Usage: pdb2reaction dft [OPTIONS]
Single-point DFT using GPU4PySCF or CPU PySCF.
Options:
-v, --verbose LEVEL Console verbosity 0-3 (default 2). 0=silent;
1=milestones only; 2=+detailed step logging
and deliverable paths; 3=everything (full
config blocks, per-file paths, DEBUG logging).
[0<=x<=3]
--help-advanced Show all options (including advanced settings)
and exit.
-i, --input FILE Input structure file (.pdb, .cif, .mmcif,
.xyz, .gjf, etc.). [required]
-q, --charge INTEGER Total charge. Required unless --ligand-charge,
YAML calc.charge, or a .gjf input gives it.
-l, --ligand-charge TEXT Total ligand charge or per-resname mapping
(e.g., GPP:-3,SAM:1) used to derive charge
when -q is omitted (requires PDB/mmCIF input
or --ref-pdb).
-m, --multiplicity INTEGER RANGE
Spin multiplicity (2S+1; inherits from .gjf
when available). [default: (1); x>=1]
--ref-pdb FILE Reference PDB/mmCIF topology to use when the
input is XYZ/GJF (keeps XYZ coordinates).
--func-basis TEXT Exchange–correlation functional and basis set
as 'FUNC/BASIS' (e.g., 'wb97m-v/6-31g**',
'wb97m-v/def2-tzvpd'). [default:
wb97m-v/def2-svp]
--scf-max-cycles, --max-cycle INTEGER RANGE
Maximum SCF iterations. [default: 100; x>=1]
--scf-tol, --conv-tol FLOAT SCF convergence tolerance (Eh). [default:
1e-09]
--dft-grid-level, --grid-level INTEGER
Numerical integration grid level (PySCF
grids.level). [default: 3]
-o, --out-dir TEXT Output directory. [default: ./result_dft/]
--dft-engine, --engine [gpu|cpu]
SCF backend: gpu (GPU4PySCF, raises error if
unavailable) or cpu (PySCF). [default: gpu]
--solvent TEXT Implicit-solvent name for native PySCF PCM/SMD
(for example water). [default: (none)]
--solvent-model [pcm|smd] Native PySCF implicit-solvent model.
[default: (smd)]
--dft-low-memory, --lowmem / --no-dft-low-memory, --no-lowmem
Use gpu4pyscf rks_lowmem.RKS for closed-shell
GPU runs, including PCM/SMD (memory-efficient
direct JK). Open-shell GPU and CPU use
standard direct-JK RKS/UKS; --no-dft-low-
memory enables density fitting. [default:
dft-low-memory]
--scf-stepwise-grid / --no-scf-stepwise-grid
Converge the SCF on a coarse grid first, then
on the final grid with the same settings.
[default: scf-stepwise-grid]
--dft-nprocs INTEGER RANGE PySCF/OpenMP CPU threads; GPU count is
unaffected. [default: (auto); x>=1]
--dft-memory, --dft-mem TEXT PySCF host RAM limit (for example 64GB or
120000MB). [default: (auto)]
--config FILE Base YAML configuration file applied before
explicit CLI options.
--show-config / --no-show-config
Print the loaded YAML file and its top-level
keys, then continue. [default: no-show-
config]
--out-json / --no-out-json Write machine-readable result.json to out_dir.
[default: no-out-json]
--dry-run / --no-dry-run Validate options and inputs without running
DFT. [default: no-dry-run]
--allow-charge-mult-mismatch Skip the cluster charge/multiplicity electron-
parity check (logs that it was skipped). Open-
shell clusters need a matching multiplicity
instead; use this only for an intentionally
nonstandard electron count.
-h, --help Show this message and exit.
