def write_final_xyz(self, unixmd_dir, istep):
""" Write final positions and velocities
:param string unixmd_dir: Directory where MD output files are written
:param integer istep: Current MD step
"""
# Write FINAL.xyz file including positions and velocities
tmp = f'{self.mol.nat:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}Position(A){"":34s}Velocity(au)'
for iat in range(self.mol.nat):
tmp += "\n" + f'{self.mol.symbols[iat]:5s}' + \
"".join([f'{self.mol.pos[iat, isp] * au_to_A:15.8f}' for isp in range(self.mol.ndim)]) \
+ "".join([f"{self.mol.vel[iat, isp]:15.8f}" for isp in range(self.mol.ndim)])
typewriter(tmp, unixmd_dir, "FINAL.xyz", "w")
def write_deco(self, unixmd_dir, istep):
""" Write XF-based decoherence information
:param string unixmd_dir: PyUNIxMD directory
:param integer istep: Current MD step
"""
# Write time-derivative density matrix elements in DOTPOTD
tmp = f'{istep + 1:9d}' + "".join(
[f'{pop:15.8f}' for pop in self.dotpopd])
typewriter(tmp, unixmd_dir, "DOTPOPD", "a")
# Write auxiliary trajectories
if (self.verbosity >= 2 and True in self.l_coh):
# Write quantum momenta
tmp = f'{self.aux.nat:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}Momentum (au)' + \
"".join(["\n" + f'{self.aux.symbols[iat]:5s}' + \
"".join([f'{self.qmom[iat, isp]:15.8f}' for isp in range(self.aux.ndim)]) for iat in range(self.aux.nat)])
typewriter(tmp, unixmd_dir, f"QMOM", "a")
# Write auxiliary variables
for ist in range(self.mol.nst):
if (self.l_coh[ist]):
# Write auxiliary phase
tmp = f'{self.aux.nat:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}Phase (au)' + \
"".join(["\n" + f'{self.aux.symbols[iat]:5s}' + \
"".join([f'{self.phase[ist, iat, isp]:15.8f}' for isp in range(self.aux.ndim)]) for iat in range(self.aux.nat)])
typewriter(tmp, unixmd_dir, f"AUX_PHASE_{ist}", "a")
# Write auxiliary trajectory movie files
tmp = f'{self.aux.nat:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}Position(A){"":34s}Velocity(au)' + \
"".join(["\n" + f'{self.aux.symbols[iat]:5s}' + \
"".join([f'{self.aux.pos[ist, iat, isp] * au_to_A:15.8f}' for isp in range(self.aux.ndim)]) + \
"".join([f"{self.aux.vel[ist, iat, isp]:15.8f}" for isp in range(self.aux.ndim)]) for iat in range(self.aux.nat)])
typewriter(tmp, unixmd_dir, f"AUX_MOVIE_{ist}.xyz", "a")
def write_sh(self, unixmd_dir, istep):
""" Write hopping-related quantities into files
:param string unixmd_dir: PyUNIxMD directory
:param integer istep: Current MD step
"""
# Write SHSTATE file
tmp = f'{istep + 1:9d}{"":14s}{self.rstate}'
typewriter(tmp, unixmd_dir, "SHSTATE", "a")
# Write SHPROB file
tmp = f'{istep + 1:9d}' + "".join(
[f'{self.prob[ist]:15.8f}' for ist in range(self.mol.nst)])
typewriter(tmp, unixmd_dir, "SHPROB", "a")
def write_deco(self, itrajectory, unixmd_dir, istep):
""" Write CT-based decoherence information
:param integer itrajectory: Index for trajectories
:param string unixmd_dir: PyUNIxMD directory
:param integer istep: Current MD step
"""
# TODO
# Write time-derivative density matrix elements in DOTPOTD
#tmp = f'{istep + 1:9d}' + "".join([f'{pop:15.8f}' for pop in self.dotpopd])
#typewriter(tmp, unixmd_dir, "DOTPOPD", "a")
# Write auxiliary trajectories
if (self.verbosity >= 2):
tmp = f'{self.nat_qm:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}sigma_x{"":5s}sigma_y{"":5s}sigma_z{"":5s}count_ntrajs' + \
"".join(["\n" + f'{self.mol.symbols[iat]:5s}' + \
"".join([f'{self.sigma_lk[itrajectory, 0, iat, idim]:15.8f}' for idim in range(self.ndim)]) + \
f'{self.count_ntrajs[itrajectory, iat]:15.8f}' for iat in range(self.nat_qm)])
typewriter(tmp, unixmd_dir, f"SIGMA", "a")
tmp = f'{self.nat_qm:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}slope' + \
"".join(["\n" + f'{self.mol.symbols[iat]:5s}' + \
"".join([f'{self.slope_i[itrajectory, iat, idim]:15.8f}' for idim in range(self.ndim)]) for iat in range(self.nat_qm)])
typewriter(tmp, unixmd_dir, f"SLOPE", "a")
# Write quantum momenta
index_lk = -1
for ist in range(self.nst):
for jst in range(ist + 1, self.nst):
index_lk += 1
tmp = f'{self.nat_qm:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}Momentum center (au)' + \
"".join(["\n" + f'{self.mol.symbols[iat]:5s}' + \
"".join([f'{self.center_lk[itrajectory, index_lk, iat, idim]:15.8f}' for idim in range(self.ndim)]) for iat in range(self.nat_qm)])
typewriter(tmp, unixmd_dir, f"CENTER_{ist}_{jst}", "a")
tmp = f'{self.nat_qm:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}Momentum (au)' + \
"".join(["\n" + f'{self.mol.symbols[iat]:5s}' + \
"".join([f'{self.qmom[itrajectory, index_lk, iat, idim]:15.8f}' for idim in range(self.ndim)]) for iat in range(self.nat_qm)])
typewriter(tmp, unixmd_dir, f"QMOM_{ist}_{jst}", "a")
for ist in range(self.nst):
for jst in range(self.nst):
if (ist != jst):
tmp = f'{istep + 1:9d}{self.K_lk[itrajectory, ist, jst]:15.8f}'
typewriter(tmp, unixmd_dir, f"K_lk_{ist}_{jst}", "a")
# Write auxiliary variables
for ist in range(self.mol.nst):
# Write auxiliary phase
tmp = f'{self.nat_qm:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}Phase (au)' + \
"".join(["\n" + f'{self.mol.symbols[iat]:5s}' + \
"".join([f'{self.phase[itrajectory, ist, iat, idim]:15.8f}' for idim in range(self.ndim)]) for iat in range(self.nat_qm)])
typewriter(tmp, unixmd_dir, f"PHASE_{ist}", "a")
def write_md_output(self, unixmd_dir, istep):
""" Write output files
:param string unixmd_dir: Directory where MD output files are written
:param integer istep: Current MD step
"""
# Write MOVIE.xyz file including positions and velocities
tmp = f'{self.mol.nat:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}Position(A){"":34s}Velocity(au)' + \
"".join(["\n" + f'{self.mol.symbols[iat]:5s}' + \
"".join([f'{self.mol.pos[iat, isp] * au_to_A:15.8f}' for isp in range(self.mol.ndim)]) + \
"".join([f"{self.mol.vel[iat, isp]:15.8f}" for isp in range(self.mol.ndim)]) for iat in range(self.mol.nat)])
typewriter(tmp, unixmd_dir, "MOVIE.xyz", "a")
# Write MDENERGY file including several energy information
tmp = f'{istep + 1:9d}{self.mol.ekin:15.8f}{self.mol.epot:15.8f}{self.mol.etot:15.8f}' \
+ "".join([f'{states.energy:15.8f}' for states in self.mol.states])
typewriter(tmp, unixmd_dir, "MDENERGY", "a")
if (self.md_type != "BOMD"):
# Write BOCOEF, BOPOP, BOCOH files
if (self.elec_object == "density"):
tmp = f'{istep + 1:9d}' + "".join([
f'{self.mol.rho.real[ist, ist]:15.8f}'
for ist in range(self.mol.nst)
])
typewriter(tmp, unixmd_dir, "BOPOP", "a")
tmp = f'{istep + 1:9d}' + "".join([f"{self.mol.rho.real[ist, jst]:15.8f}{self.mol.rho.imag[ist, jst]:15.8f}" \
for ist in range(self.mol.nst) for jst in range(ist + 1, self.mol.nst)])
typewriter(tmp, unixmd_dir, "BOCOH", "a")
elif (self.elec_object == "coefficient"):
tmp = f'{istep + 1:9d}' + "".join([f'{states.coef.real:15.8f}{states.coef.imag:15.8f}' \
for states in self.mol.states])
typewriter(tmp, unixmd_dir, "BOCOEF", "a")
if (self.l_print_dm):
tmp = f'{istep + 1:9d}' + "".join([
f'{self.mol.rho.real[ist, ist]:15.8f}'
for ist in range(self.mol.nst)
])
typewriter(tmp, unixmd_dir, "BOPOP", "a")
tmp = f'{istep + 1:9d}' + "".join([f"{self.mol.rho.real[ist, jst]:15.8f}{self.mol.rho.imag[ist, jst]:15.8f}" \
for ist in range(self.mol.nst) for jst in range(ist + 1, self.mol.nst)])
typewriter(tmp, unixmd_dir, "BOCOH", "a")
# Write NACME file
tmp = f'{istep + 1:10d}' + "".join([f'{self.mol.nacme[ist, jst]:15.8f}' \
for ist in range(self.mol.nst) for jst in range(ist + 1, self.mol.nst)])
typewriter(tmp, unixmd_dir, "NACME", "a")
# Write NACV file
if (not self.mol.l_nacme and self.verbosity >= 2):
for ist in range(self.mol.nst):
for jst in range(ist + 1, self.mol.nst):
tmp = f'{self.mol.nat_qm:6d}\n{"":2s}Step:{istep + 1:6d}{"":12s}NACV' + \
"".join(["\n" + f'{self.mol.symbols[iat]:5s}' + \
"".join([f'{self.mol.nac[ist, jst, iat, isp]:15.8f}' for isp in range(self.mol.ndim)]) for iat in range(self.mol.nat_qm)])
typewriter(tmp, unixmd_dir, f"NACV_{ist}_{jst}", "a")
def touch_file(self, unixmd_dir):
""" Routine to write PyUNIxMD output files
:param string unixmd_dir: Directory where MD output files are written
"""
# Energy information file header
tmp = f'{"#":5s}{"Step":9s}{"Kinetic(H)":15s}{"Potential(H)":15s}{"Total(H)":15s}' + \
"".join([f'E({ist})(H){"":8s}' for ist in range(self.mol.nst)])
typewriter(tmp, unixmd_dir, "MDENERGY", "w")
if (self.md_type != "BOMD"):
# BO coefficents, densities file header
if (self.elec_object == "density"):
tmp = f'{"#":5s} Density Matrix: population Re; see the manual for detail orders'
typewriter(tmp, unixmd_dir, "BOPOP", "w")
tmp = f'{"#":5s} Density Matrix: coherence Re-Im; see the manual for detail orders'
typewriter(tmp, unixmd_dir, "BOCOH", "w")
elif (self.elec_object == "coefficient"):
tmp = f'{"#":5s} BO State Coefficients: state Re-Im; see the manual for detail orders'
typewriter(tmp, unixmd_dir, "BOCOEF", "w")
if (self.l_print_dm):
tmp = f'{"#":5s} Density Matrix: population Re; see the manual for detail orders'
typewriter(tmp, unixmd_dir, "BOPOP", "w")
tmp = f'{"#":5s} Density Matrix: coherence Re-Im; see the manual for detail orders'
typewriter(tmp, unixmd_dir, "BOCOH", "w")
# NACME file header
tmp = f'{"#":5s}Non-Adiabatic Coupling Matrix Elements: off-diagonal'
typewriter(tmp, unixmd_dir, "NACME", "w")
# file header for SH-based methods
if (self.md_type == "SH" or self.md_type == "SHXF"):
tmp = f'{"#":5s}{"Step":8s}{"Running State":10s}'
typewriter(tmp, unixmd_dir, "SHSTATE", "w")
tmp = f'{"#":5s}{"Step":12s}' + "".join(
[f'Prob({ist}){"":8s}' for ist in range(self.mol.nst)])
typewriter(tmp, unixmd_dir, "SHPROB", "w")
# file header for XF-based methods
if (self.md_type == "SHXF" or self.md_type == "EhXF"):
tmp = f'{"#":5s} Time-derivative Density Matrix by decoherence: population; see the manual for detail orders'
typewriter(tmp, unixmd_dir, "DOTPOPD", "w")