def retrieve(self):
ff = FFEvaluate(self.molecule, self._parameters)
results = []
for iframe in range(self.molecule.numFrames):
self.molecule.frame = iframe
directory = os.path.join(self.directory, '%05d' % iframe)
os.makedirs(directory, exist_ok=True)
pickleFile = os.path.join(directory, 'data.pkl')
if self._completed(directory):
with open(pickleFile, 'rb') as fd:
result = pickle.load(fd)
logger.info('Loading QM data from %s' % pickleFile)
else:
result = QMResult()
result.errored = False
result.coords = self.molecule.coords[:, :, iframe:iframe + 1].copy()
if self.optimize:
opt = nlopt.opt(nlopt.LN_COBYLA, result.coords.size)
opt.set_min_objective(lambda x, _: ff.calculateEnergies(x.reshape((-1, 3)))['total'])
if self.restrained_dihedrals is not None:
for dihedral in self.restrained_dihedrals:
indices = dihedral.copy()
ref_angle = dihedralAngle(self.molecule.coords[indices, :, iframe])
def constraint(x, _):
coords = x.reshape((-1, 3))
angle = dihedralAngle(coords[indices])
return np.sin(.5*(angle - ref_angle))
opt.add_equality_constraint(constraint)
opt.set_xtol_abs(1e-3) # Similar to Psi4 default
opt.set_maxeval(1000*opt.get_dimension())
opt.set_initial_step(1e-3)
result.coords = opt.optimize(result.coords.ravel()).reshape((-1, 3, 1))
logger.info('Optimization status: %d' % opt.last_optimize_result())
result.energy = ff.calculateEnergies(result.coords[:, :, 0])['total']
result.dipole = getDipole(self.molecule)
if self.optimize:
assert opt.last_optimum_value() == result.energy # A self-consistency test
# Compute ESP values
if self.esp_points is not None:
assert self.molecule.numFrames == 1
result.esp_points = self.esp_points
distances = cdist(result.esp_points, result.coords[:, :, 0]) # Angstrom
distances *= const.physical_constants['Bohr radius'][0] / const.angstrom # Angstrom --> Bohr
result.esp_values = np.dot(np.reciprocal(distances), self.molecule.charge) # Hartree/Bohr
with open(pickleFile, 'wb') as fd:
pickle.dump(result, fd)
results.append(result)
return results
def run(self):
ff = FFEvaluate(self.molecule)
results = []
for iframe in range(self.molecule.numFrames):
self.molecule.frame = iframe
directory = os.path.join(self.directory, '%05d' % iframe)
os.makedirs(directory, exist_ok=True)
pickleFile = os.path.join(directory, 'data.pkl')
if self._completed(directory):
with open(pickleFile, 'rb') as fd:
result = pickle.load(fd)
logger.info('Loading QM data from %s' % pickleFile)
else:
result = QMResult()
result.errored = False
result.coords = self.molecule.coords[:, :, iframe:iframe + 1].copy()
if self.optimize:
opt = nlopt.opt(nlopt.LN_COBYLA, result.coords.size)
opt.set_min_objective(lambda x, _: ff.run(x.reshape((-1, 3)))['total'])
if self.restrained_dihedrals is not None:
for dihedral in self.restrained_dihedrals:
indices = dihedral.copy()
ref_angle = np.deg2rad(dihedralAngle(self.molecule.coords[indices, :, iframe]))
def constraint(x, _):
coords = x.reshape((-1, 3))
angle = np.deg2rad(dihedralAngle(coords[indices]))
return np.sin(.5*(angle - ref_angle))
opt.add_equality_constraint(constraint)
opt.set_xtol_abs(1e-3) # Similar to Psi4 default
opt.set_maxeval(1000*opt.get_dimension())
opt.set_initial_step(1e-3)
result.coords = opt.optimize(result.coords.ravel()).reshape((-1, 3, 1))
logger.info('Optimization status: %d' % opt.last_optimize_result())
result.energy = ff.run(result.coords[:, :, 0])['total']
result.dipole = self.molecule.getDipole()
if self.optimize:
assert opt.last_optimum_value() == result.energy # A self-consistency test
# Compute ESP values
if self.esp_points is not None:
assert self.molecule.numFrames == 1
result.esp_points = self.esp_points
distances = cdist(result.esp_points, result.coords[:, :, 0]) # Angstrom
distances *= const.physical_constants['Bohr radius'][0] / const.angstrom # Angstrom --> Bohr
result.esp_values = np.dot(np.reciprocal(distances), self.molecule.charge) # Hartree/Bohr
with open(pickleFile, 'wb') as fd:
pickle.dump(result, fd)
results.append(result)
return results
def retrieve(self):
results = []
for iframe in range(self.molecule.numFrames):
self.molecule.frame = iframe
directory = os.path.join(self.directory, '%05d' % iframe)
os.makedirs(directory, exist_ok=True)
pickleFile = os.path.join(directory, 'data.pkl')
molFile = os.path.join(directory, 'mol.mol2')
if self._completed(directory):
with open(pickleFile, 'rb') as fd:
result = pickle.load(fd)
logger.info('Loading data from %s' % pickleFile)
else:
start = time.clock()
result = QMResult()
result.errored = False
result.coords = self.molecule.coords[:, :,
iframe:iframe + 1].copy()
if self.optimize:
if self.minimizer is None:
self.minimizer = CustomEnergyBasedMinimizer(
self.molecule, self.calculator)
result.coords = self.minimizer.minimize(
result.coords, self.restrained_dihedrals).reshape(
(-1, 3, 1))
mol = self.molecule.copy()
mol.frame = 0
mol.coords = result.coords
mol.write(molFile)
result.energy = float(
self.calculator.calculate(result.coords,
self.molecule.element,
units='kcalmol')[0])
result.dipole = [0, 0, 0]
#if self.optimize:
# assert opt.last_optimum_value() == result.energy # A self-consistency test
finish = time.clock()
result.calculator_time = finish - start
if self._verbose:
logger.info('Custom calculator calculation time: %f s' %
result.calculator_time)
with open(pickleFile, 'wb') as fd:
pickle.dump(result, fd)
results.append(result)
return results
def run(self):
prmtop = self._get_prmtop()
system = prmtop.createSystem()
groups = {force.getForceGroup() for force in system.getForces()}
if self.optimize:
if self.restrained_dihedrals is not None:
restraint = openmm.PeriodicTorsionForce()
restraint.setForceGroup(max(groups) + 1)
for dihedral in self.restrained_dihedrals:
restraint.addTorsion(*tuple(map(int, dihedral)),
periodicity=1,
phase=0,
k=-1000 * unit.kilocalorie_per_mole)
system.addForce(restraint)
simulation = app.Simulation(
prmtop.topology, system,
openmm.VerletIntegrator(1 * unit.femtosecond),
openmm.Platform.getPlatformByName('CPU'))
results = []
molecule_copy = self.molecule.copy()
for iframe in range(self.molecule.numFrames):
self.molecule.frame = iframe
molecule_copy.frame = iframe
directory = os.path.join(self.directory, '%05d' % iframe)
os.makedirs(directory, exist_ok=True)
pickleFile = os.path.join(directory, 'data.pkl')
if self._completed(directory):
with open(pickleFile, 'rb') as fd:
results.append(pickle.load(fd))
logger.info('Loading QM data from %s' % pickleFile)
continue
simulation.context.setPositions(
self.molecule.coords[:, :, iframe] * unit.angstrom)
if self.optimize:
if self.restrained_dihedrals is not None:
for i, dihedral in enumerate(self.restrained_dihedrals):
ref_angle = dihedralAngle(
self.molecule.coords[dihedral, :, iframe])
parameters = restraint.getTorsionParameters(i)
parameters[5] = ref_angle * unit.degree
restraint.setTorsionParameters(i, *parameters)
restraint.updateParametersInContext(simulation.context)
simulation.minimizeEnergy(tolerance=0.001 *
unit.kilocalorie_per_mole)
state = simulation.context.getState(getEnergy=True,
getPositions=True,
groups=groups)
result = QMResult()
result.errored = False
result.energy = state.getPotentialEnergy().value_in_unit(
unit.kilocalorie_per_mole)
result.coords = state.getPositions(asNumpy=True).value_in_unit(
unit.angstrom).reshape((-1, 3, 1))
result.dipole = self.molecule.getDipole()
if self.esp_points is not None:
assert self.molecule.numFrames == 1
result.esp_points = self.esp_points
distances = cdist(result.esp_points,
result.coords[:, :, 0]) # Angstrom
distances *= const.physical_constants['Bohr radius'][
0] / const.angstrom # Angstrom --> Bohr
result.esp_values = np.dot(
np.reciprocal(distances),
self.molecule.charge) # Hartree/Bohr
results.append(result)
with open(pickleFile, 'wb') as fd:
pickle.dump(result, fd)
self.molecule.write(os.path.join(
directory, 'mol-init.mol2')) # Write an optimiz
molecule_copy.coords[:, :, iframe] = result.coords[:, :, 0]
molecule_copy.write(os.path.join(directory,
'mol.mol2')) # Write an optimiz
return results
def _readOutput(self, directory):
result = QMResult()
result.completed = True
xyzFile = os.path.join(directory, 'psi4out.xyz')
if os.path.exists(xyzFile):
with open(xyzFile) as f:
result.energy = float(f.readline().split()[1]) # Read the 2nd number on the 1st line
result.energy *= const.physical_constants['Hartree energy'][0]/(const.kilo*const.calorie/const.Avogadro) # Hartree to kcal/mol
result.coords = np.loadtxt(xyzFile, skiprows=2, usecols=(1, 2, 3))
result.coords = np.atleast_3d(result.coords) # TODO get rid of this
else:
result.errored = True
if self.esp_points is not None:
espFile = os.path.join(directory, 'grid_esp.dat')
if os.path.exists(espFile):
result.esp_points = self.esp_points
result.esp_values = np.loadtxt(espFile)
result.esp_values *= const.angstrom/const.physical_constants['Bohr radius'][0] # 1/Bohr to 1/Angstrom
else:
result.errored = True
outFile = os.path.join(directory, 'psi4.out')
if os.path.exists(outFile):
with open(outFile) as f:
lines = f.readlines()
for i in range(len(lines)):
if "Mulliken Charges: (a.u.)" in lines[i]:
result.mulliken = []
for j in range(self._natoms):
s = lines[i + 2 + j].split()
result.mulliken.append(float(s[5]))
if "Dipole Moment: (Debye)" in lines[i]:
s = lines[i + 1].split()
result.dipole = [float(s[1]), float(s[3]), float(s[5]), float(s[7])]
if " Traceless Quadrupole Moment: (Debye Ang)" in lines[i]:
s1, s2 = lines[i + 1].split(), lines[i + 2].split()
result.quadrupole = [float(s1[1]), float(s1[3]), float(s1[5]),
float(s2[1]), float(s2[3]), float(s2[5])]
else:
result.errored = True
return result
def _readOutput(self, directory):
result = QMResult()
with open(os.path.join(directory, 'g09.out')) as f:
fl = f.readlines()
try:
data = {}
for i in range(len(fl)):
if "Dipole moment (field-independent basis, Debye):" in fl[i]:
s = fl[i + 1].split()
data['dipole'] = [
float(s[1]),
float(s[3]),
float(s[5]),
float(s[7])
]
if "Traceless Quadrupole moment (field-independent basis, Debye-Ang):" in fl[
i]:
s1 = fl[i + 1].split()
s2 = fl[i + 2].split()
data['quadrupole'] = [
float(s1[1]),
float(s1[3]),
float(s1[5]),
float(s2[1]),
float(s2[3]),
float(s2[5])
]
if "Mulliken atomic charges:" in fl[
i] or "Mulliken charges:" in fl[i]:
data['mulliken'] = []
for j in range(self._natoms):
data['mulliken'].append(float(fl[i + 2 +
j].split()[2]))
for l in fl:
if "SCF Done: E(RHF) = " in l:
ff = l.split()
data['energy'] = float(ff[4])
if "SCF Done: E(RB3LYP) = " in l:
ff = l.split()
data['energy'] = float(ff[4])
i = 0
while i < len(fl):
if "Number Number Type X Y Z" in fl[
i]:
i += 2
data['coords'] = np.zeros((self._natoms, 3))
for j in range(self._natoms):
ff = fl[j + i].split()
data['coords'][j, 0] = float(ff[3])
data['coords'][j, 1] = float(ff[4])
data['coords'][j, 2] = float(ff[5])
else:
i += 1
i = 0
while i < len(fl):
if " Potential X Y Z" in fl[
i]:
i = i + 2 + self._natoms
data['gridesp'] = []
while not ("----" in fl[i]):
ff = fl[i].split()
data['gridesp'].append(float(ff[1]))
i += 1
data['gridesp'] = np.asarray(data['gridesp'],
dtype=np.float)
else:
i += 1
except:
data = None
if data is None:
result.errored = True
elif not ('energy' in data) or data['energy'] == 0.:
result.errored = True
else:
result.energy = data['energy']
result.energy *= const.physical_constants['Hartree energy'][0] / (
const.kilo * const.calorie / const.Avogadro
) # Hartree to kcal/mol
result.coords = np.atleast_3d(data['coords'])
if 'gridesp' in data:
result.esp_points = np.squeeze(np.asarray(self.esp_points))
result.esp_values = data['gridesp']
result.esp_values *= const.angstrom / const.physical_constants[
'Bohr radius'][0] # 1/Bohr to 1/Angstrom
if 'dipole' in data:
result.dipole = data['dipole']
if 'quadrupole' in data:
result.quadrupole = data['quadrupole']
if 'mulliken' in data:
result.mulliken = data['mulliken']
return result
def _readOutput(self, directory):
result = QMResult()
with open(os.path.join(directory, 'g09.out')) as f:
fl = f.readlines()
try:
data = {}
for i in range(len(fl)):
if "Dipole moment (field-independent basis, Debye):" in fl[i]:
s = fl[i + 1].split()
data['dipole'] = [float(s[1]), float(s[3]), float(s[5]), float(s[7])]
if "Traceless Quadrupole moment (field-independent basis, Debye-Ang):" in fl[i]:
s1 = fl[i + 1].split()
s2 = fl[i + 2].split()
data['quadrupole'] = [float(s1[1]), float(s1[3]), float(s1[5]), float(s2[1]), float(s2[3]),
float(s2[5])]
if "Mulliken atomic charges:" in fl[i] or "Mulliken charges:" in fl[i]:
data['mulliken'] = []
for j in range(self._natoms):
data['mulliken'].append(float(fl[i + 2 + j].split()[2]))
for l in fl:
if "SCF Done: E(RHF) = " in l:
ff = l.split()
data['energy'] = float(ff[4])
if "SCF Done: E(RB3LYP) = " in l:
ff = l.split()
data['energy'] = float(ff[4])
i = 0
while i < len(fl):
if "Number Number Type X Y Z" in fl[i]:
i += 2
data['coords'] = np.zeros((self._natoms, 3))
for j in range(self._natoms):
ff = fl[j + i].split()
data['coords'][j, 0] = float(ff[3])
data['coords'][j, 1] = float(ff[4])
data['coords'][j, 2] = float(ff[5])
else:
i += 1
i = 0
while i < len(fl):
if " Potential X Y Z" in fl[i]:
i = i + 2 + self._natoms
data['gridesp'] = []
while not ("----" in fl[i]):
ff = fl[i].split()
data['gridesp'].append(float(ff[1]))
i += 1
data['gridesp'] = np.asarray(data['gridesp'], dtype=np.float)
else:
i += 1
except:
data = None
if data is None:
result.errored = True
elif not ('energy' in data) or data['energy'] == 0.:
result.errored = True
else:
result.energy = data['energy']
result.energy *= const.physical_constants['Hartree energy'][0]/(const.kilo*const.calorie/const.Avogadro) # Hartree to kcal/mol
result.coords = np.atleast_3d(data['coords'])
if 'gridesp' in data:
result.esp_points = np.squeeze(np.asarray(self.esp_points))
result.esp_values = data['gridesp']
result.esp_values *= const.angstrom/const.physical_constants['Bohr radius'][0] # 1/Bohr to 1/Angstrom
if 'dipole' in data:
result.dipole = data['dipole']
if 'quadrupole' in data:
result.quadrupole = data['quadrupole']
if 'mulliken' in data:
result.mulliken = data['mulliken']
return result
def _readOutput(self, directory):
result = QMResult()
result.completed = True
xyzFile = os.path.join(directory, 'psi4out.xyz')
if os.path.exists(xyzFile):
with open(xyzFile) as f:
result.energy = float(f.readline().split()[1]) # Read the 2nd number on the 1st line
result.energy *= const.physical_constants['Hartree energy'][0]/(const.kilo*const.calorie/const.Avogadro) # Hartree to kcal/mol
result.coords = np.loadtxt(xyzFile, skiprows=2, usecols=(1, 2, 3))
result.coords = np.atleast_3d(result.coords) # TODO get rid of this
else:
result.errored = True
if self.esp_points is not None:
espFile = os.path.join(directory, 'grid_esp.dat')
if os.path.exists(espFile):
result.esp_points = self.esp_points
result.esp_values = np.loadtxt(espFile)
result.esp_values *= const.angstrom/const.physical_constants['Bohr radius'][0] # 1/Bohr to 1/Angstrom
else:
result.errored = True
outFile = os.path.join(directory, 'psi4.out')
if os.path.exists(outFile):
with open(outFile) as f:
lines = f.readlines()
for i in range(len(lines)):
if "Mulliken Charges: (a.u.)" in lines[i]:
result.mulliken = []
for j in range(self._natoms):
s = lines[i + 2 + j].split()
result.mulliken.append(float(s[5]))
if "Dipole Moment: (Debye)" in lines[i]:
s = lines[i + 1].split()
result.dipole = [float(s[1]), float(s[3]), float(s[5]), float(s[7])]
if " Traceless Quadrupole Moment: (Debye Ang)" in lines[i]:
s1, s2 = lines[i + 1].split(), lines[i + 2].split()
result.quadrupole = [float(s1[1]), float(s1[3]), float(s1[5]),
float(s2[1]), float(s2[3]), float(s2[5])]
else:
result.errored = True
return result