def main_wrapper(torComb):
"""Given a conformer (torComb) the structure is rotated to the proper
angles, then written to a file where a single point energy is evaluated.
If the energy is below a prescribed value (sysInfo.max_energy), then
proceed to a full minimization, where the final structure is then renamed
and the results written out to the terminal
"""
#Set angle in torsions object
for i in xrange(len(torsions)):
torsions[i].newAngle = np.radians(torComb.combination[i])
#Check which torsions need to be rotated
for torsion in torsions:
if torsion.newAngle != torsion.currentAngle():
#Set atoms.rotate to false
for atom in atoms:
atom.rotate = False
#Check which atoms need to be rotated & setting atom.rotate
assign_rotating_atoms(torsion.tor_atoms[1],
torsion.tor_atoms[2],
atoms)
#Rotate atoms
rotate_atoms(torsion,atoms)
#Check if atoms are too close together
if check_close_contacts(atoms):
return
#Write file for energy evaluation
torComb.filename = "new_octane"
name = TTFiles.make_filename(torComb)
TTFiles.write_xyz(atoms,torComb.filename)
#Perform single point energy evaluation
torComb.energy = TTEnergy.get_single_point_energy(torComb.filename)
#Check to see if single point energy is above the threshold for minimization
if torComb.energy > sysInfo.max_energy():
subprocess.Popen(["rm",torComb.filename])
return
#Perform minimization
torComb.min_energy = TTEnergy.get_minimum_energy(torComb.filename)
print torComb.filename,torComb.min_energy
#Clean up some files
subprocess.Popen(["mv",torComb.filename+"_2",torComb.filename])
def main_wrapper(torComb):
"""Given a conformer (torComb) the structure is rotated to the proper
angles, then written to a file where a single point energy is evaluated.
If the energy is below a prescribed value (sysInfo.max_energy), then
proceed to a full minimization, where the final structure is then renamed
and the results written out to the terminal
"""
#Set angle in torsions object
for i in xrange(len(torsions)):
torsions[i].newAngle = np.radians(torComb.combination[i])
#Check which torsions need to be rotated
for torsion in torsions:
if torsion.newAngle != torsion.currentAngle():
#Set atoms.rotate to false
for atom in atoms:
atom.rotate = False
#Check which atoms need to be rotated & setting atom.rotate
assign_rotating_atoms(torsion.tor_atoms[1], torsion.tor_atoms[2],
atoms)
#Rotate atoms
rotate_atoms(torsion, atoms)
#Check if atoms are too close together
if check_close_contacts(atoms):
return
#Write file for energy evaluation
torComb.filename = "new_octane"
name = TTFiles.make_filename(torComb)
TTFiles.write_xyz(atoms, torComb.filename)
#Perform single point energy evaluation
torComb.energy = TTEnergy.get_single_point_energy(torComb.filename)
#Check to see if single point energy is above the threshold for minimization
if torComb.energy > sysInfo.max_energy():
subprocess.Popen(["rm", torComb.filename])
return
#Perform minimization
torComb.min_energy = TTEnergy.get_minimum_energy(torComb.filename)
print torComb.filename, torComb.min_energy
#Clean up some files
subprocess.Popen(["mv", torComb.filename + "_2", torComb.filename])
#Perform minimization
torComb.min_energy = TTEnergy.get_minimum_energy(torComb.filename)
print torComb.filename,torComb.min_energy
#Clean up some files
subprocess.Popen(["mv",torComb.filename+"_2",torComb.filename])
if __name__ == '__main__':
#SET UP DATASTRUCTURES
#Generate an array of atom objects
sysInfo = SysInfo(raw_input("Filename of Tinker XYZ coordinate file: "))
atoms = TTFiles.get_xyz(sysInfo.startFile)
#Evaluate energy of starting structure to obtain a reference point
sysInfo.startEnergy = TTEnergy.get_single_point_energy(sysInfo.startFile)
#Generate an array of torsion objects
torsions = assign_torsions(atoms)
#Populate system info & list of possible torsion angles
sysInfo.nTors = len(torsions)
while (not sysInfo.deltaPhiStatus):
sysInfo.deltaPhi = float(raw_input("Delta Phi - Angle step size: "))
sysInfo.deltaPhiStatus = check_deltaPhi(sysInfo.deltaPhi)
if not sysInfo.deltaPhiStatus:
print "\n------------------------------------------"
print "Delta phi does not divide evenly into 360."
print "Please provide another value for Delta Phi"
print "------------------------------------------"
sysInfo.deltaPhiStatus, sysInfo.numberOfConformers = \
#Perform minimization
torComb.min_energy = TTEnergy.get_minimum_energy(torComb.filename)
print torComb.filename, torComb.min_energy
#Clean up some files
subprocess.Popen(["mv", torComb.filename + "_2", torComb.filename])
if __name__ == '__main__':
#SET UP DATASTRUCTURES
#Generate an array of atom objects
sysInfo = SysInfo(raw_input("Filename of Tinker XYZ coordinate file: "))
atoms = TTFiles.get_xyz(sysInfo.startFile)
#Evaluate energy of starting structure to obtain a reference point
sysInfo.startEnergy = TTEnergy.get_single_point_energy(sysInfo.startFile)
#Generate an array of torsion objects
torsions = assign_torsions(atoms)
#Populate system info & list of possible torsion angles
sysInfo.nTors = len(torsions)
while (not sysInfo.deltaPhiStatus):
sysInfo.deltaPhi = float(raw_input("Delta Phi - Angle step size: "))
sysInfo.deltaPhiStatus = check_deltaPhi(sysInfo.deltaPhi)
if not sysInfo.deltaPhiStatus:
print "\n------------------------------------------"
print "Delta phi does not divide evenly into 360."
print "Please provide another value for Delta Phi"
print "------------------------------------------"
sysInfo.deltaPhiStatus, sysInfo.numberOfConformers = \