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Anonymous

Polymatic: A Simulated Polymerization Algorithm -polymerisation procecess error

Dear users,

I have found following an error while making polymer with given Polymatic: A Simulated Polymerization Algorithm scripts.


Polymatic Simulated Polymerization

Parameters


Initial bonds:             0
Total bonds:               11
Bonds per cycle:           5
Frequency of MD type 2:    3

Maximum bond attempts:     30

Polymerization Loop


Initialization: Step 0: Error: LAMMPS energy minimization did not complete properly.

 


OUTPUT FILE SHOWN BELOW


………..   1 neighbor list requests   update every 1 steps, delay 0 steps, check yes   max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
Setting up cg style minimization …   Unit style: real

======================================================================
=

=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES =   PID 30465 RUNNING AT inspire.iict.ac.in =   EXIT CODE: 11
=   CLEANING UP REMAINING PROCESSES =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES

======================================================================
=

YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions

 Does someone have idea of resolving this issue? Thanks in advance.

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    Lauren Abbott

    The Polymatic code runs several energy minimization and molecular dynamics steps through LAMMPS during the simulated polymerization. At the end of every step, it ensures that the LAMMPS simulation ran correctly (didn't fail) before moving on to the next step.

    The error you are getting from Polymatic (LAMMPS energy minimization did not complete properly) is indicating that there was a problem with the LAMMPS energy minimization run in Step 0, such that it did not complete successfully.

    The remaining output you show is generated when LAMMPS is running and shows that there was a segmentation fault during the energy minimization. A segmentation fault can occur for a variety of reasons, so it would be impossible for me to pinpoint that problem based on only the output info you provided. I would suggest that you take a look for the last line executed in the log.lammps file generated by LAMMPS when trying to run the energy minimization. This should give you some indication as to where the problem might be occurring.

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