def test_forces_sign_far(dist):
particles = cm.ParticleGroup.from_xyz(ar_path,('constant',0.))
particles.attach_potential(cm.LJPotential(A=A_ar,B=B_ar,rcut=cut))
particles.coords[1,:] = [dist,0.,0.]
#forces for these coordinates should be, in magnitude:
assert particles.get_forces()[0][0] > 0. and \
particles.get_forces()[1][0] < 0.
def test_forces_newton_third_pair(dist):
particles = cm.ParticleGroup.from_xyz(ar_path,('constant',0.))
particles.attach_potential(cm.LJPotential(A=A_ar,B=B_ar,rcut=cut))
particles.coords[1,:] = [dist,0.,0.]
#forces for these coordinates should be, in magnitude:
assert isclose(abs(particles.get_forces()[0][0]),
abs(particles.get_forces()[1][0]),rel_tol=1e-8,abs_tol=1e-8)
def test_forces_magnitude(dist):
particles = cm.ParticleGroup.from_xyz(ar_path,('constant',0.))
particles.attach_potential(cm.LJPotential(A=A_ar,B=B_ar,rcut=cut))
particles.coords[1,:] = [dist,0.,0.]
#forces for these coordinates should be, in magnitude:
myforce = abs(12*A_ar/(dist**13)-6*B_ar/(dist**7))
assert isclose(abs(particles.get_forces()[0][0]),
myforce,rel_tol=1e-8,abs_tol=1e-8)
def test_forces_eq():
particles = cm.ParticleGroup.from_xyz(ar_path,('constant',0.))
particles.attach_potential(cm.LJPotential(A=A_ar,B=B_ar,rcut=cut))
particles.coords[1,:] = [rmin_argon,0.,0.]
#forces for these coordinates should be, in magnitude:
assert isclose(particles.get_forces()[0][0],0.,
rel_tol=1e-8,abs_tol=1e-8) \
and isclose(particles.get_forces()[1][0],0.,
rel_tol=1e-8,abs_tol=1e-8)
def test_propagate_first_ts():
ts = 5.
particles = cm.ParticleGroup.from_xyz(ar_path,('constant',0.))
particles.attach_potential(cm.LJPotential(A=A_ar,B=B_ar,rcut=cut))
particles.coords[1,:] = [4.,0.,0.]
particles.attach_propagator(cm.VerletPropagator(ts))
myforce = 12*A_ar/(4.**13)-6*B_ar/(4.**7)
upterm = (myforce/ar_mass)*ts**2
new_coord = 4. + 0.5*upterm
particles.update_coords_velocs(0)
assert isclose(new_coord,particles.coords[1][0],rel_tol=1e-8,abs_tol=1e-8)
#for j in range(10000):
# particles.update_coords_velocs(j,'reflecting_fake')
# with open("output_test.xyz","a") as myfile:
# myfile.write('100\n')
# myfile.write(f'timestep {j}\n')
# for n in range(particles.coords.shape[0]):
# x = particles.coords[n,0]
# y = particles.coords[n,1]
# z = particles.coords[n,2]
# myfile.write(f'Ar {x} {y} {z} \n')
##############################
particles = cm.ParticleGroup.from_xyz(reflecting_path,('constant',0.))
particles.coords = np.random.uniform(-9.,9.,(100,3))
particles.attach_potential(cm.LJPotential(A=A_ar,B=B_ar,rcut=cut))
particles.attach_box(-10.,10.,-10.,10.,-10.,10.)
particles.attach_propagator(cm.SteepestDescentPropagator(5.))
for j in range(1000):
particles.update_coords_velocs(j,'reflecting_velverlet')
with open("output_velver.xyz","a") as myfile:
myfile.write('100\n')
myfile.write(f'timestep {j}\n')
for n in range(particles.coords.shape[0]):
x = particles.coords[n,0]
y = particles.coords[n,1]
z = particles.coords[n,2]
myfile.write(f'Ar {x} {y} {z} \n')
import numpy as np import pycmech as cm import matplotlib.pyplot as plt water_path = './test_data/water.xyz' #sanity check for the lennard jones potential, this should look like the #argon lennard jones potential eps_argon = cm.joule2menergy(1.65e-21) sig_argon = 3.4 A_argon = 4 * eps_argon * sig_argon**12 B_argon = 4 * eps_argon * sig_argon**6 rmin_argon = 2**(1 / 6.) * sig_argon lj = cm.LJPotential(A=A_argon, B=B_argon, rcut=8.) #This plot should look like the argon lennard jones potential #with a minimum at the vertical line #and going towards 0 at the horizontal line dist = np.linspace(3.3, 8., 100) ljval = lj._lj_for_array(dist) plt.plot(dist, ljval) ylo, yhi = plt.gca().get_ylim() xlo, xhi = plt.gca().get_xlim() plt.vlines(rmin_argon, *plt.gca().get_ylim()) plt.hlines(0., *plt.gca().get_xlim(), linestyles='dashed') plt.gca().set_ylim(ylo, yhi) plt.gca().set_xlim(xlo, xhi) plt.show()
