root / ase / calculators / morse.py @ 1
Historique | Voir | Annoter | Télécharger (1,42 ko)
| 1 | 1 | tkerber | from math import exp, sqrt |
|---|---|---|---|
| 2 | 1 | tkerber | import numpy as np |
| 3 | 1 | tkerber | |
| 4 | 1 | tkerber | class MorsePotential: |
| 5 | 1 | tkerber | """Morse potential.
|
| 6 | 1 | tkerber |
|
| 7 | 1 | tkerber | Default values chosen to be similar as Lennard-Jones.
|
| 8 | 1 | tkerber | """
|
| 9 | 1 | tkerber | def __init__(self, rho0=6.0, epsilon=1.0, r0=1.0): |
| 10 | 1 | tkerber | self.epsilon = epsilon
|
| 11 | 1 | tkerber | self.rho0 = rho0
|
| 12 | 1 | tkerber | self.r0 = r0
|
| 13 | 1 | tkerber | self.positions = None |
| 14 | 1 | tkerber | |
| 15 | 1 | tkerber | def update(self, atoms): |
| 16 | 1 | tkerber | assert not atoms.get_pbc().any() |
| 17 | 1 | tkerber | if (self.positions is None or |
| 18 | 1 | tkerber | (self.positions != atoms.get_positions()).any()):
|
| 19 | 1 | tkerber | self.calculate(atoms)
|
| 20 | 1 | tkerber | |
| 21 | 1 | tkerber | def get_potential_energy(self, atoms): |
| 22 | 1 | tkerber | self.update(atoms)
|
| 23 | 1 | tkerber | return self.energy |
| 24 | 1 | tkerber | |
| 25 | 1 | tkerber | def get_forces(self, atoms): |
| 26 | 1 | tkerber | self.update(atoms)
|
| 27 | 1 | tkerber | return self._forces |
| 28 | 1 | tkerber | |
| 29 | 1 | tkerber | def get_stress(self, atoms): |
| 30 | 1 | tkerber | return np.zeros((3, 3)) |
| 31 | 1 | tkerber | |
| 32 | 1 | tkerber | def calculate(self, atoms): |
| 33 | 1 | tkerber | positions = atoms.get_positions() |
| 34 | 1 | tkerber | self.energy = 0.0 |
| 35 | 1 | tkerber | self._forces = np.zeros((len(atoms), 3)) |
| 36 | 1 | tkerber | preF = 2 * self.epsilon * self.rho0 / self.r0 |
| 37 | 1 | tkerber | for i1, p1 in enumerate(positions): |
| 38 | 1 | tkerber | for i2, p2 in enumerate(positions[:i1]): |
| 39 | 1 | tkerber | diff = p2 - p1 |
| 40 | 1 | tkerber | r = sqrt(np.dot(diff, diff)) |
| 41 | 1 | tkerber | expf = exp(self.rho0 * (1.0 - r / self.r0)) |
| 42 | 1 | tkerber | self.energy += self.epsilon * expf * (expf - 2) |
| 43 | 1 | tkerber | F = preF * expf * (expf - 1) * diff / r
|
| 44 | 1 | tkerber | self._forces[i1] -= F
|
| 45 | 1 | tkerber | self._forces[i2] += F
|
| 46 | 1 | tkerber | self.positions = positions.copy() |