quantummaterialsmodelling / vasp-phonopy-sscha Goto Github PK

Dear Luigi Ranalli,

Firstly, thanks for your vasp-phonopy-sscha code, really needed connection between SSCHA and VASP!

I'm facing the issue of generating unreasonable structure files (scf...dat or POSCAR) very similar to the issue already reported by Xinyu.

I am working on orthorhombic Pnma type BiSeI,
starting with FORCE_CONSTANTS of 2x2x2 supercell,
interpolating to 2x2x2 supercell size,
at 100 K,
having 8 qpoint files (qe format),
100 configurations.

I have uploaded FORCE_CONSTANTS and POSCAR at
https://github.com/matukumilli/BiSeI

It would be helpful if you can look in to this issue by testing the present version of code once with my files.
I hope the attached files are sufficient to reproduce the error.

Regards,
Prasad Matukumilli

Thank you very much for sharing this code!
I'm having some problems interpolating the force constants. The produced POSCAR_X is unreasonable when X is an odd number，like this
POSCAR_1

generated by phonopy
1.0
20.51030558015857 0.0 0.0947411230257034
0.0 20.860917147463063 0.0
-3.6106018498087886 0.0 20.858517349609922
Zr O
256 512
Cartesian
-438553.80855691695 -543280.1570566504 286518.73247570207
-438553.671591944 -543279.3267175994 286519.99236833915
-438552.4253739102 -543280.9669509121 286518.48628210207
-438553.2039323958 -543279.7152609768 286519.35185900383
22257.10144415168 -650241.3606646878 -26906.01525612041
22257.04413241384 -650243.0055896948 -26905.800726940302
22258.04251456885 -650241.36534403 -26906.07351934072
22256.97276405285 -650243.326194487 -26905.606374732888
676737.4450210299 440318.2365866 -1065226.153565556
676737.3888753173 440316.44367526815 -1065225.6138304048
676738.2783565173 440317.05514217593 -1065223.672337983
676736.9845212774 440315.60200564977 -1065223.2785678827
463511.2382516823 -178955.23868022897 178243.2662837978
463508.8697193315 -178954.8631244169 178242.75283586068
463509.571465863 -178956.17992234929 178243.95688892683
463510.1420496272 -178955.4577892833 178244.10510047583
-512571.4562084836 129374.96537315416 236796.2457425185
-512572.00775864033 129374.2109303694 236797.78541015953
-512571.6212766557 129374.57575351062 236798.62183244704
-512572.5869720848 129373.62711372132 236798.6442055317
-465624.63828789274 -712231.6612378139 244633.56677149824
-465624.71355332155 -712233.0207340133 244633.36209637148

……

but when X is an even number, the POSCAR_X is right,

POSCAR_2
generated by phonopy
1.0
20.51030558015857 0.0 0.0947411230257034
0.0 20.860917147463063 0.0
-3.6106018498087886 0.0 20.858517349609922
Zr O
256 512
Cartesian
-1.156085030623753 1.2059708210784816 -7.136410832497273
-1.2930499937341968 -0.4527329647789134 -7.396301335088294
-1.6483928367120877 1.0158628682616653 -6.727812692393802
-0.8698343390390317 -1.0641916639286808 -6.593387325684155
-8.901504694026082 8.487363815361661 7.135005608180705
-8.844192946183545 9.303924087477272 7.920478562602579
-8.951699910312808 7.492040942939613 7.355673368657643
-7.881949382315635 8.624526803169537 7.888531029361075
6.68065870188174 -4.944169545858398 1.8320228887938088
6.736804424631131 -3.979622948912812 2.2922898723478973
3.1275965655618143 -4.762727336411295 20.37171720594545
4.421431817404636 -4.137955406993245 20.97794937418953
-1.3266005210294092 -8.655342305462185 11.779341912553198
1.0419318397890929 -9.859262852396236 13.292791984228195
1.2310604993349252 -8.714102399657484 11.251141323743738
0.6604767469804003 -10.264600062506204 12.102932043238864
1.5849811954089108 -4.073497610752852 3.623770345081109
2.1365313621836144 -4.147419560857952 3.084104838637768
2.6409245684790688 -4.683880181715743 1.4100849567052507
3.606620009446236 -4.563604989305652 2.3877141405938107
……
how can i fix it?

Thank you very much for sharing your code!

First I follow the README, after this step “Which is your PHONOPY supercell? 3 ### On a 3x3x3 we could get a good harmonic guess”，The first error occurred : Traceback (most recent call last):
File "/home/ustb-clz/software/vasp-phonopy-sscha-main/vasp-phonopy-sscha/interface.py", line 298, in
run1.matrix_formatting()
File "/home/ustb-clz/software/vasp-phonopy-sscha-main/vasp-phonopy-sscha/interface.py", line 125, in matrix_formatting
self.dynamical_matrix = self.dynamical_matrix.drop(0, 1)
TypeError: DataFrame.drop() takes from 1 to 2 positional arguments but 3 were given

After that I modified lines 125 to 127 of interface.py self.dynamical_matrix = self.dynamical_matrix.drop([0, 1], axis=1)

I was able to continue using it, but after that “You want to use the Sobol sequence for the configurations? y/n” this issue came up.

Traceback (most recent call last):
File "/home/ustb-clz/software/vasp-phonopy-sscha-main/vasp-phonopy-sscha/interface.py", line 314, in
n_random,n_population,NQIRR = generate(None)
File "/home/ustb-clz/software/vasp-phonopy-sscha-main/vasp-phonopy-sscha/generate.py", line 92, in generate
ens = sscha.Ensemble.Ensemble(dyn, T, dyn.GetSupercell()) # (((dyn->new_dyn)
File "/home/ustb-clz/software/intel/oneapi/intelpython/latest/envs/sscha/lib/python3.10/site-packages/sscha/Ensemble.py", line 152, in init
self.dyn_0 = dyn0.Copy()
File "/home/ustb-clz/software/intel/oneapi/intelpython/latest/envs/sscha/lib/python3.10/site-packages/sscha/Ensemble.py", line 230, in setattr
self.w_0, self.pols_0 = value.DiagonalizeSupercell()
File "/home/ustb-clz/software/intel/oneapi/intelpython/latest/envs/sscha/lib/python3.10/site-packages/cellconstructor/Phonons.py", line 3635, in DiagonalizeSupercell
c_e_sc = tilde_e_qnu[itau_modes] * np.exp(1j*phase) / np.sqrt(supercell_size)
ValueError: operands could not be broadcast together with shapes (810,) (150,)

I really don't know how to fix this anymore.