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Anonymous

How to debug this error?
LAMMPS did not finish succesfully, can not continue
lmp_serial < ./bonds/bondcreate.in > out failed w/ exit code 1
---------------------------------------------------------------------------
Exception                                 Traceback (most recent call last)
 in run_all(ignore)
     35         print('Creating bonds ...')
     36         outfilelmpdat, outfilepdb = readFiles.convert_structure(infile)
---> 37         createBonds.create_bonds(outfilelmpdat, outfilepdb, bondscale, lattice_in_file, boundaries)
     38 
     39 

~/data/results/1667897/struc2lammpsdf/bin/createBonds.py in create_bonds(outfilelmpdat, outfilepdb, bondscale, files_in_lattice, user_boundaries)
     22     if return_code != 0:
     23         print('LAMMPS did not finish succesfully, can not continue')
---> 24         raise Exception('LAMMPS did not finish succesfully, can not continue')
     25     translate_write_connectivity('./bonds/new.lmpdat', './bonds/bonded.lmpdat', './bonds/pdbfile.pdb')
     26     print('Bonds have been identified')

Exception: LAMMPS did not finish succesfully, can not continue

 

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  1. 0 Like 0 Dislike

    Lorena Alzate-Vargas

    There is a problem with LAMMPS identifying bonds. Maybe your bond scale is not enough or your structure was not properly converted initially.

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