def solve(self):
#Create the initial particle from the defining string/number atoms
self.particle = NanoClass.genParticle(self.definingString, int(self.numberOfAtoms))
self.reCenter()
self.bestEnergy = self.particle.get_potential_energy()
self.bestParticle = deepcopy(self.particle)
# berendsen = NVTBerendsen(self.particle, 2.5 * units.fs, 2000, taut=0.5*100*units.fs)
berendsen = Langevin(self.particle, 5 * units.fs, units.kB * 2000, 0.005)
dyn = FIRE(atoms=self.particle)
MaxwellBoltzmannDistribution(self.particle,2000*units.kB)
CALCULATIONS=100
for i in range(CALCULATIONS):
if i%1==0:
pDone=float(i)/CALCULATIONS
self.setStatusDone(str(math.floor(pDone*100))+"% | "+self.remainingTime(pDone))
self.checkTimeout()
self.setSolution(self.getAnswer())
MaxwellBoltzmannDistribution(self.particle,2000*units.kB)
self.particle.get_potential_energy()
berendsen.run(500)
dyn.run()
self.reCenter()
testEnergy = self.particle.get_potential_energy()
if (testEnergy < self.bestEnergy):
self.bestEnergy = testEnergy
self.bestParticle = deepcopy(self.particle)
elif ((testEnergy + .5) > self.bestEnergy):
self.particle = NanoClass.genParticle(self.definingString, int(self.numberOfAtoms))
MaxwellBoltzmannDistribution(self.particle,2000*units.kB)
self.particle.get_potential_energy()
if (testEnergy < self.bestEnergy):
self.bestEnergy = testEnergy
self.bestParticle = deepcopy(self.particle)
return self.getAnswer()
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 init_dynamics(self, Nm, Nembed, V, L, dt, T):
self.L = L
# Generate the box of junk
self.__generategarbagebox__(Nm, Nembed, L, T)
# Make mol
self.mol = Atoms(symbols=self.S, positions=self.X)
# Set box and PBC
self.mol.set_cell(([[L, 0, 0], [0, L, 0], [0, 0, L]]))
self.mol.set_pbc((True, True, True))
# Set ANI calculator
self.mol.set_calculator(ANIENS(self.aens))
# Open MD output
#self.mdcrd = open(xyzfile, 'w')
# Open MD output
#self.traj = open(trjfile, 'w')
# Set the velocities corresponding to a boltzmann dist @ T/4.0
MaxwellBoltzmannDistribution(self.mol, 300.0 * units.kB)
# Declare Dyn
self.dyn = Langevin(self.mol, dt * units.fs, T * units.kB, 0.1)
def md(molecule, model, device, output, nsteps, temperature, step, friction):
start = time.time()
mm = Mol2(molecule)
pos = mm.get_coordinates()
labels = ''.join(mm.get_symbols())
device = torch.device(device)
if model.lower() == 'ani1x':
model = torchani.models.ANI1x()
elif model.lower() == 'ani1ccx':
model = torchani.models.ANI1ccx()
else:
print("unknwon model {:s}".format(model))
sys.exit(1)
assert isinstance(model, torchani.models.ANI1x) or isinstance(model, torchani.models.ANI1ccx)
atom_group = Atoms(symbols=labels, positions=pos, calculator=model.ase())
print("step {:12d}\tenergy {:12.4f}".format(0, atom_group.get_total_energy()))
dyn = Langevin(atom_group, 1*units.fs, temperature*units.kB, friction)
for i in range(nsteps):
dyn.run(step)
print("step {:12d}\tenergy {:12.4f}".format((i + 1)*step, atom_group.get_total_energy()))
mm.coordinates = atom_group.get_positions()
if output is not None:
mm.write(output + '_{:06d}.mol2'.format(i))
print("time {:12.4f}".format(time.time() - start))
sys.exit(0)
def init_dynamics(self, Nm, V, L, dt, T):
self.L = L
# Generate the box of junk
self.__generategarbagebox__(Nm, L, T)
# Make mol
self.mol = Atoms(symbols=self.S, positions=self.X)
# Set box and PBC
self.mol.set_cell(([[L, 0, 0], [0, L, 0], [0, 0, L]]))
self.mol.set_pbc((True, True, True))
# Set ANI calculator
# Set ANI calculator
self.mol.set_calculator(ANIENS(self.aens))
#self.mol.set_calculator(ANI(False))
#self.mol.calc.setnc(self.ncl[0])
# Give molecules random velocity
acc_idx = 0
vel = np.empty_like(self.X)
for n in self.Na:
rv = np.random.uniform(-V, V, size=(3))
for k in range(n):
vel[acc_idx + k, :] = rv
acc_idx += n
#print(vel)
self.mol.set_velocities(vel)
# Declare Dyn
self.dyn = Langevin(self.mol, dt * units.fs, T * units.kB, 0.1)
def __init__(self, atoms, timestep=None, temperature=None, friction=None,
trajectory=None, **kwargs):
Langevin.__init__(self, atoms, timestep, temperature, friction)
OTF.__init__(self, **kwargs)
self.md_engine = 'Langevin'
def testWithNumericalForceWithPBCEnabled(self):
# Run a Langevin thermostat dynamic for 100 steps and after the dynamic
# check once that the numerical and analytical force agree to a given
# relative tolerance
atoms = Diamond(symbol="C", pbc=True)
calculator = self.model.ase()
atoms.set_calculator(calculator)
dyn = Langevin(atoms, 5 * units.fs, 30000000 * units.kB, 0.002)
dyn.run(100)
f = atoms.get_forces()
fn = get_numeric_force(atoms, 0.001)
self.assertEqual(f, fn, rtol=0.1, atol=0.1)
def testWithNumericalForceWithPBCEnabled(self):
atoms = Diamond(symbol="C", pbc=True)
calculator = torchani.models.ANI1x().ase()
atoms.set_calculator(calculator)
dyn = Langevin(atoms, 5 * units.fs, 30000000 * units.kB, 0.002)
dyn.run(100)
f = torch.from_numpy(atoms.get_forces())
fn = get_numeric_force(atoms, 0.001)
df = (f - fn).abs().max()
avgf = f.abs().mean()
if avgf > 0:
self.assertLess(df / avgf, 0.1)
def hyster_study(edge, folder=None):
if folder == None: folder = os.getcwd()
print folder
for fileC in os.listdir(folder):
if fileC[-6:] == '.simul':
fileC = folder + fileC
_, length, _, _, v, T, dt, fric, dtheta, \
thresZ, interval, deltaY, theta, M, edge = read_simul_params_file(fileC)
mdfile = fileC[:-6] + '.traj'
traj = PickleTrajectory(mdfile, 'r')
atoms_init = traj[0]
constraints, _, twist, rend_b, rend_t = get_constraints(atoms_init, edge, \
bond, None, key = 'twist_p')
#constraints, _, rend_b, rend_t = get_constraints(atoms_init, edge, \
# bond, None, key = 'twist_p')
atoms = traj[-1]
atoms.set_constraint(constraints)
vels = (traj[-2].positions - traj[-1].positions) / (interval * dt)
atoms.set_velocities(vels)
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
view(atoms)
dyn = Langevin(atoms, dt * units.fs, T * units.kB, fric)
twist.set_angle(theta)
dyn.run(10 * interval)
view(atoms)
traj_new = PickleTrajectory(fileC[:-6] + '_hyst.traj', 'w', atoms)
mdlogf = fileC[:-6] + '_hyst.log'
do_dynamics(mdlogf, atoms, dyn, rend_b, rend_t, v, dt, deltaY, \
theta, dtheta, length, thresZ, \
interval, traj_new, M, twist)
mdhystf = fileC[:-6] + '_hyst.traj'
logfile = fileC[:-6] + '.log'
append_files(logfile, mdlogf, logfile[:-4] + '_comp.log')
call([
'ase-gui', mdfile, mdhystf, '-o', logfile[:-4] + '_comp.traj'
])
def hyster_study(edge, folder = None):
if folder == None: folder = os.getcwd()
print folder
for fileC in os.listdir(folder):
if fileC[-6:] == '.simul':
fileC = folder + fileC
_, length, _, _, v, T, dt, fric, dtheta, \
thresZ, interval, deltaY, theta, M, edge = read_simul_params_file(fileC)
mdfile = fileC[:-6] + '.traj'
traj = PickleTrajectory(mdfile, 'r')
atoms_init = traj[0]
constraints, _, twist, rend_b, rend_t = get_constraints(atoms_init, edge, \
bond, None, key = 'twist_p')
#constraints, _, rend_b, rend_t = get_constraints(atoms_init, edge, \
# bond, None, key = 'twist_p')
atoms = traj[-1]
atoms.set_constraint(constraints)
vels = (traj[-2].positions - traj[-1].positions) / (interval * dt)
atoms.set_velocities(vels)
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
view(atoms)
dyn = Langevin(atoms, dt*units.fs, T*units.kB, fric)
twist.set_angle(theta)
dyn.run(10 * interval)
view(atoms)
traj_new= PickleTrajectory(fileC[:-6] + '_hyst.traj', 'w', atoms)
mdlogf = fileC[:-6] + '_hyst.log'
do_dynamics(mdlogf, atoms, dyn, rend_b, rend_t, v, dt, deltaY, \
theta, dtheta, length, thresZ, \
interval, traj_new, M, twist)
mdhystf = fileC[:-6] + '_hyst.traj'
logfile = fileC[:-6] + '.log'
append_files(logfile, mdlogf, logfile[:-4] + '_comp.log')
call(['ase-gui', mdfile, mdhystf, '-o', logfile[:-4] + '_comp.traj'])
def _testForce(self, pbc):
atoms = Diamond(symbol="C", pbc=pbc)
builtin = torchani.neurochem.Builtins()
calculator = torchani.ase.Calculator(
builtin.species, builtin.aev_computer,
builtin.models, builtin.energy_shifter)
atoms.set_calculator(calculator)
dyn = Langevin(atoms, 5 * units.fs, 30000000 * units.kB, 0.002)
dyn.run(100)
f = torch.from_numpy(atoms.get_forces())
fn = get_numeric_force(atoms, 0.001)
df = (f - fn).abs().max()
avgf = f.abs().mean()
if avgf > 0:
self.assertLess(df / avgf, 0.1)
def run_static(self):
"""
Static run function, which uses the ASEAdapter to connect the pyiron interactive reference job with the
Langevin thermostat implemented in ASE, by setting the ASEAdapter as a replacement of the ASE atoms object.
"""
self.status.running = True
self.ref_job_initialize()
aseadapter = AseAdapter(self.ref_job, self._fast_mode)
langevin = Langevin(atoms=aseadapter,
timestep=self.input['time_step'] * units.fs,
temperature=self.input['temperature'] * units.kB,
friction=self.input['friction'],
fixcm=True)
langevin.run(self.input['ionic_steps'])
self.status.collect = True
aseadapter.interactive_close()
self._finish_job()
def solve(self):
#Create the initial particle from the defining string/number atoms
temp = 1750
mintemp = 150
self.particle = genParticle(self.definingString,int(self.numberOfAtoms))
if (len(self.particle) < 16):
temp = 1250
maxtemp = temp
berendsen = Langevin(self.particle, 2.5 * units.fs, units.kB * temp, 0.02)
# the 5.0 * units.fs is used instead of 0.1 * units.fs b/c it makes the program run faster
MaxwellBoltzmannDistribution(self.particle,units.kB * temp)
self.bestEnergy = self.particle.get_potential_energy()
self.bestParticle = deepcopy(self.particle)
self.reCenter()
self.getAnswer()
while (temp > mintemp):
berendsen = Langevin(self.particle, 2.5 * units.fs, units.kB * temp, 0.02)
berendsen.run(100)
testEnergy = self.particle.get_potential_energy()
self.bestEnergy = self.particle.get_potential_energy()
self.bestParticle = deepcopy(self.particle)
self.reCenter()
self.getAnswer()
temp -= 10
if (temp % 50 == 0):
self.bestEnergy = self.particle.get_potential_energy()
self.bestParticle = deepcopy(self.particle)
self.reCenter()
self.checkTimeout()
self.setSolution(self.getAnswer())
pDone=float(maxtemp - temp)/(maxtemp-mintemp)
self.setStatusDone(str(math.floor(pDone*100))+"% | "+self.remainingTime(pDone))
elif (temp <= mintemp):
dyn = FIRE(atoms=self.particle)
dyn.run(fmax=0.01)
self.bestEnergy = self.particle.get_potential_energy()
self.bestParticle = deepcopy(self.particle)
self.reCenter()
self.setSolution(self.getAnswer())
pDone=float(temp)/(maxtemp-mintemp)
self.setStatusDone(str(math.floor(pDone*100))+"% | "+self.remainingTime(pDone))
return self.getAnswer()
def updatevars(self):
Langevin_ASE.updatevars(self)
if len(self.atoms.constraints) == 1:
# Process the FixAtoms constraint
constr = self.atoms.constraints[0].index
self.sdpos[constr] = 0.0
self.sdmom[constr] = 0.0
self.c1[constr] = 0.0
self.c2[constr] = 0.0
self.c3[constr] = 0.0
self.c4[constr] = 0.0
self.act0[constr] = 0.0
if self._localfrict:
self.asap_md.set_vector_constants(self.prefix+"act0", self.prefix+"c3",
self.prefix+"c4", self.prefix+"pmcor",
self.prefix+"cnst")
else:
self.asap_md.set_scalar_constants(self.act0, self.c3, self.c4,
self.pmcor, self.cnst)
def langevin_dynamics(atoms, dt, tem, friction, trajectory, loginterval,
append):
dyn = Langevin(atoms,
dt * units.fs,
temperature_K=tem,
friction=friction,
rng=np.random,
trajectory=trajectory,
append_trajectory=append,
loginterval=loginterval)
return dyn
def __init__(self, atoms, timestep, temperature, friction, fixcm=True,
trajectory=None, logfile=None, loginterval=1):
assert(getattr(Langevin_ASE, "_lgv_version", 1) >= 2)
ParallelMolDynMixin.__init__(self, "Langevin", atoms)
self._uselocaldata = False # Need to store on atoms for serial simul too.
self.calculator = atoms.get_calculator()
self.asap_md = asap3._asap.Langevin(atoms, self.calculator, timestep,
self.prefix+"sdpos", self.prefix+"sdmom",
self.prefix+"c1", self.prefix+"c2",
fixcm, randint(1 << 30))
if not atoms.has('momenta'):
atoms.set_momenta(np.zeros((len(atoms), 3), float))
if atoms.constraints:
assert len(atoms.constraints) == 1
constraint = atoms.constraints[0]
assert isinstance(constraint, asap3.constraints.FixAtoms)
constraint.prepare_for_asap(atoms)
# Make all constants arrays by making friction an array
friction = friction * np.zeros(len(atoms))
Langevin_ASE.__init__(self, atoms, timestep, temperature, friction, fixcm,
trajectory, logfile, loginterval, communicator=None)
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 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_rand_dyn__(self, mid, T1, T2, dt, Nc, Ns, dS):
# Setup calculator
mol = self.mols[0].copy()
# Setup PBC if active
if self.pbc:
mol.set_cell(([[self.pbl, 0, 0],
[0, self.pbl, 0],
[0, 0, self.pbl]]))
mol.set_pbc((self.pbc, self.pbc, self.pbc))
# Setup calculator
mol.set_calculator(ANIENS(self.aens))
#mol.set_calculator(ANI(False))
#mol.calc.setnc(self.ncl[0])
# Set chemical symbols
spc = mol.get_chemical_symbols()
# Set the velocities corresponding to a boltzmann dist @ T/4.0
MaxwellBoltzmannDistribution(mol, T1 * units.kB)
# Set the thermostat
dyn = Langevin(mol, dt * units.fs, T1 * units.kB, 0.02)
dT = (T2 - T1)/Nc
#print('Running...')
for i in range(Nc):
# Set steps temperature
dyn.set_temperature((T1 + dT*i) * units.kB)
# Do Ns steps of dynamics
dyn.run(Ns)
# Return sigma
sigma = hdt.evtokcal * mol.calc.stddev
ekin = mol.get_kinetic_energy() / len(mol)
# Check for dynamics failure
if sigma > dS:
self.Nbad += 1
self.X.append(mol.get_positions())
#print('Step:', dyn.get_number_of_steps(), 'Sig:', sigma, 'Temp:',
# str(ekin / (1.5 * units.kB)) + '(' + str(T1 + dT * i) + ')')
return True,dyn.get_number_of_steps()
return False,dyn.get_number_of_steps()
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 set_lattice_params(self, md='NVE', **kwargs):
#self.lattice_model.set(**kwargs)
self.lattice_temperature = kwargs['lattice_temperature']
self.lattice_time_step = kwargs['lattice_time_step']
self.lattice_friction = kwargs['lattice_friction']
if md == 'Langevin':
self._lattice_dyn = Langevin(self.atoms,
self.lattice_time_step,
self.lattice_temperature,
self.lattice_friction,
trajectory='LattHist.traj')
elif md == 'NVE':
self._lattice_dyn = VelocityVerlet(self.atoms,
dt=self.lattice_time_step,
trajectory='LattHist.traj')
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 MD(self):
"""Molecular Dynamic"""
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase import units
from ase.md import MDLogger
from ase.io.trajectory import PickleTrajectory
from ase.md.langevin import Langevin
from ase.md.verlet import VelocityVerlet
dyndrivers = {
'Langevin': Langevin,
'None': VelocityVerlet,
}
useAsap = False
mol = self.mol
temperature = self.definedParams['temperature']
init_temperature = self.definedParams['init_temperature']
time_step = self.definedParams['time_step']
nstep = self.definedParams['nstep']
nprint = self.definedParams['nprint']
thermostat = self.definedParams['thermostat']
prop_file = os.path.join(self.definedParams['workdir'],
self.definedParams['output_prefix'] + '.out')
traj_file = os.path.join(self.definedParams['workdir'],
self.definedParams['output_prefix'] + '.traj')
MaxwellBoltzmannDistribution(mol, init_temperature * units.kB)
if thermostat == 'None':
dyn = VelocityVerlet(mol, time_step * units.fs)
elif thermostat == 'Langevin':
dyn = Langevin(mol, time_step * units.fs, temperature * units.kB,
0.01)
else:
raise ImplementationError(
method, 'Thermostat is not implemented in the MD function')
#Function to print the potential, kinetic and total energy
traj = PickleTrajectory(traj_file, "a", mol)
dyn.attach(MDLogger(dyn, mol, prop_file), interval=nprint)
dyn.attach(traj.write, interval=nprint)
dyn.run(nstep)
traj.close()
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():
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 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 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)
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()
def test(temp, frict):
output = file('Langevin.dat', 'w')
# Make a small perturbation of the momenta
atoms.set_momenta(1e-6 * np.random.random([len(atoms), 3]))
print 'Initializing ...'
predyn = VelocityVerlet(atoms, 0.5)
predyn.run(2500)
dyn = Langevin(atoms, timestep, temp, frict)
print ''
print ('Testing Langevin dynamics with T = %f eV and lambda = %f' %
(temp, frict))
ekin = atoms.get_kinetic_energy()/len(atoms)
print ekin
output.write('%.8f\n' % ekin)
print 'Equilibrating ...'
# Initial guesses for least-squares fit
a = 0.04
b = 2*frict
c = temp
params = (a,b,c)
fitdata = [(0, 2.0 / 3.0 * ekin)]
tstart = time.time()
for i in xrange(1,nequil+1):
dyn.run(nminor)
ekin = atoms.get_kinetic_energy() / len(atoms)
fitdata.append((i*nminor*timestep, 2.0/3.0 * ekin))
if usescipy and i % nequilprint == 0:
(params, chisq) = leastSquaresFit(targetfunc, params, fitdata)
print '%.6f T_inf = %.6f (goal: %f), tau = %.2f, k = %.6f' % \
(ekin, params[2], temp, 1.0/params[1], params[0])
output.write('%.8f\n' % ekin)
tequil = time.time() - tstart
print 'This took %s minutes.' % (tequil / 60)
output.write('&\n')
assert abs(temp-params[2]) < 0.25*temp, 'Least-squares fit is way off'
assert nequil*nminor*timestep > 3.0/params[1], 'Equiliberation was too short'
fitdata = np.array(fitdata)
print 'Recording statistical data - this takes ten times longer!'
temperatures = []
tstart = time.time()
for i in xrange(1,nsteps+1):
dyn.run(nminor)
ekin = atoms.get_kinetic_energy() / len(atoms)
temperatures.append(2.0/3.0 * ekin)
if i % nprint == 0:
tnow = time.time() - tstart
tleft = (nsteps-i) * tnow / i
print '%.6f (time left: %.1f minutes)' % (ekin, tleft/60)
output.write('%.8f\n' % ekin)
output.write('&\n')
output.close()
temperatures = np.array(temperatures)
mean = sum(temperatures) / len(temperatures)
print 'Mean temperature:', mean, 'eV'
print
print 'This test is statistical, and may in rare cases fail due to a'
print 'statistical fluctuation.'
print
assert abs(mean - temp) <= reltol*temp, 'Deviation is too large.'
print 'Mean temperature:', mean, ' in ', temp, ' +/- ', reltol*temp
return fitdata, params, temperatures
def run_moldy():
KC = False
# DEFINE FILES
mdfile, mdlogfile = 'md.traj', 'md.log'
atoms = make_graphene_slab(a,h,width,4,2, passivate = True)[3]
params = {'bond':bond, 'a':a, 'h':h}
params['positions'] = atoms.positions.copy()
params['pbc'] = atoms.get_pbc()
params['cell'] = atoms.get_cell().diagonal()
params['ia_dist'] = 14
params['chemical_symbols'] = atoms.get_chemical_symbols()
constraints = []
add_kc = KC_potential(params)
left = get_ind(atoms.positions.copy(), 'left', 1, bond)
rend = get_ind(atoms.positions.copy(), 'rend', atoms.get_chemical_symbols(), 0)
'''
# FIX
#zset, layer_inds = find_layers(atoms.positions.copy())
add_adh = add_adhesion(params)
add_kc = KC_potential(params)
#constraints.append(add_adh)
# END FIX
'''
fix_left = FixAtoms(indices = left)
for ind in rend:
fix_deform = FixedPlane(ind, (0., 0., 1.))
constraints.append(fix_deform)
constraints.append(fix_left)
if KC: constraints.append(add_kc)
# CALCULATOR LAMMPS
parameters = {'pair_style':'rebo',
'pair_coeff':['* * CH.airebo C H'],
'mass' :['1 12.0', '2 1.0'],
'units' :'metal',
'boundary' :'f p f'}
calc = LAMMPS(parameters=parameters)
atoms.set_calculator(calc)
# END CALCULATOR
atoms.set_constraint(constraints)
#view(atoms)
# TRAJECTORY
traj = PickleTrajectory(mdfile, 'w', atoms)
data = np.zeros((M, 6))
# DYNAMICS
dyn = Langevin(atoms, dt*units.fs, T*units.kB, 0.002)
n = 0
header = '#t [fs], d [Angstrom], epot_tot [eV], ekin_tot [eV], etot_tot [eV] \n'
log_f = open(mdlogfile, 'w')
log_f.write(header)
log_f.close()
for i in range(0, M):
#for ind in rend:
atoms[3].position[2] -= dz
dyn.run(1)
va = atoms.get_velocities()
vamax = np.linalg.norm(va[3]*0.0982269353)
#print vamax
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
data[n] = [i*dt, i*dz, epot, ekin, epot + ekin, vamax]
log_f = open(mdlogfile, 'a')
stringi = ''
for k,d in enumerate(data[n]):
if k == 0:
stringi += '%.2f ' %d
elif k == 1:
stringi += '%.6f ' %d
else:
stringi += '%.12f ' %d
log_f.write(stringi + '\n')
log_f.close()
np.savetxt(mdlogfile, data, header = header)
n += 1
if i%(int(M/100)) == 0: print 'ready = %.1f' %(i/(int(M/100))) + '%'
def runAndStudy(params_set, pot_key, save = False):
bond = params_set['bond']
T = params_set['T']
taito = params_set['taito']
dt, fric= params_set['dt'], params_set['fric']
tau = params_set['tau']
width = params_set['width']
ratio = params_set['ratio']
edge = params_set['edge']
ncores = params_set['ncores']
Ld_i = params_set['Ldilde_i']
bend, straight, [matchL_idx, matchR_idx, vec], [L_bend, L_straight], [left_idxs, right_idxs]\
= create_bend_stucture(width, ratio, Ld_i, edge, bond)
mdfile, mdlogfile, mdrelax, simulfile, folder, relaxed \
= get_fileName(pot_key, edge + '_corrStick', width, \
L_bend, L_straight, int(T), taito, key = 'corrStick')
if relaxed:
bend = PickleTrajectory(mdrelax, 'r')[-1]
else:
relaxBend(bend, left_idxs, right_idxs, edge, bond, mdrelax)
bend.set_constraint([])
shift_v = -straight.positions[matchR_idx] + (bend.positions[matchL_idx] + vec)
straight.translate(shift_v)
atoms = bend + straight
cell = [1.5*(L_bend + L_straight), L_bend + L_straight, 20]
atoms.set_cell(cell)
atoms.positions[:,2] = 3.4
trans_vec = trans_atomsKC(straight.positions[matchR_idx], edge, bond)
atoms.translate(trans_vec)
#plot_posits(atoms, edge, bond)
if edge == 'ac':
nx = int((cell[0]/5 - np.min(atoms.positions[:,0]))/(3*bond))
ny = int((cell[1]/5 - np.min(atoms.positions[:,1]))/(np.sqrt(3)*bond))
atoms.translate([nx*3.*bond, ny*np.sqrt(3)*bond, 0])
width_f = np.sqrt(3)/2.*bond*(width - 1)
elif edge == 'zz':
nx = int((cell[0]/5 - np.min(atoms.positions[:,0]))/(np.sqrt(3)*bond))
ny = int((cell[1]/5 - np.min(atoms.positions[:,1]))/(3*bond))
atoms.translate([nx*np.sqrt(3)*bond, ny*3*bond, 0])
width_f = (3./2.*width - 1)*bond
cminx, cmaxx = strip_Hend(atoms, 'right')
left_b = get_idxOfEnds(atoms, cminx, cmaxx)[0]
# CONSTRAINTS
constraints = []
constraints.append(FixAtoms(indices = left_b))
params = {}
params['positions'] = atoms.positions
params['chemical_symbols'] = atoms.get_chemical_symbols()
params['ia_dist'] = 10
params['edge'] = edge
params['bond'] = bond
params['ncores'] = ncores
add_pot = KC_potential_p(params)
constraints.append(add_pot)
atoms.set_constraint(constraints)
##
# CALCULATOR
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
##
# DYNAMICS
dyn = Langevin(atoms, dt*units.fs, T*units.kB, fric)
header = '#t [fs], shift y [Angstrom], Rad, theta [rad], hmax [A], epot_tot [eV], ekin_tot [eV], etot_tot [eV], F [eV/angst] \n'
write_line_own(mdlogfile, header, 'w')
traj = PickleTrajectory(mdfile, 'w', atoms)
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T*units.kB)
####
# SIMULATION PARAMS
nframes = 1000
M = int(20*tau/dt)
interval = int(M/nframes)
thres_cancel= 2*bond
stick = 'True'
xmax_idx = np.where(atoms.positions[:,0] == np.max(atoms.positions[:,0]))[0][0]
r_init = atoms.positions[xmax_idx].copy()
R = L_bend/np.pi*3.
print '# data_line: width, length bend, length tail, tail/bend, theta'
print width_f, L_bend, L_straight, L_straight/L_bend, width_f/(2*R)
# SIMULATION LOOP
for i in range(nframes):
print float(i)/nframes*100.
dyn.run(interval)
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
data = [i*interval*dt, epot, ekin, epot + ekin]
if save:
stringi = ''
for k,d in enumerate(data):
if k == 0:
stringi += '%.2f ' %d
elif k == 1 or k == 2:
stringi += '%.4f ' %d
else:
stringi += '%.12f ' %d
write_line_own(mdlogfile, stringi + '\n', 'a')
#print np.linalg.norm(atoms.positions[xmax_idx] - r_init)
if thres_cancel < np.linalg.norm(atoms.positions[xmax_idx] - r_init):
stick = 'false'
break
make_stick_simul_param_file(simulfile, width, L_bend, L_straight, T, \
dt, fric, interval, M, edge, stick)
return stick == 'True'
#plot_posits(atoms, edge, bond)
#view(atoms)
def printenergy(a, it, t0):
"""Function to print the potential, kinetic and total energy"""
epot = a.get_potential_energy() / len(a)
ekin = a.get_kinetic_energy() / len(a)
t_now = time()
print('Step: %4d [%6.2f]: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
'Etot = %.3feV ' % (\
it, t_now-t0, epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
return t_now
ff = PyXtal_FF(model={'system': ["Si"]}, logo=False)
ff.run(mode='predict', mliap=options.file)
calc = PyXtalFFCalculator(ff=ff)
si = bulk('Si', 'diamond', a=5.659, cubic=True)
si = si * 5
print("MD simulation for ", len(si), " atoms")
si.set_calculator(calc)
MaxwellBoltzmannDistribution(si, 1000 * units.kB)
dyn = Langevin(si, timestep=5 * units.fs, temperature_K=1000, friction=0.02)
#dyn = VelocityVerlet(si, 5*units.fs) # 2 fs time step.
t0 = time()
for i in range(10):
dyn.run(steps=1)
t_now = printenergy(si, i, t0)
t0 = t_now
# 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)
def main():
T = 300.0 # Simulation temperature
dt = 1 * units.fs # MD timestep
nsteps = 100000 # MD number of steps
mixing = [1,-1,0] # [1.0, -1.0, 0.3] # mixing weights for "real" and ML forces
lengthscale = 0.5 # KRR Gaussian width.
gamma = 1 / (2 * lengthscale**2)
grid_spacing = 0.05
# mlmodel = GaussianProcess(corr='squared_exponential',
# # theta0=1e-1, thetaL=1e-4, thetaU=1e+2,
# theta0=1.,
# random_start=100, normalize=False, nugget=1.0e-2)
mlmodel = KernelRidge(kernel='rbf',
gamma=gamma, gammaL = gamma/4, gammaU=2*gamma,
alpha=1.0e-2, variable_noise=False, max_lhood=False)
anglerange = sp.arange(0, 2*sp.pi + grid_spacing, grid_spacing)
X_grid = sp.array([[sp.array([x,y]) for x in anglerange]
for y in anglerange]).reshape((len(anglerange)**2, 2))
ext_field = None # IgnoranceField(X_grid, y_threshold=-0.075, cutoff = 3.)
# Bootstrap from initial database? uncomment
# data = sp.loadtxt('phi_psi_F.csv')
# # data[:,:2] -= 0.025 # fix because of old round_vector routine
# mlmodel.fit(data[:,:2], data[:,2])
# ext_field.update_cost(mlmodel.X_fit_, mlmodel.y)
# mlmodel.fit(X_grid, sp.zeros(len(X_grid)))
# mlmodel.fit(sp.load('X_fitD.npy'), sp.load('y_fitD.npy'))
# Prepare diagnostic visual effects.
plt.close('all')
plt.ion()
fig, ax = plt.subplots(1, 2, figsize=(24, 13))
atoms = ase.io.read('myplum.xyz')
with open('data.input', 'r') as file:
lammpsdata = file.readlines()
# Set temperature
MaxwellBoltzmannDistribution(atoms, 0.5 * units.kB * T, force_temp=True)
# Set total momentum to zero
p = atoms.get_momenta()
p -= p.sum(axis=0) / len(atoms)
atoms.set_momenta(p)
atoms.rescale_velocities(T)
# Select MD propagator
mdpropagator = Langevin(atoms, dt, T*units.kB, 1.0e-2, fixcm=True)
# mdpropagator = MLVerlet(atoms, dt, T)
# Zero-timestep evaluation and data files setup.
print("START")
pot_energy, f = calc_lammps(atoms, preloaded_data=lammpsdata)
mlmodel.accumulate_data(round_vector(atoms.colvars(), precision=grid_spacing), 0.)
# mlmodel.accumulate_data(round_vector(atoms.colvars(), precision=grid_spacing), pot_energy)
printenergy(atoms, pot_energy)
try:
os.remove('atomstraj.xyz')
except:
pass
traj = open("atomstraj.xyz", 'a')
atoms.write(traj, format='extxyz')
results, traj_buffer = [], []
# When in the simulation to update the ML fit -- optional.
teaching_points = sp.unique((sp.linspace(0, nsteps**(1/3), nsteps/20)**3).astype('int') + 1)
# MD Loop
for istep in range(nsteps):
# Flush Cholesky decomposition of K
if istep % 1000 == 0:
mlmodel.Cho_L = None
mlmodel.max_lhood = False
print("Dihedral angles | phi = %.3f, psi = %.3f " % (atoms.phi(), atoms.psi()))
do_update = (istep % 60 == 59)
t = get_time()
mdpropagator.halfstep_1of2(f)
print("TIMER 001 | %.3f" % (get_time() - t))
t = get_time()
f, pot_energy, _ = get_all_forces(atoms, mlmodel, grid_spacing, T, extfield=ext_field, mixing=mixing, lammpsdata=lammpsdata, do_update=do_update)
if do_update and mlmodel.max_lhood:
mlmodel.max_lhood = False
mdpropagator.halfstep_2of2(f)
print("TIMER 002 | %.3f" % (get_time() - t))
# manual cooldown!!!
if sp.absolute(atoms.get_kinetic_energy() / (1.5 * units.kB * atoms.get_number_of_atoms()) - T) > 100:
atoms.rescale_velocities(T)
printenergy(atoms, pot_energy/atoms.get_number_of_atoms(), step=istep)
# if do_update:
# try:
# print("Lengthscale = %.3e, Noise = %.3e" % (1/(2 * mlmodel.gamma)**0.5, mlmodel.noise.mean()))
# except:
# print("")
if istep % 60 == 59:
t = get_time()
if 'datasetplot' not in locals():
datasetplot = pl.Plot_datapts(ax[0], mlmodel)
else:
datasetplot.update()
if hasattr(mlmodel, 'dual_coef_'):
if 'my2dplot' not in locals():
my2dplot = pl.Plot_energy_n_point(ax[1], mlmodel, atoms.colvars().ravel())
else:
my2dplot.update_prediction()
my2dplot.update_current_point(atoms.colvars().ravel())
print("TIMER 003 | %.03f" % (get_time() - t))
t = get_time()
fig.canvas.draw()
print("TIMER 004 | %.03f" % (get_time() - t))
# fig.canvas.print_figure('current.png')
t = get_time()
# traj_buffer.append(atoms.copy())
# if istep % 100 == 0:
# for at in traj_buffer:
# atoms.write(traj, format='extxyz')
# traj_buffer = []
results.append(sp.array([atoms.phi(), atoms.psi(), pot_energy]))
print("TIMER 005 | %.03f" % (get_time() - t))
traj.close()
print("FINISHED")
sp.savetxt('results.csv', sp.array(results))
sp.savetxt('mlmodel.dual_coef_.csv', mlmodel.dual_coef_)
sp.savetxt('mlmodel.X_fit_.csv', mlmodel.X_fit_)
sp.savetxt('mlmodel.y.csv', mlmodel.y)
calc = None
return mlmodel
mixer_forces = [forces_full_system]
mixer_energies = [energy_full_system]
elif calc_style == "quantum":
mixer_forces = [forces_qbox_gpaw]
mixer_energies = [energy_qbox_gpaw]
mixer = Mixer(name="mixer_box",
forces=mixer_forces,
energies=mixer_energies,
debug=debug)
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:
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)
class clustergenerator():
def __init__(self,
cnstfile,
saefile,
nnfprefix,
Nnet,
solv_list,
solu_list,
gpuid=0,
sinet=False):
# Molecules list
self.solv_list = solv_list
self.solu_list = solu_list
# Number of networks
self.Nn = Nnet
# Build ANI ensemble
self.aens = ensemblemolecule(cnstfile, saefile, nnfprefix, Nnet, gpuid)
self.edgepad = 1.0
self.mindist = 2.0
#def closeoutputs(self):
# self.mdcrd.close()
# self.traj.close()
def __generategarbagebox__(self, Nm, Nembed, L, T):
self.X = np.empty((0, 3), dtype=np.float32)
self.S = []
self.C = np.zeros((Nm, 3), dtype=np.float32)
rint = np.random.randint(len(self.solv_list), size=Nm)
self.Na = np.zeros(Nm, dtype=np.int32)
self.ctd = []
pos = 0
plc = 0
for idx, j in enumerate(rint):
if idx < Nembed:
ri = np.random.randint(len(self.solu_list), size=1)
s = self.solu_list[ri[0]]['species']
xyz = self.solu_list[ri[0]]['coordinates']
nmc = self.solu_list[ri[0]]['nmdisplacements']
frc = self.solu_list[ri[0]]['forceconstant']
nms = nmt.nmsgenerator(xyz, nmc, frc, s, T, minfc=5.0E-2)
x = nms.get_Nrandom_structures(1)[0]
else:
s = self.solv_list[j]['species']
xyz = self.solv_list[j]['coordinates']
nmc = self.solv_list[j]['nmdisplacements']
frc = self.solv_list[j]['forceconstant']
nms = nmt.nmsgenerator(xyz, nmc, frc, s, T, minfc=5.0E-2)
x = nms.get_Nrandom_structures(1)[0]
# Apply a random rotation
M = rand_rotation_matrix()
x = np.dot(x, M.T)
maxd = hdn.generatedmatsd3(x).flatten().max() / 2.0
Nf = 0
fail = True
while fail:
ctr = np.random.uniform(2.0 * maxd + self.edgepad,
L - 2.0 * maxd - self.edgepad, (3))
fail = False
for cid, c in enumerate(self.ctd):
if np.linalg.norm(c[0] - ctr) < maxd + c[1] + 10.0:
# search for atoms within r angstroms
minv = 1000.0
for xi in self.X[c[2]:c[2] + self.Na[cid], :]:
for xj in x + ctr:
dij = np.linalg.norm(xi - xj)
if dij < minv:
minv = dij
if minv < self.mindist:
fail = True
Nf += 1
if not fail:
plc += 1
#print('Added:',plc)
self.ctd.append((ctr, maxd, pos))
self.X = np.vstack([self.X, x + ctr])
self.Na[idx] = len(s)
pos += len(s)
#print('Placement Complete...',plc,'-',Nf)
self.S.extend(s)
def init_dynamics(self, Nm, Nembed, V, L, dt, T):
self.L = L
# Generate the box of junk
self.__generategarbagebox__(Nm, Nembed, L, T)
# Make mol
self.mol = Atoms(symbols=self.S, positions=self.X)
# Set box and PBC
self.mol.set_cell(([[L, 0, 0], [0, L, 0], [0, 0, L]]))
self.mol.set_pbc((True, True, True))
# Set ANI calculator
self.mol.set_calculator(ANIENS(self.aens))
# Open MD output
#self.mdcrd = open(xyzfile, 'w')
# Open MD output
#self.traj = open(trjfile, 'w')
# Set the velocities corresponding to a boltzmann dist @ T/4.0
MaxwellBoltzmannDistribution(self.mol, 300.0 * units.kB)
# Declare Dyn
self.dyn = Langevin(self.mol, dt * units.fs, T * units.kB, 0.1)
# Define the printer
#def printenergy(a=self.mol, d=self.dyn, b=self.mdcrd, t=self.traj): # 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)
#
# stddev = hdn.evtokcal * a.calc.stddev
#
# t.write(str(d.get_number_of_steps()) + ' ' + str(ekin / (1.5 * units.kB)) + ' ' + str(epot) + ' ' + str(
# ekin) + ' ' + str(epot + ekin) + '\n')
# b.write(str(len(a)) + '\n' + str(ekin / (1.5 * units.kB)) + ' Step: ' + str(d.get_number_of_steps()) + '\n')
# c = a.get_positions(wrap=True)
# for j, i in zip(a, c):
# b.write(str(j.symbol) + ' ' + str(i[0]) + ' ' + str(i[1]) + ' ' + str(i[2]) + '\n')
#
# print('Step: %d Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
# 'Etot = %.3feV' ' StdDev = %.3fkcal/mol/sqrt(Na)' % (
# d.get_number_of_steps(), epot, ekin, ekin / (1.5 * units.kB), epot + ekin, stddev))
# Attach the printer
#self.dyn.attach(printenergy, interval=1)
def run_dynamics(self, Ni):
for id, nc in enumerate(self.aens.ncl):
nc.setMolecule(coords=np.array(self.mol.get_positions(),
dtype=np.float32),
types=self.mol.get_chemical_symbols())
self.dyn.run(Ni) # Do Ni steps
def __fragmentbox__(self, file, sighat):
self.X = self.mol.get_positions()
self.frag_list = []
self.Nd = 0
self.Nt = 0
self.maxsig = 0
for i in range(len(self.Na)):
si = self.ctd[i][2]
di = self.ctd[i][1]
Nai = self.Na[i]
Xci = np.sum(self.X[si:si + Nai, :], axis=0) / Nai
Xi = self.X[si:si + Nai, :]
if np.all(Xci > 4.5) and np.all(Xci <= self.L - 4.5):
if np.all(Xci > di) and np.all(Xci < self.L - di):
Xf = Xi
Sf = self.S[si:si + Nai]
Nmax = random.randint(2, 14)
Nmol = 0
for j in range(len(self.Na)):
if i != j:
sj = self.ctd[j][2]
dj = self.ctd[j][1]
Naj = self.Na[j]
Xcj = np.sum(self.X[sj:sj + Naj, :], axis=0) / Naj
Xj = self.X[sj:sj + Naj, :]
if np.all(Xcj > dj) and np.all(Xcj < self.L - dj):
dc = np.linalg.norm(Xci - Xcj)
if dc < di + dj + 5.0:
min = 10.0
for ii in range(Nai):
Xiii = Xi[ii]
for jj in range(Naj):
Xjjj = Xj[jj]
v = np.linalg.norm(Xiii - Xjjj)
if v < min:
min = v
if min < 4.5 and min > 0.70:
Xf = np.vstack([Xf, Xj])
Sf.extend(self.S[sj:sj + Naj])
Nmol += 1
if Nmol >= Nmax:
break
Xcf = np.sum(Xf, axis=0) / float(len(Sf))
Xf = Xf - Xcf
E = np.empty(5, dtype=np.float64)
for id, nc in enumerate(self.aens.ncl):
nc.setMolecule(coords=np.array(Xf, dtype=np.float32),
types=Sf)
E[id] = nc.energy()[0]
sig = np.std(hdn.hatokcal * E) / np.sqrt(Nai + Naj)
#print('Mol(',i,'): sig=',sig)
self.Nt += 1
if sig > sighat:
if sig > self.maxsig:
self.maxsig = sig
self.Nd += 1
hdn.writexyzfile(file + str(i).zfill(4) + '.xyz',
Xf.reshape(1, Xf.shape[0], 3), Sf)
self.frag_list.append(dict({'coords': Xf, 'spec': Sf}))
#print(dc, Sf, sig)
def generate_clusters(self, gcmddict, mol_sizes, id):
self.edgepad = gcmddict['edgepad']
self.mindist = gcmddict['mindist']
dstore = gcmddict['dstore']
difo = open(
dstore + 'info_data_mdcluster-' + str(id).zfill(2) + '.nfo', 'w')
difo.write('Beginning dimer generation...\n')
Nt = 0
Nd = 0
for i in range(gcmddict['Nr']):
self.init_dynamics(
mol_sizes[i],
gcmddict['Nembed'],
gcmddict['V'],
gcmddict['L'],
gcmddict['dt'],
gcmddict['T'],
)
for j in range(gcmddict['Ns']):
if j is 0:
Ni = 0
else:
Ni = gcmddict['Ni']
self.run_dynamics(Ni)
self.__fragmentbox__(
gcmddict['molfile'] + '-' + str(id).zfill(2) + '-' +
str(i).zfill(2) + '-' + str(j).zfill(4) + '_',
gcmddict['sig'])
#print('Step (',i,',',j,') [', str(self.Nd), '/', str(self.Nt),'] generated ',len(self.frag_list),' maxsig: ', self.maxsig,' dimers...')
difo.write('Step (' + str(i) + ',' + str(i) + ') [' +
str(self.Nd) + '/' + str(self.Nt) + '] generated ' +
str(len(self.frag_list)) + ' clusters. ' +
' maxsig: ' + "{:.2f}".format(self.maxsig) + '\n')
Nt += self.Nt
Nd += self.Nd
if self.maxsig > gcmddict['maxsig']:
difo.write("Terminated after: " +
"{:.2f}".format(Ni * gcmddict['Ns'] *
gcmddict['dt']) +
'fs for maxsig\n')
break
difo.flush()
#self.closeoutputs()
difo.write('Generated ' + str(Nd) + ' of ' + str(Nt) +
' tested dimers. Percent: ' +
"{:.2f}".format(100.0 * Nd / float(Nt)))
difo.close()
class dimergenerator():
def __init__(self,
cnstfile,
saefile,
nnfprefix,
Nnet,
molecule_list,
gpuid=0,
sinet=False):
# Molecules list
self.mols = molecule_list
# Number of networks
self.Nn = Nnet
# Build ANI ensemble
self.aens = ensemblemolecule(cnstfile, saefile, nnfprefix, Nnet, gpuid)
# Construct pyNeuroChem class
#self.ncl = [pync.molecule(cnstfile, saefile, nnfprefix+str(i)+'/networks/', gpuid, sinet) for i in range(self.Nn)]
def __generategarbagebox__(self, Nm, L, T):
self.X = np.empty((0, 3), dtype=np.float32)
self.S = []
self.C = np.zeros((Nm, 3), dtype=np.float32)
rint = np.random.randint(len(self.mols), size=Nm)
self.Na = np.zeros(Nm, dtype=np.int32)
self.ctd = []
pos = 0
plc = 0
attempts = 0
for idx, j in enumerate(rint):
if attempts >= 10000:
break
#x = self.mols[j]['coordinates']
#s = self.mols[j]['species']
s = self.mols[j]['species']
xyz = self.mols[j]['coordinates']
nmc = self.mols[j]['nmdisplacements']
frc = self.mols[j]['forceconstant']
nms = nmt.nmsgenerator(xyz, nmc, frc, s, T, minfc=5.0E-2)
x = nms.get_Nrandom_structures(1)[0]
# Apply a random rotation
M = rand_rotation_matrix()
x = np.dot(x, M.T)
maxd = hdn.generatedmatsd3(x).flatten().max() / 2.0
#print('after:', maxd)
fail = True
while fail and attempts < 10000:
ctr = np.random.uniform(2.0 * maxd + 1.0, L - 2.0 * maxd - 1.0,
(3))
fail = False
for cid, c in enumerate(self.ctd):
if np.linalg.norm(c[0] - ctr) < maxd + c[1] + 10.0:
# search for atoms within r angstroms
minv = 1000.0
for xi in self.X[c[2]:c[2] + self.Na[cid], :]:
for xj in x + ctr:
dij = np.linalg.norm(xi - xj)
if dij < minv:
minv = dij
if minv < 1.5:
fail = True
attempts += 1
if not fail:
plc += 1
attempts = 0
#print('Added:',plc)
self.ctd.append((ctr, maxd, pos))
self.X = np.vstack([self.X, x + ctr])
self.Na[idx] = len(s)
pos += len(s)
self.S.extend(s)
self.Na = self.Na[0:plc]
def init_dynamics(self, Nm, V, L, dt, T):
self.L = L
# Generate the box of junk
self.__generategarbagebox__(Nm, L, T)
# Make mol
self.mol = Atoms(symbols=self.S, positions=self.X)
# Set box and PBC
self.mol.set_cell(([[L, 0, 0], [0, L, 0], [0, 0, L]]))
self.mol.set_pbc((True, True, True))
# Set ANI calculator
# Set ANI calculator
self.mol.set_calculator(ANIENS(self.aens))
#self.mol.set_calculator(ANI(False))
#self.mol.calc.setnc(self.ncl[0])
# Give molecules random velocity
acc_idx = 0
vel = np.empty_like(self.X)
for n in self.Na:
rv = np.random.uniform(-V, V, size=(3))
for k in range(n):
vel[acc_idx + k, :] = rv
acc_idx += n
#print(vel)
self.mol.set_velocities(vel)
# Declare Dyn
self.dyn = Langevin(self.mol, dt * units.fs, T * units.kB, 0.1)
def run_dynamics(self, Ni):
# Open MD output
#mdcrd = open(xyzfile, 'w')
# Open MD output
#traj = open(trajfile, 'w')
# Define the printer
#def printenergy(a=self.mol, d=self.dyn): # 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('Step: %d Size: %d Energy per atom: Epot = %.3feV Ekin = %.3feV (T=%3.0fK) '
# 'Etot = %.3feV' % (d.get_number_of_steps(), len(a), epot, ekin, ekin / (1.5 * units.kB), epot + ekin))
# Attach the printer
#self.dyn.attach(printenergy, interval=4)
self.dyn.run(Ni) # Do Ni steps
# Open MD output
#mdcrd.close()
# Open MD output
#traj.close()
def __fragmentbox__(self, file, sig_cut):
self.X = self.mol.get_positions()
self.frag_list = []
self.Nd = 0
self.Nt = 0
for i in range(len(self.Na)):
si = self.ctd[i][2]
di = self.ctd[i][1]
Nai = self.Na[i]
Xci = np.sum(self.X[si:si + Nai, :], axis=0) / Nai
Xi = self.X[si:si + Nai, :]
if np.all(Xci > di) and np.all(Xci < self.L - di):
for j in range(i + 1, len(self.Na)):
sj = self.ctd[j][2]
dj = self.ctd[j][1]
Naj = self.Na[j]
Xcj = np.sum(self.X[sj:sj + Naj, :], axis=0) / Naj
Xj = self.X[sj:sj + Naj, :]
if np.all(Xcj > dj) and np.all(Xcj < self.L - dj):
dc = np.linalg.norm(Xci - Xcj)
if dc < di + dj + 6.0:
min = 10.0
for ii in range(Nai):
Xiii = Xi[ii]
for jj in range(Naj):
Xjjj = Xj[jj]
v = np.linalg.norm(Xiii - Xjjj)
if v < min:
min = v
if min < 4.2 and min > 1.1:
Xf = np.vstack([Xi, Xj])
Sf = self.S[si:si + Nai]
Sf.extend(self.S[sj:sj + Naj])
Xcf = np.sum(Xf, axis=0) / (Nai + Naj)
Xf = Xf - Xcf
E = np.empty(5, dtype=np.float64)
for id, nc in enumerate(self.aens.ncl):
nc.setMolecule(coords=np.array(
Xf, dtype=np.float32),
types=Sf)
E[id] = nc.energy()[0]
sig = np.std(
hdn.hatokcal * E) / np.sqrt(Nai + Naj)
self.Nt += 1
if sig > sig_cut:
self.Nd += 1
hdn.writexyzfile(
file + str(i).zfill(4) + '-' +
str(j).zfill(4) + '.xyz',
Xf.reshape(1, Xf.shape[0], 3), Sf)
self.frag_list.append(
dict({
'coords': Xf,
'spec': Sf
}))
from asap3 import EMT # Way too slow with ase.EMT !
size = 10
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()
def __init__(self, atoms, timestep, temperature, friction, fixcm=True,
trajectory=None, logfile=None, loginterval=1):
assert(getattr(Langevin_ASE, "_lgv_version", 1) >= 2)
ParallelMolDynMixin.__init__(self, "Langevin", atoms)
Langevin_ASE.__init__(self, atoms, timestep, temperature, friction, fixcm,
trajectory, logfile, loginterval, communicator=None)
atoms = FaceCenteredCubic(directions=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
symbol='Fe',
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)
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)