peteboyd / lammps_interface

automatic generation of LAMMPS input files for molecular dynamics simulations of MOFs
MIT License
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Error in generating raspa input from polymer cif file #56

Open sbkk000 opened 2 years ago

sbkk000 commented 2 years ago

Error in generating raspa input files from polymer cif file Operating environment:Anaconda 3 , Programs installed with conda install -c conda-forge lammps-interface Attachment is PANI03.cif document.

The error message is as follows:

$ lammps-interface -or -ff Dreiding --npt PANI03.cif

totatomlen = 1810 compute_topology_information() func: cartesian_coordinates; Elps. 0.024s func: min_img_distances; Elps. 30.202s func: compute_bonding; Elps. 30.452s func: init_typing; Elps. 30.829s func: bond_typing; Elps. 30.856s func: angles; Elps. 30.865s func: dihedrals; Elps. 30.875s func: improper_dihedrals; Elps. 30.886s Files created! -> /home/lammps-test/chitosan-PANI03/PANI03 Writing RASPA files to current WD Output cif file written to PANI03_raspa.cif 1 {'_atom_site_fract_x': '-0.25360', '_atom_site_fract_y': '1.31535', '_atom_site_fract_z': '0.07455', '_atom_site_U_iso_or_equiv': '0.00000', '_atom_site_adp_type': 'Uiso', '_atom_site_occupancy': '1.00', 'mass': 14.0067, 'molid': 444, 'element': 'N', 'cycle': False, 'rings': [], 'atomic_number': 7, 'pair_potential': lj/cut 12.500, 'h_bond_donor': False, 'h_bond_potential': None, 'tabulated_potential': False, 'table_potential': None, 'charge': 0.0, 'force_field_type': 'N_3', 'index': 1, 'ciflabel': 'N1', 'cartesian_coordinates': array([-10.72809152, 55.64351412, 3.15370356]), 'hybridization': 'sp3', 'angles': {(2, 3): {'potential': <lammps_interface.lammps_potentials.AnglePotential.CosineSquared object at 0x146b26a62f98>, 'ff_type_index': 1}, (2, 23): {'potential': <lammps_interface.lammps_potentials.AnglePotential.CosineSquared object at 0x146b26a4d278>, 'ff_type_index': 1}, (3, 23): {'potential': <lammps_interface.lammps_potentials.AnglePotential.CosineSquared object at 0x146b26a4d2b0>, 'ff_type_index': 1}}, 'impropers': {}, 'ff_type_index': 1, 'node': 1} Traceback (most recent call last): File "/home/anaconda3/envs/vaspkit/bin/lammps-interface", line 10, in sys.exit(main()) File "/home/anaconda3/envs/vaspkit/lib/python3.6/site-packages/lammps_interface/cli.py", line 35, in main write_RASPA_sim_files(sim, classifier) File "/home/anaconda3/envs/vaspkit/lib/python3.6/site-packages/lammps_interface/structure_data.py", line 1947, in write_RASPA_sim_files if(int(data['image']) > max_image): KeyError: 'image'

PANI03.cif.txt