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# Center-of-mass restraints
#
# Written by Konrad Hinsen
include "MMTK/python.pxi"
include "MMTK/numeric.pxi"
include "MMTK/core.pxi"
include "MMTK/universe.pxi"
include 'MMTK/forcefield.pxi'
cdef extern from "math.h":
double sqrt(double)
import numpy as N
cimport numpy as N
#
# Trap potential (harmonic restraint to a fixed point in space)
#
cdef class HarmonicCMTrapTerm(EnergyTerm):
cdef N.ndarray atom_indices, masses
cdef vector3 ref
cdef double k
def __init__(self, universe,
N.ndarray[N.int_t] atom_indices,
N.ndarray[N.float64_t] masses,
reference, force_constant):
cdef N.ndarray[N.float64_t] ref_array
EnergyTerm.__init__(self, universe,
"harmonic_cm_trap", ("harmonic_cm_trap",))
self.eval_func = <void *>HarmonicCMTrapTerm.evaluate
self.atom_indices = atom_indices
self.masses = masses
ref_array = reference.array
for i in range(3):
self.ref[i] = (<double *>ref_array.data)[i]
self.k = force_constant
cdef void evaluate(self, PyFFEvaluatorObject *eval,
energy_spec *input, energy_data *energy):
cdef vector3 *coordinates, *gradients
cdef N.ndarray[N.int_t] atom_indices
cdef N.ndarray[N.float_t] masses
cdef N.ndarray[N.float_t, ndim=4] fc
cdef vector3 cm, d
cdef double m, lsq, kw
cdef int i, j, n, offset
coordinates = <vector3 *>input.coordinates.data
atom_indices = self.atom_indices
masses = self.masses
# This code will never be run for a periodic universe, so
# it's safe to ignore periodic boundary conditions.
m = 0.
cm[0] = cm[1] = cm[2] = 0.
for i in atom_indices:
m += masses[i]
for j in range(3):
cm[j] += masses[i]*coordinates[i][j]
for j in range(3):
cm[j] /= m
for j in range(3):
d[j] = cm[j]-self.ref[j]
lsq = d[0]*d[0]+d[1]*d[1]+d[2]*d[2]
energy.energy_terms[self.index] = self.k*lsq
energy.energy_terms[self.virial_index] -= 2.*self.k*lsq
if energy.gradients != NULL:
gradients = <vector3 *>(<PyArrayObject *> energy.gradients).data
kw = 2.*self.k/m
for i in atom_indices:
for j in range(3):
gradients[i][j] += kw*d[j]*masses[i]
if energy.force_constants != NULL:
fc = <object>energy.force_constants
kw = 2.*self.k/(m*m)
for i in atom_indices:
for j in atom_indices:
for n in range(3):
fc [i, n, j, n] += kw*masses[i]*masses[j]
#
# Harmonic potential between two centers of mass
#
cdef class HarmonicCMDistanceTerm(EnergyTerm):
cdef N.ndarray atom_indices_1, atom_indices_2, masses
cdef double k, l0
def __init__(self, universe,
N.ndarray[N.int_t] atom_indices_1,
N.ndarray[N.int_t] atom_indices_2,
N.ndarray[N.float64_t] masses,
distance,
force_constant):
EnergyTerm.__init__(self, universe,
"harmonic_cm_distance", ("harmonic_cm_distance",))
self.eval_func = <void *>HarmonicCMDistanceTerm.evaluate
self.atom_indices_1 = atom_indices_1
self.atom_indices_2 = atom_indices_2
self.masses = masses
self.l0 = distance
self.k = force_constant
cdef void evaluate(self, PyFFEvaluatorObject *eval,
energy_spec *input, energy_data *energy):
cdef vector3 *coordinates, *gradients
cdef N.ndarray[N.int_t] atom_indices_1
cdef N.ndarray[N.int_t] atom_indices_2
cdef N.ndarray[N.float_t] masses
cdef N.ndarray[N.float_t, ndim=4] fc
cdef tensor3 fcij
cdef vector3 cm1, cm2, d
cdef double m1, m2, lsq, l, dl, deriv, w
cdef int i, j, n, offset
coordinates = <vector3 *>input.coordinates.data
atom_indices_1 = self.atom_indices_1
atom_indices_2 = self.atom_indices_2
masses = self.masses
# This code will never be run for a periodic universe, so
# it's safe to ignore periodic boundary conditions.
m1 = 0.
cm1[0] = cm1[1] = cm1[2] = 0.
for i in atom_indices_1:
m1 += masses[i]
for j in range(3):
cm1[j] += masses[i]*coordinates[i][j]
for j in range(3):
cm1[j] /= m1
m2 = 0.
cm2[0] = cm2[1] = cm2[2] = 0.
for i in atom_indices_2:
m2 += masses[i]
for j in range(3):
cm2[j] += masses[i]*coordinates[i][j]
for j in range(3):
cm2[j] /= m2
for j in range(3):
d[j] = cm2[j]-cm1[j]
lsq = d[0]*d[0]+d[1]*d[1]+d[2]*d[2]
l = sqrt(lsq)
dl = l - self.l0
energy.energy_terms[self.index] = self.k*dl*dl
energy.energy_terms[self.virial_index] -= 2.*self.k*dl*dl
if energy.gradients != NULL or energy.force_constants != NULL:
deriv = 0. if l == 0. else 2.*self.k*dl/l
if energy.gradients != NULL:
gradients = <vector3 *>(<PyArrayObject *> energy.gradients).data
deriv = 0. if l == 0. else 2.*self.k*dl/l
f1 = self.k*deriv/m1
f2 = self.k*deriv/m2
for i in atom_indices_1:
for j in range(3):
gradients[i][j] -= f1*d[j]*masses[i]
for i in atom_indices_2:
for j in range(3):
gradients[i][j] += f2*d[j]*masses[i]
if energy.force_constants != NULL:
fc = <object>energy.force_constants
for m in range(3):
for n in range(3):
fcij[m][n] = (2.*self.k-deriv)*d[m]*d[n]/lsq
fcij[m][m] += deriv
for i in atom_indices_1:
for j in atom_indices_1:
w = masses[i]*masses[j]/(m1*m1)
for m in range(3):
for n in range(3):
fc [i, m, j, n] += w*fcij[m][n]
for i in atom_indices_2:
for j in atom_indices_2:
w = masses[i]*masses[j]/(m2*m2)
for m in range(3):
for n in range(3):
fc [i, m, j, n] += w*fcij[m][n]
for i in atom_indices_1:
for j in atom_indices_2:
w = masses[i]*masses[j]/(m1*m2)
for m in range(3):
for n in range(3):
if i < j:
fc [i, m, j, n] -= w*fcij[m][n]
else:
fc [j, m, i, n] -= w*fcij[m][n]
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