Potential¶
Numerical potential energy functions for bonds, angles, dihedrals, and pairs.
Quick reference¶
The numerical kernels live in the molrs Rust extension; molpy.potential exposes
the thin Style classes that name them plus the Potentials evaluator.
| Symbol | Summary | Preferred for |
|---|---|---|
BondHarmonicStyle |
Harmonic bond style: E = k(r - r₀)² | Standard bonded interactions |
AngleHarmonicStyle |
Harmonic angle style: E = k(θ - θ₀)² | Standard angle terms |
LJ126Style |
Lennard-Jones 12-6 pair style | Standard nonbonded interactions |
ImproperHarmonicStyle |
Harmonic improper style (plus Cvff / Class2 / Periodic variants) | Out-of-plane / improper terms |
Potentials |
Deferred evaluator over a typed Frame |
Energy / force computation |
Canonical example¶
Define styles and types on a ForceField, then evaluate against a typed Frame
via ff.to_potentials(). There is no per-style to_potential() and no
parameter-array lookup; the math runs in molrs.
import molpy as mp
import numpy as np
ff = mp.ForceField(name="demo", units="real")
astyle = ff.def_atomstyle("full")
ct = astyle.def_type("CT", mass=12.011, charge=-0.18, element="C")
hc = astyle.def_type("HC", mass=1.008, charge=0.06, element="H")
bond_style = ff.def_bondstyle("harmonic")
bond_style.def_type(ct, hc, k=340.0, r0=1.09) # param name is "k", not "k0"
# Build a typed frame (atoms block + bonds block carrying a "type" column).
frame = mp.Frame()
atoms = mp.Block()
atoms.insert("x", np.array([0.0, 1.2]))
atoms.insert("y", np.array([0.0, 0.0]))
atoms.insert("z", np.array([0.0, 0.0]))
frame["atoms"] = atoms
bonds = mp.Block()
bonds.insert("atomi", np.array([0], dtype=np.uint32))
bonds.insert("atomj", np.array([1], dtype=np.uint32))
bonds.insert("type", np.array(["CT-HC"], dtype=str))
frame["bonds"] = bonds
pots = ff.to_potentials()
energy = pots.calc_energy(frame)
forces = pots.calc_forces(frame)
Related¶
Full API¶
Bond¶
bond ¶
Angle¶
angle ¶
Dihedral¶
dihedral ¶
Dihedral potential styles (facade over molrs).
DihedralCharmmStyle ¶
Bases: DihedralStyle
Dihedral charmm style.
DihedralClass2Style ¶
Bases: DihedralStyle
Dihedral class2 style.
DihedralFourierStyle ¶
Bases: DihedralStyle
Dihedral fourier style (AMBER multi-term).
DihedralMultiHarmonicStyle ¶
Bases: DihedralStyle
Dihedral multi/harmonic style.
DihedralPeriodicStyle ¶
Bases: DihedralStyle
Dihedral periodic (CHARMM-style charmm/periodic) style.
Improper¶
improper ¶
Pair¶
pair ¶
Pair (non-bonded) potential styles (facade over molrs).
PairCoulTTStyle ¶
Bases: PairStyle
Pair coul/tt — Tang−Toennies damped charge−dipole Coulomb style.
Style-level parameters: b (1/Å, default 4.5), n (default 4),
c (default 1.0).
Per-atom-type parameter: charge (e).
Damping: f_n(r) = 1 − c·exp(−b·r)·Σ_{k=0}^n (b·r)^k/k!.
Reference: Tang & Toennies, J. Chem. Phys. 80 (1984) 3726,
:doi:10.1063/1.447150.
PairTholeStyle ¶
Bases: PairStyle
Pair thole — Thole damped dipole-dipole / core-shell Coulomb style.
Per-atom-type parameters: charge (e), alpha (ų),
a_thole (dimensionless Thole damping width, default 2.6).
Damping: T(r) = 1 − (1 + s·r/2)·exp(−s·r) where
s = a_ij / (α_i·α_j)^(1/6), a_ij = (a_i + a_j)/2.
Reference: Thole, Chem. Phys. 59 (1981) 341,
:doi:10.1016/0301-0104(81)85176-2.