cspy-qrbh command

The cspy-qrbh command can be used to perform quasi-random basin-hopping crystal structure prediction.

cspy-qrbh [-h] [-c CHARGES] [-m MULTIPOLES] [-a AXIS] [-g SPACEGROUPS] [-n NUMBER_STRUCTURES]
          [--nudge NUDGE] [--adaptcell] [--asi] [--clg-chomp CLG_CHOMP | --clg-aut]
          [-p {fit,fit_disponly,fit_reponly,w99,fit_water_X,Day_halobenzenes,w99_orig_Halogens,w99_orig_H,w99rev_6311,w99rev_6311_s,w99rev_631,w99rev_pcm_6311,w99_s_cl,w99sp,w99rev_pcm_6311_and_Chloride,w99rev_pcm_6311_and_Bromide,w99rev_pcm_6311_and_Iodide,w99rev_pcm_6311_and_Halides,isoPAHAP,PAHAP,nothing,gaff2_LJ,gaff2_fit}]
          [--cutoff CUTOFF] [-r RANDOM_SEED] [--log-level LOG_LEVEL] [--keep-files]
          [--skip-header] [--status-file STATUS_FILE]
          xyz_files [xyz_files ...]

positional arguments

  • xyz_files - Xyz files containing molecules for generation

options

  • -h, --help - show this help message and exit

  • -c CHARGES, --charges CHARGES - Rank0 multipole file

  • -m MULTIPOLES, --multipoles MULTIPOLES - RankN multipole file

  • -a AXIS, --axis AXIS - Axis filename for structure minimization

  • -g SPACEGROUPS, --spacegroups SPACEGROUPS - Spacegroup set for structure generation (default: fine10)

  • -n NUMBER_STRUCTURES, --number-structures NUMBER_STRUCTURES - Number of structures for structure generation

  • --nudge NUDGE - Nudge molecules in assymetric unit that fail QR step (default: 0)

  • --adaptcell - Adaptively optimise cell parameters

  • --asi - Allow molecules to have superimposed centroids (set to true for encapsulation)

  • --clg-chomp CLG_CHOMP - Use the chomp CLG with molecular pairs from the provided database

  • --clg-aut - Use the AUT CLG with molecular pairs. If not running a CSP, a database must exist of format: [seed]-spacegroup-AU.db

  • -p POTENTIAL, --potential POTENTIAL - intermolecular potential name (default: fit)

  • --cutoff CUTOFF - dmacrys real space/repulsion-dispersion cutoff (default: calculate)

  • -r RANDOM_SEED, --random-seed RANDOM_SEED - Specify seed for random generator

  • --log-level LOG_LEVEL - Log level (default: INFO)

  • --keep-files - Keep DMACRYS and NEIGHCRYS files which, for each structure, are stored in a new directory in the pwd.

  • --skip-header - Skip the mol-CSPy header at the start of the job.

  • --status-file STATUS_FILE - Specify output status file (default: status.txt)

The cspy-qrbh is very similar to the cspy-csp command but instead, performs crystal structure prediction in which quasi-random structure generation is used to seed multiple Monte Carlo basin hopping simulations as described in the linked publication.

For more information on how to use this command, plese see the worked exmaple - Quasi-random basin hopping (QRBH) simulation of benzamide.