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gaox-qd / pysoc

PySOC: python+fortran, spin-orbit coupling, LR-TD-DFT, TDA, TD-DFTB, Gaussian 09, DFTB+
https://github.com/jzpathfinder/pysoc
Apache License 2.0
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Error running pysoc #5

Open shyamvkp opened 4 years ago

shyamvkp commented 4 years ago

Hi, I followed the instructions from http://sobereva.com/411 and used the molsoc_modified file for soc calculation. I got the below error. Can you please help me?

Traceback (most recent call last): File "/home/codes/pysoc/bin/soc.py", line 491, in write_file(mo_ene, 'mo_ene.dat', '{} ') NameError: name 'mo_ene' is not defined forrtl: No such file or directory forrtl: severe (29): file not found, unit 171, file /home/soc/soc_td_input.dat Image PC Routine Line Source soc_td 000000000041BBB6 Unknown Unknown Unknown soc_td 0000000000427AEB Unknown Unknown Unknown soc_td 0000000000407F0B Unknown Unknown Unknown soc_td 000000000040254E Unknown Unknown Unknown soc_td 00000000004024FE Unknown Unknown Unknown libc.so.6 00002B9C69DCAB35 Unknown Unknown Unknown soc_td 0000000000402409 Unknown Unknown Unknown

gaox-qd commented 4 years ago

Hi, I followed the instructions from http://sobereva.com/411 and used the molsoc_modified file for soc calculation. I got the below error. Can you please help me?

Traceback (most recent call last): File "/home/codes/pysoc/bin/soc.py", line 491, in write_file(mo_ene, 'mo_ene.dat', '{} ') NameError: name 'mo_ene' is not defined forrtl: No such file or directory forrtl: severe (29): file not found, unit 171, file /home/soc/soc_td_input.dat Image PC Routine Line Source soc_td 000000000041BBB6 Unknown Unknown Unknown soc_td 0000000000427AEB Unknown Unknown Unknown soc_td 0000000000407F0B Unknown Unknown Unknown soc_td 000000000040254E Unknown Unknown Unknown soc_td 00000000004024FE Unknown Unknown Unknown libc.so.6 00002B9C69DCAB35 Unknown Unknown Unknown soc_td 0000000000402409 Unknown Unknown Unknown

Could you reproduce the results in the examples? Otherwise it may come from your settings of Gaussian 09 or python 2.7.

shyamvkp commented 4 years ago

Hi, I tried to run the examples. While running ch2o_gaussian, I got the following error.

forrtl: severe (153): allocatable array or pointer is not allocated Image PC Routine Line Source soc_td 000000000043657E Unknown Unknown Unknown soc_td 0000000000402E44 Unknown Unknown Unknown soc_td 00000000004024FE Unknown Unknown Unknown libc.so.6 00002AF3FB231B35 Unknown Unknown Unknown soc_td 0000000000402409 Unknown Unknown Unknown

I could not identify the error source. Pls, help.

salmansey commented 4 years ago

[seyhan@login005 seyhan]$ python pysoc.py QM_code gauss_tddft open file gaussian.log [[1, 3.351], [3, 5.6721], [4, 8.0749], [5, 8.1309], [8, 9.3176]] 2 4.0271 ['ANG', 'Zeff', 'DIP'] ao_basis [['S', 1], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['P', 3], ['P', 3], ['D', 6], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['P', 3], ['P', 3], ['D', 6], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['S', 1], ['S', 1], ['S', 1], ['P', 3]] n_basis 52 hello1 hello2 open file gaussian.rwf Error when reading gaussian output Traceback (most recent call last): File "/pylon5/tr4s84p/seyhan/pysoc/bin/soc.py", line 491, in write_file(mo_ene, 'mo_ene.dat', '{} ') NameError: name 'mo_ene' is not defined input 3.35100000000000 5.67210000000000 8.07490000000000 8.13090000000000 root_s 1 2 3 4 2 6 7 9 root_t 1 2 3 4 1 3 4 5 forrtl: No such file or directory forrtl: severe (29): file not found, unit 172, file /pylon5/tr4s84p/seyhan/soc_ao.dat Image PC Routine Line Source soc_td 000000000048B27E Unknown Unknown Unknown soc_td 0000000000489D16 Unknown Unknown Unknown soc_td 0000000000449EF2 Unknown Unknown Unknown soc_td 000000000041ECCB Unknown Unknown Unknown soc_td 000000000041E232 Unknown Unknown Unknown soc_td 00000000004287F8 Unknown Unknown Unknown soc_td 0000000000406C22 Unknown Unknown Unknown soc_td 00000000004024EB Unknown Unknown Unknown soc_td 000000000040227C Unknown Unknown Unknown libc.so.6 00007FE46F9C0495 Unknown Unknown Unknown soc_td 0000000000402179 Unknown Unknown Unknown

I am also having similar errors. Any suggestion to make this work. Thank you!

gaox-qd commented 4 years ago

How about the versions of Python and Gaussian you are using now?

On Tue, Jul 7, 2020 at 4:04 PM Seyhan Salman notifications@github.com wrote:

[seyhan@login005 seyhan]$ python pysoc.py QM_code gauss_tddft open file gaussian.log [[1, 3.351], [3, 5.6721], [4, 8.0749], [5, 8.1309], [8, 9.3176]] 2 4.0271 ['ANG', 'Zeff', 'DIP'] ao_basis [['S', 1], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['P', 3], ['P', 3], ['D', 6], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['P', 3], ['P', 3], ['D', 6], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['S', 1], ['S', 1], ['S', 1], ['P', 3]] n_basis 52 hello1 hello2 open file gaussian.rwf Error when reading gaussian output Traceback (most recent call last): File "/pylon5/tr4s84p/seyhan/pysoc/bin/soc.py", line 491, in write_file(mo_ene, 'mo_ene.dat', '{} ') NameError: name 'mo_ene' is not defined input 3.35100000000000 5.67210000000000 8.07490000000000 8.13090000000000 root_s 1 2 3 4 2 6 7 9 root_t 1 2 3 4 1 3 4 5 forrtl: No such file or directory forrtl: severe (29): file not found, unit 172, file /pylon5/tr4s84p/seyhan/soc_ao.dat Image PC Routine Line Source soc_td 000000000048B27E Unknown Unknown Unknown soc_td 0000000000489D16 Unknown Unknown Unknown soc_td 0000000000449EF2 Unknown Unknown Unknown soc_td 000000000041ECCB Unknown Unknown Unknown soc_td 000000000041E232 Unknown Unknown Unknown soc_td 00000000004287F8 Unknown Unknown Unknown soc_td 0000000000406C22 Unknown Unknown Unknown soc_td 00000000004024EB Unknown Unknown Unknown soc_td 000000000040227C Unknown Unknown Unknown libc.so.6 00007FE46F9C0495 Unknown Unknown Unknown soc_td 0000000000402179 Unknown Unknown Unknown

I am also having similar errors. Any suggestion to make this work. Thank you!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jzpathfinder/pysoc/issues/5#issuecomment-655097943, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABW6RCTZEJZUWC43JGK2ZFTR2N5U7ANCNFSM4IZCV7WA .

-- Gao Xing (高星) Postdoctoral researcher Department of Chemistry University of Michigan, Ann Arbor, MI, USA gxaaas@gmail.com Politics is for the present, but an equation is for eternity!----Albert Einstein

salmansey commented 4 years ago

Thank you for your reply. I tried both g09 and g16. Same error. I don’t know how to check Python version. I am using XSEDE clusters, bridges and stampede2. Any idea?

Thanks so much for your answer again!

Sent from my iPhone

On Jul 7, 2020, at 4:46 PM, GX notifications@github.com wrote:

 How about the versions of Python and Gaussian you are using now?

On Tue, Jul 7, 2020 at 4:04 PM Seyhan Salman notifications@github.com wrote:

[seyhan@login005 seyhan]$ python pysoc.py QM_code gauss_tddft open file gaussian.log [[1, 3.351], [3, 5.6721], [4, 8.0749], [5, 8.1309], [8, 9.3176]] 2 4.0271 ['ANG', 'Zeff', 'DIP'] ao_basis [['S', 1], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['P', 3], ['P', 3], ['D', 6], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['P', 3], ['P', 3], ['D', 6], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['S', 1], ['S', 1], ['S', 1], ['P', 3]] n_basis 52 hello1 hello2 open file gaussian.rwf Error when reading gaussian output Traceback (most recent call last): File "/pylon5/tr4s84p/seyhan/pysoc/bin/soc.py", line 491, in write_file(mo_ene, 'mo_ene.dat', '{} ') NameError: name 'mo_ene' is not defined input 3.35100000000000 5.67210000000000 8.07490000000000 8.13090000000000 root_s 1 2 3 4 2 6 7 9 root_t 1 2 3 4 1 3 4 5 forrtl: No such file or directory forrtl: severe (29): file not found, unit 172, file /pylon5/tr4s84p/seyhan/soc_ao.dat Image PC Routine Line Source soc_td 000000000048B27E Unknown Unknown Unknown soc_td 0000000000489D16 Unknown Unknown Unknown soc_td 0000000000449EF2 Unknown Unknown Unknown soc_td 000000000041ECCB Unknown Unknown Unknown soc_td 000000000041E232 Unknown Unknown Unknown soc_td 00000000004287F8 Unknown Unknown Unknown soc_td 0000000000406C22 Unknown Unknown Unknown soc_td 00000000004024EB Unknown Unknown Unknown soc_td 000000000040227C Unknown Unknown Unknown libc.so.6 00007FE46F9C0495 Unknown Unknown Unknown soc_td 0000000000402179 Unknown Unknown Unknown

I am also having similar errors. Any suggestion to make this work. Thank you!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jzpathfinder/pysoc/issues/5#issuecomment-655097943, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABW6RCTZEJZUWC43JGK2ZFTR2N5U7ANCNFSM4IZCV7WA .

-- Gao Xing (高星) Postdoctoral researcher Department of Chemistry University of Michigan, Ann Arbor, MI, USA gxaaas@gmail.com Politics is for the present, but an equation is for eternity!----Albert Einstein — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

gaox-qd commented 4 years ago

It looks there are some issues on the settings of Python environment variables.

On Tue, Jul 7, 2020 at 6:21 PM Seyhan Salman notifications@github.com wrote:

Thank you for your reply. I tried both g09 and g16. Same error. I don’t know how to check Python version. I am using XSEDE clusters, bridges and stampede2. Any idea?

Thanks so much for your answer again!

Sent from my iPhone

On Jul 7, 2020, at 4:46 PM, GX notifications@github.com wrote:

 How about the versions of Python and Gaussian you are using now?

On Tue, Jul 7, 2020 at 4:04 PM Seyhan Salman notifications@github.com wrote:

[seyhan@login005 seyhan]$ python pysoc.py QM_code gauss_tddft open file gaussian.log [[1, 3.351], [3, 5.6721], [4, 8.0749], [5, 8.1309], [8, 9.3176]] 2 4.0271 ['ANG', 'Zeff', 'DIP'] ao_basis [['S', 1], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['P', 3], ['P', 3], ['D', 6], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['P', 3], ['P', 3], ['D', 6], ['S', 1], ['S', 1], ['S', 1], ['P', 3], ['S', 1], ['S', 1], ['S', 1], ['P', 3]] n_basis 52 hello1 hello2 open file gaussian.rwf Error when reading gaussian output Traceback (most recent call last): File "/pylon5/tr4s84p/seyhan/pysoc/bin/soc.py", line 491, in write_file(mo_ene, 'mo_ene.dat', '{} ') NameError: name 'mo_ene' is not defined input 3.35100000000000 5.67210000000000 8.07490000000000 8.13090000000000 root_s 1 2 3 4 2 6 7 9 root_t 1 2 3 4 1 3 4 5 forrtl: No such file or directory forrtl: severe (29): file not found, unit 172, file /pylon5/tr4s84p/seyhan/soc_ao.dat Image PC Routine Line Source soc_td 000000000048B27E Unknown Unknown Unknown soc_td 0000000000489D16 Unknown Unknown Unknown soc_td 0000000000449EF2 Unknown Unknown Unknown soc_td 000000000041ECCB Unknown Unknown Unknown soc_td 000000000041E232 Unknown Unknown Unknown soc_td 00000000004287F8 Unknown Unknown Unknown soc_td 0000000000406C22 Unknown Unknown Unknown soc_td 00000000004024EB Unknown Unknown Unknown soc_td 000000000040227C Unknown Unknown Unknown libc.so.6 00007FE46F9C0495 Unknown Unknown Unknown soc_td 0000000000402179 Unknown Unknown Unknown

I am also having similar errors. Any suggestion to make this work. Thank you!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <https://github.com/jzpathfinder/pysoc/issues/5#issuecomment-655097943 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/ABW6RCTZEJZUWC43JGK2ZFTR2N5U7ANCNFSM4IZCV7WA

.

-- Gao Xing (高星) Postdoctoral researcher Department of Chemistry University of Michigan, Ann Arbor, MI, USA gxaaas@gmail.com Politics is for the present, but an equation is for eternity!----Albert Einstein — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/jzpathfinder/pysoc/issues/5#issuecomment-655166863, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABW6RCTTGZN3IOVUOUPXM3LR2ONVHANCNFSM4IZCV7WA .

-- Gao Xing (高星) Postdoctoral researcher Department of Chemistry University of Michigan, Ann Arbor, MI, USA gxaaas@gmail.com Politics is for the present, but an equation is for eternity!----Albert Einstein

priyanandchem commented 4 months ago

Hello sir . I'm using the g09 version and got this error while running the pySOC.py file QM_code gauss_tddft open file bt-soc.log [[1, 2.595], [2, 3.6078], [3, 4.3647], [5, 4.3852], [6, 5.2711]] 4 4.3821 Error when reading gaussian output Traceback (most recent call last): File "/home/tanmoy/Downloads/pySOC-cal/pysoc/bin/soc.py", line 491, in write_file(mo_ene, 'mo_ene.dat', '{} ') NameError: name 'mo_ene' is not defined forrtl: No such file or directory forrtl: severe (29): file not found, unit 171, file /home/tanmoy/Downloads/pySOC-cal/cals/soc_td_input.dat Image PC Routine Line Source
soc_td 000000000048B27E Unknown Unknown Unknown soc_td 0000000000489D16 Unknown Unknown Unknown soc_td 0000000000449EF2 Unknown Unknown Unknown soc_td 000000000041ECCB Unknown Unknown Unknown soc_td 000000000041E232 Unknown Unknown Unknown soc_td 00000000004287F8 Unknown Unknown Unknown soc_td 000000000040755A Unknown Unknown Unknown soc_td 00000000004022D9 Unknown Unknown Unknown soc_td 000000000040227C Unknown Unknown Unknown libc.so.6 00002B9319C1B555 Unknown Unknown Unknown soc_td 0000000000402179 Unknown Unknown Unknown

gaox-qd commented 2 months ago

Which version of PySOC did you use? Perhaps you could try the version rewritten for Python 3.x by Oliver S. Lee, recently. (https://github.com/gaox-qd/pysoc)