Strategies¶

Pair potentials can be used in multiple ways in exaStamp. Depending on whether a single specy or multiple species are present in the system, one can use different variants of a pair potential or even mix them. Every pair potential X (where X is lj, buckingham, zbl, ...) provides the following operators:

Operator	Use
`X_compute_force`	One set of parameters for all atoms
`X_compute_force_symetric`	Same, each pair is computed once and the force is applied to both atoms
`X_multi_force`	One set of parameters per pair of species
`X_rigidmol_force`	Rigid molecules (only for some potentials, see each model page)
`X_plot`	Writes \(r\), \(E(r)\), \(\mathrm{d}E/\mathrm{d}r\) and a finite-difference check of \(\mathrm{d}E/\mathrm{d}r\) to a text file (`file`, default `X.csv`), for `samples` points up to `rcut`

Single specy¶

Example: Basic usage of a pair potential

lj_compute_force:
  parameters: { epsilon: 0.0104 eV , sigma: 3.4 ang }
  rcut: 8.0 ang

compute_force: lj_compute_force

Example: Symmetric variant of a pair potential

lj_compute_force_symetric:
  parameters: { epsilon: 0.0104 eV , sigma: 3.4 ang }
  rcut: 8.0 ang

compute_force: lj_compute_force_symetric

Multiple species¶

Example: Multiple species variant of a pair potential

lj_multi_force:
  rcut: 8. ang
  common_parameters: { epsilon: 0.0 , sigma: 0.0 }
  parameters:
    - { type_a: Zn , type_b: Zn , rcut: 6.10 ang , parameters: { epsilon: 2.522E-20 J , sigma: 0.244E-09 m } }
    - { type_a: Cu , type_b: Zn , rcut: 5.89 ang , parameters: { epsilon: 4.853E-20 J , sigma: 0.236E-09 m } }

compute_force: lj_multi_force

common_parameters is optional: it gives the parameters of the species pairs that are not listed in parameters.

Mixing pair potentials¶

In the presence of multiple types in the simulated sample, the compute_force_pair_multimat operator assigns a different pair potential to each pair of species. Each entry of potentials gives the two species, the potential name (lj, buckingham, exp6, zbl, coul_rf, ... — the same names as the operator prefixes), its cutoff and its parameters. Species pairs that are not listed get a zero potential.

Example: Mixing pair potentials

compute_force_pair_multimat:
  potentials:
    - { type_a: Si , type_b: Cu , potential: lj , rcut: 5.89 ang , parameters: { epsilon: 1.0 eV , sigma: 2.3 ang } }
    - { type_a: Si , type_b: Zn , potential: buckingham , rcut: 7.10 ang , parameters: { A: 1.3 eV , Rho: 1.2 ang , C: 1.5 eV*ang^6 } }
    - { type_a: Cu , type_b: Zn , potential: exp6 , rcut: 12.5 ang , parameters: { A: 37111.29 Da*kcal/g , B: 3.46350030 1/ang , C: 484.2991571 Da*kcal*ang^6/g , D: 5.0e-5 Da*kcal/g } }

compute_force: compute_force_pair_multimat

Parameters

potentials:          list, required        # { type_a, type_b, potential, rcut, parameters } for each species pair.
ghost:               bool, default false   # Also compute forces on ghost atoms.
enable_pair_weights: bool, default true    # Apply intramolecular pair weights when they exist.
symetric:            bool, default false   # Not supported: the simulation aborts if true.