def init_oop_terms(self, thresshold_zero=5e-2*angstrom):
'''
Initialize all out-of-plane terms in the system based on the oops
attribute of the system instance. All oops are given harmonic
potentials.
'''
with log.section('VAL', 3, 'Initializing'):
#get all dihedrals
from molmod.ic import opbend_dist, _opdist_low
ffatypes = [self.system.ffatypes[fid] for fid in self.system.ffatype_ids]
opdists = {}
for opdist in self.system.iter_oops():
opdist, types = term_sort_atypes(ffatypes, opdist, 'opdist')
if types in opdists.keys():
opdists[types].append(opdist)
else:
opdists[types] = [opdist]
#loop over all distinct opdist types
nharm = 0
nsq = 0
for types, oops in opdists.iteritems():
d0s = np.zeros(len(oops), float)
for i, oop in enumerate(oops):
if self.system.cell.nvec>0:
d01 = self.system.pos[oop[1]]-self.system.pos[oop[0]]
d02 = self.system.pos[oop[2]]-self.system.pos[oop[0]]
d03 = self.system.pos[oop[3]]-self.system.pos[oop[0]]
self.system.cell.mic(d01)
self.system.cell.mic(d02)
self.system.cell.mic(d03)
d0s[i] = abs(_opdist_low(d01, d02, d03, 0)[0])
else:
rs = np.array([#mind the order, is(or was) wrongly documented in molmod
self.system.pos[oop[0]],
self.system.pos[oop[1]],
self.system.pos[oop[2]],
self.system.pos[oop[3]],
])
d0s[i] = abs(opbend_dist(rs)[0])
if d0s.mean()<thresshold_zero: #TODO: check this thresshold
#add regular term harmonic in oopdist
for oop in oops:
term = self.add_term(Harmonic, [OopDist(*oop)], types, ['HC_FC_DIAG'], ['kjmol/A**2', 'A'])
self.set_params(term.index, rv0=0.0)
nharm += 1
else:
#add term harmonic in square of oopdist
log.dump('Mean absolute value of OopDist %s is %.3e A, used SQOOPDIST' %('.'.join(types), d0s.mean()/angstrom))
for oop in oops:
self.add_term(Harmonic, [SqOopDist(*oop)], types, ['PT_ALL', 'HC_FC_DIAG'], ['kjmol/A**4', 'A**2'])
nsq += 1
log.dump('Added %i Harmonic and %i SquareHarmonic out-of-plane distance terms' %(nharm, nsq))
def test_opbend_ethene():
mol = Molecule.from_file(context.get_fn("test/ethene.xyz"))
c = mol.coordinates.copy()
assert abs(ic.opbend_cos([c[0], c[5], c[4], c[3]])[0] - 1.0) < 1e-5
assert abs(ic.opbend_angle([c[0], c[5], c[4], c[3]])[0]) < 1e-5
assert abs(ic.opbend_mcos([c[0], c[5], c[4], c[3]])[0] - 1.0) < 1e-5
assert abs(ic.opbend_mangle([c[0], c[5], c[4], c[3]])[0]) < 1e-5
assert abs(ic.opbend_dist([c[0], c[5], c[4], c[3]])[0]) < 1e-5
for i in xrange(1000):
angle = np.random.uniform(-np.pi/2, np.pi/2)
radius = np.random.uniform(0, 5*angstrom)
#offset = np.random.uniform(0, 5*angstrom)
c[3] = [
radius*np.cos(angle),
0.0,
radius*np.sin(angle),
]
assert abs(ic.opbend_cos([c[0], c[5], c[4], c[3]])[0] - np.cos(angle)) < 1e-5
assert abs(ic.opbend_angle([c[0], c[5], c[4], c[3]])[0] - angle) < 1e-5
def test_opbend_ethene():
mol = Molecule.from_file(context.get_fn("test/ethene.xyz"))
c = mol.coordinates.copy()
assert abs(ic.opbend_cos([c[0], c[5], c[4], c[3]])[0] - 1.0) < 1e-5
assert abs(ic.opbend_angle([c[0], c[5], c[4], c[3]])[0]) < 1e-5
assert abs(ic.opbend_mcos([c[0], c[5], c[4], c[3]])[0] - 1.0) < 1e-5
assert abs(ic.opbend_mangle([c[0], c[5], c[4], c[3]])[0]) < 1e-5
assert abs(ic.opbend_dist([c[0], c[5], c[4], c[3]])[0]) < 1e-5
for i in xrange(1000):
angle = np.random.uniform(-np.pi / 2, np.pi / 2)
radius = np.random.uniform(0, 5 * angstrom)
#offset = np.random.uniform(0, 5*angstrom)
c[3] = [
radius * np.cos(angle),
0.0,
radius * np.sin(angle),
]
assert abs(ic.opbend_cos([c[0], c[5], c[4], c[3]])[0] -
np.cos(angle)) < 1e-5
assert abs(ic.opbend_angle([c[0], c[5], c[4], c[3]])[0] - angle) < 1e-5
def opbend_dist(self, *atoms):
''' distance plane 012 and vector 03'''
return ic.opbend_dist([self.coordinates[i]
for i in atoms])[0] / units.angstrom
def opbend_dist(self, *atoms):
''' distance plane 012 and vector 03'''
return ic.opbend_dist([self.coordinates[i]
for i in atoms])[0] / units.angstrom