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could you please help me to sort out this problem
- Biswa72
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7 years 2 weeks ago #333
by Biswa72
while generating the fragment library, the following error is showing.
Creating input MCF generation file for species 1
Running Cassandra to generate MCF files
Error attempting to parse line 906 of input file:
6 28 27 66 28 69 70 73 31 80 20 68 67 79
into at least 30 entries
This error occurred in subroutine Parse_String on step 0.
Fatal Error. Stopping program.
Creating input MCF generation file for species 2
Running Cassandra to generate MCF files
Finished generating fragments
Exiting
Traceback (most recent call last):
File "./library_setup.py", line 604, in <module>
"_1.mcf",'r')
IOError: [Errno 2] No such file or directory: 'species1/fragments/frag_1_1.mcf'
Thanking you
Creating input MCF generation file for species 1
Running Cassandra to generate MCF files
Error attempting to parse line 906 of input file:
6 28 27 66 28 69 70 73 31 80 20 68 67 79
into at least 30 entries
This error occurred in subroutine Parse_String on step 0.
Fatal Error. Stopping program.
Creating input MCF generation file for species 2
Running Cassandra to generate MCF files
Finished generating fragments
Exiting
Traceback (most recent call last):
File "./library_setup.py", line 604, in <module>
"_1.mcf",'r')
IOError: [Errno 2] No such file or directory: 'species1/fragments/frag_1_1.mcf'
Thanking you
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- emarin
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- Biswa72
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- emarin
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7 years 1 week ago #336
by emarin
Hello!
It seems that you're trying to simulate adsorption of a gas into a solid material. We recommend that you follow the procedure described in section 6.3 of the user guide. In particular, we treat a solid as a fix set of atoms whose internal degrees of freedom are not sampled. Thus, the information relevant to fragments is irrelevant in the MCF file.
Please let us know if you have more questions.
It seems that you're trying to simulate adsorption of a gas into a solid material. We recommend that you follow the procedure described in section 6.3 of the user guide. In particular, we treat a solid as a fix set of atoms whose internal degrees of freedom are not sampled. Thus, the information relevant to fragments is irrelevant in the MCF file.
Please let us know if you have more questions.
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- Biswa72
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7 years 1 week ago #337
by Biswa72
Dear Sir,
First of all very much thank you for your continuous support, as per your suggestion I followed and started the GCMC calculation, everything seems to be ok, but after some time the log file showing something like .....
Compute total energy
********************************************************************************
Starting energy components for box 1
Atomic units-Extensive
Total system energy 330871735.127
Intra molecular energy 0.000
Bond energy 0.000
Bond angle energy 0.000
Dihedral angle energy 0.000
Improper angle energy 0.000
Intra molecule vdw 330879707.967
Intra molecule q 0.000
Inter molecule vdw -7860.538
Long range correction -112.302
Inter molecule q 0.000
********************************************************************************
Run simulation
********************************************************************************
Step Move Mol Spc Box Success MaxWidth
147 delete 2 1 F no mols
148 delete 2 1 F no mols
149 delete 2 1 F no mols
150 delete 2 1 F no mols
152 delete 2 1 F no mols
154 delete 2 1 F no mols
157 delete 2 1 F no mols
159 delete 2 1 F no mols
166 delete 2 1 F no mols
170 delete 2 1 F no mols
172 delete 2 1 F no mols
174 delete 2 1 F no mols
175 delete 2 1 F no mols
179 delete 2 1 F no mols
181 delete 2 1 F no mols
182 delete 2 1 F no mols
I have attached my input file, please have a look on it.
Thank you very much.
First of all very much thank you for your continuous support, as per your suggestion I followed and started the GCMC calculation, everything seems to be ok, but after some time the log file showing something like .....
Compute total energy
********************************************************************************
Starting energy components for box 1
Atomic units-Extensive
Total system energy 330871735.127
Intra molecular energy 0.000
Bond energy 0.000
Bond angle energy 0.000
Dihedral angle energy 0.000
Improper angle energy 0.000
Intra molecule vdw 330879707.967
Intra molecule q 0.000
Inter molecule vdw -7860.538
Long range correction -112.302
Inter molecule q 0.000
********************************************************************************
Run simulation
********************************************************************************
Step Move Mol Spc Box Success MaxWidth
147 delete 2 1 F no mols
148 delete 2 1 F no mols
149 delete 2 1 F no mols
150 delete 2 1 F no mols
152 delete 2 1 F no mols
154 delete 2 1 F no mols
157 delete 2 1 F no mols
159 delete 2 1 F no mols
166 delete 2 1 F no mols
170 delete 2 1 F no mols
172 delete 2 1 F no mols
174 delete 2 1 F no mols
175 delete 2 1 F no mols
179 delete 2 1 F no mols
181 delete 2 1 F no mols
182 delete 2 1 F no mols
I have attached my input file, please have a look on it.
Thank you very much.
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- ryangmullen
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7 years 1 week ago #338
by ryangmullen
It looks like your simulation has run out of CO2 molecules. If you change
prop_freq 1000
to
prop_freq 1
you can verify that the number of CO2 molecules is indeed 0. That means your chemical potential is too low for the size of your simulation. You can fix it by increasing either the volume or the chemical potential.
Ryan
prop_freq 1000
to
prop_freq 1
you can verify that the number of CO2 molecules is indeed 0. That means your chemical potential is too low for the size of your simulation. You can fix it by increasing either the volume or the chemical potential.
Ryan
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