mmml dimer-scan¶
Reproducible rigid 1D dimer energy/force scan.
Usage¶
mmml dimer-scan --help
Options¶
usage: mmml dimer-scan [-h] [--config CONFIG]
[--calculator {physnet,spookynet,mbd,multipoles,efield,xtb,dftb3-d4,pyscf}]
[--checkpoint CHECKPOINT]
[--calculator-config CALCULATOR_CONFIG] [--method METHOD]
[--basis BASIS] [--xc XC] [--electric-field EX EY EZ]
[--slako-dir SLAKO_DIR]
[--calculator-workdir CALCULATOR_WORKDIR]
[--calculator-executable CALCULATOR_EXECUTABLE]
[--multipole-force-step ANGSTROM]
[--distance START:STOP:STEP]
[--energy-definition {interaction,total}]
[--charge CHARGE] [--spin SPIN] [--seed SEED]
[--allow-partial] [--overwrite] --output OUTPUT
[RESIDUE ...]
Run a reproducible rigid 1D dimer energy/force scan.
positional arguments:
RESIDUE One residue for a homodimer or two for a heterodimer.
Accepts campaign labels (DCM, ACE, BENZ, TIP3, MEOH) or
any CGenFF RESI name (e.g. ACO, CYBZ); non-campaign
pairs use a generic centroid–centroid orientation.
Input & configuration:
--config CONFIG YAML/JSON DimerScanConfig; command-line output/failure
flags remain available
--checkpoint CHECKPOINT
Model checkpoint/parameter path
--calculator-config CALCULATOR_CONFIG
Calculator model config JSON
--slako-dir SLAKO_DIR
DFTB+ 3ob-3-1 directory
--calculator-executable CALCULATOR_EXECUTABLE
External calculator executable
Scientific model:
--calculator {physnet,spookynet,mbd,multipoles,efield,xtb,dftb3-d4,pyscf}
Explicit ASE calculator type
--method METHOD Calculator method (for example pyscf: dft or hf)
--basis BASIS PySCF basis (default: def2-svp)
--xc XC PySCF DFT functional (default: pbe0)
--electric-field EX EY EZ
EField vector in atomic units
--multipole-force-step ANGSTROM
Central finite-difference step for learned-multipole
forces
--distance START:STOP:STEP
Inclusive distance grid in angstrom (default:
2.5:6.0:0.1)
--energy-definition {interaction,total}
--charge CHARGE
--spin SPIN Spin multiplicity for calculators that require it
Execution:
--seed SEED
Output & artifacts:
--calculator-workdir CALCULATOR_WORKDIR
External calculator scratch directory
--overwrite
--output OUTPUT
Diagnostics & safety:
-h, --help show this help message and exit
--allow-partial