QuantumLab-ZY
commented
6 months ago Your usage of openmx_postprocess is incorrect. In the readme file, I never mentioned that openmx_postprocess is used to read .scfout files; instead, it is used to generate overlap.scfout files. The usage of openmx_postprocess is similar to that of openmx, as it is essentially a modification based on openmx. By the way, when pasting parameters and structure files, I recommend using the following format:
Atoms.Number 54
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates # Unit=Ang.
1 Mo -0.0286802 1.9385361 3.3761010 7.00 7.00
2 Mo 3.3626113 1.9288630 3.3860054 7.00 7.00
3 Mo 0.0189562 7.6608930 3.3874465 7.00 7.00
4 Mo -1.6181169 4.7561361 3.4182420 7.00 7.00
5 Mo 6.6963890 1.9037534 3.4232872 7.00 7.00
6 Mo -3.3719035 7.6853933 3.4254761 7.00 7.00
flamingoXu
Dear Zhong Yang when try to use openmx_postprocess to convert my openmx.scfout into a overlap.out , the program report an err. but the Species.Number looks fine.
(GPU) root@bohrium-11924-1124454:~/test/perturbe/data_caculate/openmc_postprocess# mpirun -n 24 openmx_postprocess ./d1/openmx.scfout
The number of threads in each node for OpenMP parallelization is 1.
Welcome to OpenMX Ver. 3.9
Copyright (C), 2002-2019, T. Ozaki
OpenMX comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to
redistribute it under the constitution of the GNU-GPL.
Species.Number may be wrong.Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong.
Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong.Species.Number may be wrong.
Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. Species.Number may be wrong. The recursion method is not supported anymore.
#
Definition of Atomic Species
# Species.Number 3 <Definition.of.Atomic.Species Se Se7.0-s3p2d2 Se_PBE19 Mo Mo7.0-s3p2d2 Mo_PBE19 W W7.0-s3p2d2f1 W_PBE19 Definition.of.Atomic.Species>
#
Atoms
# Atoms.Number 54 Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU <Atoms.SpeciesAndCoordinates # Unit=Ang. 1 Mo -0.0286802 1.9385361 3.3761010 7.00 7.00 2 Mo 3.3626113 1.9288630 3.3860054 7.00 7.00 3 Mo 0.0189562 7.6608930 3.3874465 7.00 7.00 4 Mo -1.6181169 4.7561361 3.4182420 7.00 7.00 5 Mo 6.6963890 1.9037534 3.4232872 7.00 7.00 6 Mo -3.3719035 7.6853933 3.4254761 7.00 7.00 7 Mo 1.7039942 4.7615691 3.4358513 7.00 7.00 8 Mo 3.3428237 7.6583756 3.4464608 7.00 7.00 9 Mo 4.9875423 4.7740001 3.4597375 7.00 7.00 10 Se 1.6479069 6.6861775 1.6960455 3.00 3.00 11 Se 6.6620135 3.8516398 1.7150090 3.00 3.00 12 Se 8.3431634 0.9212830 1.7230284 3.00 3.00 13 Se -1.6894806 6.7494416 1.7349048 3.00 3.00 14 Se 4.9293133 0.9813151 1.7470587 3.00 3.00 15 Se 1.6218534 0.9402664 1.7546247 3.00 3.00 16 Se 3.3064606 3.8582844 1.7612616 3.00 3.00 17 Se 5.0046991 6.7349773 1.7700242 3.00 3.00 18 Se 0.0134959 3.8758717 1.7898198 3.00 3.00 19 Se -0.0214408 3.8453380 5.0316924 3.00 3.00 20 Se -1.7057505 6.7500693 5.0422239 3.00 3.00 21 Se 6.6372654 3.8306564 5.0434805 3.00 3.00 22 Se 4.9555780 6.7515701 5.0456707 3.00 3.00 23 Se 3.2974692 3.7934811 5.0594792 3.00 3.00