def test_cvlincombic_quartz():
system = get_system_quartz()
ic0 = Bond(1, 3)
ic1 = Bond(2, 5)
weights = [0.13, 0.29]
cv = CVLinCombIC(system, [ic0, ic1], weights)
value = cv.compute()
assert value == cv.get_last_computed_value()
delta0 = system.pos[3] - system.pos[1]
system.cell.mic(delta0)
ref0 = bond_length([np.zeros(3, float), delta0])[0]
delta1 = system.pos[5] - system.pos[2]
system.cell.mic(delta1)
ref1 = bond_length([np.zeros(3, float), delta1])[0]
reference = weights[0] * ref0 + weights[1] * ref1
assert np.abs(value - reference) < 1e-8
check_gpos_cv_fd(cv)
check_vtens_cv_fd(cv)
def test_iclist_quartz_bonds():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
for i, j in system.bonds:
iclist.add_ic(Bond(i, j))
dlist.forward()
iclist.forward()
for row, (i, j) in enumerate(system.bonds):
delta = system.pos[j] - system.pos[i]
system.cell.mic(delta)
assert abs(iclist.ictab[row]['value'] - bond_length([np.zeros(3, float), delta])[0]) < 1e-5
def test_cvinternalcoordinate_quartz():
system = get_system_quartz()
ic = Bond(1, 3)
cv = CVInternalCoordinate(system, ic)
value = cv.compute()
assert value == cv.get_last_computed_value()
delta = system.pos[3] - system.pos[1]
system.cell.mic(delta)
reference = bond_length([np.zeros(3, float), delta])[0]
assert np.abs(value - reference) < 1e-8
check_gpos_cv_fd(cv)
check_vtens_cv_fd(cv)
def test_iclist_quartz_bonds():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
for i, j in system.bonds:
iclist.add_ic(Bond(i, j))
dlist.forward()
iclist.forward()
for row, (i, j) in enumerate(system.bonds):
delta = system.pos[j] - system.pos[i]
system.cell.mic(delta)
assert abs(iclist.ictab[row]['value'] -
bond_length([np.zeros(3, float), delta])[0]) < 1e-5
def test_iclist_ub_water():
system = get_system_water32()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
ub = []
for i1 in xrange(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
iclist.add_ic(UreyBradley(i0, i1, i2))
ub.append((i0, i1, i2))
dlist.forward()
iclist.forward()
for row, (i0, i1, i2) in enumerate(ub):
delta = system.pos[i2] - system.pos[i0]
system.cell.mic(delta)
assert abs(iclist.ictab[row]['value'] - bond_length([np.zeros(3, float), delta])[0]) < 1e-5
def test_iclist_lastcomputed_quartz_bonds():
system = get_system_quartz()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
ics = []
for i, j in system.bonds:
ic = Bond(i, j)
ics.append(ic)
iclist.add_ic(ic)
dlist.forward()
iclist.forward()
for row, (i, j) in enumerate(system.bonds):
delta = system.pos[j] - system.pos[i]
system.cell.mic(delta)
ref = bond_length([np.zeros(3, float), delta])[0]
value = ics[row].get_last_computed_value()
assert np.abs(value - ref) < 1e-5
def test_iclist_ub_water():
system = get_system_water32()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
ub = []
for i1 in range(system.natom):
for i0 in system.neighs1[i1]:
for i2 in system.neighs1[i1]:
if i0 > i2:
iclist.add_ic(UreyBradley(i0, i1, i2))
ub.append((i0, i1, i2))
dlist.forward()
iclist.forward()
for row, (i0, i1, i2) in enumerate(ub):
delta = system.pos[i2] - system.pos[i0]
system.cell.mic(delta)
assert abs(iclist.ictab[row]['value'] -
bond_length([np.zeros(3, float), delta])[0]) < 1e-5
#!/usr/bin/env python
import argparse
import molmod as mm
import numpy as np
import mdtraj as md
def eval_pplane(atoms_xyz):
return mm.opbend_dist(atoms_xyz)[0] / mm.angstrom
CV_KIND_DICT = {
'BOND': lambda atoms_xyz: mm.bond_length(atoms_xyz)[0] / mm.angstrom,
'ANGLE': lambda atoms_xyz: mm.bend_angle(atoms_xyz)[0] / mm.deg,
'DIHEDRAL': lambda atoms_xyz: mm.dihed_angle(atoms_xyz)[0] / mm.deg,
'PPLANE': lambda atoms_xyz: eval_pplane(np.roll(atoms_xyz, -3))
}
MULTICV_KIND_DICT = {'MBOND': (2, 'BOND'),
'MANGLE': (3, 'ANGLE'),
'MDIHEDRAL': (4, 'DIHEDRAL'),
'MPPLANE': (4, 'PPLANE')}
def get_center(xyz, indices):
return np.mean(np.take(xyz, indices, axis=0), axis=0)
def get_centers(xyz, centers):
