def langevin_init_N_108_l_box_6(box_size, n_particles):
n_dim = len(box_size)
q_0 = q_opt
v_0 = np.zeros((n_particles, n_dim))
return q_0, v_0
test_config = es.SimuConfig(l_box=(6., 6., 6.),
PBC=True,
neighbor_list=False,
particle_info=[0] * 108,
n_steps=8000,
timestep=0.001,
temp=0.5,
phys_world=dummy_world)
test_md = es.MD(test_config, random_initiliazer, es.step_runners.MMC(step=0.1))
test_md.add_potential(
es.potentials.LJ(test_config, switch_start=2.5, cutoff=3.5))
test_md.run_all()
print("simu_done")
qs = test_md.traj.get_qs()
#np.save("optimized.npy",qs[-1])
Gr = es.observables.RadDistFunc(test_config, 40, [108, 0, 0])
g_r, radii = Gr.calc_radial_dist(qs, 500, 1)
import matplotlib.pyplot as plt
for _ in range(7):
plt.plot(radii, g_r[_])
plt.show()
return pot_func, force_func
def StupidInitializer3(box_size, n_particles):
# need to return a tuple of four vectors
# masses, charges, q_0 and p_0
q_0 = np.array([[0., 0.], [0., 1.]]) + box_size / 2
#v_0 = np.array([[0.5, 0.866], [-0.8, 0.6]])
v_0 = np.array([[0., 0.], [0., 0.]])
return q_0, v_0
test_config = es.SimuConfig(l_box=(8., 8.),
PBC=True,
particle_info=[0, 0],
n_steps=10000,
timestep=0.001,
temp=30,
phys_world=dummy_world)
test_md = es.MD(test_config, StupidInitializer3,
es.step_runners.Langevin(damping=0.01))
test_md.add_potential(HarmonicTrap(test_config, 100., [4., 4.]))
#test_md.add_potential(es.potentials.LJ(test_config, switch_start=2.5, cutoff=3.5))
test_md.run_all()
#print(test_md.traj.get_qs())
qs = test_md.traj.get_qs() % 8.
plt.plot(qs[:, 0, 0], qs[:, 0, 1])
plt.plot(qs[:, 1, 0], qs[:, 1, 1])
plt.show()
# 3.104 is for correct liquid water density at 300 K
l_box = 7. * np.array([2 * n, n, n])
grid=_grid([n, n, n])
q_0 = 7. * grid
#init_directions = []
q = (q_0[:, None, :] + water_shape[None, :, :]).reshape(-1, 3)
v = np.zeros((3 * n_mol, n_dim))
mol_list = []
for i in range(n_mol):
mol_list.append((0, [3 * i, 3 * i + 1, 3 * i + 2]))
particle_info = np.tile([1, 2, 2], n_mol)
return q, v, particle_info, l_box, mol_list
q, v, particle_info, l_box, mol_list = _intializer_WaterBox(3)
steps = 5000
test_config = es.SimuConfig(l_box=l_box, PBC=True, neighbor_list=False, particle_info=particle_info, mol_list=mol_list, n_steps=steps, timestep=1e-3, temp=500)
init = lambda x,y: (q, v)
test_md = es.MD(test_config, init, es.step_runners.GradientDescent())
test_md.add_potential(es.potentials.Water(test_config))
test_md.add_potential(es.potentials.LJ(test_config, switch_start=5., cutoff=7.))
test_md.add_potential(es.potentials.Coulomb(test_config))
print(es.potentials.Coulomb(test_config))
#test_md.add_potential(HarmonicTrap(test_config, 100., [4., 4.]))
#test_md.add_potential(es.potentials.LJ(test_config, switch_start=2.5, cutoff=3.5))
test_md.run_all()
#print(test_md.traj.get_qs())
qs = test_md.traj.get_qs()
pdb = es.observables.PdbWriter(test_config, 'water_opt2.pdb')
for i in range(int(steps/100)):
pdb.write_frame(qs[i * 100])
import matplotlib.pyplot as plt
from .dummies import dummy_world
def random_initiliazer(box_size, n_particles):
n_dim = len(box_size)
q_0 = np.random.uniform(0.1, 7, (n_particles, n_dim))
v_0 = np.zeros((n_particles, n_dim))
return q_0, v_0
test_config = es.SimuConfig(
l_box=(8., 8., 8.),
PBC=True,
particle_info=[0] * 40,
n_steps=2000,
timestep=0.001,
temp=30,
phys_world=dummy_world,
)
test_md = es.MD(test_config, random_initiliazer,
es.step_runners.Langevin(damping=0.01))
test_md.add_potential(
es.potentials.LJ(test_config, switch_start=2.5, cutoff=3.5))
test_md.run_all()
qs = test_md.traj.get_qs() % 8.
plt.plot(qs[:, 0, 0], qs[:, 0, 1])
plt.plot(qs[:, 1, 0], qs[:, 1, 1])
plt.show()
v_0 = np.array([[0., 0.]] * 9)
return masses, charges, q_0, v_0 * masses[:, None]
N_particles = 9
l_box = (8., 8.)
test_config = es.SimuConfig(n_dim = 2,
l_box = l_box,
n_particles = N_particles,
n_steps = 3000,
timestep = 0.001,
temp = 100,
PBC = True,
neighbour = False,
lj_flag = True,
)
test_md = es.MD(es.PhysWorld(), test_config, grid_initializer_2d, es.step_runners.Langevin(damping=0.1))
#test_md.add_global_potential(HarmonicPotential(1.))
test_md.run_all()
#print(test_md.traj.get_qs())
qs = test_md.traj.get_qs()
#plt.plot(qs[:, 0, 0]%3., qs[:, 0, 1]%3.)
#plt.plot(qs[:, 1, 0]%3., qs[:, 1, 1]%3.)
#plt.show()
import matplotlib.animation as manimation
FFMpegWriter = manimation.writers['ffmpeg']
metadata = dict(title='Movie Test', artist='Matplotlib',
comment='Movie support!')
writer = FFMpegWriter(fps=20, metadata=metadata)
mol_list = []
for i in range(n_mol):
mol_list.append((0, [3 * i, 3 * i + 1, 3 * i + 2]))
particle_info = np.tile([1, 2, 2], n_mol)
return q, v, particle_info, l_box, mol_list
q, v, particle_info, l_box, mol_list = _intializer_WaterBox(6)
steps = 2000
test_config = es.SimuConfig(l_box=l_box,
PBC=True,
particle_info=particle_info,
mol_list=mol_list,
n_steps=steps,
timestep=0.01,
temp=500)
init = lambda x, y: (q, v)
test_md = es.MD(test_config, init, es.step_runners.Langevin(damping=0.05))
test_md.add_potential(es.potentials.Water(test_config))
test_md.add_potential(es.potentials.LJ(test_config, switch_start=5.,
cutoff=7.))
test_md.add_potential(es.potentials.Coulomb(test_config))
#test_md.add_potential(HarmonicTrap(test_config, 100., [4., 4.]))
#test_md.add_potential(es.potentials.LJ(test_config, switch_start=2.5, cutoff=3.5))
test_md.run_all()
#print(test_md.traj.get_qs())
qs = test_md.traj.get_qs()
pdb = es.observables.PdbWriter(test_config, 'water_gas.pdb')
for i in range(int(steps / 10)):
pdb.write_frame(qs[i * 10])
return pot_func, force_func
def StupidInitializer3(box_size, n_particles):
# need to return a tuple of four vectors
# masses, charges, q_0 and p_0
q_0 = np.array([[0., 0.], [0., 1.]]) + box_size / 2
#v_0 = np.array([[0.5, 0.866], [-0.8, 0.6]])
v_0 = np.array([[0., 0.], [0., 0.]])
return q_0, v_0
test_config = es.SimuConfig(l_box=(8., 8.),
PBC=True,
particle_info=[0, 0],
n_steps=10000,
timestep=0.001,
temp=100,
phys_world=dummy_world)
test_md = es.MD(test_config, StupidInitializer3,
es.step_runners.MMC(step=0.05))
test_md.add_potential(HarmonicTrap(test_config, 1000., [4., 4.]))
test_md.add_potential(
es.potentials.LJ(test_config, switch_start=2.5, cutoff=3.5))
test_md.run_all()
qs = test_md.traj.get_qs()
plt.plot(qs[:, 0, 0], qs[:, 0, 1])
plt.plot(qs[:, 1, 0], qs[:, 1, 1])
plt.show()