usage: gsm [-h] -xyzfile XYZFILE [-isomers ISOMERS] -mode
{DE_GSM,SE_GSM,SE_Cross} [-only_drive]
[-package {QChem,Orca,Molpro,PyTC,TeraChemCloud,OpenMM,DFTB,TeraChem,BAGEL,xTB_lot,ase}]
[-lot_inp_file LOT_INP_FILE] [-ID ID] [-num_nodes NUM_NODES]
[-pes_type {PES,Avg_PES,Penalty_PES}]
[-adiabatic_index [ADIABATIC_INDEX ...]]
[-multiplicity [MULTIPLICITY ...]] [-FORCE_FILE FORCE_FILE]
[-RESTRAINT_FILE RESTRAINT_FILE] [-optimizer OPTIMIZER]
[-opt_print_level OPT_PRINT_LEVEL]
[-gsm_print_level GSM_PRINT_LEVEL]
[-xTB_Hamiltonian {GFN2-xTB,GFN1-xTB}] [-xTB_accuracy XTB_ACCURACY]
[-xTB_electronic_temperature XTB_ELECTRONIC_TEMPERATURE]
[-xyz_output_format XYZ_OUTPUT_FORMAT] [-solvent SOLVENT]
[-linesearch {NoLineSearch,backtrack}]
[-coordinate_type {TRIC,DLC,HDLC}] [-ADD_NODE_TOL ADD_NODE_TOL]
[-DQMAG_MAX DQMAG_MAX] [-BDIST_RATIO BDIST_RATIO]
[-CONV_TOL CONV_TOL] [-growth_direction {0,1,2}]
[-reactant_geom_fixed] [-product_geom_fixed] [-nproc NPROC]
[-charge CHARGE] [-max_gsm_iters MAX_GSM_ITERS]
[-max_opt_steps MAX_OPT_STEPS] [-only_climb] [-no_climb]
[-optimize_mesx] [-optimize_meci] [-restart_file RESTART_FILE]
[- MP_CORES] [-dont_analyze_ICs]
[-hybrid_coord_idx_file HYBRID_COORD_IDX_FILE]
[-frozen_coord_idx_file FROZEN_COORD_IDX_FILE]
[-conv_Ediff CONV_EDIFF] [-conv_dE CONV_DE] [-conv_gmax CONV_GMAX]
[-DMAX DMAX] [-sigma SIGMA] [-prim_idx_file PRIM_IDX_FILE]
[-reparametrize] [-interp_method INTERP_METHOD]
[-bonds_file BONDS_FILE] [-start_climb_immediately]
[--ase-class ASE_CLASS] [--ase-kwargs ASE_KWARGS]
Reaction path transition state and photochemistry tool
optional arguments:
-h, --help show this help message and exit
-xyzfile XYZFILE XYZ file containing reactant and, if DE-GSM, product.
-isomers ISOMERS driving coordinate file
-mode {DE_GSM,SE_GSM,SE_Cross}
GSM Type (default: DE_GSM)
-only_drive
-package {QChem,Orca,Molpro,PyTC,TeraChemCloud,OpenMM,DFTB,TeraChem,BAGEL,xTB_lot,ase}
Electronic structure theory package (default: QChem)
-lot_inp_file LOT_INP_FILE
external file to specify calculation e.g.
qstart,gstart,etc. Highly package specific.
-ID ID string identification number (default: 0)
-num_nodes NUM_NODES number of nodes for string (defaults: 9 DE-GSM, 20 SE-
GSM)
-pes_type {PES,Avg_PES,Penalty_PES}
Potential energy surface (default: PES)
-adiabatic_index [ADIABATIC_INDEX ...]
Adiabatic index (default: [0])
-multiplicity [MULTIPLICITY ...]
Multiplicity (default: [1])
-FORCE_FILE FORCE_FILE
Constant force between atoms in AU,e.g.
[(1,2,0.1214)]. Negative is tensile, positive is
compresive
-RESTRAINT_FILE RESTRAINT_FILE
Harmonic translational restraints
-optimizer OPTIMIZER The optimizer object. (default: eigenvector_follow
Recommend LBFGS for large molecules >1000 atoms)
-opt_print_level OPT_PRINT_LEVEL
Printout for optimization. 2 prints everything in opt.
-gsm_print_level GSM_PRINT_LEVEL
Printout for gsm. 1 prints ?
-xTB_Hamiltonian {GFN2-xTB,GFN1-xTB}
xTB hamiltonian
-xTB_accuracy XTB_ACCURACY
xTB accuracy
-xTB_electronic_temperature XTB_ELECTRONIC_TEMPERATURE
xTB electronic temperature
-xyz_output_format XYZ_OUTPUT_FORMAT
Format of the produced XYZ files
-solvent SOLVENT Solvent to use (xTB calculations only)
-linesearch {NoLineSearch,backtrack}
default: NoLineSearch
-coordinate_type {TRIC,DLC,HDLC}
Coordinate system (default TRIC)
-ADD_NODE_TOL ADD_NODE_TOL
Convergence tolerance for adding new node (default:
0.01)
-DQMAG_MAX DQMAG_MAX Maximum step size in single-ended mode (default: 0.8)
-BDIST_RATIO BDIST_RATIO
Reaction completion convergence in SE modes (default:
0.5)
-CONV_TOL CONV_TOL Convergence tolerance for optimizing nodes (default:
0.0005)
-growth_direction {0,1,2}
Direction adding new nodes (default: 0)
-reactant_geom_fixed Fix reactant geometry i.e. do not pre-optimize
-product_geom_fixed Fix product geometry i.e. do not pre-optimize
-nproc NPROC Processors for calculation. Python will detect
OMP_NUM_THREADS, only use this if you want to force
the number of processors
-charge CHARGE Total system charge (default: 0)
-max_gsm_iters MAX_GSM_ITERS
The maximum number of GSM cycles (default: 100)
-max_opt_steps MAX_OPT_STEPS
The maximum number of node optimizations per GSM cycle
(defaults: 3 DE-GSM, 20 SE-GSM)
-only_climb Only use climbing image to optimize TS
-no_climb Don't climb to the TS
-optimize_mesx optimize to the MESX
-optimize_meci optimize to the MECI
-restart_file RESTART_FILE
restart file
-mp_cores MP_CORES Use python multiprocessing to parallelize jobs on a
single compute node. Set OMP_NUM_THREADS, ncpus
accordingly.
-dont_analyze_ICs Don't post-print the internal coordinates primitives
and values
-hybrid_coord_idx_file HYBRID_COORD_IDX_FILE
A filename containing a list of indices to use in
hybrid coordinates. 0-Based indexed
-frozen_coord_idx_file FROZEN_COORD_IDX_FILE
A filename containing a list of indices to be frozen.
0-Based indexed
-conv_Ediff CONV_EDIFF
Energy difference convergence of optimization.
-conv_dE CONV_DE State difference energy convergence
-conv_gmax CONV_GMAX Max grad rms threshold
-DMAX DMAX
-sigma SIGMA The strength of the difference energy penalty in
Penalty_PES
-prim_idx_file PRIM_IDX_FILE
A filename containing a list of indices to define
fragments. 0-Based indexed
-reparametrize Reparametrize restart string equally along path
-interp_method INTERP_METHOD
-bonds_file BONDS_FILE
A file which contains the bond indices (0-based)
-start_climb_immediately
Start climbing immediately when restarting.
ASE:
ASE calculator options
--ase-class ASE_CLASS
ASE calculator import path, eg.
"ase.calculators.lj.LennardJones"
--ase-kwargs ASE_KWARGS
ASE calculator keyword args, as JSON dictionary, eg.
{"param_filename":"path/to/file.xml"}
Example of use:
--------------------------------
gsm -mode DE_GSM -xyzfile yourfile.xyz -package QChem -lot_inp_file qstart -ID 1
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