mmml build-crystal¶
Symmetry-aware crystals (PyXtal).
Build molecular crystals for MD. Recommended for DCM and benzene: literature
CIF + make-res atom names (--literature dcm|benz) — exact experimental unit
cell, tiled to a simulation supercell (≥28 Å edges by default) at literature ρ.
mmml make-res --res DCM --skip-energy-show
mmml build-crystal --literature dcm --monomer-pdb pdb/dcm.pdb -o pdb/dcm_crystal.pdb
mmml build-crystal --literature dcm --supercell 4,4,3 -o dcm_super.extxyz
PyXtal (uv sync --extra chem) is optional for random placement in the same
space group. DCM crystal: COD 2100015
(Pbcn, ρ≈1.97 g/cm³). Benzene: COD 4501704
(P2₁/c, ρ≈1.20 g/cm³).
mmml build-crystal \
-m "$(python -c 'from mmml.paths import default_dcm_molecule_xyz; print(default_dcm_molecule_xyz())')" \
--spg 60 --z 4 --target-density-g-cm3 1.972 -o dcm_pyxtal.extxyz
mmml build-crystal -m benzene --spg 14 --z 2 --target-density-g-cm3 1.202 -o benzene.extxyz
Liquid DCM boxes use 1.326 g/cm³ (liquid-box, md-system).
Literature vs make-res+CIF vs PyXtal tables are in the structure building guide.
Usage¶
mmml build-crystal --help
Options¶
usage: mmml build-crystal [-h] [--literature PRESET] [--from-cif PATH]
[--residue NAME] [--monomer-pdb PATH]
[--min-box-side ANG] [-m SPEC]
[--stoichiometry Z [Z ...]]
[--z Z_VALUES [Z_VALUES ...]] [--dim {0,1,2,3}]
[--spg SPACE_GROUP] [--factor FACTOR]
[--target-density-g-cm3 RHO] [--seed SEED]
[--attempts ATTEMPTS] [--no-resort]
[--supercell NX,NY,NZ] -o OUTPUT [--format OUT_FORMAT]
[--optimize] [--optimizer {bfgs,fire,lbfgs}]
[--fmax FMAX] [--max-opt-steps MAX_OPT_STEPS]
[--fix-cell] [--emt] [--quiet-opt]
Build molecular crystals: literature CIF + make-res (CHARMM names) or PyXtal
random placement with space-group symmetry.
options:
-h, --help show this help message and exit
--target-density-g-cm3 RHO
Scale cell to this mass density (g/cm³). Literature
presets use CIF ρ unless this is set. Liquid DCM ≈
1.326; crystal DCM ≈ 1.972
--supercell NX,NY,NZ Supercell repeats (literature: auto from --min-box-side
if omitted)
-o, --output OUTPUT Output path (.pdb, .xyz, .extxyz, .cif, or .npz)
--format OUT_FORMAT ASE output format override (default: inferred from
--output suffix)
Literature CIF + make-res (recommended for DCM / benzene):
--literature PRESET Bundled experimental CIF preset: dcm (Pbcn) or benz
(P2₁/c)
--from-cif PATH Override CIF path (requires --residue or --literature
for residue name)
--residue NAME CHARMM residue (DCM, BENZ) when using --from-cif without
--literature
--monomer-pdb PATH make-res monomer PDB for atom-name mapping (default:
pdb/<res>.pdb or bundled)
--min-box-side ANG Minimum supercell edge length (Å); default ≈2× CHARMM
cutnb
PyXtal random placement:
-m, --molecule SPEC Molecule specification (repeat for multi-component
crystals): XYZ/CIF path, SMILES, or chemical formula
understood by PyXtal
--stoichiometry Z [Z ...]
Formula units per molecule species (same order as
--molecule)
--z Z_VALUES [Z_VALUES ...]
Alias for stoichiometry; one value repeats for all
molecules
--dim {0,1,2,3} Crystal dimensionality (0=cluster, 3=3D periodic)
--spg, --space-group SPACE_GROUP
International space-group number
--factor FACTOR PyXtal volume factor passed to from_random
--seed SEED RNG seed for reproducible PyXtal trials
--attempts ATTEMPTS Maximum PyXtal from_random retries
--no-resort Keep PyXtal atom order in ASE export (to_ase
resort=False)
ASE optimization (optional, PyXtal path):
--optimize Relax structure with ASE after PyXtal generation
--optimizer {bfgs,fire,lbfgs}
ASE optimizer when --optimize is set
--fmax FMAX ASE force convergence (eV/Å)
--max-opt-steps MAX_OPT_STEPS
Maximum ASE optimizer steps
--fix-cell Document intent to keep the unit cell fixed (positions-
only relaxation)
--emt Use ASE EMT calculator for --optimize (smoke tests only)
--quiet-opt Suppress ASE optimizer log output
Example structures¶
More detail: Structure building guide.