def testForceAgainstDefaultNeighborList(self):
atoms = Diamond(symbol="C", pbc=False)
builtin = torchani.neurochem.Builtins()
calculator = torchani.ase.Calculator(builtin.species,
builtin.aev_computer,
builtin.models,
builtin.energy_shifter)
default_neighborlist_calculator = torchani.ase.Calculator(
builtin.species, builtin.aev_computer, builtin.models,
builtin.energy_shifter, True)
atoms.set_calculator(calculator)
dyn = Langevin(atoms, 5 * units.fs, 50 * units.kB, 0.002)
def test_energy(a=atoms):
a = a.copy()
a.set_calculator(calculator)
e1 = a.get_potential_energy()
a.set_calculator(default_neighborlist_calculator)
e2 = a.get_potential_energy()
self.assertLess(abs(e1 - e2), tol)
dyn.attach(test_energy, interval=1)
dyn.run(500)
def get_dynamics(atoms, mcfm_pot, T=300):
# ------ Set up logfiles
traj_interval = 10
thermoPrintstatus_log = open("log_thermoPrintstatus.log", "w")
outputTrajectory = open("log_trajectory.xyz", "w")
mcfmError_log = open("log_mcfmError.log", "w")
# ------ Let optimiser use the base potential and relax the per atom energies
mcfm_pot.qm_cluster.flagging_module.ema_parameter = 0.1
mcfm_pot.qm_cluster.flagging_module.qm_flag_potential_energies =\
np.ones((len(atoms), 2), dtype=float) * 1001
# ------ Minimize positions
opt = FIRE(atoms)
optimTrajectory = open("log_optimizationTrajectory.xyz", "w")
opt.attach(trajectory_writer, 1, atoms, optimTrajectory, writeResults=True)
opt.run(fmax=0.05, steps=1000)
# ------ Define ASE dyamics
sim_T = T * units.kB
MaxwellBoltzmannDistribution(atoms, 2 * sim_T)
timestep = 5e-1 * units.fs
friction = 1e-2
dynamics = Langevin(atoms, timestep, sim_T, friction, fixcm=False)
dynamics.attach(mcfm_thermo_printstatus, 100, 100, dynamics,
atoms, mcfm_pot, logfile=thermoPrintstatus_log)
dynamics.attach(trajectory_writer, traj_interval, atoms, outputTrajectory, writeResults=False)
dynamics.attach(mcfm_error_logger, 100, 100, dynamics, atoms, mcfm_pot, logfile=mcfmError_log)
return dynamics
def smash_it(system):
"""Run a simple NVT molecular dynamics simulation for 0.1 ps at 200 k using
the effective medium theory on a supplied system.
Parameters
----------
system : `ase.Atoms`
The system that is to be simulated.
Returns
-------
traj : `list` [`ase.Atoms`]
A list of `ase.Atoms` objects comprising the system's trajectory.
"""
# Tell the system to use the EMT calculator
system.set_calculator(EMT())
# Set up the NVT simulation using the Langevin thermostat
dyn = Langevin(system, 0.01 * units.fs, 200 * units.kB, 0.002)
# Create a list to hold the trajectory & a function to populate it
traj = []
def update_traj(a=system):
traj.append(a.copy())
# Attach the trajectory populator
dyn.attach(update_traj, interval=10)
# Run the molecular dynamics simulation from 10000 steps
dyn.run(10000)
# Return the trajectory
return traj
def run_md(self, f, Tmax, steps, n_steps, nmfile=None, displacement=0, min_steps=0, sig=0.34, t=0.1, nm=0, record=False):
X, S, Na, cm = hdt.readxyz2(f)
if nmfile != None:
mode=self.get_mode(nmfile, Na, mn=nm)
X=X+mode*np.random.uniform(-displacement,displacement)
X=X[0]
mol=Atoms(symbols=S, positions=X)
mol.set_calculator(ANIENS(self.net,sdmx=20000000.0))
f=os.path.basename(f)
T_eff = float(random.randrange(5, Tmax, 1)) # random T (random velocities) from 0K to TK
minstep_eff = float(random.randrange(1, min_steps, 1)) # random T (random velocities) from 0K to TK
dyn = Langevin(mol, t * units.fs, T_eff * units.kB, 0.01)
MaxwellBoltzmannDistribution(mol, T_eff * units.kB)
# steps=10000 #10000=1picosecond #Max number of steps to run
# n_steps = 1 #Number of steps to run for before checking the standard deviation
hsdt_Na=[]
evkcal=hdt.evtokcal
if record==True: #Records the coordinates at every step of the dynamics
fname = f + '_record_' + str(T_eff) + 'K' + '.xyz' #name of file to store coodinated in
def printenergy(name=fname, a=mol):
"""Function to print the potential, kinetic and total energy."""
fil= open(name,'a')
Na=a.get_number_of_atoms()
c = a.get_positions(wrap=True)
fil.write('%s \n comment \n' %Na)
for j, i in zip(a, c):
fil.write(str(j.symbol) + ' ' + str(i[0]) + ' ' + str(i[1]) + ' ' + str(i[2]) + '\n')
fil.close()
dyn.attach(printenergy, interval=1)
e=mol.get_potential_energy() #Calculate the energy of the molecule. Must be done to get the standard deviation
s=mol.calc.stddev
stddev = 0
tot_steps = 0
failed = False
while (tot_steps <= steps):
if stddev > sig and tot_steps > minstep_eff: #Check the standard deviation
self.hstd.append(stddev)
c = mol.get_positions()
s = mol.get_chemical_symbols()
Na=mol.get_number_of_atoms()
self.Na_train.append(Na)
self.coor_train.append(c)
self.S_train.append(s)
failed=True
break
else: #if the standard deviation is low, run dynamics, then check it again
tot_steps = tot_steps + n_steps
dyn.run(n_steps)
stddev = evkcal*mol.calc.stddev
c = mol.get_positions()
s = mol.get_chemical_symbols()
e=mol.get_potential_energy()
#print("{0:.2f}".format(tot_steps*t),':',"{0:.2f}".format(stddev),':',"{0:.2f}".format(evkcal*e))
return c, s, tot_steps*t, stddev, failed, T_eff
def run_md(atoms, md_temperature = 1000*kB, md_step_size = 1*fs, md_steps=100, md_interval=100, friction=0.02):
natoms=atoms.get_number_of_atoms()
#atoms.set_calculator(self.opt_calculator)
atoms_md = []
e_log = []
atoms_md.append(atoms.copy())
MaxwellBoltzmannDistribution(atoms=atoms, temp=md_temperature)
dyn = Langevin(atoms, md_step_size, md_temperature, friction)
def md_log(atoms=atoms):
atoms_md.append(atoms.copy())
epot=atoms.get_potential_energy()
ekin=atoms.get_kinetic_energy()
temp = ekin / (1.5 * kB * natoms)
e_log.append([epot, ekin, temp])
traj = Trajectory('Au_md.traj', 'w', atoms) # Output MD trajectory before it is treatment
dyn.attach(traj.write, interval=10)
dyn.attach(md_log, interval=md_interval)
dyn.run(md_steps)
return atoms_md, e_log
def md_calculation(fcp_file):
from ase import units
from ase.io.trajectory import Trajectory
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.langevin import Langevin
from ase.md import MDLogger
if 'fcc' in fcp_file:
ref_cell = read(ref_fcc)
P = np.array([[-1, 1, 1], [1, -1, 1], [1, 1, -1]])
P *= 3
atoms = make_supercell(ref_cell, P)
else:
raise ValueError("Unknown phase")
fcp = ForceConstantPotential.read(fcp_file)
fcs = fcp.get_force_constants(atoms)
calc = ForceConstantCalculator(fcs)
atoms.set_calculator(calc)
temperature = 200
number_of_MD_steps = 100
time_step = 5 # in fs
dump_interval = 10
traj_file = "data/md_" + fcp_file.split('.')[0] + '{}.traj'.format(
temperature)
log_file = "data/md_log_{}.log".format(temperature)
dyn = Langevin(atoms, time_step * units.fs, temperature * units.kB, 0.02)
logger = MDLogger(dyn,
atoms,
log_file,
header=True,
stress=False,
peratom=True,
mode='w')
traj_writer = Trajectory(traj_file, 'w', atoms)
dyn.attach(logger, interval=dump_interval)
dyn.attach(traj_writer.write, interval=dump_interval)
# run MD
MaxwellBoltzmannDistribution(atoms, temperature * units.kB)
dyn.run(number_of_MD_steps)
def test_usage(self):
atoms = fcc111('Al', size=(4, 4, 9), orthogonal=True)
atoms.set_pbc(True)
atoms.center(axis=2, vacuum=10.0)
z = atoms.positions[:, 2]
top_mask = z > z[115] - 0.1
bottom_mask = z < z[19] + 0.1
calc = EMT()
atoms.calc = calc
damping = pc.AutoDamping(C11=500 * GPa, p_c=0.2)
Pdir = 2
vdir = 0
P = 5 * GPa
v = 100.0 * m / s
dt = 1.0 * fs
T = 400.0
t_langevin = 75 * fs
gamma_langevin = 1. / t_langevin
slider = pc.SlideWithNormalPressureCuboidCell(top_mask, bottom_mask,
Pdir, P, vdir, v,
damping)
atoms.set_constraint(slider)
MaxwellBoltzmannDistribution(atoms, 2 * kB * T)
atoms.arrays['momenta'][top_mask, :] = 0
atoms.arrays['momenta'][bottom_mask, :] = 0
handle = StringIO()
beginning = handle.tell()
temps = np.zeros((len(atoms), 3))
temps[slider.middle_mask, slider.Tdir] = kB * T
gammas = np.zeros((len(atoms), 3))
gammas[slider.middle_mask, slider.Tdir] = gamma_langevin
integrator = Langevin(atoms, dt, temps, gammas, fixcm=False)
logger = pc.SlideLogger(handle, atoms, slider, integrator)
logger.write_header()
logger()
images = []
integrator.attach(logger)
integrator.attach(lambda: images.append(atoms.copy()))
integrator.run(50)
handle.seek(beginning)
pc.SlideLog(handle)
handle.close()
def md_run(origin_poscar_path, index):
print('%d' % index + ' In directory : %s' % origin_poscar_path)
atoms = read(origin_poscar_path)
calc = ANNCalculator(potentials={
"Ga": "Ga.10t-10t.nn",
"N": "N.10t-10t.nn"
})
atoms.set_calculator(calc)
MaxwellBoltzmannDistribution(atoms, 1200 * kB)
Stationary(atoms)
md = NVT(atoms, timestep=2 * fs, temperature=1000 * kB, friction=0.05)
logger = MDLogger(md, atoms, '-', stress=True)
md.attach(logger, interval=1)
traj = Trajectory(
"nvt_%s.traj" % (origin_poscar_path.split('/')[-1].split('.xsf')[0]),
"w", atoms)
md.attach(traj.write, interval=200)
md.run(40000)
def MD():
old_stdout = sys.stdout
sys.stdout = mystdout = StringIO()
orig_stdout = sys.stdout
f = open('out.txt', 'w')
sys.stdout = f
#f = open('out_' + str(temp) + '.txt', 'w')
#sys.stdout = f
Tmin = 1000
Tmax = 15000
a0 = 5.43
N = 1
atoms = Diamond(symbol='Si', latticeconstant=a0)
atoms *= (N, N, N)
atoms.set_calculator(model.calculator)
MaxwellBoltzmannDistribution(atoms, Tmin * units.kB) ###is this allowed?
Stationary(atoms) # zero linear momentum
ZeroRotation(atoms)
def printenergy(a=atoms):
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print(ekin)
traj = Trajectory('Si.traj', 'w', atoms)
for temp in np.linspace(Tmin, Tmax, 5):
dyn = Langevin(atoms, 5 * units.fs, units.kB * temp, 0.002)
dyn.attach(traj.write, interval=1)
dyn.attach(printenergy, interval=1)
dyn.run(100)
sys.stdout = orig_stdout
f.close()
def get_dynamics(atoms, mcfm_pot, T=300):
# ------ Set up logfiles
traj_interval = 10
thermoPrintstatus_log = open("log_thermoPrintstatus.log", "w")
outputTrajectory = open("log_trajectory.xyz", "w")
mcfmError_log = open("log_mcfmError.log", "w")
# ------ Let optimiser use the base potential and relax the per atom energies
mcfm_pot.qm_cluster.flagging_module.ema_parameter = 0.1
mcfm_pot.qm_cluster.flagging_module.qm_flag_potential_energies =\
np.ones((len(atoms), 2), dtype=float) * 1001
# ------ Minimize positions
opt = FIRE(atoms)
optimTrajectory = open("log_optimizationTrajectory.xyz", "w")
opt.attach(trajectory_writer, 1, atoms, optimTrajectory, writeResults=True)
opt.run(fmax=0.05, steps=1000)
# ------ Define ASE dyamics
sim_T = T * units.kB
MaxwellBoltzmannDistribution(atoms, 2 * sim_T)
timestep = 5e-1 * units.fs
friction = 1e-2
dynamics = Langevin(atoms, timestep, sim_T, friction, fixcm=False)
dynamics.attach(mcfm_thermo_printstatus,
100,
100,
dynamics,
atoms,
mcfm_pot,
logfile=thermoPrintstatus_log)
dynamics.attach(trajectory_writer,
traj_interval,
atoms,
outputTrajectory,
writeResults=False)
dynamics.attach(mcfm_error_logger,
100,
100,
dynamics,
atoms,
mcfm_pot,
logfile=mcfmError_log)
return dynamics
bottom_mask = np.loadtxt("bottom_mask.txt").astype(bool)
top_mask = np.loadtxt("top_mask.txt").astype(bool)
damp = pc.AutoDamping(C11, p_c)
slider = pc.SlideWithNormalPressureCuboidCell(top_mask, bottom_mask, Pdir, P,
vdir, v, damp)
atoms.set_constraint(slider)
calc = ASE_CALCULATOR_OBJECT # put a specific calculator here
atoms.set_calculator(calc)
temps = np.zeros((len(atoms), 3))
temps[slider.middle_mask, slider.Tdir] = kB * T
gammas = np.zeros((len(atoms), 3))
gammas[slider.middle_mask, slider.Tdir] = gamma_langevin
integrator = Langevin(atoms, dt, temps, gammas, fixcm=False)
trajectory = Trajectory('slide.traj', 'a', atoms) # append
with open('log_slide.txt', 'r', encoding='utf-8') as log_handle:
step_offset = pc.SlideLog(log_handle).step[-1]
log_handle = open('log_slide.txt', 'a', 1,
encoding='utf-8') # line buffered append
logger = pc.SlideLogger(log_handle, atoms, slider, integrator, step_offset)
integrator.attach(logger)
integrator.attach(trajectory)
integrator.run(steps_integrate)
log_handle.close()
trajectory.close()
size=(size, size, size),
pbc=True,
latticeconstant=3.5646)
view(atoms)
atoms.set_calculator(calc)
# MaxwellBoltzmannDistribution(atoms, 300 * units.kB)
# dyn = VelocityVerlet(atoms, 5 * units.fs)
T = 10
dyn = Langevin(atoms, 5 * units.fs, T * units.kB, 0.002)
traj = Trajectory('md.traj', 'w', atoms)
dyn.attach(traj.write, interval=50)
def printenergy(a):
"""Function to print the potential, kinetic and total energy"""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
printenergy(atoms)
for i in range(200):
dyn.run(50)
printenergy(atoms)
# os.makedirs(dumpVASP)
kspacing = 0.2
steps = 10
temp = 300
struc = bulk("Si", 'diamond', a=5.468728, cubic=True) * (3,3,3)
mliap = "potentials/Si-20-20.pth"
ff = PyXtal_FF(model={'system': ["Si"]}, logo=False)
ff.run(mode='predict', mliap=mliap)
calc = PyXtalFFCalculator(ff=ff)
struc.set_calculator(calc)
#struc.set_calculator(set_vasp('single', kspacing))
#energy, forces = dft_run(struc, path=dumpVASP, ncpu=16, max_time=10) # total energy
# MD
traj = Trajectory("Si.traj", 'w', struc)
MaxwellBoltzmannDistribution(struc, temperature_K=temp+50)
# NVT
dyn = Langevin(struc, timestep=0.15 * units.fs, temperature_K=temp, friction=0.004 * units.fs)
# NPT
#dyn = NPT(struc, 1. * units.fs, externalstress=0., ttime=1000*units.fs, pfactor=1000*units.fs,
# temperature_K=300)
dyn.attach(traj.write, interval=steps)
for i in range(1000):
dyn.run(steps=steps)
PrintEnergy(struc, i)
save_to_ASE_db(struc, path=ase_db)
traj.close()
if k not in ['energy', 'strain']:
del at.info[k]
# ***** Setup and run MD *****
# Initialise the dynamical system
initial_momenta = at.get_momenta()
dynamics = Langevin(at,
params.timestep,
params.sim_T * units.kB,
8e-4,
logfile=log_name)
# Save frames to the trajectory every `traj_interval` time steps
out = AtomsWriter(traj_name)
def trajectory_write(at):
atout = at.copy()
for k in atout.arrays.keys():
if k not in ['species', 'positions', 'momenta', 'numbers', 'force']:
atout.set_array(k, None)
for k in atout.info.keys():
if k not in ['energy', 'time', 'temperature', 'pbc', 'Lattice']:
del atout.info[k]
at.info['energy'] = at.get_potential_energy()
out.write(atout)
dynamics.attach(trajectory_write, params.traj_interval, at) # Save trajectory
#!simulation outputs numbered, avoids deleting exisiting results
iterFile = open("simIteration.txt", 'r+')
iteration = int(iterFile.readlines()[0]) + 1
iterFile.seek(0, 0)
iterFile.write(str(iteration))
iterFile.close()
#!Saving parameter values for each iteration of the simulation
logFile = open(".simout/logs/log" + str(iteration) + ".txt", 'w')
for p, value in params.p.iteritems():
logFile.write(p + " ==> " + str(value) + "\n")
logFile.close
crack_pos = []
traj = NetCDFTrajectory('.simout/traj' + str(iteration) + '.nc', 'w', c)
dyn.attach(traj.write, 10, dyn.atoms, arrays=['stokes', 'momenta'])
dyn.attach(find_crack_tip,
10,
dyn.atoms,
dt=params.dt * 10,
store=True,
results=crack_pos)
# run for 2000 time steps to reach steady state at initial load
for i in range(20):
dyn.run(100)
if extend_strip(dyn.atoms, params.a, params.N, params.M, params.vacuum):
set_constraints(dyn.atoms, params.a)
# start decreasing strain
#set_constraints(dyn.atoms, params.a, delta_strain=delta_strain)
atoms.set_calculator(mixer)
dyn = None
if md_style == "Langevin":
dyn = Langevin(atoms, timestep, 1.5*T*units.kB, 0.002)
elif md_style == "Verlet":
dyn = VelocityVerlet(atoms, timestep)
elif md_style == "TESTING":
dyn = DynTesting(atoms, timestep=0.1*units.fs, offset=(0.1, 0., 0.))
energy_file = None
def printenergy(a=atoms):
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
energy_file.write("%.5e,%.5e,%.5e,%.5e" %
(epot + ekin, epot, ekin, ekin/(1.5*units.kB)) + "\n")
# only enable logging for master node where rank == 0
if rank == 0:
energy_file = open("mixer_box_energy.csv", "w+b", buffering=0)
energy_file.write("total,potential,kinetic,temperature\n")
dyn.attach(printenergy, interval=log_interval)
traj = PickleTrajectory(output_file, 'w', atoms)
dyn.attach(traj.write, interval=log_interval)
printenergy()
dyn.run(steps)
d = 2.934
for R in r0list:
print 'radius',R
name=(folder,'%.1f' %R)
atoms = fcc111('Au',size=(2,2,1),a=sqrt(2)*d)
L = atoms.get_cell().diagonal()
atoms. set_cell(L)
angle = L[1]/R
atoms.rotate('y',pi/2)
atoms.translate( (-atoms[0].x,0,0) )
atoms.translate((R,0,0))
atoms = Atoms(atoms=atoms,container='Wedge')
atoms.set_container(angle=angle,height=L[0],physical=False,pbcz=True)
calc = Hotbit(SCC=False,txt='%s/optimization_%s.cal' %name,kpts=(nk,1,nk),physical_k=False)
atoms.set_calculator(calc)
traj = PickleTrajectory( 'md_R%.3f-T%.0f.traj' %(R,T),'w',atoms)
dyn = Langevin(atoms,dt*units.fs,units.kB*T,fric)
dyn.attach(MDLogger(dyn, atoms, path + 'md_R%.3f-T%.0f.log' %(R,T), header=False, stress=False,
peratom=True, mode="w"), interval = 1)
dyn.run(mdsteps)
cohesion = mean([atoms.get_potential_energy() for a in traj]) /len(atoms)
savez('%s/data_%s.npz' %name,cohesion=cohesion)
io.write('%s/extended_%s.traj' %name,atoms2)
symbol="Cu",
size=(size, size, size),
pbc=False)
# Describe the interatomic interactions with the Effective Medium Theory
atoms.set_calculator(EMT())
# We want to run MD with constant energy using the Langevin algorithm
# with a time step of 5 fs, the temperature T and the friction
# coefficient to 0.02 atomic units.
dyn = Langevin(atoms, 5 * units.fs, T * units.kB, 0.002)
def printenergy(a=atoms): # store a reference to atoms in the definition.
"""Function to print the potential, kinetic and total energy."""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
dyn.attach(printenergy, interval=50)
# We also want to save the positions of all atoms after every 100th time step.
traj = Trajectory('moldyn3.traj', 'w', atoms)
dyn.attach(traj.write, interval=50)
# Now run the dynamics
printenergy()
dyn.run(5000)
dyn = None
if md_style == "Langevin":
dyn = Langevin(atoms, timestep, 1.5 * T * units.kB, 0.002)
elif md_style == "Verlet":
dyn = VelocityVerlet(atoms, timestep)
elif md_style == "TESTING":
dyn = DynTesting(atoms, timestep=0.1 * units.fs, offset=(0.1, 0., 0.))
energy_file = None
def printenergy(a=atoms):
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
energy_file.write("%.5e,%.5e,%.5e,%.5e" % (epot + ekin, epot, ekin, ekin /
(1.5 * units.kB)) + "\n")
# only enable logging for master node where rank == 0
if rank == 0:
energy_file = open("mixer_box_energy.csv", "w+b", buffering=0)
energy_file.write("total,potential,kinetic,temperature\n")
dyn.attach(printenergy, interval=log_interval)
traj = PickleTrajectory(output_file, 'w', atoms)
dyn.attach(traj.write, interval=log_interval)
printenergy()
dyn.run(steps)
# Now let's set the calculator for ``atoms``:
atoms.set_calculator(calculator)
# Now let's minimize the structure:
print("Begin minimizing...")
opt = BFGS(atoms)
opt.run(fmax=0.001)
print()
# Now create a callback function that print interesting physical quantities:
def printenergy(a=atoms):
"""Function to print the potential, kinetic and total energy."""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print('Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV' % (epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
# We want to run MD with constant energy using the Langevin algorithm
# with a time step of 1 fs, the temperature 300K and the friction
# coefficient to 0.02 atomic units.
dyn = Langevin(atoms, 1 * units.fs, 300 * units.kB, 0.2)
dyn.attach(printenergy, interval=50)
# Now run the dynamics:
print("Beginning dynamics...")
printenergy()
dyn.run(500)
T = 1500 # Kelvin
# Set up a crystal
atoms = FaceCenteredCubic(directions=[[1,0,0],[0,1,0],[0,0,1]], symbol="Cu",
size=(size,size,size), pbc=False)
# Describe the interatomic interactions with the Effective Medium Theory
atoms.set_calculator(EMT())
# We want to run MD with constant energy using the Langevin algorithm
# with a time step of 5 fs, the temperature T and the friction
# coefficient to 0.02 atomic units.
dyn = Langevin(atoms, 5*units.fs, T*units.kB, 0.002)
#Function to print the potential, kinetic and total energy.
def printenergy(a=atoms): #store a reference to atoms in the definition.
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
print ("Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) Etot = %.3feV" %
(epot, ekin, ekin/(1.5*units.kB), epot+ekin))
dyn.attach(printenergy, interval=50)
#We also want to save the positions of all atoms after every 100th time step.
traj = PickleTrajectory("moldyn3.traj", 'w', atoms)
dyn.attach(traj.write, interval=50)
# Now run the dynamics
printenergy()
dyn.run(5000)
def sphereDynamics(R, T, params):
d = params['d'] #2.934
nk = params['nk'] #20
fmax = params['fmax'] #1E-2
fric = params['fric'] #0.002 # equilibration time tau = 10 fs/fric (= mdsteps*dt)
dt = params['dt'] #5.0
mdsteps = params['mdsteps'] #int(10/fric/dt)
path = params['path'] #'/space/tohekorh/Au_bend/files/'
uzsize = params['uz_size']
print 'radius',R
name = '%.1f' %R
# ATOMS
#atoms = fcc111('Au',size=uzsize,a=np.sqrt(2)*d)
atoms = get_opmAtomsFlat(T, params)
atoms.rotate((0,0,1), -np.pi/6, rotate_cell = True)
length1 = np.linalg.norm( atoms.get_cell()[0] )
length2 = np.linalg.norm( atoms.get_cell()[1] )
n1 = ( np.cos(np.pi/3), np.sin(np.pi/3), 0)
n2 = (-np.cos(np.pi/3), np.sin(np.pi/3), 0)
angle1 = length1/R
angle2 = length2/R
#view(atoms)
# Scale the atoms close to ball
Lx = np.linalg.norm(atoms.get_cell()[0] + atoms.get_cell()[1])
Ly = np.linalg.norm(atoms.get_cell()[0] - atoms.get_cell()[1])
phi_max = Ly/R
theta_max = Lx/R
for a in atoms:
r0 = a.position
phi = r0[1]/Ly*phi_max
theta = r0[0]/Lx*theta_max
a.position[0] = R*np.sin(theta) #*np.sin(theta)
a.position[1] = R*np.sin(phi) #a.position[1] #R*np.sin(phi) #*np.sin(theta)
a.position[2] = R*np.cos(theta)
#atoms.translate((0,0,R))
# End scaling
atoms = Atoms(atoms=atoms,container='Sphere')
atoms.set_container(angle1=angle1,angle2=angle2,n1=n1,n2=n2,mode=4)
#view(atoms.extended_copy((2,2,1)))
# FOLDERS
path_md = path + 'sphere/md_data/T=%.0f/' %T
path_opm= path + 'sphere/opm/T=%.0f/' %T
checkAndCreateFolder(path_md)
checkAndCreateFolder(path_opm)
# CALCULATOR
calc = Hotbit(SCC=False, kpts=(nk,nk,1),txt= path_opm + 'optimization_%s.cal' %name,)
atoms.set_calculator(calc)
# RELAX
opt = BFGS(atoms, trajectory= path_opm + 'optimization_%s.traj' %name)
opt.run(fmax=fmax,steps=1000)
#write(path_opm + 'opm_structure_R%.3f' %R, atoms, format='traj')
# DYNAMICS
traj = PickleTrajectory(path_md + 'md_R%.3f.traj' %R, 'w', atoms)
dyn = Langevin(atoms, dt*units.fs, units.kB*T,fric)
dyn.attach(MDLogger(dyn, atoms, path_md + 'md_R%.3f.log' %R, header=True, stress=False,
peratom=True, mode="w"), interval = 1)
dyn.attach(traj.write)
dyn.run(mdsteps)
traj.close()
# load the dynamics back.. To write the extended trajectory
traj = PickleTrajectory(path_md + 'md_R%.3f.traj' %R)
trajToExtTraj(traj, (2, 2, 1), R, T, angle1, angle2, n1, n2, path)
def cylinderDynamics(R, T, params):
nk = params['nk'] #20
fmax = params['fmax'] #1E-2
fric = params['fric'] #0.002
dt = params['dt'] #5.0
mdsteps = params['mdsteps'] #int(10/fric/dt)
path = params['path'] #'/space/tohekorh/Au_bend/files/'
print 'radius',R, '\n'
name = '%.1f' %R
# Get the optimal flat atoms , unit-cell config for this temperature:
atoms = get_opmAtomsFlat(T, params)
# Take the diagonal of the cell:
L = atoms.get_cell().diagonal()
atoms.set_cell(L)
# The wedge angle is:
angle = L[1]/R
# fiddle with atoms:
atoms.rotate('y', np.pi/2)
atoms.translate((-atoms[0].x, 0, 0) )
#view(atoms)
# Initial map for atoms, to get the on surface of cylinder:
phi_max = angle
for a in atoms:
r0 = a.position
phi = r0[1]/L[1]*phi_max
a.position[0] = R*np.cos(phi)
a.position[1] = R*np.sin(phi)
#view(atoms)
# proper number of kappa points in angle direction, if angle >= 2*pi/3 the use genuine
# physical boundary conditions and proper kappa-points. With 64 atoms in unit cell souhld not
# happen as the radius -> very small if angle = 2*pi/3 or larger.
# Check that the unit-cell angle is 2*pi/integer. This can be removed!
if (2*np.pi/angle)%1 > 0:
raise
# This does not have any effect unless angle >= 2*pi/3:
m = int(round(2*np.pi/angle))
physical = False
if m <= 3:
nk1 = m
physical = True
else:
nk1 = nk
# Set up the wedge container:
atoms = Atoms(atoms = atoms, container = 'Wedge')
atoms.set_container(angle = angle, height = L[0], physical = physical, pbcz = True)
# Check that everything looks good:
#view(atoms.extended_copy((2,1,2)))
# FOLDERS
path_opm = path + 'cylinder/opm/T=%.0f/' %T
path_md = path + 'cylinder/md_data/T=%.0f/' %T
checkAndCreateFolder(path_opm)
checkAndCreateFolder(path_md)
# CALCULATOR
calc = Hotbit(SCC=False, kpts=(nk1, 1, nk), physical_k = physical, \
txt= path_opm + 'optimization_%s.cal' %name)
atoms.set_calculator(calc)
# RELAX
opt = BFGS(atoms, trajectory= path_opm + 'optimization_%s.traj' %name)
opt.run(fmax=fmax, steps=1000)
# DYNAMICS
traj = PickleTrajectory(path_md + 'md_R%.3f.traj' %R,'w',atoms)
# Perform dynamics
dyn = Langevin(atoms, dt*units.fs, units.kB*T, fric)
dyn.attach(MDLogger(dyn, atoms, path_md + 'md_R%.3f.log' %R, header=True, stress=False,
peratom=True, mode="w"), interval = 1)
dyn.attach(traj.write)
dyn.run(mdsteps)
traj.close()
# load the dynamics back, to make exteded trajectory:
traj = PickleTrajectory(path_md + 'md_R%.3f.traj' %R)
trajToExtTraj(traj, (2, 1, 2), R, T, angle, L[0], path)
