MLFF_inference.py Command Help
Command: $SCHRODINGER/run MLFF_inference.py
usage: MLFF_inference.py [-h] [--checkpoint-file CHECKPOINT_FILE]
[--checkpoint-dir CHECKPOINT_DIR]
[--model {QRNN4,ORGANIC_CSP_MPNICE,Organic_MPNICE,Organic_MPNICE_TB,Organic_Crystals_MPNICE,Organic_Crystals_MPNICE_v1.1,Inorganic_MPNICE,Hybrid_MPNICE,Hybrid_MPNICE_O,Hybrid_MPNICE_I,QRNN_Electrolyte,UMA_sm_oc20,UMA_sm_omat,UMA_sm_omc,UMA_sm_odac,UMA_sm_omol}]
[--rmse-energy-unit {kcal,hartree,eV,meV}]
[--predict-output-head] [--read-charges]
[--atom-normalization]
[--dispersion-cutoff DISPERSION_CUTOFF]
[--external-mace-checkpoint] [--log-level LOG_LEVEL]
[--skip-dispersion] [--add-dispersion]
[--change-d3-functional {B2PLYP,PW6B95,B97-D,revPBE,B3LYP,BLYP,TPSS0,PBE0,TPSS,PBE,BP86,QRNN}]
[--model-class {QRNN,FlucQSani,SANIModel,MultiTaskQRNN,MACE,MPNICE,MPQRNN,GlideWSMPNICE,GlideWSPerAtomMPNICE}]
[--sani-label SANI_LABEL [SANI_LABEL ...]]
[--merge-labels] [--delta-learning]
[--rnn-count RNN_COUNT]
[--symmetry-functions-file SYMMETRY_FUNCTIONS_FILE]
[--num-radial-aev NUM_RADIAL_AEV]
[--min-radial-aev-distance MIN_RADIAL_AEV_DISTANCE]
[--num-rad-angular-aev NUM_RAD_ANGULAR_AEV]
[--num-angular-aev NUM_ANGULAR_AEV]
[--radial-cutoff RADIAL_CUTOFF]
[--angular-cutoff ANGULAR_CUTOFF]
[--aev-class {legacy,dynamic}] [--layers LAYERS]
[--chi-layers CHI_LAYERS] [--atom-types ATOM_TYPES]
[--use-flucq-energy] [--use-erf-lr-energy]
[--use-sigmoid-lr-energy] [--use-dispersion-energy]
[--dispersion-version {D2,D3}]
[--d3-functional {B2PLYP,PW6B95,B97-D,revPBE,B3LYP,BLYP,TPSS0,PBE0,TPSS,PBE,BP86,QRNN}]
[--use-repulsion-energy] [--use-qraev] [--use-spin]
[--spin-featurization {bare,mag,square,quartic,sraev,embedding} [{bare,mag,square,quartic,sraev,embedding} ...]]
[--use-charges] [--ligand-energy-only] [--use-qeq]
[--use-esp] [--use-chiflucq] [--dlprof]
[--sigma-offset SIGMA_OFFSET] [--sigmoid-a SIGMOID_A]
[--sigmoid-b SIGMOID_B]
[--weight-normalization [WEIGHT_NORMALIZATION]]
[--num-radial-features NUM_RADIAL_FEATURES]
[--num-angular-features NUM_ANGULAR_FEATURES]
[--node-feature-dimension NODE_FEATURE_DIMENSION]
[--mixing-type {shared,per_interaction}]
[--mixing-site {edge,node,none}]
[--qeq-class {NoQEq,LinearQEq,LinearQEqACKS2,FlexibleQEq,AlphaBetaQEq,ChargeSpinQEq,ConsistentFlexibleQEq}]
[--task-layers-split TASK_LAYERS_SPLIT]
[--num-tasks NUM_TASKS] [--calculate-electrostatics]
[--use-node-attrs] [--last-readout-only]
[--sum-interaction-charges]
[--charge-version {readout,single_feature,no_prediction}]
[--mace-type {MACE,ChargeMACE}]
[--radial-basis-version {gaussian,bessel}]
[--charge-recursion-version {linear,single_feature,single_node_attr,no_recursion,basis}]
[--use-qxraev] [--r-max R_MAX]
[--num-radial-basis NUM_RADIAL_BASIS]
[--num-cutoff-basis NUM_CUTOFF_BASIS]
[--interaction {RealAgnosticInteractionBlock,RealAgnosticResidualInteractionBlock}]
[--max-ell MAX_ELL] [--correlation CORRELATION]
[--num-interactions NUM_INTERACTIONS]
[--MLP-irreps MLP_IRREPS]
[--hidden-irreps HIDDEN_IRREPS]
[--gate {gelu,silu,tanh,abs,None}]
[--net-charge NET_CHARGE] [--net-spin NET_SPIN]
[--overwrite] [--limit-forces LIMIT_FORCES]
[--compute-stress-with-forces]
[--inference-head-index INFERENCE_HEAD_INDEX]
[--compute-charge-grad]
[--constrain-molecular-charge]
[--guess-atomic-charge-key GUESS_ATOMIC_CHARGE_KEY]
[--info-gain-kt INFO_GAIN_KT]
[--return-latent-features]
[--detach-output-head-weights] [--use-asu-speedup]
[--asu-symprec ASU_SYMPREC] [--nlist-skin NLIST_SKIN]
[--optimize-cell]
[--optimization-pressure OPTIMIZATION_PRESSURE]
[--optimization-thresh OPTIMIZATION_THRESH]
[--unstable-force-thresh UNSTABLE_FORCE_THRESH]
[--optimizer-algorithm {BFGS,FIRE}]
[--no-line-search] [--max-cycles MAX_CYCLES]
[--write-opt-path] [--freeze-heavies]
[--freeze-atoms FREEZE_ATOMS [FREEZE_ATOMS ...]]
[--fix-symmetry]
[--symmetry-precision SYMMETRY_PRECISION]
[--torsions TORSIONS] [--hydrostatic-strain]
[--sella-max-cycles SELLA_MAX_CYCLES]
[--sella-thresh SELLA_THRESH]
[--sella-use-custom-hessian]
[--sella-use-finite-hessian] [--sella-run-freq]
[--sella-order SELLA_ORDER]
[--sella-diag-every SELLA_DIAG_EVERY]
[--sella-trajectory-file SELLA_TRAJECTORY_FILE]
[--sella-logfile SELLA_LOGFILE]
[--sella-unstable-force-thresh SELLA_UNSTABLE_FORCE_THRESH]
[--neb-method NEB_METHOD] [--neb-k NEB_K]
[--neb-num-images NEB_NUM_IMAGES]
[--neb-images-min NEB_IMAGES_MIN]
[--neb-climbing-image] [--neb-fconv NEB_FCONV]
[--neb-fconv-endpoints NEB_FCONV_ENDPOINTS]
[--neb-opt-steps NEB_OPT_STEPS]
[--neb-md-temp NEB_MD_TEMP]
[--neb-total-time NEB_TOTAL_TIME]
[--neb-traj-output NEB_TRAJ_OUTPUT]
[--neb-freeze-indices NEB_FREEZE_INDICES [NEB_FREEZE_INDICES ...]]
[--neb-random-seed NEB_RANDOM_SEED] [--calc-forces]
[--calc-hessian] [--calc-stress] [--calc-dielectric]
[--calc-piezoelectric]
[--thermochemistry-temperatures THERMOCHEMISTRY_TEMPERATURES [THERMOCHEMISTRY_TEMPERATURES ...]]
[--thermochemistry-pressure THERMOCHEMISTRY_PRESSURE]
[--bandpath BANDPATH]
[--phonon-supercell-size PHONON_SUPERCELL_SIZE [PHONON_SUPERCELL_SIZE ...]]
[--phonon-delta PHONON_DELTA] [--phonon-NAC]
[--phonon-symprec PHONON_SYMPREC] [--phonon-analytic]
[--phonon-prefix PHONON_PREFIX]
[--phonopy-config PHONOPY_CONFIG]
[--ensemble {NVE,NVT,NPT}]
[--temperature TEMPERATURE] [--pressure PRESSURE]
[--total-time TOTAL_TIME] [--time-step TIME_STEP]
[--sample-interval SAMPLE_INTERVAL]
[--traj-interval TRAJ_INTERVAL]
[--ttime-factor TTIME_FACTOR]
[--ptime-factor PTIME_FACTOR]
[--bulk-modulus BULK_MODULUS]
[--md-rho-thresh MD_RHO_THRESH]
[--low-density-thresh LOW_DENSITY_THRESH]
[--restart-MD] [--random-seed RANDOM_SEED]
[--allow-strain]
[--atomic-energy-file ATOMIC_ENERGY_FILE]
[--precision {single,double}] [--track-memory]
[--mlff-data-checkpoint-key MLFF_DATA_CHECKPOINT_KEY]
[--distribute] [--distribute-by-file]
[--catch-failures] [--optimize] [--ts-optimize]
[--vibrations] [--calculate-eos] [--add-flucq-energy]
[--compute-frho] [--true-energy-key TRUE_ENERGY_KEY]
[--compute-binding-energies] [--add-solvation-energy]
[--xtb-method {GFN0-xTB,GFN1-xTB,GFN2-xTB}]
[--xtb-solvation]
[--nopbc-confining-pressure NOPBC_CONFINING_PRESSURE]
[--fep-smarts FEP_SMARTS]
[--fep-qrnn-lambda FEP_QRNN_LAMBDA]
[--fep-lj-lambda FEP_LJ_LAMBDA]
[--fep-lj-alpha FEP_LJ_ALPHA]
[--fep-lj-p-power FEP_LJ_P_POWER]
[mae_file ...]
Parser for MLFF inference routines
positional arguments:
mae_file name of input file(s) (default: [])
options:
-h, --help show this help message and exit
--checkpoint-file CHECKPOINT_FILE
Checkpoint file to load model parameters (default:
None)
--checkpoint-dir CHECKPOINT_DIR
Checkpoint directory to load ensemble parameters
(default: None)
--model {QRNN4,ORGANIC_CSP_MPNICE,Organic_MPNICE,Organic_MPNICE_TB,Organic_Crystals_MPNICE,Organic_Crystals_MPNICE_v1.1,Inorganic_MPNICE,Hybrid_MPNICE,Hybrid_MPNICE_O,Hybrid_MPNICE_I,QRNN_Electrolyte,UMA_sm_oc20,UMA_sm_omat,UMA_sm_omc,UMA_sm_odac,UMA_sm_omol}
Model name from available models (AVAILABLE_MODELS +
UMA_MODEL_NAMES) (default: None)
--rmse-energy-unit {kcal,hartree,eV,meV}
Units of energy to report RMSE in (default: kcal)
--predict-output-head
If true, simultaneously train a small NN to predict
the output head to use for each atom (default: False)
--read-charges If true use true charges as a feature (default: False)
--atom-normalization Whether to normalize the loss functions by the number
of atoms (default: False)
--dispersion-cutoff DISPERSION_CUTOFF
Radial cutoff for dispersion functions (RcNL constant)
(default: 10.0)
--external-mace-checkpoint
If true read in external MACE checkpoint from
torchsani.mace github training (default: False)
--log-level LOG_LEVEL
How much to log about this run (default: INFO)
--skip-dispersion Do not load any dispersion correction(s) the model may
have (default: False)
--add-dispersion Add a dispersion correction to the model if the model
doesn't already have one (default: False)
--change-d3-functional {B2PLYP,PW6B95,B97-D,revPBE,B3LYP,BLYP,TPSS0,PBE0,TPSS,PBE,BP86,QRNN}
Change which functional from which to pull Grimme D3
dispersion params. Default is keeping the
--d3-functional used during training. (default: None)
--model-class {QRNN,FlucQSani,SANIModel,MultiTaskQRNN,MACE,MPNICE,MPQRNN,GlideWSMPNICE,GlideWSPerAtomMPNICE}
Name of model class to train (default: MultiTaskQRNN)
--sani-label SANI_LABEL [SANI_LABEL ...]
Label(s) to train to (required) (default: [])
--merge-labels If true, merge all labels into one output head. Only
trains the last output head (default: False)
--delta-learning If true do delta learning (default: False)
--rnn-count RNN_COUNT
Number of RNN layers (default: 2)
--symmetry-functions-file SYMMETRY_FUNCTIONS_FILE
JSON file defining featurization parameters (default:
None)
--num-radial-aev NUM_RADIAL_AEV
Number of radial AEV basis functions (default: 16)
--min-radial-aev-distance MIN_RADIAL_AEV_DISTANCE
Center of smallest radial basis function (default:
0.9)
--num-rad-angular-aev NUM_RAD_ANGULAR_AEV
Number of radial AEV basis functions for use in the
angular AEV (default: 4)
--num-angular-aev NUM_ANGULAR_AEV
Number of angular basis functions of theta (default:
8)
--radial-cutoff RADIAL_CUTOFF
Maximum radial distance for radial AEVs (default: 5.2)
--angular-cutoff ANGULAR_CUTOFF
Maximum radial distance for angular AEVs (default:
3.5)
--aev-class {legacy,dynamic}
Method to calculate AEV widths/centers (default:
legacy)
--layers LAYERS JSON file defining atomic NN layers (default: /opt/sch
rodinger/suites2026-3/internal/lib/python3.11/site-
packages/torchsani/data/default_layers.json)
--chi-layers CHI_LAYERS
JSON file defining atomic NN layers for chi (charge)
prediction model (default: None)
--atom-types ATOM_TYPES
JSON file defining atom types (default: None)
--use-flucq-energy Use FlucQ total energy for LR part (default: False)
--use-erf-lr-energy Use erf truncated LR part (default: False)
--use-sigmoid-lr-energy
Use sigmoid truncated LR part (default: False)
--use-dispersion-energy
Use Grimme dispersion energy (default: False)
--dispersion-version {D2,D3}
Version of Grimme dispersion to use (default: D2)
--d3-functional {B2PLYP,PW6B95,B97-D,revPBE,B3LYP,BLYP,TPSS0,PBE0,TPSS,PBE,BP86,QRNN}
Functional from which to pull Grimme D3 dispersion
params. Default is made up unit parameters (default:
QRNN)
--use-repulsion-energy
Use Grimme repulsion energy (default: False)
--use-qraev If true use charge dependent radial AEV as feature
(default: False)
--use-spin If true predict and use partial spins as feature
(default: False)
--spin-featurization {bare,mag,square,quartic,sraev,embedding} [{bare,mag,square,quartic,sraev,embedding} ...]
Which type(s) of spin featurization to use (default:
[])
--use-charges If true use charge as a feature (default: False)
--ligand-energy-only Compute energy from ligand atoms only for protein-
ligand binding (requires ligand_atom_indicator in
database) (default: False)
--use-qeq If true equilibrate charge once it is predicted
(default: True)
--use-esp If true use ESP as feature (default: False)
--use-chiflucq Use Behler parameterization of FlucQ model (default:
False)
--dlprof Use nvtx to profile one iteration of training
(default: False)
--sigma-offset SIGMA_OFFSET
Offset for sigma in FlucQ (default: 0.0)
--sigmoid-a SIGMOID_A
a value for sigmoid damping 1/(1+exp(b*(a-x))) in
Angstrom (default: 1.1641898639866)
--sigmoid-b SIGMOID_B
b value for sigmoid damping 1/(1+exp(b*(a-x))) in
1/Angstrom (default: 16.06267205931905)
--weight-normalization [WEIGHT_NORMALIZATION]
Decouple weight matrix norm and direction. If no flag,
do not decouple. If no value as argument, decouple
weight norms and leave them constant. If a positive
float value is provided, the norm will be trainable
with the float as weight decay (default: None)
--num-radial-features NUM_RADIAL_FEATURES
Dimension of radial message features for MPNICE
(default: 32)
--num-angular-features NUM_ANGULAR_FEATURES
Dimension of angular message features for MPNICE
(default: 16)
--node-feature-dimension NODE_FEATURE_DIMENSION
Dimension of features each atom carries around for
MPNICE (default: 128)
--mixing-type {shared,per_interaction}
Whether to share radial/angular mixing over
interaction blocks (default: shared)
--mixing-site {edge,node,none}
Whether to compress node features for message passing
before or after edge formation (default: edge)
--qeq-class {NoQEq,LinearQEq,LinearQEqACKS2,FlexibleQEq,AlphaBetaQEq,ChargeSpinQEq,ConsistentFlexibleQEq}
Which class of charge/spin equilibration to use
(default: LinearQEq)
--task-layers-split TASK_LAYERS_SPLIT
Layer at which to split representation for multiple
tasks (default: 3)
--num-tasks NUM_TASKS
Number of tasks model trained to (default: 1)
--calculate-electrostatics
MACE ONLY: if true use atomic charges to calculate
electrostatic energy (default: True)
--use-node-attrs MACE ONLY: if true use node_attrs in energy readout
(default: False)
--last-readout-only MACE ONLY: if true only use last nonlinear energy
readout in MACE (default: False)
--sum-interaction-charges
MACE ONLY: if true sum charge contributions from
interaction blocks in MACE (default: False)
--charge-version {readout,single_feature,no_prediction}
MACE ONLY: version of charge prediction to use
(default: no_prediction)
--mace-type {MACE,ChargeMACE}
MACE ONLY: version of MACE to use (default:
ChargeMACE)
--radial-basis-version {gaussian,bessel}
MACE ONLY: version of radial basis to use (default:
bessel)
--charge-recursion-version {linear,single_feature,single_node_attr,no_recursion,basis}
MACE ONLY: version of charge recursion to use
(default: no_recursion)
--use-qxraev MACE ONLY: if true use charge basis (x) radial AEV as
feature (default: False)
--r-max R_MAX MACE ONLY: distance cutoff (in Ang) (default: 5.0)
--num-radial-basis NUM_RADIAL_BASIS
MACE ONLY: number of radial basis functions (default:
8)
--num-cutoff-basis NUM_CUTOFF_BASIS
MACE ONLY: number of basis functions for smooth cutoff
(default: 5)
--interaction {RealAgnosticInteractionBlock,RealAgnosticResidualInteractionBlock}
MACE ONLY: name of interaction block (default:
RealAgnosticResidualInteractionBlock)
--max-ell MAX_ELL MACE ONLY: highest ell of spherical harmonics
(default: 3)
--correlation CORRELATION
MACE ONLY: correlation order at each layer (default:
3)
--num-interactions NUM_INTERACTIONS
MACE ONLY: number of interactions (default: 2)
--MLP-irreps MLP_IRREPS
MACE ONLY: hidden irreps of the MLP in last readout
(default: 16x0e)
--hidden-irreps HIDDEN_IRREPS
MACE ONLY: irreps for hidden node states (default:
32x0e)
--gate {gelu,silu,tanh,abs,None}
MACE ONLY: non linearity for last readout (default:
silu)
--net-charge NET_CHARGE
If given, all systems will be constrained to this
charge (debugging only) (default: None)
--net-spin NET_SPIN If given, all systems will be constrained to this spin
(debugging only) (default: None)
--overwrite After wrapping atoms into central box, whether to
replace the original positions stored in ase.Atoms
object with wrapped positions (default: False)
--limit-forces LIMIT_FORCES
Atomic forces exceeding this magnitude (eV/A) will be
scaled (default: None)
--compute-stress-with-forces
If True, compute stress tensor every time forces are
requested (default: False)
--inference-head-index INFERENCE_HEAD_INDEX
MTL label for inference (-1 for Single-task or highest
index in MTL) (default: -1)
--compute-charge-grad
Compute derivative of energy with respect to charges
(default: False)
--constrain-molecular-charge
Constraint molecular charge based on formal charges
(default: False)
--guess-atomic-charge-key GUESS_ATOMIC_CHARGE_KEY
QRNN charges will be taken from this atomic property
(default: None)
--info-gain-kt INFO_GAIN_KT
Energy scale for information gain optimization, in
Hartree (default: 0.0)
--return-latent-features
Return the latent features of each atom (MPNICE only)
(default: False)
--detach-output-head-weights
Detach predicted output head weights from autograd
graph (default: False)
--use-asu-speedup Reduce the cost of a crystal calculation by only
performing inference on the ASU. (default: False)
--asu-symprec ASU_SYMPREC
Threshold for detecting symmetries in order to
determine the ASU, only used when use_asu_speedup=True
(default: 0.01)
--nlist-skin NLIST_SKIN
Skin distance (Angstrom) for neighborlist caching. The
neighborlist is built at RcNL + nlist_skin and reused
until atom/cell motion exceeds the skin buffer. Set to
0 to disable caching. (default: 0.0)
--optimize-cell Optimize cell (default: False)
--optimization-pressure OPTIMIZATION_PRESSURE
External pressure (atm) applied during optimization
(default: 0.0)
--optimization-thresh OPTIMIZATION_THRESH
Threshold on max force (in eV/A) for optimization
convergence (default: 0.01)
--unstable-force-thresh UNSTABLE_FORCE_THRESH
Maximum threshold on max force (eV/A) for stability
(default: None)
--optimizer-algorithm {BFGS,FIRE}
Choice of optimization algorithm to use in ASE
(default: BFGS)
--no-line-search Disable line search in optimizations (default: False)
--max-cycles MAX_CYCLES
Maximum number of optimization cycles (default: 500)
--write-opt-path Write optimization path (default: False)
--freeze-heavies If true freeze the positions of heavy atoms (default:
False)
--freeze-atoms FREEZE_ATOMS [FREEZE_ATOMS ...]
List of ASE atom indices to be frozen during structure
optimization (default: [])
--fix-symmetry Fix spacegroup symmetry (default: False)
--symmetry-precision SYMMETRY_PRECISION
Threshold (in Angstroms) to use for detecting symmetry
(default: 0.01)
--torsions TORSIONS List of (value, i, j, k, l) tuples defining torsions
to be constrained (value in degrees) (default: [])
--hydrostatic-strain Allow only hydrostatic strain during cell optimization
(default: False)
--sella-max-cycles SELLA_MAX_CYCLES
Maximum number of Sella optimization steps (default:
500)
--sella-thresh SELLA_THRESH
Convergence threshold for forces (Hartree/Angstrom)
(default: 0.001)
--sella-use-custom-hessian
Use analytical Hessian with finite difference fallback
(default: True)
--sella-use-finite-hessian
Force finite difference Hessian (overrides
use_custom_hessian) (default: False)
--sella-run-freq Run frequency calculation after convergence (default:
True)
--sella-order SELLA_ORDER
Saddle point order: 0 for minimization, 1 for TS
(default: 1)
--sella-diag-every SELLA_DIAG_EVERY
Frequency of Hessian diagonalization (0 = every step)
(default: 0)
--sella-trajectory-file SELLA_TRAJECTORY_FILE
Filename for Sella trajectory output (default:
sella.traj)
--sella-logfile SELLA_LOGFILE
Log file for Sella optimizer output (default: None)
--sella-unstable-force-thresh SELLA_UNSTABLE_FORCE_THRESH
Exit optimization if RMS force exceeds this value
(default: None)
--neb-method NEB_METHOD
ASE NEB method name (e.g., 'improvedtangent',
'aseneb') (default: improvedtangent)
--neb-k NEB_K NEB constant (in eV/A). If > 0, run NEB using all
input structures (default: 0.0)
--neb-num-images NEB_NUM_IMAGES
Number of images to use in the NEB path. If None, uses
provided frames as-is (default: None)
--neb-images-min NEB_IMAGES_MIN
Minimum number of images for NEB path interpolation
(default: 5)
--neb-climbing-image Whether to use a climbing image in NEB (default: True)
--neb-fconv NEB_FCONV
Threshold on max force (in eV/A) for optimization
convergence (default: 0.05)
--neb-fconv-endpoints NEB_FCONV_ENDPOINTS
Force convergence criterion for endpoint optimization,
in eV/A (default: 0.05)
--neb-opt-steps NEB_OPT_STEPS
Maximum number of optimization steps for NEB optimizer
(default: 500)
--neb-md-temp NEB_MD_TEMP
Temperature for NEB MD, in Kelvin (default: 300.0)
--neb-total-time NEB_TOTAL_TIME
Total time to run NEB MD, in ps. If 0, no MD is
performed (default: 0.0)
--neb-traj-output NEB_TRAJ_OUTPUT
Output filename for NEB MD trajectory if
neb_total_time > 0 (default: None)
--neb-freeze-indices NEB_FREEZE_INDICES [NEB_FREEZE_INDICES ...]
List of atom indices to freeze during NEB (zero-
indexed) (default: [])
--neb-random-seed NEB_RANDOM_SEED
Seed for PRNG for reproducibility in NEB MD velocity
initialization (default: None)
--calc-forces Calculate atomic forces (default: False)
--calc-hessian Calculate Hessian matrix (default: False)
--calc-stress Calculate stress tensor (default: False)
--calc-dielectric Calculate dielectric tensor (requires periodic system)
(default: False)
--calc-piezoelectric Calculate piezoelectric tensor (requires periodic
system) (default: False)
--thermochemistry-temperatures THERMOCHEMISTRY_TEMPERATURES [THERMOCHEMISTRY_TEMPERATURES ...]
List of temperatures (K) for vibrational
thermochemistry calculations (default: [298.15])
--thermochemistry-pressure THERMOCHEMISTRY_PRESSURE
Pressure in atm for thermochemistry calculations
(default: 1.0)
--bandpath BANDPATH High-symmetry k-point path for phonon bandstructure
(e.g. 'GXWKG'). Providing this option triggers the
band structure calculation. (default: None)
--phonon-supercell-size PHONON_SUPERCELL_SIZE [PHONON_SUPERCELL_SIZE ...]
Supercell size multiplier for phonon calculations
(default: [2])
--phonon-delta PHONON_DELTA
Finite displacement step size for phonon calculations
(default: 0.03)
--phonon-NAC Calculate non-analytic correction to phonons (default:
False)
--phonon-symprec PHONON_SYMPREC
Symmetry precision for phonon calculations (default:
0.01)
--phonon-analytic If True, use analytic hessian for phonon calculations
if available (default: True)
--phonon-prefix PHONON_PREFIX
Prefix for phonon output files (default: None)
--phonopy-config PHONOPY_CONFIG
Configuration file for phonopy band structure
calculations. (default: None)
--ensemble {NVE,NVT,NPT}
Ensemble for molecular dynamics (default: NVE)
--temperature TEMPERATURE
Temperature for molecular dynamics (Kelvin) (default:
300.0)
--pressure PRESSURE Pressure (atm) for NPT molecular dynamics (default:
1.0)
--total-time TOTAL_TIME
Total molecular dynamics time (ps) (default: 0.0)
--time-step TIME_STEP
Time step for molecular dynamics (fs) (default: 0.1)
--sample-interval SAMPLE_INTERVAL
Interval (frames) at which to log the MD data
(default: 100)
--traj-interval TRAJ_INTERVAL
Interval (frames) at which to collect molecular
dynamics frames (default: 100)
--ttime-factor TTIME_FACTOR
ttime-factor * time-step to obtain timescale of the
thermostat (default: 100.0)
--ptime-factor PTIME_FACTOR
ptime-factor * time-step to obtain timescale of the
barostat (default: 1000.0)
--bulk-modulus BULK_MODULUS
Bulk-modulus of substance in GPa (default: 3.0)
--md-rho-thresh MD_RHO_THRESH
MD termination threshold on ensemble uncertainty
(kcal/mol) (default: None)
--low-density-thresh LOW_DENSITY_THRESH
If not None, will exit if density is below this value
(g/cm^3) (default: None)
--restart-MD Restart MD by setting velocities from input mae file
(default: False)
--random-seed RANDOM_SEED
If given, used to seed PRNG for velocity
initialization (default: None)
--allow-strain If True, allow strain deformation in NPT ensemble
(default: False)
--atomic-energy-file ATOMIC_ENERGY_FILE
JSON file holding atomic energies to match total
energies from DFT (default: None)
--precision {single,double}
The precision to run the model in (default: single)
--track-memory Track and log peak memory at the start and end of
optimization. Reports CPU RSS on CPU runs and CUDA
allocator peak on GPU runs. (default: False)
--mlff-data-checkpoint-key MLFF_DATA_CHECKPOINT_KEY
Checkpoint filename or substring key to select
checkpoint file from MLFF_DATA directory (default:
latest_ema)
--distribute Distribute jobs using JobDJ into separate jobs per
structure (default: False)
--distribute-by-file Distribute jobs using JobDJ into separate jobs per mae
file (default: False)
--catch-failures If true catch failures as exceptions (default: False)
--optimize Optimize structure prior to computing energy (default:
False)
--ts-optimize Optimize transition state using Sella optimizer
(default: False)
--vibrations Calculate vibrational properties (auto-detects phonons
for periodic systems, molecular frequencies for non-
periodic systems) (default: False)
--calculate-eos Calculates and returns the bulk modulus (default:
False)
--add-flucq-energy If true add flucq, dispersion and atomic energy
(default: False)
--compute-frho Compute ensemble uncertainty for atomic forces
(default: False)
--true-energy-key TRUE_ENERGY_KEY
key for true energies, will compute errors to this
value if the key exists. (default:
r_j_Gas_Phase_Energy)
--compute-binding-energies
If true compute binding energies by subtracting
monomer energies (default: False)
--add-solvation-energy
If true, add xTB solvation energy to the model energy
prediction (default: False)
--xtb-method {GFN0-xTB,GFN1-xTB,GFN2-xTB}
Which xTB method to use (default: GFN2-xTB)
--xtb-solvation If true, add in xTB solvation energy (default: False)
--nopbc-confining-pressure NOPBC_CONFINING_PRESSURE
Add force towards origin, equivalent to external
pressure on sphere (default: 0.0)
--fep-smarts FEP_SMARTS
SMARTS pattern for defining the solute (first
subsystem) in FEP (default: None)
--fep-qrnn-lambda FEP_QRNN_LAMBDA
Lambda value for qrnn FEP (0=non-interacting, 1=fully
interacting) (default: 1.0)
--fep-lj-lambda FEP_LJ_LAMBDA
Lambda value for softcore LJ potential (0=regular LJ,
1=zero potential) (default: 1.0)
--fep-lj-alpha FEP_LJ_ALPHA
alpha value for controlling the strength of the
Beutler softcore LJ potential. The larger the value,
the stronger the damping effect. Only relevant when
fep-lj-mode is Beutler (default: 0.5)
--fep-lj-p-power FEP_LJ_P_POWER
p power in the Beutler softcore LJ potential. Only
relevant when fep-lj-mode is Beutler (default: 1)