def update(self, atoms):
"""
Connect the KIM pointers to values in the ase atoms class
set up neighborlist and perform calculation
"""
# here we only reinitialize the model if the number of Atoms /
# types of atoms have changed, or if the model is uninitialized
natoms = atoms.get_number_of_atoms()
ntypes = len(set(atoms.get_atomic_numbers()))
if (self.km_numberOfAtoms[0] != natoms or
self.km_numberAtomTypes[0] != ntypes or
self.cell_BC_changed(atoms)):
self.set_atoms(atoms)
if (not self.check_before_update or
(self.check_before_update and self.calculation_required(atoms, ""))):
# if the calculation is required we proceed to set the values
# of the standard things each model and atom class has
self.km_numberOfAtoms[0] = natoms
self.km_numberAtomTypes[0] = ntypes
self.km_coordinates[:] = atoms.get_positions().flatten()
if self.km_particleCharge:
km_particleCharge[:] = atoms.get_charges()
# fill the proper chemical identifiers
symbols = atoms.get_chemical_symbols()
for i in range(natoms):
self.km_atomTypes[i] = ks.KIM_API_get_species_code(self.pkim, symbols[i])
# build the neighborlist (type depends on model set by pkim)
if self.uses_neighbors:
kimnl.nbl_set_cell(atoms.get_cell().flatten(), atoms.get_pbc().flatten().astype('int8'))
kimnl.nbl_build_neighborlist(self.pkim)
ks.KIM_API_model_compute(self.pkim)
status = virial.virial_init(pkim)
status = virial.set_virial(pkim)
status = KIM_API_model_init(pkim)
atypecode = KIM_API_get_partcl_type_code(pkim, "Ar")
for i in range(numberOfAtoms[0]):
atomTypes[i] = atypecode
coordinates[:] = coords_dump.flatten()[:]
KIM_API_print(pkim)
# NNeighbors, HalfNNeighbors, neighborList, RijList = set_NeighborList(pkim, coordinates, numberOfAtoms[0], cutoff[0]*4)
# kimneighborlist.set_neigh_object(pkim, NNeighbors, HalfNNeighbors, neighborList, RijList)
kimneighborlist.nbl_build_neighborlist(pkim)
KIM_API_model_compute(pkim)
except error:
KIM_API_report_error(error.message,errno)
# print results to screen
print "--------------------------------------------------------------------------------"
print "This is Test : %s" % testname
print "Results for KIM Model : %s" % modelname
print "Forces:"
print "Atom X Y Z"
for i in range(numberOfAtoms[0]):
print "%2i %25.15e%25.15e%25.15e" % (i, forces[i*DIM + 0], forces[i*DIM + 1], forces[i*DIM + 2])
print ""
print "Energy = %20.15e" % energy[0]
