def test_switchfunction():
Coulomb = coulomb(ip.n_boxes_short_range, ip.L, ip.p_error)
assert Coulomb._coulomb__switchFunction(1.,1.,2.)==1.,"The switchfunction should be one here."
assert Coulomb._coulomb__switchFunction(2., 1., 2.) == 0., "The switchfunction should be zero here."
LJpotential = lennard_jones()
assert LJpotential._lennard_jones__switchFunction(1.,1.,2.)==1.,"The switchfunction should be one here."
assert LJpotential._lennard_jones__switchFunction(2., 1., 2.) == 0., "The switchfunction should be zero here."
def __init__(self,
positions,
properties,
velocities,
forces,
box,
Temperature,
Sigma_LJ,
Epsilon_LJ,
r_switch,
r_cut_LJ,
n_boxes_short_range,
dt,
p_rea,
p_error,
Symbols):
#check input parameters
self.positions=positions
self.R=np.linalg.norm(self.positions, axis=1)
self.N = np.size(self.positions[:,0])
first_d_Pos = np.zeros((self.N,self.N,3))
first_d_Pos[:,:,0] = np.subtract.outer(self.positions[:,0], self.positions[:,0])
first_d_Pos[:,:,1] = np.subtract.outer(self.positions[:,1], self.positions[:,1])
first_d_Pos[:,:,2] = np.subtract.outer(self.positions[:,2], self.positions[:,2])
self.d_Pos = first_d_Pos
self.labels=properties
self.velocities = velocities
self.forces = forces
self.L=box
self.T= Temperature
self.lennard_jones = lennard_jones()
self.Sigma_LJ = Sigma_LJ
self.Epsilon_LJ = Epsilon_LJ
self.dt = dt
self.p_rea = p_rea
self.n_boxes_short_range= n_boxes_short_range
self.r_switch = r_switch
self.r_cut_LJ = r_cut_LJ
# epsilon0 = (8.854 * 10^-12) / (36.938 * 10^-9) -> see Dimension Analysis
self.coulomb = coulomb(n_boxes_short_range, box, p_error, epsilon0 = epsilon_0 / (36.938 * 10**-9))
self.neighbours_coulomb, self.distances_coulomb = neighbourlist().compute_neighbourlist(positions, box[0],
0.49 * box[0])
self.r_cut_coulomb, self.k_cut, self.std = self.coulomb.compute_optimal_cutoff(p_error, box, properties, self.neighbours_coulomb, self.distances_coulomb, r_switch, 0.49 * box[0], positions)
self.neighbours_coulomb, self.distances_coulomb = neighbourlist().compute_neighbourlist(positions, box[0],
self.r_cut_coulomb)
self.coulomb.n_boxes_short_range = np.ceil( self.r_cut_coulomb/self.L[0] ).astype(int)
self.switch_parameter = self.__get_switch_parameter()
self.neighbours_LJ, self.distances_LJ= neighbourlist().compute_neighbourlist(positions, box[0], self.r_cut_LJ)
self.Symbols = Symbols
return
def test_LJ_forces():
LJ = lennard_jones()
Force = LJ.compute_forces(Test_Positions,
Sigma,
Epsilon,
Test_Labels,
Test_L,
switch_parameter,
r_switch,
neighbours)
assert np.all(Force[0, :] == -Force[1, :]), "lennard Jones force is broken"
def test_SymmetriesPotLJ2():
potential = lennard_jones()
result = potential.compute_potential(sigma=ip.sigma, epsilon=ip.epsilon, labels=ip.labels,
distances={0: [np.sqrt(12), np.sqrt(3)], 1: [np.sqrt(12), np.sqrt(12)],
2: [np.sqrt(3), np.sqrt(12)]},
neighbours=ip.neighbours, r_s=np.sqrt(3 * 2 ** 2),
r_c=np.sqrt(3 * 2 ** 2) + 0.1)
assert (abs(result[0] / result[2]) < 1 + 10 ** (
-8)), "Potential does not have the expected symmetrie. P1 and P3 should be the same."
assert (result[0] != result[1]), "Potential does not have the expected symmetrie. P1 and P2 should not be the same."
assert (result[2] != result[1]), "Potential does not have the expected symmetrie. P3 and P2 should not be the same."
return
def test_SymmetriesPotLJ():
# tests LJ Potential for with equidistant identical charges
potential = lennard_jones()
result = potential.compute_potential(sigma=ip.sigma, epsilon=ip.epsilon, labels=ip.labels,
distances=ip.distances, neighbours=ip.neighbours, r_s=np.sqrt(3 * 2 ** 2),
r_c=np.sqrt(3 * 2 ** 2) + 0.1)
assert (abs(result[0] / result[2]) < 1 + 10 ** (
-8)), "Potential does not have the expected symmetrie. P1 and P3 should be the same."
assert (abs(result[0] / result[1]) < 1 + 10 ** (
-8)), "Potential does not have the expected symmetrie. P1 and P2 should be the same."
assert (abs(result[2] / result[1]) < 1 + 10 ** (
-8)), "Potential does not have the expected symmetrie. P3 and P2 should be the same."
return