def test_vlist_peroxide_dihed_angle_cosine():
number_of_tests = 50
for i in xrange(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds = []
while len(bonds) < 3:
i0, i1 = [
int(x) for x in np.random.uniform(low=0, high=4, size=2)
] #pick 2 random atoms
if i0 == i1 or (i0, i1) in bonds or (i1, i0) in bonds: continue
if (i0, i1) in system.bonds or (i1, i0) in system.bonds:
iclist.add_ic(Bond(i0, i1))
bonds.append((i0, i1))
mult = np.random.randint(1, 4)
amp = np.random.normal(0, 1)
phi0 = np.random.uniform(0, 2 * np.pi)
vlist.add_term(Cosine(mult, amp, phi0, DihedAngle(0, 1, 2, 3)))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
angle = dihed_angle(system.pos)[0]
check_energy = 0.5 * amp * (1 - np.cos(mult * (angle - phi0)))
assert abs(energy - check_energy) < 1e-8
def test_vlist_peroxide_dihed_angle_cosine():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
mult = np.random.randint(1, 4)
amp = np.random.normal(0, 1)
phi0 = np.random.uniform(0, 2*np.pi)
vlist.add_term(Cosine(mult, amp, phi0, DihedAngle(0,1,2,3)))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
angle = dihed_angle(system.pos)[0]
check_energy = 0.5*amp*(1-np.cos(mult*(angle-phi0)))
assert abs(energy - check_energy) < 1e-8
def test_vlist_peroxide_dihed_cos_chebychev6():
number_of_tests = 50
for i in xrange(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds = []
while len(bonds) < 3:
i0, i1 = [
int(x) for x in np.random.uniform(low=0, high=4, size=2)
] #pick 2 random atoms
if i0 == i1 or (i0, i1) in bonds or (i1, i0) in bonds: continue
if (i0, i1) in system.bonds or (i1, i0) in system.bonds:
iclist.add_ic(Bond(i0, i1))
bonds.append((i0, i1))
amp = np.random.normal(0, 1)
sign = np.random.randint(2)
if sign == 0: sign = -1
vlist.add_term(Chebychev6(amp, DihedCos(0, 1, 2, 3), sign=sign))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
psi = dihed_angle(system.pos)[0]
check_energy = 0.5 * amp * (1.0 + sign * np.cos(6 * psi))
assert abs(energy - check_energy) < 1e-8
def test_vlist_peroxide_dihed_cos_chebychev6():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
amp = np.random.normal(0, 1)
sign = np.random.randint(2)
if sign==0: sign = -1
vlist.add_term(Chebychev6(amp, DihedCos(0,1,2,3), sign=sign))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
psi = dihed_angle(system.pos)[0]
check_energy = 0.5*amp*(1.0+sign*np.cos(6*psi))
assert abs(energy - check_energy) < 1e-8
def test_zero_dihed_steven():
pos = np.array([
[
3.99364178360816302e+00, 6.30763314754801546e-02,
-3.46387534695341159e+00
],
[
8.25853872852823123e+00, -2.56426319334358244e+00,
2.79913814647939019e-01
],
[
6.27951244286421861e+00, -1.73747102970232015e+00,
-2.05686744048685455e+00
],
[
8.12025850622788603e+00, -6.72445448176343996e-01,
2.91920676811204993e+00
],
])
numbers = np.array([1, 2, 3, 4])
system = System(numbers, pos)
fp = ForcePartValence(system)
fp.add_term(Cosine(3, 0.001, 0.0, DihedAngle(0, 1, 2, 3)))
gpos = np.zeros(pos.shape)
fp.compute(gpos)
# Dihedral is very nearly zero, but not exactly
assert np.abs(fp.iclist.ictab[0]['value'] -
dihed_angle(system.pos)[0]) < 1e-8
assert np.abs(fp.iclist.ictab[0]['grad']) < 1e-8
assert not np.isnan(gpos).any()
def test_gpos_vtens_dihed_angle_cosine_peroxide():
system = get_system_peroxide()
part = ForcePartValence(system)
part.add_term(Cosine(3, 1.5, 2 * np.pi / 3, DihedAngle(0, 1, 2, 3)))
print(dihed_angle(system.pos)[0] / np.pi)
check_gpos_part(system, part)
check_vtens_part(system, part)
def test_iclist_peroxide_dihedral_angle():
number_of_tests=50
for i in xrange(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# The bonds are added randomly to get different situations in the delta list
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
iclist.add_ic(DihedAngle(0,1,2,3))
dlist.forward()
iclist.forward()
assert iclist.ictab[3]['kind']==4 #assert the third ic is DihedralAngle
assert abs(iclist.ictab[3]['value'] - dihed_angle(system.pos)[0]) < 1e-5
def test_iclist_peroxide_dihedral_cos6():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
system.pos += np.random.normal(0.0, 0.1, system.pos.shape)*angstrom
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# The bonds are added randomly to get different situations in the delta list
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
iclist.add_ic(DihedCos6(0,1,2,3))
dlist.forward()
iclist.forward()
angle = dihed_angle(system.pos)[0]
print('psi=%.3f deg: target=%.6f value=%.6f' %(angle/deg, np.cos(6*angle), iclist.ictab[3]['value']))
assert abs(iclist.ictab[3]['value'] - np.cos(6*angle)) < 1e-5
def test_vlist_peroxide_dihed_angle():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
vlist.add_term(Harmonic(1.5, 0.1 , DihedAngle(0,1,2,3)))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
angle = dihed_angle(system.pos)[0]
check_energy = 0.5*1.5*(angle-0.1)**2
assert abs(energy - check_energy) < 1e-8
def test_vlist_peroxide_dihed_angle():
number_of_tests=50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
vlist = ValenceList(iclist)
bonds=[]
while len(bonds)<3:
i0, i1 = [int(x) for x in np.random.uniform(low=0,high=4,size=2)] #pick 2 random atoms
if i0==i1 or (i0,i1) in bonds or (i1,i0) in bonds: continue
if (i0,i1) in system.bonds or (i1,i0) in system.bonds:
iclist.add_ic(Bond(i0,i1))
bonds.append((i0,i1))
vlist.add_term(Harmonic(1.5, 0.1 , DihedAngle(0,1,2,3)))
dlist.forward()
iclist.forward()
energy = vlist.forward()
# calculate energy manually
angle = dihed_angle(system.pos)[0]
check_energy = 0.5*1.5*(angle-0.1)**2
assert abs(energy - check_energy) < 1e-8
def test_iclist_peroxide_dihedral_angle():
number_of_tests = 50
for i in range(number_of_tests):
system = get_system_peroxide()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# The bonds are added randomly to get different situations in the delta list
bonds = []
while len(bonds) < 3:
i0, i1 = [
int(x) for x in np.random.uniform(low=0, high=4, size=2)
] #pick 2 random atoms
if i0 == i1 or (i0, i1) in bonds or (i1, i0) in bonds: continue
if (i0, i1) in system.bonds or (i1, i0) in system.bonds:
iclist.add_ic(Bond(i0, i1))
bonds.append((i0, i1))
iclist.add_ic(DihedAngle(0, 1, 2, 3))
dlist.forward()
iclist.forward()
assert iclist.ictab[3][
'kind'] == 4 #assert the third ic is DihedralAngle
assert abs(iclist.ictab[3]['value'] -
dihed_angle(system.pos)[0]) < 1e-5
def test_iclist_peroxide_dihedral_cos6():
number_of_tests = 50
for i in range(number_of_tests):
system = get_system_peroxide()
system.pos += np.random.normal(0.0, 0.1, system.pos.shape) * angstrom
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
# The bonds are added randomly to get different situations in the delta list
bonds = []
while len(bonds) < 3:
i0, i1 = [
int(x) for x in np.random.uniform(low=0, high=4, size=2)
] #pick 2 random atoms
if i0 == i1 or (i0, i1) in bonds or (i1, i0) in bonds: continue
if (i0, i1) in system.bonds or (i1, i0) in system.bonds:
iclist.add_ic(Bond(i0, i1))
bonds.append((i0, i1))
iclist.add_ic(DihedCos6(0, 1, 2, 3))
dlist.forward()
iclist.forward()
angle = dihed_angle(system.pos)[0]
print('psi=%.3f deg: target=%.6f value=%.6f' %
(angle / deg, np.cos(6 * angle), iclist.ictab[3]['value']))
assert abs(iclist.ictab[3]['value'] - np.cos(6 * angle)) < 1e-5
def load_rotscan_g03log(fn_log, top_indexes=None):
"""Load the torsional potential from a Gaussian 03 log/output file.
Argument:
| ``fn_log`` -- The filename of the gaussian output.
Optional argument:
| ``top_indexes`` -- The atom indexes that define the rotor. These do
not have to include the atoms that define the
rotational axis. When not given, an attempt is made
to derive this information from the dihedral angle
used for the scan.
"""
# find the line that specifies the dihedral angle
with open(fn_log) as f:
found_modredundant = False
for line in f:
if line.startswith(" The following ModRedundant input section has been read:"):
found_modredundant = True
break
if not found_modredundant:
raise IOError("Could not find the ModRedundant section in the log file.")
dihedral = None
num_geoms = 0
for line in f:
line = line.strip()
if len(line) == 0:
break
else:
words = line.split()
if words[0] == "D" and (words[5] == "S" or words[5] == "F"):
if dihedral is None:
dihedral = list(int(word)-1 for word in words[1:5])
else:
raise IOError("Found multiple dihedral angle scan, which is not supported.")
if dihedral is None:
raise IOError("Could not find the dihedral angle of the rotational scan.")
# load all the energies and compute the corresponding angles
energies = []
angles = []
geometries = []
for line in f:
if line.startswith(" Input orientation:") or \
line.startswith(" Standard orientation:"):
# read the molecule
numbers = []
last_coordinates = []
## skip four lines
for i in xrange(4):
f.next()
# read atoms
for line in f:
if line.startswith(" -----"):
break
words = line.split()
numbers.append(int(words[1]))
last_coordinates.append((float(words[3]), float(words[4]), float(words[5])))
if line.startswith(" SCF Done:"):
# read the energy
last_energy = float(line[line.find("=")+1:].split()[0])
if line.startswith(" -- Stationary point found."):
# store last emergy and geometry in list
energies.append(last_energy)
last_coordinates = np.array(last_coordinates)*angstrom
geometries.append(last_coordinates)
angles.append(dihed_angle(last_coordinates[dihedral])[0])
if len(energies) == 0:
raise IOError("Could not find any stationary point")
if top_indexes is None:
# Define the molecular geometry that is used in the constructor of
# RotScan to detect the top.
from molmod.molecules import Molecule as BaseMolecule
molecule = BaseMolecule(numbers, geometries[0])
else:
molecule = None
result = RotScan(
dihedral, molecule, top_indexes,
np.array([angles, energies])
)
result.geometries = np.array(geometries)
return result
#!/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):
def load_rotscan_g03log(fn_log, top_indexes=None):
"""Load the torsional potential from a Gaussian 03 log/output file.
Argument:
| ``fn_log`` -- The filename of the gaussian output.
Optional argument:
| ``top_indexes`` -- The atom indexes that define the rotor. These do
not have to include the atoms that define the
rotational axis. When not given, an attempt is made
to derive this information from the dihedral angle
used for the scan.
"""
# find the line that specifies the dihedral angle
with open(fn_log) as f:
found_modredundant = False
for line in f:
if line.startswith(" The following ModRedundant input section has been read:"):
found_modredundant = True
break
if not found_modredundant:
raise IOError("Could not find the ModRedundant section in the log file.")
dihedral = None
num_geoms = 0
for line in f:
line = line.strip()
if len(line) == 0:
break
else:
words = line.split()
if words[0] == "D" and (words[5] == "S" or words[5] == "F"):
if dihedral is None:
dihedral = list(int(word)-1 for word in words[1:5])
else:
raise IOError("Found multiple dihedral angle scan, which is not supported.")
if dihedral is None:
raise IOError("Could not find the dihedral angle of the rotational scan.")
# load all the energies and compute the corresponding angles
energies = []
angles = []
geometries = []
for line in f:
if line.startswith(" Input orientation:") or \
line.startswith(" Standard orientation:"):
# read the molecule
numbers = []
last_coordinates = []
## skip four lines
for i in xrange(4):
f.next()
# read atoms
for line in f:
if line.startswith(" -----"):
break
words = line.split()
numbers.append(int(words[1]))
last_coordinates.append((float(words[3]), float(words[4]), float(words[5])))
if line.startswith(" SCF Done:"):
# read the energy
last_energy = float(line[line.find("=")+1:].split()[0])
if line.startswith(" -- Stationary point found."):
# store last emergy and geometry in list
energies.append(last_energy)
last_coordinates = np.array(last_coordinates)*angstrom
geometries.append(last_coordinates)
angles.append(dihed_angle(last_coordinates[dihedral])[0])
if len(energies) == 0:
raise IOError("Could not find any stationary point")
if top_indexes is None:
# Define the molecular geometry that is used in the constructor of
# RotScan to detect the top.
from molmod.molecules import Molecule as BaseMolecule
molecule = BaseMolecule(numbers, geometries[0])
else:
molecule = None
result = RotScan(
dihedral, molecule, top_indexes,
np.array([angles, energies])
)
result.geometries = np.array(geometries)
return result
def test_iclist_mil53_dihedral_angles():
system = get_system_mil53()
dlist = DeltaList(system)
iclist = InternalCoordinateList(dlist)
ic_values = []
gpos = np.zeros(system.pos.shape)
forbidden_dihedrals = [
["O_HY", "AL", "O_HY", "AL"],
["O_HY", "AL", "O_HY", "H_HY"],
["O_CA", "AL", "O_CA", "C_CA"],
]
for i1, i2 in system.bonds:
# Add bonds here to avoid that all ic signs are +1
iclist.add_ic(Bond(i2, i1))
for i0 in system.neighs1[i1]:
if i0 == i2: continue
for i3 in system.neighs1[i2]:
if i3 == i1: continue
# Compute using molmod
delta0 = system.pos[i0] - system.pos[i1]
delta1 = system.pos[i2] - system.pos[i1]
delta2 = system.pos[i3] - system.pos[i2]
system.cell.mic(delta0)
system.cell.mic(delta1)
system.cell.mic(delta2)
pos = np.zeros((4, 3))
pos[0] = system.pos[i1] + delta0
pos[1] = system.pos[i1]
pos[2] = system.pos[i1] + delta1
pos[3] = pos[2] + delta2
phi0, dphi0 = dihed_angle(pos, deriv=1)
# Compute value using yaff
iic = iclist.add_ic(DihedAngle(i0, i1, i2, i3))
ic = iclist.ictab[iic]
dlist.forward()
iclist.forward()
phi1 = ic['value']
if np.abs(phi1 - phi0) > 1e-8:
raise AssertionError(
"DihedralAngle(%d,%d,%d,%d): molmod "
"value = %12.8f yaff value = %12.8f diff = %12.2e" %
(i0, i1, i2, i3, phi0, phi1, phi0 - phi1))
# Compute derivative using yaff
gpos[:] = 0.0
ic['grad'] = 1.0
iclist.back()
dlist.back(gpos, None)
# Derivative of DihedCos fails in these cases, and DihedAngle
# derivatives are base on this
types = [
system.get_ffatype(i0),
system.get_ffatype(i1),
system.get_ffatype(i2),
system.get_ffatype(i3)
]
if types in forbidden_dihedrals or types[::
-1] in forbidden_dihedrals:
continue
ddiff = gpos[[i0, i1, i2, i3]] - dphi0
if np.any(np.abs(ddiff) > 1e-6):
raise AssertionError(
"DihedralAngle(%d,%d,%d,%d): largest "
"absolute derivative deviation = %12.2e" %
(i0, i1, i2, i3, np.amax(np.abs(ddiff))))