def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if system_changes: # if anything at all changed (could be made more fine-grained)
self.logger.pr('calculation triggered with properties={0}, system_changes={1}'.format(properties,
system_changes))
self.server.put(atoms, 0, self.label)
if self.label != 1:
# send atoms over socket, unless first time
self.logger.pr('socket calculator sending Atoms label={0}'.format(self.label))
self.server.handle_request()
# wait for results to be ready
self.logger.pr('socket calculator waiting for results label={0}'.format(self.label))
self.server.handle_request()
self.label += 1
[results] = self.server.get_results()
# we always compute energy, forces and stresses, regardless of what was requested
stress = -(results.info['virial']/results.get_volume())
self.results = {'energy': results.info['energy'],
'forces': results.arrays['force'],
'stress': full_3x3_to_Voigt_6_stress(stress)}
else:
self.logger.pr('calculation avoided with properties={0}, system_changes={1}'.format(properties,
system_changes))
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
"""EAM Calculator
atoms: Atoms object
Contains positions, unit-cell, ...
properties: list of str
List of what needs to be calculated. Can be any combination
of 'energy', 'forces'
system_changes: list of str
List of what has changed since last calculation. Can be
any combination of these five: 'positions', 'numbers', 'cell',
'pbc', 'initial_charges' and 'initial_magmoms'.
"""
Calculator.calculate(self, atoms, properties, system_changes)
# we shouldn't really recalc if charges or magmos change
if len(system_changes) > 0: # something wrong with this way
self.update(self.atoms)
self.calculate_energy(self.atoms)
if 'forces' in properties:
self.calculate_forces(self.atoms)
# check we have all the properties requested
for property in properties:
if property not in self.results:
if property is 'energy':
self.calculate_energy(self.atoms)
if property is 'forces':
self.calculate_forces(self.atoms)
def relax(self, atoms=None, properties=['energy'],
system_changes=some_changes,
flag_damping=2,
converge_eps=1.0e-3,nsteps=100,min_iteration=5,
converge_num=3,time_interval=2.0,
initial_temperature=10.0):
"""
Relax atom positions by running damped MD in pmd instead of using
optimize module in ASE.
"""
self.set(flag_damping=flag_damping,
converge_eps=converge_eps,
num_iteration=nsteps,
min_iteration=min_iteration,
num_out_energy=nsteps,
converge_num=converge_num,
time_interval=time_interval,
initial_temperature=initial_temperature,
flag_sort=1)
Calculator.calculate(self, atoms, properties, system_changes)
# print 'type(atoms),type(self.atoms)= ',type(atoms),type(self.atoms)
# print 'self.atoms = ',self.atoms
self.write_input(self.atoms, properties, system_changes)
olddir = os.getcwd()
try:
os.chdir(self.directory)
errorcode = subprocess.call(self.command, shell=True)
finally:
os.chdir(olddir)
if errorcode:
raise RuntimeError('%s returned an error: %d' %
(self.name, errorcode))
self.read_results(relax=True)
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
"""GEBF Calculator
"""
Calculator.calculate(self, atoms, properties, system_changes)
if len(system_changes) > 0: # something wrong with this way
self.update(self.atoms)
if 'energy' in properties:
self.calculate_energy(self.atoms)
if 'forces' in properties:
self.calculate_forces(self.atoms)
if 'charges' in properties:
self.calculate_charges(self.atoms)
# check we have all the properties requested
for property in properties:
if property not in self.results:
if property is 'energy':
self.calculate_energy(self.atoms)
if property is 'forces':
self.calculate_forces(self.atoms)
if property is 'charges':
self.calculate_charges(self.atoms)
#FUMPORTANT|
atoms.set_initial_charges(self.results['charges'])
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if self.qmatoms is None:
self.initialize_qm(atoms)
self.qmatoms.positions = atoms.positions[self.selection]
if self.vacuum:
self.qmatoms.positions += (self.center -
self.qmatoms.positions.mean(axis=0))
energy = self.mmcalc2.get_potential_energy(atoms)
forces = self.mmcalc2.get_forces(atoms)
energy += self.qmcalc.get_potential_energy(self.qmatoms)
qmforces = self.qmcalc.get_forces(self.qmatoms)
if self.vacuum:
qmforces -= qmforces.mean(axis=0)
forces[self.selection] += qmforces
energy -= self.mmcalc1.get_potential_energy(self.qmatoms)
forces[self.selection] -= self.mmcalc1.get_forces(self.qmatoms)
self.results['energy'] = energy
self.results['forces'] = forces
def calculate(self, atoms=None, properties=['energy'],
system_changes=None):
"""Runs a calculation, only if necessary."""
if self.calculation_required(atoms, properties):
# The subclass implementation should first call this
# implementation to set the atoms attribute.
Calculator.calculate(self, atoms, properties, system_changes)
self.write_input(atoms, properties, system_changes)
if self.command is None:
raise RuntimeError('Please set $%s environment variable ' %
('ASE_' + self.name.upper() + '_COMMAND') +
'or supply the command keyword')
olddir = os.getcwd()
try:
os.chdir(self.directory)
errorcode = subprocess.call(self.command,
stdout=subprocess.PIPE,
shell=True)
finally:
os.chdir(olddir)
if errorcode:
s = '{} returned an error: {}'
raise RuntimeError(s.format(self.name, errorcode))
# This sets self.results, and updates the atoms
self.read_results()
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
# We don't call FileIOCalculator.calculate here, because that method
# calls subprocess.call(..., shell=True), which we don't want to do.
# So, we reproduce some content from that method here.
Calculator.calculate(self, atoms, properties, system_changes)
# If a parameter file exists in the working directory, delete it
# first. If we need that file, we'll recreate it later.
localparfile = os.path.join(self.directory, '.dftd3par.local')
if os.path.isfile(localparfile):
os.remove(localparfile)
# Write XYZ or POSCAR file and .dftd3par.local file if we are using
# custom damping parameters.
self.write_input(self.atoms, properties, system_changes)
command = self._generate_command()
# Finally, call dftd3 and parse results.
with open(self.label + '.out', 'w') as f:
errorcode = subprocess.call(command, cwd=self.directory, stdout=f)
if errorcode:
raise RuntimeError('%s returned an error: %d' %
(self.name, errorcode))
self.read_results()
def calculate(self, atoms, properties, system_changes):
"""
Calculation of the energy of system and forces of all atoms.
"""
# The inherited method below just sets the atoms object,
# if specified, to self.atoms.
Calculator.calculate(self, atoms, properties, system_changes)
log = self.log
log('Calculation requested.')
images = hash_images([self.atoms])
key = images.keys()[0]
if properties == ['energy']:
log('Calculating potential energy...', tic='pot-energy')
self.descriptor.calculate_fingerprints(images=images,
log=log,
calculate_derivatives=False)
energy = self.model.get_energy(self.descriptor.fingerprints[key])
self.results['energy'] = energy
log('...potential energy calculated.', toc='pot-energy')
if properties == ['forces']:
log('Calculating forces...', tic='forces')
self.descriptor.calculate_fingerprints(images=images,
log=log,
calculate_derivatives=True)
forces = \
self.model.get_forces(self.descriptor.fingerprints[key],
self.descriptor.fingerprintprimes[key])
self.results['forces'] = forces
log('...forces calculated.', toc='forces')
def calculate(self, atoms, properties, system_changes):
# call parent method:
Calculator.calculate(self, atoms, properties, system_changes)
if not(system_changes is None):
self.update_atoms()
if 'energy' in properties:
energy = self.ff.Energy()
# energy units are kcal/mole according to http://forums.openbabel.org/Energy-units-td1574278.html
# and in Avogadro they are reported as kJ/mole ...
self.results['energy'] = energy * units.kJ / units.mol
if 'forces' in properties:
d = 0.001
F_ai = np.zeros( (self.natoms, 3) )
for iatom in xrange( self.natoms ):
for iaxis in xrange( 3 ):
obatom = self.mol.GetAtom( 1 + iatom )
vec = obatom.GetVector()
obatom.SetVector( self._shift_OBvec(vec, iaxis, d) )
self.ff.Setup( self.mol )
eplus = self.ff.Energy() * units.kJ/units.mol
obatom.SetVector( self._shift_OBvec(vec, iaxis, -2*d) )
self.ff.Setup( self.mol )
eminus = self.ff.Energy() * units.kJ/units.mol
obatom.SetVector( self._shift_OBvec(vec, iaxis, d) ) # put it back
F_ai[iatom, iaxis] = (eminus - eplus) / (2 * d)
self.results['forces'] = F_ai
def calculate(self, atoms=None, properties=['energy'],
system_changes=['positions', 'numbers', 'cell',
'pbc', 'charges', 'magmoms']):
Calculator.calculate(self, atoms, properties, system_changes)
epsilon = self.parameters.epsilon
rho0 = self.parameters.rho0
r0 = self.parameters.r0
positions = self.atoms.get_positions()
energy = 0.0
energies = np.zeros(len(self.atoms))
forces = np.zeros((len(self.atoms), 3))
preF = 2 * epsilon * rho0 / r0
for i1, p1 in enumerate(positions):
for i2, p2 in enumerate(positions[:i1]):
diff = p2 - p1
r = sqrt(np.dot(diff, diff))
expf = exp(rho0 * (1.0 - r / r0))
energy += epsilon * expf * (expf - 2)
energies[i1] += epsilon * expf * (expf - 2)
energies[i2] += epsilon * expf * (expf - 2)
F = preF * expf * (expf - 1) * diff / r
forces[i1] -= F
forces[i2] += F
self.results['energy'] = energy
self.results['forces'] = forces
self.results['potential_energies'] = energies
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
try:
results = self.checkpoint.load(atoms)
prev_atoms, results = results[0], results[1:]
try:
assert atoms_almost_equal(atoms, prev_atoms)
except AssertionError:
raise AssertionError('mismatch between current atoms and those read from checkpoint file')
self.logger.pr('retrieved results for {0} from checkpoint'.format(properties))
# save results in calculator for next time
if isinstance(self.calculator, Calculator):
if not hasattr(self.calculator, 'results'):
self.calculator.results = {}
self.calculator.results.update(dict(zip(properties, results)))
except NoCheckpoint:
if isinstance(self.calculator, Calculator):
self.logger.pr('doing calculation of {0} with new-style calculator interface'.format(properties))
self.calculator.calculate(atoms, properties, system_changes)
results = [self.calculator.results[prop] for prop in properties]
else:
self.logger.pr('doing calculation of {0} with old-style calculator interface'.format(properties))
results = []
for prop in properties:
method_name = CheckpointCalculator.property_to_method_name[prop]
method = getattr(self.calculator, method_name)
results.append(method(atoms))
_calculator = atoms.get_calculator
try:
atoms.set_calculator(self.calculator)
self.checkpoint.save(atoms, *results)
finally:
atoms.set_calculator(_calculator)
self.results = dict(zip(properties, results))
def run_calculation(self, atoms=None, properties=None,
system_changes=all_changes):
'''
Internal calculation executor. We cannot use FileIOCalculator
directly since we need to support remote execution.
This calculator is different from others.
It prepares the directory, launches the remote process and
raises the exception to signal that we need to come back for results
when the job is finished.
'''
if properties is None:
properties = ['energy']
Calculator.calculate(self, atoms, properties, system_changes)
self.write_input(self.atoms, properties, system_changes)
if self.command is None:
raise RuntimeError('Please configure RemoteQE calculator!')
olddir = os.getcwd()
errorcode=0
try:
os.chdir(self.directory)
output = subprocess.check_output(self.command, shell=True)
self.jobid=output.split()[0]
self.submited=True
#print "Job %s submitted. Waiting for it." % (self.jobid)
# Waiting loop. To be removed.
except subprocess.CalledProcessError as e:
errorcode=e.returncode
finally:
os.chdir(olddir)
if errorcode:
raise RuntimeError('%s returned an error: %d' %
(self.name, errorcode))
self.read_results()
def calculate(self, atoms=None, properties=None,
system_changes=all_changes):
'''Do the calculation.'''
if(not properties):
properties = ['energy']
Calculator.calculate(self, atoms, properties, system_changes)
if('numbers' in system_changes or
'initial_magmoms' in system_changes):
self._release_force_env()
if(self._force_env_id is None):
self._create_force_env()
n_atoms = len(self.atoms)
if('cell' in system_changes):
cell = self.atoms.get_cell()
self._send('SET_CELL %d' % self._force_env_id)
self._send(' '.join(['%.10f' % x for x in cell.flat]))
assert(self._recv() == '* READY')
if('positions' in system_changes):
self._send('SET_POS %d' % self._force_env_id)
self._send('%d' % (3 * n_atoms))
for pos in self.atoms.get_positions():
self._send('%.10f %.10f %.10f' % (pos[0], pos[1], pos[2]))
self._send('*END')
assert(float(self._recv()) >= 0) # max change -> ignore
assert(self._recv() == '* READY')
self._send('EVAL_EF %d' % self._force_env_id)
assert(self._recv() == '* READY')
self._send('GET_E %d' % self._force_env_id)
self.results['energy'] = float(self._recv()) * Hartree
assert(self._recv() == '* READY')
forces = np.zeros(shape=(n_atoms, 3))
self._send('GET_F %d' % self._force_env_id)
assert(int(self._recv()) == 3 * n_atoms)
for i in range(n_atoms):
line = self._recv()
forces[i, :] = [float(x) for x in line.split()]
assert(self._recv() == '* END')
assert(self._recv() == '* READY')
self.results['forces'] = forces * Hartree / Bohr
self._send('GET_STRESS %d' % self._force_env_id)
line = self._recv()
assert(self._recv() == '* READY')
stress = np.array([float(x) for x in line.split()]).reshape(3, 3)
assert(np.all(stress == np.transpose(stress))) # should be symmetric
# Convert 3x3 stress tensor to Voigt form as required by ASE
stress = np.array([stress[0, 0], stress[1, 1], stress[2, 2],
stress[1, 2], stress[0, 2], stress[0, 1]])
self.results['stress'] = stress * Hartree / Bohr**3
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
energy, forces = 0, np.zeros((self.N, 3))
e, f = self._calculate_harm(atoms)
energy += e
forces += f
e, f = self._calculate_soft(atoms)
energy += e
forces += f
self.results = {'energy': energy, 'forces': forces}
def calculate(self, atoms=None, properties=['energy', 'forces'], system_changes=['positions']):
Calculator.calculate(self, atoms, properties, system_changes)
if 'energy' in properties:
self.results['energy'] = self.energy(atoms)
if 'forces' in properties:
F = self.forces(atoms)
if self.noZ:
F[:,-1] = 0
self.results['forces'] = F
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms)
self.kpts = kpts2ndarray(self.parameters.kpts, atoms)
icell = atoms.get_reciprocal_cell() * 2 * np.pi * Bohr
n = 7
offsets = np.indices((n, n, n)).T.reshape((n**3, 1, 3)) - n // 2
eps = 0.5 * (np.dot(self.kpts + offsets, icell)**2).sum(2).T
eps.sort()
self.eigenvalues = eps[:, :20] * Ha
self.results = {'energy': 0.0}
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms)
self.kpts = kpts2ndarray(self.parameters.kpts, atoms)
icell = atoms.get_reciprocal_cell() * 2 * np.pi * Bohr
n = 7
offsets = np.indices((n, n, n)).T.reshape((n**3, 1, 3)) - n // 2
eps = 0.5 * (np.dot(self.kpts + offsets, icell)**2).sum(2).T
eps.sort()
self.eigenvalues = eps[:, :20] * Ha
self.results = {'energy': 0.0}
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
julia_atoms = ASEAtoms(atoms)
self.results = {}
if 'energy' in properties:
self.results['energy'] = julia.energy(self.julip_calculator, julia_atoms)
if 'forces' in properties:
self.results['forces'] = np.array(julia.forces(self.julip_calculator, julia_atoms))
if 'stress' in properties:
self.results['stress'] = np.array(julia.stress(self.julip_calculator, julia_atoms))
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms)
cf_by_name = self.corrFunc.get_cf_by_cluster_names(
atoms, self.eci.keys())
energy = 0.0
for key, value in self.eci.items():
energy += value * cf_by_name[key]
self.results["energy"] = energy * len(
atoms) # Should not return energy per atom!
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
#chem_symbols = list(set(atoms.get_chemical_symbols()))
#self.ff = PyXtal_FF(model={'system': chem_symbols}, logo=self.parameters.logo)
#self.ff.run(mode='predict', mliap=self.parameters.mliap)
# base potential
if self.parameters.ff._descriptors['base_potential']:
self.base_potential = ZBL(
self.parameters.ff._descriptors['base_potential']['inner'],
self.parameters.ff._descriptors['base_potential']['outer'],
atomic_energy=True)
base_results = self.base_potential.calculate(atoms)
base_energy = base_results['energy']
base_forces = base_results['force']
base_stress = base_results['stress'] # eV/A^3
base_energies = base_results['energies']
else:
base_energy = 0
base_forces = np.zeros([len(atoms), 3])
base_stress = np.zeros([6])
base_energies = 0.
desp = compute_descriptor(self.parameters.ff._descriptors, atoms)
energies, forces, stress = self.parameters.ff.model.calculate_properties(
desp, bforce=True, bstress=True)
self.desp = desp
self.results['energies'] = energies + base_energies
self.results['energy'] = energies.sum() + base_energy
self.results['free_energy'] = energies.sum() + base_energy
self.results['forces'] = forces + base_forces
# pyxtal_ff and lammps uses: xx, yy, zz, xy, xz, yz
# ase uses: xx, yy, zz, yz, xz, xy
# from eV/A^3 to GPa
self.results['stress_zbl'] = base_stress / units.GPa
self.results['energy_zbl'] = base_energy
self.results['forces_zbl'] = base_forces
self.results['stress_ml'] = stress
self.results['energy_ml'] = energies.sum()
self.results['forces_ml'] = forces
# ase counts the stress differently
if self.style == 'ase':
self.results['stress'] = -(stress * units.GPa +
base_stress)[[0, 1, 2, 5, 4, 3]]
else:
self.results['stress'] = self.results['stress_zbl'] + self.results[
'stress_ml']
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
natoms = len(self.atoms)
sigma = self.parameters.sigma
epsilon = self.parameters.epsilon
rc = self.parameters.rc
if rc is None:
rc = 3 * sigma
if 'numbers' in system_changes:
self.nl = NeighborList([rc / 2] * natoms, self_interaction=False)
self.nl.update(self.atoms)
positions = self.atoms.positions
cell = self.atoms.cell
e0 = 4 * epsilon * ((sigma / rc)**12 - (sigma / rc)**6)
energy = 0.0
forces = np.zeros((natoms, 3))
stress = np.zeros((3, 3))
for a1 in range(natoms):
neighbors, offsets = self.nl.get_neighbors(a1)
cells = np.dot(offsets, cell)
d = positions[neighbors] + cells - positions[a1]
r2 = (d**2).sum(1)
c6 = (sigma**2 / r2)**3
c6[r2 > rc**2] = 0.0
energy -= e0 * (c6 != 0.0).sum()
c12 = c6**2
energy += 4 * epsilon * (c12 - c6).sum()
f = (24 * epsilon * (2 * c12 - c6) / r2)[:, np.newaxis] * d
forces[a1] -= f.sum(axis=0)
for a2, f2 in zip(neighbors, f):
forces[a2] += f2
stress += np.dot(f.T, d)
if 'stress' in properties:
if self.atoms.number_of_lattice_vectors == 3:
stress += stress.T.copy()
stress *= -0.5 / self.atoms.get_volume()
self.results['stress'] = stress.flat[[0, 4, 8, 5, 2, 1]]
else:
raise PropertyNotImplementedError
self.results['energy'] = energy
self.results['free_energy'] = energy
self.results['forces'] = forces
def calculate(self, atoms=None,
properties=['energy'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
natoms = len(self.atoms)
sigma = self.parameters.sigma
epsilon = self.parameters.epsilon
rc = self.parameters.rc
if rc is None:
rc = 3 * sigma
if 'numbers' in system_changes:
self.nl = NeighborList([rc / 2] * natoms, self_interaction=False)
self.nl.update(self.atoms)
positions = self.atoms.positions
cell = self.atoms.cell
e0 = 4 * epsilon * ((sigma / rc)**12 - (sigma / rc)**6)
energy = 0.0
forces = np.zeros((natoms, 3))
stress = np.zeros((3, 3))
for a1 in range(natoms):
neighbors, offsets = self.nl.get_neighbors(a1)
cells = np.dot(offsets, cell)
d = positions[neighbors] + cells - positions[a1]
r2 = (d**2).sum(1)
c6 = (sigma**2 / r2)**3
c6[r2 > rc**2] = 0.0
energy -= e0 * (c6 != 0.0).sum()
c12 = c6**2
energy += 4 * epsilon * (c12 - c6).sum()
f = (24 * epsilon * (2 * c12 - c6) / r2)[:, np.newaxis] * d
#print d
#print r2**.5
#print offsets
#print f
#print neighbors
forces[a1] -= f.sum(axis=0)
for a2, f2 in zip(neighbors, f):
forces[a2] += f2
stress += np.dot(f.T, d)
#stress = np.dot(stress, cell)
stress += stress.T.copy()
stress *= -0.5 / self.atoms.get_volume()
self.results['energy'] = energy
self.results['forces'] = forces
self.results['stress'] = stress.flat[[0, 4, 8, 5, 2, 1]]
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
nat = len(self.atoms)
atnums = self.atoms.numbers
atnums_in_system = set(atnums)
i_n, j_n, dr_nc, abs_dr_n = neighbour_list(
'ijDd', self.atoms, self.dict)
e_n = np.zeros_like(abs_dr_n)
de_n = np.zeros_like(abs_dr_n)
for params, pair in enumerate(self.dict):
if pair[0] == pair[1]:
mask1 = atnums[i_n] == pair[0]
mask2 = atnums[j_n] == pair[0]
mask = np.logical_and(mask1, mask2)
e_n[mask] = self.f[pair](abs_dr_n[mask])
de_n[mask] = self.df[pair](abs_dr_n[mask])
if pair[0] != pair[1]:
mask1 = np.logical_and(
atnums[i_n] == pair[0], atnums[j_n] == pair[1])
mask2 = np.logical_and(
atnums[i_n] == pair[1], atnums[j_n] == pair[0])
mask = np.logical_or(mask1, mask2)
e_n[mask] = self.f[pair](abs_dr_n[mask])
de_n[mask] = self.df[pair](abs_dr_n[mask])
epot = 0.5*np.sum(e_n)
# Forces
df_nc = -0.5*de_n.reshape(-1, 1)*dr_nc/abs_dr_n.reshape(-1, 1)
# Sum for each atom
fx_i = np.bincount(j_n, weights=df_nc[:, 0], minlength=nat) - \
np.bincount(i_n, weights=df_nc[:, 0], minlength=nat)
fy_i = np.bincount(j_n, weights=df_nc[:, 1], minlength=nat) - \
np.bincount(i_n, weights=df_nc[:, 1], minlength=nat)
fz_i = np.bincount(j_n, weights=df_nc[:, 2], minlength=nat) - \
np.bincount(i_n, weights=df_nc[:, 2], minlength=nat)
# Virial
virial_v = -np.array([dr_nc[:, 0]*df_nc[:, 0], # xx
dr_nc[:, 1]*df_nc[:, 1], # yy
dr_nc[:, 2]*df_nc[:, 2], # zz
dr_nc[:, 1]*df_nc[:, 2], # yz
dr_nc[:, 0]*df_nc[:, 2], # xz
dr_nc[:, 0]*df_nc[:, 1]]).sum(axis=1) # xy
self.results = {'energy': epot,
'stress': virial_v/self.atoms.get_volume(),
'forces': np.transpose([fx_i, fy_i, fz_i])}
def calculate(self,
atoms=None,
properties=["energy"],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
image = atoms
natoms = len(image)
energy = 0.0
forces = np.zeros((natoms, 3))
self.results["energy"] = energy
self.results["forces"] = forces
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
natoms = len(self.atoms)
k = self.parameters.k
tolerAngs = self.parameters.tolerAngs
tolerMult = self.parameters.tolerMult
cutoff = self.parameters.cutoff
if 'numbers' in system_changes:
# Want agregation? cutoff > 2.00
# Want uniform? cutoff < 1.50
# Directional? cutoff < 1.25
self.nl = NeighborList([cutoff / 2] * natoms,\
self_interaction=False)
self.nl.update(self.atoms)
positions = self.atoms.positions
cell = self.atoms.cell
energy = 0.0
forces = np.zeros((natoms, 3))
stress = np.zeros((3, 3))
for a1 in range(natoms):
neighbors, offsets = self.nl.get_neighbors(a1)
# print(neighbors)
cells = np.dot(offsets, cell)
vecBond = positions[neighbors] + cells - positions[a1]
lenBond = np.sqrt((vecBond**2).sum(1))
covalBl = covalRadii[self.atoms.get_atomic_numbers()[a1]]+\
covalRadii[self.atoms.get_atomic_numbers()[neighbors]]
compress = covalBl - lenBond
energy += k / 2 * ((compress)**2).sum()
# only repulsion
compress[covalBl - lenBond < tolerAngs] = 0.0
compress[lenBond / covalBl > 1 - tolerMult] = 0.0
# # also attraction
# compress[np.abs(covalBl - lenBond) < tolerAngs] = 0.0
# compress[np.abs(1 - lenBond / covalBl) < tolerMult] = 0.0
f = k * (compress)[:, np.newaxis] * vecBond
forces[a1] -= f.sum(axis=0)
for a2, f2 in zip(neighbors, f):
forces[a2] += f2
self.results['energy'] = energy
self.results['free_energy'] = energy
self.results['forces'] = forces
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
results = [
self.calculator.get_property(prop, atoms) for prop in properties
]
# Only count evaluation if system (typically the position)
# has changed
if system_changes:
self.n_evals += 1
self.results = dict(zip(properties, results))
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
R = atoms.get_positions()
charges = self.get_virtual_charges(atoms)
pbc = atoms.pbc
energy = 0.0
forces = np.zeros_like(atoms.get_positions())
for m in range(len(atoms)):
D = R[m + 1:] - R[m]
shift = np.zeros_like(D)
for i, periodic in enumerate(pbc):
if periodic:
L = atoms.cell.diagonal()[i]
shift[:, i] = (D[:, i] + L / 2) % L - L / 2 - D[:, i]
D += shift
d2 = (D**2).sum(1)
d = d2**0.5
x1 = d > self.rc - self.width
x2 = d < self.rc
x12 = np.logical_and(x1, x2)
y = (d[x12] - self.rc + self.width) / self.width
t = np.zeros(len(d)) # cutoff function
t[x2] = 1.0
t[x12] -= y**2 * (3.0 - 2.0 * y)
dtdd = np.zeros(len(d))
dtdd[x12] -= 6.0 / self.width * y * (1.0 - y)
c6 = (self.sigma**2 / d2)**3
c12 = c6**2
e_lj = 4 * self.epsilon * (c12 - c6)
e_c = k_c * charges[m + 1:] * charges[m] / d
energy += np.dot(t, e_lj)
energy += np.dot(t, e_c)
F = (24 * self.epsilon *
(2 * c12 - c6) / d2 * t - e_lj * dtdd / d)[:, None] * D
forces[m] -= F.sum(0)
forces[m + 1:] += F
F = (e_c / d2 * t)[:, None] * D \
- (e_c * dtdd / d)[:, None] * D
forces[m] -= F.sum(0)
forces[m + 1:] += F
self.results['energy'] = energy
self.results['forces'] = forces
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
# construct neighbor list
i_p, j_p, r_p, r_pc = neighbour_list('ijdD',
atoms=atoms,
cutoff=self.cutoff)
nb_atoms = len(self.atoms)
nb_pairs = len(i_p)
# normal vectors
n_pc = (r_pc.T / r_p).T
nx_p, ny_p, nz_p = n_pc.T
# construct triplet list
first_i = first_neighbours(nb_atoms, i_p)
ij_t, ik_t = triplet_list(first_i)
# calculate energy
G_t = self.G(r_pc[ij_t], r_pc[ik_t])
xi_p = np.bincount(ij_t, weights=G_t, minlength=nb_pairs)
F_p = self.F(r_p, xi_p)
epot = 0.5 * np.sum(F_p)
d1G_t = self.d1G(r_pc[ij_t], r_pc[ik_t])
d2F_d2G_t = (self.d2F(r_p[ij_t], xi_p[ij_t]) *
self.d2G(r_pc[ij_t], r_pc[ik_t]).T).T
# calculate forces (per pair)
fx_p = \
self.d1F(r_p, xi_p) * n_pc[:, 0] + \
self.d2F(r_p, xi_p) * np.bincount(ij_t, d1G_t[:, 0], minlength=nb_pairs) + \
np.bincount(ik_t, d2F_d2G_t[:, 0], minlength=nb_pairs)
fy_p = \
self.d1F(r_p, xi_p) * n_pc[:, 1] + \
self.d2F(r_p, xi_p) * np.bincount(ij_t, d1G_t[:, 1], minlength=nb_pairs) + \
np.bincount(ik_t, d2F_d2G_t[:, 1], minlength=nb_pairs)
fz_p = \
self.d1F(r_p, xi_p) * n_pc[:, 2] + \
self.d2F(r_p, xi_p) * np.bincount(ij_t, d1G_t[:, 2], minlength=nb_pairs) + \
np.bincount(ik_t, d2F_d2G_t[:, 2], minlength=nb_pairs)
# collect atomic forces
fx_n = 0.5 * (np.bincount(i_p, weights=fx_p) -
np.bincount(j_p, weights=fx_p))
fy_n = 0.5 * (np.bincount(i_p, weights=fy_p) -
np.bincount(j_p, weights=fy_p))
fz_n = 0.5 * (np.bincount(i_p, weights=fz_p) -
np.bincount(j_p, weights=fz_p))
f_n = np.transpose([fx_n, fy_n, fz_n])
self.results = {'energy': epot, 'forces': f_n}
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
P = atoms.positions
D = np.array([P - p for p in P]) # all distance vectors
d = (D**2).sum(2)**0.5
dd = d - self.target
d.ravel()[::len(d) + 1] = 1 # avoid dividing by zero
d4 = d**4
e = 0.5 * (dd**2 / d4).sum()
f = -2 * ((dd * (1 - 2 * dd / d) / d**5)[..., np.newaxis] * D).sum(0)
self.results = {'energy': e, 'forces': f}
def calculate(
self,
atoms=None,
properties=["energy", "forces", "stress"],
system_changes=["positions", "numbers", "cell", "pbc"],
):
"""
Inherited method from the ase Calculator class that is called by
get_property()
Parameters
----------
atoms : Atoms
Atoms object whose properties are desired
properties : list of str
List of what needs to be calculated. Can be any combination
of 'energy', 'forces' and 'stress'.
system_changes : list of str
List of what has changed since last calculation. Can be any
combination of these six: 'positions', 'numbers', 'cell',
and 'pbc'.
"""
Calculator.calculate(self, atoms, properties, system_changes)
# Update KIM API input data and neighbor list, if necessary
if system_changes:
if self.need_neigh_update(atoms, system_changes):
self.update_neigh(atoms, self.species_map)
self.energy = np.array([0.0], dtype=np.double)
self.forces = np.zeros([self.num_particles[0], 3], dtype=np.double)
self.update_compute_args_pointers(self.energy, self.forces)
else:
self.update_kim_coords(atoms)
self.kim_model.compute(self.compute_args, self.release_GIL)
energy = self.energy[0]
forces = self.assemble_padding_forces()
try:
volume = atoms.get_volume()
stress = self.compute_virial_stress(self.forces, self.coords, volume)
except ValueError: # Volume cannot be computed
stress = None
# Quantities passed back to ASE
self.results["energy"] = energy
self.results["free_energy"] = energy
self.results["forces"] = forces
self.results["stress"] = stress
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if system_changes:
self.results = {}
if 'energy' in properties and 'energy' not in self.results:
e1 = self.calc1.get_potential_energy(atoms)
e2 = self.calc2.get_potential_energy(atoms)
self.results['energy'] = e1 + e2
if 'forces' in properties and 'forces' not in self.results:
f1 = self.calc1.get_forces(atoms)
f2 = self.calc2.get_forces(atoms)
self.results['forces'] = f1 + f2
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
dataset = TestDataset(images=atoms,
descriptor=self.model.descriptor,
Gs=self.Gs,
fprange=self.fp_scaling,
label=self.model.label)
fp_length = dataset.fp_length()
unique_atoms = dataset.unique()
architecture = copy.copy(self.model.structure)
architecture.insert(0, fp_length)
batch_size = len(dataset)
dataloader = DataLoader(dataset,
batch_size,
collate_fn=dataset.collate_test,
shuffle=False)
if properties == ['energy']:
model = FullNN(unique_atoms,
architecture,
"cpu",
forcetraining=False)
elif properties == ['forces']:
model = FullNN(unique_atoms,
architecture,
"cpu",
forcetraining=True)
model.load_state_dict(torch.load(self.label))
model.eval()
for batch in dataloader:
input_data = [batch[0], len(batch[1]), unique_atoms]
for element in unique_atoms:
input_data[0][element][0] = input_data[0][element][
0].requires_grad_(True)
fp_primes = batch[2]
energy, forces = model(input_data, fp_primes)
energy = (energy * self.target_sd) + self.target_mean
energy = np.concatenate(energy.detach().numpy())
if properties == ['forces']:
forces = (forces * self.target_sd).detach().numpy()
if self.lj:
lj_energy, lj_forces, _ = self.lj_model.lj_pred([atoms],
self.fitted_params,
self.params_dict)
lj_energy = np.squeeze(lj_energy)
energy += lj_energy
if properties == ['forces']:
forces += lj_forces
self.results["energy"] = float(energy)
self.results["forces"] = forces
def calculate(self, atoms=None, properties=['energy'],
system_changes=[]):
Calculator.calculate(self, atoms, properties, system_changes)
# only one property allowed
assert(len(properties) == 1)
# make sure we have a water molecule, and identify O, H1, H2
chemical_formula = self.atoms.get_chemical_formula(mode='all')
if chemical_formula == 'OHH':
o = 0
h1= 1
h2 =2
elif chemical_formula == 'HOH':
o = 1
h1= 0
h2 =2
elif chemical_formula == 'HHO':
o = 2
h1= 0
h2 =1
else:
raise RuntimeError("chemical formula '{}' is not a water molecule!".format(chemical_formula))
# compute internal coordinates, both stretch coordinates q1, q2 in [bohr] and theta in radians
pos=atoms.get_positions() / Bohr
#q1_tmp = (pos[h1] - pos[o]) / Bohr
#q2_tmp = (pos[h2] - pos[o]) / Bohr
#
#q1 = np.linalg.norm(q1_tmp)
#q2 = np.linalg.norm(q2_tmp)
#
#q1_norm = q1_tmp / q1
#q2_norm = q2_tmp / q2
#q_norm_sum = q1_norm + q2_norm
#q_norm_sum_norm = q_norm_sum / np.linalg.norm(q_norm_sum)
#
#theta = 2.0 * abs(np.arcsin(np.linalg.norm(np.cross(q1_norm,q_norm_sum_norm))))
q1,q2,theta = get_internal_coords_h2o(pos[o], pos[h1], pos[h2])
if properties[0] == 'energy':
V =0.0
V= h2o_pjt2.pots(q1,q2,theta)
self.results['energy'] = V * Ha
if properties[0] == 'forces':
self.results['forces'] = self.calculate_numerical_forces(atoms, d=0.00000001)
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
# natoms = len(self.atoms)
# positions = self.atoms.positions
# cell = self.atoms.cell
self.results['energy'] = self.energy
self.results['forces'] = self.forces
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if system_changes:
self.results = {}
if 'energy' in properties and 'energy' not in self.results:
self.results['energy'] = 0.0
for constraint in self.constraint:
self.results['energy'] += constraint.adjust_potential_energy(
atoms)
if 'forces' in properties and 'forces' not in self.results:
self.results['forces'] = np.zeros((len(atoms), 3))
for constraint in self.constraint:
constraint.adjust_forces(atoms, self.results['forces'])
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
X = [self.atoms]
managers = self.representation.transform(X)
energy = self.model.predict(managers)
forces = -self.model.predict(managers, compute_gradients=True)
self.results['energy'] = energy
self.results['free_energy'] = energy
self.results['forces'] = forces
def calculate(self, atoms, properties, system_changes):
"""Calculation of the energy of system and forces of all atoms."""
# The inherited method below just sets the atoms object,
# if specified, to self.atoms.
Calculator.calculate(self, atoms, properties, system_changes)
if properties == ['energy']:
energy = self.model.calculate_energy(atoms)
self.results['energy'] = energy[0]
if properties == ['forces']:
forces = self.model.calculate_forces(atoms)
self.results['forces'] = forces[0]
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
julia_atoms = ASEAtoms(atoms)
julia_atoms = convert(julia_atoms)
self.results = {}
if 'energy' in properties:
self.results['energy'] = energy(self.julip_calculator, julia_atoms)
if 'forces' in properties:
self.results['forces'] = np.array(
forces(self.julip_calculator, julia_atoms))
if 'stress' in properties:
voigt_stress = full_3x3_to_voigt_6_stress(
np.array(stress(self.julip_calculator, julia_atoms)))
self.results['stress'] = voigt_stress
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
E = 0.0
R = atoms.positions
F = np.zeros_like(R)
for a, r in enumerate(R):
D = R - r
d = (D**2).sum(1)**0.5
x = d - 1.0
E += np.vdot(x, x)
d[a] = 1
F -= (x / d)[:, None] * D
energy = 0.25 * E
self.results = {'energy': energy, 'forces': F}
def calculate(self, atoms=None, properties=None, system_changes=all_changes):
"""calculate and store energy"""
if not properties:
properties = 'energy'
"""
If system_changes, atoms etc will be updated.
"""
Calculator.calculate(self, atoms, properties, system_changes)
e_old = self.ann_model.predict(self.atoms)[0][0]
self.results['energy'] = float(e_old)
self.results['forces'] = np.array(self.cal_force(e_old))
def calculate(self,
atoms=None,
properties=None,
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
image = atoms
natoms = len(image)
energy = 0.0
forces = np.zeros((natoms, 3))
self.results["energy"] = energy
self.results["forces"] = forces
self.results["stress"] = -np.array([0, 0, 0, 0, 0, 0])
self.results["force_stds"] = zeros_like(forces)
atoms.info["max_force_stds"] = np.nanmax(self.results["force_stds"])
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
E = 0.0
R = atoms.positions
F = np.zeros_like(R)
for a, r in enumerate(R):
D = R - r
d = (D**2).sum(1)**0.5
x = d - 1.0
E += np.vdot(x, x)
d[a] = 1
F -= (x / d)[:, None] * D
energy = 0.25 * E
self.results = {'energy': energy, 'forces': F}
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
data_object = self.a2g.convert(atoms)
batch = data_list_collater([data_object])
predictions = self.trainer.predict(batch,
per_image=False,
disable_tqdm=True)
if self.trainer.name == "s2ef":
self.results["energy"] = predictions["energy"].item()
self.results["forces"] = predictions["forces"].cpu().numpy()
elif self.trainer.name == "is2re":
self.results["energy"] = predictions["energy"].item()
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
data_object = self.a2g.convert(atoms)
batch = data_list_collater([data_object])
if self.pbc_graph:
edge_index, cell_offsets, neighbors = radius_graph_pbc(
batch, 6, 50, batch.pos.device)
batch.edge_index = edge_index
batch.cell_offsets = cell_offsets
batch.neighbors = neighbors
predictions = self.trainer.predict(batch)
self.results["energy"] = predictions["energy"][0]
self.results["forces"] = predictions["forces"][0]
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
# start_time2 = time.time()
## make up for stress
## TODO
# stress_ani = np.zeros((1, 3))
stress_ani = np.zeros(6)
if self.Setup or self.nc.ncl[0].request_setup():
# Setup molecule for MD
natoms = len(self.atoms)
atom_symbols = self.atoms.get_chemical_symbols()
xyz = self.atoms.get_positions()
self.nc.set_molecule(xyz.astype(np.float32), atom_symbols)
self.nc.set_pbc(self.atoms.get_pbc()[0],
self.atoms.get_pbc()[1],
self.atoms.get_pbc()[2])
self.Setup = False
else:
xyz = self.atoms.get_positions()
# Set the conformers in NeuroChem
self.nc.set_coordinates(xyz.astype(np.float32))
# TODO works only for 3D periodic. For 1,2D - update np.zeros((3,3)) part
pbc_inv = (np.linalg.inv(self.atoms.get_cell())).astype(
np.float32) if atoms.pbc.all() else np.zeros(
(3, 3), dtype=np.float32)
self.nc.set_cell((self.atoms.get_cell()).astype(np.float32),
pbc_inv)
energy, force, stddev = self.nc.compute_mean_props()
self.stddev = conv_au_ev * stddev
self.results['energy'] = conv_au_ev * energy
if 'forces' in properties:
forces = conv_au_ev * force
# restrain atoms
for i in self.reslist:
forces[i] = 0.0
self.results['forces'] = -forces
self.results['stress'] = conv_au_ev * stress_ani
def calculate(self,
atoms=None,
properties=["energy"],
system_changes=all_changes):
if self.calculation_required(atoms, properties):
Calculator.calculate(self, atoms)
posinp = Posinp.from_ase(atoms)
job = Job(posinp=posinp, calculator=self.schnetpackcalculator)
for prop in properties:
job.run(prop)
results = {}
for prop, result in zip(job.results.keys(), job.results.values()):
results[prop] = np.squeeze(result)
self.results = results
def calculate(self,
atoms=None,
properties=['energy'],
system_changes=all_changes):
Calculator.calculate(self, atoms, properties, system_changes)
self.write_pw_input(atoms)
self.run_pw()
Ep = self.parse_E()
F = self.parse_F(atoms)
# s = self.parse_Stress()
self.results['energy'] = Ep
self.results['forces'] = F
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
i_n, j_n, dr_nc, abs_dr_n = neighbour_list('ijDd', self.atoms,
self._db_cutoff)
epot, virial_v, forces_ic = self.energy_virial_and_forces(
self.atoms.numbers, i_n, j_n, dr_nc, abs_dr_n)
self.results = {
'energy': epot,
'free_energy': epot,
'stress': virial_v / self.atoms.get_volume(),
'forces': forces_ic
}
def calculate(self, atoms=None, properties=['energy'],
system_changes=['positions', 'numbers', 'cell',
'pbc', 'charges','magmoms']):
Calculator.calculate(self, atoms)
calc_molcell = self.molcell.copy()
calc_molcell.atom = ase_atoms_to_pyscf(atoms)
calc_molcell.a = atoms.cell
calc_molcell.build(None,None)
self.mf = self.mf_class(calc_molcell)
for key in self.mf_dict:
self.mf.__dict__[key] = self.mf_dict[key]
self.results['energy']=self.mf.scf()
self.results['mf']=self.mf
def calculate(self, atoms=None, properties=['energy'],
system_changes=some_changes):
Calculator.calculate(self, atoms, properties, system_changes)
self.write_input(self.atoms, properties, system_changes)
olddir = os.getcwd()
try:
os.chdir(self.directory)
errorcode = subprocess.call(self.command, shell=True)
finally:
os.chdir(olddir)
if errorcode:
raise RuntimeError('%s returned an error: %d' %
(self.name, errorcode))
self.read_results()
def calculate(self, atoms=None, properties=['energy'],
system_changes=['positions', 'numbers', 'cell']):
Calculator.calculate(self, atoms, properties, system_changes)
if not system_changes:
return
if 'numbers' in system_changes:
self.close()
self._run_vasp(atoms)
new = read(os.path.join(self.path, 'vasprun.xml'), index=-1)
self.results = {'free_energy': new.get_potential_energy(force_consistent=True),
'energy': new.get_potential_energy(),
'forces': new.get_forces()[self.resort],
'stress': new.get_stress()}
def calculate(
self,
atoms=None,
properties=["energy"],
system_changes=["positions", "numbers", "cell", "pbc", "charges", "magmoms"],
):
Calculator.calculate(self, atoms)
calc_molcell = self.molcell.copy()
calc_molcell.atom = ase_atoms_to_pyscf(atoms)
calc_molcell.h = atoms.cell
calc_molcell.build(None, None)
self.mf = self.mf_class(calc_molcell)
for key in self.mf_dict:
self.mf.__dict__[key] = self.mf_dict[key]
self.results["energy"] = self.mf.scf()
self.results["mf"] = self.mf
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if system_changes:
if 'energy' in self.results:
del self.results['energy']
if 'forces' in self.results:
del self.results['forces']
if 'energy' not in self.results:
if self.permutation is None:
crd = np.reshape(atoms.get_positions(), (1, len(atoms), 3))
else:
crd = np.reshape(atoms.get_positions()
[self.permutation[0, :]], (1, len(atoms), 3))
sander.set_positions(crd)
e, f = sander.energy_forces()
self.results['energy'] = e.tot * units.kcal / units.mol
if self.permutation is None:
self.results['forces'] = (np.reshape(np.array(f),
(len(atoms), 3)) *
units.kcal / units.mol)
else:
ff = np.reshape(np.array(f), (len(atoms), 3)) * \
units.kcal / units.mol
self.results['forces'] = ff[self.permutation[1, :]]
if 'forces' not in self.results:
if self.permutation is None:
crd = np.reshape(atoms.get_positions(), (1, len(atoms), 3))
else:
crd = np.reshape(atoms.get_positions()[self.permutation[0, :]],
(1, len(atoms), 3))
sander.set_positions(crd)
e, f = sander.energy_forces()
self.results['energy'] = e.tot * units.kcal / units.mol
if self.permutation is None:
self.results['forces'] = (np.reshape(np.array(f),
(len(atoms), 3)) *
units.kcal / units.mol)
else:
ff = np.reshape(np.array(f), (len(atoms), 3)) * \
units.kcal / units.mol
self.results['forces'] = ff[self.permutation[1, :]]
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if self.np_atoms is None:
self.initialize_np(atoms)
if self.sp_atoms is None:
self.initialize_sp(atoms)
energy = 0
forces = np.zeros(shape=(len(atoms), 3))
## 1. Nanoparticle
self.np_atoms.positions = atoms.positions[self.np_selection]
if self.vacuum:
self.np_atoms.positions += (self.center -
self.np_atoms.positions.mean(axis=0))
energy += self.np_calc.get_potential_energy(self.np_atoms)
np_forces = self.np_calc.get_forces(self.np_atoms)
if self.vacuum:
np_forces -= np_forces.mean(axis=0)
forces[self.np_selection] += np_forces
## 2. Support. Copy-Paste. TODO: make loop over subsystems
self.sp_atoms.positions = atoms.positions[self.sp_selection]
if self.vacuum:
self.sp_atoms.positions += (self.center -
self.sp_atoms.positions.mean(axis=0))
energy += self.sp_calc.get_potential_energy(self.sp_atoms)
sp_forces = self.sp_calc.get_forces(self.sp_atoms)
if self.vacuum:
sp_forces -= sp_forces.mean(axis=0)
forces[self.sp_selection] += sp_forces
## 3. INTERACTION
if self.ia_calc is not None:
ienergy, inpforces, ispforces = self.ia_calc.calculate(
self.np_atoms, self.sp_atoms, (0, 0, 0))
forces[self.np_selection] += inpforces
forces[self.sp_selection] += ispforces
energy += ienergy
## 4. return result
self.results['energy'] = energy
self.results['forces'] = forces
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if not(system_changes is None):
self.update_atoms()
species = set(atoms.numbers)
charges = [atom.charge for atom in atoms]
energy = 0.0
forces = np.zeros((len(atoms), 3))
chems = atoms.get_chemical_symbols()
for i, R1, symb1, Q1 in zip(count(), atoms.positions, chems, charges):
for j, R2, symb2, Q2 in zip(count(), atoms.positions, chems, charges):
if j<=i:
continue
pair = _tup2str((symb1,symb2))
if pair not in self.parameters:
continue
A, rho, C = self.parameters[pair]
D = R1 - R2
d2 = (D**2).sum()
if (d2 > 0.001):
d = np.sqrt(d2)
coul = COUL_COEF*Q1*Q2/d
Aexp = A*np.exp(-d/rho)
Cr6 = C/d2**3
energy += Aexp - Cr6 + coul
force = (1/rho*Aexp - 6/d*Cr6 + coul/d)*D/d
forces[i, :] += force
forces[j, :] += -force
if 'energy' in properties:
self.results['energy'] = energy
if 'forces' in properties:
self.results['forces'] = forces
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if isinstance(self.calculator, Calculator):
results = [self.calculator.get_property(prop, atoms)
for prop in properties]
else:
results = []
for prop in properties:
method_name = self.property_to_method_name[prop]
method = getattr(self.calculator, method_name)
results.append(method(atoms))
if 'energy' in properties or 'energies' in properties:
self.energy_evals.setdefault(self.label, 0)
self.energy_evals[self.label] += 1
try:
energy = results[properties.index('energy')]
except IndexError:
energy = sum(results[properties.index('energies')])
logger.info('energy call count=%d energy=%.3f',
self.energy_evals[self.label], energy)
self.results = dict(zip(properties, results))
if 'forces' in self.results:
fmax = self.fmax.setdefault(self.label, [])
walltime = self.walltime.setdefault(self.label, [])
forces = self.results['forces'].copy()
energy_count = self.energy_count.setdefault(self.label, [])
energy_evals = self.energy_evals.setdefault(self.label, 0)
energy_count.append(energy_evals)
for constraint in atoms.constraints:
constraint.adjust_forces(atoms, forces)
fmax.append(abs(forces).max())
walltime.append(time.time())
logger.info('force call fmax=%.3f', fmax[-1])
if self.dumpjson:
self.write_json('dump.json')
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
a = self.parameters['a']
rc = self.parameters['rc']
k = self.parameters['k']
beta = self.parameters['beta']
energies = np.zeros(len(atoms))
forces = np.zeros((len(atoms), 3))
velocities = (atoms.get_momenta().T/atoms.get_masses()).T
i, j, dr, r = neighbour_list('ijDd', atoms, rc)
if len(i) > 0:
dr_hat = (dr.T/r).T
dv = velocities[j] - velocities[i]
de = 0.5*k*(r - a)**2 # spring energies
e = 0.5*de # half goes to each end of spring
f = (k*(r - a)*dr_hat.T).T + beta*dv
energies[:] = np.bincount(i, e)
for kk in range(3):
forces[:, kk] = np.bincount(i, weights=f[:, kk])
energy = energies.sum()
# add energy 0.5*k*(rc - a)**2 for each broken bond
if len(i) < self.crystal_bonds:
de = 0.5*k*(rc - a)**2
energy += 0.5*de*(self.crystal_bonds - len(i))
# Stokes dissipation
if 'stokes' in atoms.arrays:
b = atoms.get_array('stokes')
forces -= (velocities.T*b).T
self.results = {'energy': energy,
'forces': forces}
def calculate(self, atoms, properties, system_changes):
Calculator.calculate(self, atoms, properties, system_changes)
if self.qmatoms is None:
self.initialize(atoms)
self.mmatoms.set_positions(atoms.positions[~self.mask])
self.qmatoms.set_positions(atoms.positions[self.mask])
if self.vacuum:
shift = self.center - self.qmatoms.positions.mean(axis=0)
self.qmatoms.positions += shift
else:
shift = (0, 0, 0)
self.embedding.update(shift)
ienergy, iqmforces, immforces = self.interaction.calculate(
self.qmatoms, self.mmatoms, shift)
qmenergy = self.qmatoms.get_potential_energy()
mmenergy = self.mmatoms.get_potential_energy()
energy = ienergy + qmenergy + mmenergy
print('Energies: {0:12.3f} {1:+12.3f} {2:+12.3f} = {3:12.3f}'
.format(ienergy, qmenergy, mmenergy, energy), file=self.output)
qmforces = self.qmatoms.get_forces()
mmforces = self.mmatoms.get_forces()
mmforces += self.embedding.get_mm_forces()
forces = np.empty((len(atoms), 3))
forces[self.mask] = qmforces + iqmforces
forces[~self.mask] = mmforces + immforces
self.results['energy'] = energy
self.results['forces'] = forces
def calculate(self, atoms=None, properties=['energy'],
system_changes=all_changes):
sim = self.sim
# check that only things we actually pass to PINY are changed
if not self.changes.issuperset(system_changes):
msg = 'Not all changes are supported: {:s}'.format(str(system_changes))
raise NotImplementedError(msg)
# update PINY positions, recalculate ghosts and set them back in atoms
sim.set_x((atoms.get_positions() / units.Bohr)[:,:,np.newaxis])
atoms.set_positions(sim.get_x()[:,:,0] * units.Bohr)
# now call parent method to remember the atoms, with ghosts updated
Calculator.calculate(self, atoms=atoms)
# run and extract results
sim.update()
self.results = {
'energy': sim.get_V().item() * units.Ha,
'forces': - sim.get_dV_dx()[:,:,0] * units.Ha / units.Bohr
}
