 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 Sat Dec 3 15:24:38 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 3 Dec 2005 15:24:38 +0100 Subject: [Pw_forum] another two problems about the pseudopotential In-Reply-To: <20051203030739.13759.qmail@web15606.mail.cnb.yahoo.com> References: <20051203030739.13759.qmail@web15606.mail.cnb.yahoo.com> Message-ID: <200512031524.38523.giannozz@nest.sns.it> On Saturday 03 December 2005 04:07, li yan wrote: > what's the meaning fo PBX PBC? PBX = "Perdew-Becke-Ernzerhof gradient correction to exchange" PBC = "Perdew-Becke-Ernzerhof gradient correction to correlation" > I do some work about AgCl, the pseudopontential of Ag is given > by fhi98pp, while for Cl , i generated the pseudopotential with pwscf. > But the scf.out said that DFT is inconsistent. there used to be some inconsistency in the name of the PBE gradient corrected functional. Now all codes (atomic, converters, pwscf) use the same logic (or lack of it). > So can I change directly the PBX PBC to PBE PBE in Cl.UPF to achieve > the consistent of the DFT for Ag and Cl? yes, you can 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 ylin at shell.cas.usf.edu Mon Dec 5 01:32:47 2005 From: ylin at shell.cas.usf.edu (You Lin) Date: Sun, 4 Dec 2005 19:32:47 -0500 (EST) Subject: [Pw_forum] Re: Pw_forum digest, Vol 1 #825 - 3 msgs In-Reply-To: <20051204063509.9826.41228.Mailman@democritos.sissa.it> References: <20051204063509.9826.41228.Mailman@democritos.sissa.it> Message-ID: Dear Paolo: Thanks for the response. Yes, it works. However, it is still a mistery to me that Rahman-Parrinello damped md does break sysmmetry in this case. Your help is greatly appreciated. On Sun, 4 Dec 2005 pw_forum-request at pwscf.org wrote: > From: Paolo Giannozzi > Organization: Scuola Normale Superiore > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Help about vc-relax > Date: Sat, 3 Dec 2005 10:39:13 +0100 > Reply-To: pw_forum at pwscf.org > > On Wednesday 23 November 2005 22:48, You Lin wrote: > > > I'm trying to do a variable cell relaxation [...] > > The code stops at the second step [...] > > The error message gives no hint. > > well, it gives a hint, if you know what it means (which is far > from obvious)... > > > from checkallsym : error # 2 > > not orthogonal operation > > this means that the variable-cell relaxation has broken the > original symmetry of the unit cell. Since the number of k-points > depends on the symmetry of the cell, the run has to be stopped. > Possible solutions: > - start with a nonsymmetric cell > - use a symmetry-conserving algorithm: the Wentzcovitch algorithm > (cell_dynamics='damp-w') shouldn't break the symmetry > > 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 > > --__--__-- > > Message: 3 > From: Paolo Giannozzi > Organization: Scuola Normale Superiore > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] another two problems about the pseudopotential > Date: Sat, 3 Dec 2005 15:24:38 +0100 > Reply-To: pw_forum at pwscf.org > > On Saturday 03 December 2005 04:07, li yan wrote: > > > what's the meaning fo PBX PBC? > > PBX = "Perdew-Becke-Ernzerhof gradient correction to exchange" > PBC = "Perdew-Becke-Ernzerhof gradient correction to correlation" > > > I do some work about AgCl, the pseudopontential of Ag is given > > by fhi98pp, while for Cl , i generated the pseudopotential with pwscf. > > But the scf.out said that DFT is inconsistent. > > there used to be some inconsistency in the name of the PBE gradient > corrected functional. Now all codes (atomic, converters, pwscf) use > the same logic (or lack of it). > > > So can I change directly the PBX PBC to PBE PBE in Cl.UPF to achieve > > the consistent of the DFT for Ag and Cl? > > yes, you can > > 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 > > > End of Pw_forum Digest > ________________________________________ You Lin Department of Physics University of South Florida 4202 East Fowler Avenue Tampa, FL 33620 ________________________________________ Tel: (813)396-9220 [Office] Homepage: http://shell.cas.usf.edu/~ylin ________________________________________ From ylin at shell.cas.usf.edu Mon Dec 5 01:48:15 2005 From: ylin at shell.cas.usf.edu (You Lin) Date: Sun, 4 Dec 2005 19:48:15 -0500 (EST) Subject: [Pw_forum] Help about vc-relax In-Reply-To: <20051204063509.9826.41228.Mailman@democritos.sissa.it> References: <20051204063509.9826.41228.Mailman@democritos.sissa.it> Message-ID: Dear Paolo: Still got a question: After my first run, I wish to start a from the silicon.save by changing the control option: restart_mode='restart' Then the the code reported: Program PWSCF v.3.0 starts ... Today is 4Dec2005 at 19:42: 4 Ultrasoft (Vanderbilt) Pseudopotentials Current dimensions of program pwscf are: ntypx = 10 npk = 40000 lmax = 3 nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 Starting configuration read from file silicon.save Reading file silicon.save warning: symmetry operation # 25 not allowed. fractional translation: 0.2578067 0.2525927 0.2401578 in crystal coordinates %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from checkallsym : error # 1 not orthogonal operation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ---------------- End of output -------------------------------- The symmetry is wrong again? I was using symmetry-conserving algorithm: the Wentzcovitch algorithm (cell_dynamics='damp-w'). And it runs fine if I start from scratch. Thanks for the help in advance. ________________________________________ You Lin Department of Physics University of South Florida 4202 East Fowler Avenue Tampa, FL 33620 ________________________________________ Tel: (813)396-9220 [Office] Homepage: http://shell.cas.usf.edu/~ylin ________________________________________ From cbarreteau at cea.fr Mon Dec 5 08:34:35 2005 From: cbarreteau at cea.fr (Cyrille Barreteau) Date: Mon, 5 Dec 2005 08:34:35 +0100 (CET) Subject: [Pw_forum] problem of convergence In-Reply-To: <200512031524.38523.giannozz@nest.sns.it> References: <20051203030739.13759.qmail@web15606.mail.cnb.yahoo.com> <200512031524.38523.giannozz@nest.sns.it> Message-ID: <45930.132.166.17.128.1133768075.squirrel@dsm-mail> Dear pwscf users and developpers, I am trying to do a pwscf calculation of a 100 iron surface. I first performed a scf calculation on a 11 layers thick slab without any difficulty. But to get a better description of the surface I have tried to perform a calculation with a thicker slab: 20 atomic layers. Then comes the difficulty: the scf cycle never converges. After 46 iterations the estimated scf accuracy is huge (see below). Any hint to improve convergency? -decreasing mixing? -changing occupation -changing degauss... thank you in advance Cyrille ==================================================== iteration # 46 ecut= 35.00 ryd beta=0.30 Davidson diagonalization with overlap ethr = 2.46E-03, avg # of iterations = 6.7 total cpu time spent up to now is 228848.87 secs total energy = -1200.62214988 ryd estimated scf accuracy < 4756.34124938 ryd total magnetization = 10.95 Bohr mag/cell absolute magnetization = 11.56 Bohr mag/cell ===================================================== Here is the input file: ============================================== &control calculation='scf' title='Fe 001 20 layers + vacuum' restart_mode='from_scratch', prefix='fe_surf_001_gga' pseudo_dir = '/home/barreto/SOFTWARE/pseudo/', outdir='tmp' / &system ibrav = 6, celldm(1) = 5.42351511431617127800 , celldm(3)=13, nat= 20, ntyp= 1,nbnd=150,nspin=2, ecutwfc = 35.0, ecutrho=250.,starting_magnetization(1)=0.3, occupations='smearing', smearing='methfessel-paxton', degauss=0.025 / &electrons conv_thr = 1.0d-8 mixing_beta = 0.3 / ATOMIC_SPECIES Fe 55.847 Fe_us_gga_d2.1.8.pseudo.UPF ATOMIC_POSITIONS Fe 0.000000000000000 0.000000000000000 -5.25000000000000 Fe 0.500000000000000 0.500000000000000 -4.75000000000000 Fe 0.000000000000000 0.000000000000000 -4.25000000000000 Fe 0.500000000000000 0.500000000000000 -3.75000000000000 Fe 0.000000000000000 0.000000000000000 -3.25000000000000 Fe 0.500000000000000 0.500000000000000 -2.75000000000000 Fe 0.000000000000000 0.000000000000000 -2.25000000000000 Fe 0.500000000000000 0.500000000000000 -1.75000000000000 Fe 0.000000000000000 0.000000000000000 -1.25000000000000 Fe 0.500000000000000 0.500000000000000 -0.75000000000000 Fe 0.000000000000000 0.000000000000000 -0.25000000000000 Fe 0.000000000000000 0.000000000000000 0.25000000000000 Fe 0.500000000000000 0.500000000000000 0.75000000000000 Fe 0.000000000000000 0.000000000000000 1.25000000000000 Fe 0.500000000000000 0.500000000000000 1.75000000000000 Fe 0.000000000000000 0.000000000000000 2.25000000000000 Fe 0.500000000000000 0.500000000000000 2.75000000000000 Fe 0.000000000000000 0.000000000000000 3.25000000000000 Fe 0.500000000000000 0.500000000000000 3.75000000000000 Fe 0.000000000000000 0.000000000000000 4.25000000000000 Fe 0.500000000000000 0.500000000000000 4.75000000000000 Fe 0.000000000000000 0.000000000000000 5.25000000000000 K_POINTS automatic 14 14 1 0 0 0 ========================================================== -- ================================================================== Cyrille Barreteau | phone : +33 (0)1 69 08 29 51 CEA Saclay | fax : +33 (0)1 69 08 84 46 DSM/DRECAM/SPCSI | email : cyrille.barreteau at cea.fr Batiment 462 | 91191 Gif sur Yvette Cedex FRANCE ~~~~~~~~~~~~~~~~~~~~~~~~ http://www-drecam.cea.fr/spcsi/index.php http://www-drecam.cea.fr/Images/Pisp/cbarreteau/cbarreteau_fr.html http://www-drecam.cea.fr/Phocea/Membres/Cours/index.php ================================================================== From degironc at sissa.it Mon Dec 5 09:25:01 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 05 Dec 2005 09:25:01 +0100 Subject: [Pw_forum] problem of convergence References: <20051203030739.13759.qmail@web15606.mail.cnb.yahoo.com> <200512031524.38523.giannozz@nest.sns.it> <45930.132.166.17.128.1133768075.squirrel@dsm-mail> Message-ID: <4393F95D.5060103@sissa.it> try changing mixing_mode to local-TF. It should damp charge sloshing. stefano Cyrille Barreteau wrote: >Dear pwscf users and developpers, > >I am trying to do a pwscf calculation of a 100 iron surface. >I first performed a scf calculation on a 11 layers thick >slab without any difficulty. But to get a better description >of the surface I have tried to perform a calculation with >a thicker slab: 20 atomic layers. Then comes the difficulty: >the scf cycle never converges. After 46 iterations the >estimated scf accuracy is huge (see below). >Any hint to improve convergency? > -decreasing mixing? > -changing occupation > -changing degauss... > > thank you in advance > Cyrille > >==================================================== > iteration # 46 ecut= 35.00 ryd beta=0.30 > Davidson diagonalization with overlap > ethr = 2.46E-03, avg # of iterations = 6.7 > > total cpu time spent up to now is 228848.87 secs > > total energy = -1200.62214988 ryd > estimated scf accuracy < 4756.34124938 ryd > > total magnetization = 10.95 Bohr mag/cell > absolute magnetization = 11.56 Bohr mag/cell >===================================================== > >Here is the input file: > >============================================== > &control > calculation='scf' > title='Fe 001 20 layers + vacuum' > restart_mode='from_scratch', > prefix='fe_surf_001_gga' > pseudo_dir = '/home/barreto/SOFTWARE/pseudo/', > outdir='tmp' > / > &system > ibrav = 6, celldm(1) = 5.42351511431617127800 , celldm(3)=13, > nat= 20, ntyp= 1,nbnd=150,nspin=2, > ecutwfc = 35.0, ecutrho=250.,starting_magnetization(1)=0.3, > occupations='smearing', smearing='methfessel-paxton', degauss=0.025 > / > &electrons > conv_thr = 1.0d-8 > mixing_beta = 0.3 > / >ATOMIC_SPECIES > Fe 55.847 Fe_us_gga_d2.1.8.pseudo.UPF >ATOMIC_POSITIONS >Fe 0.000000000000000 0.000000000000000 -5.25000000000000 >Fe 0.500000000000000 0.500000000000000 -4.75000000000000 >Fe 0.000000000000000 0.000000000000000 -4.25000000000000 >Fe 0.500000000000000 0.500000000000000 -3.75000000000000 >Fe 0.000000000000000 0.000000000000000 -3.25000000000000 >Fe 0.500000000000000 0.500000000000000 -2.75000000000000 >Fe 0.000000000000000 0.000000000000000 -2.25000000000000 >Fe 0.500000000000000 0.500000000000000 -1.75000000000000 >Fe 0.000000000000000 0.000000000000000 -1.25000000000000 >Fe 0.500000000000000 0.500000000000000 -0.75000000000000 >Fe 0.000000000000000 0.000000000000000 -0.25000000000000 >Fe 0.000000000000000 0.000000000000000 0.25000000000000 >Fe 0.500000000000000 0.500000000000000 0.75000000000000 >Fe 0.000000000000000 0.000000000000000 1.25000000000000 >Fe 0.500000000000000 0.500000000000000 1.75000000000000 >Fe 0.000000000000000 0.000000000000000 2.25000000000000 >Fe 0.500000000000000 0.500000000000000 2.75000000000000 >Fe 0.000000000000000 0.000000000000000 3.25000000000000 >Fe 0.500000000000000 0.500000000000000 3.75000000000000 >Fe 0.000000000000000 0.000000000000000 4.25000000000000 >Fe 0.500000000000000 0.500000000000000 4.75000000000000 >Fe 0.000000000000000 0.000000000000000 5.25000000000000 >K_POINTS automatic > 14 14 1 0 0 0 >========================================================== > > > > > > > > > > From degironc at sissa.it Mon Dec 5 09:34:51 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Mon, 05 Dec 2005 09:34:51 +0100 Subject: [Pw_forum] Help about vc-relax References: <20051204063509.9826.41228.Mailman@democritos.sissa.it> Message-ID: <4393FBAB.3040706@sissa.it> The problem is that symmetry is a properties of the structure and PR has broken it so you cannot continue the broken run, even by damp-w. You can of course start from scratch using the "broken" structure. The code will find less symmetry w.r.t. to the original run, will generate the needed k-points and will go on. About your question on why PR braek the symmetry... there is a discussion of this problem in Renata Wentzcovitch's original work *Invariant molecular-dynamics approach to structural phase transitions * R. M. Wentzcovitch Phys. Rev. B *44*, 2358-2361 (1991) stefano You Lin wrote: >Dear Paolo: > >Still got a question: After my first run, I wish to start a from the >silicon.save by changing the control option: > >restart_mode='restart' > >Then the the code reported: > > Program PWSCF v.3.0 starts ... > Today is 4Dec2005 at 19:42: 4 > > Ultrasoft (Vanderbilt) Pseudopotentials > > Current dimensions of program pwscf are: > > ntypx = 10 npk = 40000 lmax = 3 > nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 > > Starting configuration read from file silicon.save > > Reading file silicon.save > warning: symmetry operation # 25 not allowed. fractional >translation: > 0.2578067 0.2525927 0.2401578 in crystal coordinates > > >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > from checkallsym : error # 1 > not orthogonal operation > >%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > stopping ... >---------------- End of output -------------------------------- > >The symmetry is wrong again? I was using symmetry-conserving algorithm: >the Wentzcovitch algorithm (cell_dynamics='damp-w'). And it runs fine >if I start from scratch. > >Thanks for the help in advance. > >________________________________________ > >You Lin > >Department of Physics >University of South Florida >4202 East Fowler Avenue >Tampa, FL 33620 >________________________________________ > >Tel: (813)396-9220 [Office] > >Homepage: http://shell.cas.usf.edu/~ylin >________________________________________ > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From giannozz at nest.sns.it Mon Dec 5 10:01:55 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 5 Dec 2005 10:01:55 +0100 Subject: [Pw_forum] Help about vc-relax In-Reply-To: References: <20051204063509.9826.41228.Mailman@democritos.sissa.it> Message-ID: <200512051001.55512.giannozz@nest.sns.it> On Monday 05 December 2005 01:48, You Lin wrote: > Still got a question: After my first run, I wish to start a from the > silicon.save by changing the control option: > > restart_mode='restart' > > Then the the code reported: > [....] > from checkallsym : error # 1 > not orthogonal operation > The symmetry is wrong again? I was using symmetry-conserving > algorithm: the Wentzcovitch algorithm (cell_dynamics='damp-w'). > And it runs fine if I start from scratch. if the SAME job gives different results when - started for N steps and then restarted for M more steps - started for N+M steps please provide a test job 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 Mon Dec 5 10:45:31 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 5 Dec 2005 10:45:31 +0100 Subject: [Pw_forum] another two problems about the pseudopotential In-Reply-To: <20051203030739.13759.qmail@web15606.mail.cnb.yahoo.com> References: <20051203030739.13759.qmail@web15606.mail.cnb.yahoo.com> Message-ID: <200512051045.31277.giannozz@nest.sns.it> On Saturday 03 December 2005 04:07, li yan wrote: > in the example about the generation of the pseudopotential for Al > given by version 3.0. in the pseudo-gen part, the configuration is > [Ne] 3s2 3p1 3d-1, while in the pseudo-test part, the configuration > is [Ne] 3s2 3p1 3d0, why? "negative number flags the unbound states" > is given by the input_ld1. the d state is used to generate the local potential, but one should not attempt to calculate a bound state for 3d. The negative occupancy is just a flag of this situation. 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 ylin at shell.cas.usf.edu Mon Dec 5 18:21:56 2005 From: ylin at shell.cas.usf.edu (You Lin) Date: Mon, 5 Dec 2005 12:21:56 -0500 (EST) Subject: [Pw_forum] Help about vc-relax In-Reply-To: <20051204063509.9826.41228.Mailman@democritos.sissa.it> References: <20051204063509.9826.41228.Mailman@democritos.sissa.it> Message-ID: I don't know how to post as a follow up. But here's the test job: ---- Start of the script ---- #!/bin/sh EXAMPLE_DIR=`pwd` # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use pw.x to calculate the total energy and" $ECHO "the band structure of four simple systems: Si, Al, Cu, Ni." # set the needed environment variables . ../environment_variables rm -rf $EXAMPLE_DIR/results # required executables and pseudopotentials BIN_LIST="pw.x" PSEUDO_LIST="Si.vbc.UPF Al.vbc.UPF Cu.pz-d-rrkjus.UPF NiUS.RRKJ3.UPF" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" $ECHO $ECHO " running pw.x as: $PW_COMMAND" $ECHO ecut=18. #UPF=SiPBE_nc.UPF #UPF=Si.vbc.UPF #UPF=Si.pbe-n-van.UPF #UPF=Si.pw91-n-van.UPF #UPF=Si.pbe-rrkj.UPF UPF=Si.pz-vbc.UPF for diago in david ; do #for celldm in 6.08 6.18 6.28 6.38 6.48 6.58 6.68 6.78 6.88 ; do for celldm in 09.80 ; do # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" #rm -rf $TMP_DIR/* $ECHO " done" # self-consistent calculation cat > si.scf.$diago.in << EOF &control calculation = 'vc-relax' restart_mode='from_scratch', prefix='silicon', tstress = .true. tprnfor = .true. pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/', nstep = 100 / &system ibrav= 0, celldm(1) =$celldm, nat= 2, ntyp= 1, ecutwfc =$ecut / &electrons diagonalization='$diago' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 / &ions upscale=10 / &cell cell_dynamics='damp-w' press=0. wmass=.1 / ATOMIC_SPECIES Si 28.086 $UPF ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.25 0.25 0.25 CELL_PARAMETERS -0.500000 0.000000 0.500000 0.000000 0.500000 0.500000 -0.500000 0.500000 0.000000 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 EOF $ECHO " running the scf calculation for Si...\c" $PW_COMMAND < si.scf.$diago.in > si.scf.$diago.$celldm.out $ECHO " done" done done $ECHO $ECHO "$EXAMPLE_DIR : done" ---- End of the script ---- This is a script for relaxing Si fcc structure for 100 steps using Wentzcovitch algorithm from scratch. I can run this script from scratch for 100 steps (nstep=100) with no error. But if I run it for 50 steps(set nstep=50) and continue from there by changing the line restart_mode='from_scratch', to restart_mode='restart', Then it reports: ---- Start of output ---- Program PWSCF v.3.0 starts ... Today is 5Dec2005 at 12:19:12 Ultrasoft (Vanderbilt) Pseudopotentials Current dimensions of program pwscf are: ntypx = 10 npk = 40000 lmax = 3 nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 Starting configuration read from file silicon.save Reading file silicon.save warning: symmetry operation # 6 not allowed. fractional translation: 0.2454073 0.2637782 0.2454073 in crystal coordinates warning: symmetry operation # 10 not allowed. fractional translation: 0.2454073 0.2637782 0.2454073 in crystal coordinates warning: symmetry operation # 14 not allowed. fractional translation: 0.2454073 0.2637782 0.2454073 in crystal coordinates warning: symmetry operation # 25 not allowed. fractional translation: 0.2454073 0.2637782 0.2454073 in crystal coordinates warning: symmetry operation # 41 not allowed. fractional translation: 0.2454073 0.2637782 0.2454073 in crystal coordinates warning: symmetry operation # 45 not allowed. fractional translation: 0.2454073 0.2637782 0.2454073 in crystal coordinates %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from checkallsym : error # 1 not orthogonal operation %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... ---- End of output ---- So I AM using Wentzcovitch algorithm in both cases. (M=50 and N=50) But it seems the "restart" mode changed the symmetry?? Thanks for the help. > Still got a question: After my first run, I wish to start a from the > silicon.save by changing the control option: > > restart_mode='restart' > > Then the the code reported: > [....] > from checkallsym : error # 1 > not orthogonal operation > The symmetry is wrong again? I was using symmetry-conserving > algorithm: the Wentzcovitch algorithm (cell_dynamics='damp-w'). > And it runs fine if I start from scratch. if the SAME job gives different results when - started for N steps and then restarted for M more steps - started for N+M steps please provide a test job 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 ________________________________________ You Lin Department of Physics University of South Florida 4202 East Fowler Avenue Tampa, FL 33620 ________________________________________ Tel: (813)396-9220 [Office] Homepage: http://shell.cas.usf.edu/~ylin ________________________________________ From proffess at yandex.ru Mon Dec 5 18:41:11 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Mon, 5 Dec 2005 20:41:11 +0300 (MSK) Subject: [Pw_forum] Help about vc-relax In-Reply-To: References: <20051204063509.9826.41228.Mailman@democritos.sissa.it> Message-ID: <43947BB7.000008.17497@mfront8.yandex.ru> Dear PWscf authors/users, I would like to add the next comment: I "successfully reproduced" this errors in my vc-relax calculations using 'damp-w' algoritm. The one studied system has no any symmetry, but when I fully restarted the calculations I got the error in >> from checkallsym : error # 1 >> not orthogonal operation Other system has a symmetry, and after a lot of steps I got the same error. I am not sure, that I have this error with 2.1.5 version (I did a lot vc-relax calculations). Thanks, Sergey From konstantin_kudin at yahoo.com Mon Dec 5 19:47:31 2005 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Mon, 5 Dec 2005 10:47:31 -0800 (PST) Subject: [Pw_forum] Help about vc-relax (and Espresso 3.0) In-Reply-To: <43947BB7.000008.17497@mfront8.yandex.ru> Message-ID: <20051205184731.21812.qmail@web52007.mail.yahoo.com> Sergey and others, Please do try all your traditional jobs with version 3.0, unless the bugs are identified they cannot be fixed! Kostya --- Sergey Lisenkov wrote: > Dear PWscf authors/users, > > I would like to add the next comment: I "successfully reproduced" > this errors in my vc-relax calculations using 'damp-w' algoritm. The > one studied system has no any symmetry, but when I fully restarted > the calculations I got the error in > > >> from checkallsym : error # 1 > >> not orthogonal operation > > Other system has a symmetry, and after a lot of steps I got the same > error. I am not sure, that I have this error with 2.1.5 version (I > did a lot vc-relax calculations). > > Thanks, > Sergey > _______________________________________________ > 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 ylin at shell.cas.usf.edu Mon Dec 5 22:29:01 2005 From: ylin at shell.cas.usf.edu (You Lin) Date: Mon, 5 Dec 2005 16:29:01 -0500 (EST) Subject: [Pw_forum] Help about vc-relax In-Reply-To: <20051204063509.9826.41228.Mailman@democritos.sissa.it> References: <20051204063509.9826.41228.Mailman@democritos.sissa.it> Message-ID: Dear Sir: For the symmetry broken problem, I am running the v 3.0. Please refer to the output file I presented. So the symmetry broken problem exists even in the latest version of pwscf. Thanks for the help. Best Regards, ________________________________________ You Lin Department of Physics University of South Florida 4202 East Fowler Avenue Tampa, FL 33620 ________________________________________ Tel: (813)396-9220 [Office] Homepage: http://shell.cas.usf.edu/~ylin ________________________________________ From proffess at yandex.ru Tue Dec 6 00:13:27 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Tue, 6 Dec 2005 02:13:27 +0300 (MSK) Subject: [Pw_forum] error from aainit Message-ID: <4394C997.000001.05373@webmail9.yandex.ru> Dear PWscf authors, I have got this error using serial version of pwscf code (3.0) on sgi altix machine. The same job is working on our other machine (intel xeon em64t cluster). %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from aainit : error # 14 mx dimension too small %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Any idea how to solve it? Thanks, Sergey From ding at sissa.it Tue Dec 6 09:11:37 2005 From: ding at sissa.it (Xunlei Ding) Date: Tue, 06 Dec 2005 09:11:37 +0100 Subject: [Pw_forum] question on ecutwfc and ecutrho Message-ID: <1133856697.21895.50.camel@cresole.cm.sissa.it> Dear all, I am now doing a calculation on a adsorption system. To determine the ecutwfc and ecutrho, I calculate the scf energies of a (3*2*5) slab with two adsorbed CO2. unit:ryd ecutwfc ecutrho total energy 24 288 -2725.94125538 case1 32 140 -2726.54980713 case2 32 200 -2726.06221809 case3 35 288 -2726.04364368 case4 Question1: It is said that the ecutrho should be about 4*ecutwfc, but why the difference between case2 and case3 is so large? Question2: It the difference between case3 and case4 small? (The adsorption energy is less than 0.5eV. ) Question3: Can I determine the suitable values for ecutwfc and ecutrho from these data? Thank you! Yours, Ding From degironc at sissa.it Tue Dec 6 09:27:53 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 06 Dec 2005 09:27:53 +0100 Subject: [Pw_forum] question on ecutwfc and ecutrho References: <1133856697.21895.50.camel@cresole.cm.sissa.it> Message-ID: <43954B89.8060909@sissa.it> When using US pseudopotentials cutoff for rho is usually much largere than 4 times the cutoff for wfc. ecutwfc and ecutrho are properties of the pseudopotentials not of the particular structure. Choose a simple structure and compute etot vs ecutwfc keeping ecutrho at the default value. look for convergence of total energy down to about a mryd/atom. at this point the choice (ecutwfc, ecutrho=4ecutwfc) is a good set but probably ecutwfc could be chosen smaller with no loss of accuracy. fix ecutrho to the determined value and progressively reduce ecutwfc to see up to where you can go. stefano From your data I cannot tell, it is usually better to change one parameter at a time. Probably ecutrho=288 is fine and and 32-35 is ok for ecutwfc while 24 is not. Xunlei Ding wrote: >Dear all, > >I am now doing a calculation on a adsorption system. >To determine the ecutwfc and ecutrho, >I calculate the scf energies of a (3*2*5) slab with two adsorbed CO2. > >unit:ryd >ecutwfc ecutrho total energy >24 288 -2725.94125538 case1 >32 140 -2726.54980713 case2 >32 200 -2726.06221809 case3 >35 288 -2726.04364368 case4 > >Question1: It is said that the ecutrho should be about 4*ecutwfc, but >why the difference between case2 and case3 is so large? > >Question2: It the difference between case3 and case4 small? (The >adsorption energy is less than 0.5eV. ) > >Question3: Can I determine the suitable values for ecutwfc and ecutrho >from these data? > >Thank you! > >Yours, >Ding > > >_______________________________________________ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum > > From Giovanni.Cantele at na.infn.it Tue Dec 6 09:46:34 2005 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Tue, 06 Dec 2005 09:46:34 +0100 Subject: [Pw_forum] EXX In-Reply-To: <43954B89.8060909@sissa.it> References: <1133856697.21895.50.camel@cresole.cm.sissa.it> <43954B89.8060909@sissa.it> Message-ID: <43954FEA.5060105@na.infn.it> Dear all, as far I understand, implementation of hybrid functionals (exx.f90) is in progress within Quantum-ESPRESSO. Is it already possible to test it? If yes, I find in some parts of the code lines like #if defined (EXX) ... #endif So, should I both recompile the code with -DEXX option and add some specific variable in the input file? Thanks for help, Giovanni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. G Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: Giovanni.Cantele at na.infn.it Web: http://people.na.infn.it/~cantele **************** RICERCA E FUTURO CAMMINANO INSIEME: DA 41 MESI I LAVORATORI DELLA RICERCA HANNO IL CONTRATTO SCADUTO, IL FUTURO NON DEVE SCADERE! per maggiori info: http://www.ge.cnr.it/rsu/rsu.htm **************** From giannozz at nest.sns.it Tue Dec 6 09:59:37 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 6 Dec 2005 09:59:37 +0100 Subject: [Pw_forum] Help about vc-relax In-Reply-To: References: <20051204063509.9826.41228.Mailman@democritos.sissa.it> Message-ID: <200512060959.37984.giannozz@nest.sns.it> On Monday 05 December 2005 22:29, You Lin wrote: > For the symmetry broken problem, I am running the v 3.0 [...] > So the symmetry broken problem exists even in the latest version of pwscf. this is clear. What is not clear is whether it is a new problem or wheter it existed already in previous versions 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 satchel1979 at gmail.com Tue Dec 6 11:38:21 2005 From: satchel1979 at gmail.com (chen zhengzheng) Date: Tue, 6 Dec 2005 18:38:21 +0800 Subject: [Pw_forum] My Compiling Error Message-ID: <2cb3d9ad0512060238y708b9e97nd21156b3999f20f4@mail.gmail.com> Dear Sir, I have downloaded the espresso-2.1.3 and compiled it on our cluster (Linux Debian) following the user guide: ./configure make all Then I got the error message as follows: make[1]: Entering directory `/home/chenzz01/espresso-2.1.3/PWNC' ifc -Vaxlib -O2 -tpp6 -I. -I../include -I../Modules -I../PW -I../PH -cl,./intel.pcl -fpp -D__LINUX -D__INTEL -D__FFTW -D__USE_INTERNAL_FFTW -c becmod.f90 Error FCE01 : Could not open program unit catalog list file ./intel.pcl compilation aborted for becmod.f90 (code 1) make[1]: *** [becmod.o] Error 1 make[1]: Leaving directory `/home/chenzz01/espresso-2.1.3/PWNC' make: *** [nc] Error 2 and at the same time all the executable files were generated, example01 can also run but with the message ** Address Error". I do not know why. Could you please give any suggestions to tackle this problem? Thank you very much. Yours Z.Z. Chen -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20051206/5aa47165/attachment.htm From cbarreteau at cea.fr Tue Dec 6 14:41:12 2005 From: cbarreteau at cea.fr (Cyrille Barreteau) Date: Tue, 6 Dec 2005 14:41:12 +0100 (CET) Subject: [Pw_forum] problem of convergence In-Reply-To: <4393F95D.5060103@sissa.it> References: <20051203030739.13759.qmail@web15606.mail.cnb.yahoo.com> <200512031524.38523.giannozz@nest.sns.it> <45930.132.166.17.128.1133768075.squirrel@dsm-mail> <4393F95D.5060103@sissa.it> Message-ID: <47557.132.166.17.128.1133876472.squirrel@dsm-mail> Grazie Mille Stefano. Quesaco local-TF? What is exactly this local-TF mixing scheme? Do you have any reference? It seems very efficient for slabs (and probably clusters). cyrille On Lun 5 d?cembre 2005 9:25, Stefano de Gironcoli a ?crit : > try changing mixing_mode to local-TF. > It should damp charge sloshing. > > stefano > > Cyrille Barreteau wrote: > >>Dear pwscf users and developpers, >> >>I am trying to do a pwscf calculation of a 100 iron surface. >>I first performed a scf calculation on a 11 layers thick >>slab without any difficulty. But to get a better description >>of the surface I have tried to perform a calculation with >>a thicker slab: 20 atomic layers. Then comes the difficulty: >>the scf cycle never converges. After 46 iterations the >>estimated scf accuracy is huge (see below). >>Any hint to improve convergency? >> -decreasing mixing? >> -changing occupation >> -changing degauss... >> >> thank you in advance >> Cyrille >> >>==================================================== >> iteration # 46 ecut= 35.00 ryd beta=0.30 >> Davidson diagonalization with overlap >> ethr = 2.46E-03, avg # of iterations = 6.7 >> >> total cpu time spent up to now is 228848.87 secs >> >> total energy = -1200.62214988 ryd >> estimated scf accuracy < 4756.34124938 ryd >> >> total magnetization = 10.95 Bohr mag/cell >> absolute magnetization = 11.56 Bohr mag/cell >>===================================================== >> >>Here is the input file: >> >>============================================== >> &control >> calculation='scf' >> title='Fe 001 20 layers + vacuum' >> restart_mode='from_scratch', >> prefix='fe_surf_001_gga' >> pseudo_dir = '/home/barreto/SOFTWARE/pseudo/', >> outdir='tmp' >> / >> &system >> ibrav = 6, celldm(1) = 5.42351511431617127800 , celldm(3)=13, >> nat= 20, ntyp= 1,nbnd=150,nspin=2, >> ecutwfc = 35.0, ecutrho=250.,starting_magnetization(1)=0.3, >> occupations='smearing', smearing='methfessel-paxton', degauss=0.025 >> / >> &electrons >> conv_thr = 1.0d-8 >> mixing_beta = 0.3 >> / >>ATOMIC_SPECIES >> Fe 55.847 Fe_us_gga_d2.1.8.pseudo.UPF >>ATOMIC_POSITIONS >>Fe 0.000000000000000 0.000000000000000 -5.25000000000000 >>Fe 0.500000000000000 0.500000000000000 -4.75000000000000 >>Fe 0.000000000000000 0.000000000000000 -4.25000000000000 >>Fe 0.500000000000000 0.500000000000000 -3.75000000000000 >>Fe 0.000000000000000 0.000000000000000 -3.25000000000000 >>Fe 0.500000000000000 0.500000000000000 -2.75000000000000 >>Fe 0.000000000000000 0.000000000000000 -2.25000000000000 >>Fe 0.500000000000000 0.500000000000000 -1.75000000000000 >>Fe 0.000000000000000 0.000000000000000 -1.25000000000000 >>Fe 0.500000000000000 0.500000000000000 -0.75000000000000 >>Fe 0.000000000000000 0.000000000000000 -0.25000000000000 >>Fe 0.000000000000000 0.000000000000000 0.25000000000000 >>Fe 0.500000000000000 0.500000000000000 0.75000000000000 >>Fe 0.000000000000000 0.000000000000000 1.25000000000000 >>Fe 0.500000000000000 0.500000000000000 1.75000000000000 >>Fe 0.000000000000000 0.000000000000000 2.25000000000000 >>Fe 0.500000000000000 0.500000000000000 2.75000000000000 >>Fe 0.000000000000000 0.000000000000000 3.25000000000000 >>Fe 0.500000000000000 0.500000000000000 3.75000000000000 >>Fe 0.000000000000000 0.000000000000000 4.25000000000000 >>Fe 0.500000000000000 0.500000000000000 4.75000000000000 >>Fe 0.000000000000000 0.000000000000000 5.25000000000000 >>K_POINTS automatic >> 14 14 1 0 0 0 >>========================================================== >> >> >> >> >> >> >> >> >> >> > > > > > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From alexdiazortiz at gmail.com Tue Dec 6 18:26:17 2005 From: alexdiazortiz at gmail.com (Alejandro Diaz Ortiz) Date: Tue, 6 Dec 2005 11:26:17 -0600 Subject: [Pw_forum] espresso on mac os x Message-ID: <4CBACB7C-EDEF-46A1-BE7E-11FE130B0182@gmail.com> Hi, I am a new espresso user and I am trying to install it first in an Apple computer before putting it into a linux cluster. I tried the shortest way to install espresso, i.e., ./configure and then make all, but it did not work. Before I engage in a battle against the OS X, I wanted to know if someone has already installed expresso in an Apple machine---I have OS X 10.4, g95, gcc tools---and willing to share the make.sys and the necessary tricks. Thanks, Alex From giannozz at nest.sns.it Tue Dec 6 18:27:24 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 6 Dec 2005 18:27:24 +0100 Subject: [Pw_forum] My Compiling Error In-Reply-To: <2cb3d9ad0512060238y708b9e97nd21156b3999f20f4@mail.gmail.com> References: <2cb3d9ad0512060238y708b9e97nd21156b3999f20f4@mail.gmail.com> Message-ID: <200512061827.24708.giannozz@nest.sns.it> On Tuesday 06 December 2005 11:38, chen zhengzheng wrote: > I have downloaded the espresso-2.1.3 there are newer versions > Error FCE01 : Could not open program unit catalog list file ./intel.pcl intel compiler v.6 is very old and no longer supported. Try to use "configure.old". 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 akohlmey at vitae.cmm.upenn.edu Tue Dec 6 19:01:47 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Tue, 6 Dec 2005 13:01:47 -0500 (EST) Subject: [Pw_forum] espresso on mac os x In-Reply-To: <4CBACB7C-EDEF-46A1-BE7E-11FE130B0182@gmail.com> Message-ID: On Tue, 6 Dec 2005, Alejandro Diaz Ortiz wrote: AO> Hi, hi alex, AO> I am a new espresso user and I am trying to install it first in an AO> Apple computer before putting it into a linux cluster. I tried the AO> shortest way to install espresso, i.e., ./configure and then make AO> all, but it did not work. Before I engage in a battle against the OS AO> X, I wanted to know if someone has already installed expresso in an AO> Apple machine---I have OS X 10.4, g95, gcc tools---and willing to AO> share the make.sys and the necessary tricks. Thanks, the default configuration (yest there is one and it was tested) for mac os x was created for use with the ibm xlf compiler. you may have to fiddle a bit with the various settings to make this work with g95. it is probably easier, you start with the linux machine right away. what did not work on the mac, btw? axel. AO> AO> Alex AO> AO> _______________________________________________ AO> Pw_forum mailing list AO> Pw_forum at pwscf.org AO> http://www.democritos.it/mailman/listinfo/pw_forum AO> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From andrea.vittadini at unipd.it Wed Dec 7 12:29:37 2005 From: andrea.vittadini at unipd.it (Andrea Vittadini) Date: 07 Dec 2005 12:29:37 +0100 Subject: [Pw_forum] crystal coordinates and ibrav=12 Message-ID: <1133954977.11829.9.camel@icaro> Hi all, anybody tried to run PWSCF calculations on a Monoclinic cell (ibrav=12) with "crystal" coordinates? I used two coordinates sets, both with the following cell parameters: celldm(1)= 7.154503 celldm(2)= 2.759416 celldm(3)= 1.000000 celldm(4)= 0.362396 As far as I can see, sets 1&2 should be (approximately) equivalent, yet set #1 gives strange results. I tried both espresso 2.1.4 and 3.0: no change. The following are the coordinates sets: ============= set #1 =============== ATOMIC_POSITIONS {crystal} O 0.95595 0.95595 0.50000 O 0.54405 0.04405 0.00000 O 0.20596 0.20595 0.00000 O 0.79405 0.29405 0.50000 O 0.95596 0.45596 0.00000 O 0.54405 0.54405 0.50000 O 0.20596 0.70596 0.50000 O 0.79405 0.79405 0.00000 Ti 0.00000 0.00000 0.00000 Ti 0.75000 0.25000 0.00000 Ti 0.00000 0.50000 0.50000 Ti 0.75000 0.75000 0.50000 ============= set #2 =============== ATOMIC_POSITIONS O 0.0000000 -0.1132771 0.5000000 O 0.5000000 0.1132771 0.0000000 O 0.0000000 0.5296840 0.0000000 O 0.5000000 0.7562383 0.5000000 O 0.5000000 1.1726452 0.0000000 O 0.0000000 1.3991994 0.5000000 O 0.5000000 1.8156063 0.5000000 O 0.0000000 2.0421606 0.0000000 Ti 0.0000000 0.0000000 0.0000000 Ti 0.5000000 0.6429612 0.0000000 Ti 0.5000000 1.2859223 0.5000000 Ti 0.0000000 1.9288834 0.5000000 ======================================= -- ------------------------------------------------------------------------------- Andrea Vittadini Istituto di Scienze e Tecnologie Molecolari del CNR CNR Institute of Molecular Science and Technologies Indirizzo/Address: Dip. Scienze Chimiche EMAIL : andrea.vittadini at unipd.it via Marzolo 1 PHONE : +39 049 827 5235 I-35131 Padova, Italy FAX : +39 049 827 5161 ------------------------------------------------------------------------------- From giannozz at nest.sns.it Wed Dec 7 14:07:34 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 7 Dec 2005 14:07:34 +0100 Subject: [Pw_forum] crystal coordinates and ibrav=12 In-Reply-To: <1133954977.11829.9.camel@icaro> References: <1133954977.11829.9.camel@icaro> Message-ID: <200512071407.34078.giannozz@nest.sns.it> On Wednesday 07 December 2005 12:29, Andrea Vittadini wrote: > anybody tried to run PWSCF calculations on a Monoclinic cell > (ibrav=12) with "crystal" coordinates? I didn't! > I used two coordinates sets, both with the following cell parameters: > celldm(1)= 7.154503 celldm(2)= 2.759416 celldm(3)= 1.000000 > celldm(4)= 0.362396 > > As far as I can see, sets 1&2 should be (approximately) equivalent, yet > set #1 gives strange results. the code prints both the crystal axis and the cartesian atomic coordinates in 2pi/a units (if it doesn't, try "verbosity='high'"). From such data you should be able to find out what is happening. This is what the axis for the monoclinic P, i.e. ibrav=12, should look like: ============================= a1 = (a,0,0), a2= (b*sin(gamma), b*cos(gamma), 0), a3 = (0, 0, c) where gamma is the angle between axis a and b, celldm(1)=a, celldm(2)=b/a, celldm(3)=c/a, celldm(4)=cos(ab) (see file Doc/INPUT_PW towards the end) 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 Wed Dec 7 15:54:35 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 7 Dec 2005 15:54:35 +0100 Subject: [Pw_forum] error from aainit In-Reply-To: <4394C997.000001.05373@webmail9.yandex.ru> References: <4394C997.000001.05373@webmail9.yandex.ru> Message-ID: <200512071554.35748.giannozz@nest.sns.it> On Tuesday 06 December 2005 00:13, Sergey Lisenkov wrote: > I have got this error using serial version of pwscf code (3.0) on sgi altix > machine. compiler, libraries? there is a Make.altix in install/, have a look at it 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 Wed Dec 7 16:44:11 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Wed, 7 Dec 2005 18:44:11 +0300 (MSK) Subject: [Pw_forum] error from aainit In-Reply-To: <200512071554.35748.giannozz@nest.sns.it> References: <4394C997.000001.05373@webmail9.yandex.ru> <200512071554.35748.giannozz@nest.sns.it> Message-ID: <4397034B.000003.30452@webmail11.yandex.ru> >On Tuesday 06 December 2005 00:13, Sergey Lisenkov wrote: >compiler, libraries? there is a Make.altix in install/, have a look at it > The make.sys file is based on Make.altix in install/ Compilers -ifort8.1, ifort9.0 libraries - scsl, or mkl8.0 In all cases the error was the same. Sergey From yay451 at mail.usask.ca Wed Dec 7 21:16:41 2005 From: yay451 at mail.usask.ca (Yansun Yao) Date: Wed, 07 Dec 2005 14:16:41 -0600 Subject: [Pw_forum] Unit of displacements Message-ID: <1133986601.43974329e8c23@webmail.usask.ca> Dear Pwscf users, Could you please tell me the unit using for the displacements in dynamical matrix files, generated by ph.x? Is it in Bohradius , alat or crystal coordinates? Thank you in advance! Yansun Yao University of Saskatchewan From liyanpcl at yahoo.com.cn Thu Dec 8 02:49:09 2005 From: liyanpcl at yahoo.com.cn (li yan) Date: Thu, 8 Dec 2005 09:49:09 +0800 (CST) Subject: [Pw_forum] about the generation of the pseudopotential Message-ID: <20051208014909.95990.qmail@web15607.mail.cnb.yahoo.com> dear all, i followed the examples about the generation of the pseudopotential given by 3.0. in the generation part, for Al, the configuration is [Ne] 3s2 3p1 3d-1, is the number which flags the unbound state fixed to -1 or any negtive number? In the test part, the configuration is [Ne] 3s2 3p1 3d 0. why this config is different from that in the generation part? in the inputp, how can i determin the rcut, ener and the unboud states' ocs? and why the rcut is equel to the rcutus. as far as i know, the rcutus is larger than rcut. regards. --------------------------------- ????G??????????????????? ?????D????????? -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20051208/23d254b4/attachment.htm From pwscfklt at gmail.com Thu Dec 8 16:17:38 2005 From: pwscfklt at gmail.com (Konzern) Date: Thu, 8 Dec 2005 10:17:38 -0500 Subject: [Pw_forum] problem with ph.x Message-ID: Hi everyone, I am trying to use the ph.x of espresso 3.0 to do some calculations concerning phonons. However, when I tried to run the example in example06, something unexpected happened. There was no problem with pw.x, the scf finished very soon. But when it turned to phonon calculations, the porgram seemed to be idle after generating alas.dyn2. I am running the program with 4 cpus; the ph.x has been idle for more than 10 hours. Attached is all the related files. Any idea? Thank you. Besides, I found that there is some problem to run pp.x by mpirun. When I use 2 cpus, the program also idled, while with 1 cpu, there is no problem. Konzern -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20051208/1de1592c/attachment.htm From pwscfklt at gmail.com Thu Dec 8 16:19:33 2005 From: pwscfklt at gmail.com (Konzern) Date: Thu, 8 Dec 2005 10:19:33 -0500 Subject: [Pw_forum] problem with ph.x In-Reply-To: References: Message-ID: Hi everyone, I am trying to use the ph.x of espresso 3.0 to do some calculations concerning phonons. However, when I tried to run the example in example06, something unexpected happened. There was no problem with pw.x, the scf finished very soon. But when it turned to phonon calculations, the porgram seemed to be idle after generating alas.dyn2. I am running the program with 4 cpus; the ph.x has been idle for more than 10 hours. Attached is all the related files. Any idea? Thank you. Besides, I found that there is some problem to run pp.x by mpirun. When I use 2 cpus, the program also idled, while with 1 cpu, there is no problem. Konzern -- sorry, forgot the attachment just now. -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20051208/e0313073/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: ph.tar.gz Type: application/x-gzip Size: 8923 bytes Desc: not available Url : /pipermail/attachments/20051208/e0313073/attachment.bin From degironc at sissa.it Fri Dec 9 09:29:58 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Fri, 9 Dec 2005 09:29:58 +0100 (CET) Subject: [Pw_forum] Unit of displacements In-Reply-To: <1133986601.43974329e8c23@webmail.usask.ca> References: <1133986601.43974329e8c23@webmail.usask.ca> Message-ID: Dynamical matrices are written in atomic units : Ryd/bohr^2 stefano On Wed, 7 Dec 2005, Yansun Yao wrote: > Dear Pwscf users, > Could you please tell me the unit using for the displacements in dynamical > matrix files, generated by ph.x? Is it in Bohradius , alat or crystal > coordinates? > Thank you in advance! > Yansun Yao > University of Saskatchewan > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > From shein at ihim.uran.ru Fri Dec 9 12:13:00 2005 From: shein at ihim.uran.ru (Igor R. Shein) Date: Fri, 09 Dec 2005 16:13:00 +0500 Subject: [Pw_forum] Pseudopotentials for 5-f elements Message-ID: <439966BC.5050305@ihim.uran.ru> Dear sirs, I have generated full relativistic pseudopotential for Th: ******************************************************** &input title='Th', zed=90.0, rmax = 200, rel=2, iswitch=3, rlderiv=2.50, eminld=-4.0, emaxld=4.0, deld=0.02, nld=5, config='[Rn] 6d2 7s2', dft='PBE' / &inputp pseudotype=3, lloc=0, file_pseudopw='Th_rel.RRKJ3', nlcc=.true., rcore=1.2, rcloc=3.5 / 5 6D 3 2 2.00 0.00 2.10 2.10 1.50 6D 3 2 0.00 -0.20 2.10 2.10 1.50 6D 3 2 0.00 0.00 2.10 2.10 2.50 6D 3 2 0.00 -0.20 2.10 2.10 2.50 7S 1 0 2.00 0.00 2.60 2.60 0.50 *********************************** in view of the spin - orbital parameters and for metal Th lattice parameter is 9.49 a.u.(experimental - 9.60775 a.u.). But I do not manage to understand, how is correctly necessary to generate pseudopotentials in view of 5-f elements. Yours faithfully, PhD Igor R. Shein From j.kendrick at bradford.ac.uk Fri Dec 9 15:31:02 2005 From: j.kendrick at bradford.ac.uk (John Kendrick) Date: Fri, 9 Dec 2005 14:31:02 -0000 Subject: [Pw_forum] Problems with running Nudged Elastic Band - Address Error Message-ID: <000701c5fccd$2e43aed0$0a02a8c0@TOSH> Hi, I wonder if some one can give me some help. Ive been using pwscf to perform some optimisations of a crystal lattice of transition metal oxides with some pleasing results as to predictions of lattice constants. I have now started to look at using the nudged elastic band method to follow proton migration in the lattice. But I am getting ** Address Error **. I then looked at Example 17, with is the H-HH transition state using NEB and got the same error. I am running on a linux cluster. I have checked out the latest version of the software from cvs. Compiler is intel fortran 7.1 (I tried 8.0 and got compilation problems, we don't have access to 9) MPI ch is 1.2.5.2-1 compiled with above compiler The compilation is for the parallel version of the code. Output from the run looks like this.... ========================================================== Program PWSCF v.3.0 starts ... Today is 9Dec2005 at 11:29:39 Parallel version (MPI) Number of processors in use: 1 Ultrasoft (Vanderbilt) Pseudopotentials Current dimensions of program pwscf are: ntypx = 10 npk = 40000 lmax = 3 nchix = 6 ndmx = 2000 nbrx = 14 nqfx = 8 gamma-point specific algorithms are used p0_24355: p4_error: interrupt SIGSEGV: 11 ============================================================= Could some one give me some pointers as to where to start looking? Thanks John Make.sys looks like this; # make.sys. Generated from make.sys.in by configure. # compilation rules .SUFFIXES : .SUFFIXES : .o .c .f .f90 .f90.o: $(MPIF90) $(F90FLAGS) -c $< .f.o: $(F77) $(FFLAGS) -c $< .c.o: $(CC) $(CFLAGS) -c $< CC = icc MPICC = mpicc CFLAGS = -O3 $(DFLAGS) $(IFLAGS) CPP = icc -E CPPFLAGS = $(DFLAGS) $(IFLAGS) F90 = ifc MPIF90 = mpif90 F90FLAGS = $(FFLAGS) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) F90FLAGS_NOOPT = $(FFLAGS_NOOPT) -nomodule -fpp $(FDFLAGS) $(IFLAGS) $(MODFLAGS) F77 = ifc MPIF77 = mpif77 FFLAGS = -Vaxlib -O2 -tpp6 FFLAGS_NOOPT = -O0 LD = mpif90 LDFLAGS = -Vaxlib AR = ar ARFLAGS = ruv RANLIB = echo BLAS_LIBS = -L/usr/local/Cluster-Apps/mkl61/lib/32 -lmkl_ia32 -lguide -lpthread LAPACK_LIBS = -lmkl_lapack FFT_LIBS = -L/home/software/lib -lfftw MPI_LIBS = MASS_LIBS = # ----------------------------- # application-specific settings # See include/defs.h.README for a list of precompilation options # (possible arguments to -D or -U) and their meaning DFLAGS = -D__LINUX -D__INTEL -D__FFTW -D__MPI -D__PARA FDFLAGS = $(DFLAGS) IFLAGS = -I../include -I/home/software/include MODFLAGS = -I. -I../Modules -I../PW -I../PH -I../iotk/src -I../CPV LIBOBJS = ../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a # LIBS must contain the location of all needed external libraries LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FFT_LIBS) $(MPI_LIBS) $(MASS_LIBS) # MYLIB can be one of the following (depending on LIBS): # blas : compile the local copy of blas routines # lapack : compile the local copy of lapack routines # blas_and_lapack : all of the above - use this for a quick test # or if you don't have an optimized blas/lapack library # lapack_ibm : compile only lapack routines not present in IBM ESSL # use this together with IBM ESSL # lapack_t3e : compile only lapack routines not present in T3E scilib # use this together with T3E scilib # lapack_mkl : compile only lapack routines not present in Intel MKL # use this together with Intel MKL MYLIB = lapack_mkl Dr John Kendrick Institute of Pharmaceutical Innovation University of Bradford Bradford BD7 1DP Tel: +44(0)1274 236101 Fax: +44(0)1274 236166 Email: J.Kendrick#bradford.ac.uk From yay451 at mail.usask.ca Fri Dec 9 15:48:23 2005 From: yay451 at mail.usask.ca (Yansun Yao) Date: Fri, 09 Dec 2005 08:48:23 -0600 Subject: [Pw_forum] Unit of displacements In-Reply-To: References: <1133986601.43974329e8c23@webmail.usask.ca> Message-ID: <1134139703.439999374a925@webmail.usask.ca> Dear Stefano Thank you! Could you please also tell me the unit used in atomic displacements (eigenvectors dividied by the square mass)? Yansun Quoting Stefano de Gironcoli : > Dynamical matrices are written in atomic units : Ryd/bohr^2 > stefano > > On Wed, 7 Dec 2005, Yansun Yao wrote: > > > Dear Pwscf users, > > Could you please tell me the unit using for the displacements in > dynamical > > matrix files, generated by ph.x? Is it in Bohradius , alat or crystal > > coordinates? > > Thank you in advance! > > Yansun Yao > > University of Saskatchewan > > _______________________________________________ > > 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 > From giannozz at nest.sns.it Fri Dec 9 16:18:04 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 9 Dec 2005 16:18:04 +0100 Subject: [Pw_forum] Unit of displacements In-Reply-To: <1134139703.439999374a925@webmail.usask.ca> References: <1133986601.43974329e8c23@webmail.usask.ca> <1134139703.439999374a925@webmail.usask.ca> Message-ID: <200512091618.04417.giannozz@nest.sns.it> On Friday 09 December 2005 15:48, Yansun Yao wrote: > Thank you! Could you please also tell me the unit used in atomic > displacements (eigenvectors dividied by the square mass)? masses are in atomic (rydberg) units: mass of one electron = 0.5, one atomic mass unit = 911.444 -- 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 Dec 9 18:36:26 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 9 Dec 2005 18:36:26 +0100 Subject: [Pw_forum] Problems with running Nudged Elastic Band - Address Error In-Reply-To: <000701c5fccd$2e43aed0$0a02a8c0@TOSH> References: <000701c5fccd$2e43aed0$0a02a8c0@TOSH> Message-ID: <200512091836.26485.giannozz@nest.sns.it> On Friday 09 December 2005 15:31, John Kendrick wrote: > Number of processors in use: 1 > p0_24355: p4_error: interrupt SIGSEGV: 11 maybe you should first try if it works when compiled for serial execution. With one processor, the code does no communication at all. Compilation and execution problems with PC's and PC clusters are discussed at length in the users' guide. A sizable percentage of messages in this list are about the same subject. In summary, most errors of such a kind in parallel execution are due to bad compilers or libraries. If you find any evidence that there is something wrong with the algorithm, please submit enough data so that the problem can be reproduced 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 yonasb at yahoo.com Fri Dec 9 20:15:34 2005 From: yonasb at yahoo.com (Yonas Abraham) Date: Fri, 9 Dec 2005 11:15:34 -0800 (PST) Subject: [Pw_forum] espresso-3.0 bug? Message-ID: <20051209191534.65985.qmail@web32002.mail.mud.yahoo.com> in a PGI 64 compiler under AMD optron system with mpich enabled, I can't compile CP. here is the error msg cpp -P -traditional -D__LINUX64 -D__PGI -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include fpmdpp.f90 -o fpmdpp.F90 mpif90 -fast -r8 -D__LINUX64 -D__PGI -D__FFTW -D__USE_INTERNAL_FFTW -D__MPI -D__PARA -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c fpmdpp.F90 -o fpmdpp.o PGF90-S-0155-prefix is use associated and cannot be redeclared (fpmdpp.F90: 46) 0 inform, 0 warnings, 1 severes, 0 fatal for fpmd_postproc make[1]: *** [fpmdpp.o] Error 2 I can see that fpmd_postproc USE's xml_io_base.f90, which intern uses prefix variable from io_files module. I have compiled the same code under other 32 bit AMD machile, but that didn't cought this bug. /yonas From degironc at sissa.it Tue Dec 13 13:55:08 2005 From: degironc at sissa.it (Stefano de Gironcoli) Date: Tue, 13 Dec 2005 13:55:08 +0100 Subject: [Pw_forum] EXX References: <1133856697.21895.50.camel@cresole.cm.sissa.it> <43954B89.8060909@sissa.it> <43954FEA.5060105@na.infn.it> Message-ID: <439EC4AC.4050404@sissa.it> Hybrid functionals (currently only HF and PBE0) are kind of implemented in PWscf. "Kind of" means under development, basically untested and unsupported (even less than other features). It only works with NCPP and, since no HF or PBE0 pseudopotential generation in available, one needs to force the DFT from input using input_dft variable in system namelist. Forces are ok, stress are not. It is VERY slow and I don't know if it will be possible to improve on that. My suggestion is to wait sometime, until at least an example is provided. If you still want to use it, be very carefull and report mis-behaviors to me (not to get a quick fix, but to help in the development) In order to use it one should define -DEXX in DFLAGS in make.sys and recompile everything stefano Giovanni Cantele wrote: > Dear all, > as far I understand, implementation of hybrid functionals > (exx.f90) is in progress within Quantum-ESPRESSO. > > Is it already possible to test it? > > If yes, I find in some parts of the code lines like > #if defined (EXX) > ... > #endif > > So, should I both recompile the code with -DEXX option > and add some specific variable in the input file? > > Thanks for help, > Giovanni > From giannozz at nest.sns.it Mon Dec 12 15:41:02 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 12 Dec 2005 15:41:02 +0100 Subject: [Pw_forum] espresso-3.0 bug? In-Reply-To: <20051209191534.65985.qmail@web32002.mail.mud.yahoo.com> References: <20051209191534.65985.qmail@web32002.mail.mud.yahoo.com> Message-ID: <200512121541.02148.giannozz@nest.sns.it> On Friday 09 December 2005 20:15, Yonas Abraham wrote: > I can see that fpmd_postproc USE's xml_io_base.f90, > which intern uses prefix variable from io_files module. > > I have compiled the same code under other 32 bit AMD > machile, but that didn't cought this bug. there is a PRIVATE declaration in xml_io_base.f90: only those variables that are declared PUBLIC should be visible, I think (I am no f90 expert). So the bug might be in the PGI compiler and not in quantum-espresso 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 Dec 12 15:53:18 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 12 Dec 2005 15:53:18 +0100 Subject: [Pw_forum] Pseudopotentials for 5-f elements In-Reply-To: <439966BC.5050305@ihim.uran.ru> References: <439966BC.5050305@ihim.uran.ru> Message-ID: <200512121553.18250.giannozz@nest.sns.it> On Friday 09 December 2005 12:13, Igor R. Shein wrote: > I have generated full relativistic pseudopotential for Th [...] > in view of the spin - orbital parameters and for metal Th lattice > parameter is 9.49 a.u.(experimental - 9.60775 a.u.). > But I do not manage to understand, how is correctly necessary to > generate pseudopotentials in view of 5-f elements. I do not manage to understand what your problem is. Is it the discrepancy between the theoretical and experimental lattice parameter? it doesn't look that bad. You have to carefully check the convergence of your calculations, the effects of the various approximations, etc. . Remember that DFT has serious limitations in strongly correlated materials. 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 Dec 12 15:59:10 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 12 Dec 2005 15:59:10 +0100 Subject: [Pw_forum] error from aainit In-Reply-To: <4397034B.000003.30452@webmail11.yandex.ru> References: <4394C997.000001.05373@webmail9.yandex.ru> <200512071554.35748.giannozz@nest.sns.it> <4397034B.000003.30452@webmail11.yandex.ru> Message-ID: <200512121559.10644.giannozz@nest.sns.it> On Wednesday 07 December 2005 16:44, Sergey Lisenkov wrote: > >compiler, libraries? there is a Make.altix in install/, have a look at it > > The make.sys file is based on Make.altix in install/ > > Compilers -ifort8.1, ifort9.0 > libraries - scsl, or mkl8.0 > > In all cases the error was the same. unless you have convincing evidence of the contrary, I will assume it is a compiler bug, or a problem with libraries (the only thing I can think of is an unexpected behavior in random number generation). If you want to try to find convincing evidence, just compare what "aainit" does when it works and when it doesn't: it is a rather simple routine 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 shaposh at isp.nsc.ru Mon Dec 12 16:09:43 2005 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Mon, 12 Dec 2005 21:09:43 +0600 Subject: [Pw_forum] CP dynamics with Nose thermostat Message-ID: <1134400183.3044.6.camel@m00> Hello to all, i am trying to make CP dynamics for the Si slab with 144 Si atoms. I use Nose thermostat and "tempw" = 300K. However, after some relaxation, ionic temperature reaches ~500K and oscillates around. What is going on? What would be the best strategy for performing CP dynamics with Nose thermostat activated? Regards, Alex From proffess at yandex.ru Mon Dec 12 17:09:46 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Mon, 12 Dec 2005 19:09:46 +0300 (MSK) Subject: [Pw_forum] error from aainit In-Reply-To: <200512121559.10644.giannozz@nest.sns.it> References: <4394C997.000001.05373@webmail9.yandex.ru> <200512071554.35748.giannozz@nest.sns.it> <4397034B.000003.30452@webmail11.yandex.ru> <200512121559.10644.giannozz@nest.sns.it> Message-ID: <439DA0CA.000001.14257@pantene.yandex.ru> Dear Paolo, >unless you have convincing evidence of the contrary, I will assume >it is a compiler bug, or a problem with libraries (the only thing I can >think of is an unexpected behavior in random number generation). >If you want to try to find convincing evidence, just compare what >"aainit" does when it works and when it doesn't: it is a rather simple >routine I compiled 2.1.5 version with the same compiler/libraries, etc. This version works fine - there is no that error. I will look at newer version and try to find what causes the problem. Sergey From j.kendrick at Bradford.ac.uk Mon Dec 12 17:38:02 2005 From: j.kendrick at Bradford.ac.uk (John Kendrick) Date: Mon, 12 Dec 2005 16:38:02 -0000 Subject: [Pw_forum] Problems with running Nudged Elastic Band - Address Error Message-ID: <000001c5ff3a$6edab460$7650358f@TOSH> I did as suggested, and got a failure running my example on a single node. I tracked this down to a compiler problem with intel_7.1. In routine path_base.f90 The statement d_R(:,i) = d_R(:,i) / image_spacing(i) Was requiring the allocation of a very large temporary array. I replaced ':' by '1:dim' in the above line and all looks OK! Thanks John Dr John Kendrick Institute of Pharmaceutical Innovation University of Bradford Bradford BD7 1DP Tel: +44(0)1274 236101 Fax: +44(0)1274 236166 Email: J.Kendrick at bradford.ac.uk ========================================================== On Friday 09 December 2005 15:31, John Kendrick wrote: > Number of processors in use: 1 > p0_24355: p4_error: interrupt SIGSEGV: 11 maybe you should first try if it works when compiled for serial execution. With one processor, the code does no communication at all. Compilation and execution problems with PC's and PC clusters are discussed at length in the users' guide. A sizable percentage of messages in this list are about the same subject. In summary, most errors of such a kind in parallel execution are due to bad compilers or libraries. If you find any evidence that there is something wrong with the algorithm, please submit enough data so that the problem can be reproduced 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 Tue Dec 13 09:50:32 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 13 Dec 2005 09:50:32 +0100 Subject: [Pw_forum] problem with ph.x In-Reply-To: References: Message-ID: <200512130950.32170.giannozz@nest.sns.it> On Thursday 08 December 2005 16:19, Konzern wrote: > the ph.x has been idle for more than 10 hours. if you run interactively and print the output at the terminal, you will see the code crashing during a diagonalization. Sometimes parallel jobs remain in a hung state after a crash. I don't know why it crashes, though. 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 Tue Dec 13 10:35:57 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 13 Dec 2005 10:35:57 +0100 Subject: [Pw_forum] CP dynamics with Nose thermostat In-Reply-To: <1134400183.3044.6.camel@m00> References: <1134400183.3044.6.camel@m00> Message-ID: <200512131035.57926.giannozz@nest.sns.it> On Monday 12 December 2005 16:09, Alexander Shaposhnikov wrote: > i am trying to make CP dynamics for the Si slab with 144 Si atoms. > I use Nose thermostat and "tempw" = 300K. However, after some > relaxation, ionic temperature reaches ~500K and oscillates around. this is the correct behaviour: the Nose' thermostat may lead to large temperature oscillations. See this message and the related thread: http://www.democritos.it/pipermail/pw_forum/2005-June/002549.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 wmbmacam at lg.ehu.es Tue Dec 13 18:22:18 2005 From: wmbmacam at lg.ehu.es (=?UTF-8?B?TWlndWVsIE1hcnTDrW5leiBDYW5hbGVz?=) Date: Tue, 13 Dec 2005 18:22:18 +0100 Subject: [Pw_forum] Relax error Message-ID: <439F034A.6070104@lg.ehu.es> Good afternoon everybody, I was testing some pseudopotentials, and one of these tests consisted in the H-H distance in equilibrium. So I did a relax run with pw.x. It worked OK. I copied the final positions into the input and then re-ran the test (with higher convergence criteria). However, this time I got an error (also appears with the same convergence criteria from the first run). The last lines of the output are: entering subroutine stress ... total stress (ryd/bohr**3) (kbar) P= -0.05 -0.00000031 0.00000002 0.00000002 -0.05 0.00 0.00 0.00000002 -0.00000031 0.00000002 0.00 -0.05 0.00 0.00000002 0.00000002 -0.00000031 0.00 0.00 -0.05 searching for next position (pslinmin)... Eold = -2.33845221 Etot = -2.33845221 DEold = -0.00000101 DEtot = -0.00000158 linmin: 2nd order interpolation plus 3rd order corrections %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from linmin : error # 2 unexpected error %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping ... I would be glad if anyone more knowledgeable than me suggested anything. From calculation=md to running CPMD (though it is an USPP...) to dancing and singing round the computer while it is running. Thanks in advance, Miguel PS: Am I asking too much accuracy? Or is the idea of a second relaxation run plain stupid? -- ---------------------------------------- Miguel Mart?nez Canales Dto. F?sica de la Materia Condensada UPV/EHU Facultad de Ciencia y Tecnolog?a Apdo. 644 48080 Bilbao (Spain) Fax: +34 94 601 3500 Tlf: +34 94 601 5437 ---------------------------------------- 2005 International Year of Physics "The only things you can't avoid in life are death, taxes and Ubuntu reviews." Robert Storey From giannozz at nest.sns.it Tue Dec 13 18:29:39 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Tue, 13 Dec 2005 18:29:39 +0100 Subject: [Pw_forum] Relax error In-Reply-To: <439F034A.6070104@lg.ehu.es> References: <439F034A.6070104@lg.ehu.es> Message-ID: <200512131829.39467.giannozz@nest.sns.it> On Tuesday 13 December 2005 18:22, Miguel Mart?nez Canales wrote: > PS: Am I asking too much accuracy? you are -- 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 pwscfklt at gmail.com Wed Dec 14 03:11:52 2005 From: pwscfklt at gmail.com (L.T. Kong) Date: Tue, 13 Dec 2005 21:11:52 -0500 Subject: [Pw_forum] problem with ph.x References: <200512130950.32170.giannozz@nest.sns.it> Message-ID: <003001c60053$c0393ce0$0b02a8c0@konzern> Thank you, Paolo. I did not found the problem, either. I have tried to use mpirun -np 2 ph.x -npool 2, and it works; and if I use mpirun -np 1 ph.x, it still works well. However, it fails in other situations. I don't know if it is the problem of parallelization of both q-points and k-points ( Just a speculation) simultaneously. Thanks. Konzern ----- Original Message ----- From: "Paolo Giannozzi" To: Sent: Tuesday, December 13, 2005 3:50 AM Subject: Re: [Pw_forum] problem with ph.x > On Thursday 08 December 2005 16:19, Konzern wrote: > >> the ph.x has been idle for more than 10 hours. > > if you run interactively and print the output at the terminal, > you will see the code crashing during a diagonalization. > Sometimes parallel jobs remain in a hung state after a crash. > I don't know why it crashes, though. > > 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 ferretti.andrea at unimore.it Wed Dec 14 11:46:42 2005 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Wed, 14 Dec 2005 11:46:42 +0100 (CET) Subject: [Pw_forum] WanT second public release Message-ID: Dear friends and colleagues, it is our great pleasure to announce the second public release of the WanT suite of codes for ab initio electronic transport and maximally-localized Wannier functions calculations at: http://www.wannier-transport.org WanT is an open-source, GNU General Public License suite of codes that provides an integrated approach for the study of coherent electronic transport in nanostructures. The core methodology combines state-of-the-art Density Functional Theory (DFT), plane-wave, norm-conserving pseudopotentials calculations with a Green's functions method based on the Landauer formalism to describe quantum conductance. The essential connection between the two, and a crucial step in the calculation, is the use of the maximally-localized Wannier function representation to introduce naturally the ground-state electronic structure into the lattice Green's function approach at the basis of the evaluation of the quantum conductance. Moreover, the knowledge of the Wannier functions of the system allows for the direct link between the electronic transport properties of the device with the nature of the chemical bonds, providing insight onto the mechanisms that govern electron flow at the nanoscale. WanT calculations will provide the user with: - Quantum conductance spectrum for a bulk (infinite, periodic) system and for a lead-conductor-lead geometry - Density of states spectrum in the conductor region - Centers and spreads of the maximally-localized Wannier functions of the system New features of version 2.0.0: - complete code restyling (number of executable, internal data representation, repository) - new iotk (XML-like) interface with quantum-ESPRESSO package - new user interface (input file formats and calculation steps) - test suite enlarged and improved - important performance issues addressed (e.g. different scaling for large systems) - improved numerical stability and machine portability - implementation of ultra-soft pseudopotentials in the calculation of Wannier functions and related quantities - implementation of "conditioned" localization and penalty functionals in Wannier minimization - implementation of restart procedure - implementation of k-point summations in transport calculations - upgraded postprocessing suite (e.g. supported fmts in plot.x) and enlarged Feel free to forward this message to all the people you think might be interested. Arrigo Calzolari, Andrea Ferretti and Marco Buongiorno Nardelli, on behalf of the WanT developers team. -- 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From shaposh at isp.nsc.ru Thu Dec 15 14:50:46 2005 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Thu, 15 Dec 2005 19:50:46 +0600 Subject: [Pw_forum] Pw.x : relaxation in crystall coordinates? Message-ID: <1134654646.2726.6.camel@m00> Hello, is it possible to make structural relaxation with input coordinates in "crystall" units? Total force always calculated = 0 and no relaxation is done. The same system input in "alat" units (coordinates taken from pw.x output) have non-zero total force. Thanks. From akohlmey at vitae.cmm.upenn.edu Thu Dec 15 15:02:37 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Thu, 15 Dec 2005 09:02:37 -0500 (EST) Subject: [Pw_forum] Pw.x : relaxation in crystall coordinates? In-Reply-To: <1134654646.2726.6.camel@m00> Message-ID: On Thu, 15 Dec 2005, Alexander Shaposhnikov wrote: AS> Hello, hi! AS> is it possible to make structural relaxation with input coordinates AS> in "crystall" units? Total force always calculated = 0 and no yes. of course. AS> relaxation is done. The same system input in "alat" units (coordinates AS> taken from pw.x output) have non-zero total force. this is because of the limited numerical accuracy in the output. seems like in your starting configuration, the forces cancel exactly due to symmetry. just break the symmetry for 1-2 atoms in the input by adding a small displacement and you should see a similar behavior as when using alat based coordinates. axel. AS> AS> Thanks. AS> AS> _______________________________________________ AS> Pw_forum mailing list AS> Pw_forum at pwscf.org AS> http://www.democritos.it/mailman/listinfo/pw_forum AS> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shaposh at isp.nsc.ru Thu Dec 15 15:14:13 2005 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Thu, 15 Dec 2005 20:14:13 +0600 Subject: [Pw_forum] Pw.x : relaxation in crystall coordinates? In-Reply-To: References: Message-ID: <1134656053.2726.13.camel@m00> Hi, this idea comes to in the first place. So, i made some distortion in crystall coordinates "by hand". To my great surprise, the total force still was zero! I made a run with nosym=.TRUE., still no effect. (And in alat units total force is not that small, by the way.) I use the latest cvs version. No changes wrt 3.0. Regards, Alex On Thu, 2005-12-15 at 09:02 -0500, Axel Kohlmeyer wrote: > On Thu, 15 Dec 2005, Alexander Shaposhnikov wrote: > > AS> Hello, > > hi! > > AS> is it possible to make structural relaxation with input coordinates > AS> in "crystall" units? Total force always calculated = 0 and no > > yes. of course. > > AS> relaxation is done. The same system input in "alat" units (coordinates > AS> taken from pw.x output) have non-zero total force. > > this is because of the limited numerical accuracy in the output. > seems like in your starting configuration, the forces cancel exactly > due to symmetry. just break the symmetry for 1-2 atoms in the input > by adding a small displacement and you should see a similar behavior > as when using alat based coordinates. > > axel. > > AS> > AS> Thanks. > AS> > AS> _______________________________________________ > AS> Pw_forum mailing list > AS> Pw_forum at pwscf.org > AS> http://www.democritos.it/mailman/listinfo/pw_forum > AS> > From giannozz at nest.sns.it Thu Dec 15 16:38:05 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 15 Dec 2005 16:38:05 +0100 Subject: [Pw_forum] Pw.x : relaxation in crystall coordinates? In-Reply-To: <1134654646.2726.6.camel@m00> References: <1134654646.2726.6.camel@m00> Message-ID: <200512151638.05512.giannozz@nest.sns.it> On Thursday 15 December 2005 14:50, Alexander Shaposhnikov wrote: > is it possible to make structural relaxation with input coordinates > in "crystall" units? Total force always calculated = 0 and no > relaxation is done. The same system input in "alat" units (coordinates > taken from pw.x output) have non-zero total force. the code prints cartesian coordinates, always. Please check whether you get different results with the same set of coordinates. If so, please submit an test job 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 coldwind1978 at yahoo.com.cn Fri Dec 16 02:58:38 2005 From: coldwind1978 at yahoo.com.cn (=?gb2312?q?=D5=EB=D2=B6=20=D6=EC?=) Date: Fri, 16 Dec 2005 09:58:38 +0800 (CST) Subject: [Pw_forum] what is the meaning of the error " error in DGETRF" Message-ID: <20051216015838.63886.qmail@web15804.mail.cnb.yahoo.com> Dear All users: i am new users, when i relax supperlattice "BaTiO3/SrTiO3", the error appeared: from invmat : error # 2 error in DGETRF ,please tell me why? Regards zhuzhenye __________________________________________________ ??????????????? http://cn.mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20051216/6262dea8/attachment.htm From shaposh at isp.nsc.ru Fri Dec 16 12:17:39 2005 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Fri, 16 Dec 2005 17:17:39 +0600 Subject: [Pw_forum] Pw.x : relaxation in crystall coordinates? In-Reply-To: <200512151638.05512.giannozz@nest.sns.it> References: <1134654646.2726.6.camel@m00> <200512151638.05512.giannozz@nest.sns.it> Message-ID: <1134731859.20470.10.camel@m00> Here is (minimum) tests job: //////// &CONTROL calculation = 'relax' , restart_mode = 'from_scratch' , outdir = '/scr/tmp/zro2t' , pseudo_dir= '/home/alex/programs/espresso-current/pseudo/', prefix = zro2t , tprnfor = .true., / &SYSTEM ibrav = 6, celldm(1) = 6.88, celldm(3) = 1.448, nat = 6, ntyp = 2, ecutwfc = 55, / &ELECTRONS diagonalization = 'david', / &IONS ion_dynamics='bfgs', / ATOMIC_SPECIES Zr 91.00000 Zr.pbe-nsp-van.UPF O 16.00000 O.pbe-rrkjus.UPF ATOMIC_POSITIONS {crystall} Zr 0.750000000 0.250000000 0.250000000 0 0 0 Zr 0.250000000 0.750000000 0.750000000 0 0 0 O 0.250000000 0.250000000 0.454600000 0 0 0 O 0.750000000 0.750000000 0.545400000 0 0 0 O 0.250000000 0.250000000 0.954600000 0 0 0 O 0.750000000 0.750000000 0.045400000 0 0 0 K_POINTS {automatic} 4 4 3 0 0 0 ////////// Atomic positions in alat : Zr 0.7500000 0.2500000 0.3620000 Zr 0.2500000 0.7500000 1.0860000 O 0.2500000 0.2500000 0.6582608 O 0.7500000 0.7500000 0.7897392 O 0.2500000 0.2500000 1.3822608 O 0.7500000 0.7500000 0.0657392 In the case of {crystall} coordinates, total force is always zero. Regards, Alex On Thu, 2005-12-15 at 16:38 +0100, Paolo Giannozzi wrote: > On Thursday 15 December 2005 14:50, Alexander Shaposhnikov wrote: > > > is it possible to make structural relaxation with input coordinates > > in "crystall" units? Total force always calculated = 0 and no > > relaxation is done. The same system input in "alat" units (coordinates > > taken from pw.x output) have non-zero total force. > > the code prints cartesian coordinates, always. Please check whether > you get different results with the same set of coordinates. If so, > please submit an test job > > Paolo > From giannozz at nest.sns.it Fri Dec 16 13:07:55 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 16 Dec 2005 13:07:55 +0100 Subject: [Pw_forum] Pw.x : relaxation in crystall coordinates? In-Reply-To: <1134731859.20470.10.camel@m00> References: <1134654646.2726.6.camel@m00> <200512151638.05512.giannozz@nest.sns.it> <1134731859.20470.10.camel@m00> Message-ID: <200512161307.55391.giannozz@nest.sns.it> On Friday 16 December 2005 12:17, Alexander Shaposhnikov wrote: > ATOMIC_POSITIONS {crystall} "crystal", actually (but this is not relevant, provided the string matches "crystal). > Zr 0.750000000 0.250000000 0.250000000 0 0 0 > Zr 0.250000000 0.750000000 0.750000000 0 0 0 > O 0.250000000 0.250000000 0.454600000 0 0 0 > O 0.750000000 0.750000000 0.545400000 0 0 0 > O 0.250000000 0.250000000 0.954600000 0 0 0 > O 0.750000000 0.750000000 0.045400000 0 0 0 > [...] In the case of {crystall} coordinates, total force is always zero. of course it is: you are setting it to zero. From INPUT_PW: X x y z {if_pos(1) if_pos(2) if_pos(3)} where : X Character: label of the atom as specified in ATOMIC_SPECIES x, y, z Real: atomic positions if_pos: Integer: component i of the force for this atom is multiplied by if_pos(i), which must be 0 or 1. Used to keep selected atoms and/or selected components fixed in neb, smd, MD dynamics or structural optimization run If you set these to zero, you set to zero the forces 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 shaposh at isp.nsc.ru Fri Dec 16 13:22:08 2005 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Fri, 16 Dec 2005 18:22:08 +0600 Subject: [Pw_forum] Pw.x : relaxation in crystall coordinates? In-Reply-To: <200512161307.55391.giannozz@nest.sns.it> References: <1134654646.2726.6.camel@m00> <200512151638.05512.giannozz@nest.sns.it> <1134731859.20470.10.camel@m00> <200512161307.55391.giannozz@nest.sns.it> Message-ID: <1134735728.20470.13.camel@m00> Silly me:) Thank you! On Fri, 2005-12-16 at 13:07 +0100, Paolo Giannozzi wrote: > On Friday 16 December 2005 12:17, Alexander Shaposhnikov wrote: > > > ATOMIC_POSITIONS {crystall} > > "crystal", actually (but this is not relevant, provided the string > matches "crystal). > > > Zr 0.750000000 0.250000000 0.250000000 0 0 0 > > Zr 0.250000000 0.750000000 0.750000000 0 0 0 > > O 0.250000000 0.250000000 0.454600000 0 0 0 > > O 0.750000000 0.750000000 0.545400000 0 0 0 > > O 0.250000000 0.250000000 0.954600000 0 0 0 > > O 0.750000000 0.750000000 0.045400000 0 0 0 > > > [...] In the case of {crystall} coordinates, total force is always zero. > > of course it is: you are setting it to zero. From INPUT_PW: > > X x y z {if_pos(1) if_pos(2) if_pos(3)} > > where : > > X Character: label of the atom as specified in ATOMIC_SPECIES > x, y, z Real: atomic positions > if_pos: Integer: component i of the force for this atom is multiplied > by if_pos(i), which must be 0 or 1. Used to keep selected atoms > and/or selected components fixed in neb, smd, MD dynamics or > structural optimization run > > If you set these to zero, you set to zero the forces > > Paolo > From shaposh at isp.nsc.ru Fri Dec 16 16:35:50 2005 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Fri, 16 Dec 2005 21:35:50 +0600 Subject: [Pw_forum] PW.x : restart of mpi jobs with disk_io='high' broken? Message-ID: <1134747350.20470.36.camel@m00> Hello. Sorry again for the silly posts about relaxation:) What i have found : Restart of mpi jobs with NCPU>1 and disk_io set to 'high' seems to be broken. It hangs with the last message "Starting wfc from file". 'normal' or 'low' have no problem, as well as 'high' on just one CPU. Regards, Alex From konstantin_kudin at yahoo.com Fri Dec 16 20:35:10 2005 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Fri, 16 Dec 2005 11:35:10 -0800 (PST) Subject: [Pw_forum] PW.x : restart of mpi jobs with disk_io='high' broken? In-Reply-To: <1134747350.20470.36.camel@m00> Message-ID: <20051216193510.3429.qmail@web52013.mail.yahoo.com> Please report if you can restart with the following options: startingpot='file' startingwfc='atomic' Kostya --- Alexander Shaposhnikov wrote: > Hello. Sorry again for the silly posts about relaxation:) > > What i have found : > Restart of mpi jobs with NCPU>1 and disk_io set to 'high' > seems to be broken. It hangs with the last message "Starting wfc from > file". 'normal' or 'low' have no problem, as well as 'high' on just > one > CPU. > > Regards, > Alex > > _______________________________________________ > 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 ykzhou at gmail.com Sat Dec 17 01:46:11 2005 From: ykzhou at gmail.com (y.k. zhou) Date: Fri, 16 Dec 2005 18:46:11 -0600 Subject: [Pw_forum] what is the meaning of the error " error in DGETRF" In-Reply-To: <20051216015838.63886.qmail@web15804.mail.cnb.yahoo.com> References: <20051216015838.63886.qmail@web15804.mail.cnb.yahoo.com> Message-ID: On 12/15/05, ?? ? wrote: > Dear All users: > i am new users, when i relax supperlattice "BaTiO3/SrTiO3", the error > appeared: from invmat : error # 2 > error in DGETRF > ,please tell me why? > Hi, dgetrf is a LAPACK subroutine for LU factorization of a general matrix using partial pivoting with row interchanges. The output value of info for SUBROUTINE DGETRF( M, N, A, LDA, IPIV, INFO ) is commented (in the source code) as: * INFO (output) INTEGER * = 0: successful exit * < 0: if INFO = -i, the i-th argument had an illegal value * > 0: if INFO = i, U(i,i) is exactly zero. The factorization * has been completed, but the factor U is exactly * singular, and division by zero will occur if it is used * to solve a system of equations. regards, -ykz From mousumi at jncasr.ac.in Sun Dec 18 09:32:14 2005 From: mousumi at jncasr.ac.in (Mousumi Upadhyay Kahaly) Date: Sun, 18 Dec 2005 14:02:14 +0530 (IST) Subject: [Pw_forum] coloured STM Message-ID: <51679.202.41.111.151.1134894734.squirrel@202.41.111.151> Dear all, We could get some black & white STM imgaes for our system of study. Getting coloured STM imgaes will help me more. Will any of you please tell me, how to get coloured STM imgaes using PWSCF (post-processing)? best regards, mousumi. From akohlmey at vitae.cmm.upenn.edu Sun Dec 18 12:28:11 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Sun, 18 Dec 2005 06:28:11 -0500 (EST) Subject: [Pw_forum] coloured STM In-Reply-To: <51679.202.41.111.151.1134894734.squirrel@202.41.111.151> Message-ID: On Sun, 18 Dec 2005, Mousumi Upadhyay Kahaly wrote: MK> Dear all, dear mousumi, MK> We could get some black & white STM imgaes for our system of study. MK> MK> Getting coloured STM imgaes will help me more. Will any of you MK> please tell me, how to get coloured STM imgaes using PWSCF MK> (post-processing)? if everything else fails, use a image manipulation program, e.g. gimp, to map the grey value to a color gradient. it is a rather simple procedure. see the respective manual. axel. MK> MK> best regards, MK> mousumi. MK> _______________________________________________ MK> Pw_forum mailing list MK> Pw_forum at pwscf.org MK> http://www.democritos.it/mailman/listinfo/pw_forum MK> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From shaposh at isp.nsc.ru Mon Dec 19 08:16:17 2005 From: shaposh at isp.nsc.ru (Alexander Shaposhnikov) Date: Mon, 19 Dec 2005 13:16:17 +0600 Subject: [Pw_forum] PW.x : restart of mpi jobs with disk_io='high' broken? In-Reply-To: <20051216193510.3429.qmail@web52013.mail.yahoo.com> References: <20051216193510.3429.qmail@web52013.mail.yahoo.com> Message-ID: <1134976577.2726.3.camel@m00> No, cannot restart with disk_io='high' in any case. Can anybody confirm this? Is there any real use for disk_io='high' performance-wise (for large jobs and high-speed io)? Regards, Alex On Fri, 2005-12-16 at 11:35 -0800, Konstantin Kudin wrote: > Please report if you can restart with the following options: > > startingpot='file' > startingwfc='atomic' > > Kostya > > --- Alexander Shaposhnikov wrote: > > > Hello. Sorry again for the silly posts about relaxation:) > > > > What i have found : > > Restart of mpi jobs with NCPU>1 and disk_io set to 'high' > > seems to be broken. It hangs with the last message "Starting wfc from > > file". 'normal' or 'low' have no problem, as well as 'high' on just > > one > > CPU. > > > > Regards, > > Alex > > > > _______________________________________________ > > 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 From swblelia at sw.ehu.es Mon Dec 19 15:44:24 2005 From: swblelia at sw.ehu.es (Aritz Leonardo) Date: Mon, 19 Dec 2005 15:44:24 +0100 Subject: [Pw_forum] honeycomb In-Reply-To: <200511301752.03946.giannozz@nest.sns.it> References: <1133365055.6874.10.camel@swpc50.sw.ehu.es> <438DCA68.7000604@sissa.it> <1133368691.7813.2.camel@swpc50.sw.ehu.es> <200511301752.03946.giannozz@nest.sns.it> Message-ID: <1135003464.1135.68.camel@swpc50.sw.ehu.es> El mi?, 30-11-2005 a las 17:52 +0100, Paolo Giannozzi escribi?: > On Wednesday 30 November 2005 17:38, Aritz Leonardo wrote: > > > I have drawn in xcrysden one monolayer and does not look good at all. > > ibrav=4, celldm(1)=a (in atomic units), celldm(3)=c/a, nat=4, ntyp=1 > > ATOMIC_POSITIONS (alat) > C 0.0 0.000000000 0.0 > C 0.0 0.577350270 0.0 I think that this line should be changed > C 0.0 0.000000000 c/(2a) by--> C 0.0 0.577350270 c/(2a) > C 0.5 0.288675135 c/(2a) > > P. From konstantin_kudin at yahoo.com Mon Dec 19 16:55:39 2005 From: konstantin_kudin at yahoo.com (Konstantin Kudin) Date: Mon, 19 Dec 2005 07:55:39 -0800 (PST) Subject: [Pw_forum] PW.x : restart of mpi jobs with disk_io='high' broken? In-Reply-To: <1134976577.2726.3.camel@m00> Message-ID: <20051219155539.1707.qmail@web52001.mail.yahoo.com> Alexander, Please do provide a test job with output so that it is possible to reproduce your bug. Otherwise the request resembles "my computer does not work!" type of complaints. Kostya --- Alexander Shaposhnikov wrote: > No, cannot restart with disk_io='high' in any case. > Can anybody confirm this? > Is there any real use for disk_io='high' performance-wise (for large > jobs and high-speed io)? > > Regards, > Alex > > On Fri, 2005-12-16 at 11:35 -0800, Konstantin Kudin wrote: > > Please report if you can restart with the following options: > > > > startingpot='file' > > startingwfc='atomic' > > > > Kostya > > > > --- Alexander Shaposhnikov wrote: > > > > > Hello. Sorry again for the silly posts about relaxation:) > > > > > > What i have found : > > > Restart of mpi jobs with NCPU>1 and disk_io set to 'high' > > > seems to be broken. It hangs with the last message "Starting wfc > from > > > file". 'normal' or 'low' have no problem, as well as 'high' on > just > > > one > > > CPU. > > > > > > Regards, > > > Alex > > > > > > _______________________________________________ > > > 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 > > _______________________________________________ > 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 giannozz at nest.sns.it Mon Dec 19 22:44:21 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Mon, 19 Dec 2005 22:44:21 +0100 Subject: [Pw_forum] honeycomb In-Reply-To: <1135003464.1135.68.camel@swpc50.sw.ehu.es> References: <1133365055.6874.10.camel@swpc50.sw.ehu.es> <200511301752.03946.giannozz@nest.sns.it> <1135003464.1135.68.camel@swpc50.sw.ehu.es> Message-ID: <200512192244.21915.giannozz@nest.sns.it> On Monday 19 December 2005 15:44, Aritz Leonardo wrote: > > ATOMIC_POSITIONS (alat) > > C 0.0 0.000000000 0.0 > > C 0.0 0.577350270 0.0 > > I think that this line should be changed > > > C 0.0 0.000000000 c/(2a) by--> C 0.0 0.577350270 c/(2a) > > C 0.5 0.288675135 c/(2a) it seems to me they are the same. In both cases you two layers of hexagons, stacked one above the other, displaced in such a way that the the two sublattices of the second layer are either above one of the sublattices of the first layer, or above the centers of the hexagons od the first layer. 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 sir_puding at tut.by Wed Dec 21 10:32:38 2005 From: sir_puding at tut.by (sir_puding at tut.by) Date: Wed, 21 Dec 2005 11:32:38 +0200 Subject: [Pw_forum] Is it possible FPMD + Magnetic + Electric Fields within Espresso? In-Reply-To: References: Message-ID: <12317457.20051221113238@tut.by> Greatings, everyone. I'm looking for an instrument to perform some modelling of nanostructures. Is it possible in Espresso to simulate molecular dynamics in electric and magnetic fields? Sergey. From giannozz at nest.sns.it Wed Dec 21 16:37:14 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 21 Dec 2005 16:37:14 +0100 Subject: [Pw_forum] Is it possible FPMD + Magnetic + Electric Fields within Espresso? In-Reply-To: <12317457.20051221113238@tut.by> References: <12317457.20051221113238@tut.by> Message-ID: <200512211637.14216.giannozz@nest.sns.it> On Wednesday 21 December 2005 10:32, sir_puding at tut.by wrote: > Greatings, everyone. I'm looking for an instrument to perform some > modelling of nanostructures. Is it possible in Espresso to simulate > molecular dynamics in electric and magnetic fields? it is possible to perform molecular dynamics simulations under an electric field, but not in a magnetic field 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 lee0su at MIT.EDU Thu Dec 22 00:47:15 2005 From: lee0su at MIT.EDU (Young-Su Lee) Date: Wed, 21 Dec 2005 18:47:15 -0500 Subject: [Pw_forum] calculation = "nscf" with CP Message-ID: <43A9E983.6000600@mit.edu> Dear CP developers, I've been using "calculation = nscf" option with CP version 2.0. I found that this option is disabled in Espresso version 3.0 and managed to turn it on. If I understand correctly, the only necessary change to make "nscf" option work is to read charge density in subroutine rhoofr. What worries me is that the results from two versions are different. The occupied 4 states are fine and eigenvalues are the same as those from self-consistent calculations in both cases. Ver 2.0 ================================================ total energy = -4.06675 a.u. kinetic energy = 9.34798 a.u. electrostatic energy = -7.34356 a.u. esr = 0.29882 a.u. eself = 7.97885 a.u. pseudopotential energy = -3.09480 a.u. n-l pseudopotential energy = 0.19565 a.u. exchange-correlation energy = -3.17201 a.u. average potential = -0.02336 a.u. eigenvalues at k-point: 0.000 0.000 0.000 -16.96 -9.38 -9.38 -9.38 -0.55 0.83 0.88 0.89 0.89 1.04 1.06 1.81 1.97 2.09 2.21 2.23 2.24 2.34 2.38 2.44 Ver 3.0 ================================================= total energy = -4.07598 Hartree a.u. kinetic energy = 9.33894 Hartree a.u. electrostatic energy = -7.34357 Hartree a.u. esr = 0.29882 Hartree a.u. eself = 7.97885 Hartree a.u. pseudopotential energy = -3.09481 Hartree a.u. n-l pseudopotential energy = 0.19548 Hartree a.u. exchange-correlation energy = -3.17202 Hartree a.u. average potential = 0.00000 Hartree a.u. Eigenvalues (eV), kp = 1 , spin = 1 -16.96 -9.38 -9.38 -9.38 -0.55 0.80 0.88 0.89 0.89 1.03 1.05 1.81 1.97 2.09 2.18 2.21 2.22 2.31 2.35 2.42 ======================================================== Is there any significant change from 2.0 to 3.0 ? I'd really appreciate if anyone can give me some advice about which subroutines I should look at. Young-Su Lee P.S.* Two minor bugs 1. subroutine read_rho_xml in Modules/xml_io_base.f90 The following two lines should go before IF( kowner(k) == mpime ) THEN statement IF ( kowner( k ) /= ionode_id ) & CALL mp_put( rho_plane, rho_plane, mpime, ionode_id, kowner(k), k ) 2. subroutine vofrho in CPV/cplib.f90 The variable "vave" should be from module energies. It's locally defined now and average potential is always zero in output. From giannozz at nest.sns.it Thu Dec 22 16:42:18 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 22 Dec 2005 16:42:18 +0100 Subject: [Pw_forum] calculation = "nscf" with CP In-Reply-To: <43A9E983.6000600@mit.edu> References: <43A9E983.6000600@mit.edu> Message-ID: <200512221642.18717.giannozz@nest.sns.it> On Thursday 22 December 2005 00:47, Young-Su Lee wrote: > What worries me is that the results from two versions are different. > The occupied 4 states are fine and eigenvalues are the same as those > from self-consistent calculations in both cases. > > Ver 2.0 ================================================ > > total energy = -4.06675 a.u. > [...] > Ver 3.0 ================================================= > > total energy = -4.07598 Hartree a.u. > [..] > Is there any significant change from 2.0 to 3.0 ? there are many, but hopefully none that changes the results from good to bad! One change that may slightly affect the results is the way pseudopotentials are interpolated. Try to reduce the value of the parameter "refg", controlling the accuracy of the interpolation, in namelist &control from its default value 0.05. You should be able to find the same results that you find by setting tpstab=.false. (no interpolation) in file CPV/pseudopot.f90 Thank you for the minor bugs 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 lee0su at MIT.EDU Fri Dec 23 00:09:04 2005 From: lee0su at MIT.EDU (Young-Su Lee) Date: Thu, 22 Dec 2005 18:09:04 -0500 Subject: [Pw_forum] calculation = "nscf" with CP In-Reply-To: <43AB2C55.60908@mit.edu> References: <43AB2C55.60908@mit.edu> Message-ID: <43AB3210.4030202@mit.edu> Thank you for the suggestions. I set tpstab=.false. and set refg and mmx to be identical to ver 2.0, but it doesn't help. Even in the case of self-consistent calculation, average potential is quite different while all other values are almost the same. Inside the subroutine vofrho after CALL exch_corr_h(nspin,rhog,rhor,rhoc,sfac,exc,dxc) sum of the elements of rhor is different. I'm using C.pbe-rrkjus.UPF and H.pbe-rrkjus.UPF. ver 2.0 ========================================== total energy = -8.07495 a.u. kinetic energy = 5.42399 a.u. electrostatic energy = -7.34356 a.u. esr = 0.29882 a.u. eself = 7.97885 a.u. pseudopotential energy = -3.09480 a.u. n-l pseudopotential energy = 0.11144 a.u. exchange-correlation energy = -3.17201 a.u. average potential = -0.02336 a.u. eigenvalues at k-point: 0.000 0.000 0.000 -16.96 -9.38 -9.38 -9.38 ver 3.0 ========================================== total energy = -8.07495 Hartree a.u. kinetic energy = 5.42401 Hartree a.u. electrostatic energy = -7.34357 Hartree a.u. esr = 0.29882 Hartree a.u. eself = 7.97885 Hartree a.u. pseudopotential energy = -3.09481 Hartree a.u. n-l pseudopotential energy = 0.11143 Hartree a.u. exchange-correlation energy = -3.17202 Hartree a.u. average potential = -0.02397 Hartree a.u. Eigenvalues (eV), kp = 1 , spin = 1 -16.96 -9.38 -9.38 -9.38 >there are many, but hopefully none that changes the results from >good to bad! One change that may slightly affect the results is the >way pseudopotentials are interpolated. Try to reduce the value of >the parameter "refg", controlling the accuracy of the interpolation, >in namelist &control from its default value 0.05. You should be able >to find the same results that you find by setting tpstab=.false. (no >interpolation) in file CPV/pseudopot.f90 > >Thank you for the minor bugs > >Paolo > > > From giannozz at nest.sns.it Fri Dec 23 16:26:23 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Fri, 23 Dec 2005 16:26:23 +0100 Subject: [Pw_forum] calculation = "nscf" with CP In-Reply-To: <43AB3210.4030202@mit.edu> References: <43AB2C55.60908@mit.edu> <43AB3210.4030202@mit.edu> Message-ID: <200512231626.23436.giannozz@nest.sns.it> On Friday 23 December 2005 00:09, Young-Su Lee wrote: > ver 2.0 ========================================== > total energy = -8.07495 a.u. > [...] > ver 3.0 ========================================== > total energy = -8.07495 Hartree a.u. I don't really see a problem here. The error on the total energy is a quadratic function of the error on the charge density. This is not true for the single pieces composing the total energy, so the latter will be more sensitive than the total energy to lack of self-consistency. The average potential, in particular, is very sensitive to errors because gradient-corrected functionals have a nasty numerical behavior for \rho=>0 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 pwscfklt at gmail.com Fri Dec 23 17:30:36 2005 From: pwscfklt at gmail.com (Konzern) Date: Fri, 23 Dec 2005 11:30:36 -0500 Subject: [Pw_forum] convergence of pw.x Message-ID: Hi everyone, Merry Christmas and Happy New Year to you. But I have a problem. I am using pwscf (version 2.1.5) to calculate the phonon of a slab. In the scf calculations, I set the parameter of conv_thr as 1.0d-12, and so in the nscf where calculation='phonon'. The scf converged successfully, while the nscf just could not converge, there was always some " xx eigenvalues not converged." So I have to increase the conv_thr of nscf run to 1.0d-10 or so, and this time, it could converge finally, although there was still some "yy eigenvalues not converged" ( yy=1 or 2) duing the calculation. I don't know what is wrong with this. In my expectation, the nscf should be able to converge easily based on the previous scf run, at least, to the save accuracy level. Could you tell to what extent will this affect the resultant frequencies? i.e., can I still believe in the resultant frequencies? The threshhold I used in ph.x is 1.0d-14; I tried to use conv_thr=1.0d-10 in both scf and nscf while tr2_ph=1.0d-12 in ph.x, the resultant frequencies were "wrong" ( too many imaginary ones). Thanks. Konzern -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20051223/9985e9ef/attachment.htm From giannozz at nest.sns.it Sat Dec 24 11:13:47 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 24 Dec 2005 11:13:47 +0100 Subject: [Pw_forum] convergence of pw.x In-Reply-To: References: Message-ID: <200512241113.47074.giannozz@nest.sns.it> On Friday 23 December 2005 17:30, Konzern wrote: > In the scf calculations, I set the parameter of conv_thr as 1.0d-12 this is very small. Typical values are 1.0d-6 to 1.0d-8. This number is an estimate for the self-consistency error on the energy. Note that the threshold for the phonon calculation is a different quantity (average error on the potential or something like this) > while the nscf just could not converge, there was always some > " xx eigenvalues not converged." as long as xx is small, it shouldn't be such a big deal, especially if you have empty states (these are the state that tend to converge more slowly) > The threshhold I used in ph.x is 1.0d-14; I tried to use conv_thr=1.0d-10 in > both scf and nscf while tr2_ph=1.0d-12 in ph.x, the resultant frequencies > were "wrong" ( too many imaginary ones). if you change all convergence parameters at the same time, it is impossible to understand which are relevant and which are not. 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 hplan at pku.edu.cn Sat Dec 24 12:28:46 2005 From: hplan at pku.edu.cn (Hai-Ping Lan) Date: Sat, 24 Dec 2005 19:28:46 +0800 Subject: [Pw_forum] about phonon calculations Message-ID: <200512241928464948382@pku.edu.cn> Dear Colleagues : I have compiled ESPRESSO 2.1.5 package in AMD operon workstations. But i cannot perform phonon calculations parallelly. Would anyone else have happened to this problem? ????????Hai-Ping Lan ????????hplan at pku.edu.cn ??????????2005-12-24 From leoant21 at hotmail.com Sun Dec 25 11:01:37 2005 From: leoant21 at hotmail.com (=?gb2312?B?1cUguumx8g==?=) Date: Sun, 25 Dec 2005 10:01:37 +0000 Subject: [Pw_forum] Question on calculation on LiNiO2 Message-ID: Dear all, Now I am doing some calculation on LiNiO2, the scf calculation has been completed, but when I try to do band and dos calculation, there are some problems as follow(appear in both band and dos calculations): %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from efermit: error # 1 unexpected error %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% stopping... Please help me and give me some possible solution. Best regards. Hongbin Zhang _________________________________________________________________ ?????????????? MSN Messenger: http://messenger.msn.com/cn From vdiep at ictp.it Sun Dec 25 17:43:45 2005 From: vdiep at ictp.it (Diep Vinh Quang) Date: Sun, 25 Dec 2005 17:43:45 +0100 (CET) Subject: [Pw_forum] Single Chain of molecule In-Reply-To: References: <20051204063509.9826.41228.Mailman@democritos.sissa.it> Message-ID: <33022.10.38.44.221.1135529025.squirrel@webmail3.ictp.trieste.it> Dear Pwscf users, Could you please tell me what is the value of "ibrav" for one dimensional system? For example, I would like to calculate the band structure of a chain of Polyethylene C2H4. I can constructe the position of the atoms but I don't know how to declare the bravais lattice. Any helps are appricated. Bests Vinh Ps. Ex ATOMIC_POSITIONS {angstrom} C -0.6295585950 -0.4167504952 0 H 0.0115649288 -1.048383796 0 H -1.270682119 -1.048383796 0 C 0.6295585950 0.4167504952 0 H -0.0115649288 1.048383796 0 H 1.270682119 1.048383796 0 From akohlmey at vitae.cmm.upenn.edu Sun Dec 25 19:29:27 2005 From: akohlmey at vitae.cmm.upenn.edu (Axel Kohlmeyer) Date: Sun, 25 Dec 2005 13:29:27 -0500 (EST) Subject: [Pw_forum] Single Chain of molecule In-Reply-To: <33022.10.38.44.221.1135529025.squirrel@webmail3.ictp.trieste.it> Message-ID: On Sun, 25 Dec 2005, Diep Vinh Quang wrote: VQ> Dear Pwscf users, dear vinh, VQ> Could you please tell me what is the value of "ibrav" for one dimensional system? there is none. with a code like pwscf, you always have a system that is periodic in three dimension. VQ> For example, I would like to calculate the band structure of a chain of Polyethylene VQ> C2H4. I can constructe the position of the atoms but I don't know how to declare the VQ> bravais lattice. your best shot is probably using a large enough orthorhombic supercell, e.g. ibrav=8, a=2.5182343800, b=10.0, c=10.0 you have to make sure that b and c are large enough, so that the periodic images do not influence each other. since your system is pretty non-polar this should work well. regards, axel. VQ> VQ> Any helps are appricated. VQ> VQ> Bests VQ> VQ> Vinh VQ> Ps. Ex ATOMIC_POSITIONS {angstrom} VQ> C -0.6295585950 -0.4167504952 0 VQ> H 0.0115649288 -1.048383796 0 VQ> H -1.270682119 -1.048383796 0 VQ> C 0.6295585950 0.4167504952 0 VQ> H -0.0115649288 1.048383796 0 VQ> H 1.270682119 1.048383796 0 VQ> VQ> _______________________________________________ VQ> Pw_forum mailing list VQ> Pw_forum at pwscf.org VQ> http://www.democritos.it/mailman/listinfo/pw_forum VQ> -- ======================================================================= Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From giannozz at nest.sns.it Wed Dec 28 17:34:08 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Wed, 28 Dec 2005 17:34:08 +0100 Subject: [Pw_forum] Question on calculation on LiNiO2 In-Reply-To: References: Message-ID: <200512281734.08953.giannozz@nest.sns.it> On Sunday 25 December 2005 11:01, ? ?? wrote: > Now I am doing some calculation on LiNiO2, the scf calculation has been > completed, but when I try to do band and dos calculation, there are some > problems as follow(appear in both band and dos calculations): >[..] > from efermit: error # 1 > unexpected error This is (sort of) explained in the users' guide: ============================= Possible reasons: - serious error in data, such as bad number of electrons, insufficient number of bands, absurd value of broadening (efermig), or too few tetrahedra (efermit); - [...] ============================= You should use tetrahedra only together with uniform grids (i.e. automatic k-points), not when calculating selected directions in the k-space. 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 proffess at yandex.ru Thu Dec 29 02:04:07 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Thu, 29 Dec 2005 04:04:07 +0300 (MSK) Subject: [Pw_forum] pwscf code on CRAY-X1 Message-ID: <43B33607.000003.02812@ariel.yandex.ru> Dear all, Does anybode compile espresso code (3.0) on Cray-X1 machine? I tried to do it but the compilation was failed with some routines from iotk. It seems it is because in iotk_config.h file there are no any definitions for Cray machine. Also configure define some flags "D__X1 -D__X1_COA", but they are absent in any source files. Also, the configure does not print -D__T3E flag - currently used for Cray machines. Any hints and suggestins are higly appreciated. Thanks, Sergey Total errors detected in iotk_fmt.f90: 1 ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -e Z -F -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_fmt.F90 -o iotk_fmt.o cpp -P -C -traditional -D__X1 -D__X1_COA -D__T3E -D__FFTW -D__USE_INTERNAL_FFTW -I../include iotk_misc.f90 -o iotk_misc.F90 CC-11 cpp: ERROR File = /tmp/sergey/PWSCF/espresso-3.0/iotk/src/../include/iotk_config.h, Line = 84 The indicated directive is not a recognized preprocessing directive. #warn unknown architecture, please add to iotk_config.h ^ Total errors detected in iotk_misc.f90: 1 ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -e Z -F -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_misc.F90 -o iotk_misc.o string = "logical(kind="//trim(iotk_itoa(__IOTK_LOGICAL1))//")" ^ ftn-1725 ftn: ERROR IOTK_PRINT_KINDS_X, File = iotk_misc.F90, Line = 325, Column = 44 Unexpected syntax while parsing the assignment statement : "operand" was expected but found "_". string = "integer(kind="//trim(iotk_itoa(__IOTK_INTEGER1))//")" ^ ftn-1725 ftn: ERROR IOTK_PRINT_KINDS_X, File = iotk_misc.F90, Line = 327, Column = 44 Unexpected syntax while parsing the assignment statement : "operand" was expected but found "_". string = "real(kind="//trim(iotk_itoa(__IOTK_REAL1))//")" ^ ftn-1725 ftn: ERROR IOTK_PRINT_KINDS_X, File = iotk_misc.F90, Line = 329, Column = 41 Unexpected syntax while parsing the assignment statement : "operand" was expected but found "_". string = "character(kind="//trim(iotk_itoa(__IOTK_CHARACTER1))//")" ^ ftn-1725 ftn: ERROR IOTK_PRINT_KINDS_X, File = iotk_misc.F90, Line = 331, Column = 46 Unexpected syntax while parsing the assignment statement : "operand" was expected but found "_". Cray Fortran: Version 5.4.0.0 (u5016f94044i30086p54142a54005e54004x9403) Cray Fortran: Wed Dec 28, 2005 15:57:25 Cray Fortran: Compile time: 3.2700 seconds Cray Fortran: 824 source lines Cray Fortran: 4 errors, 0 warnings, 0 other messages, 0 ansi Cray Fortran: "explain ftn-message number" gives more information about each message *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) From cjtan at OptimaNumerics.com Thu Dec 29 08:24:24 2005 From: cjtan at OptimaNumerics.com (C J Kenneth Tan -- OptimaNumerics) Date: Thu, 29 Dec 2005 07:24:24 +0000 (UTC) Subject: [Pw_forum] pwscf code on CRAY-X1 In-Reply-To: <43B33607.000003.02812@ariel.yandex.ru> References: <43B33607.000003.02812@ariel.yandex.ru> Message-ID: Sergey, I don't have the answers that you are looking for, but I see that the T3E is an MPP machine while the X1 is a vector machine. Kenneth Tan ----------------------------------------------------------------------- C J Kenneth Tan, PhD OptimaNumerics Ltd Telephone: +44 798 941 7838 E-mail: cjtan at OptimaNumerics.com Telephone: +44 207 099 4428 Web: http://www.OptimaNumerics.com Facsimile: +44 207 100 4572 ----------------------------------------------------------------------- On 2005-12-29 04:04 +0300 Sergey Lisenkov (proffess at yandex.ru) wrote: > Date: Thu, 29 Dec 2005 04:04:07 +0300 (MSK) > From: Sergey Lisenkov > Reply-To: pw_forum at pwscf.org > To: pw_forum at pwscf.org > Subject: [Pw_forum] pwscf code on CRAY-X1 > > Dear all, > > Does anybode compile espresso code (3.0) on Cray-X1 machine? I tried to do it but the compilation was failed with some routines from iotk. It seems it is because in iotk_config.h file there are no any definitions for Cray machine. Also configure define some flags "D__X1 -D__X1_COA", but they are absent in any source files. Also, the configure does not print -D__T3E flag - currently used for Cray machines. > > Any hints and suggestins are higly appreciated. > > Thanks, > Sergey > > Total errors detected in iotk_fmt.f90: 1 > ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -e Z -F -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_fmt.F90 -o iotk_fmt.o > cpp -P -C -traditional -D__X1 -D__X1_COA -D__T3E -D__FFTW -D__USE_INTERNAL_FFTW -I../include iotk_misc.f90 -o iotk_misc.F90 > CC-11 cpp: ERROR File = /tmp/sergey/PWSCF/espresso-3.0/iotk/src/../include/iotk_config.h, Line = 84 > The indicated directive is not a recognized preprocessing directive. > > #warn unknown architecture, please add to iotk_config.h > ^ > > Total errors detected in iotk_misc.f90: 1 > ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -e Z -F -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_misc.F90 -o iotk_misc.o > > string = "logical(kind="//trim(iotk_itoa(__IOTK_LOGICAL1))//")" > ^ > ftn-1725 ftn: ERROR IOTK_PRINT_KINDS_X, File = iotk_misc.F90, Line = 325, Column = 44 > Unexpected syntax while parsing the assignment statement : "operand" was expected but found "_". > > string = "integer(kind="//trim(iotk_itoa(__IOTK_INTEGER1))//")" > ^ > ftn-1725 ftn: ERROR IOTK_PRINT_KINDS_X, File = iotk_misc.F90, Line = 327, Column = 44 > Unexpected syntax while parsing the assignment statement : "operand" was expected but found "_". > > string = "real(kind="//trim(iotk_itoa(__IOTK_REAL1))//")" > ^ > ftn-1725 ftn: ERROR IOTK_PRINT_KINDS_X, File = iotk_misc.F90, Line = 329, Column = 41 > Unexpected syntax while parsing the assignment statement : "operand" was expected but found "_". > > string = "character(kind="//trim(iotk_itoa(__IOTK_CHARACTER1))//")" > ^ > ftn-1725 ftn: ERROR IOTK_PRINT_KINDS_X, File = iotk_misc.F90, Line = 331, Column = 46 > Unexpected syntax while parsing the assignment statement : "operand" was expected but found "_". > > Cray Fortran: Version 5.4.0.0 (u5016f94044i30086p54142a54005e54004x9403) > Cray Fortran: Wed Dec 28, 2005 15:57:25 > Cray Fortran: Compile time: 3.2700 seconds > Cray Fortran: 824 source lines > Cray Fortran: 4 errors, 0 warnings, 0 other messages, 0 ansi > Cray Fortran: "explain ftn-message number" gives more information about each message > *** Error code 1 (bu21) > *** Error code 1 (bu21) > *** Error code 1 (bu21) > _______________________________________________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > From giannozz at nest.sns.it Thu Dec 29 10:45:26 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Thu, 29 Dec 2005 10:45:26 +0100 Subject: [Pw_forum] pwscf code on CRAY-X1 In-Reply-To: <43B33607.000003.02812@ariel.yandex.ru> References: <43B33607.000003.02812@ariel.yandex.ru> Message-ID: <200512291045.26619.giannozz@nest.sns.it> On Thursday 29 December 2005 02:04, Sergey Lisenkov wrote: > Does anybody compile espresso code (3.0) on Cray-X1 machine? > I tried to do it but the compilation was failed with some routines > from iotk. It seems it is because in iotk_config.h file there are no > any definitions for Cray machine. try to replace iotk/include/iotk_config.h with the attached version. It should work for any (non-buggy) compiler, but it was never tested > Also configure define some flags "D__X1 -D__X1_COA", but they are > absent in any source files. they shouldn't be there, but they are harmless anyway > Also, the configure does not print -D__T3E flag T3E was a completely different - and by now extinct, I guess - machine 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: iotk_config.h Type: text/x-chdr Size: 2413 bytes Desc: not available Url : /pipermail/attachments/20051229/b8fee77d/attachment.h From proffess at yandex.ru Fri Dec 30 00:43:05 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Fri, 30 Dec 2005 02:43:05 +0300 (MSK) Subject: [Pw_forum] pwscf code on CRAY-X1 In-Reply-To: <200512291045.26619.giannozz@nest.sns.it> References: <43B33607.000003.02812@ariel.yandex.ru> <200512291045.26619.giannozz@nest.sns.it> Message-ID: <43B47489.000006.18234@webmail12.yandex.ru> Dear Paolo, >try to replace iotk/include/iotk_config.h with the attached version. >It should work for any (non-buggy) compiler, but it was never tested So, it seems, we have buggy compiler, because it doesn't work with the same error message in the same file. Sergey From proffess at yandex.ru Fri Dec 30 02:48:54 2005 From: proffess at yandex.ru (Sergey Lisenkov) Date: Fri, 30 Dec 2005 04:48:54 +0300 (MSK) Subject: [Pw_forum] pwscf code on CRAY-X1 In-Reply-To: <200512291045.26619.giannozz@nest.sns.it> References: <43B33607.000003.02812@ariel.yandex.ru> <200512291045.26619.giannozz@nest.sns.it> Message-ID: <43B49206.000004.23769@webmail12.yandex.ru> Dear all, I have reached a little bit of proggress in compiling after playing with "cpp" options. But the compilation was stopped again with the error in another file: ... cpp -N -P -C -D__FFTW -D__USE_INTERNAL_FFTW -I../include iotk_files_interf.f90 -o iotk_files_interf.F90 ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_files_interf.F90 -o iotk_files_interf.o cpp -N -P -C -D__FFTW -D__USE_INTERNAL_FFTW -I../include iotk_files.f90 -o iotk_files.F90 ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_files.F90 -o iotk_files.o cpp -N -P -C -D__FFTW -D__USE_INTERNAL_FFTW -I../include iotk_fmt.f90 -o iotk_fmt.F90 ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_fmt.F90 -o iotk_fmt.o cpp -N -P -C -D__FFTW -D__USE_INTERNAL_FFTW -I../include iotk_misc.f90 -o iotk_misc.F90 ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_misc.F90 -o iotk_misc.o cpp -N -P -C -D__FFTW -D__USE_INTERNAL_FFTW -I../include iotk_module.f90 -o iotk_module.F90 ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_module.F90 -o iotk_module.o cpp -N -P -C -D__FFTW -D__USE_INTERNAL_FFTW -I../include iotk_scan.f90 -o iotk_scan.F90 ftn -s default64 -dp -rma -e0 -O scalar3,stream3,vector3,nointerchange -Z -O inline5 -D__FFTW -D__USE_INTERNAL_FFTW -I../include -I. -I../Modules -I../PW -I../PH -I../iotk/src -c iotk_scan.F90 -o iotk_scan.o control = modulo(header,iotk_ncontrol+1) ^ ftn-774 ftn: ERROR IOTK_SCAN_TAG_X, File = iotk_scan.F90, Line = 501, Column = 17 Improper intrinsic argument type or inconsistent types. Cray Fortran: Version 5.4.0.0 (u5016f94044i30086p54142a54005e54004x9403) Cray Fortran: Thu Dec 29, 2005 16:47:16 Cray Fortran: Compile time: 3.3100 seconds Cray Fortran: 922 source lines Cray Fortran: 1 errors, 0 warnings, 0 other messages, 0 ansi Cray Fortran: "explain ftn-message number" gives more information about each message *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) I looked at source code (from iotk) and see that there is no definitions of "modulo". I looked at cray documentation and found only this one: modulo(3i) NAME MODULO -- Modulo function SYNOPSIS MODULO ([A=]a, [P=]p) IMPLEMENTATION UNICOS/mp Cray Fortran STANDARDS Fortran DESCRIPTION The MODULO function returns the remainder of a divided by p using modulo math. The result always has the sign of the modulo base, p. This function accepts the following arguments: a Must be of type integer or real p Must be of the same type and kind type parameter as a MODULO is an elemental function. The name of this intrinsic cannot be passed as an argument. RETURN VALUES The result type and type parameter are the same as a. When a is of type integer, if p is not equal to zero, MODULO (a, p) has the value r such that a = q * p + r, where q is an integer. The inequality 0 <= r < p holds if p > 0, and p < r <= 0 holds if p < 0. If p = 0, the result is 0. When a is of type real, if p is not equal to zero, the value of the result is a - FLOOR (a / p) * p. The result can be a NaN when that value is available. Is that the code needs? Thanks, Sergey From ferretti.andrea at unimore.it Fri Dec 30 12:28:09 2005 From: ferretti.andrea at unimore.it (Andrea Ferretti) Date: Fri, 30 Dec 2005 12:28:09 +0100 (CET) Subject: [Pw_forum] pwscf code on CRAY-X1 In-Reply-To: <43B49206.000004.23769@webmail12.yandex.ru> References: <43B33607.000003.02812@ariel.yandex.ru> <200512291045.26619.giannozz@nest.sns.it> <43B49206.000004.23769@webmail12.yandex.ru> Message-ID: Hi, On Fri, 30 Dec 2005, Sergey Lisenkov wrote: > control = modulo(header,iotk_ncontrol+1) > ^ > ftn-774 ftn: ERROR IOTK_SCAN_TAG_X, File = iotk_scan.F90, Line = 501, Column = 17 > Improper intrinsic argument type or inconsistent types. > It seems that the compiler complains due to a kind mismatch among the two integer arguments of the function MODULO: header is defined as (iotk_scan.f90 and iotk_base.f90 ) integer ( __IOTK_HEADER_KIND ) :: header where, from iotk_auxmacros.h #ifndef __IOTK_HEADER_KIND # define __IOTK_HEADER_KIND selected_int_kind(8) #endif iotk_ncontrol+1 is instead a default integer (iotk_base.f90) In std fortran 90, shouldn't the MODULO function be able to implicitly convert among kinds ?? or is it an extension to the std ?? anyway, if this is the problem, I guess some shorter integer exists on this machine, causing __IOTK_HEADER_KIND to be different from default... a quick and dirty fix may be changing __IOTK_HEADER_KIND to the default in iotk_auxmacros.h: #ifndef __IOTK_HEADER_KIND # define __IOTK_HEADER_KIND kind(1) #endif I am not so sure this is the problem (but it should be easy to check), and if it is, I am not sure other troubles are not coming up due to the kind modification... hope it helps 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 Please, if possible, don't send me MS Word or PowerPoint attachments Why? See: http://www.gnu.org/philosophy/no-word-attachments.html From hqzhou at nju.edu.cn Sat Dec 31 04:59:07 2005 From: hqzhou at nju.edu.cn (Huiqun Zhou) Date: Sat, 31 Dec 2005 11:59:07 +0800 Subject: [Pw_forum] About neb and smd Message-ID: <005401c60dbe$8d1f1690$1d00a8c0@solarflare> Dear list-users, Could anyone give me a pointer whether it's theoretically reasonable to investigate solid state transition induced by pressure using NEB or string method? Any references are appreciated. Happy New Year! Huiqun Zhou -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20051231/eb9997e8/attachment.htm From yuwen_66 at yahoo.com Sat Dec 31 06:11:20 2005 From: yuwen_66 at yahoo.com (W. YU) Date: Fri, 30 Dec 2005 21:11:20 -0800 (PST) Subject: [Pw_forum] alkali metal pseudopotentials Message-ID: <20051231051120.65709.qmail@web51006.mail.yahoo.com> Dear PW users, Happy and brighter new year! I have some problmes on using the alkali pseudopotentials; 1. Has anybody know any real system usage of the pseudopotenals of Li, Na, and K (both LDA and GGA) provided by the PW web? 2. I did some calculations on alkali hydrides such as LiH and NaH. For LiH, the LDA using Von Barth and Car scheme give a much smaller lattice constant while GGA using uspp and a ld1-generated TM type Norm-conserving LDA pseudopotential or the LDA pseudopotential converted from FHI format give much larger lattice constants than the experimental result. Bearing in mind the small mass of this system, the vibrating energy should play an important role and the theoretical LDA lattice constant would be much smaller. For NaH system, the VBC LDA gives a lattice constant very close to the experimental one and the GGA gives larger lattice constant. When the vibrating effect (Zero point energy and temperature effect) is taken into account, the resulting lattice constant is much larger than the experiment. While a full-potential calculation with both LDA and GGA give much smaller lattice constants for both LiH and NaH than experimental ones. Now it seems that the calculations using pseudopotentials cannot give systematic results for LiH and NaH even with VBC norm-conserving pseudopotentials---that is, a much smaller zero-temperature lattice constant with a major improvement when the zero-point energy is included, but still less than or just close to the experimental one. (Note, the none-linear-core corrections are used on all alkali atom pseudopotentials). In this case, can I still trust the pseudopotential of Li and/or Na? thanks a lot! W. YU __________________________________________ Yahoo! DSL ? Something to write home about. Just $16.99/mo. or less. dsl.yahoo.com From liyanpcl at yahoo.com.cn Sat Dec 31 14:31:56 2005 From: liyanpcl at yahoo.com.cn (li yan) Date: Sat, 31 Dec 2005 21:31:56 +0800 (CST) Subject: [Pw_forum] questions about the ph.x Message-ID: <20051231133156.80486.qmail@web15609.mail.cnb.yahoo.com> dear all, i am calculating the phonon frequency of an X-point for AgI. both the scf and nscf parts are completed, but there is an erorr in the file agi.ph.out, that is %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% from read_namelists : error # 1 reading namelist control %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% the iput codes about the agi.ph.in is cat > agi.ph.in << EOF phonon of AgI except Gamma &inputph tr2_ph=1.0d-16, prefix='agi', amass(1)=107.87, amass(2)=126.90, outdir='$TMP_DIR/', fildyn='dyn.$ic', / 0.2500000 0.1443376 0.0000000 EOF $PARA_PREFIX $PW_ROOT/bin/pw.x $PARA_POSTFIX < agi.ph.in >agi.ph.out would you please tell me the reason for this case? best regards __________________________________________________ ??????????????? http://cn.mail.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: /pipermail/attachments/20051231/b8982ebe/attachment.htm From giannozz at nest.sns.it Sat Dec 31 15:40:59 2005 From: giannozz at nest.sns.it (Paolo Giannozzi) Date: Sat, 31 Dec 2005 15:40:59 +0100 Subject: [Pw_forum] questions about the ph.x In-Reply-To: <20051231133156.80486.qmail@web15609.mail.cnb.yahoo.com> References: <20051231133156.80486.qmail@web15609.mail.cnb.yahoo.com> Message-ID: <200512311540.59214.giannozz@nest.sns.it> On Saturday 31 December 2005 14:31, li yan wrote: > $PARA_PREFIX $PW_ROOT/bin/pw.x $PARA_POSTFIX < agi.ph.in >agi.ph.out the name of the executable for phonon calculations is ph.x 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 akohlmey at cmm.upenn.edu Sat Dec 31 23:15:49 2005 From: akohlmey at cmm.upenn.edu (Axel Kohlmeyer) Date: Sat, 31 Dec 2005 17:15:49 -0500 (EST) Subject: [Pw_forum] alkali metal pseudopotentials In-Reply-To: <20051231051120.65709.qmail@web51006.mail.yahoo.com> References: <20051231051120.65709.qmail@web51006.mail.yahoo.com> Message-ID: On Fri, 30 Dec 2005, W. YU wrote: > Dear PW users, dear w. yu, > Happy and brighter new year! > > I have some problmes on using the alkali > pseudopotentials; > > 1. Has anybody know any real system usage of the > pseudopotenals of Li, Na, and K (both LDA and GGA) > provided by the PW web? some papers are actually mentioned in the details section of the webpages, and the vanderbilt uspps are also posted on the vanderbilt website and have been used in different codes as well. > 2. I did some calculations on alkali hydrides such as > LiH and NaH. For LiH, the LDA using Von Barth and Car > scheme give a much smaller lattice constant while GGA > using uspp and a ld1-generated TM type Norm-conserving there are several points to consider here: LDA functionals in general are known for overbinding, as are GGA for underbinding. the difference from the experimental lattice constant can be easily 5% or even more. some people claim, that using LDA at the experimental lattice constant gives the most consistent results for (pure) alkali metals. binary compounds (and beyond) are - of course - more tricky. using pseudopotentials with only one valence electron for (partially) ionic compounds, is tricky as well. i would suggest comparing to a 'semi-core' (or in the case of Li all-electron) pseudopotential. > LDA pseudopotential or the LDA pseudopotential > converted from FHI format give much larger lattice > constants than the experimental result. Bearing in last time i checked, the FHI converter did not support NLCC, so that potential may be totally bogus. please recheck. > mind the small mass of this system, the vibrating > energy should play an important role and the > theoretical LDA lattice constant would be much > smaller. For NaH system, the VBC LDA gives a lattice > constant very close to the experimental one and the > GGA gives larger lattice constant. When the vibrating > effect (Zero point energy and temperature effect) is > taken into account, the resulting lattice constant is > much larger than the experiment. While a > full-potential calculation with both LDA and GGA gives can you please elabotrate, what you mean be 'full-potential' calculation. > much smaller lattice constants for both LiH and NaH > than experimental ones. Now it seems that the > calculations using pseudopotentials cannot give > systematic results for LiH and NaH even with VBC > norm-conserving pseudopotentials---that is, a much > smaller zero-temperature lattice constant with a major > improvement when the zero-point energy is included, > but still less than or just close to the experimental > one. > > (Note, the none-linear-core corrections are used on > all alkali atom pseudopotentials). > > In this case, can I still trust the pseudopotential of > Li and/or Na? i have tested zv=3 pseudopotentials for Li (LDA and several GGAs) vanderbilt uspps and troullier-martins nc and less well tested Na semi-core potentials (also uspps and nc) and matching hydrogen PPs. you probably will have to test them for your system as well, but give me a holler if you are interested. axel. > > thanks a lot! > > W. YU > > ======================================================================= Axel Kohlmeyer e-mail: akohlmey at cmm.upenn.edu, tel: ++1-215-898-1582 Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.