from dataclasses import dataclass
from math import sqrt
import os
from pathlib import Path
import re
import shutil
import subprocess
import warnings
from jinja2 import Template
import numpy as np
import pyparsing as pp
# from pysisyphus.calculators.cosmo_data import COSMO_RADII
from pysisyphus.calculators.OverlapCalculator import (
GroundStateContext,
OverlapCalculator,
)
from pysisyphus.calculators.parser import (
parse_turbo_gradient,
parse_turbo_ccre0_ascii,
parse_turbo_mos,
# parse_turbo_exstates,
parse_turbo_exstates_re as parse_turbo_exstates,
)
from pysisyphus.helpers_pure import file_or_str, get_random_path
from pysisyphus.wavefunction.excited_states import make_density_matrices_for_root
[docs]
@dataclass
class ExSpectrumRoot:
root: int
sym: str
exc_energy: float
osc_vel: float
osc_len: float
@file_or_str(".exspectrum")
def parse_exspectrum(text: str) -> list[ExSpectrumRoot]:
"""Parse root data from exspectrum file."""
ex_roots = list()
for line in text.strip().split("\n"):
line = line.strip()
is_comment = line.startswith("#")
is_empty = line == ""
if is_comment or is_empty:
continue
# root, sym, energy_au, energy_ev, energy_cm⁻¹, energy_nm, osc_vel, osc_len
root, sym, exc_energy, *_, osc_vel, osc_len = line.split()
root = int(root)
exc_energy = float(exc_energy)
osc_vel = float(osc_vel)
osc_len = float(osc_len)
ex_root = ExSpectrumRoot(
root=root,
sym=sym,
exc_energy=exc_energy,
osc_vel=osc_vel,
osc_len=osc_len,
)
ex_roots.append(ex_root)
return ex_roots
[docs]
def index_strs_for_atoms(atoms):
indices = dict()
for i, atom in enumerate(atoms, 1):
indices.setdefault(atom.lower(), list()).append(i)
pairs = dict()
for key, values in indices.items():
pairs[key] = list()
i_end = len(values) - 1
start = None
for i, v in enumerate(values):
if start is None:
start = v
if (i == i_end) or (v + 1 != values[i + 1]):
end = None if (start == v) else v
pairs[key].append((start, end))
start = None
atom_strs = dict()
for key, prs in pairs.items():
tmp = list()
for start, end in prs:
if end is None:
itm = str(start)
else:
itm = f"{start}-{end}"
tmp.append(itm)
atom_str = f"{key} " + ",".join(tmp)
atom_strs[key] = atom_str
return atom_strs
[docs]
def get_cosmo_data_groups(atoms, epsilon, rsolv=None, refind=None, dcosmo_rs=None):
cosmo_dgs = {
"cosmo": {
"epsilon": epsilon,
},
"cosmo_out": "file=out.ccf",
"cosmo_data": "file=cosmo_transfer.tmp",
}
if rsolv is not None:
cosmo_dgs["cosmo"]["rsolv"] = rsolv
if refind is not None:
cosmo_dgs["cosmo"]["refind"] = refind
# Transform atom list into TURBOMOLE-style compressed indices
# H, H, H, O, O, H, O
# is transformed to
# h 1-3, 6
# o 4-5, 7
# etc.
index_strs = index_strs_for_atoms(atoms)
cosmo_atom_strs = list()
cosmo_atoms = dict()
# This does not yet work; so we stick with the default radii.
# for key, index_str in index_strs.items():
# TODO: reenable COSMO_RADII import
# radius = COSMO_RADII[key].radius
# cosmo_atoms[index_str] = f"\nradius={radius:.6f}"
# cosmo_dgs["cosmo_atoms"] = cosmo_atoms
if dcosmo_rs:
cosmo_dgs["dcosmo_rs"] = f"file={dcosmo_rs}"
return cosmo_dgs
DATA_GROUP_TPL = Template(
"""
{% for dg in data_groups %}
${{ dg }}
{% for key, value in data_groups[dg].items() %}
{{ key }}{% if value %} ={{ value }}{% endif %}
{% endfor %}
{% endfor %}
""",
trim_blocks=True,
lstrip_blocks=True,
)
SIMPLE_INPUT_TPL = Template(
"""
$atoms
basis={{ basis }}
$coord file=coord
$grad file=gradient
$symmetry c1
$eht charge={{ charge }} unpaired={{ unpaired }}
{{ data_groups }}
$end
"""
)
[docs]
def render_data_groups(raw_data_groups):
data_groups = dict()
for dg, kws in raw_data_groups.items():
# datagroup w/o keywords
if kws is None:
data_groups[dg] = dict()
# datagroup w/ one keyword on same line. Here we just merge the name and the keyword,
# so they appear on the same line.
elif type(kws) in (str, int, float):
data_groups[f"{dg} {kws}"] = dict()
# Otherwise a dict is expected
elif type(kws) == dict:
data_groups[dg] = kws
else:
raise Exception(f"Can't handle input '{dg}': '{kws}'!")
return DATA_GROUP_TPL.render(data_groups=data_groups)
[docs]
def parse_frozen_nmos(text: str) -> tuple[list[tuple[int, int], tuple[int, int]], bool]:
"""Determine number of occ. & and virt. orbitals used in ES calculations."""
frozen_re = re.compile(
r"number of non-frozen orbitals\s+:\s+(?P<nmos>\d+)"
r"\s+number of non-frozen occupied orbitals :\s+(?P<nocc>\d+)"
)
matches = frozen_re.findall(text)
mo_nums = list()
for nmos, nocc in matches:
nmos = int(nmos)
nocc = int(nocc)
nvirt = nmos - nocc
mo_nums.append((nocc, nvirt))
restricted = len(mo_nums) == 1
if restricted:
mo_nums.append((0, 0))
return mo_nums, restricted
@file_or_str(
"ciss_a", "ucis_a", "sing_a", "unrs_a", "dipl_a", exact=True, add_exts=True
)
def parse_ci_coeffs(
text: str,
nocc_a: int,
nvirt_a: int,
nocc_b: int,
nvirt_b: int,
restricted_same_ab=False,
):
"""Parse CI coefficients from escf/egrad calculations."""
states_data = Turbomole.parse_td_vectors(text)
expect_a = nocc_a * nvirt_a
expect_b = nocc_b * nvirt_b
shape_a = (nocc_a, nvirt_a)
shape_b = (nocc_b, nvirt_b)
Xa = np.zeros((len(states_data), *shape_a))
Ya = np.zeros((len(states_data), *shape_a))
Xb = np.zeros((len(states_data), *shape_b))
Yb = np.zeros((len(states_data), *shape_b))
# Whether a Y vector is present
with_deexc = len(states_data[0]["vector"]) == 2 * (expect_a + expect_b)
if with_deexc:
XpYa = np.empty(shape_a)
XmYa = np.empty(shape_a)
XpYb = np.empty(shape_b)
XmYb = np.empty(shape_b)
for i, state_data in enumerate(states_data):
coeffs = np.array(state_data["vector"])
# TD-DFT/TD-HF
if with_deexc:
start = 0
# X + Y
XpYa[:] = coeffs[start : start + expect_a].reshape(shape_a)
start += expect_a
XpYb = coeffs[start : start + expect_b].reshape(shape_b)
start += expect_b
# X - Y
XmYa[:] = coeffs[start : start + expect_a].reshape(shape_a)
start += expect_a
XmYb = coeffs[start : start + expect_b].reshape(shape_b)
start += expect_b
# Recover X and Y vectors from X + Y and X - Y
Xa[i] = (XpYa + XmYa) / 2.0
Ya[i] = XpYa - Xa[i]
Xb[i] = (XpYb + XmYb) / 2.0
Yb[i] = XpYb - Xb[i]
# TDA/CIS
else:
Xa[i] = coeffs[:expect_a].reshape(shape_a)
Xb[i] = coeffs[expect_a:].reshape(shape_b)
if restricted_same_ab and Xb.size == 0:
Xb = Xa.copy()
Yb = Ya.copy()
return Xa, Ya, Xb, Yb
[docs]
def get_density_matrices_for_root(
log_fn, vec_fn, root, rlx_vec_fn=None, Ca=None, Cb=None
):
with open(log_fn) as handle:
text = handle.read()
# Number of non-frozen/active molecular orbitals
((nfocc_a, nfvirt_a), (nfocc_b, nfvirt_b)), restricted = parse_frozen_nmos(text)
# Transition density
Xa, Ya, Xb, Yb = parse_ci_coeffs(vec_fn, nfocc_a, nfvirt_a, nfocc_b, nfvirt_b)
# Relaxed density correction; there is never a deexciation part
if rlx_vec_fn:
ov_corr_a, _, ov_corr_b, _ = parse_ci_coeffs(
rlx_vec_fn, nfocc_a, nfvirt_a, nfocc_b, nfvirt_b
)
# We expect only one root in dipl_a
assert ov_corr_a.shape[0] == 1
ov_corr_a = ov_corr_a[0]
assert ov_corr_b.shape[0] == 1
ov_corr_b = ov_corr_b[0]
else:
ov_corr_a = None
ov_corr_b = None
return make_density_matrices_for_root(
root - 1, restricted, Xa, Ya, Xb, Yb, ov_corr_a, ov_corr_b, Ca, Cb
)
[docs]
class TurbomoleGroundStateContext(GroundStateContext):
def __enter__(self):
super().__enter__()
self.energy_cmd_bak = self.calc.energy_cmd
self.calc.energy_cmd = self.calc.scf_cmd
def __exit__(self, exc_type, exc_value, exc_traceback):
super().__exit__(exc_type, exc_value, exc_traceback)
self.calc.energy_cmd = self.energy_cmd_bak
[docs]
class Turbomole(OverlapCalculator):
conf_key = "turbomole"
_set_plans = (
"out",
"control",
"alpha",
"beta",
"ccres",
"exspectrum",
"exstates",
"mos",
"mwfn_wf",
("ciss_a", "td_vec_fn"),
("sing_a", "td_vec_fn"),
("ucis_a", "td_vec_fn"),
("unrs_a", "td_vec_fn"),
("dipl_a", "rlx_vec_fn"),
)
def __init__(
self,
control_path=None,
numfreq=False,
simple_input=None,
double_mol_path=None,
cosmo_kwargs=None,
wavefunction_dump=True,
**kwargs,
):
super().__init__(**kwargs)
assert (control_path is not None) or (
simple_input is not None
), "Please either provide a prepared 'control_path' or 'simple_input'!"
# Handle simple input
if simple_input:
control_path = (self.out_dir / get_random_path("control_path")).absolute()
self.log(
"Set 'control_path' to '{control_path}'. Creating 'control' from simple input in it."
)
try:
control_path.mkdir()
except FileExistsError:
# Clean directory if already exists
for fn in control_path.iterdir():
fn.unlink()
control_str = control_from_simple_input(
simple_input, charge=self.charge, mult=self.mult
)
with open(control_path / "control", "w") as handle:
handle.write(control_str)
# End of simple input handling
# Set provided control_path or use the one generated for simple_input
self.control_path = Path(control_path).absolute()
self.numfreq = numfreq
self.double_mol_path = double_mol_path
if self.double_mol_path:
self.double_mol_path = Path(self.double_mol_path)
# Check if the overlap matrix will be printed and assert
# that no SCF iterations are done.
if self.double_mol_path:
with open(self.double_mol_path / "control") as handle:
text = handle.read()
assert re.search(r"\$intsdebug\s*sao", text) and re.search(
r"\$scfiterlimit\s*0", text
), ("Please set " "$intsdebug sao and $scfiterlimit 0 !")
self.cosmo_kwargs = cosmo_kwargs
if self.cosmo_kwargs:
assert (
"epsilon" in self.cosmo_kwargs
), "If 'cosmo_kwargs' is given 'epsilon' must be specified!"
self.wavefunction_dump = wavefunction_dump
self.to_keep = (
"control",
"mos",
"alpha",
"beta",
"out",
"ciss_a",
"ucis_a",
"sing_a",
"unrs_a",
"dipl_a",
"gradient",
"__ccre*",
"exstates",
"coord",
"mwfn_wf:wavefunction.molden",
"input.xyz",
"pc_gradients",
"nprhessian",
"exspectrum",
)
self.parser_funcs = {
"energy": self.parse_energy,
"force": self.parse_force,
"hessian": self.parse_hessian,
"double_mol": self.parse_double_mol,
"noparse": lambda path: None,
}
# Turbomole uses the 'control' file implicitly
self.inp_fn = ""
self.out_fn = "turbomole.out"
# MO coefficient files
self.mos = None
self.alpha = None
self.beta = None
# Prepare base_cmd
with open(self.control_path / "control") as handle:
text = handle.read()
scf_cmd = "dscf"
second_cmd = "grad"
# Check for RI
self.ri = ("$rij" in text) or ("$rik" in text)
if self.ri:
scf_cmd = "ridft"
second_cmd = "rdgrad"
self.log("Found RI calculation.")
self.uhf = ("$uhf" in text) or (self.mult > 1)
# It seems as they changed whats written in the control file in version 7.7
try:
self.set_occ_and_mo_nums(text)
except TypeError:
warnings.warn(
"Parsing of occupied and virtual MO numbers failed! Disabling "
"excited state tracking!"
)
self.track = False
assert not (("$exopt" in text) and ("$ricc2" in text)), (
"Found $exopt and $ricc2 in the control file! $exopt is used "
"for TD-DFT/TDA gradients whereas $ricc2 with 'geoopt ...' "
"leads to ricc2 gradients. Please delete one of the keywords!"
)
self.td = False
self.td_vec_fn = None
self.ricc2 = False
self.ricc2_opt = False
# Check for excited state calculation
if "$exopt" in text:
exopt_re = r"\$exopt\s*(\d+)"
self.root = int(re.search(exopt_re, text)[1])
second_cmd = "egrad"
self.prepare_td(text)
self.td = True
elif "$soes" in text:
second_cmd = "escf"
self.td = True
self.prepare_td(text)
elif ("$ricc2" in text) and ("$excitations" in text):
self.ricc2 = True
self.ricc2_opt = "geoopt" in text
second_cmd = "ricc2"
self.prepare_td(text)
self.root = self.get_ricc2_root(text)
try:
frozen_mos = int(re.search(r"implicit core=\s*(\d+)", text)[1])
except TypeError:
frozen_mos = 0
self.frozen_mos = frozen_mos
self.log(f"Found {self.frozen_mos} frozen orbitals.")
if self.track:
assert self.td or self.ricc2, (
"track=True can only be used "
"in connection with excited state calculations."
)
# Right now this can't handle a root flip from some excited state
# to the ground state ... Then we would need grad/rdgrad again,
# instead of egrad.
self.scf_cmd = scf_cmd
self.second_cmd = second_cmd
self.numforce_cmd = f"{self.second_cmd}; NumForce -central -d 0.005"
if self.ri:
self.numforce_cmd += " -ri"
# Setup several cmds, depending on the calc type
def get_cmd(cmd):
return ";".join((self.scf_cmd, cmd))
if self.td:
self.energy_cmd = get_cmd("escf")
self.forces_cmd = get_cmd("egrad")
self.hessian_cmd = "not_yet_implemented"
elif self.ricc2:
ricc2_cmd = get_cmd("ricc2")
self.energy_cmd = ricc2_cmd
self.forces_cmd = ricc2_cmd
self.hessian_cmd = "not_yet_implemented"
else:
self.energy_cmd = self.scf_cmd
self.forces_cmd = get_cmd(second_cmd)
self.hessian_cmd = (
get_cmd(self.numforce_cmd) if self.numfreq else get_cmd("aoforce")
)
self.log("Prepared commands:")
self.log("\tEnergy cmd: " + self.energy_cmd)
self.log("\tForces cmd: " + self.forces_cmd)
self.log("\tHessian cmd: " + self.hessian_cmd)
if self.td or self.ricc2 and (self.root is None):
warnings.warn(
"No root set! Either include '$exopt' for TDA/TDDFT or "
"'geoopt' for ricc2 in the control or supply a value for 'root'! "
)
[docs]
def set_occ_and_mo_nums(self, text):
# Determine number of basis functions
nbf_re = r"nbf\(AO\)=(\d+)"
nbf = int(re.search(nbf_re, text)[1])
self.occ_mos = None
self.virt_mos = None
# Determine number of occupied orbitals
if not self.uhf:
# Sometimes Turbomole does NOT use a range, but only a single integer,
# e.g., for hydrogen (H_2).
occ_re = r"closed shells\s+(\w)\s*(\d+)-?(\d*)"
occ_mobj = re.search(occ_re, text)
occ_mos = occ_mobj[3]
if occ_mos == "":
occ_mos = occ_mobj[2]
self.occ_mos = int(occ_mos)
self.log(f"Found {self.occ_mos} occupied MOs.")
# Number of spherical basis functions. May be different from CAO
# Determine number of virtual orbitals
self.virt_mos = nbf - self.occ_mos
else:
alpha_re = r"alpha shells\s+(\w)\s*\d+-(\d+)"
alpha_mos = int(re.search(alpha_re, text)[2])
self.log(f"Found {alpha_mos} occupied alpha MOs.")
beta_re = r"beta shells\s+(\w)\s*\d+-(\d+)"
beta_mos = int(re.search(beta_re, text)[2])
self.log(f"Found {beta_mos} occupied beta MOs.")
[docs]
def get_ricc2_root(self, text):
regex = r"geoopt.+?state=\((.+?)\)"
mobj = re.search(regex, text)
if not mobj:
root = None
elif mobj[1] == "x":
root = 0
else:
assert mobj[1].startswith("a "), "symmetry isn't supported!"
root = int(mobj[1][-1])
return root
[docs]
def prepare_td(self, text):
self.log("Preparing for excited state (gradient) calculations")
self.td_vec_fn = None
self.ci_coeffs = None
self.mo_inds = None
[docs]
def prepare_point_charges(self, point_charges):
"""$point_charges
<x> <y> <z> <q>
"""
lines = [f"{x:.12} {y:.12f} {z:.12f} {q:.12f}" for x, y, z, q in point_charges]
return "$point_charges\n\t" + "\n".join(lines)
[docs]
def sub_control(self, pattern, repl, log_msg="", **kwargs):
path = self.path_already_prepared
assert path
self.log(f"Updating control file in '{path}' {log_msg}")
control_path = path / "control"
with open(control_path) as handle:
text = handle.read()
text = re.sub(pattern, repl, text, **kwargs)
with open(control_path, "w") as handle:
handle.write(text)
[docs]
def append_control(self, to_append, log_msg="", **kwargs):
self.sub_control(r"\$end", f"{to_append}\n$end", log_msg, **kwargs)
[docs]
def get_pal_env(self):
env_copy = os.environ.copy()
env_copy["PARA_ARCH"] = "SMP"
env_copy["PARNODES"] = str(self.pal)
env_copy["SMPCPUS"] = str(self.pal)
return env_copy
[docs]
def store_and_track(self, results, func, atoms, coords, **prepare_kwargs):
if self.track:
prev_run_path = self.last_run_path
self.store_overlap_data(atoms, coords)
# Redo the calculation with the updated root
if self.track_root():
self.calc_counter += 1
results = func(atoms, coords, **prepare_kwargs)
self.last_run_path = prev_run_path
try:
shutil.rmtree(self.last_run_path)
except FileNotFoundError:
self.log(f"'{self.last_run_path}' has already been deleted!")
results["all_energies"] = self.parse_all_energies()
return results
[docs]
def get_energy(self, atoms, coords, **prepare_kwargs):
self.prepare_input(atoms, coords, "energy", **prepare_kwargs)
kwargs = {
"calc": "energy",
"shell": True,
"hold": self.track,
"env": self.get_pal_env(),
"cmd": self.energy_cmd,
}
results = self.run(None, **kwargs)
results = self.store_and_track(
results, self.get_energy, atoms, coords, **prepare_kwargs
)
return results
[docs]
def get_all_energies(self, atoms, coords, **prepare_kwargs):
results = self.get_energy(atoms, coords, **prepare_kwargs)
with open(self.out) as handle:
text = handle.read()
((nfocc_a, nfvirt_a), (nfocc_b, nfvirt_b)), restricted = parse_frozen_nmos(text)
results["td_1tdms"] = parse_ci_coeffs(
self.td_vec_fn,
nfocc_a,
nfvirt_a,
nfocc_b,
nfvirt_b,
restricted_same_ab=True,
)
return results
[docs]
def get_forces(self, atoms, coords, cmd=None, **prepare_kwargs):
self.prepare_input(atoms, coords, "force", **prepare_kwargs)
if cmd is None:
cmd = self.forces_cmd
kwargs = {
"calc": "force",
"shell": True, # To allow chained commands like 'ridft; rdgrad'
"hold": self.track, # Keep the files for WFOverlap
"env": self.get_pal_env(),
"cmd": cmd,
}
# Use inp=None because we don't use any dedicated input besides
# the previously prepared control file and the current coords.
results = self.run(None, **kwargs)
results = self.store_and_track(
results, self.get_forces, atoms, coords, **prepare_kwargs
)
return results
[docs]
def get_hessian(self, atoms, coords, **prepare_kwargs):
if self.td or self.ricc2:
raise Exception("ricc2 or TD-DFT/TDA hessian not yet supported!")
self.prepare_input(atoms, coords, "hessian", **prepare_kwargs)
kwargs = {
"calc": "hessian",
"shell": True, # To allow chained commands like 'ridft; rdgrad'
"hold": self.track,
"env": self.get_pal_env(),
"cmd": self.hessian_cmd,
}
results = self.run(None, **kwargs)
results = self.store_and_track(
results, self.get_hessian, atoms, coords, **prepare_kwargs
)
return results
[docs]
def get_stored_wavefunction(self, **kwargs):
return self.load_wavefunction_from_file(self.mwfn_wf, **kwargs)
[docs]
def get_wavefunction(self, atoms, coords, **prepare_kwargs):
with TurbomoleGroundStateContext(self):
results = self.get_energy(atoms, coords, **prepare_kwargs)
results["wavefunction"] = self.get_stored_wavefunction()
return results
[docs]
def get_relaxed_density(self, atoms, coords, root, **prepare_kwargs):
root_bak = self.root
self.root = root
results = self.get_forces(atoms, coords, **prepare_kwargs)
self.root = root_bak
if self.uhf:
with open(self.alpha) as handle:
text = handle.read()
Ca = parse_turbo_mos(text)
with open(self.beta) as handle:
text = handle.read()
Cb = parse_turbo_mos(text)
else:
with open(self.mos) as handle:
text = handle.read()
Ca = parse_turbo_mos(text)
Cb = Ca.copy()
Pa, Pb = get_density_matrices_for_root(
self.out, self.td_vec_fn, root, rlx_vec_fn=self.rlx_vec_fn, Ca=Ca, Cb=Cb
)
density = np.stack((Pa, Pb), axis=0)
results["density"] = density
return results
[docs]
def run_calculation(self, atoms, coords, **prepare_kwargs):
return self.get_energy(atoms, coords, **prepare_kwargs)
[docs]
def run_double_mol_calculation(self, atoms, coords1, coords2):
if not self.double_mol_path:
self.log(
"Skipping double molecule calculations as double mol "
"path is not specified.!"
)
return None
self.log("Running double molecule calculation")
double_atoms = atoms + atoms
double_coords = np.hstack((coords1, coords2))
self.prepare_input(double_atoms, double_coords, "double_mol")
kwargs = {
"calc": "double_mol",
"shell": True,
"keep": False,
"hold": True,
"cmd": self.scf_cmd,
"env": self.get_pal_env(),
}
results = self.run(None, **kwargs)
return results
[docs]
def parse_double_mol(self, path):
"""Parse a double molecule overlap matrix from Turbomole output
to be used with WFOWrapper."""
with open(path / self.out_fn) as handle:
text = handle.read()
regex = r"OVERLAP\(SAO\)\s+-+([\d\.E\-\s*\+]+)\s+-+"
ovlp_str = re.search(regex, text)[1]
ovlp = np.array(ovlp_str.strip().split(), dtype=np.float64)
mo_num = self.occ_mos + self.virt_mos
double_mo_num = 2 * mo_num
full_ovlp = np.zeros((double_mo_num, double_mo_num))
full_ovlp[np.tril_indices(double_mo_num)] = ovlp
double_mol_S = full_ovlp[mo_num:, :mo_num]
return double_mol_S
[docs]
def parse_mos(self):
pass
[docs]
def parse_energy(self, path):
with open(path / self.out_fn) as handle:
text = handle.read()
en_regex = re.compile(r"Total energy\s*:?\s*=?\s*([\d\-\.]+)", re.IGNORECASE)
tot_ens = en_regex.findall(text)
# Only modify energy when self.root is set; otherwise stick with the GS energy.
if self.td and self.root is not None:
# Drop ground state energy that is repeated. That is why we don't subtract
# 1 from self.root.
tot_en = tot_ens[1:][self.root]
elif self.ricc2 and self.ricc2_opt:
results = parse_turbo_gradient(path)
tot_en = results["energy"]
elif self.ricc2 and not self.ricc2_opt:
raise Exception("Implement me!")
else:
tot_en = tot_ens[0]
tot_en = float(tot_en)
return {
"energy": tot_en,
}
@staticmethod
@file_or_str(".sing_a", ".ciss_a")
def parse_tddft_tden(text):
eigval_re = re.compile(r"(\d+)\s+eigenvalue\s+=\s+([\d\.\-D\+]+)")
eigvals = eigval_re.findall(text)
state_inds, exc_ens = zip(*eigvals)
exc_ens = [exc_en.replace("D", "E") for exc_en in exc_ens]
return np.array(exc_ens, dtype=float)
[docs]
def parse_all_energies(self):
# Parse eigenvectors from escf/egrad calculation
gs_energy = self.parse_gs_energy()
# if self.root and self.second_cmd in ("escf", "egrad"):
if self.second_cmd in ("escf", "egrad") and hasattr(self, "exspectrum"):
# I don't know why, but sometimes sing_a contains wrong excitation energies...
# exc_energies = Turbomole.parse_tddft_tden(self.td_vec_fn)
roots = parse_exspectrum(self.exspectrum)
exc_energies = np.array([root.exc_energy for root in roots])
# Parse eigenvectors from ricc2 calculation
elif self.second_cmd == "ricc2":
with open(self.exstates) as handle:
exstates_text = handle.read()
exc_energies_by_model = parse_turbo_exstates(exstates_text)
# Drop CCS and take energies from whatever model was used
exc_energies = [
(model, exc_ens)
for model, exc_ens in exc_energies_by_model.items()
if model != "CCS"
]
assert len(exc_energies) == 1
_, exc_energies = exc_energies[0]
else:
exc_energies = np.array(list())
if exc_energies.size == 0:
all_energies = np.array((gs_energy,))
else:
all_energies = np.full(len(exc_energies) + 1, gs_energy)
all_energies[1:] += exc_energies
return all_energies
[docs]
def parse_ci_coeffs(self):
if self.second_cmd in ("escf", "egrad"):
with open(self.td_vec_fn) as handle:
text = handle.read()
ci_coeffs = self.parse_td_vectors(text)
ci_coeffs = [cc["vector"] for cc in ci_coeffs]
# Parse eigenvectors from ricc2 calculation
elif self.second_cmd == "ricc2":
ci_coeffs = [self.parse_cc2_vectors(ccre) for ccre in self.ccres]
ci_coeffs = np.array(ci_coeffs)
states = ci_coeffs.shape[0]
tden_size = self.occ_mos * self.virt_mos
if ci_coeffs.shape[1] == (2 * tden_size):
self.log("TDDFT calculation with X and Y vectors present. ")
XpY = ci_coeffs[:, :tden_size]
XmY = ci_coeffs[:, tden_size:]
X = (XpY + XmY) / 2.0
Y = XpY - X
else:
X = ci_coeffs
Y = np.zeros_like(X)
tden_shape = (states, self.occ_mos, self.virt_mos)
X = X.reshape(tden_shape)
Y = Y.reshape(tden_shape)
return X, Y
[docs]
def parse_force(self, path):
results = parse_turbo_gradient(path)
return results
[docs]
def parse_hessian(self, path, fn=None):
if fn is None:
if self.numfreq:
fn = path / "numforce" / "nprhessian"
else:
fn = path / "nprhessian"
with open(fn) as handle:
text = handle.read()
split = text.strip().split()
assert split[0] == "$nprhessian"
assert split[-1] == "$end"
def is_float(str_):
return "." in str_
hess_items = [item for item in split if is_float(item)]
coord_num = int(sqrt(len(hess_items)))
assert coord_num**2 == len(hess_items)
hessian = np.array(hess_items, dtype=float).reshape(-1, coord_num)
energy = self.parse_energy(path)["energy"]
results = {
"energy": energy,
"hessian": hessian,
}
return results
[docs]
@staticmethod
def parse_td_vectors(text):
"""For TDA calculations only the X vector is present in the
ciss_a/etc. file. In TDDFT calculations there are twise as
much items compared with TDA. The first half corresponds to
(X+Y) and the second half to (X-Y). X can be calculated as
X = ((X+Y)+(X-Y))/2. Y is then given as Y = (X+Y)-X. The
normalization can then by checked as
np.concatenate((X, Y)).dot(np.concatenate((X, -Y)))
and should be 1."""
def to_float(s, loc, toks):
match = toks[0].replace("D", "E")
return float(match)
float_ = pp.Word(pp.nums + ".-D+").setParseAction(to_float)
integer = pp.Word(pp.nums).setParseAction(lambda t: int(t[0]))
float_chrs = pp.nums + "D.+-"
float_20 = pp.Word(float_chrs, exact=20).setParseAction(to_float)
word = pp.Word(pp.alphanums)
line_word = word().setWhitespaceChars(" ")
line = pp.Group(pp.Optional(word) + line_word[...])("title")
title = pp.Literal("$title") + pp.Optional(line)
symmetry = pp.Literal("$symmetry") + pp.Word(pp.alphanums).setResultsName(
"symmetry"
)
tensor_dim = pp.Literal("$tensor space dimension") + integer.setResultsName(
"tensor_dim"
)
scfinstab = pp.Literal("$scfinstab") + pp.Word(pp.alphanums).setResultsName(
"scfinstab"
)
subspace_dim = pp.Literal(
"$current subspace dimension"
) + integer.setResultsName("subspace_dim")
converged = pp.Literal("$current iteration converged")
eigenpairs = pp.Literal("$eigenpairs")
eigenpair = pp.Group(
integer.setResultsName("state")
+ pp.Literal("eigenvalue =")
+ float_.setResultsName("eigenvalue")
+ pp.Group(pp.OneOrMore(float_20)).setResultsName("vector")
)
end = pp.Literal("$end")
parser = (
title
+ symmetry
+ tensor_dim
+ scfinstab
+ subspace_dim
+ converged
+ eigenpairs
+ pp.OneOrMore(eigenpair).setResultsName("eigenpairs")
+ end
)
result = parser.parseString(text)
states = result["subspace_dim"]
eigenpairs = result["eigenpairs"]
eigenpair_list = [eigenpairs[i].asDict() for i in range(states)]
return eigenpair_list
[docs]
def parse_cc2_vectors(self, ccre):
with open(ccre) as handle:
text = handle.read()
coeffs = parse_turbo_ccre0_ascii(text)
coeffs = coeffs.reshape(-1, self.virt_mos)
eigenpairs_full = np.zeros((self.occ_mos, self.virt_mos))
eigenpairs_full[self.frozen_mos :, :] = coeffs
"""
from_inds, to_inds = np.where(np.abs(eigenpairs_full) > 0.1)
for i, (from_, to_) in enumerate(zip(from_inds, to_inds)):
sq = eigenpairs_full[from_, to_]**2
print(f"{from_+1:02d} -> {to_+self.occ_mos+1:02d}: {sq:.2%}")
print()
"""
return eigenpairs_full
[docs]
def parse_gs_energy(self):
"""Several places are possible:
$subenergy from control file
total energy from turbomole.out
Final MP2 energy from turbomole.out with ADC(2)
Final CC2 energy from turbomole.out with CC(2)
"""
float_re = r"([\d\-\.E]+)"
regexs = [
# CC2 ground state energy
("out", r"Final CC2 energy\s*:\s*" + float_re, 0),
# ADC(2) ground state energy
("out", r"Final MP2 energy\s*:\s*" + float_re, 0),
("control", r"\$subenergy.*$\s*" + float_re, re.MULTILINE),
# DSCF ground state energy
("out", r"total energy\s*=\s*" + float_re, 0),
# From egrad when a rootflip occured. Then only the excited
# state calculation will be redone and the ground state calculation
# won't be present in the out-file.
("out", r"Ground state\s*?Total energy:\s+" + float_re, re.MULTILINE),
]
for file_attr, regex, flag in regexs:
regex_ = re.compile(regex, flags=flag)
with open(getattr(self, file_attr)) as handle:
text = handle.read()
mobj = regex_.search(text)
try:
gs_energy = float(mobj[1])
self.log(
f"Parsed ground state energy from '{file_attr}' using "
f"regex '{regex[:11]}'."
)
return gs_energy
except TypeError:
continue
raise Exception("Couldn't parse ground state energy!")
[docs]
def prepare_overlap_data(self, path):
all_energies = self.parse_all_energies()
X, Y = self.parse_ci_coeffs()
self.log(f"Reading MO coefficients from '{self.mos}'.")
with open(self.mos) as handle:
text = handle.read()
C = parse_turbo_mos(text)
self.log(f"Reading electronic energies from '{self.out}'.")
return C, X, Y, all_energies
[docs]
def run_after(self, path):
# Convert binary CCRE0 files to ASCII for easier parsing
for ccre in path.glob("CCRE0-*"):
cmd = f"ricctools -dump {ccre.name}".split()
result = subprocess.Popen(
cmd, cwd=path, stdout=subprocess.PIPE, stderr=subprocess.PIPE
)
result.wait()
# ricctools seem to crash sometimes, even though the respective ASCII
# ccre-files are generated.
subprocess.run(
"actual -r".split(),
cwd=path,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
if self.wavefunction_dump or self.td:
self.make_molden(path)
# With ricc2 we probably have a frozen core that we have to disable
# temporarily before creating the molden file. Afterwards we restore
# the original control file with the frozen core.
elif self.ricc2:
# Backup original control file
ctrl_backup = path / "control.backup"
shutil.copy(path / "control", ctrl_backup)
# We have to remove line with implicit core in the control file
with open(path / "control") as handle:
text = handle.read()
lines = text.split("\n")
lines = [l for l in lines if "implicit core" not in l]
with open(path / "control", "w") as handle:
handle.write("\n".join(lines))
self.make_molden(path)
# Restore control backup
shutil.copy(ctrl_backup, path / "control")
[docs]
@staticmethod
def make_molden(path):
cmd = "tm2molden norm".split()
fn = "wavefunction.molden"
stdin = f"""{fn}
"""
res = subprocess.Popen(
cmd,
cwd=path,
universal_newlines=True,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
)
stdout, stderr = res.communicate(stdin)
res.terminate()
[docs]
def get_chkfiles(self):
if self.uhf:
chkfiles = {
"alpha": self.alpha,
"beta": self.beta,
}
else:
chkfiles = {
"mos": self.mos,
}
return chkfiles
[docs]
def set_chkfiles(self, chkfiles):
try:
if self.uhf:
alpha = chkfiles["alpha"]
beta = chkfiles["beta"]
self.alpha = alpha
self.beta = beta
self.log(f"Set chkfile '{alpha}' and '{beta}' as alpha and beta.")
else:
mos = chkfiles["mos"]
self.mos = mos
self.log(f"Set chkfile '{mos}' as mos.")
except KeyError:
self.log("Found no chkfile information in chkfiles!")
def __str__(self):
return "Turbomole calculator"