mmml neb¶
Nudged elastic band (NEB) path sampling with PhysNet.
Usage¶
mmml neb --help
Options¶
usage: mmml neb [-h] [--config CONFIG] [--checkpoint CHECKPOINT]
[--initial INITIAL] [--final FINAL] [--output-dir OUTPUT_DIR]
[--n-images N_IMAGES] [--fmax FMAX] [--climb | --no-climb]
[--interpolate {idpp,linear}] [--optimizer {BFGS,FIRE,MDMin}]
[--neb-method {improvedtangent,aseneb,eb,spline,string}]
[--spring-k SPRING_K]
[--shared-calculator | --no-shared-calculator]
[--max-steps MAX_STEPS] [--plot | --no-plot] [--overwrite]
[--pair I,J]
Nudged elastic band (NEB) path sampling with a PhysNet / MMML checkpoint as the
ASE calculator.
Input & configuration:
--config CONFIG YAML/JSON NebConfig; CLI flags override file values when
set
--checkpoint CHECKPOINT
PhysNet / MMML checkpoint
Scientific model:
--neb-method {improvedtangent,aseneb,eb,spline,string}
ASE NEB force method (default: improvedtangent)
--shared-calculator, --no-shared-calculator
Share one ASE calculator across images (default: on)
Execution:
--max-steps MAX_STEPS
Optional optimizer step cap (default: unlimited until
fmax)
Output & artifacts:
--output-dir, -o OUTPUT_DIR
Directory for neb.traj / neb.xyz / profile / plot /
summary
--plot, --no-plot Write neb_plot.png (default: on)
--overwrite Overwrite existing artifacts in --output-dir
Diagnostics & safety:
-h, --help show this help message and exit
Other options:
--initial INITIAL Reactant / initial XYZ
--final FINAL Product / final XYZ
--n-images N_IMAGES Total band images including endpoints (default: 11)
--fmax FMAX Force convergence threshold in eV/Å (default: 0.05)
--climb, --no-climb Enable climbing-image NEB (default: off)
--interpolate {idpp,linear}
Band interpolation method (default: idpp)
--optimizer {BFGS,FIRE,MDMin}
Band optimizer (default: BFGS)
--spring-k SPRING_K NEB spring constant (default: 0.1)
--pair I,J Atom-index pair to log as a distance column
(repeatable). Default for 9-atom NH3–CH3Cl: 1,2 (N–C)
and 0,2 (Cl–C).
CLI adapter for ASE NEB sampling with an MMML PhysNet checkpoint. Usage: mmml
neb \ --checkpoint examples/m/kl.json \ --initial examples/m/neb/reag_0_opt.xyz
\ --final examples/m/neb/prod_0_opt.xyz \ --output-dir artifacts/nh3_ch3cl/neb \
--n-images 11 --fmax 0.05