def __iter__(self):
if type(self.filename) == type(''):
f = open(self.filename)
opened = True
# First eight lines are header
header = [f.readline() for i in range(8)]
# Rest of file is data array
data = np.loadtxt(f)
lattice = fzeros((3, 3))
for i in [1, 2, 3]:
lattice[:, i] = [float(x) for x in header[i + 1].split()[1:]]
if self.vacuum is not None:
lattice += np.diag(self.vacuum)
at = Atoms(n=len(data), lattice=lattice)
at.pos[...] = data[:, 3:6].T
at.set_atoms(self.z)
at.add_property('tag', data[:, 1].astype(int))
at.add_property('mass', data[:, 2])
at.add_property('velo', data[:, 6:9].T)
at.add_property('epot', data[:, 9])
if self.fix_tags is not None:
at.add_property('move_mask', 1)
for tag in self.fix_tags:
at.move_mask[at.tag == tag] = 0
if opened:
f.close()
yield at
def dict2atoms(row):
from quippy.elasticity import stress_matrix
at = row.toatoms(add_additional_information=True)
f = None
try:
f = at.get_forces()
except RuntimeError:
pass
e = None
try:
e = at.get_potential_energy()
except RuntimeError:
pass
v = None
try:
v = -stress_matrix(at.get_stress()) * at.get_volume()
except RuntimeError:
pass
at = Atoms(at) # convert to quippy Atoms
if f is not None:
at.add_property('force', f.T)
if e is not None:
at.params['energy'] = e
if v is not None:
at.params['virial'] = v
if 'key_value_pairs' in atoms.params:
atoms.params.update(atoms.params['key_value_pairs'])
del atoms.params['key_value_pairs']
if 'data' in atoms.params:
for (key, value) in atoms.params['data'].items():
key = str(key) # avoid unicode strings
value = np.array(value)
if value.dtype.kind == 'U':
value = value.astype(str)
if value.dtype.kind != 'S':
value = value.T
try:
at.add_property(key, value)
except (TypeError, RuntimeError):
at.params[key] = value
return at
def ASEReader(source, format=None):
"""
Helper routine to load from ASE trajectories
"""
from ase.io import read
from ase.atoms import Atoms as AseAtoms
from quippy.elasticity import stress_matrix
format_converter = {
'POSCAR': 'vasp',
'CONTCAR': 'vasp',
'OUTCAR': 'vasp-out',
'vasprun.xml': 'vasp-xml'
}
format = format_converter.get(format, format)
images = read(source, index=slice(None, None, None), format=format)
if isinstance(images, AseAtoms):
images = [images]
for at in images:
f = None
try:
f = at.get_forces()
except RuntimeError:
pass
e = None
try:
e = at.get_potential_energy(force_consistent=True)
except RuntimeError:
pass
v = None
try:
v = -stress_matrix(at.get_stress()) * at.get_volume()
except RuntimeError:
pass
at = Atoms(at) # convert to quippy Atoms
if f is not None:
at.add_property('force', f.T)
if e is not None:
at.params['energy'] = e
if v is not None:
at.params['virial'] = v
yield at
def ASEReader(source):
"""
Helper routine to load from ASE trajectories
"""
from ase.io import read
from ase.atoms import Atoms as AseAtoms
from quippy.elasticity import stress_matrix
images = read(source, index=slice(None, None, None))
if isinstance(images, AseAtoms):
images = [images]
for at in images:
f = None
try:
f = at.get_forces()
except RuntimeError:
pass
e = None
try:
e = at.get_potential_energy()
except RuntimeError:
pass
v = None
try:
v = -stress_matrix(at.get_stress()) * at.get_volume()
except RuntimeError:
pass
at = Atoms(at) # convert to quippy Atoms
if f is not None:
at.add_property('force', f.T)
if e is not None:
at.params['energy'] = e
if v is not None:
at.params['virial'] = v
yield at
def CP2KOutputReader(fh,
module=None,
type_map=None,
kind_map=None,
format=None):
# mapping from run type to (default module index, list of available module)
run_types = {
'QS': ['QUICKSTEP'],
'QMMM': ['FIST', 'QM/MM', 'QUICKSTEP'],
'MM': ['FIST']
}
filename, lines = read_text_file(fh)
run_type = cp2k_run_type(cp2k_output=lines)
if type_map is None:
type_map = {}
if kind_map is None:
kind_map = {}
try:
available_modules = run_types[run_type]
except KeyError:
raise ValueError('Unknown CP2K run type %s' % run_type)
if module is None:
module = available_modules[0]
try:
cell_index = available_modules.index(module)
except ValueError:
raise ValueError("Don't know how to read module %s from file %s" %
(module, filename))
cell_lines = [
i for i, line in enumerate(lines) if line.startswith(" CELL| Vector a")
]
if cell_lines == []:
raise ValueError("Cannot find cell in file %s" % filename)
try:
cell_line = cell_lines[cell_index]
except IndexError:
raise ValueError(
"Cannot find cell with index %d in file %s for module %s" %
(cell_index, filename, module))
lattice = fzeros((3, 3))
for i in [0, 1, 2]:
lattice[:,
i + 1] = [float(c) for c in lines[cell_line + i].split()[4:7]]
try:
start_line = lines.index(
" MODULE %s: ATOMIC COORDINATES IN angstrom\n" % module)
except ValueError:
raise ValueError(
"Cannot find atomic positions for module %s in file %s" %
(module, filename))
kinds = []
species = []
Zs = []
pos = []
masses = []
Zeffs = []
types = []
qeffs = []
for line in lines[start_line + 4:]:
if line.strip() == '':
break
if module == 'FIST':
atom, kind, typ, x, y, z, qeff, mass = line.split()
types.append(typ)
Z = type_map.get(typ, 0)
kind = int(kind)
if Z == 0:
Z = kind_map.get(kind, 0)
Zs.append(Z)
qeffs.append(float(qeff))
else:
atom, kind, sp, Z, x, y, z, Zeff, mass = line.split()
species.append(sp)
Zs.append(int(Z))
Zeffs.append(float(Zeff))
kinds.append(int(kind))
pos.append([float(x), float(y), float(z)])
masses.append(float(mass))
at = Atoms(n=len(kinds), lattice=lattice)
at.pos[...] = farray(pos).T
at.set_atoms(Zs)
at.add_property('mass', farray(masses) * MASSCONVERT)
at.add_property('kind', kinds)
if module == 'FIST':
at.add_property('type', ' ' * TABLE_STRING_LENGTH)
at.add_property('qm', False)
at.qm[:] = (at.type.stripstrings()
== '_QM_') | (at.type.stripstrings() == '_LNK')
at.type[...] = s2a(types, TABLE_STRING_LENGTH)
at.add_property('qeff', qeffs)
else:
at.species[...] = s2a(species, TABLE_STRING_LENGTH)
at.add_property('zeff', Zeffs)
yield at
def read_xml_output(xmlfile,energy_from=None, extract_forces=False, extract_dipole=False, datafile=None, cluster=None):
#parse an xml output file and return cluster with updated info
# datafile tells which energies, forces to look for, cluster Atoms object which gets returned, this is echoed in the xml file so can be left out
# If extract_forces is not given and the FORCE keyword is found in datafile, the default is to set extract_forces=True
log = logging.getLogger('molpro_driver')
if datafile is None:
datafile=MolproDatafile(xml=xmlfile)
if 'FORCE' in datafile:
extract_forces=True
energy_names = OrderedDict()
energy_names['CCSD(T)-F12'] = ["total energy"]
energy_names['CCSD(T)'] = ["total energy"]
energy_names['MP2'] = ["total energy"]
energy_names['DF-MP2'] = ["total energy"]
energy_names['DF-RMP2'] = ["energy"]
energy_names['RKS'] = ["Energy"]
energy_names['RHF'] = ["Energy"]
energy_names['DF-RHF'] = ["Energy"]
energy_names['HF'] = ["Energy"]
energy_names['DF-HF'] = ["Energy"]
#etc
gradient_names = OrderedDict()
gradient_names['CCSD(T)'] =[""]
gradient_names['RKS'] =['RKS GRADIENT']
gradient_names['MP2'] =['MP2 GRADIENT']
all_methods=OrderedDict()
all_methods['HF']=["RHF"]
all_methods['DF-HF']=["RHF"]
all_methods['RHF']=["RHF"]
all_methods['DF-RHF']=["RHF"]
all_methods['MP2']=["MP2"]
all_methods['DF-MP2']=["MP2"]
all_methods['DF-RMP2']=["DF-RMP2"]
all_methods['RKS']=["RKS"]
all_methods['CCSD(T)-F12']=["CCSD(T)-F12a","CCSD(T)-F12b"]
all_methods['CCSD(T)']=["CCSD(T)"]
if energy_from is None:
log.critical("don't know which energy to extract, use keyword energy_from with options "+str([all_methods[k] for k in iter(all_methods)]).replace('[','').replace(']',''))
#loop through datafile to look for methods.
calcs=[] #holds the keys for getting correct method, energy_name, gradient_name
data_keys_upper = [key.upper() for key in datafile._keys]
for key in all_methods._keys:
if key in data_keys_upper:
calcs.append(key)
dom = minidom.parse(xmlfile)
elements=[]
position_matrix=[]
cml = dom.documentElement.getElementsByTagName('cml:atomArray')
for l in cml[0].childNodes:
if l.nodeType== 1:
element=l.attributes['elementType'].value.encode('ascii','ignore')
elements.append(atomic_number(element))
posx = l.attributes['x3'].value.encode('ascii','ignore')
posy = l.attributes['y3'].value.encode('ascii','ignore')
posz = l.attributes['z3'].value.encode('ascii','ignore')
position_matrix.append([float(posx),float(posy),float(posz)])
if cluster is None:
cluster = Atoms(n=len(elements))
cluster.set_atoms(elements)
position_matrix=farray(position_matrix).T
if not 'ANGSTROM' in datafile._keys and not 'angstrom' in datafile._keys:
position_matrix = position_matrix * (1.0/0.529177249)
cluster.pos[:,:]=position_matrix
#note this leaves the lattice undefined
#now look for each of these energies in xml file
energy_found=False
props = dom.documentElement.getElementsByTagName('property')
for prop in props:
prop_name = prop.attributes['name'].value.encode('ascii','ignore')
prop_method = prop.attributes['method'].value.encode('ascii','ignore')
for calc in calcs:
if prop_name in energy_names[calc] and prop_method in all_methods[calc]:
energy_param_name="_".join([prop_method,prop_name])
energy_param_name=energy_param_name.replace(" ","_")
#log.info("found "+energy_param_name)
# dated routines for finding monomer pairs, triplets in Topology module
energy_param=prop.attributes['value'].value.encode('ascii','ignore')
my_energy=energy_param_name
i_en=1
while my_energy in cluster.params.iterkeys():
i_en+=1
my_energy='_'.join([energy_param_name,str(i_en)])
cluster.params[my_energy] = float(energy_param) * HARTREE
if prop_method == energy_from:
cluster.params['Energy']=float(energy_param) * HARTREE
energy_found=True
elif extract_dipole and prop_name=='Dipole moment':
dipole_param_name="_".join([prop_method,prop_name])
dipole_param_name=dipole_param_name.replace(" ","_")
log.info("found dipole moment: "+dipole_param_name)
dipole_param=prop.attributes['value'].value.encode('ascii','ignore')
cluster.params[dipole_param_name]=dipole_param
if not energy_found:
log.critical("couldn't find energy from "+energy_from+" prop method : "+prop_method)
# read gradients if requested
if extract_forces:
if not cluster.has_property('force'):
cluster.add_property('force', 0.0, n_cols=3)
grads = dom.documentElement.getElementsByTagName('gradient')
force_matrix = grads[0].childNodes[0].data.split('\n')
force_matrix = [str(i).split() for i in force_matrix]
for i in force_matrix:
try:
force_matrix.remove([])
except ValueError:
break
force_matrix = [[(-1.0 * HARTREE / BOHR) * float(j) for j in i]
for i in force_matrix]
cluster.force[:] =farray(force_matrix).T
if len(grads) != 1:
for k in range(1,len(grads)):
my_force='force%s'%str(k+1)
force_matrix = grads[k].childNodes[0].data.split('\n')
force_matrix = [str(i).split() for i in force_matrix]
for i in force_matrix:
try:
force_matrix.remove([])
except ValueError:
break
force_matrix = [[(-1.0 * HARTREE / BOHR) * float(j) for j in i]
for i in force_matrix]
cluster.add_property(my_force,farray(force_matrix).T)
return cluster
def CubeReader(f, property_name='charge', discard_repeat=True, format=None):
def convert_line(line, *fmts):
return (f(s) for f, s in zip(fmts, line.split()))
if type(f) == type(''):
f = open(f)
opened = True
# First two lines are comments
comment1 = f.readline()
comment2 = f.readline()
# Now number of atoms and origin
n_atom, origin_x, origin_y, origin_z = convert_line(
f.readline(), int, float, float, float)
origin = farray([origin_x, origin_y, origin_z]) * BOHR
# Next three lines define number of voxels and shape of each element
shape = [0, 0, 0]
voxel = fzeros((3, 3))
for i in (1, 2, 3):
shape[i - 1], voxel[1, i], voxel[2, i], voxel[3, i] = convert_line(
f.readline(), int, float, float, float)
at = Atoms(n=n_atom, lattice=voxel * BOHR * shape)
at.add_property(property_name, 0.0)
prop_array = getattr(at, property_name)
# Now there's one line per atom
for i in frange(at.n):
at.z[i], prop_array[i], at.pos[1,
i], at.pos[2,
i], at.pos[3,
i] = convert_line(
f.readline(),
int, float,
float, float,
float)
at.pos[:, i] *= BOHR
at.set_atoms(at.z)
# Rest of file is volumetric data
data = np.fromiter((float(x) for x in f.read().split()), float, count=-1)
if data.size != shape[0] * shape[1] * shape[2]:
raise IOError("Bad array length - expected shape %r, but got size %d" %
(shape, data.size))
# Save volumetric data in at.data
data = farray(data.reshape(shape))
# Discard periodic repeats?
if discard_repeat:
at.data = data[:-1, :-1, :-1]
shape = [s - 1 for s in shape]
at.set_lattice(voxel * BOHR * shape, False)
at.params['comment1'] = comment1
at.params['comment2'] = comment2
at.params['origin'] = origin
at.params['shape'] = shape
# save grids in at.grid_x, at.grid_y, at.grid_z
if at.is_orthorhombic:
at.grid_x, at.grid_y, at.grid_z = np.mgrid[origin[1]:origin[1] +
at.lattice[1, 1]:shape[0] *
1j, origin[2]:origin[2] +
at.lattice[2, 2]:shape[1] *
1j, origin[3]:origin[3] +
at.lattice[3, 3]:shape[2] *
1j]
if opened:
f.close()
yield at
lotf_spring_hops=2,
test_mode=params.test_mode,
save_clusters=params.save_clusters,
force_restart=params.force_restart)
atoms.set_calculator(qmmm_pot)
system_timer('init_fm_pot')
if not params.continuation and not params.classical:
print 'Finding initial Quantum Core positions...'
if geom =='disloc':
atoms = set_quantum_disloc(atoms)
elif geom=='crack':
mom = [3.0 for at in range(len(atoms))]
atoms.set_initial_magnetic_moments(mom)
atoms.add_property('hybrid', 0, overwrite=True)
atoms.add_property('hybrid_vec', 0, overwrite=True)
atoms.add_property('hybrid_1', 0)
atoms.add_property('hybrid_mark_1', 0)
crackpos = atoms.info['CrackPos']
qm_list_old = []
qm_list = update_hysteretic_qm_region(atoms, [], crackpos, params.qm_inner_radius,
params.qm_outer_radius,
update_marks=False)
atoms.hybrid[qm_list] = HYBRID_ACTIVE_MARK
atoms.hybrid_vec[qm_list] = HYBRID_ACTIVE_MARK
atoms.hybrid_1[qm_list] = HYBRID_ACTIVE_MARK
atoms.hybrid_mark_1[qm_list] = HYBRID_ACTIVE_MARK
atoms.params['core'] = crackpos
print HYBRID_ACTIVE_MARK
print 'Core Found. No. Quantum Atoms:', sum(atoms.hybrid[:])
def PosCelReader(basename=None,
pos='pos.in',
cel='cel.in',
force='force.in',
energy='energy.in',
stress='stress.in',
species_map={
'O': 1,
'Si': 2
},
cel_angstrom=False,
pos_angstrom=False,
rydberg=True,
format=None):
if basename is not None:
basename = os.path.splitext(basename)[0]
pos = '%s.pos' % basename
cel = '%s.cel' % basename
energy = '%s.ene' % basename
stress = '%s.str' % basename
force = '%s.for' % basename
doenergy = os.path.exists(energy)
doforce = os.path.exists(force)
dostress = os.path.exists(stress)
if isinstance(pos, str): pos = open(pos)
if isinstance(cel, str): cel = open(cel)
if doenergy and isinstance(energy, str): energy = open(energy)
if doforce and isinstance(force, str): force = open(force)
if dostress and isinstance(stress, str): stress = open(stress)
pos = iter(pos)
cel = iter(cel)
if doenergy: energy = iter(energy)
if doforce: force = iter(force)
if dostress: stress = iter(stress)
pos.next() # throw away blank line at start
if doforce: force.next()
rev_species_map = dict(zip(species_map.values(), species_map.keys()))
while True:
poslines = list(
itertools.takewhile(
lambda L: L.strip() != '' and not L.strip().startswith('STEP'),
pos))
if poslines == []:
break
cellines = list(itertools.islice(cel, 4))
#lattice = farray([ [float(x) for x in L.split()] for L in cellines[1:4] ]).T
lattice = fzeros((3, 3))
for i in (1, 2, 3):
lattice[:, i] = [float(x) for x in cellines[i].split()]
if not cel_angstrom: lattice *= BOHR
at = Atoms(n=len(poslines), lattice=lattice)
at.pos[:] = farray([[float(x) for x in L.split()[0:3]]
for L in poslines]).T
if not pos_angstrom: at.pos[:] *= BOHR
species = [rev_species_map[int(L.split()[3])] for L in poslines]
elements = [
not el.isdigit() and atomic_number(el) or el for el in species
]
at.set_atoms(elements)
if doenergy:
at.params['energy'] = float(energy.next().split()[0])
if rydberg:
at.params['energy'] *= RYDBERG
if dostress:
stress_lines = list(itertools.islice(stress, 4))
virial = farray([[float(x) for x in L.split()]
for L in stress_lines[1:4]])
virial *= at.cell_volume() / (10.0 * GPA)
at.params['virial'] = virial
if doforce:
at.add_property('force', 0.0, n_cols=3)
force_lines = list(
itertools.takewhile(lambda L: L.strip() != '', force))
if len(force_lines) != at.n:
raise ValueError("len(force_lines) (%d) != at.n (%d)" %
(len(force_lines), at.n))
at.force[:] = farray([[float(x) for x in L.split()[0:3]]
for L in force_lines]).T
if rydberg:
at.force[:] *= RYDBERG / BOHR
yield at
class Potential(_potential.Potential):
__doc__ = update_doc_string(
_potential.Potential.__doc__,
r"""
The :class:`Potential` class also implements the ASE
:class:`ase.calculators.interface.Calculator` interface via the
the :meth:`get_forces`, :meth:`get_stress`, :meth:`get_stresses`,
:meth:`get_potential_energy`, :meth:`get_potential_energies`
methods. This simplifies calculation since there is no need
to set the cutoff or to call :meth:`~quippy.atoms.Atoms.calc_connect`,
as this is done internally. The example above reduces to::
atoms = diamond(5.44, 14)
atoms.rattle(0.01)
atoms.set_calculator(pot)
forces = atoms.get_forces()
print forces
Note that the ASE force array is the transpose of the QUIP force
array, so has shape (len(atoms), 3) rather than (3, len(atoms)).
The optional arguments `pot1`, `pot2` and `bulk_scale` are
used by ``Sum`` and ``ForceMixing`` potentials (see also
wrapper class :class:`ForceMixingPotential`)
An :class:`quippy.mpi_context.MPI_context` object can be
passed as the `mpi_obj` argument to restrict the
parallelisation of this potential to a subset of the
The `callback` argument is used to implement the calculation of
the :class:`Potential` in a Python function: see :meth:`set_callback` for
an example.
In addition to the builtin QUIP potentials, it is possible to
use any ASE calculator as a QUIP potential by passing it as
the `calculator` argument to the :class:`Potential` constructor, e.g.::
from ase.calculators.morse import MorsePotential
pot = Potential(calculator=MorsePotential)
`cutoff_skin` is used to set the :attr:`cutoff_skin` attribute.
`atoms` if given, is used to set the calculator associated
with `atoms` to the new :class:`Potential` instance, by calling
:meth:'.Atoms.set_calculator`.
.. note::
QUIP potentials do not compute stress and per-atom stresses
directly, but rather the virial tensor which has units of stress
:math:`\times` volume, i.e. energy. If the total stress is
requested, it is computed by dividing the virial by the atomic
volume, obtained by calling :meth:`.Atoms.get_volume`. If per-atom
stresses are requested, a per-atom volume is needed. By default
this is taken to be the total volume divided by the number of
atoms. In some cases, e.g. for systems containing large amounts of
vacuum, this is not reasonable. The ``vol_per_atom`` calc_arg can
be used either to give a single per-atom volume, or the name of an
array in :attr:`.Atoms.arrays` containing volumes for each atom.
""",
signature=
'Potential(init_args[, pot1, pot2, param_str, param_filename, bulk_scale, mpi_obj, callback, calculator, cutoff_skin, atoms])'
)
callback_map = {}
def __init__(self,
init_args=None,
pot1=None,
pot2=None,
param_str=None,
param_filename=None,
bulk_scale=None,
mpi_obj=None,
callback=None,
calculator=None,
cutoff_skin=1.0,
atoms=None,
fpointer=None,
finalise=True,
error=None,
**kwargs):
self.atoms = None
self._prev_atoms = None
self.energy = None
self.energies = None
self.forces = None
self.stress = None
self.stresses = None
self.elastic_constants = None
self.unrelaxed_elastic_constants = None
self.numeric_forces = None
self._calc_args = {}
self._default_quantities = []
self.cutoff_skin = cutoff_skin
if callback is not None or calculator is not None:
if init_args is None:
init_args = 'callbackpot'
if param_filename is not None:
param_str = open(param_filename).read()
if init_args is None and param_str is None:
raise ValueError('Need one of init_args,param_str,param_filename')
if init_args is not None:
if init_args.lower().startswith('callbackpot'):
if not 'label' in init_args:
init_args = init_args + ' label=%d' % id(self)
else:
# if param_str missing, try to find default set of QUIP params
if param_str is None and pot1 is None and pot2 is None:
param_str = quip_xml_parameters(init_args)
if kwargs != {}:
if init_args is not None:
init_args = init_args + ' ' + dict_to_args_str(kwargs)
else:
init_args = dict_to_args_str(kwargs)
_potential.Potential.__init__(self,
init_args,
pot1=pot1,
pot2=pot2,
param_str=param_str,
bulk_scale=bulk_scale,
mpi_obj=mpi_obj,
fpointer=fpointer,
finalise=finalise,
error=error)
if init_args is not None and init_args.lower().startswith(
'callbackpot'):
_potential.Potential.set_callback(self, Potential.callback)
if callback is not None:
self.set_callback(callback)
if calculator is not None:
self.set_callback(calculator_callback_factory(calculator))
if atoms is not None:
atoms.set_calculator(self)
__init__.__doc__ = _potential.Potential.__init__.__doc__
def calc(self,
at,
energy=None,
force=None,
virial=None,
local_energy=None,
local_virial=None,
args_str=None,
error=None,
**kwargs):
if not isinstance(args_str, basestring):
args_str = dict_to_args_str(args_str)
kw_args_str = dict_to_args_str(kwargs)
args_str = ' '.join((self.get_calc_args_str(), kw_args_str, args_str))
if isinstance(energy, basestring):
args_str = args_str + ' energy=%s' % energy
energy = None
if isinstance(energy, bool) and energy:
args_str = args_str + ' energy'
energy = None
if isinstance(force, basestring):
args_str = args_str + ' force=%s' % force
force = None
if isinstance(force, bool) and force:
args_str = args_str + ' force'
force = None
if isinstance(virial, basestring):
args_str = args_str + ' virial=%s' % virial
virial = None
if isinstance(virial, bool) and virial:
args_str = args_str + ' virial'
virial = None
if isinstance(local_energy, basestring):
args_str = args_str + ' local_energy=%s' % local_energy
local_energy = None
if isinstance(local_energy, bool) and local_energy:
args_str = args_str + ' local_energy'
local_energy = None
if isinstance(local_virial, basestring):
args_str = args_str + ' local_virial=%s' % local_virial
local_virial = None
if isinstance(local_virial, bool) and local_virial:
args_str = args_str + ' local_virial'
local_virial = None
potlog.debug(
'Potential invoking calc() on n=%d atoms with args_str "%s"' %
(len(at), args_str))
_potential.Potential.calc(self, at, energy, force, virial,
local_energy, local_virial, args_str, error)
calc.__doc__ = update_doc_string(
_potential.Potential.calc.__doc__,
"""In Python, this method is overloaded to set the final args_str to
:meth:`get_calc_args_str`, followed by any keyword arguments,
followed by an explicit `args_str` argument if present. This ordering
ensures arguments explicitly passed to :meth:`calc` will override any
default arguments.""")
@staticmethod
def callback(at_ptr):
from quippy import Atoms
at = Atoms(fpointer=at_ptr, finalise=False)
if 'label' not in at.params or at.params[
'label'] not in Potential.callback_map:
raise ValueError('Unknown Callback label %s' % at.params['label'])
Potential.callback_map[at.params['label']](at)
def set_callback(self, callback):
"""
For a :class:`Potential` of type `CallbackPot`, this method is
used to set the callback function. `callback` should be a Python
function (or other callable, such as a bound method or class
instance) which takes a single argument, of type
:class:`~quippy.atoms.Atoms`. Information about which quantities should be
computed can be obtained from the `calc_energy`, `calc_local_e`,
`calc_force`, and `calc_virial` keys in `at.params`. Results
should be returned either as `at.params` entries (for energy and
virial) or by adding new atomic properties (for forces and local
energy).
Here's an example implementation of a simple callback::
def example_callback(at):
if at.calc_energy:
at.params['energy'] = ...
if at.calc_force:
at.add_property('force', 0.0, n_cols=3)
at.force[:,:] = ...
p = Potential('CallbackPot')
p.set_callback(example_callback)
p.calc(at, energy=True)
print at.energy
...
"""
Potential.callback_map[str(id(self))] = callback
def wipe(self):
"""
Mark all quantities as needing to be recalculated
"""
self.energy = None
self.energies = None
self.forces = None
self.stress = None
self.stresses = None
self.numeric_forces = None
self.elastic_constants = None
self.unrelaxed_elastic_constants = None
def update(self, atoms):
"""
Set the :class:`~quippy.atoms.Atoms` object associated with this :class:`Potential` to `atoms`.
Called internally by :meth:`get_potential_energy`,
:meth:`get_forces`, etc. Only a weak reference to `atoms` is
kept, to prevent circular references. If `atoms` is not a
:class:`quippy.atoms.Atoms` instance, then a copy is made and a
warning will be printed.
"""
# we will do the calculation in place, to minimise number of copies,
# unless atoms is not a quippy Atoms
if isinstance(atoms, Atoms):
self.atoms = weakref.proxy(atoms)
else:
potlog.debug(
'Potential atoms is not quippy.Atoms instance, copy forced!')
self.atoms = Atoms(atoms)
# check if atoms has changed since last call
if self._prev_atoms is not None and self._prev_atoms.equivalent(
self.atoms):
return
# Mark all quantities as needing to be recalculated
self.wipe()
# do we need to reinitialise _prev_atoms?
if self._prev_atoms is None or len(self._prev_atoms) != len(
self.atoms) or not self.atoms.connect.initialised:
self._prev_atoms = Atoms()
self._prev_atoms.copy_without_connect(self.atoms)
self._prev_atoms.add_property('orig_pos', self.atoms.pos)
else:
# _prev_atoms is OK, update it in place
self._prev_atoms.z[...] = self.atoms.z
self._prev_atoms.pos[...] = self.atoms.pos
self._prev_atoms.lattice[...] = self.atoms.lattice
# do a calc_connect(), setting cutoff_skin so full reconnect will only be done when necessary
self.atoms.set_cutoff(self.cutoff(), cutoff_skin=self.cutoff_skin)
potlog.debug(
'Potential doing calc_connect() with cutoff %f cutoff_skin %r' %
(self.atoms.cutoff, self.cutoff_skin))
self.atoms.calc_connect()
# Synonyms for `update` for compatibility with ASE calculator interface
def initialize(self, atoms):
self.update(atoms)
def set_atoms(self, atoms):
self.update(atoms)
def calculation_required(self, atoms, quantities):
self.update(atoms)
for quantity in quantities:
if getattr(self, quantity) is None:
return True
return False
def calculate(self, atoms, quantities=None):
"""
Perform a calculation of `quantities` for `atoms` using this Potential.
Automatically determines if a new calculation is required or if previous
results are still appliciable (i.e. if the atoms haven't moved since last call)
Called internally by :meth:`get_potential_energy`, :meth:`get_forces`, etc.
"""
if quantities is None:
quantities = ['energy', 'forces', 'stress']
# Add any default quantities
quantities = set(self.get_default_quantities() + quantities)
if len(quantities) == 0:
raise RuntimeError('Nothing to calculate')
if not self.calculation_required(atoms, quantities):
return
args_map = {
'energy': {
'energy': None
},
'energies': {
'local_energy': None
},
'forces': {
'force': None
},
'stress': {
'virial': None
},
'numeric_forces': {
'force': 'numeric_force',
'force_using_fd': True,
'force_fd_delta': 1.0e-5
},
'stresses': {
'local_virial': None
},
'elastic_constants': {},
'unrelaxed_elastic_constants': {}
}
# list of quantities that require a call to Potential.calc()
calc_quantities = [
'energy', 'energies', 'forces', 'numeric_forces', 'stress',
'stresses'
]
# list of other quantities we know how to calculate
other_quantities = ['elastic_constants', 'unrelaxed_elastic_constants']
calc_args = {}
calc_required = False
for quantity in quantities:
if quantity in calc_quantities:
calc_required = True
calc_args.update(args_map[quantity])
elif quantity not in other_quantities:
raise RuntimeError(
"Don't know how to calculate quantity '%s'" % quantity)
if calc_required:
self.calc(self.atoms, args_str=dict_to_args_str(calc_args))
if 'energy' in quantities:
self.energy = float(self.atoms.energy)
if 'energies' in quantities:
self.energies = self.atoms.local_energy.view(np.ndarray)
if 'forces' in quantities:
self.forces = self.atoms.force.view(np.ndarray).T
if 'numeric_forces' in quantities:
self.numeric_forces = self.atoms.numeric_force.view(np.ndarray).T
if 'stress' in quantities:
stress = -self.atoms.virial.view(
np.ndarray) / self.atoms.get_volume()
# convert to 6-element array in Voigt order
self.stress = np.array([
stress[0, 0], stress[1, 1], stress[2, 2], stress[1, 2],
stress[0, 2], stress[0, 1]
])
if 'stresses' in quantities:
lv = np.array(self.atoms.local_virial) # make a copy
vol_per_atom = self.get('vol_per_atom',
self.atoms.get_volume() / len(atoms))
if isinstance(vol_per_atom, basestring):
vol_per_atom = self.atoms.arrays[vol_per_atom]
self.stresses = -lv.T.reshape(
(len(atoms), 3, 3), order='F') / vol_per_atom
if 'elastic_constants' in quantities:
cij_dx = self.get('cij_dx', 1e-2)
cij = fzeros((6, 6))
self.calc_elastic_constants(self.atoms,
fd=cij_dx,
args_str=self.get_calc_args_str(),
c=cij,
relax_initial=False,
return_relaxed=False)
if not get_fortran_indexing():
cij = cij.view(np.ndarray)
self.elastic_constants = cij
if 'unrelaxed_elastic_constants' in quantities:
cij_dx = self.get('cij_dx', 1e-2)
c0ij = fzeros((6, 6))
self.calc_elastic_constants(self.atoms,
fd=cij_dx,
args_str=self.get_calc_args_str(),
c0=c0ij,
relax_initial=False,
return_relaxed=False)
if not get_fortran_indexing():
c0ij = c0ij.view(np.ndarray)
self.unrelaxed_elastic_constants = c0ij
def get_potential_energy(self, atoms):
"""
Return potential energy of `atoms` calculated with this Potential
"""
self.calculate(atoms, ['energy'])
return self.energy
def get_potential_energies(self, atoms):
"""
Return array of atomic energies calculated with this Potential
"""
self.calculate(atoms, ['energies'])
return self.energies.copy()
def get_forces(self, atoms):
"""
Return forces on `atoms` calculated with this Potential
"""
self.calculate(atoms, ['forces'])
return self.forces.copy()
def get_numeric_forces(self, atoms):
"""
Return forces on `atoms` computed with finite differences of the energy
"""
self.calculate(atoms, ['numeric_forces'])
return self.numeric_forces.copy()
def get_stress(self, atoms):
"""
Return stress tensor for `atoms` computed with this Potential
Result is a 6-element array in Voigt notation:
[sigma_xx, sigma_yy, sigma_zz, sigma_yz, sigma_xz, sigma_xy]
"""
self.calculate(atoms, ['stress'])
return self.stress.copy()
def get_stresses(self, atoms):
"""
Return the per-atoms virial stress tensors for `atoms` computed with this Potential
"""
self.calculate(atoms, ['stresses'])
return self.stresses.copy()
def get_elastic_constants(self, atoms):
"""
Calculate elastic constants of `atoms` using this Potential.
Returns 6x6 matrix :math:`C_{ij}` of elastic constants.
The elastic contants are calculated as finite difference
derivatives of the virial stress tensor using positive and
negative strains of magnitude the `cij_dx` entry in
``calc_args``.
"""
self.calculate(atoms, ['elastic_constants'])
return self.elastic_constants.copy()
def get_unrelaxed_elastic_constants(self, atoms):
"""
Calculate unrelaxed elastic constants of `atoms` using this Potential
Returns 6x6 matrix :math:`C^0_{ij}` of unrelaxed elastic constants.
The elastic contants are calculated as finite difference
derivatives of the virial stress tensor using positive and
negative strains of magnitude the `cij_dx` entry in
:attr:`calc_args`.
"""
self.calculate(atoms, ['unrelaxed_elastic_constants'])
return self.unrelaxed_elastic_constants.copy()
def get_default_quantities(self):
"Get the list of quantities to be calculated by default"
return self._default_quantities[:]
def set_default_quantities(self, quantities):
"Set the list of quantities to be calculated by default"
self._default_quantities = quantities[:]
def get(self, param, default=None):
"""
Get the value of a ``calc_args`` parameter for this :class:`Potential`
Returns ``None`` if `param` is not in the current ``calc_args`` dictionary.
All calc_args are passed to :meth:`calc` whenever energies,
forces or stresses need to be re-computed.
"""
return self._calc_args.get(param, default)
def set(self, **kwargs):
"""
Set one or more calc_args parameters for this Potential
All calc_args are passed to :meth:`calc` whenever energies,
forces or stresses need to be computed.
After updating the calc_args, :meth:`set` calls :meth:`wipe`
to mark all quantities as needing to be recaculated.
"""
self._calc_args.update(kwargs)
self.wipe()
def get_calc_args(self):
"""
Get the current ``calc_args``
"""
return self._calc_args.copy()
def set_calc_args(self, calc_args):
"""
Set the ``calc_args`` to be used subsequent :meth:`calc` calls
"""
self._calc_args = calc_args.copy()
def get_calc_args_str(self):
"""
Get the ``calc_args`` to be passed to :meth:`calc` as a string
"""
return dict_to_args_str(self._calc_args)
def get_cutoff_skin(self):
return self._cutoff_skin
def set_cutoff_skin(self, cutoff_skin):
self._cutoff_skin = cutoff_skin
self._prev_atoms = None # force a recalculation
cutoff_skin = property(get_cutoff_skin,
set_cutoff_skin,
doc="""
The `cutoff_skin` attribute is only relevant when the ASE-style
interface to the Potential is used, via the :meth:`get_forces`,
:meth:`get_potential_energy` etc. methods. In this case the
connectivity of the :class:`~quippy.atoms.Atoms` object for which
the calculation is requested is automatically kept up to date by
using a neighbour cutoff of :meth:`cutoff` + `cutoff_skin`, and
recalculating the neighbour lists whenever the maximum displacement
since the last :meth:`Atoms.calc_connect` exceeds `cutoff_skin`.
""")
