Unable to generate the fragment molecules

  • wthor1
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5 years 1 month ago #588 by wthor1
Dear all,

Recently I've tried to use cassandra on my system, it should be a polymer, and I've some questions on it.
When I'm trying to generate the fragments using library_setup.py, it generated the error message as shown:

----
Creating input MCF generation file for species 1
Running Cassandra to generate MCF files
Error attempting to parse line 562 of input file:
2 22 6 1 2 3 4 5 23 24 26 28 36 53 7
into at least 24 entries
This error occurred in subroutine Parse_String on step 0.
Fatal Error. Stopping program.
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL
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'
----

I've generated the mcf files using mcfgen.py, and this error occurs.
I was wondering is there any upper limits for the fragments atomic info?

Thank you in advance!

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5 years 1 month ago #590 by emarin
Could you share your files? what polymer are you trying to simulate? could you share an image?

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5 years 1 month ago #592 by wthor1
When I check the fragment info from the mcfgen.py, maybe there are quit many rings in my system (I am using monomer at the moment), so the fragments connectivity are a little messy, I decide to redefine the fragments and it is as shown as image below:



After that, I did not get the error as shown above, and at least 2 fragments are generated (better than last time, nothing generated?), however, I get error like this:

"""
Scanning input file
Number of species found: 1
The MCF file number 1 is: pilot_ATM.mcf
Species 1 has 17 fragments
Molecules with rings found. These are:
Species 1 has 5 rings.


Creating input MCF generation file for species 1
Running Cassandra to generate MCF files

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7FE304F47E08
#1 0x7FE304F46F90
#2 0x7FE3046784AF
#3 0x489BFB in participation_
#4 0x4783E6 in mcf_control_
#5 0x409D86 in MAIN__ at main.f90:?
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_3_1.mcf'
"""

I rechecked my structure and the connectivity, I guess it should be fine so I've no idea what's the mistake I've done here.

Any suggestion or correction please?

Much appreciated and have a good day!

I attach my mcf file also for better reference.

File Attachment:

File Name: pilot_ATM.mcf
File Size:29 KB
Attachments:

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