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] [-g SPACEGROUPS] [-a AXIS] [-n NUMBER_STRUCTURES]
          [-r RANDOM_SEED]
          [-p {fit,fit_boron,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_Halides,isoPAHAP,PAHAP}]
          [--cutoff CUTOFF] [--status-file STATUS_FILE] [--clg-old] [--log-level LOG_LEVEL]
          [--keep-files]
          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
-g SPACEGROUPS, --spacegroups SPACEGROUPS - Spacegroup set for structure generation (default: fine10)
-a AXIS, --axis AXIS - Axis filename for structure minimization
-n NUMBER_STRUCTURES, --number-structures NUMBER_STRUCTURES - Number of structures in total
-r RANDOM_SEED, --random-seed RANDOM_SEED - Specify seed for random generator
-p POTENTIAL, --potential POTENTIAL - intermolecular potential name (default: fit)
--cutoff CUTOFF - dmacrys real space/repulsion-dispersion cutoff (default: calculate)
--status-file STATUS_FILE - Specify output status file (default: status.txt)
--clg-old - Use the old version of the CLG
--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.

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.