Hello,
please answer one question related to modeling using epx.x program for
graphene modified by hydrogen atoms. It is not clear to me how to select in the input file epx.in the values of parameters nqs{cartezian} and parameters xq(1), xq(2), xq(3) for this material.
Thank you for your reply.
Valery
Hi Valery,
I think https://docs.epw-code.org/doc/Inputs.html#nqs will help you to understand the input flags.
xq(1), xq(2), xq(3) are the phonon wavevectors of the coarse grid. Must be in the same order as prefix_q* listed in dvscf_dir. You can copy these from the beginning of the phonon output file.
If you are using the latest versions of the code, you do not need to specify them explicitly, and are calculated internally with respect to nq1, nq2, and nq3.
Best,
Hari Paudyal
Hi Hari Paudyal.
Thank you for your reply.
Please answer one more question related to modeling using epw.x program for graphene modified by hydrogen atoms. I calculated parameters xq(1), xq(2), xq(3) for this material with the program ph.x and passed it in program epw.x. Text of input file listed here. But when I ran the epw.x program, I got the answer “Error in routine epw_setup (1): coarse k-mesh needs to be strictly positive in 1st BZ stopping “.
I do not know if it is possible to simulate such systems or if I have made some mistakes.
Valery
–
&inputepw
prefix = ‘./’
amass(1) = 12.011
amass(2) = 1.0079
outdir = ‘./’
elph = .true.
kmaps = .false.
epbwrite = .true.
epbread = .false.
epwwrite = .true.
epwread = .false.
nbndsub = 4
nbndskip = 0
wannierize = .true.
num_iter = 300
iprint = 2
dis_win_max = 12
dis_froz_max= 7
iverbosity = 0
elecselfen = .false.
phonselfen = .true.
a2f = .true.
fsthick = 2.80284905 ! eV
eptemp = 300 ! K
degaussw = 0.1 ! eV
dvscf_dir = ‘./’
filukk = ‘./C2H1.ukk’
nk1 = 12
nk2 = 12
nk3 = 12
nq1 = 12
nq2 = 12
nq3 = 12
nqf1 = 20
nqf2 = 20
nqf3 = 20
nkf1 = 10
nkf2 = 10
nkf3 = 10
! The list of qpoints below must be identical
! to ../phonons/qlist.dat
/
31 cartesian
0.000000000 0.000000000 0.000000000
0.000000000 0.115470054 0.000000000
0.000000000 0.230940108 0.000000000
0.000000000 0.346410162 0.000000000
0.000000000 0.461880215 0.000000000
0.000000000 -0.577350269 0.000000000
0.100000000 0.057735027 0.000000000
0.100000000 0.173205081 0.000000000
0.100000000 0.288675135 0.000000000
0.100000000 0.404145188 0.000000000
0.100000000 0.519615242 0.000000000
0.200000000 0.115470054 0.000000000
0.200000000 0.230940108 0.000000000
0.200000000 0.346410162 0.000000000
0.200000000 0.461880215 0.000000000
0.200000000 0.577350269 0.000000000
0.200000000 0.000000000 0.000000000
0.300000000 0.173205081 0.000000000
0.300000000 0.288675135 0.000000000
0.300000000 0.404145188 0.000000000
0.300000000 0.519615242 0.000000000
0.300000000 -0.057735027 0.000000000
0.400000000 0.230940108 0.000000000
0.400000000 0.346410162 0.000000000
0.400000000 0.461880215 0.000000000
0.400000000 0.577350269 0.000000000
0.400000000 -0.115470054 0.000000000
0.400000000 0.000000000 0.000000000
-0.500000000 -0.288675135 0.000000000
-0.500000000 -0.173205081 0.000000000
-0.500000000 -0.057735027 0.000000000
Program EPW v.5.0.0 starts on 16Apr2021 at 14:37: 0
Serial version
Reading data from directory: ././.save/
IMPORTANT: XC functional enforced from input :
Exchange-correlation = PBE ( 1 4 3 4 0 0)
Any further DFT definition will be discarded
Please, verify this is what you really want
file C.pbe-rrkjus.UPF: wavefunction(s) 2S 2P renormalized
file H.pbe-rrkjus.UPF: wavefunction(s) 1S renormalized
Error in routine epw_setup (1):
coarse k-mesh needs to be strictly positive in 1st BZ
stopping …
Dear Valery:
/
31 cartesian
0.000000000 0.000000000 0.000000000
The q-point list should be given in Cartesian units and as Hari mentioned, its format should follow the specific form described at https://docs.epw-code.org/doc/Inputs.html#structure-of-the-input-data .
Well, is there a specific reason to use the old version of EPW? I strongly suggest you to use the latest version of EPW (EPW v5.3.1).
Sincerely,
H. Lee
Dear H.Lee
Thank you for your reply. But what is wrong with these points. The points I am using are from the ph.x program and I used according to Hari recommendations in his previous letter. If the 5.0 program version is not correct and cannot do the simulation of this structure, then I will install the 5.3.1 version in the future.
Sincerely,
Valery
Dear Valery:
First, I don’t know about EPW v5.0, but you might need to add the fourth column of weight as described at https://docs.epw-code.org/doc/Inputs.html#structure-of-the-input-data .
I guess that even in EPW v5.0, the weights are internally ignored; so you can use the weight of 1.0 for all q points.
nk1 = 12
nk2 = 12
nk3 = 12
nq1 = 12
nq2 = 12
nq3 = 12
nqf1 = 20
nqf2 = 20
nqf3 = 20
nkf1 = 10
nkf2 = 10
nkf3 = 10
Second, your system is a 2D system and probably, in your scf, nscf, and ph calculations, you might use the number of grid of 1 along the kz direction.
(Could you confirm that you used the grid of “12 12 1” from your nscf and ph calculations?)
Thus, please replace the above part by the following:
nk1 = 12
nk2 = 12
nk3 = 1
nq1 = 12
nq2 = 12
nq3 = 1
nqf1 = 20
nqf2 = 20
nqf3 = 1
nkf1 = 10
nkf2 = 10
nkf3 = 1
Sincerely,
H. Lee
Good afternoon,
Thank you for your reply, but my problem has not yet been solved. Now I am trying to put the new version of QE-6.7 on my computer, but there are problems here. Therefore, for the time being, I work in QE-6.3. These days, I tried to solve a similar problem for SiC material, using the files that were in the examples of the program QE-6.3. The program epw.x for SiC material started to simulate when I put the largest grid with the number of points 216 (for the grid 666=216). With less number of points I got the same error as for my variant with graphene. So maybe I also need to use the exact grid with more number of points 144 (for 12121 grid). If this is the case, then how do I get a grid with this number of points, because the ph.x program only gives me 63 points. I inform you that I have fulfilled all your comments made in the last letter. Maybe with QE-6.7 program everything will be easier and my problem will be solved. Excuse me for my persistence, but I am very interested in research of electron-phononon interaction in two-dimensional materials.
Respectfully,
Mishchenka Valery
Dear Mishchenka Valery:
First, I would suggest you again to use the recent version of EPW (v5.3.1) since it is much easier for me to keep track of the (potential) issues you encounter.
In addition, I would like to look at all of your inputs and outputs (scf.in, scf.out, nscf.in, nscf.out, ph.in, ph.out, epw.in, and epw.out).
Sincerely,
H. Lee
Dear H. Lee,
I received your last letter where you offer me to send input and output files obtained with program QE-6.3. However, taking into account your repeatedly stated recommendation to use EPW 5.3.1 program, I installed program QE-6.7. With its help I ran programs pw.x and ph.x for my variant of simulation with graphene and obtained satisfactory results.
However, the installation of the EPW program, which came with QE-6.7, ended unsuccessfully and a message was received in the end:
Make: *** [epw] Error 1
In the long text that accompanied the installation, I read two warnings.
The first one was:
Unable to download www.netlib.org/lapack/lapack-3.6.1.tgz.
Then I downloaded this archive and extracted it into the Lapack folder.
The second of them:
Unable to download wannier90. …copy files located here: https://codeload.github.com/wannier-developers/wannier90/tar.gz/v3.1.0.
However I haven’t found above mentioned files in this path.
How can I solve this problems? Thanks for the answer!
Best regards,
Mishchenka Valery.
Dear Mishchenka Valery:
Unable to download wannier90. …copy files located here: > https://codeload.github.com/wannier-dev > … .gz/v3.1.0.
I can download the file at https://codeload.github.com/wannier-developers/wannier90/tar.gz/v3.1.0 .
If you are using the clusters at the HPC center, you had better consult with the staffs there about the installation failure.
Sincerely,
H. Lee
Dear H. Lee,
Thanks for your letter, I installed the lapack-3.6.1 and wannier90-v3.1.0 in the EPW and Install folders in the common directory. However, again the installation of the EPW program, which came with QE-6.7, failed and a same message was received:
Make: *** [epw] Error 1
Maybe the folders lapack-3.6.1 and wannier90-v3.1.0 have to be installed in another location. I work alone and don’t have a cluster of machines.
How can I solve this problems? Thanks for the answer!
Best regards,
Mishchenka Valery.
Translated with www.DeepL.com/Translator (free version)
Dear H. Lee,
Thanks for your letter, I installed the lapack-3.6.1 and wannier90-v3.1.0 in the EPW and Install folders in the common directory. However, again the installation of the EPW program, which came with QE-6.7, failed and a same message was received:
Make: *** [epw] Error 1
Maybe the folders lapack-3.6.1 and wannier90-v3.1.0 have to be installed in another location. I work alone and don’t have a cluster of machines.
How can I solve this problems? Thanks for the answer!
Best regards,
Mishchenka Valery.
Dear H. Lee,
Thank you for your letter and help, I have installed the EPW 5.3 program in my computer.
When I run the program to execute with input file C2H1.epw.in, I get an error:
Xml data file ././.save/data-file-schema.xml not found
Now I try to solve this problem.
Best regards,
Mishchenka Valery.
Dear H. Lee,
I received your letter where you offer me to send the input and output files obtained for the study of graphene with hydrogen atoms. Taking into account your recommendation, I used EPW 5.3.1 and QE-6.7 programs in the last calculations. The execution of programs pw.x and ph.x passed without remarks. But when I ran EPW 5.3.1 using the file C2H1.epw.in, I got a warning:
Error in routine epw_setup(1):
coarse k-mesh needs to be strictly positive in 1st BZ
stopping …
I attach in .rar form the texts of C2H1.scf.in, C2H1.scf.out, C2H1.ph.in, C2H1.ph.out, C2H1.epw.in, C2H1.epw.out.
How can I solve these problems? Maybe use a more accurate mesh for k? Thanks for the answer!
Best regards,
Mishchenka Valery.
Dear Mishchenka Valery:
In addition, I would like to look at all of your inputs and outputs (scf.in, scf.out, nscf.in, nscf.out, ph.in, ph.out, epw.in, and epw.out).
Although I asked you to provide all inputs and outputs, I can’t find some inputs and outputs in your attached files.
Error in routine epw_setup(1):
coarse k-mesh needs to be strictly positive in 1st BZ
stopping …
I need to look at nscf.in, but I guess that you didn’t provide the k-point list on the full BZ with the range of [0, 1) from kmesh.pl in Wannier90.
I would suggest you to study and understand fully the examples in the EPW package before the production run for your research.
Sincerely,
H. Lee
Dear H. Lee,
Thank you for your reply. Please find enclosed texts of files C2H1.ph.in, C2H1B.epw.in, C2H1B.epw.out.
Files C2H1B.epw.in, C2H1B.epw.out I created today for 12x12x1 grid with program kmesh.pl located in Wannier90. I could not attach the files C2H1.scf.in, C2H1.scf.out, C2H1.ph.out to this e-mail for some unknown to me reason. I will try to send the files C2H1.scf.in, C2H1.scf.out, C2H1.ph.out in the next letter.
The EPW 5.3.1 program gives me a warning when I use C2H1B.epw.in:
Error in routine epw_setup(1):
coarse k-mesh needs to be strictly positive in BZ
Stopping …
How can i solve this problem ? Thanks for the answer!
Best regards,
Mishchenka Valery.
Dear H. Lee,
In addition to my previous letter, I am sending you the texts of files C2H1.scf.in, C2H1.scf.out, and C2H1.ph.out.
Best regards,
Mishchenka Valery.
Dear H. Lee,
In addition to my previous letter, I am sending you the texts of files C2H1.nscf.in, C2H1.nscf.out.
Best regards,
Mishchenka Valery.
Dear mishchenka:
I have difficulty with viewing the contents of rar files.
Please (1) use other compressed file formats such as tar, tar.gz, or zip or (2) upload the original files (not compressed).
Sincerely,
H. Lee
Dear H. Lee,
Thank you for your reply, excuse me for many letters. I will try to send you texts of C2H1.scf.in, C2H1.scf.out, C2H1.ph.in, C2H1.ph.out, C2H1.epw.in, C2H1.epw.out files with .tar.gz extension by one or several letters.
I was looking at examples of modeling on your website of different materials, and SiC material in particular, using the EPW program. I noticed that after running the ph.x program and before running the epw.x program an additional program pp.py is used. However, when running the pp.py program from the QE-6.7 program suite for my material, I got the answer:
bash: /home/user/ge-6.7/EPW/bin/pp.py: permission denied.
When I looked at the files in the SiC example material, I noticed that another program, pp.py, was being used. When running this program on the SiC material
/home/user/qe-6.7/qe-6.7/EPW/examples/sic/phonons/pp.py
I get the response:
from: can’t read /var/mail/builtins
/home/user/qe-6.7/qe-6.7/EPW/examples/sic/phonons/pp.py: line 7: import: command not found
/home/user/qe-6.7/qe-6.7/EPW/examples/sic/phonons/pp.py: line 8: import: command not found
/home/user/qe-6.7/qe-6.7/EPW/examples/sic/phonons/pp.py: line 11: syntax error near unexpected token ‘(’
/home/user/qe-6.7/qe-6.7/EPW/examples/sic/phonons/pp.py: line 11: ‘prefix = input (‘Enter the prefix used for PH calculations (e.g. diam)\n’)’
Maybe my simulation problems are related to the correct and proper execution of the pp.py program. However, in order to run this program, I need instructions and explanations on how to run this program. Thank you for your reply.
I am sending two versions of files with the .epx extension. I tried different ways to run the epw.x file.
Best regards,
Mishchenka Valery.