[Pw_forum] FFT parallel bug with GCC+MPICH2 under Windows
Hi, QE developers and users, I am trying to compile 6.2 version QE under Windows with MPICH2 parallel. After successfully compiling, I noticed the software took place error at very beginning as following: Parallelization info sticks: dense smooth PW G-vecs:dense smooth PW Min 0 0 000 0 Max 1 1 111 1 Sum 1 1 111 1 Since the same problem was seen in previous version (5.4.0), so I tried to modify the code in file FFTXLib/stick_base.f90. However, it was noticed that the source code of stick_base.f90 was changed a lot. Using the similar method as done for v5.4.0, the same error remained. More detailed. In v5.4.0, a simple modification in subroutine stick_maps can solve the trouble, but in v6.2, there is no stick_maps which was replaced by stick_map_allocation, stick_map_set, stick_map_index and stick_map_deallocate. Simply changing the similar part in stick_map_set does not lead to right parallization information. By adding more break points, it was found the array size of st was defined by lb(2) and ub(2). But, four elements in the two arrays all equaled to ZERO. Because stick_map_set was called by get_sticks, lb(2) and ub(2), corresponding to smap%lb(2) and smap%ub(2), were checked at beginning of the subroutine. Unfortunately, they also equaled to ZERO. The following tracing was suspended owing to no idea which subroutine calls get_sticks. It is also noticed that this problem can be only occurred while compiling QE with GCC and official MPICH2 (1.4.1p1, in win64 msi) through MinGW platform (including MinGW, MinGW-w64, Msys2, etc). Could any people suggest me how to avoid / solve this probem? Thank you very much in advance, Best Regards, -- GAO Zhe, Dr., Senior Research Engineer, Gypsum Activity R - Asia, Saint-Gobain Research Shanghai Co., Ltd., No. 55, Wenjing-road, Minhang-district, Shanghai, China, Tel: +86-21-5475-7251 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Crystal space group
Hi, Paolo, Thank you very much. I really did not notice this change in versions. Best Regards, -- GAO Zhe, Dr., Research Engineer, Gypsum Activity R - Asia, Saint-Gobain Research Shanghai Co., Ltd., No. 55, Wenjing-road, Minhang-district, Shanghai, China, Tel: +86-21-5475-7251 At 2016-12-23 22:42:49, "Paolo Giannozzi" <p.gianno...@gmail.com> wrote: From the Doc/release-notes file: New in 5.1.1 version: [..] * Added possibility to provide structure via space-group number and Wyckoff positions --- (5.1.1 was released 2 years ago). Related variables are "space_group" and the "crystal_sg" option for ATOMIC_POSITIONS. They are explained in the documentation On Fri, Dec 23, 2016 at 3:12 PM, GAO Zhe <flux_ra...@163.com> wrote: Hi, Paliwal, You may use the small tool - spacegroup - in ELK package to convert space group number to ibrav=0 + CELL_PARAMETERS set. Or, you could also choose the small code - cif2cell - to complete the space group number to the format PWscf uses. Kind Regards, -- GAO Zhe, Dr., Research Engineer, Gypsum Activity R - Asia, Saint-Gobain Research Shanghai Co., Ltd., No. 55, Wenjing-road, Minhang-district, Shanghai, China, Tel: +86-21-5475-7251 At 2016-12-23 16:10:48, "Uttam Paliwal" <uttam...@gmail.com> wrote: Hi how to provide crustal space group number (eg 216 for zinc blende type) instead of ibrav lebel. -- ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum -- 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
Re: [Pw_forum] Crystal space group
Hi, Paliwal, You may use the small tool - spacegroup - in ELK package to convert space group number to ibrav=0 + CELL_PARAMETERS set. Or, you could also choose the small code - cif2cell - to complete the space group number to the format PWscf uses. Kind Regards, -- GAO Zhe, Dr., Research Engineer, Gypsum Activity R - Asia, Saint-Gobain Research Shanghai Co., Ltd., No. 55, Wenjing-road, Minhang-district, Shanghai, China, Tel: +86-21-5475-7251 At 2016-12-23 16:10:48, "Uttam Paliwal" <uttam...@gmail.com> wrote: Hi how to provide crustal space group number (eg 216 for zinc blende type) instead of ibrav lebel. -- ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Cannot allocate FFT (Trouble-shooting)
Dear QE users and developers, The problem has been solved, so I just reply my own mail. In QE version 5.4.0, it was found the error information from PW/src/allocate_fft.f90, but the real issue was raised from the subroutine sticks_maps defined in FFTXLib/stick_base.f90. Just before the end of sticks_maps subroutine, the function MPI_ALLREDUCE is used. However, the first parameter MPI_IN_PLACE could not work with certain cases of MPICH2. Thus, the members of three integer arrays, st, stw and sts, become all zero. So far, I just added three internal "shadows" integer arrays, _st_, _stw_ and _sts_. They copied all the members of st, stw and sts before calling MPI_ALLREDUCE. Thereafter, MPI_IN_PLACE are replaced by the "shadows". After recompiling the code under MinGW with GNU compiler, the source code package of QE 5.4.0 was compiled to Windows 32-bit parallel executable files. Several computations has been done under Windows, it proved that the modified code is able to provide similar speed and the same results as running under Unix/Linux. Please do not hesitate to let me know if one wants to test the Windows - parallel version QE 5.4.0. Best Regards, -- GAO Zhe, Dr., Research Engineer, Gypsum Activity R - Asia, Saint-Gobain Research Shanghai Co., Ltd., No. 55, Wenjing-road, Minhang-district, Shanghai, China, Tel: +86-21-5475-7251 At 2016-10-16 11:01:46, "GAO Zhe" <flux_ra...@163.com> wrote: Dear QE users and developers, I am trying to compile QE 5.4.0 under MinGW-32 with MPICH2. However, pw.x met error while allocating FFT as following: G-vector sticks info sticks: dense smooth PW G-vecs:dense smooth PW Sum 0 0 000 0 %% Error in routine allocate_fft (1): wrong ngm %% During compiling, the only warning information was occurred for zhpev_drv.f90 in LAXlib as: gfortran -O3 -static -x f95-cpp-input -D__WIN32 -D__FFTW3 -D__GFORTRAN -D__STD_F95 -D__MPI -D__PARA -I../include -I/$(MPICH_TOP)/include -I/local/include -I../ELPA/src -c zhpev_drv.f90 mpif.h:511.11: Included at zhpev_drv.f90:14: SAVE /MPIFCMB1/, /MPIFCMB2/ 1 Warning: SAVE statement at (1) follows blanket SAVE statement mpif.h:512.11: Included at zhpev_drv.f90:14: SAVE /MPIFCMB3/, /MPIFCMB4/, /MPIFCMB5/, /MPIFCMB6/ 1 Warning: SAVE statement at (1) follows blanket SAVE statement mpif.h:513.11: Included at zhpev_drv.f90:14: SAVE /MPIFCMB7/, /MPIFCMB8/ 1 Warning: SAVE statement at (1) follows blanket SAVE statement So far, I have no idea why the strange error took place. Would you like to share some comments with me how to avoiding the error? Many thanks. Best Regards, -- GAO Zhe, Dr., Research Engineer, Gypsum Activity R - Asia, Saint-Gobain Research Shanghai Co., Ltd., No. 55, Wenjing-road, Minhang-district, Shanghai, China, Tel: +86-21-5475-7251 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] How to solve the "wrong ngm" error in allocate_fft() that shows up only in parallel mode?
Hi, Suchit, Have you solved the allocate_fft() error for your Windows version QE? Actually, I met the similar problem as you. But, it still seems slightly different. The series version of QE 5.4.0 had been compiled under MinGW 32-bit with gfortran and cc. It runs well. The allocate_fft() error, for me, only occurred if I tried to compile parallel version QE, no matter for which version (I have tried from 5.0.2 to 6.0.0) the same problem took place. The only warning information was the last rows of mpif.h Warning info: for QE 6.0.0: while compiling FFTXlib/stick_base.f90 and FFTXlib/fft_types.f90: at end of mpif.h, SAVE statement at (1) follows blanket SAVE statement. for QE 5.4.0: while compiling LAXlib/zhpev_drv.f90, the same. According to 8 years ago discussion, it seems to be the true reason: https://trac.mpich.org/projects/mpich/ticket/208 Two versions of gfortran (5.4.0 under cygwin 32-bit and 4.6.2 under mingw 32-bit) had been tested, the same problem remained. 32-bit MPICH2-1.4.1p1 was used for all parallel compiling. Would you like to share your idea with me for solving the allocate_fft error? Thank you very much, Best Regards, -- GAO Zhe, Dr., Research Engineer, Gypsum Activity R - Asia, Saint-Gobain Research Shanghai Co., Ltd., No. 55, Wenjing-road, Minhang-district, Shanghai, China, Tel: +86-21-5475-7251 At 2016-05-23 00:25:36, "Suchit" <such.e...@gmail.com> wrote: Dear All, I am trying to install and use the parallel version of Quantum Espresso 5.4.0. During the "./configure" step, the parallel machine is detected successfully, and "make all" also does not return any errors. However, when I run a simple Silicon example, I end up with an allocate_fft error, and it appears that the ngm value in the program is incorrect. I also ran configure and make on QE-5.4.0 successfully by disabling parallel mode, and found that the same Silicon example works well without any allocate_fft and ngm errors. Below I provide contents from three files. The "Si.scf.in" is the input file to pw.x. The "Si.scf-SerialMode.out" is the output of pw.x built by disabling the parallel mode, and SCF converges without errors -- below I have only shown the first few lines for brevity. The "Si.scf-ParallelMode.out" is the output of pw.x built by enabling parallel mode (default option). The "wrong ngm" error in allocate_fft() can be seen, also all the values in the "G vectors stick info" are zeroed out. I am using 64-bit Cygwin for this work. During configure step for both serial and parallel modes I use the internal BLAS, LAPACK, and FFT libraries. Thanks for any help you might have to offer. With Best Regards, --Suchit Si.scf.in starts here title = 'Silicon' , calculation = 'scf' , restart_mode = 'from_scratch' , outdir = './out' , pseudo_dir = '/cygdrive/c/Users/sbhattarai/Documents/QuantumEspresso/espresso-5.4.0/pseudo' prefix = 'Si' , iprint = 1 , / ibrav = 2, celldm(1) = 10, nat = 2, ntyp = 1, nbnd = 10 ecutwfc = 30 , ecutrho = 120 , / mixing_mode = 'plain' , mixing_beta = 0.7 , diagonalization = 'cg' , / ATOMIC_SPECIES Si 28.08600 Si.pbe-hgh.UPF ATOMIC_POSITIONS alat Si 0.00.00.0 Si 0.250000.250000.25000 K_POINTS gamma # End of Si.scf.in # ### Start of first few lines of Si.scf-SerialMode.out # Program PWSCF v.5.4.0 starts on 22May2016 at 8:42:27 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/quote Serial version Waiting for input... Reading input from standard input Current dimensions of program PWSCF are: Max number of different atomic species (ntypx) = 10 Max number of k-points (npk) = 4 Max angular momentum in pseudopotentials (lmaxx) = 3 gamma-point specific algorithms are used G-vector sticks info sticks: dense smooth PW G-vecs:dense smooth PW Sum 421 421109 5577 5577 701 Tot 211 211 55 Title: Silicon
[Pw_forum] Cannot allocate FFT
Dear QE users and developers, I am trying to compile QE 5.4.0 under MinGW-32 with MPICH2. However, pw.x met error while allocating FFT as following: G-vector sticks info sticks: dense smooth PW G-vecs:dense smooth PW Sum 0 0 000 0 %% Error in routine allocate_fft (1): wrong ngm %% During compiling, the only warning information was occurred for zhpev_drv.f90 in LAXlib as: gfortran -O3 -static -x f95-cpp-input -D__WIN32 -D__FFTW3 -D__GFORTRAN -D__STD_F95 -D__MPI -D__PARA -I../include -I/$(MPICH_TOP)/include -I/local/include -I../ELPA/src -c zhpev_drv.f90 mpif.h:511.11: Included at zhpev_drv.f90:14: SAVE /MPIFCMB1/, /MPIFCMB2/ 1 Warning: SAVE statement at (1) follows blanket SAVE statement mpif.h:512.11: Included at zhpev_drv.f90:14: SAVE /MPIFCMB3/, /MPIFCMB4/, /MPIFCMB5/, /MPIFCMB6/ 1 Warning: SAVE statement at (1) follows blanket SAVE statement mpif.h:513.11: Included at zhpev_drv.f90:14: SAVE /MPIFCMB7/, /MPIFCMB8/ 1 Warning: SAVE statement at (1) follows blanket SAVE statement So far, I have no idea why the strange error took place. Would you like to share some comments with me how to avoiding the error? Many thanks. Best Regards, -- GAO Zhe, Dr., Research Engineer, Gypsum Activity R - Asia, Saint-Gobain Research Shanghai Co., Ltd., No. 55, Wenjing-road, Minhang-district, Shanghai, China, Tel: +86-21-5475-7251 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Error in routine check_tempdir
Hi, Paolo,
Thank you very much,
I removed the following sentence in PW/src/input.f90, and re-compiled pw.x by
gfortran under MinGW. Now, it works well for scf, nscf and bands calculations
(it has been only tested these three tasks so far).
IF ( ios > 0 ) CALL errore ('check_tempdir','tmp_dir cannot be opened',1)
Best Regards,
--
GAO Zhe, Dr.,
Research Engineer,
Gypsum Activity R - Asia,
Saint-Gobain Research Shanghai Co., Ltd.,
No. 55, Wenjing-road, Minhang-district, Shanghai, China,
Tel: +86-21-5475-7251
At 2016-08-10 15:07:19, "Paolo Giannozzi" <p.gianno...@gmail.com> wrote:
>You find check_tempdir in PW/src/input.f90. It is used only there.
>
>Paolo
>
>On Tue, Aug 9, 2016 at 10:19 AM, GAO Zhe <flux_ra...@163.com> wrote:
>> Dear all,
>>
>> I have compiled QE 5.4.0 through gfortran (4.6.2) and gcc (4.6.2) under
>> MinGW of Windows 7 (32-bit). However, when I run the pw.exe, it gives an
>> error as the blue information. Even reading the input files successfully run
>> before, the same error occurred. It seems the program can create the temp
>> directory assigned by outdir variable, but, it cannot generate the save
>> folder - ${prefix}.save.
>> As a confirmation of authority of directory, the older version - 5.1.2 (also
>> compiled by same compilers and environment) - was tested on the same input
>> files and all runs were succeed.
>> Would you like to let me know how to overcome this problem, or let me know
>> the location of sub-routine of check_tempdir.
>> Many thanks,
>> Best Regards,
>>
>> Program PWSCF v.5.4.0 starts on 9Aug2016 at 16: 6:14
>>
>> This program is part of the open-source Quantum ESPRESSO suite
>> for quantum simulation of materials; please cite
>> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>> URL http://www.quantum-espresso.org;,
>> in publications or presentations arising from this work. More details
>> at
>> http://www.quantum-espresso.org/quote
>>
>> Serial version
>> Waiting for input...
>> Reading input from standard input
>>
>> Current dimensions of program PWSCF are:
>> Max number of different atomic species (ntypx) = 10
>> Max number of k-points (npk) = 4
>> Max angular momentum in pseudopotentials (lmaxx) = 3
>>
>>
>> %%%%%%%%%%
>> Error in routine check_tempdir (1):
>> tmp_dir cannot be opened
>>
>> %%
>>
>> stopping ...
>> STOP 1
>>
>> --
>> GAO Zhe, Dr.,
>> Research Engineer,
>> Gypsum Activity R - Asia,
>> Saint-Gobain Research Shanghai Co., Ltd.,
>> No. 55, Wenjing-road, Minhang-district, Shanghai, China,
>> Tel: +86-21-5475-7251
>>
>>
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum@pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
>
>--
>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
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[Pw_forum] Error in routine check_tempdir
Dear all,
I have compiled QE 5.4.0 through gfortran (4.6.2) and gcc (4.6.2) under MinGW
of Windows 7 (32-bit). However, when I run the pw.exe, it gives an error as the
blue information. Even reading the input files successfully run before, the
same error occurred. It seems the program can create the temp directory
assigned by outdir variable, but, it cannot generate the save folder -
${prefix}.save.
As a confirmation of authority of directory, the older version - 5.1.2 (also
compiled by same compilers and environment) - was tested on the same input
files and all runs were succeed.
Would you like to let me know how to overcome this problem, or let me know the
location of sub-routine of check_tempdir.
Many thanks,
Best Regards,
Program PWSCF v.5.4.0 starts on 9Aug2016 at 16: 6:14
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org;,
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Serial version
Waiting for input...
Reading input from standard input
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 4
Max angular momentum in pseudopotentials (lmaxx) = 3
%%
Error in routine check_tempdir (1):
tmp_dir cannot be opened
%%
stopping ...
STOP 1
--
GAO Zhe, Dr.,
Research Engineer,
Gypsum Activity R - Asia,
Saint-Gobain Research Shanghai Co., Ltd.,
No. 55, Wenjing-road, Minhang-district, Shanghai, China,
Tel: +86-21-5475-7251
___
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[Pw_forum] Is the results of structural relaxiation by pwscf accurate?
According to the pointview of methods/theories implemented in DFT codes, all of the relaxed structures from QE, VASP and CASTEP are definitely reliable. But, these codes use different pseudo-potentials, which induce slight fluctuation to the final structure. Most important, all the structures should be obtained from the converged computational parameters. Otherwise, there is no code being able to provide "reliable" structure. -- GAO Zhe, Dr., Research Engineer, Quartz, Saint-Gobain Research (Shanghai), No. 55, Wenjing-road, Minhang-district, Shanghai, China At 2013-04-30 00:42:32,"???" <18733462676 at 163.com> wrote: dear all According to my trying with different software,i found that there is a large difference between relaxiation with pwscf and other software(e.g.vasp and castep),So i want to know wh ether the relaxiation of pwscf is reliable? And can you provide some suggestions? ?? -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130430/1f17b799/attachment.html
[Pw_forum] Not convergence of the scf in phonon calculation
First of all, please make sure that the model you computed has been fully relaxed. Then, while the model was big, the lower alpha_mix(1), default as 0.7, may be helpful for the SCF convergence during ph.x process. -- GAO Zhe, Dr., Research Engineer, Quartz, Saint-Gobain Research (Shanghai), No. 55, Wenjing-road, Minhang-district, Shanghai, China At 2013-04-29 09:47:18,"???" <18733462676 at 163.com> wrote: dear all when I computed the scf of phonon,the convergnece is always not attained,I tried changing the "tr2_ph" and "alpha_mixing" to accelarate the speed of convergnece ,But the results is not ideal.So i want to know what can i do to perform the convergence of phonon.e.g.which parameters can be changed ? ?? -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130429/0e417189/attachment.html
[Pw_forum] nscf calculation error
The output file has given the error info as follow: 24 Error in routine card_occupations (1): 25 Missing occupations, end of file reached You may simply add " occupations = ' tetrahedra ' " in the namelist for NSCF calculation. -- GAO Zhe, Dr., Research Engineer, Quartz, Saint-Gobain Research (Shanghai), Wenjing-Road 55#, Minhang, Shanghai, China At 2013-03-24 07:29:41,"Kopinjol Baishya" wrote: Hi, I was trying to run the silver ion in quantum espresso. The scf calculation runs fine but the nscf calculation gives me an error and the job crashes. Here is the nscf input file: 2 calculation='nscf' 3 prefix='silver', 4 pseudo_dir='/scratch/scratchdirs/kopinjol/Calculations/Projects/GW-Yambo/Ag/Ag-ion/Y ambo/ReCalc/Cnvg-Tests/PwScf-Cnvg-tests/Ecutwfc-100-Ecutrho-170/cdm-19.2', 5 outdir = '/scratch/scratchdirs/kopinjol/Calculations/Projects/GW-Yambo/Ag/Ag-ion/Yam bo/ReCalc/Cnvg-Tests/PwScf-Cnvg-tests/Ecutwfc-100-Ecutrho-170/cdm-19.2/SAVE', 6 wf_collect=.true., 7 verbosity='high', 8 / 9 10 ibrav= 1, celldm(1) = 19.2, nat= 1, ntyp= 1, 11 occupations = 'from_input', 12 nspin=1, 13 nosym = .false. 14 force_symmorphic=.true., 15 tot_charge = +1, 16 nbnd = 200, 17 ecutwfc = 100.0, 18 ecutrho = 170.0 19 / 20 21 diago_thr_init = 1.0e-6 22 diago_full_acc = .true. 23 / 24 ATOMIC_SPECIES 25 Ag 107.87 Ag.UPF 26 ATOMIC_POSITIONS 27 Ag 0.00 0.00 0.00 28 K_POINTS gamma 29 OCCUPATIONS 30 2 2 2 2 2 0 0 0 0 0 0 0 0 0 31 And here is the output file with the error: 2 Program PWSCF v.5.0.2 (svn rev. 9392) starts on 6Feb2013 at 8:25:40 3 4 This program is part of the open-source Quantum ESPRESSO suite 5 for quantum simulation of materials; please cite 6 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); 7 URL http://www.quantum-espresso.org;, 8 in publications or presentations arising from this work. More details at 9 http://www.quantum-espresso.org/quote.php 10 11 Parallel version (MPI & OpenMP), running on 192 processor cores 12 Number of MPI processes: 192 13 Threads/MPI process: 1 14 R & G space division: proc/nbgrp/npool/nimage = 192 15 16 Current dimensions of program PWSCF are: 17 Max number of different atomic species (ntypx) = 10 18 Max number of k-points (npk) = 4 19 Max angular momentum in pseudopotentials (lmaxx) = 3 20 Waiting for input... 21 Reading input from standard input 22 23 %% 24 Error in routine card_occupations (1): 25 Missing occupations, end of file reached 26 %% 27 28 stopping ... 29 Application 14955548 exit codes: 134 30 Application 14955548 exit signals: Killed 31 Application 14955548 resources: utime ~20s, stime ~0s Rss ~9536 inblocks ~1085175 outblocks ~2891880 I would really appreciate if someone could direct me as to what might be going wrong! Thanks in advance, Kopinjol Baishya Graduate Student, Materials Modeling Group, UIC -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130324/5fcb1449/attachment.html
[Pw_forum] pdos files connot bw generated by projwfc.x
Dear ??: I am not sure whether I guess correctly. But according to my memory, the PDOS calculations requires symmetry analyze. Thus, I recommend you to set lsym=.t., and use projwfc.x running your input. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-11-06 21:55:31,"???" wrote: Dear Lorenzo, I've tried your suggestion, but "filpdos".pdos_tot and "filpdos".pdos_atm#N(X)_wfc#M(l) are still missing. here's my new input: prefix = '2Fe-gaussian-A' , outdir = '/home/enixchen/SHHsu/2Fe/QE/A/gaussian-scf1/tmp' , filpdos = '/home/enixchen/SHHsu/2Fe/QE/A/gaussian-scf1/2Fe-gaussian-A-PDOS' , filproj = '/home/enixchen/SHHsu/2Fe/QE/A/gaussian-scf1/2Fe-gaussian-A-PROJ' , ngauss = 0 , degauss = 0.0003 , kresolveddos = .false. , Emin = -8 , Emax = 5 , DeltaE = 0.01 , lsym = .false. , tdosinboxes = .false. , #n_proj_boxes = 3 , #irmin = 1 , #irmax = 240 , #plotboxes = .true. , / I sill only get 2Fe-gaussian-A-PROJ.up and 2Fe-gaussian-A-PROJ.down, and the ouput looks similar. Are there any further suggestions? Thank you very much!! here is the output: Program PROJWFC v.4.3.2starts on 6Nov2012 at 21:42: 9 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 2 processors R & G space division: proc/pool =2 Info: using nr1, nr2, nr3 values from input Info: using nr1s, nr2s, nr3s values from input file Fe.pbe-nd-rrkjus.UPF: wavefunction(s) 4S renormalized file Fe.pbe-nd-rrkjus.UPF: wavefunction(s) 4S renormalized Parallelization info sticks: dense smooth PW G-vecs:dense smooth PW Min 157677844 1958 1845827 647241 80912 Max 157687845 1959 1845830 647246 80913 Sum 31535 15689 3917 3691657 1294487 161825 negative rho (up, down): 0.160E-03 0.160E-03 Gaussian broadening (read from input): ngauss,degauss= 00.000300 Gaussian broadening (read from input): ngauss,degauss= 00.000300 Calling projwave Atomic states used for projection (read from pseudopotential files): state # 1: atom 1 (Fe1), wfc 1 (l=0 m= 1) state # 2: atom 1 (Fe1), wfc 2 (l=2 m= 1) state # 3: atom 1 (Fe1), wfc 2 (l=2 m= 2) state # 4: atom 1 (Fe1), wfc 2 (l=2 m= 3) state # 5: atom 1 (Fe1), wfc 2 (l=2 m= 4) state # 6: atom 1 (Fe1), wfc 2 (l=2 m= 5) state # 7: atom 2 (Fe2), wfc 1 (l=0 m= 1) state # 8: atom 2 (Fe2), wfc 2 (l=2 m= 1) state # 9: atom 2 (Fe2), wfc 2 (l=2 m= 2) state # 10: atom 2 (Fe2), wfc 2 (l=2 m= 3) state # 11: atom 2 (Fe2), wfc 2 (l=2 m= 4) state # 12: atom 2 (Fe2), wfc 2 (l=2 m= 5) k = 0.00 0.00 0.00 e( 1) =-7.68838 eV psi = 0.957*[# 5]+0.033*[# 3]+ |psi|^2 = 0.992 e( 2) =-7.58964 eV psi = 0.636*[# 3]+0.244*[# 4]+0.078*[# 2]+0.020*[# 5]+0.012*[# 6]+ |psi|^2 = 0.991 e( 3) =-7.57765 eV |psi|^2 = 0.991 e( 3) =-7.57765 eV psi = 0.715*[# 4]+0.232*[# 3]+0.018*[# 6]+0.013*[# 2]+0.013*[# 5]+ |psi|^2 = 0.991 e( 4) =-7.12819 eV psi = 0.899*[# 2]+0.089*[# 3]+0.002*[# 4]+0.001*[# 5]+ |psi|^2 = 0.992 e( 5) =-6.52681 eV psi = 0.965*[# 6]+0.029*[# 4]+ |psi|^2 = 0.996 e( 6) =-5.20161 eV psi = 0.955*[# 1]+0.036*[# 7]+0.001*[# 11]+ |psi|^2 = 0.993 e( 7) =-4.26929 eV psi = 0.987*[# 12]+0.011*[# 10]+0.001*[# 11]+ |psi|^2 = 1.000 e( 8) =-4.24529 eV psi = 0.616*[# 7]+0.349*[# 8]+0.021*[# 1]+0.012*[# 9]+ |psi|^2 = 0.998 e( 9) =-3.94093 eV psi = 0.617*[# 8]+0.343*[# 7]+0.021*[# 9]+0.015*[# 1]+ |psi|^2 = 0.996 e( 10) =-3.42297 eV psi = 0.512*[# 10]+0.461*[# 9]+0.015*[# 8]+0.005*[# 11]+0.005*[# 12]+ |psi|^2 = 1.000 e( 11) =-3.42204 eV psi = 0.495*[# 9]+0.476*[# 10]+0.018*[# 8]+0.006*[# 12]+0.005*[# 11]+ |psi|^2 = 1.000 e( 12) =-2.90414 eV psi = 0.984*[# 11]+0.011*[# 9]+0.001*[# 12]+0.001*[# 1]+ |psi|^2 = 0.997 k = 0.000
[Pw_forum] Density of states
Dear Peng: To show the difference between DOSes, the best way is put the Fermi level at same place. Normally, (E-Ef) is preferred by lots of researches as the variable of x-axes. Manually shifting DOS for matching is not a good idea, since HOMO should be the standard and adjusted to the same position (although Fermi level given by PWscf is LUMO for semiconductor or insulator). BTW, in PWscf, nscf calculation also provides Fermi energy, which usually is slightly different with that from scf calculation and displayed by setting verbosity='high' in namelist. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-09-08 01:16:39,"Peng Chen" wrote: Dear All, I calculated the total density of states (in the attachment) for both afm and fm states of an insulator. I shifted the curves so that the band gap starts at 0 eV. In the top figure, the Fermi energy obtained from the scf calculation falls between the gap. So if I plot Fermi surface, can I get reliable result? In the bottom figure, I shifted the spin down DOS of fm state so that it can match with the spin down DOS of afm state. I am not sure if that is the right way to show the DOS difference of these two states. Another question is about the accuracy of calculation. In the scf calculation, I made the total energy converged within 0.001 Ry with related to the ecutwfc, degauss, kpoints... Then I did band structure calculation. Can I say the error of calculated band energy is within 0.001 Ry? Best Regards. Peng -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120908/7e79df07/attachment.htm
[Pw_forum] W full relativistic pseudopotential
Dear Yingchun:
Few days ago, Prof. Marzari provided the compiled "pslib" in this maillist. Any
one can download them at: http://theossrv1.epfl.ch/index.php?n=Main.Links
For example, in rel-pbe, you can find W.rel-pbe-spn-rrkjus.UPF, the basic
information of this file is:
author="ADC"
date="15Jun2012"
comment=""
element=" W"
pseudo_type="USPP"
relativistic="full"
is_ultrasoft="T"
is_paw="F"
is_coulomb="F"
has_so="T"
has_wfc="F"
has_gipaw="F"
paw_as_gipaw="F"
core_correction="T"
functional="PBE"
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
At 2012-09-07 17:00:32,"???" wrote:
>Dear All,
>I need W full relativistic pseudopotential to check the spin-orbital
>effect on band structure.
>However, I found that there is no such pseudopotential in QE
>pseudolist and pslibrary0.2.5.
>Would you please kindly help me to solve this problem?
>Thank you in advance.
>Best,
>--
>Y. C. Cheng
>Department of Physics
>Nanjing University
>Nanjing 210093
>P. R. China
>Tel: 86-25-83592907
>Email: yccheng.nju at gmail.com
>___
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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[Pw_forum] 110-direction Vs 110-point calculation
Dear S. Chab: Definitely, I am not clear about your system. Which is the 4x4x4 M-P mesh? for k-points or q-points? If it is for k-points, then I think it is too small. But any way, I think the convergence test and well relaxation should be done before phonon calculation. For the [110] direction, which means the path from Gamma to X, in your system. X is just a point in FBZ and corresponds to (110) or (1/2, 1/2, 0) based on different cells. Of course, you can directly calculate frequencies by specifying a series of q-points along [110] direction in ph.x. But, running the whole phonon dispersion at converged q-mesh and only draw Gamma->X out is better choice. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-08-14 21:18:39,"Satyananda Chab" wrote: Dear Users, I am trying to calculate the full phonon spectrum of a ferromagnetic alloy but the results that I found are not matching with literature. So I want to know (1) How to assign 110-direction for a grid calculation? (2)Whether calculating phonon spectrum from Gamma to X point along 110 direction is the same as that of a single point calculation at 110 point for this particular point. (3)Will both calculations give the same frequencies at 110 point? (4)My phonon spectrum do not match previous papers. Is there anything to do with grid size?(I used 4X4X4 Monkhorst pack ) If anybody throw me some light on these questions, i will be very happy. Thanking you in advance SATYANAND CH Junior Research Fellow Department of Physics Gauhati University Guwahati 781014 (+91)950-895-6853 email: csatya11 at gmail.com me as that of a single point calculation at 110 point. (3)Will both calculations give the same frequencies at 110 point? (4)My phonon spectrum do not match previous papers. Is there anything to do with grid size?(I used 4X4X4 Monkhorst pack ) If anybody of you throw me some light, i will be very happy. Thanking you in advance SATYA NANDA CH Junior Research Fellow Department of Physics Gauhati University Guwahati 781014 (+91)950-895-6853 email: csatya11 at gmail.com -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120814/0ce1f11c/attachment.htm
[Pw_forum] phonon calculation
Dear Abolore Musari: In my opinion, lots of paper ran DFPT at 4x4x4 q-mesh. Sometimes (not often), 3x3x3 q-mesh may also provide reasonable results. The easiest way may be similar as k-mesh test, you can gradually increase the q-mesh from 2x2x2 to NxNxN until the frequencies converged (the threshold can be defined by yourself). -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-08-12 12:47:12,"Abolore Musari" wrote: >Dear sir. >Sir l just want to ask how do l know the proper nq1 nq2 nq3 to use in >my phonon calculation after my scf calculation. >Am sorry l ask this type of question l will be so happy if u can kindly explain >thanks >Musari. A.A >UNAAB Nigeria >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120812/47d22f3d/attachment.htm
[Pw_forum] piezoelectric constant
Dear Alex: I think you can try Berry Phase implemented in the program pw.x. Reference: David Vanderbilt, Berry-phase theory of proper piezoelectric response, J. Phys. Chem. Solids, 61 (2000), 147 -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-08-11 13:47:20,"Alex Mariani" wrote: Dear all Iwantto calculatethepiezoelectric constant for PbTio3. Howdo using the QE code? What istheprocedure? Pleasehelpme? best regards Alex Mariani Magadh University Department of Physics -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120811/eec99524/attachment.htm
[Pw_forum] optical properties
For your purpose, I think QE + Yambo will help you a lot~ -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-08-05 19:38:46,"Sohail Ahmad" wrote: | Dear All I am using QE 4.2.1 I would like to know that can we use QE to calculate optical properties.dielectric function,energy loss function,absorption and reflectance spectra Sohail KKU Saudi Arabia | -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120805/480448b2/attachment.htm
[Pw_forum] Input error?
The possibilities I guessed: 1, Do you have authority to access that directory? 2, Do you have enough HDD space for the wavefunction file? 3, How about cleaning the directory /home/.../exec/ and re-running the task? -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-07-19 05:05:13,"Pedro Augusto F. P. Moreira" wrote: > Dear all, > > I am trying to pw.x, but the following error happens: > > > %% > task # 0 > from diropn : error #10 > error opening /home/pedro/Documentos/espresso-5.0/exec/h2o.wfc1 > > %% > > I imagine that the pw.x should open the wcf1 file. Am I rigth? Can >anyone say why this error is happening? I managed to run the same >simulation, but with an isolated molecule. My input follows below. > > Thanks, > > Pedro > >-- >Pedro Moreira > >IFGW - Unicamp - Brazil > ># > >calculation='relax', >restart_mode='from_scratch', >pseudo_dir='/home/pedro/Documentos/espresso-5.0/pseudo', >outdir='/home/pedro/Documentos/espresso-5.0/exec', >prefix='h2o', >tprnfor = .true., >nstep = 1, >/ > >ibrav = 0, >nat = 1080, ntyp = 2, >ecutwfc = 70.0, ecutrho = 850.0, >/ > >electron_maxstep = 500, >/ > >/ >ATOMIC_SPECIES >H 1.00790 H.blyp-van_ak.UPF >O 15.9994 O.blyp-van_ak.UPF >CELL_PARAMETERS angstrom >22.15 0.000 0.000 >0.000 23.02 0.000 >0.000 0.000 21.55 >K_POINTS crystal >1 >0. 0. 0. 1.00e+00 >ATOMIC_POSITIONS angstrom > >1080 atoms >## >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120719/965a40e2/attachment.htm
[Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed".
By the way, do you want to calculate the FCC structure (diamond structure)? If so, your model/structure is definitely wrong~ For FCC, the primitive cell contains two atoms, one at (0,0,0), another at (1/4,1/4,1/4), and the cell vectors should be as you used. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-07-18 16:41:23,"bamidele ibrahim" wrote: Dear GAO, Thanks for the explanation, i have tried it , it produced the same result. Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. From: GAO Zhe <flux_ra...@163.com> To: PWSCF Forum Sent: Wednesday, July 18, 2012 10:30 AM Subject: Re: [Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed". If there is no model/structure problem, then you can try to set diagonalization='cg' in namelist, although this method will decrease the calculation speed due to the poor parallel performance. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-07-18 13:30:15,"bamidele ibrahim" wrote: Dear all, I am running scf calculation and relax with the input file below: calculation = 'relax', prefix='MgSe' pseudo_dir='/home/adetunji/espresso-4.3/pslibrary.0.2.5/pz/PSEUDOPOTENTIALS', outdir='./', / ibrav=0, nat=8, celldm(1)= 11.32, ntyp=2, ecutwfc = 50.0, / mixing_beta = 0.9 conv_thr = 1.0d-9 / ion_dynamics ='bfgs' / ATOMIC_SPECIES Mg 24.305 Mg.pz-n-kjpaw.UPF Se 78.963 Se.pz-n-kjpaw.UPF CELL_PARAMETERS 0.000 0.49 0.49 0.49 0.000 0.49 0.49 0.49 0.000 ATOMIC_POSITIONS Mg 0. 0. 0. Mg 0. 0.5000 0.5000 Mg 0.5000 0. 0.5000 Mg 0.5000 0.5000 0. Se 0.2500 0.2500 0.2500 Se 0.7500 0.7500 0.2500 Se 0.7500 0.2500 0.7500 Se 0.2500 0.7500 0.7500 K_POINTS (automatic) 6 6 6 1 1 1 In both cases, it crashes and produces this error: from cdiaghg : error #42 diagonalization (ZHEGV*) failed %% Can anybody in the house tell me what i have done wrong. Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120718/11555ea8/attachment-0001.htm
[Pw_forum] scf calculation crashed for "diagonalization (ZHEGV*) failed".
If there is no model/structure problem, then you can try to set diagonalization='cg' in namelist, although this method will decrease the calculation speed due to the poor parallel performance. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-07-18 13:30:15,"bamidele ibrahim" wrote: Dear all, I am running scf calculation and relax with the input file below: calculation = 'relax', prefix='MgSe' pseudo_dir='/home/adetunji/espresso-4.3/pslibrary.0.2.5/pz/PSEUDOPOTENTIALS', outdir='./', / ibrav=0, nat=8, celldm(1)= 11.32, ntyp=2, ecutwfc = 50.0, / mixing_beta = 0.9 conv_thr = 1.0d-9 / ion_dynamics ='bfgs' / ATOMIC_SPECIES Mg 24.305 Mg.pz-n-kjpaw.UPF Se 78.963 Se.pz-n-kjpaw.UPF CELL_PARAMETERS 0.000 0.49 0.49 0.49 0.000 0.49 0.49 0.49 0.000 ATOMIC_POSITIONS Mg 0. 0. 0. Mg 0. 0.5000 0.5000 Mg 0.5000 0. 0.5000 Mg 0.5000 0.5000 0. Se 0.2500 0.2500 0.2500 Se 0.7500 0.7500 0.2500 Se 0.7500 0.2500 0.7500 Se 0.2500 0.7500 0.7500 K_POINTS (automatic) 6 6 6 1 1 1 In both cases, it crashes and produces this error: from cdiaghg : error #42 diagonalization (ZHEGV*) failed %% Can anybody in the house tell me what i have done wrong. Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120718/e7c44ee2/attachment.htm
[Pw_forum] help
That means the parameter or format for the card K_POINTS {automatic} is wrong
in your Si.band.in.
Please provide your input file, no person can point out the exact error due to
the lack of information.
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
At 2012-07-16 21:29:38,"Nyaruanda Calvince" wrote:
am a new user .
am running mpirun -np 2 pw.x < Si.band.in > Si.band.out calculation. The
following is my output:
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org;,
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
Parallel version (MPI), running on 2 processors
R & G space division: proc/pool =2
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 4
Max angular momentum in pseudopotentials (lmaxx) = 3
Waiting for input...
Reading input from stdin
%%
from card_kpoints : error # 1
error while reading automatic k points
%%
stopping ...
Additionally, from my command line the following error messages appear after
the above run command.
may you help me please.
Regards
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[Pw_forum] Bad data for namelist object mixing_mode
how about writing it as: mixing_mode = 'local-TF' , ? -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-07-13 19:55:05,"Ramesh Kumar" wrote: Dear Users, When I run 'relax' calculation of TiO2 with v.4.3.1, it is running successfully. The same file, if I run in v.5.0, its giving an error "Bad data for namelist object mixing_mode" and if I remove the mixing_mode from the input file, in v.5.0 also it is running successfully. Please some one help me in this regard. I am giving the input here calculation = "relax", pseudo_dir = "/opt/espresso-4.3.1/pseudo-hcl", title = "TiO2-supercell-3x1x2 at 25Ry", verbosity = "high", outdir = "/tmp", wfcdir = "/tmp", nstep = 300, forc_conv_thr = 1.0D-2, restart_mode = "from_scratch", disk_io = "high", / ibrav = 14, A = 10.2395, B = 11.3526, C = 18.8588, cosAB = 0, cosAC = 0, cosBC = 0, nat = 72, ntyp = 2, ecutwfc = 25, / electron_maxstep = 500, diago_david_ndim = 6, mixing_beta = 0.1, mixing_mode = local-TF, / ion_dynamics = 'bfgs', / ATOMIC_SPECIES O16.000 O.pw91-van_ak.UPF Ti 47.862 Ti.pw91-nsp-van.UPF ATOMIC_POSITIONS angstrom Ti 7.802601390 0.0 0.731726700 Ti 7.802601390 3.78420 0.731726700 Ti 7.802601390 7.56840 0.731726700 Ti 9.189153004 -0.006515422 4.448918595 Ti 9.189954718 3.775789308 4.449899070 - - - O0.824867440 -0.004475915 3.563076597 O0.824908130 3.791766218 3.563292452 O0.824597987 7.563798394 3.561725593 K_POINTS automatic 1 1 1 0 0 0 Thank you in advance. - With Best Regards: CH. Ramesh Kumar Ph.D Student, Computational Chemistry Lab, Indian Institute of Chemical Technology(IICT), Tarnaka, Hyderabad. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120713/0f66c42a/attachment.htm
[Pw_forum] Calculation of Gibbs free energies
According to my experience, the general process is right, but, this general process is normally working for crystal rather than amorphous, liquid and gas. Since the contribution from vibration is not that much in those matter, for example, transition contributes much more in gas phase. Therefore, Monte Carlo or Molecular Dynamic could be better choice in these cases. Technically, in your calculation, H2O molecule may exist in a box, therefore only the Gamma phonon calculation is meaningful. Since q2r means fitting the finite samplings of dynamic matrics to infinite interatomic force constants, only one point is not that reliable to find good aproach of IFCs. Actually, since vibrational free energy is defined with the term of hv, you can derectly obtain Fvib from your first step. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-07-10 22:44:56,"Torstein Fjermestad" wrote: > Dear all, > > In one of my projects I would need to compute the Gibbs free energies > of structures along a reaction path. After looking through the QE > webpage, the pw_forum, and the documentation in the quantum espresso > installation directory I think I understand the general procedure: > > 1. one calculates the phonons > 2. one computes the interatomic Force Constants with the q2r.x program > 3. one uses the matdyn.x to produce input for the F_QHA.x program > 4. with the F_QHA.x program one can compute the Gibbs free energy and > other thermodynamical properties. > > (please correct me if I have misunderstood this general procedure) > > The problem is that I have so far only managed to complete step 1, to > compute the phonons. I am currently doing test calculations on a water > molecule and this is the input file of the phonon calculation: > > phonons of H2O in super cell at Gamma > > outdir='./', > prefix='h2o', > amass(1)=1.01, > amass(2)=16.01, > fildyn='h2o.dynG', > trans= .true. > / > 0.0 0.0 0.0 > > I then try to run the q2r.x calculation with the following input: > > test of q2r calculation > > fildyn='h2o.dynG', > flfrc='h2o-output-q2r.fc', > zasr='no' > > This calculation crashes presumably because it expects a file called > h2o.dynG0. But from where do I get this file? As far as I can see the > phonon calculation only produces the file h2o.dynG, not a h2o.dynG0 > file. > > I am completely lost at the moment so I would appreciate if anyone > could help me with carrying out the q2r calculation correctly. > > Thank you very much in advance, > > Yours sincerely, > > Torstein Fjermestad, > University of Oslo, > Norway > > > > > > > > > > > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120711/534bf766/attachment.htm
[Pw_forum] Error #19 MoS2 ecutoff convergence test
Well, the error actually is very small, please check carefully next time, since
this must only due to your own careless~
in , to define the number of band, we use the parameter "nbnd" instead
of "nband"..
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
At 2012-07-10 17:09:37,"Sohail Ahmad" wrote:
| Dear QE users
I am unable to understand the reason behind error #19
Kindly help
http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 4
Max angular momentum in pseudopotentials (lmaxx) = 3
Waiting for input...
%%
from read_namelists : error #19
reading namelist system
%%
stopping ...
---
#!/bin/sh
for i in 30 35 40 45 50 55 60 65
do
#j=$[$i*8]
echo " calculation ecutoff $i is running "
cat >> MoS2$i.in << EOF
calculation = 'scf',
restart_mode = 'from_scratch',
prefix = 'MoS2',
pseudo_dir = '/home/sohail/espresso-4.2.1/pseudo',
outdir = './OUT'
/
ibrav = 4, celldm(1) = 5.9715031, celldm(3) = 3.89, nat = 6, ntyp = 2,
ecutwfc = $i,
ecutrho = 300,
nband = 10,
occupations = 'smearing', smearing = 'gaussian', degauss= 0.001,
nspin = 2,
starting_magnetization(1) = 0.5d0,
/
mixing_beta = 0.3,
conv_thr = 1.0d-9,
/
ATOMIC_SPECIES
Mo 95.96 Mo.pbe-paw-nh.UPF
S 32.06 S.pbe-van_bm.UPF
ATOMIC_POSITIONS {crystal}
Mo 0. 0.6667 0.2500
Mo 0.6667 0. 0.7500
S 0. 0.6667 0.6200
S 0.6667 0. 0.1200
S 0.6667 0. -0.6200
S 0. 0.6667 -0.1200
K_POINTS AUTOMATIC
4 4 4 1 1 1
EOF
pw.x < MoS2$i.in> MoS2$i.out
rm -rf OUT/*
done
---
Sohail Ahmad
King Khalid University
Saudi Arabia
|
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[Pw_forum] Equation of state with PW.x
Dear Furman: I think, the easier and better way to make such a "compress" is using isostatic pressure, which can be specified by parameter "press" in "cell" namelist, especially for the un-cubic system. For example, in HCP structure, the cell is determined by "a" and "a/c", while the volume changing, not only "a", but also "a/c" ratio changes, too. Therefore, you can do a batch of "vc-relax" tasks with different press and gather the final volume and total energy to fit EOS. The aim compress, as 10% or 20% shrinkage, can be found from EOS fitting result, where you can obtain the P-V curve. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-06-08 15:17:36,"David Furman" wrote: Hello dear users and developers, I'm trying to calculate the equation of state of Europium oxide, but I have some doubts regarding my procedure. I have the xyz coordinates of the unit cell in angstroms which I put into atom_positions and also define the needed celldm's(). I'm interested to compress the material to different values (say, 0%, 10% and 20% volumetric compression) and calculate the total energy each time. Do I have to change the given initial xyz coordinates in atom_positions AND the celldm() , or just change the celldm() accordingly to the compression and pw.x will do the proper changes to the positions of the atoms ? I have done some calculations with uncompressed unit cell and with 20% compressed unit cell (by changing to the proper compressed celldm() values) but the difference in energy was about 0.5 Ry which i believe to be quite small. (Of course I checked previously for convergence). Am I doing it wrong ? Any help will be greatly appreciated David Furman, Graduate Student| Fritz Haber Research Center for Molecular Dynamics, The Hebrew University of Jerusalem | +972-8656-8909 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120609/d4fdf803/attachment-0001.htm
[Pw_forum] error with open64 compilers
For AMD machine, you can try the free version of PathScale, which shares the libraries with open64, but has better compability. Further, according to my experience, even for AMD machine, ifort+MKL provide higher efficiency than PathSclae+AMCL, this may be mainly caused by the missing of FFTW (only FFT) in AMCL. Of course, I have not tested every possibility, hope you can find better compiler and math-libraries combination in AMD platform. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-06-05 17:11:03,Arturo wrote: Now it gives me another error: mpif90 -O3 -ftpp -D__FFTW -D__MPI -D__PARA -I../include -I../../iotk/src -I../../Modules -I. -c cglib.f90 real(DP) :: zmat( MAXVAL(descla(:)%nrlx), nudx, nspin ), fmat( MAXVAL(descla(:)%nrlx), nudx, nspin ), fdiag( nx ) ^ openf95-870 openf90: ERROR CALCMT, File = cglib.f90, Line = 25, Column = 25 The intrinsic call "MAXVAL" is not valid in a specification expression. real(kind=DP)z0( MAXVAL(descla(:)%nrlx), nudx, nspin ) ^ openf95-870 openf90: ERROR ROTATE, File = cglib.f90, Line = 102, Column = 28 The intrinsic call "MAXVAL" is not valid in a specification expression. We have a machine with AMD interlagos processor and the vendor recommend us to use this compiler Open64 from AMD. Thanks for your help!! Arturo El 05/06/12 10:49, Lorenzo Paulatto escribi?: On Tue, Jun 5, 2012 at 10:32 AM, Arturo wrote: real(dp), parameter :: fac = (1.d0/2.d0) * 1.d0/(3.d0*pi**2)**(1.d0/3.d0) ^ openf95-206 openf90: ERROR DO_RDG, File = elf.f90, Line = 203, Column = 70 The exponent in a constant initialization expression must be type integer. How can I solve it? Open the file with a text editor and replace the right-hand-side expression with its result: 0.161620459673995d0 But, where did you find this compiler? And, I'm just curious, why did you choose it? Are you sure it is reliable? bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 ___ Pw_forum mailing list Pw_forum at pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum -- Arturo Giner Gracia HPC research group System Administrator Instituto de Biocomputaci?n y F?sica de Sistemas Complejos (BIFI) Universidad de Zaragoza e-mail: artginer at bifi.es phone: (+34) 976762992 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120605/f315d752/attachment-0001.htm
[Pw_forum] Finite Temperature Schrödinger Equation.
I haven't found any efficiency and powerful method to solve Schrodinger Equ with temperature effect. But the paper you mentioned, was published in "International Journal of Theoretical Physics", which is an open access journal with IF=0.67. I briefly read that paper, but I do not think one can directly use such a method into practicing and I am also afraid there r some problems in the equations. If you really wanna obtain some properties (ex. band info) from DFT, the semi-emperical AHC method or DFPT method may give you some help. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea ? 2012-06-02 22:24:40?"Hongsheng Zhao" ??? >Hi all, > >I've learned that the "Finite Temperature Schr?dinger Equation" from here: > >http://arxiv.org/abs/1005.2751 > >Basically, I've two issues on the above paper: > >1- Does someone has any hints on how to realize it in pwscf? > >2- Besides this method, are there other methods for taking the >temperature into effect within Schr?dinger Equation? Which is the most >feasible schedule till now? > >Regards >-- >Hongsheng Zhao >School of Physics and Electrical Information Science, >Ningxia University, Yinchuan 750021, China >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120603/8dc04d33/attachment.htm
[Pw_forum] The phonon frequency unit in matdyn.x v5.0
Thank you very much Prof. Giannozzi, I think I caught your idea. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-05-23 00:45:57,"Paolo Giannozzi" wrote: >On Tue, 2012-05-22 at 11:20 +0800, GAO Zhe wrote: > >> Now, in matdyn.x v5.0, if I did not set amass(i), the output frequency >> would be in some other unit. > >output frequencies are in the same units, but maybe the mass is not >what you expect, or what should have been. There have been some >changes in the internal units of mass. From Doc/release-notes: > * atomic masses in the code are in amu unless otherwise stated >This might have some unexpected consequences. > >P. > >Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120523/52bad8d3/attachment.htm
[Pw_forum] The phonon frequency unit in matdyn.x v5.0 (sorry for the wrong Fig in last one)
Dear QE developer and users: I am so sorry that I attached the wrong Fig in last email~ This is the right comparason~ -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/e458b15e/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: Compare.png Type: image/png Size: 69768 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120522/e458b15e/attachment-0001.png
[Pw_forum] The phonon frequency unit in matdyn.x v5.0
Dear QE developer and users: I am using QE 5.0 now. I am not sure whether I did not read the manual carefully. But when I use the matdyn.x as in QE 4.3.2, the output unit became different. Detail: In matdyn.x v4.x, one did not have to set the parameters amass(i) and the element mass can be read from IFCs file. The output frequency was in cm^(-1) unit. Now, in matdyn.x v5.0, if I did not set amass(i), the output frequency would be in some other unit. I though it was THz, but I compared it with the output from matdyn.x v4.3.2 by the same IFCs, the arbitrary value was a little bit higher than when unit in THz. The same issue was found when calculate phonon DOS. However, if I added amass(i) parameters, all of the result would be in cm^(-1) unit. The comparason for with and without amass(i) in matdyn.x v5.0 is shown as the accessory, which was from the example of Fe_AFM in PlotPhon. By the way, when I used 'crystal' method for ASR in matdyn.x v4.3, the results from with and without amass(i) has some different in low frequency acoustics bratches as: With amass(i): 0.01 0.00 0.00 6.53593.08293.2829 155.3803 173.4756 173.4207 232.7133 232.7937 237.6018 280.0328 280.1047 283.2520 0.02 0.00 0.00 13.05336.16616.5649 155.4117 173.5031 173.2838 232.4662 232.7895 237.6108 279.8124 280.0984 283.2260 Without amass(i): 0.01 0.00 0.00 3.08293.28296.5359 155.3803 173.4207 173.4756 232.7133 232.7937 237.6018 280.0328 280.1047 283.2520 0.02 0.00 0.00 6.16616.5649 13.0533 155.4117 173.2838 173.5031 232.4662 232.7895 237.6108 279.8124 280.0984 283.2260 -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120522/2fa09642/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: Fe_AFM.Thz.png Type: image/png Size: 75739 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20120522/2fa09642/attachment-0001.png
[Pw_forum] Conversion from conventional to primitive cell
How about trying the spacegroup code in Exciting or ELK package? At 2012-05-04 21:31:48,"Peng Chen" wrote: Dear All, Is there any tools (free) to convert a conventional unit cell to a primitive cell? Recently, I tried to convert atom positions from a face centered orthorhombic unit cell (space group cmca, basis vectors: a,b,c) to its primitive cell. I used basis vectors: 1/2(a,0,c), 1/2(a,b,0),1/2(0,b,c). But it looks they are not the correct ones because the chemical formula in this unit cell is not the same as that in conventional unit cell. -- Best Regards. Peng -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120504/204bfc82/attachment.htm
[Pw_forum] convergence NOT achieved after 100 iterations: stopping
How about trying to fix the movement for BN-sheet and just move H atoms. The
BN-sheet may achieve a concavity during "relax" process. For the absorption of
H2, the concavity will vanish and a plane-BN finally be obtained. But for
single H atom, I am not sure whether one can ignore such an effect.
By the way, is it reasonable that only one H atom was absorped instead of
diatom H2 molecule?
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
At 2012-04-27 09:20:20,"Cao TF" wrote:
Dear QE users
Recently, I have done some calculation of BN sheet with hydrogen atoms adsorbed
on it. The problem is that when I let hydrogen atoms adsorb on the N atoms. The
calculation is hard to converge. Although, I have changed mixing_beta and the
number of K points. The problem have not been solved. Dose anyone have some
experience on such kind of calculations? Any suggestions will be greatly
appreciated. Here is my input file.
title = 'graphene layer' ,
calculation = 'relax' ,
restart_mode = 'restart' ,
outdir = './tmp' ,
pseudo_dir = '/lustre/ISSP2/tfcao/pseudo' ,
prefix = 'graphene' ,
tprnfor = .TRUE. ,
nstep = 400 ,
/
ibrav = 8 ,
a = 15.026832 , b = 13.014 , c = 15.0 ,
nat = 74 ,
ntyp = 3 ,
starting_magnetization(1) = 0.5 ,
occupations = 'smearing' ,
nosym = .TRUE. ,
degauss = 0.005 ,
smearing = 'mp' ,
nspin = 2 ,
ecutwfc = 30.0 ,
ecutrho = 300.0 ,
/
conv_thr = 1.0d-7 ,
mixing_mode = 'local-TF' ,
mixing_beta = 0.1 ,
diagonalization = 'cg' ,
/
ion_dynamics = 'bfgs' ,
pot_extrapolation = 'atomic' ,
/
ATOMIC_SPECIES
B 10.811 B.pbe-n-van.UPF
N 14.00674 N.pbe-rrkjus.UPF
H 1.0 H.pbe-rrkjus.UPF
ATOMIC_POSITIONS crystal
ATOMIC_POSITIONS crystal
N 0.000 0.000 0.5000 0 0 0
B 0.000 0.1100 0.5000
N 8.0005E-02 0.1700 0.5000
B 8.0005E-02 0.2800 0.5000
N 0.000 0.3299 0.5000
B 0.000 0.4400 0.5000
N 8.0005E-02 0.5000 0.5000
B 8.0005E-02 0.6099 0.5000
N 0.000 0.6597 0.5000
B 0.000 0.7696 0.5000
N 8.0005E-02 0.8296 0.5000
B 8.0005E-02 0.9394 0.5000
N 0.1700 0.000 0.5000
B 0.1700 0.1100 0.5000
N 0.2500 0.1700 0.5000
B 0.2500 0.2800 0.5000
N 0.1700 0.3299 0.5000
B 0.1700 0.4400 0.5000
N 0.2500 0.5000 0.5000
B 0.2500 0.6099 0.5000
N 0.1700 0.6597 0.5000
B 0.1700 0.7696 0.5000
N 0.2500 0.8296 0.5000
B 0.2500 0.9394 0.5000
N 0.3400 0.000 0.5000
B 0.3400 0.1100 0.5000
N 0.4198 0.1700 0.5000
B 0.4198 0.2800 0.5000
N 0.3400 0.3299 0.5000
B 0.3400 0.4400 0.5000
N 0.4198 0.5000 0.5000
B 0.4198 0.6099 0.5000
N 0.3400 0.6597 0.5000
B 0.3400 0.7696 0.5000
N 0.4198 0.8296 0.5000
B 0.4198 0.9394 0.5000
N 0.5101 0.000 0.5000
B 0.5101 0.1100 0.5000
N 0.58333403 0.1700 0.5000
B 0.58333403 0.2800 0.5000
N 0.5101 0.3299 0.5000
B 0.5101 0.4400 0.5000
N 0.58333403 0.5000 0.5000
B 0.58333403 0.6099 0.5000
N 0.5101 0.6597 0.5000
B 0.5101 0.7696 0.5000
N 0.58333403 0.8296 0.5000
B 0.58333403 0.9394 0.5000
N 0.6800 0.000 0.5000
B 0.6800 0.1100 0.5000
N 0.75000101 0.1700 0.5000
B 0.75000101 0.2800 0.5000
N 0.6800 0.3299 0.5000
B 0.6800 0.4400 0.5000
N 0.75000101 0.5000 0.5000
B 0.75000101 0.6099 0.5000
N 0.6800 0.6597 0.5000
B 0.6800 0.7696 0.5000
N 0.75000101 0.8296 0.5000
B 0.75000101 0.9394 0.5000
N 0.8498 0.000 0.5000
B 0.8498 0.1100 0.5000
N 0.91666800 0.1700 0.5000
B 0.91666800 0.2800 0.5000
N 0.8498 0.3299 0.5000
B 0.8498 0.4400 0.5000
N 0.91666800 0.5000 0.5000
B 0.91666800 0.6099 0.5000
N 0.8498 0.6597 0.5000
B 0.8498 0.7696 0.5000
N 0.91666800 0.8296 0.5000
B 0.91666800 0.9394 0.5000
H 0.5000 0.6600 0.56900670
H 0.6800 0.3300 0.56900670
K_POINTS {automatic}
8 8 1 0 0 0
==
Teng Fei Cao
==
Research Laboratory for Computational Materials Sciences,
Instutue of Solid State Physics,the Chinese Academy of Sciences,
P.O.Box 1129, Hefei 230031, P.R.China
Tel: 86-551-5591464-326(office)
Fax: 86-551-5591434
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[Pw_forum] bismuth fully relativistic pseudopotential needed
The PSLibrary contents the pseudo-potential of ultrasoft full-rel Bi as: title='Bi', zed=83, rel=$nrel, config='[Xe] 4f14 5d10 6s2 6p3 6d-2', iswitch=3, dft='$gfun', / pseudotype=3, file_pseudopw='Bi.$fct-dn-rrkjus.UPF', author='ADC', lloc=-2, rcloc=2.2, which_augfun='PSQ', rmatch_augfun_nc=.true., nlcc=.true., new_core_ps=.true., nlcc=.true., new_core_ps=.true., rcore=1.4, tm=.true., / 6 6S 1 0 2 0 1.6 2.2 0 6S 1 0 0 0.2 1.6 2.2 0 6P 2 1 3 0 1.6 2.3 0 6P 2 1 0 0.2 1.6 2.3 0 5D 3 2 10 0 0.9 2 0 5D 3 2 0 2.5 0.9 2 0 -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-04-18 17:27:50,"???" wrote: Hi ,all I want to calculate properties of Bi2Se3 concerning spin orbit coupling , however attempt to find the full relativistic ultrasoft PBE pseudopotential of bismuth failed . Will you be kind enough to supply me with the pseudopotential file ??? -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120418/b4ae638b/attachment.htm
[Pw_forum] Any Norm-conserved PP database for Pwscf?
Oh, that is nice, thank you very much for providing this information. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-04-12 20:00:53,"Lorenzo Paulatto" wrote: >On Thu, 12 Apr 2012 10:40:50 +0200, GAO Zhe wrote: >> I remember that ph.x can deal with ultrasoft pseudo-potential (may not >> work with PAW pseudo-potential > >PAW dataset are supported by the phonon code. > > >bests >-- >Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 >phone: +33 (0)1 44275 084 / skype: paulatz >www: http://www-int.impmc.upmc.fr/~paulatto/ >mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120412/a13a2034/attachment.htm
[Pw_forum] Any Norm-conserved PP database for Pwscf?
I remember that ph.x can deal with ultrasoft pseudo-potential (may not work with PAW pseudo-potential)~ According to my own experience, since NCPP alway requires high cut-off energy, it will cost more time for phonon calculation~ Or, this website: http://www.sas.upenn.edu/rappegroup/htdocs/Research/psp_gga.html, provides norm-conserving pseudo-potential parameters for certain elements (a little big harder pp, so the cut-off around 100Ry is required). You can use opium code to generate UPF format pp based on the parameters. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-04-12 14:55:34,"Sheleon Zhang" wrote: >Hello, >Recently,i am going to perform the photon calulations for some crystal, >but most of the pp for atoms are not nc formatted. at first, i want to >covert the abinit nc-pp to pwscf using phi2upf.x, but when it read the >second line of nc-pp file contains znatom, zion, pspdat,programme failed >with 'Fortran runtime error: Bad real number in item 1 of list input' or >'forrtl: severe (59): list-directed I/O syntax error, unit 1,'. i check >the code,but cant find anything wierd.Please guide me how to solve this >promblem. >Thanks in advanced > > > >Best regards! > >Sheleon >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120412/02e3396a/attachment.htm
[Pw_forum] help on convergence
Dear Ibrahim at least, you need to: 1, increasing your ecutwfc little bit, 25Ry is normally not good enough; 2, adding ecutrho, which should be equal to 8~12 times of ecutwfc, due to you were using ultrasoft pp 3, the most important one, you'd better add crystal after ATOMIC_POSITIONS, I remember the default one may be alat. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-04-08 21:08:47,"bamidele ibrahim" wrote: Dear all, I am working on TiO2 and running scf for this compound, i have not been able to get a convergence. I will be delighted if i can get help on this from any expert. I have with this mail the input file for the scf. Adetunji Bamidele Ibrahim(PhD Student) Department of physics,University of Agriculture, Abeokuta, Ogun State,Nigeria. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120409/74745f75/attachment.htm
[Pw_forum] How to plot the potential curve during pseudopotential generation?
The one you need may be in the name of ld1ps.wfc, you can draw it by gnuplot or xmgrace. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-04-04 18:58:36,"??" wrote: >Dear all, > >When I am using the ld1.x to generate a pseudopotential, I want to plot the >potential curve (pseudo V-r curve) to see how it fitting the all-electron >case. However, I cannot find any file containing such potential. And could you >guide me how to find it? Thank you very much? > >Warmest regards, > >Plato Tao > > > >-- >--- >PH.D. candidate Peng Tao >Magnetism and Magnetic Materials Division >National Laboratory for Material Science >Institute of Metal Research, Chinese Academy of Sciences >Phone +86-024-83978751 >--- > > > > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120404/af2d35a1/attachment.htm
[Pw_forum] error two atoms overlap
Since your system is simple cubic, and your first and second atoms position are (0,0,0) and (-1,0,0), which are both at the vertex position of a cubic, thus the 1st and 2nd atoms at exactly same position (please think about the translation in crystal). Actually, in you input file, atom 1~4 aimed the same position. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-27 06:33:35,"mohamed makhyoun" wrote: | Dear All: By running the given input file for pw.x I get the error: from check_atoms : error # 1 atoms # 1 and # 2 overlap! Although I checked the input by XCRYSDEN visualization program and nothing is wrong. I appreciate any help. Best Regard Mohamed ### calculation = 'scf' , prefix='cu3nbs4' restart_mode = 'from_scratch' , outdir = '$TMP_DIR/' , pseudo_dir = '/home/mohamed/espresso/exec/pseudo' , verbosity = 'default' , / ibrav=1 celldm(1)= 10.397 , nat = 20, ntyp = 3, ecutwfc = 60. , nbnd=90, / conv_thr=1.0D-8 , / ATOMIC_SPECIES Nb 92.9064 Nb.pbe-sR-sc-us.UPF Cu 63.546Cu.pbe-sR-us.UPF S 32.06 S.pbe-van-bm.UPF ATOMIC_POSITIONS crystal Nb 0.0 0.0 0.0 Nb -1.0 0.0 0.0 Nb 0.0 0.0 -1.0 Nb 1.0 0.0 0.0 Cu 0.5 0.0 0.0 Cu 0.0 0.0 -0.5 Cu -0.5 0.0 0.0 Cu 0.0 -0.5 0.0 Cu 0.0 0.5 0.0 Cu 0.0 0.0 0.5 S0.242599953 0.242599953 0.242599953 S0.242599953 -0.242599953 -0.242599953 S -0.242599953 0.242599953 -0.242599953 S -0.242599953 -0.242599953 0.242599953 S -0.757400047 0.242599953 0.242599953 S0.242599953 0.242599953 -0.757400047 S -0.757400047 -0.242599953 -0.242599953 S0.757400047 0.242599953 -0.242599953 S -0.242599953 -0.242599953 -0.757400047 S0.757400047 -0.242599953 0.242599953 K_POINTS gamma | -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120327/e0400c5c/attachment.htm
[Pw_forum] Problem with QE4.0.3
If you have installed ifort and MKL, then you can add ifort into environment
variables. For example, the 64bit ifort installed in /opt/intel, by writing
source /opt/intel/bin/compilervars.sh intel64 into your ${HOME}/.bashrc
software will find MKL automaticly.
BTW, lmkl_lapack.so is looked from an old version of ifort or mkl.
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
At 2012-03-25 21:44:20,"Ajit Vallabhaneni" wrote:
>Dear users,
>
> I am trying to install QE V4.0.3 for some purpose although i
> installed V4.3.2 before. I followed the same procedure as 4.3.2
> (./configure-> make PW,PH) after loading the same modules. I am able to
> generate the pw.x and ph.x files but they are not working properly.
>
>
>[avallabh at hansen-fe00 bin]$ ./pw.x
>./pw.x: error while loading shared libraries: libmkl_lapack.so: cannot open
>shared object file: No such file or directory
>
>
> Please let me know how should i fix this. I didnot have this problem
> with V4.3.2.
>
>
>Thanks
>Ajit
>___
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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[Pw_forum] error in reading namelist system
Dear Gabriele:
I am afraid it has to be if one wanted to calculate electron-phonon
interactions, although la2F is not mentioned in INPUT_PW and PWgui. This
parameter helps to form a la2F data file in outdir from SCF and will be used by
ph.x once setting elph = .true.
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
At 2012-03-23 00:54:04,"Gabriele Sclauzero"
wrote:
Dear Elie,
are you sure that this la2F keyword is part of the pw.x namelist?
Anyway, it's always good practice to specify which version of QE you are using
as well as the compiler.
If you are using version 4.3.2 with some versions of the Intel 12.x.x compiler,
there could be some problems with the new handling of the input files.
Indeed, what I have observed is that lines longer than 80 characters are split
when the original input is copied to the input_tmp.in file.
This can possibly lead to a wrong interpretation of your input.
Is this the case for you?
HTH
GS
Il giorno 22/mar/2012, alle ore 15.07, Elie M ha scritto:
Dear all,
I am trying to run an scf calculation but the code complains:
" from read_namelists : error #19
reading namelist system"
I have checked into my but could not find anything wrong.
"
prefix='elphmono',
calculation='scf',
restart_mode='from_scratch',
verbosity='high',
tprnfor=.true.,
pseudo_dir = '/home_cluster/fis718/eliemouj/espresso-4.3.2/pseudo',
outdir='/home_cluster/fis718/eliemouj/espresso-4.3.2/monographene/MONODIR',
/
ibrav= 4, celldm(1) =4.608737, celldm(3)=4.53666, nat=2, ntyp= 1, ecutwfc
=32, occupations='smearing', smearing='methfessel-paxton', degauss=0.01,
la2F=.true.
/
conv_thr=1.D-9,
mixing_beta=0.1D0,
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
ATOMIC_POSITIONS crystal
C 0.00 0.00 0.00
C 0.33 -0.33 0.00
K_POINTS {automatic}
50 50 1 0 0 0 "
Can anyone spot anything wrong with it. Thank you all
Elie Moukaes
University of Nottingham
NG7 2RD
UK
___
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Pw_forum at pwscf.org
http://www.democritos.it/mailman/listinfo/pw_forum
? Gabriele Sclauzero, EPFL SB ITP CSEA
PH H2 462, Station 3, CH-1015 Lausanne
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[Pw_forum] error in reading namelist system
How about adding a "," after la2F = .true. as: ... la2F = .true. , / -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-22 23:17:54,"Elie M" wrote: There is nothing wrong with the pseudo_dir or outdir otherwise it would have complained that the directory does not exist. This is really weird. I cannot find any errors in the part Elie > Date: Thu, 22 Mar 2012 10:25:38 -0400 > From: avallabh at purdue.edu > To: elie.moujaes at hotmail.co.uk > CC: pw_forum at pwscf.org > Subject: Re: [Pw_forum] error in reading namelist system > > Elie, > > I am able to run your script with out any errors. Please check the names of > pseudo_dir and out_dir in your file. > > Thanks > Ajit -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120325/9ef7e8f1/attachment.htm
[Pw_forum] LDA+U or GGA+U?
Dear QE developer and users: I just began to try LDA+U method in QE, by adding lda_plus_u = .true. and Hubbard_U(i) parameters to scf input file, where the U value was determined by following M.Cococcioni's thesis and Prof. Marzari's paper (PRL, 97, 103001). However, when I check other code about this area, I found these days they are using GGA+U as well. Such like in VASP, I saw they mentioned in forum that LDA or GGA is just depends on XC in pseudo-potential. And in the case of Abinit, the official example is calculated by PBE-PAW pseudo-potential. Therefore, I am wondering that, if I setted lda_plus_u = .true. and used GGA pseudo-potential, may I say I am using GGA+U method? Since when I tried in that way, I saw the output is as: LDA+U calculation, Hubbard_lmax = 2 atomic species L Hubbard U Hubbard alpha Any suggestion is welcome. Thanks. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120312/b685b995/attachment.htm
[Pw_forum] Eyvaz Isaev
I am so sad to hear such a bad news. Without Prof. Isaev's kind help, I might not overcome the difficulty in calculations by PWscf and write my papers. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-02 15:44:11,"Paolo Giannozzi" wrote: >I have the regret to announce that Prof. Dr. Eyvaz Isaev, >author of QHA and PlotPhon packages, passed away on Sept.11, 2011 > >P. >-- >Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120303/6f564f2f/attachment.htm
[Pw_forum] Error in using bands_FS.x to get Fermi surface,
I checked the code of bands_FS.f90, and found like this: open(12,file='input_FS') read(12,*) n_start, n_last read(12,*) E_fermi read(12,*) sysname read(12,*) na,nb, nc read(12,*) x(1),x(2),x(3) read(12,*) y(1),y(2),y(3) read(12,*) z(1),z(2),z(3) So I am just wondering whether it can work well, if you change your input file name as "input_FS", and run only by the command bands_FS.x < CWrium.fs.in > CWrium.fs.out, where CWrium.fs.in is a nscf calculation input file with the K_Points obtained by kvec_FS.x. The more ditailed process is in example 08. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-03-02 11:08:12,"Chan-Woo Lee" wrote: Dear QE developers and users, I am trying to get Fermi surface using kvecs_FS.x and bands_FS.x. I have followed example08 and have succeeded to get K-points using kvecs_FS.x. However, I got following error message when I execute bands_FS.x: At line 230 of file bands_FS.f90 Fortran runtime error: Bad real number in item 13 of list input Line 230 of bands_FS.f90 is about reading spin-up energies?. But I have no idea why the code is not working. FYI, I added my input files for kvecs_FS.x and bands_FS.x: kvecs_FS.in: 0.317093 0.00 0.00 0.00 0.317093 0.00 0.00 0.00 0.317093 12 12 12 CWrium input_FS.in: 10 14 22.8158 CWrium 12 12 12 0.317093 0.00 0.00 0.00 0.317093 0.00 0.00 0.00 0.317093 Here, 10 14 are min. and max. band no. (no. of bands for my SCF calc. is 20), and 22.8158 is Fermi energy. Again, your help will truly be appreciated. I cc?ed Dr. Eyvaz Isaev who is the author of the two codes. Sincerely, Chan-Woo --- Chan-Woo Lee, Ph.D. Postdoctoral Research Associate Department of Chemistry University of Pennsylvania 231 South 34th Street Philadelphia, PA 19104-6323 Phone: 1-215-898-3564 (Office) -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120302/ddc3f215/attachment.htm
[Pw_forum] POPULATION OF CHARGE
in the output of projwfc.x, Lowdin Charge -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-23 20:06:56,"bhabya sahoo" wrote: can espresso give the population of charge in in each orbital? b d sahoo reserch scolar mumbai -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120223/e72caf4f/attachment.htm
[Pw_forum] LATTICE PARAMETER FOR InAs/GaAs QUANTUM DOT
You can find structure information here: http://rruff.geo.arizona.edu/AMS/amcsd.php -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-21 01:51:10,"michael onyeaju" wrote: Dear Q.E User I am currently working on strained InAs spherical quantum dot emberded in GaAs substrate but find it difficult to get the number of atom per unit cell (the lattice parameter), please can some one help me out Onyeaju, Michael Department of Physics, Faculty of Science, University of Port Harcourt Phone:+2348068118468 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120221/d167f530/attachment.htm
[Pw_forum] How we can give Temperature to equilibrium system (T=o)
You can obtain thermodynamics properties at finite temperature by calculating phonon (ph.x) and treating phonon through QHA method. If temperature was high, you may need an-harmonic calculation by d3.x -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-09 22:49:27,"bramha pandey" wrote: Dear QE users... i want to know how we can introduce the temperature in our equilibrium system(i.e after running scf with proper setting of lattice parameter, ecut and k point, we get ground state total energy(T=0) in scf run). As i read somewhere that SCF will gives the minimum total energy at T=0, because in DFT there is no term of temperature. May be i am wrong but can we introduce temperature by changing the any parameter in input file of pw.x. Actualy i want to generate the phonon by the thermal excitation in my input file by increasing the temperature of my system or any other means by which i can generate phonon for thermo-dynamical property calculation of the system. Any type of help will be appreciable . -- Thanks and Regards Bramha Prasad Pandey Assistant Professor (Electronics and Communication Engg) GLA Group of Institutions, Mathura. Ph. No. 08954143009 email id pandey.bramha at gmail.com bpglaitm at yahoo.co.in -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/84ba8dc9/attachment.htm
[Pw_forum] Calculation stopped at the beginning of ph.x process
Dear QE developer and users:
At first, I want to say thanks to Alex Kohlmeyer, who made me realized I still
can run the calculation by normal user access.
I compiled pw.x and ph.x, again, by mpich2 1.4.1p1 which was compiled by PGI
fortran 9.0 (trial version). The pw.x calculation among 12 nodes (24 cores) was
very nice. But when I run the ph.x, the calculation stopped at the initial step.
The terminate displayed as:
mpirun -machinefile nodes -np 24 ${KKK}/ph.x -npool 3 -in ${KKK}/binary.ph.in >
${KKK}/binary.ph.out
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 2
.
application called MPI_Abort(MPI_COMM_WORLD, 0) - process 23
And I checked the output file, binary.ph.out, it did not show the information
about process stopping:
Parallel version (MPI), running on24 processors
K-points division: npool =3
R & G space division: proc/pool =8
Ultrasoft (Vanderbilt) Pseudopotentials
Info: using nr1, nr2, nr3 values from input
Info: using nr1s, nr2s, nr3s values from input
Message from routine read_ions :
PP will be read from ./
Parallelization info
sticks: dense smooth PW G-vecs:dense smooth PW
Min 253 253 72 8611 86111298
Max 254 254 73 8614 86141301
Sum202520255776889168891 10395
Dynamical matrices for ( 3, 3, 3,) uniform grid of q-points
( 4q-points):
N xq(1) xq(2) xq(3)
1 0.0 0.0 0.0
2 0.0 0.0 0.3
3 0.0 0.3 0.3
4 0.3 0.3 0.3
Calculation of q =0.000 0.000 0.000
rank 3 in job 73 node01_35097 caused collective abort of all ranks
exit status of rank 3: killed by signal 9
..
rank 22 in job 73 node01_35097 caused collective abort of all ranks
exit status of rank 22: killed by signal 9
Why did this problem occurred? I ran the same input file in my own computer,
with mpich2 1.4.1p1 and ifort 12. It worked well at least up to the "break
point". Is this problem caused by the fortran compilor PGI 9.0?
Looking forward to any suggestion.
Thanks a lot.
--
GAO Zhe
CMC Lab, Materials Science & Engineering Department,
Seoul National University, South Korea
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[Pw_forum] The iotk error occurrd in ph.x
Dear Axel, thank you very much. I will try ifort+mpich2 in my own directory, hoping it works and the newest ifort 12 can work in Fedora 7. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-02-08 22:12:02,"Axel Kohlmeyer" wrote: >2012/2/8 GAO Zhe : >> Dear QE developer and users >> I am using an old cluster for calculation, where mpich2 1.2.1 was compiled >> by gortran 4.1.2 in Fedora 7 x86_64. >> The pw.x calculations were fine, but when I was executing ph.x, the iotk >> error occurred (no matter multi-nodes or single-core, this error occurred as >> soon as the input file read by ph.x) : >> # FROM IOTK LIBRARY, VERSION 1.2.0 >> # UNRECOVERABLE ERROR (ierr=1) >> # ERROR IN: iotk_scan_end (iotk_scan.f90:241) >> # CVS Revision: 1.23 >> # foundl >> # ERROR IN: iotk_close_read (iotk_files.f90:746) >> # CVS Revision: 1.20 >> As I known, such a problem is due to the bug of compiler, i.e., gfortran >> 4.1.2. However, since I just have the normal user authority in this cluster, >> I cannot upgrade gfortran or install other fortran compiler. Even mpich2 was >> installed in /usr, so I cannot re-compile it. > >yes, you can compile and install both the GCC compilers >(including gfortran) and the MPI library without superuser >privilege and override the system defaults. it just takes >some effort and requires reading of the corresponding >documentation. i have done both many times on very >different machines without having root access. > >axel. > > >> In such a case, do I have to give up the phonon calculaitons in this cluster >> ? >> >> -- >> GAO Zhe >> CMC Lab, Materials Science & Engineering Department, >> Seoul National University, South Korea >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > >-- >Dr. Axel Kohlmeyer >akohlmey at gmail.com http://goo.gl/1wk0 > >College of Science and Technology >Temple University, Philadelphia PA, USA. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120209/d413b127/attachment.htm
[Pw_forum] The iotk error occurrd in ph.x
Dear QE developer and users I am using an old cluster for calculation, where mpich2 1.2.1 was compiled by gortran 4.1.2 in Fedora 7 x86_64. The pw.x calculations were fine, but when I was executing ph.x, the iotk error occurred (no matter multi-nodes or single-core, this error occurred as soon as the input file read by ph.x) : # FROM IOTK LIBRARY, VERSION 1.2.0 # UNRECOVERABLE ERROR (ierr=1) # ERROR IN: iotk_scan_end (iotk_scan.f90:241) # CVS Revision: 1.23 # foundl # ERROR IN: iotk_close_read (iotk_files.f90:746) # CVS Revision: 1.20 As I known, such a problem is due to the bug of compiler, i.e., gfortran 4.1.2. However, since I just have the normal user authority in this cluster, I cannot upgrade gfortran or install other fortran compiler. Even mpich2 was installed in /usr, so I cannot re-compile it. In such a case, do I have to give up the phonon calculaitons in this cluster ? -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120208/37513e5d/attachment.htm
[Pw_forum] query on e-ph tutorial
This problem happens during diagonalize the matrix. At least there are two methods to solve this problem: Firstly, changing the diagonalization method to CG, which requires to modify the PH code; secondly, increasing empty bands by "nbnd" parameter in the input file of pw.x. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-01-30 22:48:10,"Ajit Vallabhaneni" wrote: >Dear Paolo, > >Sorry for sending my response to your personal email. I didn't > see it before.Here is my question. > > I tried example 7 with the same parameters given. But the > al.elph.in (with nq1=nq2=nq3=4) was terminated with the following message: > > >Band Structure Calculation > Davidson diagonalization with overlap > > %% > from cdiaghg : error #19 > diagonalization (ZHEGV*) failed > %% > > stopping ... > > >Is this because of the small mesh size (16x16x16)? > >Thanks >Ajit >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120131/ec7f58ba/attachment-0001.htm
[Pw_forum] help regarding fqha.x
You can use the QHA module in QE, which gives you more detailed result. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-01-28 22:11:54,"bramha pandey" wrote: Good evening to all QE users I wanted to calculate the thermodynamical property of system using QE. i was trying to use fqha.x code which was giving only free energy at each temperature. but i require other properties of thermodynamic like cv, internal energy etc. how can i get other properties of thermodynamic using fqha.x. Thanks in advanced for your valuable comments. -- Thanks and Regards Bramha Prasad Pandey Assistant Professor (Electronics and Communication Engg) GLA Group of Institutions, Mathura. Ph. No. 08954143009 email id pandey.bramha at gmail.com bpglaitm at yahoo.co.in -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120130/2d585bfd/attachment.htm
[Pw_forum] problen to run q2r.x code.
The function of q2r.x is summarizing a series of dynamic matrics and transferring to real space force constants by FFT. Such series dyn files, declaring as fildyn='*' in the input file of q2r.x, are named as *0, *1, *2,..., where *0 contains the dyn files list. Therefore, when you have only one dyn file, it is not recommanded to form the force constants. Or, if you really want, you can make a file, let's call it dyn.G0, and write such contents in it: 1 1 1 1 0.000E+00 0.000E+00 0.000E+00 Then change the file name of dyn.G to dyn.G1, and using q2r.x by the input: zasr = 'simple' , fildyn = 'dyn.G' , flfrc = 'fc' , / I do not guarantee such a method can help you to achieve meaningful result -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-01-27 00:22:08,"bramha pandey" wrote: Dear QE Users.. good evening. i got a problem when running the q2r.x code for obtaing the IFC file. I am using QE-4.3.2 on ubantu 11.10 of 32 bits the error is shown file /home/espresso-4.2/phcal/si/ dyn.G0 not found reading grid info from input but i have a file of dyn.G not dyn.G0. I have also look in q2r.f90 file. >>>> nr1,nr2,nr3: dimensions of the FFT grid formed by the q-point grid ! nfile : number of files containing C(q_n), n=1,nfile ! followed by nfile cards: ! filin : name of file containing C(q_n) ! The name and order of files is not important as long as q=0 is the first<<<< I am unable to exploit the meaning of above statement due to my new entrance in QE. Thanks in advanced for your valuable time and suggestions. -- Thanks and Regards Bramha Prasad Pandey Assistant Professor (Electronics and Communication Engg) GLA Group of Institutions, Mathura. Ph. No. 08954143009 email id pandey.bramha at gmail.com bpglaitm at yahoo.co.in -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120127/16dfd6b9/attachment.htm
[Pw_forum] Which subroutine is related to the atomic displacement in DFPT
Do you mean the displacement modes in DFPT, as: Atomic displacements: "There are", i3, "irreducible representations" May the code mode_group.f90 be able to give you some idea~ -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-01-13 00:20:57,"Caloma Trumica" wrote: Hi Professor, Can you comment on this thread. Question again, how to induce the perturbation in PWSCF? Many Thanks. On Thu, Jan 12, 2012 at 10:06 AM, Lorenzo Paulatto wrote: On Thu, 12 Jan 2012 15:47:06 +0100, Caloma Trumica wrote: > Isn't it either by atomic displacement or electric field? It's done by density functional perturbation theory (DFPT). If you have never heard it before, you can start with these slides by Stefano baroni (http://stefano.baroni.me/presentations_files/lecture-ictp-Jan2011.pdf) and/or from chapter 19.3 in R.M. Martin's book (Electronic Structure, 2004) and follow the references to go in depth. bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120113/73d72b8e/attachment.htm
[Pw_forum] Can ph.x use 'cg' diagonalization?
Prof. GIannozzi, thank you very much. It is really helpful to me. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2012-01-07 17:11:01,"Paolo Giannozzi" wrote: > >On Jan 7, 2012, at 2:35 , GAO Zhe wrote: > >> Is it possible to use conjugate gradient in ph.x ? > >edit routine "set_defaults_pw.f90", change "isolve=0" to >"isolve=1", recompile > >P. >--- >Paolo Giannozzi, Dept of Chemistry, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120107/514b76d1/attachment.htm
[Pw_forum] Can ph.x use 'cg' diagonalization?
Dear QE developer and users: I am using ph.x to calculate phonon dispersion. But I met a problem during my computation. My structure needs 12 dynamic matrics files. But after 3 *.dyn file were calculated, the error occurred during band structure calculation: Band Structure Calculation Davidson diagonalizaion with overlap %%% from cdiaghg: error #126 diagonalization (ZHEGV*) failed %%% Therefore, I changed to diagonalization='cg' in scf calculation and recalculate it, the problem remained. It seemed no matter which diag method I used in scf calculation, only Davidson algorithm is used in ph.x. Is it possible to use conjugate gradient in ph.x ? Thanks a lot. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120107/3238828b/attachment.htm
[Pw_forum] Does QE support the old MPICH and gfortran?
Dear QE developer and users: I borrowed a cluster from other department. During configure the QE package, both of v4.3.2 and v4.1.3, it showed "Parallel environment not detected". Then I checked ./install/config.log ( in QE v4.3.2 ), and found the error message like: configure:2884: mpif90 -V >&5 f95: '-V' must come at the start of the command line configure:2887: $? = 1 configure:2895: checking whether we are using the GNU Fortran compiler configure:2914: mpif90 -c -g -O2 conftest.F >&5 configure:2920: $? = 0 configure:2937: result: yes configure:2943: checking whether mpif90 accepts -g configure:2960: mpif90 -c -g conftest.f90 >&5 configure:2966: $? = 0 configure:2982: result: yes configure:3353: WARNING: parallel compiler mpif90 uses gfortran, but serial compiler mpif90 was detected configure:3355: WARNING: assuming F90=gfortran, discarding mpif90 The cluster is running on Fedora release 8. mpi version is mpif90 for 1.2.7 (release) of : 2005/11/04 11:54:51, which was compiled by gfortran ( gcc version 4.1.2 20070925 (Red Hat 4.1.2-33) ). Each node is based on Intel dual-core CPU. The parallel environment can be detected by Abinit ( unfortunately, Abinit cannot pass the mpi compiling as well, even I tried Abinit v5.3.5, which was released in 2007 ). Do I have to use an older version ( ealier than 4.1.3 ) QE? Or, are there some other methods to overcome this problem? Since this cluster does not belong to our lab, we cannot update the mpi version and install ifort. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/edaca07c/attachment.htm
[Pw_forum] software to draw phonon spectra for windows
Cygwin + gnuplot is a good choice~ Or, you can use the OriginLab or QtiPlot demo version. At 2011-12-14 04:10:04,"Liwei Geng" wrote: Dear all, Could anyone please suggest me some free software to draw phonon spectra under windows XP systems? Great thanks! Best regards, Liwei -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111214/1822d1d7/attachment.htm
[Pw_forum] How to achieve the convergence of Ecutrho?
Actually, the standard of convergency for cut-off energy is not how much dE the system gained, but whether dE/dCut is near to 0 enough. Definitely, such a threahold, for dE/dCut, is also determined by yourself. The example from you was too extreme. Thinking about 100Ry as step, your result are too rough to hold the slope information. But when 10^(-5)Ry was using, even though it should give the very fine dE/dCut information as well, the results may be not good due to the accuracy of DFT, numerical methods, and computer limitation ( please consider the length of float and double float variable ). P.S.: Therefore, I think such question is not the one of sci. & tech. rather than your thinking method. This may be the reason that no person reply such a post in emuch. -- GAO Zhe CMC Lab, Materials Science & Engineering Department, Seoul National University, South Korea At 2011-12-13 15:43:04,"??" wrote: >Dear all, > >I've asked sevral people about the convergence criteria of Ecutrho test. They >point out that the convergence will be achieved when the difference between >two adjacent scf calculation is smaller than 0.1 meV. However, they are not >very sure about the step length. From my view, the step length may pose huge >effects on our calculation. Consider the cases of step lengths are 100 Ry and >0.1Ry respectively, the latter will be convergent immediately while the >former will not be so fast. > >For the resons above, I'm really confused now. And could any nice guy show me >the strict judgement of the convergence for Ecutrho? Thank you very much! > >Yours, >Plato Tao > >-- >--- >PH.D. candidate Peng Tao >Magnetism and Magnetic Materials Division >National Laboratory for Material Science >Institute of Metal Research, Chinese Academy of Sciences >Phone +86-024-83978751 >--- > > > > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111213/07d5406c/attachment.htm
[Pw_forum] PlotPhon Examples
*.fc is generated from dynamics matrics by q2r.x. The script in examples just organizes several programs, matdyn.x, k_for_bands.x, bands_to_gnuplot.x and E_min_max.x, working one by one with certain data exchanging. Through pw.x and ph.x, you can just obtain dynamics matrics. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-11-21 15:32:17,W2AGZ wrote: To All (especially Eyvas), Are the input scripts used to generate the .fc files for the two Al examples and Fe from pw.x and ph.x available? Thanks, -Paul Paul Michael Grant, PhD Physicist and Science Writer Senior Life Fellow, American Physical Society Fellow, Institute of Physics, United Kingdom Staff Associate, Jet Propulsion Laboratory, NASA (2011) Visiting Scholar, Applied Physics, Stanford (2005-2008) EPRI Science Fellow (Retired) IBM Research Staff Member Emeritus Principal, W2AGZ Technologies w2agz at w2agz.com http://www.w2agz.com -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2021/71487f30/attachment.htm
[Pw_forum] calculation of lattice parameter and angle of rhombohedral structure
Yes, that is my mistake. The denominator should be (|a| |b|). Furthermore, I just wanted to say A as the angle between vector a and b~~~ Definitely, in rhombohedral structure, alpha = beta = gamma~ -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-11-17 18:15:17,"Gabriele Sclauzero" wrote: Dear all, I think that (using GAO Zhe's notation) both b (*) c / (|b| |c|) and a (*) b / (|a| |b|) should give the same result, because in the rhombohedral lattice the three basis vectors form equal angles with each other. Obviously, a (*) b / (|a (*) b|) is not correct because it would always give 1 or -1 (and I believe it was just a typo). HTH GS On 11/17/2011 06:49 AM, Huiqun Zhou wrote: I'm afraid the formula for calculating cosA should be cosA = b (*) c / (|b| | c|) dr. zhou huiqun @earth sciences, nanjing university, china - Original Message - From:GAO Zhe To:PWSCF Forum Sent: Wednesday, November 16, 2011 8:53 PM Subject: Re: [Pw_forum] calculation of lattice parameter and angle of rhombohedral structure the three basis vectors of rhombohedral are (after relaxation) : a = ( 0.636439417 -0.367448469 0.640642896 ) b = ( 0.0 0.734896938 0.640642896 ) c = ( -0.636439417 -0.367448469 0.640642896 ) then the lattice paremeter should be: A = sqrt (a1^2+a2^2+a3^2) * alat = 8.05092296 a.u. . The angle between two vectors can be calculated by: cosA = a (*) b / |a (*) b|, where a and b are basis vectors, (*) represents the dot product. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-11-16 20:14:38,"yedu kondalu" wrote: Dear users, I did the optimization for a compound using variable cell approximation using PWSCF, which belongs to the space group R3m(160) Rhombohedral representation. The primitive vectors in terms of lattice parameter a = 8.25791360 a.u. a(1) = ( 0.619505 -0.357671 0.698774 ) a(2) = ( 0.00 0.715343 0.698774 ) a(3) = ( -0.619505 -0.357671 0.698774 ) after completion of optimization step, the primitive vectors CELL_PARAMETERS (alat= 8.25791360) 0.636439417 -0.367448469 0.640642896 0.0 0.734896938 0.640642896 -0.636439417 -0.367448469 0.640642896 can u please explain me how can I calculate the lattice parameter a and the angle (alpha) ??? Thanks in advance Regards Yedukondalu -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2017/6df9938a/attachment.htm
[Pw_forum] calculation of lattice parameter and angle of rhombohedral structure
the three basis vectors of rhombohedral are (after relaxation) : a = ( 0.636439417 -0.367448469 0.640642896 ) b = ( 0.0 0.734896938 0.640642896 ) c = ( -0.636439417 -0.367448469 0.640642896 ) then the lattice paremeter should be: A = sqrt (a1^2+a2^2+a3^2) * alat = 8.05092296 a.u. . The angle between two vectors can be calculated by: cosA = a (*) b / |a (*) b|, where a and b are basis vectors, (*) represents the dot product. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-11-16 20:14:38,"yedu kondalu" wrote: Dear users, I did the optimization for a compound using variable cell approximation using PWSCF, which belongs to the space group R3m(160) Rhombohedral representation. The primitive vectors in terms of lattice parameter a = 8.25791360 a.u. a(1) = ( 0.619505 -0.357671 0.698774 ) a(2) = ( 0.00 0.715343 0.698774 ) a(3) = ( -0.619505 -0.357671 0.698774 ) after completion of optimization step, the primitive vectors CELL_PARAMETERS (alat= 8.25791360) 0.636439417 -0.367448469 0.640642896 0.0 0.734896938 0.640642896 -0.636439417 -0.367448469 0.640642896 can u please explain me how can I calculate the lattice parameter a and the angle (alpha) ??? Thanks in advance Regards Yedukondalu -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2016/bd9126e6/attachment.htm
[Pw_forum] problem about pp.x: namelist plot not found or invalid
Thank you very much for your patient. since the bash script was a little bit complex, the careless and low level error occurred. Next time, I will check my input more carefully. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-11-15 19:50:18,"Guido Fratesi" wrote: >No, the order within the namelist is not important, but you solved the >problem by correctly typing the variable names. >GF > >Il 11/15/2011 12:47 PM, GAO Zhe ha scritto: >> Oh, I am sorry to bother~ I have found the problem. >> This problem occurred when filepp(i) have not been written together, i.e.: >> filepp(1) >> filepp(2) >> >> filepp(max) >> weight(1) >> weight(2) >> >> weight(max) >> is the only right way to create the input file. >> >> >> At 2011-11-15 19:29:46,"GAO Zhe" wrote: >> >> Dear QE developer and users: >> Hi >> I am using pp.x to generate the charge density file on certain >> surface. The work for namelist, , worked very well. >> However, when I wanna summary the results from to xcrysden >> file, the error occurred: >> chdens, namelist plot not found or invalid, exiting >> Actually, I changed chdens.f90 a little bit on INTEGER, PARAMETER :: >> nfilemax = 30, but I do not think this is the reason to meet such a >> problem~ Since if I create a short input file by PWGUI, then it >> works well. However, even if the short one created by myself, the >> same error happened. >> Now, I need to summary more than 20 |psi|^2files due to the density >> k-points mesh, so it is impossible to build the input file via >> PWGUI's help. >> I checked chdens.f90, again, but I cannot understand the meaning of >> error~ >> Any suggetstion will be welcome. >> P.S.: This is my input file (the file have generated in the >> previous steps) : >> >> / >> >> nfile = 27 , >> filpp(1) = 'CD_1.dat' , >> weight(1) = 0.016 , >> filpp(2) = 'CD_2.dat' , >> weight(2) = 0.032 , >> filpp(3) = 'CD_3.dat' , >> weight(3) = 0.032 , >> filpp(4) = 'CD_4.dat' , >> weight(4) = 0.032 , >> filpp(5) = 'CD_5.dat' , >> weight(5) = 0.064 , >> filpp(6) = 'CD_6.dat' , >> weight(6) = 0.064 , >> filpp(7) = 'CD_7.dat' , >> weight(7) = 0.032 , >> filpp(8) = 'CD_8.dat' , >> weight(8) = 0.064 , >> filpp(9) = 'CD_9.dat' , >> weight(9) = 0.064 , >> filpp(10) = 'CD_10.dat' , >> weight(10) = 0.032 , >> filpp(11) = 'CD_11.dat' , >> weight(11) = 0.064 , >> filpp(12) = 'CD_12.dat' , >> weight(12) = 0.064 , >> filpp(13) = 'CD_13.dat' , >> weight(13) = 0.064 , >> filpp(14) = 'CD_14.dat' , >> weight(14) = 0.128 , >> filpp(15) = 'CD_15.dat' , >> weight(15) = 0.128 , >> filpp(16) = 'CD_16.dat' , >> weight(16) = 0.064 , >> filpp(17) = 'CD_17.dat' , >> weight(17) = 0.128 , >> filpp(18) = 'CD_18.dat' , >> weight(18) = 0.128 , >> filpp(19) = 'CD_19.dat' , >> weight(19) = 0.032 , >> filpp(20) = 'CD_20.dat' , >> weight(20) = 0.064 , >> filpp(21) = 'CD_21.dat' , >> weight(21) = 0.064 , >> filpp(22) = 'CD_22.dat' , >> weight(22) = 0.064 , >> filpp(23) = 'CD_23.dat' , >> weight(23) = 0.128 , >> filpp(24) = 'CD_24.dat' , >> weight(24) = 0.128 , >> filpp(25) = 'CD_25.dat' , >> weight(25) = 0.064 , >> filpp(26) = 'CD_26.dat' , >> weight(26) = 0.128 , >> filpp(27) = 'CD_27.dat' , >> weight(27) = 0.128 , >> fileout = 'CDresult.xsf' , >> iflag = 2 , >> output_format = 3 , >> e1(1) = 2.0, >> e1(2) = 0.0, >> e1(3) = 0.0, >> e2(1) = 0.0, >> e2(2) = 2.0, >> e2(3) = 0.0, >> x0(1) = 0.0, >> x0(2) = 0.0, >> x0(3) = 0.0, >> nx = 45 , >> ny = 45 , >> / >> >> >> >> -- >> GAO Zhe >> CMC Lab, MSE, SNU, Seoul, S.Korea >> >> >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > >-- >Guido Fratesi > >Dipartimento di Scienza dei Materiali >Universita` degli Studi di Milano-Bicocca >via Cozzi 53, 20125 Milano, Italy >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2015/d2b65c9c/attachment.htm
[Pw_forum] problem about pp.x: namelist plot not found or invalid
I am sorry, this is my mistake, but I thing the order of filepp(i) and weight(i) could be another problem. At 2011-11-15 19:44:40,"Guido Fratesi" wrote: >Dear Gao Zhe, >"filpp" should be "filepp", at least. >Guido > >Il 11/15/2011 12:29 PM, GAO Zhe ha scritto: >> Dear QE developer and users: >> Hi >> I am using pp.x to generate the charge density file on certain surface. >> The work for namelist, , worked very well. >> However, when I wanna summary the results from to xcrysden >> file, the error occurred: >> chdens, namelist plot not found or invalid, exiting >> Actually, I changed chdens.f90 a little bit on INTEGER, PARAMETER :: >> nfilemax = 30, but I do not think this is the reason to meet such a >> problem~ Since if I create a short input file by PWGUI, then it works >> well. However, even if the short one created by myself, the same error >> happened. >> Now, I need to summary more than 20 |psi|^2files due to the density >> k-points mesh, so it is impossible to build the input file via PWGUI's help. >> I checked chdens.f90, again, but I cannot understand the meaning of error~ >> Any suggetstion will be welcome. >> P.S.: This is my input file (the file have generated in the >> previous steps) : >> >> / >> >> nfile = 27 , >> filpp(1) = 'CD_1.dat' , >> weight(1) = 0.016 , >> filpp(2) = 'CD_2.dat' , >> weight(2) = 0.032 , >> filpp(3) = 'CD_3.dat' , >> weight(3) = 0.032 , >> filpp(4) = 'CD_4.dat' , >> weight(4) = 0.032 , >> filpp(5) = 'CD_5.dat' , >> weight(5) = 0.064 , >> filpp(6) = 'CD_6.dat' , >> weight(6) = 0.064 , >> filpp(7) = 'CD_7.dat' , >> weight(7) = 0.032 , >> filpp(8) = 'CD_8.dat' , >> weight(8) = 0.064 , >> filpp(9) = 'CD_9.dat' , >> weight(9) = 0.064 , >> filpp(10) = 'CD_10.dat' , >> weight(10) = 0.032 , >> filpp(11) = 'CD_11.dat' , >> weight(11) = 0.064 , >> filpp(12) = 'CD_12.dat' , >> weight(12) = 0.064 , >> filpp(13) = 'CD_13.dat' , >> weight(13) = 0.064 , >> filpp(14) = 'CD_14.dat' , >> weight(14) = 0.128 , >> filpp(15) = 'CD_15.dat' , >> weight(15) = 0.128 , >> filpp(16) = 'CD_16.dat' , >> weight(16) = 0.064 , >> filpp(17) = 'CD_17.dat' , >> weight(17) = 0.128 , >> filpp(18) = 'CD_18.dat' , >> weight(18) = 0.128 , >> filpp(19) = 'CD_19.dat' , >> weight(19) = 0.032 , >> filpp(20) = 'CD_20.dat' , >> weight(20) = 0.064 , >> filpp(21) = 'CD_21.dat' , >> weight(21) = 0.064 , >> filpp(22) = 'CD_22.dat' , >> weight(22) = 0.064 , >> filpp(23) = 'CD_23.dat' , >> weight(23) = 0.128 , >> filpp(24) = 'CD_24.dat' , >> weight(24) = 0.128 , >> filpp(25) = 'CD_25.dat' , >> weight(25) = 0.064 , >> filpp(26) = 'CD_26.dat' , >> weight(26) = 0.128 , >> filpp(27) = 'CD_27.dat' , >> weight(27) = 0.128 , >> fileout = 'CDresult.xsf' , >> iflag = 2 , >> output_format = 3 , >> e1(1) = 2.0, >> e1(2) = 0.0, >> e1(3) = 0.0, >> e2(1) = 0.0, >> e2(2) = 2.0, >> e2(3) = 0.0, >> x0(1) = 0.0, >> x0(2) = 0.0, >> x0(3) = 0.0, >> nx = 45 , >> ny = 45 , >> / >> >> >> >> -- >> GAO Zhe >> CMC Lab, MSE, SNU, Seoul, S.Korea >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > >-- >Guido Fratesi > >Dipartimento di Scienza dei Materiali >Universita` degli Studi di Milano-Bicocca >via Cozzi 53, 20125 Milano, Italy >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2015/69f67b40/attachment-0001.htm
[Pw_forum] problem about pp.x: namelist plot not found or invalid
Oh, I am sorry to bother~ I have found the problem. This problem occurred when filepp(i) have not been written together, i.e.: filepp(1) filepp(2) filepp(max) weight(1) weight(2) weight(max) is the only right way to create the input file. At 2011-11-15 19:29:46,"GAO Zhe" wrote: Dear QE developer and users: Hi I am using pp.x to generate the charge density file on certain surface. The work for namelist, , worked very well. However, when I wanna summary the results from to xcrysden file, the error occurred: chdens, namelist plot not found or invalid, exiting Actually, I changed chdens.f90 a little bit on INTEGER, PARAMETER :: nfilemax = 30, but I do not think this is the reason to meet such a problem~ Since if I create a short input file by PWGUI, then it works well. However, even if the short one created by myself, the same error happened. Now, I need to summary more than 20 |psi|^2 files due to the density k-points mesh, so it is impossible to build the input file via PWGUI's help. I checked chdens.f90, again, but I cannot understand the meaning of error~ Any suggetstion will be welcome. P.S.: This is my input file (the file have generated in the previous steps) : / nfile = 27 , filpp(1) = 'CD_1.dat' , weight(1) = 0.016 , filpp(2) = 'CD_2.dat' , weight(2) = 0.032 , filpp(3) = 'CD_3.dat' , weight(3) = 0.032 , filpp(4) = 'CD_4.dat' , weight(4) = 0.032 , filpp(5) = 'CD_5.dat' , weight(5) = 0.064 , filpp(6) = 'CD_6.dat' , weight(6) = 0.064 , filpp(7) = 'CD_7.dat' , weight(7) = 0.032 , filpp(8) = 'CD_8.dat' , weight(8) = 0.064 , filpp(9) = 'CD_9.dat' , weight(9) = 0.064 , filpp(10) = 'CD_10.dat' , weight(10) = 0.032 , filpp(11) = 'CD_11.dat' , weight(11) = 0.064 , filpp(12) = 'CD_12.dat' , weight(12) = 0.064 , filpp(13) = 'CD_13.dat' , weight(13) = 0.064 , filpp(14) = 'CD_14.dat' , weight(14) = 0.128 , filpp(15) = 'CD_15.dat' , weight(15) = 0.128 , filpp(16) = 'CD_16.dat' , weight(16) = 0.064 , filpp(17) = 'CD_17.dat' , weight(17) = 0.128 , filpp(18) = 'CD_18.dat' , weight(18) = 0.128 , filpp(19) = 'CD_19.dat' , weight(19) = 0.032 , filpp(20) = 'CD_20.dat' , weight(20) = 0.064 , filpp(21) = 'CD_21.dat' , weight(21) = 0.064 , filpp(22) = 'CD_22.dat' , weight(22) = 0.064 , filpp(23) = 'CD_23.dat' , weight(23) = 0.128 , filpp(24) = 'CD_24.dat' , weight(24) = 0.128 , filpp(25) = 'CD_25.dat' , weight(25) = 0.064 , filpp(26) = 'CD_26.dat' , weight(26) = 0.128 , filpp(27) = 'CD_27.dat' , weight(27) = 0.128 , fileout = 'CDresult.xsf' , iflag = 2 , output_format = 3 , e1(1) = 2.0, e1(2) = 0.0, e1(3) = 0.0, e2(1) = 0.0, e2(2) = 2.0, e2(3) = 0.0, x0(1) = 0.0, x0(2) = 0.0, x0(3) = 0.0, nx = 45 , ny = 45 , / -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2015/5769bf63/attachment.htm
[Pw_forum] problem about pp.x: namelist plot not found or invalid
Dear QE developer and users: Hi I am using pp.x to generate the charge density file on certain surface. The work for namelist, , worked very well. However, when I wanna summary the results from to xcrysden file, the error occurred: chdens, namelist plot not found or invalid, exiting Actually, I changed chdens.f90 a little bit on INTEGER, PARAMETER :: nfilemax = 30, but I do not think this is the reason to meet such a problem~ Since if I create a short input file by PWGUI, then it works well. However, even if the short one created by myself, the same error happened. Now, I need to summary more than 20 |psi|^2 files due to the density k-points mesh, so it is impossible to build the input file via PWGUI's help. I checked chdens.f90, again, but I cannot understand the meaning of error~ Any suggetstion will be welcome. P.S.: This is my input file (the file have generated in the previous steps) : / nfile = 27 , filpp(1) = 'CD_1.dat' , weight(1) = 0.016 , filpp(2) = 'CD_2.dat' , weight(2) = 0.032 , filpp(3) = 'CD_3.dat' , weight(3) = 0.032 , filpp(4) = 'CD_4.dat' , weight(4) = 0.032 , filpp(5) = 'CD_5.dat' , weight(5) = 0.064 , filpp(6) = 'CD_6.dat' , weight(6) = 0.064 , filpp(7) = 'CD_7.dat' , weight(7) = 0.032 , filpp(8) = 'CD_8.dat' , weight(8) = 0.064 , filpp(9) = 'CD_9.dat' , weight(9) = 0.064 , filpp(10) = 'CD_10.dat' , weight(10) = 0.032 , filpp(11) = 'CD_11.dat' , weight(11) = 0.064 , filpp(12) = 'CD_12.dat' , weight(12) = 0.064 , filpp(13) = 'CD_13.dat' , weight(13) = 0.064 , filpp(14) = 'CD_14.dat' , weight(14) = 0.128 , filpp(15) = 'CD_15.dat' , weight(15) = 0.128 , filpp(16) = 'CD_16.dat' , weight(16) = 0.064 , filpp(17) = 'CD_17.dat' , weight(17) = 0.128 , filpp(18) = 'CD_18.dat' , weight(18) = 0.128 , filpp(19) = 'CD_19.dat' , weight(19) = 0.032 , filpp(20) = 'CD_20.dat' , weight(20) = 0.064 , filpp(21) = 'CD_21.dat' , weight(21) = 0.064 , filpp(22) = 'CD_22.dat' , weight(22) = 0.064 , filpp(23) = 'CD_23.dat' , weight(23) = 0.128 , filpp(24) = 'CD_24.dat' , weight(24) = 0.128 , filpp(25) = 'CD_25.dat' , weight(25) = 0.064 , filpp(26) = 'CD_26.dat' , weight(26) = 0.128 , filpp(27) = 'CD_27.dat' , weight(27) = 0.128 , fileout = 'CDresult.xsf' , iflag = 2 , output_format = 3 , e1(1) = 2.0, e1(2) = 0.0, e1(3) = 0.0, e2(1) = 0.0, e2(2) = 2.0, e2(3) = 0.0, x0(1) = 0.0, x0(2) = 0.0, x0(3) = 0.0, nx = 45 , ny = 45 , / -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2015/2b7315c2/attachment.htm
[Pw_forum] k-path for phonon
In my opinion, having chosen the k-path by xcrysden, you can modify the k-path file in QE/PlotPhon/Include, then the full k-path can be generated by QE/PlotPhon/bin/k_for_bands.x -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-11-03 18:58:16,"?ric Germaneau" wrote: Dear all, I got confused about how to generate k-path for matdyn.in file. I just realized that xcrysgen does not have option to write k-vectors in 2pi/a unit Would you please tell me hoe you proceed? Thank you, ?ric. -- Be the change you wish to see in the world ? Mahatma Gandhi ? Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China Please, if possible, don't send me MS Word or PowerPoint attachments Why? See:http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2003/3af90932/attachment.htm
[Pw_forum] Raman spectra calculatio using QE
If you are using K_POINTS gamma in scf but still wanna use ph.x for further calculaiton, why not try changing K_POINTS gamma to: K_POINTS 1 0.0 0.0 0.0 Or, you can using phcg.x as the follower of K_POINTS gamma case. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-27 04:36:00,wumindt2 wrote: Dear All, Is there anyone have done Raman spectra using QE? I tried to run the SiH4 example which could be downloaded from the QE website. The process i did is very simple, after scf calculation using the defalt sih4.scf.in file, i ran the sih4.nm.in file using ph.x. But i got an error as " cannot start from pw.x data file using Gamma-point tricks". So what's wrong with my calculation? Thanks for any help! Best regards, Min WU -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111027/aaff2516/attachment.htm
[Pw_forum] Partial phonon DOS
You can just use QHA in QE after IFCs calculated, then ph-pdos will be obtained directly. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-24 14:23:18,"jayashree.pan at jncasr.ac.in" wrote: Hi, I am a new Quantum Espresso user. I am doing phonon calculation and I also want to do partial phonon DOS using QE. There are some old posts from Prof.Eyvaz Isaev and Dr.Subhradip Ghosh, where they ware talking about it. Please help me if anyone know how to do it. Thank you. Jayashree -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111024/a0faad14/attachment.htm
[Pw_forum] compilation QHA code
You problem came from here: fortran -FR -c Mean_square_displacement.f90 make: fortran: Command not found Check carefully for each "makefile" and make sure that all of the compiler name is cerect. Moreover, it is suggeted to use ifort or other fortran compiler rather than gfortran for QHA, since gfortran does not support un-integer as step-length in loop. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-11 18:50:47,"bhabya sahoo" wrote: when i compile QHA the error gives gfortan -O3 -c tetra.f make: gfortan: Command not found make: *** [tetra.o] Error 127 gfortran -O3 -c Debye.f90 Debye.f90:144.8: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer Debye.f90:144.11: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Start expression in DO loop at (1) must be integer Debye.f90:144.24: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: End expression in DO loop at (1) must be integer Debye.f90:144.31: do T = T_low_start, T_low, T_low_delta 1 Warning: Deleted feature: Step expression in DO loop at (1) must be integer Debye.f90:177.4: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Loop variable at (1) must be integer Debye.f90:177.7: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Start expression in DO loop at (1) must be integer Debye.f90:177.16: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: End expression in DO loop at (1) must be integer Debye.f90:177.24: do T = T_low+5, T_high, T_high_delta 1 Warning: Deleted feature: Step expression in DO loop at (1) must be integer gfortran -O3 -c Debye_T.f gfortran -O3 -c debye3.f gfortran -O3 -c cheval.f gfortran -O3 -c d1mach.f gfortran -static -o Debye.x Debye.o Debye_T.o debye3.o cheval.o d1mach.o fortran -FR -c Mean_square_displacement.f90 make: fortran: Command not found make: *** [Mean_square_displacement.o] Error 127 ln: creating symbolic link `tetra.x': File exists ln: creating symbolic link `phonon_dos.x': File exists ln: creating symbolic link `Debye.x': File exists ln: creating symbolic link `Atom_projected_properties.x': File exists ln: creating symbolic link `F_QHA.x': File exists ln: creating symbolic link `Ghost_DOS.x': File exists ln: creating symbolic link `Partial_phonon_DOS.x': File exists ln: creating symbolic link `Mean_square_displacement.x': File exists ln: creating symbolic link `atom_info.x': File exists bds at Planck:~/bhabya/espresso-4.3/QHA$ what should i do b d sahoo reserch scholar barc mumbai -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111011/a7df13dc/attachment.htm
[Pw_forum] Is it possible to calculate free energy of graphite at specified temperature?
Dear Prof. Giannozzi: Thank you very much for your attention on my question. I still have a problem about graphite phonon. I saw a lot of persons calculated that, including prof. Marzari. However, all of their calculations were based on xy-plane, i.e., Gamma-M-K-Gamma q-path, even one of papers mentioned about calculating IFC through nk1*nk2, 2-dimensional MP grid. Therefore, I am wondering that, if I calculate IFC in 2D, does QHA work on this 2D-IFC? -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea ? 2011-10-10 14:30:52?"Paolo Giannozzi" ??? > >On Oct 10, 2011, at 20:11 , ?ric Germaneau wrote: > >> Also usually people use a supercell to compute phonon. > >people using linear response do not need any supercell > >P. >--- >Paolo Giannozzi, Dept of Chemistry, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111010/1f24e7b2/attachment-0001.htm
[Pw_forum] Is it possible to calculate free energy of graphite at specified temperature?
Dear Eric, Thank you very much for your reply. I haven't calculated graphite, and when I tried to calculate it, I was in dormitory, at where I cannot download any paper.. After reading your suggestion, I searched a paper publised at Solid State Communications 131, 141-152, it clearly showed that the phonon dispersion of graphite is stable. I think I may use too small cut-off and k-points due to my poor performance of laptop~ I will try it, again, for a better relaxation and result. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-11 01:05:44,"?ric Germaneau" wrote: Hey Gao, Well, I have a naive question/reply. Why do you get imaginary frequencies? I'd be very surprised of graphite instability at 0K ... Is you structure relaxed enough? This structure has been so much studied, have you ever read such graphite properties before? May experts can tell us more about it. ?ric. On 10/10/2011 12:37 AM, GAO Zhe wrote: Thank you for your kindly reply. Well, normally, if we found imaginary frequency in phonon dispersion, it indicates that this structure is not stable or, at least, unstable at 0K. Therefore, the vibrational free energy becomes unmeaningful because of the imaginary value. However, as we know, graphite is stable phase in a wild temperature range, including 0K. And when we discuss about formation free energy of carbide at specified temperature, graphite is used as reference pure material instead of diamond. This means that the free energy of graphite really exists. Therefore, I wondered whether there are some methods, for example, improving the graphite model, can deal with this problem and calculate vibrational free energy of graphite. Or, whether it is possible that we canneglect the vibration including z-direction and only consider vibration in xy-plane. -- GAO Zhe CMC Lab, MSE , SNU, Seoul, S.Korea At 2011-10-09 20:52:02,"bhabya sahoo" wrote: no because it is not valid for negative frequncy in phonon spectrum 2011/10/9 GAO Zhe Dear QE developer and users: I am using QE 4.3.2 to calculate phonon and thermaldynamis properties of materials. These days, I need to find the Gibbs (or Helmholtz) Free energy of carbon. Thus, I compared diamond and graphite phases at 0K. As a result, graphite provides lower energy per carbon atom (about 0.3eV/atom lower than of diamond). However, the phonon dispersion result shows that the imaginary frequency occurred at Gamma, H, A and K, so it is impossible by using QHA to find the vibrational free energy at specified temperature. The graphite model I used is: ibrav = 0 , celldm(1) = 1.889725989 , CELL_PARAMETERS 2.130421558318710 -1.22460182690 0.000 0.000 2.459998920365380 0.000 0.000 0.000 6.800 ATOMIC_POSITIONS crystal C 0. 0. 0.2500 C 0. 0. 0.7500 C 0.3330 0.6669 0.2500 C -0.3330 -0.6669 0.7500 Is there any other methods or models can calculate the free energy of graphite at specified temperature? Any suggestion will be welcome. Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea ___ 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.orghttp://www.democritos.it/mailman/listinfo/pw_forum -- Be the change you wish to see in the world ? Mahatma Gandhi ? Dr. ?ric Germaneau Graduate University of Chinese Academy of Sciences College of Physical Sciences Yuquan Road 19A Beijing 100049 China Please, if possible, don't send me MS Word or PowerPoint attachments Why? See:http://www.gnu.org/philosophy/no-word-attachments.html -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111010/c2241d00/attachment-0001.htm
[Pw_forum] Is it possible to calculate free energy of graphite at specified temperature?
Thank you for your kindly reply. Well, normally, if we found imaginary frequency in phonon dispersion, it indicates that this structure is not stable or, at least, unstable at 0K. Therefore, the vibrational free energy becomes unmeaningful because of the imaginary value. However, as we know, graphite is stable phase in a wild temperature range, including 0K. And when we discuss about formation free energy of carbide at specified temperature, graphite is used as reference pure material instead of diamond. This means that the free energy of graphite really exists. Therefore, I wondered whether there are some methods, for example, improving the graphite model, can deal with this problem and calculate vibrational free energy of graphite. Or, whether it is possible that we canneglect the vibration including z-direction and only consider vibration in xy-plane. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-09 20:52:02,"bhabya sahoo" wrote: no because it is not valid for negative frequncy in phonon spectrum 2011/10/9 GAO Zhe Dear QE developer and users: I am using QE 4.3.2 to calculate phonon and thermaldynamis properties of materials. These days, I need to find the Gibbs (or Helmholtz) Free energy of carbon. Thus, I compared diamond and graphite phases at 0K. As a result, graphite provides lower energy per carbon atom (about 0.3eV/atom lower than of diamond). However, the phonon dispersion result shows that the imaginary frequency occurred at Gamma, H, A and K, so it is impossible by using QHA to find the vibrational free energy at specified temperature. The graphite model I used is: ibrav = 0 , celldm(1) = 1.889725989 , CELL_PARAMETERS 2.130421558318710 -1.22460182690 0.000 0.000 2.459998920365380 0.000 0.000 0.000 6.800 ATOMIC_POSITIONS crystal C 0. 0. 0.2500 C 0. 0. 0.7500 C 0.3330 0.6669 0.2500 C -0.3330 -0.6669 0.7500 Is there any other methods or models can calculate the free energy of graphite at specified temperature? Any suggestion will be welcome. Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111010/4bc0b240/attachment-0001.htm
[Pw_forum] Is it possible to calculate free energy of graphite at specified temperature?
Dear QE developer and users: I am using QE 4.3.2 to calculate phonon and thermaldynamis properties of materials. These days, I need to find the Gibbs (or Helmholtz) Free energy of carbon. Thus, I compared diamond and graphite phases at 0K. As a result, graphite provides lower energy per carbon atom (about 0.3eV/atom lower than of diamond). However, the phonon dispersion result shows that the imaginary frequency occurred at Gamma, H, A and K, so it is impossible by using QHA to find the vibrational free energy at specified temperature. The graphite model I used is: ibrav = 0 , celldm(1) = 1.889725989 , CELL_PARAMETERS 2.130421558318710 -1.22460182690 0.000 0.000 2.459998920365380 0.000 0.000 0.000 6.800 ATOMIC_POSITIONS crystal C 0. 0. 0.2500 C 0. 0. 0.7500 C 0.3330 0.6669 0.2500 C -0.3330 -0.6669 0.7500 Is there any other methods or models can calculate the free energy of graphite at specified temperature? Any suggestion will be welcome. Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111009/62e49347/attachment.htm
[Pw_forum] problems with pp.x for parallel processing
In my opinion, the easiest way to solve this problem is to add wf_collect=.t.
in nscf calculation "input" file, then use pp.x output without
parallelism.
--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
At 2011-10-08 02:09:04,"Natalia Pavlenko" wrote:
>I tried two different possibilities: first, I used the same number of pools
>("-npool 2") in nscf and in pp.x. In this case I received the message:
>-
>from local_dos : error # 1
> problems with xk_pool
>--
>Second, I tried to run pp.x without setting the option npool
>(just pp.x < case_rho.in > case_rho.out), in this case I get the following
>message after the crash:
>--
>from postproc : error # 1
>pw.x run with a different number of pools. Use wf_collect=.true.
>---
>
>Best regards, N. Pavlenko
>Dr. Natalia Pavlenko
>Institute for Condensed Matter Physics,
>Lviv, Ukraine
>
>Tel.: +38-0322-707401
>Fax: +38-0322-761158
>
>
>
>--- On Fri, 10/7/11, Paolo Giannozzi wrote:
>
>> From: Paolo Giannozzi
>> Subject: Re: [Pw_forum] problems with pp.x for parallel processing
>> To: "PWSCF Forum"
>> Date: Friday, October 7, 2011, 10:40 AM
>>
>> On Oct 7, 2011, at 18:19 , Natalia Pavlenko wrote:
>>
>> > I am trying to calculate charge density plots using
>> pp.x for 8
>> > parallel
>> > processors. The scf and nscf calculations are
>> successfully finished.
>> > With pp.x, I receive the following warning after the
>> CRASH:
>>
>> you didn't try to run on a diferent number of pools from
>> the one
>> used in the nscf calculation?
>>
>> P.
>> ---
>> Paolo Giannozzi, Dept of
>> Chemistry,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>>
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>___
>Pw_forum mailing list
>Pw_forum at pwscf.org
>http://www.democritos.it/mailman/listinfo/pw_forum
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[Pw_forum] Can we obtain anharmonic vibration energy from s3.x?
Dear QE developer and users: I am using ph.x and QHA to calculate thermodynamics properties of some compositions and their solid-solutions. However, for some materials and their solid-solution, the results shows agaist to the thermodynamics "general sense", for example, DeltaG,Delta Gibbs Free Energy, lower than ideal solution at low temperature but higher at high temperature. But in "general sense", the ideal solution line cannot be overcome, that means if one solution's DeltaG was once lower than ideal solution's, then ideal solution line should be its limitation even at very high temperature. Therefore, I want to check whether this phenomenon was due to anharmonic effect or not. I have known that we can calculate anharmonic dynamic matrix for specified q-point by s3.x code, but I also want to know whether we can gather the anharmonic dynamic matrics to form IFC and anharmonic-phDOS. Moreover, if we can obtain IFC and phDOS for anharmonic case, is it possible to calculate Fvib from them? Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111005/19689af9/attachment.htm
[Pw_forum] CuO bulk Error during compilation
Since you defined there are 2 types of elements, but in ATOMIC_POSITIONS, you defined 3 kinds, i.e., Cu1, Cu2 and O1. You have at least 2 choices. 1, remove the number behind elements' symble and combined Cu1 and Cu2 as one element, Cu; 2, change the parameter ntyp from 2 to 3. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-10-02 19:08:53,"ambesh dixit" wrote: Dear all, I tried to compile bulk CuO SCF calculation using following input file, which i built. calculation = 'scf' , restart_mode = 'from_scratch' , outdir = '/home/espresso/espresso-4.3.2/tmpCuO/' , pseudo_dir = '/home/espresso/espresso-4.3.2/pseudo/' , prefix = 'CuO' , tstress = .true. , tprnfor = .true. , / ibrav = 12, celldm(1) = 5.137, celldm(2) = 0.91356823, celldm(3) = 0.66731555, celldm(4) = -0.165839393, nat = 8, ntyp = 2, ecutwfc = 35 , ecutrho = 240.0 , nbnd = 50, occupations = 'smearing' , degauss = 0.01 , smearing = 'gaussian' , nspin = 2 , starting_magnetization(1) = 0.50, starting_magnetization(2) = -0.50, / conv_thr = 1.0d-6 , mixing_mode = 'plain' , mixing_beta = 0.3 , mixing_fixed_ns = 0, / ATOMIC_SPECIES Cu163.546 Cu.pbe-paw_kj.UPF Cu263.546 Cu.pbe-paw_kj.UPF O1 15.99940 O.pbe-rrkjus.UPF ATOMIC_POSITIONS crystal Cu1 0.25000 0.25000 0.0 Cu2 0.75000 0.75000 0.0 Cu2 0.75000 0.25000 0.5 Cu1 0.25000 0.75000 0.5 O10.0 0.41987 0.25000 O10.0 0.58043 0.75000 O10.5 0.91957 0.25000 O10.5 0.08013 0.75000 K_POINTS automatic 4 4 4 0 0 0 After running pw.x i got following error Warning: cardO1 15.9994 O.PBE-RRKJUS.UPF ignored %% from read_cards : error # 5 species O1 in ATOMIC_POSITIONS is nonexistent %% stopping ... I dont understand why, evenwhen i visualize using VESTA or xcrysden, there is no problem in getting right monoclinic structure. Kindly suggest where is problem. Thanks -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111002/2d4bf0dd/attachment.htm
[Pw_forum] installing input file builder: gdis-0.99
To Jinghui: I haven't tried GDIS. But, I still think you can start the software through terminate, then some error may display if it doesn't work. To Eric: Now, the lastest version is 0.99, you can download from: https://df.arcs.org.au/ARCS/worldview/GDIS/ -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-30 10:30:44,"He Jinghui" wrote: >Dear All: > >I was wondering who has successively installed the latest version of >gdis: 0.99. Now the official release version is 0.90-3, but it doesn't >support the pwscf input/output file format. I tried to use cvs to >download the 0.99 version and to install it. The installation went well >without any error, but after installation, the software cannot start a >GUI, exit without any error message. Any idea? >Thank you in advance! > >OS: linux mint 10 -64 bit gnome >no library files missing reported > >regards >He Jinghui >Department of Chemistry >national university of Singapore > > > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110930/08dd1f73/attachment.htm
[Pw_forum] Error running dos.x
Why not trywf_collect = .true. anddisk_io = 'default' in pw.x ? At least, when I calculatednscf afterscf, it does not work if disk_io = 'low'. The similar thing may occur indos.x case. Good luck. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-29 04:01:43,"Zhiting Tian" wrote: >Dear all, > >I am running dos.x. I have succeeded in running it couple of times. But for >most of the time, I get the error message: > %%% > task # 0 > from pp_check_file : error # 2 > file /home/.../PbSedos.save not found > %%% > >But I have checked and the folder PbSedos.save is definitely there. I am using >the same version of espresso and I don't think version should be a problem. > >Sometimes, I get the error message: > > from dos : error # 1 > pools not implemented, or incorrect file read > > >Or > > reading inputpp namelist > > > >Anyone could give me some hints? > >Thanks, >Zhiting Tian >Department of Mechanical Engineering >Massachusetts Institute of Technology >Cambridge, MA 02139 >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110929/13b66832/attachment.htm
[Pw_forum] problem about ibrav no.
I do not know whether your structure was right or not unless you provide the data base of MoSi. However, you can determine the strcutre by CELL_PARAMETER and ATOMIC_POSITIONS, which can be obtained by the utility, spacegroup, in ELK/Exciting code according ICSD. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-28 14:27:48,"amar shugani" wrote: Respected sir, my compound is molybdenum disilicide .when i am putting ibrav no. 7 correct structure is not forming when i am giving 6 structure is same as given on crystal structure site but MoSi2 is bct for which ibrav no. is 7 sir,guide me about this and tell me whether my input file and structure is correct or not -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110928/c5f19f84/attachment.htm
[Pw_forum] mpif90 compiler that uses ifort
In my case, I installed ifort 2011 at first, and then compiled OpenMPI by ifort with command: ./configure --prefix=/ FC=ifort After "make install" OpenMPI, the $MPIBIN=/**/OpenMPI/bin and $MPILIB=/***/OpenMPI/Lib have been added into .bashrc file through the method: $PATH=$MPIBIN:$PATH and $LD_LIBRARY_PATH=$MPILIB:$LD_LIBRARY_PATH. When compiling QE v4.3.2, only ./configure was needed, then ifort and mpif90 would be chosen automaticly (if compiled before, "make clean" first) Hope this method can work in your case. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-27 00:30:06,"Ahmad Yassin" wrote: Hello all; I had a problem in installing QE 4.0.3 using Intel Compiler... the ./configure step runs smooth if using gcc and gfortran, but when using icc and ifort it gives me the following warnings: configure: WARNING: serial/parallel compiler mismatch detected configure: WARNING: parallel compiler mpif90 uses gfortran, but serial compiler is ifort looking it up, I found a previous email in the mailing list (http://www.democritos.it/pipermail/pw_forum/2009-June/013265.html) stating that you have a mismatch between parallel (mpif90) and serial (gfortran) compiler. This is something "configure" warns you about. Use "./configure F90=gfortran", or, better, install a mpif90 compiler that uses ifort I tried to reinstall OpenMPI, using icc and ifort to compile its source, but the conflict is still there... Is there anyway to make mpif90 use ifort ? or is there any other parallel compiler using ifort? Ahmad Yassin -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110927/caefa21c/attachment-0001.htm
[Pw_forum] Problem of the energy of orbital in ld1.x with PDOS
Even though I cannot give you any suggestion to generate a better NCPP for Ru, you can try to convert a fhi NCPP to UPF by upftools/fhi2upf.x. Here: http://www.sas.upenn.edu/rappegroup/htdocs/Research/psp_gga.html#Ru3, you can find both of the fhi file and parameters. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-24 17:45:49,WF wrote: >Hello everyone, > I recently do a vc-relax calculation of Ru metal of PBE >norm-conserving PP. > >The PP input is like this, which is slightly modified from that in >atomic_doc: >-- > > title='Ru', > zed=44.0, > rel=1, > config='[Kr] 4d6.0 5s2.0 5p0', > iswitch=3, > dft='pbe' > / > > pseudotype=2, > file_pseudopw='Ru.pbe-rrkjnc.UPF', > author='TM', > lloc=0, > nlcc=.true., > rcore = 0.9, > / >3 >5P 2 1 0.00 -0.099963 2.40 2.40 0.0 >4D 3 2 6.00 0.00 1.90 2.40 0.0 >5S 1 0 2.00 0.00 2.30 2.40 0.0 >-- > >If the 5P energy is set to 0.00 ( which means energy of all-electron >calculation ), the a axis of result is identical to that when the energy is >set to -0.09963 ( the all electron result copied from ld1.x output ). >However, in .UPF file, 2 wavefunctions and 3 projectors are generated if the >energy is 0.00, all of 4D, 5S and 5P will appear in PDOS ( by projwfc.x ), >but only 2 projectors are obtained otherwise and 5P will not appear in >further PDOS calculation. I don't know how to make PDOS of all of 4D, 5S and >5P if the energy is not 0.00. Can anyone give some advices ? Thanks. > >Best regards, > >Wu F > >--- >F, Wu >College of Chemistry and Molecular Engineering >Peking University >-- > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110924/75069ebf/attachment.htm
[Pw_forum] Does VCA method give positive formation energy?
Dear QE developers and users: Hi. I am using Quantum-ESPRESSO v4.2.1 to deal with DFPT and QHA. Because of the computational limitation of my PC, I chose VCA method to compare the phonon dispersion and thermo-properties change as a function of compositions. The system I calculated was ZrC-ZrN. Since based on our experiments, we have known that the Zr(CN) solid-solution is possible to produce. PW91 xc-functional has been selected at 13x13x13 k-points mesh with ecutwfc=40Ry and ecutrho=400Ry. The q-mesh was 4x4x4. Structure of ZrC, ZrN and Zr(CN) is Fm-3m (NaCl Structure). The Vanderbilt ultrasoft pseudo-potential of C and N were combined by virtual.x in certain ratio. However, I found the formation energy: Ff[T, Zr(CNx)] = F[T, Zr(CNx)] - (1-x) * F[T, ZrC] - x * F[T, ZrN] was always positive number. Then, I checked ZrC, ZrN and Zr(CN0.5) carefully by both of 'vc-relax' and E-V curve for total energy calculation. Finally, I found thatE[Zr(CN0.5)] - 0.5 * E[ZrC] - 0.5 * E[ZrN] was about +0.4Ry/cell, that means+525.088kJ/mol. According to thermodynamics principle, Zr(CN0.5) cannot be prepared. However, when I tried supercell-doping method, the formation energy was negative ( about-10kJ/mol ). Therefore, I want to know why VCA method gives positive formation energy. Is it reasonable? If it should be like this, then can we believe the phonon result from VCA as reliable one? Any suggestion will be welcomed. Thanks. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110923/b7d640da/attachment.htm
[Pw_forum] elastic constants
In my opinion, the methods, to find elastic constants for both of CsCl-structure and NaCl-structure, should be same principlely, because of the cubic lattice. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-18 23:09:27,"bhabya sahoo" wrote: can any one suggest me how to find the elastic constants in CsCl phase because i know by distortion stress strain relation i can find the elastic constants in B 1 phase (nacl) by orthorombhic and tetragonal distortion what is the difference between two phase determining the elastic constants b d sahoo(reserch scholar) barc mumbai -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110919/d178f073/attachment.htm
[Pw_forum] from check_atoms : error #
Definitely, this error means that No.1 and No.2 atoms were at same or very close position. You'd better check your ATOMIC_POSITIONS instead of changing ibrav. Without your "input" file, I cannot tell any thing detailed. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-17 19:57:19,"ramesh kumar" wrote: Dear All I am trying to make a tetragonal supercell with 32 atoms but got this error from check_atoms : error # 1 atoms # 1 and # 2 overlap! I tried searching forum got the answer like because of the equivalent atom positions it shows the error. So i tried to use p1 space group (triclinic cell) but i am unable to get rid of the error. Anyboday faced this problem earlier please help me in this regard... Thankyou With regards K. Ramesh Kumar Research Scholar Department of Physics IIT-Madras Chennai-600 036 Treat yourself at a restaurant, spa, resort and much more withRediff Deal ho jaye! -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110917/76715521/attachment.htm
[Pw_forum] SCF errror with the converted pseudopotential
Therefore, you have to use the examples at atomic_doc/***_library, too. The problem of fhi-ncpp converting, may be solved only by Abinit or FHI98 developers, because of the lack of basic information in pp files. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-14 19:25:54,lucking-pine wrote: Hi, Paolo Thanks for your advice.But the main problem I want to know is if the way which I converted pseudopotential is right or wrong?And could tell me the reason? The information is very few by only reading atomic_doc/pseudo-gen.pdf. 2011/9/14 Paolo Giannozzi On Sep 13, 2011, at 16:38 , lucking-pine wrote: > from readpp : error # 2 > inconsistent DFT read http://www.quantum-espresso.org/user_guide/ node52.html#SECTION000121060 --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222 ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110916/295624e3/attachment.htm
[Pw_forum] regarding structural optimization
Because of your question without any details, I can only answer it generally. For getting convergency lattice parameter by energy-volume method, you can read the paper,Acta Materialia 54 (2006) 1641-1657, in which the author discussed that issue by Wien2k code. Or, if you want to use "vc-relax", you'd better decrease the convergence threshold to very small number with convergence cutoff energy, k-mesh and so on. One more to be noted is that the minimum energy configuration corresponds to zero force, but minimum enthalpy corresponds to zero force and stress. In "vc-relax" case, we try to find zero both for force and stress instead of only for total energy. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-14 17:14:08,"kondaiah samudrala" wrote: Dear all, I am doing test calculations for orthorhombic layered compounds having van der waals forces. i calculated the volume by varying c/a, b/a and a with energy and taken the minimum values of c/a, b/a and a. But my volume change is surprisingly 2% with experimental ( even van der waals forces having). I tried with the "vc-relax" for same system i found 12% volume change with experimental.I tried with psedopotentials also and the results are same. I am very thankful any to solve this problem. Thanks in advance S.Appalakondaiah Research Scholar University of hyderabad Hyderabad India -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110916/3bc17b0d/attachment.htm
[Pw_forum] Is it necessary to clear outdir / wfcdir before calculation?
At least, there are three methods to avoid the effect of last calculation. restart_mode = 'from_scratch' or change prefix or rm -rf $TempDIR/* -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-08 13:41:38,WF wrote: Hello everyone, Recently I make a small bash script to run a lot of small pw.x calculation one by one. But all of them use same outdir and wfcdir. They are temporary directories and I don?t need them ( I only need scf energy, so stdout is enough ). Is it necessary to delete them before starting a new calculation ? Because I have done a lot of calculation, I would like to verify whether this will affect the results to determine whether I should modify the script to restart my calculation again, or just use these result. Best regards, Wu F --- F, Wu College of Chemistry and Molecular Engineering Peking University -- -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110908/22bea0be/attachment.htm
[Pw_forum] Pseudopotential for Terbium in upf file
You can try to generate Tb's UPF PP by ld1.x, or transfer from CASTEP's PP file to UPF by usp2upf, which can be downloaded from http://www2.tcm.phy.cam.ac.uk/onetep/Main/Utilities. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-08 05:14:53,"Chengyang Li" wrote: >Dear Users > > >I'm trying to find the pseudopotential for Terbium but it seems like there is >no upf file about Terbium. Does any one can share the codes or give me some >advice? Thank you. > > > > >Chengyang Li > >Department of Physics >Western Michigan Univerisity > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110908/2436fc85/attachment.htm
[Pw_forum] All electron calculation
QE is pseudo-potential method DFT software instead of all-electron method, unless you make all-electron pseudo-potential by using ld1.x ( I do not guarantee it could be successful ). If you really wanna use all-electron method, you'd better to use the DFT software implemented FLAPW, such like Wien2k. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-08 00:45:45,"Tram Bui" wrote: Dear Everyone, I'm trying to run a quick all electron calculation for Cs. where I have the input file(cs.in) as below: title='Cs', zed=55.0, iswitch=1, dft='PBE', config='[Xe] 6s1 5d0 6p0 ' / then I run bin/pw.x cs.out. I got an error message saying "from read_namelists : error # 1 reading namelist control" what might have been wrong in my code? is pw.x is the right command for all electron calculation? Thank you very much, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110908/cb0ef0d9/attachment-0001.htm
[Pw_forum] (no subject)
According to your input information, nat=48, I think you wanted to make 2x2x2
rutile-TiO2 supercell with a substitutional Nb. However, you setted celldm(1)
and ATOMIC_POSITIONS wrong.
You may set celldm(1)=1 and keep CELL_PARAMETERS; or keep celldm(1)=8.7 and set
CELL_PARAMETERS as
2.000 0.000 0.000
0.000 2.000 0.000
0.000 0.000 1.288
For ATOMIC_POSITIONS, you may set it as:
ATOMIC_POSITIONS {crystal}
O 0.1523998693948630 0.1523998693948630 0.
O 0.3476001306051368 0.3476001306051368 0.
O 0.0976001306051369 0.4023998693948629 0.2501
O 0.4023998693948629 0.0976001306051369 0.2501
O 0.6523998693948631 0.1523998693948630 0.
O 0.8476001306051368 0.3476001306051368 0.
O 0.5976001306051370 0.4023998693948629 0.2501
O 0.9023998693948629 0.0976001306051369 0.2501
O 0.1523998693948630 0.6523998693948631 0.
O 0.3476001306051368 0.8476001306051368 0.
O 0.0976001306051369 0.9023998693948629 0.2501
O 0.4023998693948629 0.5976001306051370 0.2501
O 0.6523998693948631 0.6523998693948631 0.
O 0.8476001306051368 0.8476001306051368 0.
O 0.5976001306051370 0.9023998693948629 0.2501
O 0.9023998693948629 0.5976001306051370 0.2501
O 0.1523998693948630 0.1523998693948630 0.5000
O 0.3476001306051368 0.3476001306051368 0.5000
O 0.0976001306051369 0.4023998693948629 0.7501
O 0.4023998693948629 0.0976001306051369 0.7501
O 0.6523998693948631 0.1523998693948630 0.5000
O 0.8476001306051368 0.3476001306051368 0.5000
O 0.5976001306051370 0.4023998693948629 0.7501
O 0.9023998693948629 0.0976001306051369 0.7501
O 0.1523998693948630 0.6523998693948631 0.5000
O 0.3476001306051368 0.8476001306051368 0.5000
O 0.0976001306051369 0.9023998693948629 0.7501
O 0.4023998693948629 0.5976001306051370 0.7501
O 0.6523998693948631 0.6523998693948631 0.5000
O 0.8476001306051368 0.8476001306051368 0.5000
O 0.5976001306051370 0.9023998693948629 0.7501
O 0.9023998693948629 0.5976001306051370 0.7501
Ti -0. -0. 0.
Ti 0.2498 0.2498 0.2501
Ti 0.5000 -0. 0.
Ti 0.7498 0.2498 0.2501
Ti -0. 0.5000 0.
Ti 0.2498 0.7498 0.2501
Ti 0.5000 0.5000 0.
Ti 0.7498 0.7498 0.2501
Ti -0. -0. 0.5000
Ti 0.2498 0.2498 0.7501
Ti 0.5000 -0. 0.5000
Ti 0.7498 0.2498 0.7501
Ti -0. 0.5000 0.5000
Ti 0.2498 0.7498 0.7501
Ti 0.5000 0.5000 0.5000
Ti 0.7498 0.7498 0.7501
--
GAO Zhe
CMC Lab, MSE, SNU, Seoul, S.Korea
At 2011-09-07 20:22:30,"Winfred Mulwa" wrote:
Dear all
I have tried doing a vc-relax on the attached TiO2 rutile supercell,
the calculations stop after a few minutes without giving any error.
What might be the problem?
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[Pw_forum] about PWscf PP generation
Of course, since the element Xe already has 5s2 and 5p2~ you can change parameter "config" like: '[Xe] 5d1 6s1.5 6p0.5' -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-09-04 20:37:09,"Robin H" wrote: Hello everyone, I used revisedPBE to generate PWscf PP of La atom.But for the first time I met a mistake like this Program LD1 v.4.3.1starts on 4Sep2011 at 19:53:36 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URLhttp://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO Parallel version (MPI), running on 1 processors %% from el_config : error #12 wavefunction 5S found too many times %% stopping ... [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 0) - process 0 since the input is like this title='La' zed=57. rel=1, config='[Xe] 5s2.00 5p6.00 6s2.00 5d1.00', iswitch=3, dft='revPBE' / lloc=1, pseudotype=3, nlcc=.true., tm=.true., file_pseudopw='La.revPBE.UPF', / 5 5D 3 2 1.00 0.00 2.20 2.20 5D 3 2 0.00 0.05 2.20 2.20 6S 1 0 2.00 0.00 2.20 2.20 6S 1 0 0.00 0.05 2.20 2.20 5P 2 1 6.00 0.00 2.20 2.00 Is there anything wrong in my electric configuration of La? as I changed like this : title='La' zed=57. rel=1, config='[Xe] 5s2.00 5p6.00 6s1.50 5d1.00 6p0.50', iswitch=3, dft='revPBE' / lloc=1, pseudotype=3, nlcc=.true., tm=.true., file_pseudopw='La.revPBE.UPF', / 5 5S 1 0 2.00 0.00 2.20 2.20 5P 2 1 6.00 0.00 2.20 2.20 5D 3 2 1.00 0.00 2.20 2.20 6S 1 0 1.50 0.00 2.20 2.20 6P 2 1 0.50 0.00 2.20 2.00 the error is still exist like the fomer.what's the error suggest ?I'm wondered that how to write the list of states following the namelist of tried to find some information in the reference of PWscf to make me clear,but this part seemed hard to understand,hope everyone who is sophisticated at PP generation to give me some tips, I'm appreciated. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110904/42f82997/attachment.htm
[Pw_forum] Can not find minimum free energy by QHA
Prof. Giannozzi: Thank you very much for your kindly reply. I think this is my problem to understand Fvib. I have also checked Axel van de Walle's Ph.D thesis, and found that free energy should be Fvib+Fconf-TSvib-TSconf. In 0GPa pressure case, Fconf should equal to total energy. Therefore I cannot obtain the right Free Energy vs Volume curve as a result of using Fvib alone. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-30 03:42:31,"Paolo Giannozzi" wrote: > >On Aug 22, 2011, at 4:36 , GAO Zhe wrote: > >> However, the free energy kept decreasing as a monotone decreasing >> function of lattice parameter > >you mean: the "vibrational free energy" alone, or "the sum of the >energy and of the vibrational free energy"? the vibrational free >energy should be a small correction to the total energy. > >P. >--- >Paolo Giannozzi, Dept of Chemistry, >Univ. Udine, via delle Scienze 208, 33100 Udine, Italy >Phone +39-0432-558216, fax +39-0432-558222 > > > > >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110831/0419a2d7/attachment.htm
[Pw_forum] phonon instability
Dear Prof. Baroni: Thank you very much for your reply. However, what I wanted to say is, although QE doesn't support frozen-ph as a "function", it can still be calculated through certain steps. Just as elastic constant calculation, we can calculate in any DFT code, but only several code provide it as a "function", such as CASTEP. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-25 03:30:00,"Stefano Baroni" wrote: On Aug 24, 2011, at 8:21 PM, GAO Zhe wrote: As I know, frozen phonon method is not implemented in QE. ??? *ANY* code able to perform total-energy and atomic-force calculations can be used to do frozen phonons ... SB --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110825/5d4a632d/attachment.htm
[Pw_forum] phonon instability
As I know, frozen phonon method is not implemented in QE. You can use frozen-ph method either by the free software "phon", http://www.homepages.ucl.ac.uk/~ucfbdxa/, or make it manually like this tutorial: http://www.abinit.org/documentation/helpfiles/for-v6.8/tutorial/lesson_rf1.html, even though it is from Abinit. After all, once we have DFPT, why do you wanna frozen-ph ? -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-25 02:06:10,"bhabya sahoo" wrote: i am doing the linear response calculation so how can i do frozen phonon calculation On Wed, Aug 24, 2011 at 10:54 PM, Mike Mehl wrote: To keep from boring everyone, I'm taking this off-line. If anyone else wants to participate in the discussion please let me know and I'll add you to the conversation. On 08/24/2011 01:07 PM, bhabya sahoo wrote: > ok but i have seen many papers that this B2 unstability due to some > anaharmonic contributions > or it may be due to band closing phenomenon > can u explain this more correctly because i am doing calculation on > transition metal carbides > On Wed, Aug 24, 2011 at 9:01 PM, Mike Mehl <mailto:Michael.Mehl at nrl.navy.mil>> wrote: > -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110825/7832f808/attachment.htm
[Pw_forum] partial band structure
You can obtain projected DOS by projwfc.x, more detail at the beginning of PP/projwfc.f90 -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-23 00:21:11,"bhabya sahoo" wrote: hallo i am doing calculation of band structure in DOS there is no option of getting partial density of states can i calculate that plesase give me suggetions b d sahoo, reserch scolar barc mmbai -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110823/8166fb57/attachment.htm
[Pw_forum] usage of recover=.true.
If you are afraid of losing files, you can copy the corresponding files out as backup before restarting. I just tried restart DFPT once, about 2 months ago. I remember just recover = .t. was needed and everything was fine~ How about the error message in your new output file? -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:27:33,"Elie Moujaes" wrote: Thank you.I hope it works as I definitely do not want to lose the 105 modes..It took 7 days to do that. But how to re execute the ph.x command..I tried doing the usual: /..././ph.x GB60.phG.out but it exited. Is there another way to restart the command? Thanks again Elie Date: Mon, 22 Aug 2011 22:21:25 +0800 From:flux_ray12 at 163.com To:pw_forum at pwscf.org Subject: Re: [Pw_forum] usage of recover=.true. If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:06:49,"Elie Moujaes" wrote: Dear all, I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? Thanks Elie Moujaes University of Nottingham NG7 2RD UK ___ Pw_forum mailing listPw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/88d00709/attachment.htm
[Pw_forum] usage of recover=.true.
If you specify the right outdir path and prefix name, then the restarted one will definitely begin from 106th mode, since 105 modes have been finished. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-22 22:06:49,"Elie Moujaes" wrote: Dear all, I am doing phonon calculations for a large system at the Gamma point (I have 180 irreducible representations (modes) to work out). The server was shut for a day. I have used in my input file recover=.true. I have reached representation 106 before the server broke down. Does it mean that If I executed the command ph.x again, the calculations will start from where it was interrupted?if not, what can i do to not lose what has been done? Thanks Elie Moujaes University of Nottingham NG7 2RD UK -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110822/ca0a9564/attachment.htm
[Pw_forum] convergence of Phonon
I think you can try to reduce the alpha_mix(1), 0.7 by default, for a better convergency~ P.S.: This suggestion was original from by Prof. Isaev, and it works well in a lot of cases. -- GAO Zhe CMC Lab, MSE, SNU, Seoul, S.Korea At 2011-08-09 15:24:17,"mayank gupta" wrote: >Dear all > > >I am doing phonon calculation of a magnetic system, have not included >any magnetic interaction on it. I am calculating phonon at 2x2x2 mesh >(6 q points). I got the phonon frequency +ve at 5 q point while at >one q point it is negative. I have check this with 24 x24x24 k point >and with very high ecut and observed this particular phonon mode >doesn't converge with k point while rest is converged. is it because >of not taking in to account the magnetic part or something else. > > > >-- >Mayank > >BHABHA ATOMIC RESEARCH CENTER >MUMBAI, INDIA >Office: 022-25595606 >Home: 9920397437 / 9869834437 >___ >Pw_forum mailing list >Pw_forum at pwscf.org >http://www.democritos.it/mailman/listinfo/pw_forum -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110809/f25e0307/attachment.htm
