# fix the slabs
top_indices = simu.get_indices_z_more_than(11)
bottom_indices = simu.get_indices_z_less_than(-3.5)
simu.fix_positions(top_indices)
simu.fix_positions(bottom_indices)
simu.print_stats_during_simulation(interval=50.0)
# save the trajectory in a new file (so that we don't overwrite the old one)
simu.save_trajectory_during_simulation(interval=50.0, filename='test.traj')
# run for a while to let the system find a stable configuration
simu.run_simulation(time=2000.0)
# push the top slab down
simu.remove_constraints()
simu.fix_velocities(top_indices, [0, 0, -0.002])
simu.fix_positions(bottom_indices)
threshold = 3.0
low_indices = simu.get_indices_z_less_than(threshold)
# approach the surface until the first silver atoms reach it
# this can be monitored, e.g., by counting the atoms below a certain
# threshold
while len(low_indices) == len(simu.get_indices_z_less_than(threshold)):
simu.run_simulation(100.0)
# write the geometry file - remember to read the correct trajectory
ft.trajectory_to_xyz(filename_in='test.traj')
#! /usr/bin/env python import friction_tools as ft # create the simulation containing two atoms simu = ft.FrictionSimulation() simu.create_atoms(element='C', positions=[[0, 0, 0], [6, 0, 0]]) # create an interaction between the two atoms simu.create_interaction(['C', 'C'], strength=10.0, equilibrium_distance=5.0) # give the atoms some initial velocities vs = [[0.1, 0, 0], [-0.1, 0, 0]] simu.set_velocities(indices=range(2), velocity=vs) # tell that we want to run the simulation with default settings simu.create_dynamics() # tell that we want to record the movement of the atoms simu.save_trajectory_during_simulation(interval=5) # run the simulation for 1000 fs print "starting simulation" simu.run_simulation(time=1000.0) print "finished simulation" # after finishing, create an xyz-file for viewing what happened ft.trajectory_to_xyz()
def main(strengths):
moving_slab_material = 'Ag'
moving_slab_xy = 3 # 3
moving_slab_z = 2 # 2
fixed_slab_material = 'Au'
fixed_slab_xy = 5 # 5
fixed_slab_z = 2 # 2
element_charges = {
'Au': 0.01,
'Ag': 0.005
}
element_lj_strengths = strengths
"""= {
'Au': 1.0,
'Ag': 0.5
}"""
# Create simulation object
sim = ft.FrictionSimulation()
# Calculate thresholds for being in touch with the surface
contact_threshold = math.ceil(10.0 / float(moving_slab_xy)) * moving_slab_z
velocity_threshold_x = 0.04
# Create the two slabs and store their indices
# TODO: Edit to use z-config
sim.create_slab(
element=fixed_slab_material,
xy_cells=fixed_slab_xy,
z_cells=2,
top_z=0.0
)
sim.create_slab(
element=moving_slab_material,
xy_cells=moving_slab_xy,
z_cells=2,
bottom_z=5.0
)
fixed_mat_indices = sim.get_indices_by_element(fixed_slab_material)
moving_mat_indices = sim.get_indices_by_element(moving_slab_material)
# TODO: Edit to use z-config
bottom_indices = sim.get_indices_z_less_than(-2) # Bottom row of fixed materials atoms
top_indices = sim.get_indices_z_more_than(8.0) # Top row of moving materials atoms
# Create interactions
create_lj_interactions(element_lj_strengths)
# create_coulomb_interactions(element_charges) # Currently too slow!
# Create dynamics and configure the setup
sim.create_dynamics(dt=1.0, temperature=300)
# Fix the bottom slab and make the top slab move down
sim.fix_positions(bottom_indices)
sim.add_constant_force(top_indices, [0, 0, -0.1])
# sim.fix_velocities(top_indices, [0, 0, -0.005], [True, True, True])
sim.set_temperature(300) # Try to reset the temperature
# Save tmps, print stats and time the simulation
sim.save_trajectory_during_simulation(interval=50.0)
sim.print_stats_during_simulation(interval=50.0)
t0 = time.time()
print('Starting the simulation')
print(sim.get_avg_forces(moving_mat_indices))
while len(sim.get_indices_z_more_than(contact_threshold)):
print(len(sim.get_indices_z_more_than(contact_threshold)))
print(sim.get_avg_velocity(moving_mat_indices))
print(sim.get_avg_forces(moving_mat_indices))
sim.run_simulation(500)
print('Moving slab hit the fixed slab.')
sim.remove_constraints()
print('Starting friction measurement phase.')
xpos0 = [p[0] for p in sim.get_positions(indices=moving_mat_indices)]
friction_initial_velocity_x(0.005, 0.1)
xpos1 = [p[0] for p in sim.get_positions(indices=moving_mat_indices)]
xdiff = []
for i in range(0, len(xpos0)):
xdiff.append(xpos1[i] - xpos0[i])
out = open('ownpos.txt', 'w')
for i in range(0, len(xpos0)):
out.write('{0}\n'.format(xpos0[i], xpos1[i]))
out.close()
print('All done, generating simulation file.')
print(sim.get_avg_forces(moving_mat_indices))
sim.write_positions_to_file(indices=moving_mat_indices)
sim.write_average_position_to_file(indices=moving_mat_indices)
sim.write_velocities_to_file(indices=moving_mat_indices)
ft.trajectory_to_xyz()
#=====================
#>>>>> MAIN 2 <<<<<<<<
#=====================
#sim = ft.FrictionSimulation()
## Calculate thresholds for being in touch with the surface
#contact_threshold = math.ceil(10.0 / float(moving_slab_xy)) * moving_slab_z
#velocity_threshold_x = 0.04
## Create the two slabs and store their indices
## TODO: Edit to use z-config
#sim.create_slab(element=fixed_slab_material, xy_cells=fixed_slab_xy, z_cells=2, top_z=0.0)
#sim.create_slab(element=moving_slab_material, xy_cells=moving_slab_xy, z_cells=2, bottom_z=5.0)
#fixed_mat_indices = sim.get_indices_by_element(fixed_slab_material)
#moving_mat_indices = sim.get_indices_by_element(moving_slab_material)
## TODO: Edit to use z-config
#bottom_indices = sim.get_indices_z_less_than(-2) # Bottom row of fixed materials atoms
#top_indices = sim.get_indices_z_more_than(8.0) # Top row of moving materials atoms
## Create interactions
#create_lj_interactions(element_lj_strengths)
#create_coulomb_interactions(element_charges) # Currently too slow!
## Create dynamics and configure the setup
#sim.create_dynamics(dt=1.0, temperature=300)
## Fix the bottom slab and make the top slab move down
#sim.fix_positions(bottom_indices)
#sim.add_constant_force(top_indices, [0, 0, -0.1])
## sim.fix_velocities(top_indices, [0, 0, -0.005], [True, True, True])
#sim.set_temperature(300) # Try to reset the temperature
## Save tmps, print stats and time the simulation
#sim.save_trajectory_during_simulation(interval=50.0)
#sim.print_stats_during_simulation(interval=50.0)
#t0 = time.time()
#print('Starting the simulation')
#while len(sim.get_indices_z_more_than(contact_threshold)):
#print(len(sim.get_indices_z_more_than(contact_threshold)))
#print(sim.get_avg_velocity(moving_mat_indices))
#sim.run_simulation(500)
#print('Moving slab hit the fixed slab.')
#print('Starting friction measurement phase.')
#friction_constant_velocity_x([initial_velocity, 0.0, 0.0])
#print('All done, generating simulation file.')
#ft.trajectory_to_xyz()
def main(strengths):
moving_slab_material = 'Ag'
moving_slab_xy = 3 # 3
moving_slab_z = 2 # 2
fixed_slab_material = 'Au'
fixed_slab_xy = 5 # 5
fixed_slab_z = 2 # 2
element_charges = {'Au': 0.01, 'Ag': 0.005}
element_lj_strengths = strengths
"""= {
'Au': 1.0,
'Ag': 0.5
}"""
# Create simulation object
sim = ft.FrictionSimulation()
# Calculate thresholds for being in touch with the surface
contact_threshold = math.ceil(10.0 / float(moving_slab_xy)) * moving_slab_z
velocity_threshold_x = 0.04
# Create the two slabs and store their indices
# TODO: Edit to use z-config
sim.create_slab(element=fixed_slab_material,
xy_cells=fixed_slab_xy,
z_cells=2,
top_z=0.0)
sim.create_slab(element=moving_slab_material,
xy_cells=moving_slab_xy,
z_cells=2,
bottom_z=5.0)
fixed_mat_indices = sim.get_indices_by_element(fixed_slab_material)
moving_mat_indices = sim.get_indices_by_element(moving_slab_material)
# TODO: Edit to use z-config
bottom_indices = sim.get_indices_z_less_than(
-2) # Bottom row of fixed materials atoms
top_indices = sim.get_indices_z_more_than(
8.0) # Top row of moving materials atoms
# Create interactions
create_lj_interactions(element_lj_strengths)
# create_coulomb_interactions(element_charges) # Currently too slow!
# Create dynamics and configure the setup
sim.create_dynamics(dt=1.0, temperature=300)
# Fix the bottom slab and make the top slab move down
sim.fix_positions(bottom_indices)
sim.add_constant_force(top_indices, [0, 0, -0.1])
# sim.fix_velocities(top_indices, [0, 0, -0.005], [True, True, True])
sim.set_temperature(300) # Try to reset the temperature
# Save tmps, print stats and time the simulation
sim.save_trajectory_during_simulation(interval=50.0)
sim.print_stats_during_simulation(interval=50.0)
t0 = time.time()
print('Starting the simulation')
print(sim.get_avg_forces(moving_mat_indices))
while len(sim.get_indices_z_more_than(contact_threshold)):
print(len(sim.get_indices_z_more_than(contact_threshold)))
print(sim.get_avg_velocity(moving_mat_indices))
print(sim.get_avg_forces(moving_mat_indices))
sim.run_simulation(500)
print('Moving slab hit the fixed slab.')
sim.remove_constraints()
print('Starting friction measurement phase.')
xpos0 = [p[0] for p in sim.get_positions(indices=moving_mat_indices)]
friction_initial_velocity_x(0.005, 0.1)
xpos1 = [p[0] for p in sim.get_positions(indices=moving_mat_indices)]
xdiff = []
for i in range(0, len(xpos0)):
xdiff.append(xpos1[i] - xpos0[i])
out = open('ownpos.txt', 'w')
for i in range(0, len(xpos0)):
out.write('{0}\n'.format(xpos0[i], xpos1[i]))
out.close()
print('All done, generating simulation file.')
print(sim.get_avg_forces(moving_mat_indices))
sim.write_positions_to_file(indices=moving_mat_indices)
sim.write_average_position_to_file(indices=moving_mat_indices)
sim.write_velocities_to_file(indices=moving_mat_indices)
ft.trajectory_to_xyz()
#=====================
#>>>>> MAIN 2 <<<<<<<<
#=====================
#sim = ft.FrictionSimulation()
## Calculate thresholds for being in touch with the surface
#contact_threshold = math.ceil(10.0 / float(moving_slab_xy)) * moving_slab_z
#velocity_threshold_x = 0.04
## Create the two slabs and store their indices
## TODO: Edit to use z-config
#sim.create_slab(element=fixed_slab_material, xy_cells=fixed_slab_xy, z_cells=2, top_z=0.0)
#sim.create_slab(element=moving_slab_material, xy_cells=moving_slab_xy, z_cells=2, bottom_z=5.0)
#fixed_mat_indices = sim.get_indices_by_element(fixed_slab_material)
#moving_mat_indices = sim.get_indices_by_element(moving_slab_material)
## TODO: Edit to use z-config
#bottom_indices = sim.get_indices_z_less_than(-2) # Bottom row of fixed materials atoms
#top_indices = sim.get_indices_z_more_than(8.0) # Top row of moving materials atoms
## Create interactions
#create_lj_interactions(element_lj_strengths)
#create_coulomb_interactions(element_charges) # Currently too slow!
## Create dynamics and configure the setup
#sim.create_dynamics(dt=1.0, temperature=300)
## Fix the bottom slab and make the top slab move down
#sim.fix_positions(bottom_indices)
#sim.add_constant_force(top_indices, [0, 0, -0.1])
## sim.fix_velocities(top_indices, [0, 0, -0.005], [True, True, True])
#sim.set_temperature(300) # Try to reset the temperature
## Save tmps, print stats and time the simulation
#sim.save_trajectory_during_simulation(interval=50.0)
#sim.print_stats_during_simulation(interval=50.0)
#t0 = time.time()
#print('Starting the simulation')
#while len(sim.get_indices_z_more_than(contact_threshold)):
#print(len(sim.get_indices_z_more_than(contact_threshold)))
#print(sim.get_avg_velocity(moving_mat_indices))
#sim.run_simulation(500)
#print('Moving slab hit the fixed slab.')
#print('Starting friction measurement phase.')
#friction_constant_velocity_x([initial_velocity, 0.0, 0.0])
#print('All done, generating simulation file.')
#ft.trajectory_to_xyz()
def init_simulation(simulation_time=1000,
element_surf='Au',
dims_surf=(20, 8, 5),
element_obj='C',
dims_obj=(3, 3, 3),
set_force=[0.0, 0.0, -0.02],
set_interval=10,
root_path='/u/76/tolland1/unix/Desktop/',
set_folder_name='initialise_number'):
"""
Initialises a surface without periodic boundary conditions and a brick on top of the surface:
:param simulation_time: Simulation time
:param element_surf: Chemical symbol for the surface element.
:param dims_surf: Dimensions in (x, y, z) format
:param element_obj: Chemical symbol for the object element.
:param dims_obj: Dimensions in (x, y, z) format
:param set_force: Force acting on the object.
:param set_interval: Interval for gathering data. (How often the gathered data is saved.)
:param root_path: Root path for saving data.
:param set_folder_name: The folder where the simulations is initialised. If already exists, existing one is overwritten
:return: Trajectory of the initialised simulation saved in the folder defined.
"""
# Lennard-Jones constants
lennardjones_surf = [1.0, 1.414]
lennardjones_obj = [1.0, 1.414]
lennardjones_surfojb = [0.1, 1.414]
'''
Define the initialise folder and save it to initialise.pkl
Save simulation details and sate to file
'''
folder_path = root_path + set_folder_name + '/'
et.init_dir(path=folder_path)
output = open('initialise.pkl', 'wb')
pickle.dump(obj=folder_path, file=output)
output.close()
configs = [element_surf,
dims_surf,
element_obj,
dims_obj,
set_force,
lennardjones_surf,
lennardjones_obj,
lennardjones_surfojb]
output = open(folder_path + 'simulation_config.pkl', 'wb')
pickle.dump(obj=configs, file=output)
output.close()
date_and_time = datetime.datetime.today()
get_date = date_and_time.strftime('%d.%m.%Y')
get_time = date_and_time.strftime('%H:%M:%S')
output = open(folder_path + 'info.txt', 'w')
info = 'Date: {0}\nTime: {1}\nSimulation time: {2}\nSurface: {3} {4}\nObject: {5} {6}\nForce: {7}'
output.write(info.format(get_date,
get_time,
simulation_time,
element_surf,
dims_surf,
element_obj,
dims_obj,
set_force))
output.close()
'''
Simulation
'''
simulation = ft.FrictionSimulation()
'''
Non-periodic Surface.
Bottom of the surface is fixed in its initial position.
'''
positions_surf = et.brick(x_width=dims_surf[0],
y_width=dims_surf[1],
z_width=dims_surf[2],
x_pos=0,
y_pos=0,
z_pos=-2 * dims_surf[2])
simulation.create_atoms(element=element_surf,
positions=positions_surf)
# Fix positions of the bottom
bottom_indices = simulation.get_indices_z_less_than(z_limit=-2 * dims_surf[2] + 0.5)
simulation.fix_positions(indices=bottom_indices, xyz=[True, True, True])
# For restricting thermostat
indices_surf_unfixed = simulation.get_indices_z_more_than(z_limit=-2 * dims_surf[2])
'''
Object.
'''
positions_obj = et.brick(x_width=dims_obj[0],
y_width=dims_obj[1],
z_width=dims_obj[2],
x_pos=2,
y_pos=dims_surf[1] - dims_obj[1],
z_pos=2)
simulation.create_atoms(element=element_obj,
positions=positions_obj)
indices_obj = simulation.get_indices_by_element(element=element_obj)
# Force
if set_force is None:
print 'Force is not set.\nRemember to add a force when running the actual simulation'
else:
simulation.add_constant_force(indices=indices_obj, force=set_force)
# Interacting lennard-jones forces between the particles.
simulation.create_interaction([element_surf, element_surf],
strength=lennardjones_surf[0],
equilibrium_distance=lennardjones_surf[1])
simulation.create_interaction([element_obj, element_obj],
strength=lennardjones_obj[0],
equilibrium_distance=lennardjones_obj[1])
simulation.create_interaction([element_surf, element_obj],
strength=lennardjones_surfojb[0],
equilibrium_distance=lennardjones_surfojb[1])
simulation.list_atoms()
simulation.create_dynamics(dt=1.0,
temperature=300,
coupled_indices=indices_surf_unfixed,
strength=0.01)
# Trajectory
simulation.save_trajectory_during_simulation(interval=set_interval,
filename=folder_path + 'simulation.traj')
simulation.print_stats_during_simulation(interval=5.0)
# Time the simulation
t0 = time.time()
simulation.run_simulation(time=simulation_time)
t1 = time.time()
runtime = "{ti} s".format(ti=str(int(t1 - t0)))
output = open(folder_path + 'info.txt', 'a')
output.write('\nRuntime: {0}'.format(runtime))
output.close()
print 'Time taken {0}'.format(runtime)
# Convert .traj to .xyz
ft.trajectory_to_xyz(filename_in=folder_path + 'simulation.traj',
filename_out=folder_path + 'simulation.xyz')
def read_and_run_simulation(simulation_time=1000,
set_velocity=[0.50, 0.0, 0.0],
set_force=None,
set_interval=1,
root_path='/u/76/tolland1/unix/Desktop/',
set_folder_name='simulation_number'):
"""
Run a simulation from initialised trajectory.
:param simulation_time: Simulation time
:param set_velocity: The velocity given to object.
:param set_force: The force acting on the object. Default is None, which loads the force used in the initialising. If value is given it will be used instead of the force in the initialisement.
:param set_interval: Interval for gathering data. (How often the gathered data is saved.)
:param root_path: Root path for saving data.
:param set_folder_name: The folder where the simulations is saved. If already exists, existing one is overwritten
:return: Trajectory of the simulation saved in the folder defined.
"""
# Initialise folder to root path
folder_path = root_path + set_folder_name + '/'
et.init_dir(path=folder_path)
# load initialised simulation
infile = open('initialise.pkl', 'rb')
folder_load = pickle.load(file=infile)
infile.close()
infile = open(folder_load + 'simulation_config.pkl', 'rb')
configs = pickle.load(file=infile)
infile.close()
[
element_surf, dims_surf, element_obj, dims_obj, get_force,
lennardjones_surf, lennardjones_obj, lennardjones_surfojb
] = configs
if set_force is None:
set_force = get_force
date_and_time = datetime.datetime.today()
get_date = date_and_time.strftime('%d.%m.%Y')
get_time = date_and_time.strftime('%H:%M:%S')
output = open(folder_path + 'info.txt', 'w')
info = 'Date: {0}\nTime: {1}\nSimulation time: {2}\nSurface: {3} {4}\nObject: {5} {6}\nForce: {7}\nVelocity: {8}'
output.write(
info.format(get_date, get_time, simulation_time, element_surf,
dims_surf, element_obj, dims_obj, set_force, set_velocity))
output.close()
'''
Simulation
'''
simulation = ft.FrictionSimulation()
simulation.continue_from_trajectory(filename=folder_load +
'simulation.traj')
# Fix positions of the bottom slab
bottom_indices = simulation.get_indices_z_less_than(
z_limit=-2 * dims_surf[2] + 0.1)
simulation.fix_positions(indices=bottom_indices, xyz=[True, True, True])
# For restricting thermostat
indices_surf_unfixed = simulation.get_indices_z_more_than(z_limit=-2 *
dims_surf[2])
# Velocities
indices_obj = simulation.get_indices_by_element(element=element_obj)
velocities_obj = np.ones([len(indices_obj), 3], dtype='float')
velocities_obj = velocities_obj * np.array(set_velocity)
simulation.set_velocities(indices=indices_obj, velocity=velocities_obj)
# Force
if set_force is None:
print 'Force is not set.'
else:
simulation.add_constant_force(indices=indices_obj, force=set_force)
# Interacting lennard-jones forces between the particles.
simulation.create_interaction([element_surf, element_surf],
strength=lennardjones_surf[0],
equilibrium_distance=lennardjones_surf[1])
simulation.create_interaction([element_obj, element_obj],
strength=lennardjones_obj[0],
equilibrium_distance=lennardjones_obj[1])
simulation.create_interaction([element_surf, element_obj],
strength=lennardjones_surfojb[0],
equilibrium_distance=lennardjones_surfojb[1])
#
simulation.list_atoms()
#
simulation.create_dynamics(dt=1.0,
temperature=300,
coupled_indices=indices_surf_unfixed,
strength=0.01)
# Trajectory
simulation.save_trajectory_during_simulation(interval=set_interval,
filename=folder_path +
'simulation.traj')
# Energy and Temperature
simulation.gather_energy_and_temperature_during_simulation(
interval=set_interval, filename=folder_path + 'energy.txt')
# Work
simulation.gather_total_work_during_simulation(
interval=set_interval,
indices=indices_surf_unfixed,
filename=folder_path + 'work_tot_surf.txt')
simulation.gather_total_work_during_simulation(interval=set_interval,
indices=indices_obj,
filename=folder_path +
'work_tot_obj.txt')
# Average positions
simulation.gather_average_position_during_simulation(
interval=set_interval,
filename=folder_path + 'avr_positions_surf.txt',
indices=indices_surf_unfixed)
simulation.gather_average_position_during_simulation(
interval=set_interval,
filename=folder_path + 'avr_positions_obj.txt',
indices=indices_obj)
# Velocities
simulation.gather_velocities_during_simulation(
interval=simulation_time,
filename=folder_path + 'velocities_surf.txt',
indices=indices_surf_unfixed)
simulation.gather_velocities_during_simulation(interval=simulation_time,
filename=folder_path +
'velocities_obj.txt',
indices=indices_obj)
# Print Stats during simulation
simulation.print_stats_during_simulation(interval=5.0)
# Time the simulation
t0 = time.time()
simulation.run_simulation(time=simulation_time)
t1 = time.time()
runtime = "{ti} s".format(ti=str(int(t1 - t0)))
output = open(folder_path + 'info.txt', 'a')
output.write('\nRuntime: {0}'.format(runtime))
output.close()
print 'Time taken {0}'.format(runtime)
# Convert .traj to .xyz
ft.trajectory_to_xyz(filename_in=folder_path + 'simulation.traj',
filename_out=folder_path + 'simulation.xyz')
constraint = 0
if constraint == 1:
# prevent the gold slab from moving
simu.fix_positions(au_indices)
elif constraint == 2:
# prevent the bottom of the gold slab from moving
simu.fix_positions(bottom_indices)
elif constraint == 3:
# create 'ghost' atoms at the bottom of the slab and attach the bottom to them
simu.duplicate_atoms(element='C', indices=bottom_indices)
c_indices = simu.get_indices_by_element('C')
simu.attach_with_springs(c_indices,
bottom_indices,
strength=1.0,
cutoff=3.0)
simu.fix_positions(c_indices)
# time the simulation
import time
t0 = time.time()
print "starting simulation"
simu.run_simulation(time=2000.0)
print "finished simulation"
t1 = time.time()
print "time taken {ti} s".format(ti=str(int(t1 - t0)))
ft.trajectory_to_xyz(filename_out='simulation-diffa.xyz')