Anonymous @ on
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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Lorena Alzate-Vargas @ on
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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