def calculate(self, atoms):
self.positions = atoms.get_positions()
pos = self.positions[:]
scmepos = self.positions[:]
truepos = pos[:]
self.cell = atoms.get_cell()
cell = self.cell
numatoms = self.numatoms
nummols = self.molnum
# Atomwise MIC PBCs needed for SCME
n = np.zeros(np.shape(scmepos))
c_mid = cell.diagonal() * 0.5
n = np.rint((c_mid - pos) / cell.diagonal())
scmepos += n * cell.diagonal()
scme_atoms = atoms[:]
scme_atoms.set_positions(scmepos)
# Convert to scme coordinates
scme_atoms = self.ase_to_scme(scme_atoms)
scme_coords = scme_atoms.get_positions()
scme_coords = scme_coords.transpose()
# Call SCME
# with shape tests:
eF = np.reshape(self.eF, np.shape(self.eF), order="F")
defield = np.reshape(self.defield, np.shape(self.defield), order="F")
# print np.shape(defield)
# eQM = np.zeros([3,nummols])
testin = np.zeros([3, 3, nummols])
testin = testin.reshape(3, 3, nummols, order="F")
ff, epot, et, qpole = scme.main(scme_coords, cell.diagonal(), eF, defield)
# CONVERT UNITS HERE! 1D = 0.20819434 e*Ang
# SCME forces: Debye^2/Ang^3 ... which explains
# convFactor = 14.39975841d0 / 4.803206799d0**2
# and Elvars 1/4.8 = 0.208 ish ...
# f = np.reshape(ff,[numatoms,3],order='F')
f = np.reshape(ff, [numatoms, 3])
# testout = testout.reshape(nummols,3,3,order='F')
# Convert force array back to ase coordinates
aseforces = self.f_scme_to_ase(f)
# H's get Ey and Ez ... HACKING
et = et.transpose() # F-> P
# et = np.reshape(et,[numatoms])
# CHECK THIS PLEASE! WHERES THE REINDEXING?
# update atoms with the new charges
self.dipoles = et.reshape(nummols, 3)
self.qpoles = qpole
self.atoms = atoms
self.forces = aseforces
self.energy = epot
def calculate(self,atoms):
self.positions = atoms.get_positions()
pos = self.positions[:]
scmepos = self.positions[:]
truepos = pos[:]
self.cell = atoms.get_cell()
cell = self.cell
numatoms = self.numatoms
nummols = self.molnum
# Atomwise MIC PBCs needed for SCME
n = np.zeros(np.shape(scmepos))
c_mid = cell.diagonal() * 0.5
n = np.rint((c_mid - pos) / cell.diagonal())
scmepos += n * cell.diagonal()
scme_atoms = atoms[:]
scme_atoms.set_positions(scmepos)
# Convert to scme coordinates
scme_atoms = self.ase_to_scme(scme_atoms)
scme_coords = scme_atoms.get_positions()
scme_coords = scme_coords.transpose()
# Call SCME
# with shape tests:
eF = np.reshape(self.eF, np.shape(self.eF), order='F')
deF = np.reshape(self.deF, np.shape(self.deF), order='F')
#print np.shape(deF)
#eQM = np.zeros([3,nummols])
testin = np.zeros([3,3,nummols])
testin = testin.reshape(3,3,nummols,order='F')
eF = -1* eF / unit.Debye
deF = -1* deF / unit.Debye
ff,epot,eT,dipole,qpole = scme.main(scme_coords,cell.diagonal(),eF,deF)
# also get eT out: total field.
#f = np.reshape(ff,[numatoms,3],order='F')
f = np.reshape(ff,[numatoms,3])
#testout = testout.reshape(nummols,3,3,order='F')
# Convert force array back to ase coordinates
aseforces = self.f_scme_to_ase(f)
dipole = -1 * dipole*unit.Debye # go back to ase units
dipole = dipole.transpose() # F-> P
eT = eT * unit.Debye
eT = eT.transpose() # F-> P
# update calc and atoms
self.dipoles = dipole.reshape(nummols, 3)
#self.qpoles = qpole NO QPOLES RIGHT NOW PLEASE
self.qpoles = np.zeros(np.shape(qpole))
self.atoms = atoms
self.forces = aseforces
self.energy = epot
self.eT = eT