IBI potential generator
Get the input:
Generate an amorphous structure with deposit for each pristine phase, and a mixed phase.
Convert the Deposit output to xyz:
babel structure.mol2 structure.xyz
Generate the xyz file in center of geometry and (if the COG+ picture is used) into an orientation file that defines the orientation of a molecular axis defined by two atoms in the molecules. There is a very crude tool available to do this.
python tools/get_cog_orientation_v2.py infile id0 id1 no_atoms_of_second_mol
This tool prints "cogs.dat", "orientations.npy" and "mol_type_list.dat". The parameters id0 and id1 are two atoms along the molecular axis. The distinction between two different molecules is done via the numbers of atoms (not the best of methods...), and the number of the second molecule is supplied in "no_atoms_of_second_mol"
This step needs to be done for both the pristine structures and the mixed morphology.
IBI on the pristine morphologies
Run IBI on two pristine systems separately. Here we recommend to look at the settings files provided in the "FromSCtoCOGplus/examples/get_pot_X" directory containing example input and settings files (for X = C60 and DNTT):
- adapt settings (system size, input file names)
- if errors like potential not going to zero, toy around with cutoffs (rdf_edge_cutoff, rdf_cutoff_begin, rdf_cutoff_end. rdf_edge_cutoff > cutoff_end > cutoff_begin required)
- parallel_IBI may change convergence
- for extended molecules: set no_mol_atoms > 1 and mol_length (between 1.0 and 1.2 for DNTT). Adapt parameters to get good convergence.
- try to run IBI with IBI_pot_gen_single_phase.py
- WARNING: If system too small, only small ranges in the rdf can be covered (up to half the box size, so rdf_edge_cutoff < 0.5*box_size required) Then, the first peak might be fine but the overall relaxation could be funny.
- Make sure not to run in frustration (energy output of MD should be < 0)
- Check if the minimum of the potential is where you expect it to be, otherwise change settings.
IBI on the mixed morphology
Now run IBI on the mixed system. Please check the settings_mixed in the "FromSCtoCOGplus/examples/get_pot_mixed" directory and modify, if needed:
- copy aa and bb potential files from pristine fit into execution folder for the mixed IBI run.
- adapt 'pot_aa: "pot_file_aa.dat"' and 'pot_bb: "pot_file_bb.dat"' to settings
- set no_mol_types: 2
- set no_mol_atoms and mol_length (now arrays with two elements)
- set mol_type_file (see above) in settings. This contains a list with entries 0 or 1 to identify molecule species.
- try to run IBI with IBI_pot_gen_mixed_phase.py
NOTE: does not work well for interfaces
The results of the search are