Dear All,
Recently, I am working with ATAT in order to get the vibration free energy using the bond stiffness versus bond length approximation. When I run `fitsvsl -f’, I confront an error saying:
Singular matrix in lu_decomposition
Segmentation fault (core dumped)
BTW, I am using Quantum ESPRESSO code linked with ATAT. I really appreciate it if you let me know how I should fix this problem. Thank you for your help.
Regards,
Mahdi
Ok, this is helpful. Can you send me a tar file with the relevant input files. (i.e. everything but the very large input/output files from espresso). I can then debug this. Sorry I first had to rule out simple errors.
Thank you for your help and interest. Actually, I tried to upload the tar file here, but it seems that my file is not uploaded here. Woud you please let me know how I should sent it to you?
email to [email protected] but make sure you made it small.
Dear Professor Van De Walle,
I would like to inform you that I sent the tar file to the email that you mentioned.
I believe the issue is that you did not specify or did not specify a large enough value of the -er parameter when you generated the perturbations. er must be at least 2 or 3 times the nearest neighbor distance. This parameter controls the size of the supercell used, which is needed to be able to separately identify different force constants (otherwise the atoms and their periodic image move together).
BTW, if you do automate the force conversion, please feel free to share your script!
Thank you so much for your explanation. Actually, in files that I sent to you, I used the -er value equal to 3. Now, I want to test with -er equal to 5. I will update you about what I get. Hopefully, after getting the results successfully, I will prepare the script file and put it here for free.
Regards,
Mahdi
in the first step I have done by hand. after that I will write a script for this calculation.
Actually, the force.out file includes the values of force vectors on each atom after the scf run in Qunatum ESPRESSO. I converted them to eV/angstrom based on your guidance, but still I get segmentation fault.
nrtc@linux-gfye:~/Downloads/0000> ls /vol_/*/force.out
0/vol_0/p+0.2_3_0/force.out 3/vol_0/p+0.2_3_0/force.out 4/vol_1/p+0.2_3_1/force.out
0/vol_1/p+0.2_3_0/force.out 3/vol_0/p+0.2_3_1/force.out 4/vol_1/p+0.2_3_2/force.out
1/vol_0/p+0.2_3_0/force.out 3/vol_0/p+0.2_3_2/force.out 5/vol_0/p+0.2_3_0/force.out
1/vol_1/p+0.2_3_0/force.out 3/vol_1/p+0.2_3_0/force.out 5/vol_0/p+0.2_3_1/force.out
2/vol_0/p+0.2_3_0/force.out 3/vol_1/p+0.2_3_1/force.out 5/vol_0/p+0.2_3_2/force.out
2/vol_0/p+0.2_3_1/force.out 3/vol_1/p+0.2_3_2/force.out 5/vol_1/p+0.2_3_0/force.out
2/vol_0/p+0.2_3_2/force.out 4/vol_0/p+0.2_3_0/force.out 5/vol_1/p+0.2_3_1/force.out
2/vol_1/p+0.2_3_0/force.out 4/vol_0/p+0.2_3_1/force.out 5/vol_1/p+0.2_3_2/force.out
2/vol_1/p+0.2_3_1/force.out 4/vol_0/p+0.2_3_2/force.out
2/vol_1/p+0.2_3_2/force.out 4/vol_1/p+0.2_3_0/force.out
nrtc@linux-gfye:~/Downloads/0000> cat /vol_/*/force.out
0 0 -0.0022
0 0 0.0022
0 0 -0.0019
0 0 0.0019
0 0 -0.003414727922566
0 0 0.003414727922566
0 0 -0.002988983980392
0 0 0.002988983980392
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0.000788691127382 0.000544747291233 0.000726187629641
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0.000971843181772 0.000436358059231 -0.000731771612000
This usually means there is not enough data to fit the model.
Do you see files called vol_//force.out ?
The qe interface someone contributed to the code does not seem to parse the forces calculated by the ab initio code, so this is likely the issue.
It would be great if you could contribute a fix to this. You need to convert the espresso output files into a file called force.out that contains the forces acting on each atom, one 3d vector per line (space-separated) and expressed in units of eV/angstrom.
Thank you for your quick response,
These are the whole result that I got after running the fitsvsl -f which were come out in the terminal. 6 main points (ground state points) and 27 folders including force.out files have been produced. I was wondering if these numbers of produced data are enough for fitting or not?? Could you please let me know how many force.out files are needed in order to fit appropriately?
nrtc@linux-gfye:~/Downloads/0000> fitsvsl -f
0) Reading 0/vol_0/p+0.2_3_0
The question is what is the output of
ls */vol_*/*/force.out
cat */vol_*/*/force.out
Also, which script did you use to convert to/from the espresso input/output?
Similar question. Please help
Segmentation error actually occurs during the execution of a program over a system. It can be fixed by some modification on the program. You may just visit Epson printer not printing to get the entire details about the error.