[Pw_forum] "Too many g vector" error in vc-relax
Hi, I am attempting to optimize unit cell for a H2MnO4 compound using vc-relax in ase-espresso. I have got the following strange error: "too many g-vectors" I have used a e-cut of 45 Ry. I think this error has some thing to do with the e-cut. During cell relaxation, it seems that the size of the cell changes significantly by ~10 Angstrom^3. The have taken a cell_factor of 5,much larger than the default value, i.e.,1.2. Any help will be appreciated, Best, Reza ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Documentation on atomic velocities
Dear Ilya, Thanks for your replies. Just to confirm I understood correctly, are the atomic velocities saved in the temporary files so that restarting with restart_mode='restart' will resume the dynamics continuously? And concerning my original questions, can the velocities be written to the ordinary output file using some undocumented option? Many thanks for the support to users. Time is gold and you give it away. I really appreciate it. Luis E. Gonzalez Universidad de Valladolid. On Tue, 21 Mar 2017, Ilya Ryabinkin wrote: > By the way, to resume an interrupted MD run you DON'T need > ATOMIC_VELOCITIES. They are useful only if you'd like to start (for > whatever reason) with a setup with non-zero *initial* velocities (like > I needed once). > > The right way is to use restart_mode = 'restart' with all temporary > files available from the previous (interrupted) step. > > The reason is simple: to restart Verlrt algorithm you need more than > initial velocities. > > > -- > I. > > On Tue, Mar 21, 2017 at 9:13 PM, Ilya Ryabinkin wrote: >> Dear Luis: >> Indeed, there is an undocumented option: pw.x reads the card >> ATOMIC_VELOCITIES once the option >> >> &IONS >>ion_velocities = 'from_input', >> / >> >> is provided. >> >> They are given in Ry/bohr, no other units are accepted. >> >> -- >> Ilya >> >> >> On Tue, Mar 21, 2017 at 6:53 PM, luisen >> wrote: >>> >>> Sorry for not being precise enough. I am using the MD calculation in pw.x >>> >>> Luis E. Gonzalez >>> Univ. de Valladolid >>> Spain. >>> >>> >>> On Tue, 21 Mar 2017, LEUNG Clarence wrote: >>> Dear Luis, Do you use the cpmd of cp.x or the md in pw.x? Thanks. Clarence City university of Hong Kong Original message From: luisen Date: 21/03/2017 20:42 (GMT+08:00) To: pw_forum@pwscf.org Subject: [Pw_forum] Documentation on atomic velocities Dear developers, I am interested in using atomic velocities generated in previous MD runs in order to continue the MD calculation after a finished job (finished either gracefully or abruptly). I made a small program to compute the velocities from the positions and modified slightly the code in order to read the velocities from a file upon initialization if this file was present. It is however an ad-hoc solution. I have seen in the last distribution (6.1) that there is the possibility of using a section in the input file named ATOMIC_VELOCITIES. My question is if there is any documentation for its use, and if there is any flag so as to output the velocities (in addition to positions) to the output file, for later use as input in a subsequent run. Yours, Luis Enrique Gonzalez Universidad de Valladolid ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >> >> >> >> -- >> *** >> Ilya Ryabinkin >> Postdoctoral Scholar >> Physical and Environmental Sciences >>University of Toronto Scarborough >> http://www.utsc.utoronto.ca/~aizmaylov/Members.html >> *** > > > > -- > *** >Ilya Ryabinkin > Postdoctoral Scholar > Physical and Environmental Sciences > University of Toronto Scarborough > http://www.utsc.utoronto.ca/~aizmaylov/Members.html > *** > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Band Structure related Query
I think there is some example on Si band structure, I do not know the file number etc. On Mar 22, 2017 11:14 AM, "Anindya Bose" wrote: > Dear Sir, > In quantum espresso, I want to see a band structure consisting of 6 > valence bands and 6 conduction bands only.What is the way to do it > directly.I will be waiting for the answer. > > Thanks and regards, > Anindya Bose > Research Fellow, > IIIT Allahabad > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Band Structure related Query
Dear Sir, In quantum espresso, I want to see a band structure consisting of 6 valence bands and 6 conduction bands only.What is the way to do it directly.I will be waiting for the answer. Thanks and regards, Anindya Bose Research Fellow, IIIT Allahabad ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Absolute energy values
Hi all, how do we get absolute energy values (HOMO, LUMO, Fermi) in QE? From what I understand the values in the output are relative values and not absolute. In VASP (other DFT based software) there is a formula for getting absolute values, is there any solution in QE also? -- Vipul S. Ghemud Ph.D. student. Dept of Physics, SPPU, Ganeshkhind, Pune- 411007. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Documentation on atomic velocities
By the way, to resume an interrupted MD run you DON'T need ATOMIC_VELOCITIES. They are useful only if you'd like to start (for whatever reason) with a setup with non-zero *initial* velocities (like I needed once). The right way is to use restart_mode = 'restart' with all temporary files available from the previous (interrupted) step. The reason is simple: to restart Verlrt algorithm you need more than initial velocities. -- I. On Tue, Mar 21, 2017 at 9:13 PM, Ilya Ryabinkin wrote: > Dear Luis: > Indeed, there is an undocumented option: pw.x reads the card > ATOMIC_VELOCITIES once the option > > &IONS >ion_velocities = 'from_input', > / > > is provided. > > They are given in Ry/bohr, no other units are accepted. > > -- > Ilya > > > On Tue, Mar 21, 2017 at 6:53 PM, luisen wrote: >> >> Sorry for not being precise enough. I am using the MD calculation in pw.x >> >> Luis E. Gonzalez >> Univ. de Valladolid >> Spain. >> >> >> On Tue, 21 Mar 2017, LEUNG Clarence wrote: >> >>> Dear Luis, >>> Do you use the cpmd of cp.x or the md in pw.x? >>> >>> Thanks. >>> >>> Clarence >>> City university of Hong Kong >>> >>> >>> Original message >>> From: luisen >>> Date: 21/03/2017 20:42 (GMT+08:00) >>> To: pw_forum@pwscf.org >>> Subject: [Pw_forum] Documentation on atomic velocities >>> >>> >>> Dear developers, >>> >>> I am interested in using atomic velocities generated in previous MD runs >>> in order to continue the MD calculation after a finished job (finished >>> either gracefully or abruptly). >>> I made a small program to compute the velocities from the positions and >>> modified slightly the code in order to read the velocities from a file >>> upon initialization if this file was present. It is however an ad-hoc >>> solution. >>> >>> I have seen in the last distribution (6.1) that there is the possibility >>> of using a section in the input file named ATOMIC_VELOCITIES. >>> >>> My question is if there is any documentation for its use, and if there >>> is any flag so as to output the velocities (in addition to positions) to >>> the output file, for later use as input in a subsequent run. >>> >>> Yours, >>> >>> Luis Enrique Gonzalez >>> Universidad de Valladolid >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > *** > Ilya Ryabinkin > Postdoctoral Scholar > Physical and Environmental Sciences >University of Toronto Scarborough > http://www.utsc.utoronto.ca/~aizmaylov/Members.html > *** -- *** Ilya Ryabinkin Postdoctoral Scholar Physical and Environmental Sciences University of Toronto Scarborough http://www.utsc.utoronto.ca/~aizmaylov/Members.html *** ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Documentation on atomic velocities
Dear Luis: Indeed, there is an undocumented option: pw.x reads the card ATOMIC_VELOCITIES once the option &IONS ion_velocities = 'from_input', / is provided. They are given in Ry/bohr, no other units are accepted. -- Ilya On Tue, Mar 21, 2017 at 6:53 PM, luisen wrote: > > Sorry for not being precise enough. I am using the MD calculation in pw.x > > Luis E. Gonzalez > Univ. de Valladolid > Spain. > > > On Tue, 21 Mar 2017, LEUNG Clarence wrote: > >> Dear Luis, >> Do you use the cpmd of cp.x or the md in pw.x? >> >> Thanks. >> >> Clarence >> City university of Hong Kong >> >> >> Original message >> From: luisen >> Date: 21/03/2017 20:42 (GMT+08:00) >> To: pw_forum@pwscf.org >> Subject: [Pw_forum] Documentation on atomic velocities >> >> >> Dear developers, >> >> I am interested in using atomic velocities generated in previous MD runs >> in order to continue the MD calculation after a finished job (finished >> either gracefully or abruptly). >> I made a small program to compute the velocities from the positions and >> modified slightly the code in order to read the velocities from a file >> upon initialization if this file was present. It is however an ad-hoc >> solution. >> >> I have seen in the last distribution (6.1) that there is the possibility >> of using a section in the input file named ATOMIC_VELOCITIES. >> >> My question is if there is any documentation for its use, and if there >> is any flag so as to output the velocities (in addition to positions) to >> the output file, for later use as input in a subsequent run. >> >> Yours, >> >> Luis Enrique Gonzalez >> Universidad de Valladolid >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- *** Ilya Ryabinkin Postdoctoral Scholar Physical and Environmental Sciences University of Toronto Scarborough http://www.utsc.utoronto.ca/~aizmaylov/Members.html *** ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Documentation on atomic velocities
Sorry for not being precise enough. I am using the MD calculation in pw.x Luis E. Gonzalez Univ. de Valladolid Spain. On Tue, 21 Mar 2017, LEUNG Clarence wrote: Dear Luis, Do you use the cpmd of cp.x or the md in pw.x? Thanks. Clarence City university of Hong Kong Original message From: luisen Date: 21/03/2017 20:42 (GMT+08:00) To: pw_forum@pwscf.org Subject: [Pw_forum] Documentation on atomic velocities Dear developers, I am interested in using atomic velocities generated in previous MD runs in order to continue the MD calculation after a finished job (finished either gracefully or abruptly). I made a small program to compute the velocities from the positions and modified slightly the code in order to read the velocities from a file upon initialization if this file was present. It is however an ad-hoc solution. I have seen in the last distribution (6.1) that there is the possibility of using a section in the input file named ATOMIC_VELOCITIES. My question is if there is any documentation for its use, and if there is any flag so as to output the velocities (in addition to positions) to the output file, for later use as input in a subsequent run. Yours, Luis Enrique Gonzalez Universidad de Valladolid ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Documentation on atomic velocities
Dear Luis, Do you use the cpmd of cp.x or the md in pw.x? Thanks. Clarence City university of Hong Kong Original message From: luisen Date: 21/03/2017 20:42 (GMT+08:00) To: pw_forum@pwscf.org Subject: [Pw_forum] Documentation on atomic velocities Dear developers, I am interested in using atomic velocities generated in previous MD runs in order to continue the MD calculation after a finished job (finished either gracefully or abruptly). I made a small program to compute the velocities from the positions and modified slightly the code in order to read the velocities from a file upon initialization if this file was present. It is however an ad-hoc solution. I have seen in the last distribution (6.1) that there is the possibility of using a section in the input file named ATOMIC_VELOCITIES. My question is if there is any documentation for its use, and if there is any flag so as to output the velocities (in addition to positions) to the output file, for later use as input in a subsequent run. Yours, Luis Enrique Gonzalez Universidad de Valladolid ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Documentation on atomic velocities
Dear developers, I am interested in using atomic velocities generated in previous MD runs in order to continue the MD calculation after a finished job (finished either gracefully or abruptly). I made a small program to compute the velocities from the positions and modified slightly the code in order to read the velocities from a file upon initialization if this file was present. It is however an ad-hoc solution. I have seen in the last distribution (6.1) that there is the possibility of using a section in the input file named ATOMIC_VELOCITIES. My question is if there is any documentation for its use, and if there is any flag so as to output the velocities (in addition to positions) to the output file, for later use as input in a subsequent run. Yours, Luis Enrique Gonzalez Universidad de Valladolid ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] NEB first_last_opt
Sorry, the only one *who* can think through it...:-) G. Quoting Aleksandra Oranskaia : > Hello dear QE users, > > I have a question regarding pre-optimization of starting and ending > points of NEB. > > Dealing with multi-scale simulation of a vacancy migration in a huge > supercell (say, 350-400 atoms), should one make a pre-optimization > of starting and ending points of a path? > > I tried both ways and came to the conclusion that pre-optimization > pushes the system away from the minimum energy path (leading to the > increased barriers), because pre-optimization implies too deep > restructuring towards deeper minimums rather than the local minimums > closest to the minimum energy pathway. > In my opinion it is more physical if a migration corresponds to a > minimum energy pathway AND minimum restructuring. > > If you would simulate vacancy migration in a huge supercell with NEB > optimization, would you optimize starting and ending points? Why? > > > Thanks in advance and hope to hear your opinions and reasonings, > > Regards, > Alex. > -- > > -- > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] NEB first_last_opt
Dear Aleksandra > I tried both ways and came to the conclusion that pre-optimization > pushes the system away from the minimum energy path (leading to the > increased barriers) This is indeed the expected behavior. If your first and last images were potential energy minimum configurations, even if local ones, the pre-optimization 'relax' calculations would let them unchanged, or almost unchanged because only in the case of high symmetry systems input coordinates are "exactly" in a local minimum. This implies that your first and last images are not potential energy minimum configurations, and the code correctly optimizes them, and this of course lowers the potential energy and raises the potential energy barrier connecting the two configurations. > In my opinion it is more physical if a migration corresponds to a > minimum energy pathway AND minimum restructuring. I'm not sure I understand this sentence. If you don't start from/end to a local minimum why do you gain more physical insight into your NEB simulation? If you want to drive your system through some intermediate local minimum which permits the lowering of the global barriers across the PES, you can use the intermediate_image feature. If in the end you find the same high barriers then three interpretations can be given: 1) your initial physical guess is wrong and in the "real" system vacancies do not exist/do not migrate; 2) The DFT level of theory used to perform the NEB calculation is not accurate and does not provide reliable numbers for transition states/barriers; 3) the migration occur through some redox process in which there is a change in the charge state of the defect which lowers the barrier. You are the only one that can think through this... HTH Giuseppe Quoting Aleksandra Oranskaia : > Hello dear QE users, > > I have a question regarding pre-optimization of starting and ending > points of NEB. > > Dealing with multi-scale simulation of a vacancy migration in a huge > supercell (say, 350-400 atoms), should one make a pre-optimization > of starting and ending points of a path? > > I tried both ways and came to the conclusion that pre-optimization > pushes the system away from the minimum energy path (leading to the > increased barriers), because pre-optimization implies too deep > restructuring towards deeper minimums rather than the local minimums > closest to the minimum energy pathway. > In my opinion it is more physical if a migration corresponds to a > minimum energy pathway AND minimum restructuring. > > If you would simulate vacancy migration in a huge supercell with NEB > optimization, would you optimize starting and ending points? Why? > > > Thanks in advance and hope to hear your opinions and reasonings, > > Regards, > Alex. > -- > > -- > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] NEB first_last_opt
Hello dear QE users, I have a question regarding pre-optimization of starting and ending points of NEB. Dealing with multi-scale simulation of a vacancy migration in a huge supercell (say, 350-400 atoms), should one make a pre-optimization of starting and ending points of a path? I tried both ways and came to the conclusion that pre-optimization pushes the system away from the minimum energy path (leading to the increased barriers), because pre-optimization implies too deep restructuring towards deeper minimums rather than the local minimums closest to the minimum energy pathway. In my opinion it is more physical if a migration corresponds to a minimum energy pathway AND minimum restructuring. If you would simulate vacancy migration in a huge supercell with NEB optimization, would you optimize starting and ending points? Why? Thanks in advance and hope to hear your opinions and reasonings, Regards, Alex. -- -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Problem with PP in version 6.0
On Mon, Mar 20, 2017 at 11:01 PM, gangotri dey wrote: > I think there is a problem with version 6.0 in the section PP for cube file > generation. Does anyone face the same problem? which problem? -- Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
