Fragment Python Script Crash Work-Around
- piskuliche
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8 years 1 month ago #97
by piskuliche
This is more of an FYI, rather than a question.
For some reason, when /library_setup.py is run to generate the fragment files during simulation preparation, with version 1.1 of Cassandra, it does not create all of the files needed to run a simulation.
Running version 1.1 alone causes the following to occur:
After experimentation, it became clear that when you run this same script with Cassandra version 1.0, and then run it again with version 1.1 the fragment files are generated properly.
Hope this helps those of you that encountered this problem as well.
For some reason, when /library_setup.py is run to generate the fragment files during simulation preparation, with version 1.1 of Cassandra, it does not create all of the files needed to run a simulation.
Running version 1.1 alone causes the following to occur:
*********Cassandra setup*********
Cassandra location: /data/piskuliche/Software/Cassandra.exe
Scanning input file...
Number of species found: 1
The MCF file number 1 is: ethylene_oxide.mcf
Species 1 has 1 fragments
Molecules with rings found. These are:
Species 1 has 1 rings.
Creating input MCF generation file for species 1...
Done...
Running Cassandra to generate MCF files...
Done...
Traceback (most recent call last):
File "/data/piskuliche/Cassandra/Scripts/Frag_Library_Setup/library_setup.py", line 540, in <module>
"_1.mcf",'r')
IOError: [Errno 2] No such file or directory: 'species1/fragments/frag_1_1.mcf'After experimentation, it became clear that when you run this same script with Cassandra version 1.0, and then run it again with version 1.1 the fragment files are generated properly.
Hope this helps those of you that encountered this problem as well.
The following user(s) said Thank You: jshah46545
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