def main():
M = Molecule(opts.coords)
if len(M.molecules) != 1:
raise RuntimeError(
'Input coordinates must be a single contiguous molecule')
if opts.phi1 == None:
raise RuntimeError(
'phi1 (the first quartet of atoms) must be provided')
xyzout = []
commout = []
xyzcsh = []
commcsh = []
if opts.phi2 != None: # Two dimensional scan
for inc1 in range(0, 360, opts.scan):
for inc2 in range(0, 360, opts.scan):
xyzrot, clash = get_rotated_xyz(M, [opts.phi1, opts.phi2],
[inc1, inc2])
print(inc1, inc2, "Clash" if clash else "Ok")
comm = "Dihedrals %s, %s set to %i, %i" % (str(
opts.phi1), str(opts.phi2), inc1, inc2)
if clash:
xyzcsh.append(xyzrot.copy())
commcsh.append(comm)
else:
xyzout.append(xyzrot.copy())
commout.append(comm)
else: # One dimensional scan
for inc1 in range(0, 360, opts.scan):
xyzrot, clash = get_rotated_xyz(M, [opts.phi1], [inc1])
print(inc1, "Clash" if clash else "Ok")
comm = "Dihedral %s set to %i" % (str(opts.phi1), inc1)
if clash:
xyzcsh.append(xyzrot.copy())
commcsh.append(comm)
else:
xyzout.append(xyzrot.copy())
commout.append(comm)
if len(xyzout) > 0:
M.xyzs = xyzout
M.comms = commout
M.write(
os.path.splitext(opts.coords)[0] + "_out" +
os.path.splitext(opts.coords)[1])
if len(xyzcsh) > 0:
M.xyzs = xyzcsh
M.comms = commcsh
M.write(
os.path.splitext(opts.coords)[0] + "_clash" +
os.path.splitext(opts.coords)[1])
def write_fb_target_abinitio(self, records):
""" Write a list of {'energy': xxx, 'molecule': xxx, 'name': xxx} records into a new target folder """
# prepare folder for writing
target_name = 'abinitio_bond_angles'
target_folder = os.path.join(self.out_folder, target_name)
os.mkdir(target_folder)
os.chdir(target_folder)
# load data into a fb Molecule
out_m = Molecule()
out_m.elem = self.m.elem.copy()
out_m.xyzs = []
out_m.qm_energies = []
out_m.comms = []
for record in records:
qcmol = record['molecule']
energy = record['energy']
name = record.get('name', 'created by FBTargetBuilder')
m = self.qc_molecule_to_fb_molecule(qcmol)
assert m.elem == out_m.elem, 'Elements list of resulting qcmol is not consistent with self.m'
# append geometry
out_m.xyzs.append(m.xyzs[0])
# append energy
out_m.qm_energies.append(energy)
# append name
out_m.comms.append(name)
# write output
print(
f"Writing {len(records)} frames into targets/abinitio_bond_angles/traj.xyz"
)
out_m.write('traj.xyz')
print(
f"Writing {len(records)} frames into targets/abinitio_bond_angles/qdata.txt"
)
out_m.write('qdata.txt')
def main():
M = Molecule(opts.coords)
if len(M.molecules) != 1:
raise RuntimeError('Input coordinates must be a single contiguous molecule')
if opts.phi1 == None:
raise RuntimeError('phi1 (the first quartet of atoms) must be provided')
xyzout = []
commout = []
xyzcsh = []
commcsh = []
if opts.phi2 != None: # Two dimensional scan
for inc1 in range(0, 360, opts.scan):
for inc2 in range(0, 360, opts.scan):
xyzrot, clash = get_rotated_xyz(M, [opts.phi1, opts.phi2], [inc1, inc2])
print(inc1, inc2, "Clash" if clash else "Ok")
comm = "Dihedrals %s, %s set to %i, %i" % (str(opts.phi1), str(opts.phi2), inc1, inc2)
if clash:
xyzcsh.append(xyzrot.copy())
commcsh.append(comm)
else:
xyzout.append(xyzrot.copy())
commout.append(comm)
else: # One dimensional scan
for inc1 in range(0, 360, opts.scan):
xyzrot, clash = get_rotated_xyz(M, [opts.phi1], [inc1])
print(inc1, "Clash" if clash else "Ok")
comm = "Dihedral %s set to %i" % (str(opts.phi1), inc1)
if clash:
xyzcsh.append(xyzrot.copy())
commcsh.append(comm)
else:
xyzout.append(xyzrot.copy())
commout.append(comm)
if len(xyzout) > 0:
M.xyzs = xyzout
M.comms = commout
M.write(os.path.splitext(opts.coords)[0]+"_out"+os.path.splitext(opts.coords)[1])
if len(xyzcsh) > 0:
M.xyzs = xyzcsh
M.comms = commcsh
M.write(os.path.splitext(opts.coords)[0]+"_clash"+os.path.splitext(opts.coords)[1])
from forcebalance.readfrq import read_frq_gen
# Frequency output file.
fout = sys.argv[1]
# Mode number, starting from 1.
modenum = int(sys.argv[2])
if modenum == 0:
raise RuntimeError("Start mode number from one, please")
frqs, modes, intens, elem, xyz = read_frq_gen(fout)
M = Molecule()
M.elem = elem[:]
M.xyzs = []
xmode = modes[modenum - 1]
xmode /= (np.linalg.norm(xmode)/np.sqrt(M.na))
xmode *= 0.3 # Reasonable vibrational amplitude
spac = np.linspace(0, 1, 101)
disp = np.concatenate((spac, spac[::-1][1:], -1*spac[1:], -1*spac[::-1][1:-1]))
for i in disp:
M.xyzs.append(xyz+i*xmode.reshape(-1,3))
M.comms = ['Vibrational Mode %i Frequency %.3f Displacement %.3f' % (modenum, frqs[modenum-1], disp[i]*(np.linalg.norm(xmode)/np.sqrt(M.na))) for i in range(len(M))]
M.write(os.path.splitext(fout)[0]+'.mode%03i.xyz' % modenum)
import os, sys, re
import numpy as np
from forcebalance.molecule import Molecule
from forcebalance.readfrq import read_frq_psi
# Psi4 output file.
psiout = sys.argv[1]
# Mode number, starting from 1.
modenum = int(sys.argv[2])
frqs, modes, elem, xyz = read_frq_psi(psiout)
M = Molecule()
M.elem = elem[:]
M.xyzs = []
xmode = modes[modenum - 1]
xmode /= (np.linalg.norm(xmode)/np.sqrt(M.na))
xmode *= 0.3 # Reasonable vibrational amplitude
spac = np.linspace(0, 1, 101)
disp = np.concatenate((spac, spac[::-1][1:], -1*spac[1:], -1*spac[::-1][1:-1]))
for i in disp:
M.xyzs.append(xyz+i*xmode)
M.comms = ['Vibrational Mode %i Frequency %.3f Displacement %.3f' % (modenum, frqs[modenum-1], disp[i]*(np.linalg.norm(xmode)/np.sqrt(M.na))) for i in range(len(M))]
M.write(os.path.splitext(psiout)[0]+'.mode%03i.xyz' % modenum)
