From 35a641d49325faa3899e4c0837fc7466cdff57ab Mon Sep 17 00:00:00 2001 From: Alon Grinberg Dana Date: Sun, 5 Apr 2026 21:33:50 +0300 Subject: [PATCH 1/3] Added the Arkane xTB ESS adapter --- arkane/ess/__init__.py | 1 + arkane/ess/factory.py | 5 +- arkane/ess/xtb.py | 347 +++++++++++++++++++++++++++++++++++++++++ 3 files changed, 352 insertions(+), 1 deletion(-) create mode 100644 arkane/ess/xtb.py diff --git a/arkane/ess/__init__.py b/arkane/ess/__init__.py index ffd1e36bfba..6c9307ebcf7 100644 --- a/arkane/ess/__init__.py +++ b/arkane/ess/__init__.py @@ -39,3 +39,4 @@ from arkane.ess.psi4_parser import Psi4Log from arkane.ess.qchem import QChemLog from arkane.ess.terachem import TeraChemLog +from arkane.ess.xtb import XTBLog diff --git a/arkane/ess/factory.py b/arkane/ess/factory.py index ca0baee26c6..ef156afc18d 100644 --- a/arkane/ess/factory.py +++ b/arkane/ess/factory.py @@ -102,9 +102,12 @@ def ess_factory(fullpath: str, elif 'terachem' in line: ess_name = 'TeraChemLog' break + elif 'x t b' in line or 'xtb version' in line: + ess_name = 'XTBLog' + break line = f.readline().lower() if ess_name is None: raise InputError(f'The file at {fullpath} could not be identified as a ' - f'Gaussian, Molpro, Orca, Psi4, QChem, or TeraChem log file.') + f'Gaussian, Molpro, Orca, Psi4, QChem, TeraChem, or xTB log file.') return _registered_ess_adapters[ess_name](path=fullpath, check_for_errors=check_for_errors, scratch_directory=scratch_directory) diff --git a/arkane/ess/xtb.py b/arkane/ess/xtb.py new file mode 100644 index 00000000000..d0c9b39ea24 --- /dev/null +++ b/arkane/ess/xtb.py @@ -0,0 +1,347 @@ +#!/usr/bin/env python3 + +############################################################################### +# # +# RMG - Reaction Mechanism Generator # +# # +# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), # +# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) # +# # +# Permission is hereby granted, free of charge, to any person obtaining a # +# copy of this software and associated documentation files (the 'Software'), # +# to deal in the Software without restriction, including without limitation # +# the rights to use, copy, modify, merge, publish, distribute, sublicense, # +# and/or sell copies of the Software, and to permit persons to whom the # +# Software is furnished to do so, subject to the following conditions: # +# # +# The above copyright notice and this permission notice shall be included in # +# all copies or substantial portions of the Software. # +# # +# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # +# DEALINGS IN THE SOFTWARE. # +# # +############################################################################### + +""" +Arkane ESS adapter for xTB (extended Tight Binding) output files. +Supports geometry (V2000 and $coord/Turbomol formats), energy, frequencies, +ZPE, and conformer loading. +""" + +import logging +import re + +import numpy as np + +import rmgpy.constants as constants +from rmgpy.statmech import ( + Conformer, + HarmonicOscillator, + IdealGasTranslation, + LinearRotor, + NonlinearRotor, +) + +from arkane.common import ( + get_element_mass, + get_principal_moments_of_inertia, + symbol_by_number, +) +from arkane.exceptions import LogError +from arkane.ess.adapter import ESSAdapter +from arkane.ess.factory import register_ess_adapter + +logger = logging.getLogger(__name__) + +BOHR_TO_ANGSTROM = constants.a0 * 1e10 # ~0.52918 Angstrom +INERTIA_ZERO_TOL = 1e-4 # amu*angstrom^2 + + +def _normalize_symbol(raw: str) -> str: + """Normalize an element symbol from xTB output (e.g. 'c' -> 'C', 'cl' -> 'Cl').""" + if len(raw) == 1: + return raw.upper() + return raw[0].upper() + raw[1:].lower() + + +class XTBLog(ESSAdapter): + """ + Arkane ESS adapter for xTB output files. + + Parses output from the xtb program (https://github.com/grimme-lab/xtb), + including geometry, electronic energy, vibrational frequencies, and + thermochemical data. + + Supported geometry formats: + - V2000 (SDF/Molfile) block from ``--opt`` outputs + - Turbomol ``$coord`` block (Bohr) from ``--opt`` outputs + Frequency-only (``--hess``) outputs do not embed a geometry. + """ + + def check_for_errors(self): + """Check for common xTB errors in the output file.""" + with open(self.path, 'r') as f: + for line in f: + if 'ERROR' in line and 'SETUP' not in line: + raise LogError(f'xTB error found in {self.path}: {line.strip()}') + if 'abnormal termination' in line.lower(): + raise LogError(f'xTB job terminated abnormally in {self.path}') + + def get_number_of_atoms(self) -> int: + """ + Return the number of atoms from the xTB output. + + Tries the explicit 'number of atoms' line first, then falls + back to counting atoms in the geometry block. + """ + with open(self.path, 'r') as f: + for line in f: + if 'number of atoms' in line: + return int(line.split()[-1]) + try: + coord, _, _ = self.load_geometry() + return len(coord) + except LogError: + pass + raise LogError(f'Could not determine the number of atoms in {self.path}') + + def load_geometry(self): + """ + Load the molecular geometry from the xTB output file. + + Supports two formats found in xTB ``--opt`` outputs: + - **V2000 (SDF/Molfile)**: Cartesian coordinates in Angstroms. + - **Turbomol ``$coord``**: Cartesian coordinates in Bohr (converted to Angstroms). + + Frequency-only (``--hess``) outputs do not embed a geometry and will raise. + + Returns: + Tuple of (coord, number, mass): + coord: np.ndarray (n, 3) in Angstroms + number: np.ndarray (n,) atomic numbers + mass: np.ndarray (n,) atomic masses in amu + """ + with open(self.path, 'r') as f: + lines = f.readlines() + coord, number, mass = self._parse_v2000(lines) + if not coord: + coord, number, mass = self._parse_turbomol_coord(lines) + if not coord: + raise LogError(f'Could not find geometry in {self.path}') + return (np.array(coord, dtype=np.float64), + np.array(number, dtype=int), + np.array(mass, dtype=np.float64)) + + @staticmethod + def _parse_v2000(lines): + """Parse V2000 (SDF/Molfile) geometry block. Returns (coord, number, mass) or empty lists.""" + coord, number, mass = [], [], [] + for i, line in enumerate(lines): + if 'V2000' in line: + n_atoms = int(line.split()[0]) + coord, number, mass = [], [], [] + for j in range(i + 1, i + 1 + n_atoms): + tokens = lines[j].split() + x, y, z = float(tokens[0]), float(tokens[1]), float(tokens[2]) + symbol = tokens[3] + coord.append([x, y, z]) + mass_i, num_i = get_element_mass(symbol) + number.append(num_i) + mass.append(mass_i) + return coord, number, mass + + @staticmethod + def _parse_turbomol_coord(lines): + """Parse Turbomol $coord block (Bohr). Converts to Angstroms.""" + coord, number, mass = [], [], [] + in_coord = False + for line in lines: + stripped = line.strip() + if stripped == '$coord': + in_coord = True + coord, number, mass = [], [], [] + continue + if in_coord: + if stripped.startswith('$'): + break + tokens = stripped.split() + if len(tokens) >= 4: + try: + x = float(tokens[0]) * BOHR_TO_ANGSTROM + y = float(tokens[1]) * BOHR_TO_ANGSTROM + z = float(tokens[2]) * BOHR_TO_ANGSTROM + symbol = _normalize_symbol(tokens[3]) + coord.append([x, y, z]) + mass_i, num_i = get_element_mass(symbol) + number.append(num_i) + mass.append(mass_i) + except (ValueError, KeyError): + break + return coord, number, mass + + def load_energy(self, zpe_scale_factor=1.): + """ + Load the electronic energy in J/mol from the xTB output. + + Returns the last ``total energy`` value found. The zero-point energy + is NOT included. + """ + e_elect = None + with open(self.path, 'r') as f: + for line in f: + if ':: total energy' in line: + match = re.search(r'(-?\d+\.\d+)\s+Eh', line) + if match: + e_elect = float(match.group(1)) + elif 'TOTAL ENERGY' in line and 'Eh' in line: + match = re.search(r'(-?\d+\.\d+)\s+Eh', line) + if match: + e_elect = float(match.group(1)) + if e_elect is None: + raise LogError(f'Unable to find energy in xTB output file {self.path}') + return e_elect * constants.E_h * constants.Na + + def load_zero_point_energy(self): + """ + Load the zero-point energy in J/mol from the xTB output. + Only available in frequency (``--hess``) calculations. + """ + zpe = None + with open(self.path, 'r') as f: + for line in f: + if ':: zero point energy' in line or 'zero-point vibrational energy' in line.lower(): + match = re.search(r'(\d+\.\d+)\s+Eh', line) + if match: + zpe = float(match.group(1)) + if zpe is None: + raise LogError(f'Unable to find zero-point energy in xTB output file {self.path}') + return zpe * constants.E_h * constants.Na + + def _load_all_frequencies(self): + """ + Load ALL vibrational frequencies from the last eigval block in the xTB output, + including near-zero (translational/rotational) and negative (imaginary) modes. + + xTB prints frequencies twice (after Hessian and in Frequency Printout). + Returns the last complete set. + """ + all_blocks, current_block = [], [] + with open(self.path, 'r') as f: + for line in f: + if line.strip().startswith('eigval :'): + values = line.split(':')[1].split() + current_block.extend(float(v) for v in values) + elif current_block and not line.strip().startswith('eigval'): + all_blocks.append(current_block) + current_block = [] + if current_block: + all_blocks.append(current_block) + return all_blocks[-1] if all_blocks else [] + + def _load_frequencies(self): + """ + Load positive (real) vibrational frequencies in cm^-1. + Filters out translational/rotational modes (near-zero) and imaginary (negative). + """ + return [f for f in self._load_all_frequencies() if f > 0.1] + + def _load_spin_multiplicity(self): + """ + Determine spin multiplicity from the xTB output. + + xTB reports ``spin`` as S (not 2S+1), so multiplicity = 2*S + 1. + Some xTB versions use ``--uhf N`` where N = number of unpaired electrons. + Default to singlet. + """ + with open(self.path, 'r') as f: + for line in f: + # Format: " spin : 0.5" + if 'spin' in line: + parts = line.split() + if parts and parts[0] == 'spin': + s = float(parts[-1]) + return int(2 * s + 1) + # Also check for unpaired electrons in setup block + if 'unpaired' in line and ':' in line: + parts = line.split(':') + try: + n_unpaired = int(parts[-1].strip()) + return n_unpaired + 1 + except ValueError: + pass + return 1 + + def load_conformer(self, symmetry=None, spin_multiplicity=0, optical_isomers=None, label=''): + """ + Load the molecular degree of freedom data from an xTB output file. + + Requires geometry to be available in the log file (optimization outputs). + For frequency-only outputs, geometry must be loaded from a separate file. + + Returns: + Tuple of (Conformer, unscaled_frequencies). + """ + if optical_isomers is None or symmetry is None: + _optical_isomers, _symmetry, _ = self.get_symmetry_properties() + if optical_isomers is None: + optical_isomers = _optical_isomers + if symmetry is None: + symmetry = _symmetry + + if spin_multiplicity == 0: + spin_multiplicity = self._load_spin_multiplicity() + + unscaled_frequencies = self._load_frequencies() + modes = [] + + # Translation + coord, number, mass = self.load_geometry() + modes.append(IdealGasTranslation(mass=(sum(mass), "amu"))) + + # Rotation — use tolerance for linear molecule detection + symbols = [symbol_by_number[i] for i in number] + inertia = list(get_principal_moments_of_inertia(coord, numbers=number, symbols=symbols)[0]) + if inertia and not all(abs(i) < INERTIA_ZERO_TOL for i in inertia): + nonzero = [i for i in inertia if abs(i) >= INERTIA_ZERO_TOL] + if len(nonzero) < len(inertia): + # Linear molecule: one or more moments are ~zero + modes.append(LinearRotor(inertia=(max(nonzero), "amu*angstrom^2"), symmetry=symmetry)) + else: + modes.append(NonlinearRotor(inertia=(nonzero, "amu*angstrom^2"), symmetry=symmetry)) + + # Vibration + if unscaled_frequencies: + modes.append(HarmonicOscillator(frequencies=(unscaled_frequencies, "cm^-1"))) + + return Conformer(E0=(0.0, "kJ/mol"), + modes=modes, + spin_multiplicity=spin_multiplicity, + optical_isomers=optical_isomers), unscaled_frequencies + + def load_negative_frequency(self): + """Load the first imaginary (negative) frequency in cm^-1 for a transition state.""" + neg_freqs = [f for f in self._load_all_frequencies() if f < -0.1] + if not neg_freqs: + raise LogError(f'No imaginary frequencies found in {self.path}') + return neg_freqs[0] + + def load_force_constant_matrix(self): + """xTB writes a separate hessian file; not parsed from the main output.""" + return None + + def load_scan_energies(self): + raise NotImplementedError('Rotor scans are not supported by the xTB adapter.') + + def load_scan_pivot_atoms(self): + raise NotImplementedError('Rotor scans are not supported by the xTB adapter.') + + def load_scan_frozen_atoms(self): + raise NotImplementedError('Rotor scans are not supported by the xTB adapter.') + + +register_ess_adapter('XTBLog', XTBLog) From 181595f7486388d60ffc9d2d5913ff3217cb5d15 Mon Sep 17 00:00:00 2001 From: Alon Grinberg Dana Date: Sun, 5 Apr 2026 21:34:05 +0300 Subject: [PATCH 2/3] Tests: Arkane xTB --- arkane/data/xTB/CO2_xtb.out | 538 ++++++++++++++++++++++++ arkane/data/xTB/NCC_xTB.out | 302 ++++++++++++++ arkane/data/xTB/TS_NH2+N2H3_xtb.out | 429 +++++++++++++++++++ arkane/data/xTB/freq.out | 395 ++++++++++++++++++ arkane/data/xTB/output.out | 525 ++++++++++++++++++++++++ arkane/data/xTB/xtb_opt_1.out | 610 ++++++++++++++++++++++++++++ arkane/data/xTB/xtb_opt_2.out | 581 ++++++++++++++++++++++++++ test/arkane/ess/xtbTest.py | 348 ++++++++++++++++ 8 files changed, 3728 insertions(+) create mode 100644 arkane/data/xTB/CO2_xtb.out create mode 100644 arkane/data/xTB/NCC_xTB.out create mode 100644 arkane/data/xTB/TS_NH2+N2H3_xtb.out create mode 100644 arkane/data/xTB/freq.out create mode 100644 arkane/data/xTB/output.out create mode 100644 arkane/data/xTB/xtb_opt_1.out create mode 100644 arkane/data/xTB/xtb_opt_2.out create mode 100644 test/arkane/ess/xtbTest.py diff --git a/arkane/data/xTB/CO2_xtb.out b/arkane/data/xTB/CO2_xtb.out new file mode 100644 index 00000000000..3eed4a15bb2 --- /dev/null +++ b/arkane/data/xTB/CO2_xtb.out @@ -0,0 +1,538 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.5.1 (b24c23e) compiled by 'conda@728c89f4b128' on 2022-07-12 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, C. Hölzer + A. Katbashev, J. Koopman, C. Lavigne, S. Lehtola, F. März, M. Müller, + F. Musil, H. Neugebauer, J. Pisarek, C. Plett, P. Pracht, F. Pultar, + J. Seibert, P. Shushkov, S. Spicher, M. Stahn, M. Steiner, T. Strunk, + J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/25 at 05:22:50.670 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : xtb input.in --ohess + coordinate file : input.in + omp threads : 24 + + ID Z sym. atoms + 1 8 o 1, 3 + 2 6 c 2 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 12 : + : # atomic orbitals 12 : + : # shells 6 : + : # electrons 16 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -10.1007538 -0.101008E+02 0.106E+01 4.97 0.0 T + 2 -10.0837734 0.169804E-01 0.574E+00 3.59 1.0 T + 3 -10.0773402 0.643318E-02 0.626E+00 5.06 1.0 T + 4 -10.1510321 -0.736919E-01 0.259E-01 4.20 1.0 T + 5 -10.1510272 0.488608E-05 0.921E-02 4.19 1.0 T + 6 -10.1510323 -0.506258E-05 0.265E-02 4.20 2.2 T + 7 -10.1510345 -0.226921E-05 0.418E-03 4.20 13.8 T + 8 -10.1510346 -0.196644E-07 0.156E-03 4.20 37.0 T + 9 -10.1510346 -0.850277E-08 0.674E-06 4.20 8561.2 T + 10 -10.1510346 -0.710543E-13 0.255E-06 4.20 22676.3 T + + *** convergence criteria satisfied after 10 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.7653646 -20.8266 + 2 2.0000 -0.7649366 -20.8150 + 3 2.0000 -0.6584822 -17.9182 + 4 2.0000 -0.6147223 -16.7274 + 5 2.0000 -0.6084645 -16.5572 + 6 2.0000 -0.6084645 -16.5572 + 7 2.0000 -0.5293643 -14.4047 + 8 2.0000 -0.5293643 -14.4047 (HOMO) + 9 -0.3750715 -10.2062 (LUMO) + 10 -0.3750715 -10.2062 + 11 -0.2101496 -5.7185 + 12 0.2402001 6.5362 + ------------------------------------------------------------- + HL-Gap 0.1542928 Eh 4.1985 eV + Fermi-level -0.4522179 Eh -12.3055 eV + + SCC (total) 0 d, 0 h, 0 min, 0.403 sec + SCC setup ... 0 min, 0.010 sec ( 2.419%) + Dispersion ... 0 min, 0.003 sec ( 0.781%) + classical contributions ... 0 min, 0.010 sec ( 2.444%) + integral evaluation ... 0 min, 0.000 sec ( 0.036%) + iterations ... 0 min, 0.286 sec ( 70.971%) + molecular gradient ... 0 min, 0.094 sec ( 23.285%) + printout ... 0 min, 0.000 sec ( 0.057%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -10.135996710859 Eh :: + :: gradient norm 0.370268159994 Eh/a0 :: + :: HOMO-LUMO gap 4.198520838595 eV :: + ::.................................................:: + :: SCC energy -10.151034559557 Eh :: + :: -> isotropic ES 0.030700273527 Eh :: + :: -> anisotropic ES 0.002732467907 Eh :: + :: -> anisotropic XC 0.003162451907 Eh :: + :: -> dispersion -0.000668659270 Eh :: + :: repulsion energy 0.015037855445 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ----------------------------------------------------------- + | ===================== | + | A N C O P T | + | ===================== | + | Approximate Normal Coordinate | + | Rational Function Optimizer | + ----------------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : optimization level normal : + : max. optcycles 200 : + : ANC micro-cycles 20 : + : degrees of freedom 4 : + :.................................................: + : RF solver davidson : + : write xtbopt.log true : + : linear (good luck) true : + : energy convergence 0.5000000E-05 Eh : + : grad. convergence 0.1000000E-02 Eh/α : + : maximium RF displ. 1.0000000 : + : Hlow (freq-cutoff) 0.1000000E-01 : + : Hmax (freq-cutoff) 5.0000000 : + : S6 in model hess. 20.0000000 : + ................................................... + +generating ANC from model Hessian ... +Using Lindh-Hessian (1995) + Shifting diagonal of input Hessian by 0.0000000000000000 + Lowest eigenvalues of input Hessian + 0.000000 0.000000 0.000000 0.000000 0.000000 0.215176 + 0.215176 0.561115 1.673465 + Highest eigenvalues + 0.000000 0.000000 0.215176 0.215176 0.561115 1.673465 + + +........................................................................ +.............................. CYCLE 1 .............................. +........................................................................ + 1 -10.1510346 -0.101510E+02 0.444E-08 4.20 0.0 T + 2 -10.1510346 0.177636E-14 0.438E-08 4.20 100000.0 T + 3 -10.1510346 0.000000E+00 0.118E-08 4.20 100000.0 T + SCC iter. ... 0 min, 0.092 sec + gradient ... 0 min, 0.072 sec + * total energy : -10.1359967 Eh change -0.1243450E-13 Eh + gradient norm : 0.3702682 Eh/α predicted 0.0000000E+00 (-100.00%) + displ. norm : 0.4969294 α lambda -0.1839972E+00 + maximum displ.: 0.4969294 α in ANC's #3, #1, #2, ... + +........................................................................ +.............................. CYCLE 2 .............................. +........................................................................ + 1 -10.3526738 -0.103527E+02 0.234E+00 7.05 0.0 T + 2 -10.3544820 -0.180822E-02 0.145E+00 6.75 1.0 T + 3 -10.3547344 -0.252415E-03 0.774E-01 6.94 1.0 T + 4 -10.3552207 -0.486288E-03 0.757E-02 6.86 1.0 T + 5 -10.3552194 0.132848E-05 0.224E-02 6.86 2.6 T + 6 -10.3552209 -0.153895E-05 0.171E-03 6.86 33.8 T + 7 -10.3552209 -0.351930E-08 0.157E-04 6.85 366.6 T + 8 -10.3552209 -0.336442E-11 0.372E-06 6.85 15531.4 T + SCC iter. ... 0 min, 0.234 sec + gradient ... 0 min, 0.086 sec + * total energy : -10.2874264 Eh change -0.1514297E+00 Eh + gradient norm : 0.1913381 Eh/α predicted -0.1147166E+00 ( -24.24%) + displ. norm : 0.4321505 α lambda -0.8268689E-01 + maximum displ.: 0.4321505 α in ANC's #3, #4, #1, ... + +........................................................................ +.............................. CYCLE 3 .............................. +........................................................................ + 1 -10.5022216 -0.105022E+02 0.282E+00 11.07 0.0 T + 2 -10.5040084 -0.178678E-02 0.164E+00 10.81 1.0 T + 3 -10.5040388 -0.304142E-04 0.476E-01 10.88 1.0 T + 4 -10.5040796 -0.408503E-04 0.682E-02 10.84 1.0 T + 5 -10.5040795 0.881504E-07 0.695E-03 10.84 8.3 T + 6 -10.5040796 -0.107646E-06 0.117E-03 10.84 49.4 T + 7 -10.5040796 -0.753690E-10 0.848E-05 10.84 680.9 T + 8 -10.5040796 -0.688694E-11 0.142E-06 10.84 40655.2 T + SCC iter. ... 0 min, 0.238 sec + gradient ... 0 min, 0.084 sec + * total energy : -10.2681402 Eh change 0.1928617E-01 Eh + gradient norm : 0.3875581 Eh/α predicted -0.4906449E-01 (-354.40%) + displ. norm : 0.2684634 α lambda -0.1040451E+00 + maximum displ.: 0.2684634 α in ANC's #3, #1, #2, ... + +........................................................................ +.............................. CYCLE 4 .............................. +........................................................................ + 1 -10.4154030 -0.104154E+02 0.191E+00 7.94 0.0 T + 2 -10.4168194 -0.141640E-02 0.113E+00 8.19 1.0 T + 3 -10.4169413 -0.121900E-03 0.560E-01 8.07 1.0 T + 4 -10.4170767 -0.135356E-03 0.636E-02 8.11 1.0 T + 5 -10.4170772 -0.501209E-06 0.617E-03 8.12 9.4 T + 6 -10.4170773 -0.811078E-07 0.850E-04 8.12 67.9 T + 7 -10.4170773 -0.107153E-09 0.297E-05 8.12 1942.5 T + SCC iter. ... 0 min, 0.196 sec + gradient ... 0 min, 0.084 sec + * total energy : -10.3076013 Eh change -0.3946106E-01 Eh + gradient norm : 0.0442511 Eh/α predicted -0.5577199E-01 ( 41.33%) + displ. norm : 0.0274909 α lambda -0.1216500E-02 + maximum displ.: 0.0274909 α in ANC's #3, #4, #2, ... + +........................................................................ +.............................. CYCLE 5 .............................. +........................................................................ + 1 -10.4269290 -0.104269E+02 0.178E-01 8.37 0.0 T + 2 -10.4269396 -0.106159E-04 0.105E-01 8.35 1.0 T + 3 -10.4269401 -0.488665E-06 0.480E-02 8.36 1.2 T + 4 -10.4269412 -0.110765E-05 0.548E-03 8.36 10.5 T + 5 -10.4269412 -0.196353E-08 0.167E-04 8.36 345.1 T + 6 -10.4269412 -0.965628E-11 0.805E-05 8.36 717.1 T + SCC iter. ... 0 min, 0.174 sec + gradient ... 0 min, 0.089 sec + * total energy : -10.3083872 Eh change -0.7858751E-03 Eh + gradient norm : 0.0125378 Eh/α predicted -0.6087097E-03 ( -22.54%) + displ. norm : 0.0108672 α lambda -0.1362493E-03 + maximum displ.: 0.0108672 α in ANC's #3, #4, #1, ... + +........................................................................ +.............................. CYCLE 6 .............................. +........................................................................ + 1 -10.4307891 -0.104308E+02 0.714E-02 8.46 0.0 T + 2 -10.4307908 -0.170189E-05 0.420E-02 8.45 1.4 T + 3 -10.4307909 -0.747659E-07 0.190E-02 8.46 3.0 T + 4 -10.4307911 -0.166970E-06 0.218E-03 8.45 26.5 T + 5 -10.4307911 -0.306100E-09 0.575E-05 8.45 1003.4 T + 6 -10.4307911 -0.241585E-12 0.312E-05 8.45 1853.1 T + SCC iter. ... 0 min, 0.180 sec + gradient ... 0 min, 0.081 sec + * total energy : -10.3084521 Eh change -0.6494850E-04 Eh + gradient norm : 0.0006476 Eh/α predicted -0.6813368E-04 ( 4.90%) + displ. norm : 0.0008006 α lambda -0.3461407E-06 + maximum displ.: 0.0008006 α in ANC's #3, #4, #1, ... + +........................................................................ +.............................. CYCLE 7 .............................. +........................................................................ + 1 -10.4305084 -0.104305E+02 0.528E-03 8.45 0.0 T + 2 -10.4305084 -0.935862E-08 0.311E-03 8.45 18.6 T + 3 -10.4305084 -0.421489E-09 0.141E-03 8.45 40.9 T + 4 -10.4305084 -0.915616E-09 0.162E-04 8.45 356.8 T + 5 -10.4305084 -0.173372E-11 0.412E-06 8.45 14005.4 T + SCC iter. ... 0 min, 0.145 sec + gradient ... 0 min, 0.090 sec + * total energy : -10.3084522 Eh change -0.1243137E-06 Eh + gradient norm : 0.0003367 Eh/α predicted -0.1728305E-06 ( 39.03%) + displ. norm : 0.0002739 α lambda -0.5879194E-07 + maximum displ.: 0.0002739 α in ANC's #3, #4, #1, ... + + *** GEOMETRY OPTIMIZATION CONVERGED AFTER 7 ITERATIONS *** + +------------------------------------------------------------------------ + total energy gain : -0.1724555 Eh -108.2175 kcal/mol + total RMSD : 0.4030910 a0 0.2133 Å + total power (kW/mol): -64.6831340 (step) -221.2344 (real) +------------------------------------------------------------------------ + + ANCopt (total) 0 d, 0 h, 0 min, 2.047 sec + optimizer setup ... 0 min, 0.000 sec ( 0.004%) + model hessian ... 0 min, 0.000 sec ( 0.001%) + ANC generation ... 0 min, 0.000 sec ( 0.002%) + coordinate transformation ... 0 min, 0.000 sec ( 0.001%) + single point calculation ... 0 min, 2.002 sec ( 97.802%) + optimization log ... 0 min, 0.001 sec ( 0.038%) + hessian update ... 0 min, 0.044 sec ( 2.127%) + rational function ... 0 min, 0.000 sec ( 0.010%) + +================ + final structure: +================ +$coord + -2.16138153091286E+00 5.20613777548114E-16 1.14673985615952E-18 o + -8.95200516010515E-08 -6.14906634635295E-16 1.14218571599872E-16 c + 2.16138162043291E+00 4.79212730686445E-16 -2.64708229938330E-17 o +$eht charge=0 unpaired=0 +$periodic 0 +$end + + Bond Distances (Angstroems) + --------------------------- +O1-C2=1.1438 C2-O1=1.1438 C2-O3=1.1438 O3-C2=1.1438 + O C Rav=1.1438 sigma=0.0000 Rmin=1.1438 Rmax=1.1438 2 + + selected bond angles (degree) + -------------------- +O3-C2-O1=180.00 + + selected dihedral angles (degree) + --------------------------------- + + ------------------------------------------------- + | Final Singlepoint | + ------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : # basis functions 12 : + : # atomic orbitals 12 : + : # shells 6 : + : # electrons 16 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -10.4305084 -0.104305E+02 0.342E-07 8.45 0.0 T + 2 -10.4305084 0.532907E-14 0.186E-07 8.45 100000.0 T + 3 -10.4305084 0.177636E-14 0.936E-08 8.45 100000.0 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.8107966 -22.0629 + 2 2.0000 -0.7966721 -21.6786 + 3 2.0000 -0.6648029 -18.0902 + 4 2.0000 -0.6634459 -18.0533 + 5 2.0000 -0.6634459 -18.0533 + 6 2.0000 -0.5998444 -16.3226 + 7 2.0000 -0.5344372 -14.5428 + 8 2.0000 -0.5344372 -14.5428 (HOMO) + 9 -0.2240446 -6.0966 (LUMO) + 10 -0.2240446 -6.0966 + 11 0.3095444 8.4231 + 12 1.3634789 37.1021 + ------------------------------------------------------------- + HL-Gap 0.3103926 Eh 8.4462 eV + Fermi-level -0.3792409 Eh -10.3197 eV + + SCC (total) 0 d, 0 h, 0 min, 0.201 sec + SCC setup ... 0 min, 0.006 sec ( 2.736%) + Dispersion ... 0 min, 0.011 sec ( 5.648%) + classical contributions ... 0 min, 0.006 sec ( 2.905%) + integral evaluation ... 0 min, 0.000 sec ( 0.067%) + iterations ... 0 min, 0.096 sec ( 47.486%) + molecular gradient ... 0 min, 0.083 sec ( 41.110%) + printout ... 0 min, 0.000 sec ( 0.032%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -10.308452243026 Eh :: + :: gradient norm 0.000336725868 Eh/a0 :: + :: HOMO-LUMO gap 8.446212794931 eV :: + ::.................................................:: + :: SCC energy -10.430508422218 Eh :: + :: -> isotropic ES 0.032323956216 Eh :: + :: -> anisotropic ES 0.003405391673 Eh :: + :: -> anisotropic XC 0.000434262888 Eh :: + :: -> dispersion -0.000687147517 Eh :: + :: repulsion energy 0.122056180790 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Numerical Hessian | + ------------------------------------------------- +step length : 0.00500 +SCC accuracy : 0.30000 +Hessian scale factor : 1.00000 +frozen atoms in % : 0.00000 0 +RMS gradient : 0.00034 +estimated CPU time 0.00 min +estimated wall time 0.00 min + +writing file . + + vibrational frequencies (cm⁻¹) +eigval : 0.00 0.00 0.00 0.00 0.00 600.70 +eigval : 600.70 1424.29 2592.18 + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.8107966 -22.0629 + 2 2.0000 -0.7966721 -21.6786 + 3 2.0000 -0.6648029 -18.0902 + 4 2.0000 -0.6634459 -18.0533 + 5 2.0000 -0.6634459 -18.0533 + 6 2.0000 -0.5998444 -16.3226 + 7 2.0000 -0.5344372 -14.5428 + 8 2.0000 -0.5344372 -14.5428 (HOMO) + 9 -0.2240446 -6.0966 (LUMO) + 10 -0.2240446 -6.0966 + 11 0.3095444 8.4231 + 12 1.3634789 37.1021 + ------------------------------------------------------------- + HL-Gap 0.3103926 Eh 8.4462 eV + Fermi-level -0.3792409 Eh -10.3197 eV + + # Z covCN q C6AA α(0) + 1 8 o 0.856 -0.232 18.599 5.782 + 2 6 c 1.711 0.464 21.601 7.524 + 3 8 o 0.856 -0.232 18.599 5.782 + + Mol. C6AA /au·bohr⁶ : 174.800064 + Mol. C8AA /au·bohr⁸ : 4029.888003 + Mol. α(0) /au : 19.088404 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + + --------------------------------------------------------------------------- + # Z sym total # sym WBO # sym WBO # sym WBO + --------------------------------------------------------------------------- + 1 8 o 2.370 -- 2 c 1.968 3 o 0.402 + 2 6 c 3.936 -- 1 o 1.968 3 o 1.968 + 3 8 o 2.370 -- 2 c 1.968 1 o 0.402 + --------------------------------------------------------------------------- + +Topologies differ in total number of bonds +Writing topology from bond orders to xtbtopo.mol + +molecular dipole: + x y z tot (Debye) + q only: -0.000 0.000 0.000 + full: -0.000 0.000 0.000 0.000 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: -2.169 0.000 1.084 0.000 -0.000 1.084 +Molecule has the following symmetry elements: (i) (Cinf) (C2) 2*(sigma) +It seems to be the Dinfh point group diff --git a/arkane/data/xTB/NCC_xTB.out b/arkane/data/xTB/NCC_xTB.out new file mode 100644 index 00000000000..4437d65f6c4 --- /dev/null +++ b/arkane/data/xTB/NCC_xTB.out @@ -0,0 +1,302 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.5.1 (b24c23e) compiled by 'conda@728c89f4b128' on 2022-07-12 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, C. Hölzer + A. Katbashev, J. Koopman, C. Lavigne, S. Lehtola, F. März, M. Müller, + F. Musil, H. Neugebauer, J. Pisarek, C. Plett, P. Pracht, F. Pultar, + J. Seibert, P. Shushkov, S. Spicher, M. Stahn, M. Steiner, T. Strunk, + J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/25 at 04:54:15.181 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : xtb input.in + coordinate file : input.in + omp threads : 24 + + ID Z sym. atoms + 1 7 n 1 + 2 6 c 2, 3 + 3 1 h 4-10 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 19 : + : # atomic orbitals 19 : + : # shells 13 : + : # electrons 20 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -10.8729960 -0.108730E+02 0.292E+00 11.01 0.0 T + 2 -10.8929483 -0.199524E-01 0.155E+00 11.27 1.0 T + 3 -10.8936747 -0.726402E-03 0.682E-01 11.31 1.0 T + 4 -10.8937471 -0.723836E-04 0.975E-02 11.23 1.0 T + 5 -10.8937514 -0.431045E-05 0.454E-02 11.23 1.0 T + 6 -10.8937519 -0.433308E-06 0.996E-03 11.23 3.2 T + 7 -10.8937520 -0.145291E-06 0.204E-03 11.23 15.5 T + 8 -10.8937520 -0.295992E-08 0.302E-04 11.23 104.8 T + 9 -10.8937520 -0.577529E-10 0.101E-04 11.23 312.6 T + + *** convergence criteria satisfied after 9 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6265775 -17.0500 + ... ... ... ... + 4 2.0000 -0.5194537 -14.1351 + 5 2.0000 -0.5163789 -14.0514 + 6 2.0000 -0.4884890 -13.2925 + 7 2.0000 -0.4537369 -12.3468 + 8 2.0000 -0.4523900 -12.3102 + 9 2.0000 -0.4388175 -11.9408 + 10 2.0000 -0.3630745 -9.8798 (HOMO) + 11 0.0494719 1.3462 (LUMO) + 12 0.1260207 3.4292 + 13 0.1321555 3.5961 + 14 0.1464083 3.9840 + 15 0.1742217 4.7408 + ... ... ... + 19 0.2783726 7.5749 + ------------------------------------------------------------- + HL-Gap 0.4125464 Eh 11.2260 eV + Fermi-level -0.1568013 Eh -4.2668 eV + + SCC (total) 0 d, 0 h, 0 min, 0.434 sec + SCC setup ... 0 min, 0.003 sec ( 0.758%) + Dispersion ... 0 min, 0.015 sec ( 3.539%) + classical contributions ... 0 min, 0.011 sec ( 2.561%) + integral evaluation ... 0 min, 0.027 sec ( 6.269%) + iterations ... 0 min, 0.286 sec ( 65.962%) + molecular gradient ... 0 min, 0.086 sec ( 19.712%) + printout ... 0 min, 0.005 sec ( 1.187%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -10.752192838993 Eh :: + :: gradient norm 0.017368634110 Eh/a0 :: + :: HOMO-LUMO gap 11.225958754700 eV :: + ::.................................................:: + :: SCC energy -10.893752005864 Eh :: + :: -> isotropic ES 0.012212916399 Eh :: + :: -> anisotropic ES 0.004311068440 Eh :: + :: -> anisotropic XC 0.010072177729 Eh :: + :: -> dispersion -0.003443587089 Eh :: + :: repulsion energy 0.141558330550 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6265775 -17.0500 + 2 2.0000 -0.5920275 -16.1099 + 3 2.0000 -0.5610626 -15.2673 + 4 2.0000 -0.5194537 -14.1351 + 5 2.0000 -0.5163789 -14.0514 + 6 2.0000 -0.4884890 -13.2925 + 7 2.0000 -0.4537369 -12.3468 + 8 2.0000 -0.4523900 -12.3102 + 9 2.0000 -0.4388175 -11.9408 + 10 2.0000 -0.3630745 -9.8798 (HOMO) + 11 0.0494719 1.3462 (LUMO) + 12 0.1260207 3.4292 + 13 0.1321555 3.5961 + 14 0.1464083 3.9840 + 15 0.1742217 4.7408 + 16 0.1783232 4.8524 + 17 0.2369989 6.4491 + 18 0.2534620 6.8971 + 19 0.2783726 7.5749 + ------------------------------------------------------------- + HL-Gap 0.4125464 Eh 11.2260 eV + Fermi-level -0.1568013 Eh -4.2668 eV + + # Z covCN q C6AA α(0) + 1 7 n 2.629 -0.343 28.846 7.977 + 2 6 c 3.730 0.030 20.157 6.409 + 3 6 c 3.750 -0.106 22.587 6.778 + 4 1 h 0.860 0.136 1.503 1.920 + 5 1 h 0.860 0.131 1.535 1.941 + 6 1 h 0.924 0.003 3.014 2.715 + 7 1 h 0.924 0.032 2.557 2.501 + 8 1 h 0.924 0.036 2.508 2.477 + 9 1 h 0.924 0.034 2.529 2.487 + 10 1 h 0.924 0.048 2.349 2.397 + + Mol. C6AA /au·bohr⁶ : 628.954400 + Mol. C8AA /au·bohr⁸ : 12386.610898 + Mol. α(0) /au : 37.600519 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + + --------------------------------------------------------------------------- + # Z sym total # sym WBO # sym WBO # sym WBO + --------------------------------------------------------------------------- + 1 7 n 2.993 -- 2 c 1.020 5 h 0.970 4 h 0.968 + 2 6 c 3.988 -- 1 n 1.020 3 c 1.019 7 h 0.976 + 6 h 0.973 + 3 6 c 3.996 -- 2 c 1.019 8 h 0.987 10 h 0.987 + 9 h 0.986 + 4 1 h 0.982 -- 1 n 0.968 + 5 1 h 0.983 -- 1 n 0.970 + 6 1 h 1.000 -- 2 c 0.973 + 7 1 h 0.999 -- 2 c 0.976 + 8 1 h 0.999 -- 3 c 0.987 + 9 1 h 0.999 -- 3 c 0.986 + 10 1 h 0.998 -- 3 c 0.987 + --------------------------------------------------------------------------- + +Topologies differ in total number of bonds +Writing topology from bond orders to xtbtopo.mol + +molecular dipole: + x y z tot (Debye) + q only: 0.003 -0.023 0.184 + full: 0.166 -0.066 0.538 1.440 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: 1.022 -0.244 0.347 0.365 -0.168 -1.368 + q+dip: 1.494 -0.410 0.893 1.651 -0.993 -2.387 + full: 1.871 -0.443 0.872 1.346 -0.769 -2.743 + + + ------------------------------------------------- + | TOTAL ENERGY -10.752192838993 Eh | + | GRADIENT NORM 0.017368634110 Eh/α | + | HOMO-LUMO GAP 11.225958754700 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/25 at 04:54:15.712 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.532 sec + * cpu-time: 0 d, 0 h, 0 min, 12.160 sec + * ratio c/w: 22.878 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.434 sec + * cpu-time: 0 d, 0 h, 0 min, 9.928 sec + * ratio c/w: 22.856 speedup + diff --git a/arkane/data/xTB/TS_NH2+N2H3_xtb.out b/arkane/data/xTB/TS_NH2+N2H3_xtb.out new file mode 100644 index 00000000000..7985d0efe4c --- /dev/null +++ b/arkane/data/xTB/TS_NH2+N2H3_xtb.out @@ -0,0 +1,429 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.5.1 (b24c23e) compiled by 'conda@728c89f4b128' on 2022-07-12 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, C. Hölzer + A. Katbashev, J. Koopman, C. Lavigne, S. Lehtola, F. März, M. Müller, + F. Musil, H. Neugebauer, J. Pisarek, C. Plett, P. Pracht, F. Pultar, + J. Seibert, P. Shushkov, S. Spicher, M. Stahn, M. Steiner, T. Strunk, + J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/25 at 05:40:34.195 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : xtb input.in --hess + coordinate file : input.in + omp threads : 24 + + ID Z sym. atoms + 1 7 n 1, 4, 7 + 2 1 h 2, 3, 5, 6, 8 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + +q/qsh data taken from xtbrestart +CAMM data taken from xtbrestart + + ................................................... + : SETUP : + :.................................................: + : # basis functions 17 : + : # atomic orbitals 17 : + : # shells 11 : + : # electrons 20 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? true : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -10.8541976 -0.108542E+02 0.478E+00 0.77 0.0 T + 2 -10.8519591 0.223848E-02 0.832E+00 1.15 1.0 T + 3 -10.9247349 -0.727758E-01 0.679E+00 0.44 1.0 T + 4 -11.1151403 -0.190405E+00 0.402E+00 1.05 1.0 T + 5 -11.0968475 0.182927E-01 0.354E+00 0.99 1.0 T + 6 -11.1356853 -0.388377E-01 0.356E+00 0.42 1.0 T + 7 -11.1361959 -0.510646E-03 0.338E+00 0.39 1.0 T + 8 -11.0815338 0.546621E-01 0.325E+00 0.04 1.0 T + 9 -10.9657623 0.115771E+00 0.598E+00 0.25 1.0 T + 10 -10.9813757 -0.156135E-01 0.562E+00 0.16 1.0 T + 11 -11.0850405 -0.103665E+00 0.296E+00 0.58 1.0 T + 12 -11.1090041 -0.239636E-01 0.287E+00 0.55 1.0 T + 13 -11.1231508 -0.141467E-01 0.269E+00 0.39 1.0 T + 14 -11.1434646 -0.203138E-01 0.177E+00 0.13 1.0 T + 15 -11.1474659 -0.400126E-02 0.133E+00 0.10 1.0 T + 16 -11.1468049 0.660925E-03 0.122E+00 0.10 1.0 T + 17 -11.0997765 0.470284E-01 0.318E+00 0.03 1.0 T + 18 -11.1245114 -0.247349E-01 0.230E+00 0.22 1.0 T + 19 -11.1499837 -0.254723E-01 0.689E-01 0.03 1.0 T + 20 -11.1447688 0.521491E-02 0.126E+00 0.10 1.0 T + 21 -11.1437502 0.101859E-02 0.130E+00 0.01 1.0 T + 22 -11.1458133 -0.206309E-02 0.115E+00 0.10 1.0 T + 23 -11.1495056 -0.369235E-02 0.793E-01 0.03 1.0 T + 24 -11.1509990 -0.149338E-02 0.600E-01 0.07 1.0 T + 25 -11.1522716 -0.127261E-02 0.344E-01 0.04 1.0 T + 26 -11.1526765 -0.404833E-03 0.212E-01 0.06 1.0 T + 27 -11.1528564 -0.179882E-03 0.105E-01 0.05 1.0 T + 28 -11.1529043 -0.479848E-04 0.470E-02 0.05 1.0 T + 29 -11.1529137 -0.933667E-05 0.222E-02 0.05 1.6 T + 30 -11.1529162 -0.252341E-05 0.408E-03 0.05 8.7 T + 31 -11.1529162 -0.506488E-07 0.306E-03 0.05 11.5 T + 32 -11.1529163 -0.301140E-07 0.182E-03 0.05 19.5 T + 33 -11.1529163 -0.156650E-07 0.215E-04 0.05 164.4 T + 34 -11.1529163 0.216634E-09 0.347E-04 0.05 101.8 T + + *** convergence criteria satisfied after 34 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6878200 -18.7165 + ... ... ... ... + 4 2.0000 -0.5614664 -15.2783 + 5 2.0000 -0.5454139 -14.8415 + 6 2.0000 -0.5183795 -14.1058 + 7 2.0000 -0.4603694 -12.5273 + 8 2.0000 -0.4090447 -11.1307 + 9 2.0000 -0.3904638 -10.6251 + 10 1.4572 -0.3423259 -9.3152 (HOMO) + 11 0.5428 -0.3404496 -9.2641 (LUMO) + 12 -0.0197704 -0.5380 + 13 0.0427379 1.1630 + 14 0.1212398 3.2991 + 15 0.1278854 3.4799 + ... ... ... + 17 0.2388268 6.4988 + ------------------------------------------------------------- + HL-Gap 0.0018763 Eh 0.0511 eV + Fermi-level -0.3413878 Eh -9.2896 eV + + SCC (total) 0 d, 0 h, 0 min, 1.199 sec + SCC setup ... 0 min, 0.009 sec ( 0.751%) + Dispersion ... 0 min, 0.021 sec ( 1.752%) + classical contributions ... 0 min, 0.010 sec ( 0.830%) + integral evaluation ... 0 min, 0.020 sec ( 1.669%) + iterations ... 0 min, 1.050 sec ( 87.616%) + molecular gradient ... 0 min, 0.088 sec ( 7.371%) + printout ... 0 min, 0.000 sec ( 0.008%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -11.067932211213 Eh :: + :: gradient norm 0.044042780703 Eh/a0 :: + :: HOMO-LUMO gap 0.051055839133 eV :: + ::.................................................:: + :: SCC energy -11.152916291942 Eh :: + :: -> isotropic ES 0.029139599864 Eh :: + :: -> anisotropic ES 0.002736060526 Eh :: + :: -> anisotropic XC 0.017808727226 Eh :: + :: -> dispersion -0.002230701284 Eh :: + :: repulsion energy 0.084983559547 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Numerical Hessian | + ------------------------------------------------- +step length : 0.00500 +SCC accuracy : 0.30000 +Hessian scale factor : 1.00000 +frozen atoms in % : 0.00000 0 +RMS gradient : 0.04405 !! INCOMPLETELY OPTIMIZED GEOMETRY !! +estimated CPU time 0.02 min +estimated wall time 0.00 min + +writing file . + + projected vibrational frequencies (cm⁻¹) +eigval : -0.00 -0.00 -0.00 0.00 0.00 0.00 +eigval : -781.89 139.33 236.79 327.73 471.51 690.72 +eigval : 827.09 915.23 1056.62 1185.04 1315.85 1347.33 +eigval : 1424.36 1497.04 3181.14 3367.54 3433.32 3467.59 + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6878196 -18.7165 + 2 2.0000 -0.6237956 -16.9743 + 3 2.0000 -0.5877989 -15.9948 + 4 2.0000 -0.5614663 -15.2783 + 5 2.0000 -0.5454136 -14.8415 + 6 2.0000 -0.5183796 -14.1058 + 7 2.0000 -0.4603691 -12.5273 + 8 2.0000 -0.4090446 -11.1307 + 9 2.0000 -0.3904640 -10.6251 + 10 1.4574 -0.3423267 -9.3152 (HOMO) + 11 0.5426 -0.3404496 -9.2641 (LUMO) + 12 -0.0197701 -0.5380 + 13 0.0427381 1.1630 + 14 0.1212399 3.2991 + 15 0.1278853 3.4799 + 16 0.1978072 5.3826 + 17 0.2388270 6.4988 + ------------------------------------------------------------- + HL-Gap 0.0018771 Eh 0.0511 eV + Fermi-level -0.3413882 Eh -9.2896 eV + + # Z covCN q C6AA α(0) + 1 7 n 2.651 -0.217 25.747 7.536 + 2 1 h 0.860 0.162 1.321 1.801 + 3 1 h 1.296 0.231 0.947 1.519 + 4 7 n 2.699 -0.194 25.208 7.457 + 5 1 h 0.860 0.162 1.319 1.799 + 6 1 h 0.860 0.181 1.207 1.721 + 7 7 n 1.343 -0.433 29.864 7.794 + 8 1 h 0.859 0.108 1.730 2.060 + + Mol. C6AA /au·bohr⁶ : 449.984263 + Mol. C8AA /au·bohr⁸ : 8598.507649 + Mol. α(0) /au : 31.686407 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + + --------------------------------------------------------------------------- + # Z sym total # sym WBO # sym WBO # sym WBO + --------------------------------------------------------------------------- + 1 7 n 2.845 -- 4 n 1.128 2 h 0.962 3 h 0.570 + 7 n 0.178 + 2 1 h 0.973 -- 1 n 0.962 + 3 1 h 0.946 -- 1 n 0.570 7 n 0.364 + 4 7 n 3.163 -- 1 n 1.128 5 h 0.958 6 h 0.945 + 7 n 0.128 + 5 1 h 0.971 -- 4 n 0.958 + 6 1 h 0.961 -- 4 n 0.945 + 7 7 n 1.664 -- 8 h 0.988 3 h 0.364 1 n 0.178 + 4 n 0.128 + 8 1 h 0.988 -- 7 n 0.988 + --------------------------------------------------------------------------- + +Topologies differ in total number of bonds +Writing topology from bond orders to xtbtopo.mol + +molecular dipole: + x y z tot (Debye) + q only: -1.588 0.009 0.342 + full: -1.927 -0.171 0.894 5.417 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: -2.416 1.215 0.857 0.584 0.526 1.560 +Molecule has no symmetry elements +It seems to be the C1 point group + q+dip: -1.976 -0.198 -0.541 1.330 1.113 2.518 + full: -1.727 -0.022 -0.415 1.348 1.270 2.141 + + ------------------------------------------------- + | Frequency Printout | + ------------------------------------------------- + projected vibrational frequencies (cm⁻¹) +eigval : -0.00 -0.00 -0.00 0.00 0.00 0.00 +eigval : -781.89 139.33 236.79 327.73 471.51 690.72 +eigval : 827.09 915.23 1056.62 1185.04 1315.85 1347.33 +eigval : 1424.36 1497.04 3181.14 3367.54 3433.32 3467.59 + reduced masses (amu) + 1: 12.12 2: 11.73 3: 12.46 4: 12.33 5: 12.01 6: 10.98 7: 4.41 8: 1.76 + 9: 9.60 10: 4.15 11: 6.89 12: 4.75 13: 4.81 14: 3.48 15: 2.74 16: 10.71 + 17: 3.60 18: 1.96 19: 1.62 20: 1.77 21: 1.86 22: 1.83 23: 1.46 24: 2.15 + IR intensities (km·mol⁻¹) + 1: 2.82 2: 10.07 3: 0.26 4: 1.70 5: 12.02 6: 12.77 7:168.96 8: 45.26 + 9: 0.96 10: 51.09 11: 49.16 12:118.12 13:115.92 14: 82.29 15: 38.59 16: 69.80 + 17: 25.25 18: 94.03 19: 46.21 20: 9.84 21: 53.59 22: 4.79 23: 10.08 24: 1.41 + Raman intensities (amu) + 1: 0.00 2: 0.00 3: 0.00 4: 0.00 5: 0.00 6: 0.00 7: 0.00 8: 0.00 + 9: 0.00 10: 0.00 11: 0.00 12: 0.00 13: 0.00 14: 0.00 15: 0.00 16: 0.00 + 17: 0.00 18: 0.00 19: 0.00 20: 0.00 21: 0.00 22: 0.00 23: 0.00 24: 0.00 + output can be read by thermo (or use thermo option). + writing molden fake output. + recommended (thermochemical) frequency scaling factor: 1.0 + ------------------------------------------------- + | Thermodynamic Functions | + ------------------------------------------------- + +c1 symmetry found (for desy threshold: 0.10E+00) used in thermo + + ................................................... + : SETUP : + :.................................................: + : # frequencies 17 : + : # imaginary freq. 1 : + : linear? false : + : only rotor calc. false : + : symmetry c1 : + : rotational number 1 : + : scaling factor 1.0000000 : + : rotor cutoff 50.0000000 cm⁻¹ : + : imag. cutoff -20.0000000 cm⁻¹ : + :.................................................: + + mode ω/cm⁻¹ T·S(HO)/kcal·mol⁻¹ T·S(FR)/kcal·mol⁻¹ T·S(vib) + ------------------------------------------------------------------------ + 1 139.33 -0.83870 ( 98.37%) -0.75242 ( 1.63%) -0.83729 + 2 236.79 -0.54469 ( 99.80%) -0.59554 ( 0.20%) -0.54479 + ------------------------------------------------------------------------ + + temp. (K) partition function enthalpy heat capacity entropy + cal/mol cal/K/mol cal/K/mol J/K/mol + 298.15 VIB 4.57 1328.586 9.523 7.470 + ROT 0.278E+05 888.752 2.981 23.316 + INT 0.127E+06 2217.338 12.504 30.786 + TR 0.312E+27 1481.254 4.968 37.454 + TOT 3698.5919 17.4721 68.2401 285.5166 + + T/K H(0)-H(T)+PV H(T)/Eh T*S/Eh G(T)/Eh + ------------------------------------------------------------------------ + 298.15 0.589408E-02 0.625845E-01 0.324231E-01 0.301614E-01 + ------------------------------------------------------------------------ + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: THERMODYNAMIC :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total free energy -11.037770792106 Eh :: + ::.................................................:: + :: total energy -11.067932210697 Eh :: + :: zero point energy 0.056690417480 Eh :: + :: G(RRHO) w/o ZPVE -0.026528998888 Eh :: + :: G(RRHO) contrib. 0.030161418591 Eh :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: +imag cut-off (cm-1) : 5.00 + found 1 significant imaginary frequency + writing imag mode distorted coords to xtbhess.coord + for further optimization. + + ------------------------------------------------- + | TOTAL ENERGY -11.067932210697 Eh | + | TOTAL ENTHALPY -11.005347711824 Eh | + | TOTAL FREE ENERGY -11.037770792106 Eh | + | GRADIENT NORM 0.044051109476 Eh/α | + | HOMO-LUMO GAP 0.051079223054 eV | + ------------------------------------------------- +######################################################################## +[WARNING] Runtime exception occurred +-1- hessian_numhess: Hessian on incompletely optimized geometry! +######################################################################## + +------------------------------------------------------------------------ + * finished run on 2022/07/25 at 05:40:35.738 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 1.542 sec + * cpu-time: 0 d, 0 h, 0 min, 35.521 sec + * ratio c/w: 23.030 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 1.199 sec + * cpu-time: 0 d, 0 h, 0 min, 27.666 sec + * ratio c/w: 23.074 speedup + analytical hessian: + * wall-time: 0 d, 0 h, 0 min, 0.252 sec + * cpu-time: 0 d, 0 h, 0 min, 5.763 sec + * ratio c/w: 22.840 speedup + diff --git a/arkane/data/xTB/freq.out b/arkane/data/xTB/freq.out new file mode 100644 index 00000000000..f7d46b23c43 --- /dev/null +++ b/arkane/data/xTB/freq.out @@ -0,0 +1,395 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.3.3 (71d3805) compiled by 'conda@b85dec0bf610' on 2021-01-07 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN1-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + with help from (in alphabetical order) + C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher, M. Checinski, + S. Dohm, S. Ehlert, S. Ehrlich, F. März, H. Neugebauer, J. Pisarek, + P. Pracht, P. Shushkov, and S. Spicher. + + * started run on 2026/04/05 at 21:13:14.497 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/alon/anaconda3/envs/xtb_env/bin/xtb mol.sdf --hess --gfn2 --parallel --uhf 1 --chrg 0 + coordinate file : mol.sdf + omp threads : 28 + number of atoms : 10 + number of electrons : 19 + charge : 0 + spin : 0.5 + first test random number : 0.65715491998447 + + ID Z sym. atoms + 1 6 C 1-3 + 2 1 H 4-10 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 19 : + : # atomic orbitals 19 : + : # shells 13 : + : # electrons 19 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -10.0416711 -0.100417E+02 0.261E+00 10.94 0.0 T + 2 -10.0633074 -0.216363E-01 0.128E+00 11.04 1.0 T + 3 -10.0636420 -0.334646E-03 0.626E-01 11.05 1.0 T + 4 -10.0637056 -0.635153E-04 0.802E-02 11.02 1.0 T + 5 -10.0637056 -0.179674E-07 0.178E-02 11.02 1.8 T + 6 -10.0637060 -0.424862E-06 0.287E-03 11.02 11.0 T + 7 -10.0637060 -0.813378E-08 0.880E-04 11.02 36.0 T + 8 -10.0637060 -0.139483E-08 0.213E-04 11.02 148.8 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6061683 -16.4947 + ... ... ... ... + 4 2.0000 -0.4986683 -13.5695 + 5 2.0000 -0.4853163 -13.2061 + 6 2.0000 -0.4739663 -12.8973 + 7 2.0000 -0.4615788 -12.5602 + 8 2.0000 -0.4406775 -11.9914 + 9 2.0000 -0.4305099 -11.7148 + 10 1.0000 -0.2854557 -7.7676 (HOMO) + 11 0.1195484 3.2531 (LUMO) + 12 0.1500368 4.0827 + 13 0.1796854 4.8895 + 14 0.1856294 5.0512 + 15 0.1978893 5.3848 + ... ... ... + 19 0.3654091 9.9433 + ------------------------------------------------------------- + HL-Gap 0.4050041 Eh 11.0207 eV + Fermi-level -0.2204682 Eh -5.9992 eV + + SCC (total) 0 d, 0 h, 0 min, 0.001 sec + SCC setup ... 0 min, 0.000 sec ( 4.544%) + Dispersion ... 0 min, 0.000 sec ( 3.231%) + classical contributions ... 0 min, 0.000 sec ( 1.655%) + integral evaluation ... 0 min, 0.000 sec ( 17.352%) + iterations ... 0 min, 0.001 sec ( 41.202%) + molecular gradient ... 0 min, 0.000 sec ( 27.611%) + printout ... 0 min, 0.000 sec ( 3.837%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -9.907945789900 Eh :: + :: gradient norm 0.000167508372 Eh/a0 :: + :: HOMO-LUMO gap 11.020722679226 eV :: + ::.................................................:: + :: SCC energy -10.063706015090 Eh :: + :: -> isotropic ES 0.002969205741 Eh :: + :: -> anisotropic ES 0.003814162232 Eh :: + :: -> anisotropic XC 0.007249074358 Eh :: + :: -> dispersion -0.003488521930 Eh :: + :: repulsion energy 0.155759193674 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Numerical Hessian | + ------------------------------------------------- +step length : 0.00500 +SCC accuracy : 0.30000 +Hessian scale factor : 1.00000 +frozen atoms in % : 0.00000 0 +RMS gradient : 0.00017 +estimated CPU time 0.00 min +estimated wall time 0.00 min + +writing file . + + projected vibrational frequencies (cm-1) +eigval : -0.00 -0.00 -0.00 0.00 0.00 0.00 +eigval : 63.60 78.48 387.35 421.10 940.62 946.86 +eigval : 956.71 1028.72 1167.73 1180.95 1343.10 1393.57 +eigval : 1405.68 1465.51 1475.29 1481.36 1484.29 2854.51 +eigval : 2860.02 2993.19 2993.57 3004.99 3009.56 3104.88 + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6061685 -16.4947 + 2 2.0000 -0.5856626 -15.9367 + 3 2.0000 -0.5406394 -14.7115 + 4 2.0000 -0.4986683 -13.5695 + 5 2.0000 -0.4853160 -13.2061 + 6 2.0000 -0.4739665 -12.8973 + 7 2.0000 -0.4615787 -12.5602 + 8 2.0000 -0.4406776 -11.9914 + 9 2.0000 -0.4305100 -11.7148 + 10 1.0000 -0.2854551 -7.7676 (HOMO) + 11 0.1195485 3.2531 (LUMO) + 12 0.1500364 4.0827 + 13 0.1796854 4.8895 + 14 0.1856298 5.0512 + 15 0.1978891 5.3848 + 16 0.2104543 5.7268 + 17 0.2219295 6.0390 + 18 0.3220796 8.7642 + 19 0.3654094 9.9433 + ------------------------------------------------------------- + HL-Gap 0.4050036 Eh 11.0207 eV + Fermi-level -0.2204679 Eh -5.9992 eV + + # Z covCN q C6AA α(0) + 1 6 C 3.752 -0.096 22.389 6.748 + 2 6 C 3.751 -0.096 22.389 6.748 + 3 6 C 2.882 -0.072 29.797 8.949 + 4 1 H 0.923 0.044 2.396 2.421 + 5 1 H 0.924 0.039 2.463 2.454 + 6 1 H 0.925 0.039 2.457 2.451 + 7 1 H 0.925 0.039 2.458 2.452 + 8 1 H 0.924 0.039 2.462 2.454 + 9 1 H 0.923 0.044 2.396 2.421 + 10 1 H 0.926 0.019 2.751 2.594 + + Mol. C6AA /au·bohr⁶ : 671.387425 + Mol. C8AA /au·bohr⁸ : 14020.731634 + Mol. α(0) /au : 39.690034 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + + --------------------------------------------------------------------------- + # Z sym total # sym WBO # sym WBO # sym WBO + --------------------------------------------------------------------------- + 1 6 C 3.988 -- 3 C 1.079 6 H 0.978 5 H 0.973 + 4 H 0.940 + 2 6 C 3.988 -- 3 C 1.079 7 H 0.978 8 H 0.973 + 9 H 0.940 + 3 6 C 3.142 -- 2 C 1.079 1 C 1.079 10 H 0.976 + 4 1 H 0.946 -- 1 C 0.940 + 5 1 H 0.984 -- 1 C 0.973 + 6 1 H 0.991 -- 1 C 0.978 + 7 1 H 0.991 -- 2 C 0.978 + 8 1 H 0.984 -- 2 C 0.973 + 9 1 H 0.946 -- 2 C 0.940 + 10 1 H 0.999 -- 3 C 0.976 + --------------------------------------------------------------------------- + + +molecular dipole: + x y z tot (Debye) + q only: -0.095 -0.086 0.006 + full: -0.141 -0.089 0.052 0.444 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: 0.060 -0.134 0.180 0.234 -0.555 -0.240 + q+dip: 0.015 0.235 0.399 0.377 -0.497 -0.414 + full: 0.025 0.052 0.231 0.225 -0.555 -0.256 + + ------------------------------------------------- + | Frequency Printout | + ------------------------------------------------- + projected vibrational frequencies (cm-1) +eigval : -0.00 -0.00 -0.00 0.00 0.00 0.00 +eigval : 63.60 78.48 387.35 421.10 940.62 946.86 +eigval : 956.71 1028.72 1167.73 1180.95 1343.10 1393.57 +eigval : 1405.68 1465.51 1475.29 1481.36 1484.29 2854.51 +eigval : 2860.02 2993.19 2993.57 3004.99 3009.56 3104.88 + reduced masses (amu) + 1: 9.19 2: 8.92 3: 9.23 4: 9.15 5: 9.42 6: 5.79 7: 1.20 8: 3.43 + 9: 6.62 10: 4.08 11: 8.02 12: 2.52 13: 2.96 14: 4.29 15: 6.86 16: 5.59 + 17: 6.97 18: 3.32 19: 2.84 20: 1.82 21: 1.73 22: 1.85 23: 1.48 24: 1.74 + 25: 1.75 26: 1.57 27: 1.56 28: 1.77 29: 1.76 30: 1.82 + IR intensities (amu) + 1: 0.07 2: 0.09 3: 0.08 4: 0.09 5: 0.11 6: 0.14 7: 0.00 8: 0.15 + 9: 0.13 10: 0.22 11: 0.08 12: 0.03 13: 0.04 14: 0.07 15: 0.20 16: 0.31 + 17: 0.50 18: 0.22 19: 0.06 20: 0.05 21: 0.05 22: 0.06 23: 0.04 24: 0.12 + 25: 0.28 26: 0.19 27: 0.18 28: 0.03 29: 0.27 30: 0.32 + Raman intensities (amu) + 1: 0.00 2: 0.00 3: 0.00 4: 0.00 5: 0.00 6: 0.00 7: 0.00 8: 0.00 + 9: 0.00 10: 0.00 11: 0.00 12: 0.00 13: 0.00 14: 0.00 15: 0.00 16: 0.00 + 17: 0.00 18: 0.00 19: 0.00 20: 0.00 21: 0.00 22: 0.00 23: 0.00 24: 0.00 + 25: 0.00 26: 0.00 27: 0.00 28: 0.00 29: 0.00 30: 0.00 +Molecule has the following symmetry elements: (sigma) +It seems to be the Cs point group + output can be read by thermo (or use thermo option). + writing molden fake output. + recommended (thermochemical) frequency scaling factor: 1.0 + ------------------------------------------------- + | Thermodynamic Functions | + ------------------------------------------------- + +cs symmetry found (for desy threshold: 0.10E+00) used in thermo + + ................................................... + : SETUP : + :.................................................: + : # frequencies 24 : + : # imaginary freq. 0 : + : linear? false : + : only rotor calc. false : + : symmetry cs : + : rotational number 1 : + : scaling factor 1.0000000 : + : rotor cutoff 50.0000000 cm⁻¹ : + : imag. cutoff -20.0000000 cm⁻¹ : + :.................................................: + + mode ω/cm⁻¹ T·S(HO)/kcal·mol⁻¹ T·S(FR)/kcal·mol⁻¹ T·S(vib) + ------------------------------------------------------------------------ + 1 63.60 -1.29469 ( 72.35%) -0.98363 ( 27.65%) -1.20869 + 2 78.48 -1.17128 ( 85.86%) -0.92163 ( 14.14%) -1.13597 + ------------------------------------------------------------------------ + + temp. (K) partition function enthalpy heat capacity entropy + cal/mol cal/K/mol cal/K/mol J/K/mol + 298.15 VIB 17.2 1534.753 9.629 10.395 + ROT 0.176E+05 888.752 2.981 22.409 + INT 0.303E+06 2423.506 12.610 32.805 + TR 0.274E+27 1481.254 4.968 37.192 + TOT 3904.7597 17.5778 69.9961 292.8635 + + T/K H(0)-H(T)+PV H(T)/Eh T*S/Eh G(T)/Eh + ------------------------------------------------------------------------ + 298.15 0.622263E-02 0.928878E-01 0.332574E-01 0.596304E-01 + ------------------------------------------------------------------------ + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: THERMODYNAMIC :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total free energy -9.848315378832 Eh :: + ::.................................................:: + :: total energy -9.907945789911 Eh :: + :: zero point energy 0.086665171024 Eh :: + :: G(RRHO) w/o ZPVE -0.027034759946 Eh :: + :: G(RRHO) contrib. 0.059630411079 Eh :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | TOTAL ENERGY -9.907945789911 Eh | + | TOTAL ENTHALPY -9.815057988157 Eh | + | TOTAL FREE ENERGY -9.848315378832 Eh | + | GRADIENT NORM 0.000167778724 Eh/α | + | HOMO-LUMO GAP 11.020709553837 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2026/04/05 at 21:13:14.519 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.022 sec + * cpu-time: 0 d, 0 h, 0 min, 0.125 sec + * ratio c/w: 5.689 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.001 sec + * cpu-time: 0 d, 0 h, 0 min, 0.005 sec + * ratio c/w: 3.550 speedup + numerical hessian: + * wall-time: 0 d, 0 h, 0 min, 0.015 sec + * cpu-time: 0 d, 0 h, 0 min, 0.107 sec + * ratio c/w: 7.094 speedup + diff --git a/arkane/data/xTB/output.out b/arkane/data/xTB/output.out new file mode 100644 index 00000000000..c2555503ff0 --- /dev/null +++ b/arkane/data/xTB/output.out @@ -0,0 +1,525 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.3.3 (71d3805) compiled by 'conda@b85dec0bf610' on 2021-01-07 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN1-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + with help from (in alphabetical order) + C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher, M. Checinski, + S. Dohm, S. Ehlert, S. Ehrlich, F. März, H. Neugebauer, J. Pisarek, + P. Pracht, P. Shushkov, and S. Spicher. + + * started run on 2026/04/05 at 21:13:11.373 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/alon/anaconda3/envs/xtb_env/bin/xtb mol.sdf --opt tight --gfn2 --parallel --uhf 1 --chrg 0 + coordinate file : mol.sdf + omp threads : 28 + number of atoms : 10 + number of electrons : 19 + charge : 0 + spin : 0.5 + first test random number : 0.49640547205832 + + ID Z sym. atoms + 1 6 C 1-3 + 2 1 H 4-10 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 19 : + : # atomic orbitals 19 : + : # shells 13 : + : # electrons 19 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -10.0416711 -0.100417E+02 0.261E+00 10.94 0.0 T + 2 -10.0633074 -0.216363E-01 0.128E+00 11.04 1.0 T + 3 -10.0636420 -0.334646E-03 0.626E-01 11.05 1.0 T + 4 -10.0637056 -0.635153E-04 0.802E-02 11.02 1.0 T + 5 -10.0637056 -0.179674E-07 0.178E-02 11.02 1.8 T + 6 -10.0637060 -0.424862E-06 0.287E-03 11.02 11.0 T + 7 -10.0637060 -0.813378E-08 0.880E-04 11.02 36.0 T + 8 -10.0637060 -0.139483E-08 0.213E-04 11.02 148.8 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6061683 -16.4947 + ... ... ... ... + 4 2.0000 -0.4986683 -13.5695 + 5 2.0000 -0.4853163 -13.2061 + 6 2.0000 -0.4739663 -12.8973 + 7 2.0000 -0.4615788 -12.5602 + 8 2.0000 -0.4406775 -11.9914 + 9 2.0000 -0.4305099 -11.7148 + 10 1.0000 -0.2854557 -7.7676 (HOMO) + 11 0.1195484 3.2531 (LUMO) + 12 0.1500368 4.0827 + 13 0.1796854 4.8895 + 14 0.1856294 5.0512 + 15 0.1978893 5.3848 + ... ... ... + 19 0.3654091 9.9433 + ------------------------------------------------------------- + HL-Gap 0.4050041 Eh 11.0207 eV + Fermi-level -0.2204682 Eh -5.9992 eV + + SCC (total) 0 d, 0 h, 0 min, 0.001 sec + SCC setup ... 0 min, 0.000 sec ( 3.932%) + Dispersion ... 0 min, 0.000 sec ( 3.355%) + classical contributions ... 0 min, 0.000 sec ( 1.553%) + integral evaluation ... 0 min, 0.000 sec ( 17.193%) + iterations ... 0 min, 0.001 sec ( 38.483%) + molecular gradient ... 0 min, 0.000 sec ( 32.733%) + printout ... 0 min, 0.000 sec ( 2.267%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -9.907945789900 Eh :: + :: gradient norm 0.000167508372 Eh/a0 :: + :: HOMO-LUMO gap 11.020722679226 eV :: + ::.................................................:: + :: SCC energy -10.063706015090 Eh :: + :: -> isotropic ES 0.002969205741 Eh :: + :: -> anisotropic ES 0.003814162232 Eh :: + :: -> anisotropic XC 0.007249074358 Eh :: + :: -> dispersion -0.003488521930 Eh :: + :: repulsion energy 0.155759193674 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ----------------------------------------------------------- + | ===================== | + | A N C O P T | + | ===================== | + | Approximate Normal Coordinate | + | Rational Function Optimizer | + ----------------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : optimization level tight : + : max. optcycles 200 : + : ANC micro-cycles 20 : + : degrees of freedom 24 : + :.................................................: + : RF solver davidson : + : write xtbopt.log true : + : linear? false : + : energy convergence 0.1000000E-05 Eh : + : grad. convergence 0.8000000E-03 Eh/α : + : maximium RF displ. 1.0000000 : + : Hlow (freq-cutoff) 0.1000000E-01 : + : Hmax (freq-cutoff) 5.0000000 : + : S6 in model hess. 20.0000000 : + ................................................... + +generating ANC from model Hessian ... +Using Lindh-Hessian (1995) + Shifting diagonal of input Hessian by 2.3540512790611329E-003 + Lowest eigenvalues of input Hessian + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.010000 0.012932 0.020193 0.036542 0.064021 0.064540 + 0.067460 0.076667 0.112683 0.118968 0.123604 0.125717 + Highest eigenvalues + 1.066348 1.078735 1.114279 1.122396 1.332034 1.453783 + + +........................................................................ +.............................. CYCLE 1 .............................. +........................................................................ + 1 -10.0637060 -0.100637E+02 0.257E-05 11.02 0.0 T + 2 -10.0637060 -0.211209E-11 0.119E-05 11.02 2658.6 T + 3 -10.0637060 -0.284217E-13 0.540E-06 11.02 5857.7 T + SCC iter. ... 0 min, 0.000 sec + gradient ... 0 min, 0.000 sec + * total energy : -9.9079458 Eh change -0.1044143E-10 Eh + gradient norm : 0.0001678 Eh/α predicted 0.0000000E+00 (-100.00%) + displ. norm : 0.0014254 α lambda -0.4426483E-07 + maximum displ.: 0.0013651 α in ANC's #2, #16, #11, ... + + *** GEOMETRY OPTIMIZATION CONVERGED AFTER 1 ITERATIONS *** + +------------------------------------------------------------------------ + total energy gain : -0.0000000 Eh -0.0000 kcal/mol + total RMSD : 0.0000000 a0 0.0000 Å + total power (kW/mol): -0.0000000 (step) -0.0000 (real) +------------------------------------------------------------------------ + + ANCopt (total) 0 d, 0 h, 0 min, 0.002 sec + optimizer setup ... 0 min, 0.000 sec ( 1.192%) + model hessian ... 0 min, 0.000 sec ( 24.216%) + ANC generation ... 0 min, 0.000 sec ( 3.716%) + coordinate transformation ... 0 min, 0.000 sec ( 0.080%) + single point calculation ... 0 min, 0.001 sec ( 63.861%) + optimization log ... 0 min, 0.000 sec ( 1.172%) + hessian update ... 0 min, 0.000 sec ( 0.030%) + rational function ... 0 min, 0.000 sec ( 2.525%) + +================ + final structure: +================ + + xtb 04052621133D +xtb: 6.3.3 (71d3805) + 10 9 0 0 0 999 V2000 + -1.2948 0.0509 -0.1043 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2116 -1.5150 1.2916 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0825 -0.1905 0.7057 C 0 0 0 0 0 3 0 0 0 0 0 0 + -2.1457 0.3557 0.5210 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1316 0.8533 -0.8243 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5938 -0.8508 -0.6375 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1856 -2.3148 0.6674 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2852 -1.6592 1.4153 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2390 -1.6264 2.2879 H 0 0 0 0 0 0 0 0 0 0 0 0 + 0.4901 0.6581 1.0398 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 3 1 0 0 0 0 + 1 4 1 0 0 0 0 + 1 5 1 0 0 0 0 + 1 6 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 7 1 0 0 0 0 + 2 8 1 0 0 0 0 + 2 9 1 0 0 0 0 + 3 10 1 0 0 0 0 +M END +$$$$ + + Bond Distances (Angstroems) + --------------------------- +C1-C3=1.4779 C1-H4=1.0991 C1-H5=1.0904 C1-H6=1.0894 C2-C3=1.4779 C2-H7=1.0895 +C2-H8=1.0903 C2-H9=1.0991 C3-C1=1.4779 C3-C2=1.4779 C3-H10=1.0769 H4-C1=1.0991 +H5-C1=1.0904 H6-C1=1.0894 H7-C2=1.0895 H8-C2=1.0903 H9-C2=1.0991 H10-C3=1.0769 + C H Rav=1.0907 sigma=0.0069 Rmin=1.0769 Rmax=1.0991 7 + C C Rav=1.4779 sigma=0.0000 Rmin=1.4779 Rmax=1.4779 2 + + selected bond angles (degree) + -------------------- +H4-C1-C3=111.63 H5-C1-C3=111.06 H5-C1-H4=106.71 H6-C1-C3=110.99 +H6-C1-H4=107.19 H6-C1-H5=109.09 H7-C2-C3=110.99 H8-C2-C3=111.07 +H8-C2-H7=109.08 H9-C2-C3=111.63 H9-C2-H7=107.18 H9-C2-H8=106.70 +C2-C3-C1=121.80 H10-C3-C1=118.52 H10-C3-C2=118.52 + + selected dihedral angles (degree) + --------------------------------- +C2-C3-C1-H4= 88.76 C2-C3-C1-H5=207.71 C2-C3-C1-H6=329.24 H10-C3-C1-H4=281.25 +H10-C3-C1-H5= 40.20 H10-C3-C1-H6=161.74 C1-C3-C2-H7= 30.75 C1-C3-C2-H8=152.29 +C1-C3-C2-H9=271.24 H10-C3-C2-H7=198.26 H10-C3-C2-H8=319.79 H10-C3-C2-H9= 78.75 + ------------------------------------------------- + | Final Singlepoint | + ------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : # basis functions 19 : + : # atomic orbitals 19 : + : # shells 13 : + : # electrons 19 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -10.0637060 -0.100637E+02 0.969E-07 11.02 0.0 T + 2 -10.0637060 0.355271E-14 0.589E-07 11.02 53664.1 T + 3 -10.0637060 0.177636E-14 0.271E-07 11.02 100000.0 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6061685 -16.4947 + ... ... ... ... + 4 2.0000 -0.4986683 -13.5695 + 5 2.0000 -0.4853160 -13.2061 + 6 2.0000 -0.4739665 -12.8973 + 7 2.0000 -0.4615787 -12.5602 + 8 2.0000 -0.4406775 -11.9914 + 9 2.0000 -0.4305100 -11.7148 + 10 1.0000 -0.2854551 -7.7676 (HOMO) + 11 0.1195485 3.2531 (LUMO) + 12 0.1500364 4.0827 + 13 0.1796854 4.8895 + 14 0.1856298 5.0512 + 15 0.1978891 5.3848 + ... ... ... + 19 0.3654094 9.9433 + ------------------------------------------------------------- + HL-Gap 0.4050036 Eh 11.0207 eV + Fermi-level -0.2204679 Eh -5.9992 eV + + SCC (total) 0 d, 0 h, 0 min, 0.001 sec + SCC setup ... 0 min, 0.000 sec ( 3.904%) + Dispersion ... 0 min, 0.000 sec ( 3.670%) + classical contributions ... 0 min, 0.000 sec ( 2.216%) + integral evaluation ... 0 min, 0.000 sec ( 20.357%) + iterations ... 0 min, 0.000 sec ( 22.730%) + molecular gradient ... 0 min, 0.000 sec ( 43.201%) + printout ... 0 min, 0.000 sec ( 3.306%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -9.907945789911 Eh :: + :: gradient norm 0.000167776370 Eh/a0 :: + :: HOMO-LUMO gap 11.020710061302 eV :: + ::.................................................:: + :: SCC energy -10.063706015100 Eh :: + :: -> isotropic ES 0.002969138307 Eh :: + :: -> anisotropic ES 0.003814175600 Eh :: + :: -> anisotropic XC 0.007249059940 Eh :: + :: -> dispersion -0.003488523956 Eh :: + :: repulsion energy 0.155759193674 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6061685 -16.4947 + 2 2.0000 -0.5856626 -15.9367 + 3 2.0000 -0.5406394 -14.7115 + 4 2.0000 -0.4986683 -13.5695 + 5 2.0000 -0.4853160 -13.2061 + 6 2.0000 -0.4739665 -12.8973 + 7 2.0000 -0.4615787 -12.5602 + 8 2.0000 -0.4406775 -11.9914 + 9 2.0000 -0.4305100 -11.7148 + 10 1.0000 -0.2854551 -7.7676 (HOMO) + 11 0.1195485 3.2531 (LUMO) + 12 0.1500364 4.0827 + 13 0.1796854 4.8895 + 14 0.1856298 5.0512 + 15 0.1978891 5.3848 + 16 0.2104543 5.7268 + 17 0.2219295 6.0390 + 18 0.3220796 8.7642 + 19 0.3654094 9.9433 + ------------------------------------------------------------- + HL-Gap 0.4050036 Eh 11.0207 eV + Fermi-level -0.2204679 Eh -5.9992 eV + + # Z covCN q C6AA α(0) + 1 6 C 3.752 -0.096 22.389 6.748 + 2 6 C 3.751 -0.096 22.389 6.748 + 3 6 C 2.882 -0.072 29.797 8.949 + 4 1 H 0.923 0.044 2.396 2.421 + 5 1 H 0.924 0.039 2.463 2.454 + 6 1 H 0.925 0.039 2.457 2.451 + 7 1 H 0.925 0.039 2.458 2.452 + 8 1 H 0.924 0.039 2.462 2.454 + 9 1 H 0.923 0.044 2.396 2.421 + 10 1 H 0.926 0.019 2.751 2.594 + + Mol. C6AA /au·bohr⁶ : 671.387423 + Mol. C8AA /au·bohr⁸ : 14020.731625 + Mol. α(0) /au : 39.690034 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + + --------------------------------------------------------------------------- + # Z sym total # sym WBO # sym WBO # sym WBO + --------------------------------------------------------------------------- + 1 6 C 3.988 -- 3 C 1.079 6 H 0.978 5 H 0.973 + 4 H 0.940 + 2 6 C 3.988 -- 3 C 1.079 7 H 0.978 8 H 0.973 + 9 H 0.940 + 3 6 C 3.142 -- 2 C 1.079 1 C 1.079 10 H 0.976 + 4 1 H 0.946 -- 1 C 0.940 + 5 1 H 0.984 -- 1 C 0.973 + 6 1 H 0.991 -- 1 C 0.978 + 7 1 H 0.991 -- 2 C 0.978 + 8 1 H 0.984 -- 2 C 0.973 + 9 1 H 0.946 -- 2 C 0.940 + 10 1 H 0.999 -- 3 C 0.976 + --------------------------------------------------------------------------- + + +molecular dipole: + x y z tot (Debye) + q only: -0.095 -0.086 0.006 + full: -0.141 -0.089 0.052 0.444 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: 0.060 -0.134 0.180 0.234 -0.555 -0.240 + q+dip: 0.015 0.235 0.399 0.377 -0.497 -0.414 + full: 0.025 0.052 0.231 0.225 -0.555 -0.256 + + ------------------------------------------------- + | Geometry Summary | + ------------------------------------------------- + + molecular mass/u : 43.0877930 + center of mass at/Å : -0.4072910 -0.5684548 0.6322305 + moments of inertia/u·Å² : 0.1317621E+02 0.6015876E+02 0.6707902E+02 +rotational constants/cm⁻¹ : 0.1279399E+01 0.2802191E+00 0.2513100E+00 + + * 9 selected distances + + # Z # Z value/Å + 1 6 C 3 6 C 1.4778516 + 2 6 C 3 6 C 1.4778612 (max) + 1 6 C 4 1 H 1.0990605 + 1 6 C 5 1 H 1.0903577 + 1 6 C 6 1 H 1.0893880 + 2 6 C 7 1 H 1.0895290 + 2 6 C 8 1 H 1.0902808 + 2 6 C 9 1 H 1.0991197 + 3 6 C 10 1 H 1.0768545 (min) + + * 2 distinct bonds (by element types) + + Z Z # av. dist./Å max./Å min./Å + 1 H 6 C 7 1.0906557 1.0991197 1.0768545 + 6 C 6 C 2 1.4778564 1.4778612 1.4778516 + + +optimized geometry written to: xtbopt.sdf + + + ------------------------------------------------- + | TOTAL ENERGY -9.907945789911 Eh | + | GRADIENT NORM 0.000167776370 Eh/α | + | HOMO-LUMO GAP 11.020710061302 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2026/04/05 at 21:13:11.382 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.009 sec + * cpu-time: 0 d, 0 h, 0 min, 0.024 sec + * ratio c/w: 2.601 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.001 sec + * cpu-time: 0 d, 0 h, 0 min, 0.005 sec + * ratio c/w: 3.559 speedup + ANC optimizer: + * wall-time: 0 d, 0 h, 0 min, 0.003 sec + * cpu-time: 0 d, 0 h, 0 min, 0.009 sec + * ratio c/w: 3.256 speedup + diff --git a/arkane/data/xTB/xtb_opt_1.out b/arkane/data/xTB/xtb_opt_1.out new file mode 100644 index 00000000000..d6237eeca75 --- /dev/null +++ b/arkane/data/xTB/xtb_opt_1.out @@ -0,0 +1,610 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.5.1 (b24c23e) compiled by 'conda@728c89f4b128' on 2022-07-12 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN1-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for ALPB and GBSA implicit solvation: + * S. Ehlert, M. Stahn, S. Spicher, S. Grimme, J. Chem. Theory Comput., + 2021, 17, 4250-4261. DOI: 10.1021/acs.jctc.1c00471 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + for SPH calculations refer to: + * S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714 + DOI: 10.1021/acs.jctc.0c01306 + + with help from (in alphabetical order) + P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher + M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, C. Hölzer + A. Katbashev, J. Koopman, C. Lavigne, S. Lehtola, F. März, M. Müller, + F. Musil, H. Neugebauer, J. Pisarek, C. Plett, P. Pracht, F. Pultar, + J. Seibert, P. Shushkov, S. Spicher, M. Stahn, M. Steiner, T. Strunk, + J. Stückrath, T. Rose, and J. Unsleber + + * started run on 2022/07/25 at 06:22:17.589 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : xtb input.in --opt vtight + coordinate file : input.in + omp threads : 24 + + ID Z sym. atoms + 1 6 c 1-3 + 2 8 o 4 + 3 1 h 5-8 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 20 : + : # atomic orbitals 20 : + : # shells 12 : + : # electrons 22 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -12.5907958 -0.125908E+02 0.538E+00 3.37 0.0 T + 2 -12.6188145 -0.280187E-01 0.268E+00 2.55 1.0 T + 3 -12.6192585 -0.444029E-03 0.199E+00 3.03 1.0 T + 4 -12.6250726 -0.581411E-02 0.537E-01 2.77 1.0 T + 5 -12.6268146 -0.174195E-02 0.171E-01 2.81 1.0 T + 6 -12.6269634 -0.148778E-03 0.548E-02 2.81 1.0 T + 7 -12.6269686 -0.527887E-05 0.241E-02 2.80 1.5 T + 8 -12.6269688 -0.151179E-06 0.404E-03 2.80 8.8 T + 9 -12.6269688 -0.347712E-07 0.259E-03 2.80 13.6 T + 10 -12.6269689 -0.379188E-07 0.361E-04 2.80 97.9 T + 11 -12.6269689 -0.539755E-09 0.166E-04 2.80 212.5 T + + *** convergence criteria satisfied after 11 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.7131568 -19.4060 + ... ... ... ... + 5 2.0000 -0.5434007 -14.7867 + 6 2.0000 -0.5422567 -14.7556 + 7 2.0000 -0.5353638 -14.5680 + 8 2.0000 -0.4951196 -13.4729 + 9 2.0000 -0.4772995 -12.9880 + 10 2.0000 -0.4486040 -12.2071 + 11 2.0000 -0.4083156 -11.1108 (HOMO) + 12 -0.3053152 -8.3080 (LUMO) + 13 -0.1944273 -5.2906 + 14 0.0741552 2.0179 + 15 0.1201398 3.2692 + 16 0.1383174 3.7638 + ... ... ... + 20 0.6182951 16.8247 + ------------------------------------------------------------- + HL-Gap 0.1030004 Eh 2.8028 eV + Fermi-level -0.3568154 Eh -9.7094 eV + + SCC (total) 0 d, 0 h, 0 min, 0.497 sec + SCC setup ... 0 min, 0.007 sec ( 1.327%) + Dispersion ... 0 min, 0.020 sec ( 3.928%) + classical contributions ... 0 min, 0.009 sec ( 1.851%) + integral evaluation ... 0 min, 0.029 sec ( 5.846%) + iterations ... 0 min, 0.339 sec ( 68.271%) + molecular gradient ... 0 min, 0.093 sec ( 18.730%) + printout ... 0 min, 0.000 sec ( 0.043%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -12.460800594006 Eh :: + :: gradient norm 0.049225784306 Eh/a0 :: + :: HOMO-LUMO gap 2.802782657527 eV :: + ::.................................................:: + :: SCC energy -12.626968863833 Eh :: + :: -> isotropic ES 0.022798934510 Eh :: + :: -> anisotropic ES 0.000527167465 Eh :: + :: -> anisotropic XC 0.007727951902 Eh :: + :: -> dispersion -0.003176771789 Eh :: + :: repulsion energy 0.166167967131 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ----------------------------------------------------------- + | ===================== | + | A N C O P T | + | ===================== | + | Approximate Normal Coordinate | + | Rational Function Optimizer | + ----------------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : optimization level verytight : + : max. optcycles 200 : + : ANC micro-cycles 20 : + : degrees of freedom 18 : + :.................................................: + : RF solver davidson : + : write xtbopt.log true : + : linear? false : + : energy convergence 0.1000000E-06 Eh : + : grad. convergence 0.2000000E-03 Eh/α : + : maximium RF displ. 1.0000000 : + : Hlow (freq-cutoff) 0.1000000E-01 : + : Hmax (freq-cutoff) 5.0000000 : + : S6 in model hess. 20.0000000 : + ................................................... + +generating ANC from model Hessian ... +Using Lindh-Hessian (1995) + Shifting diagonal of input Hessian by 7.5988932457269481E-004 + Lowest eigenvalues of input Hessian + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.010000 0.015374 0.027151 0.034216 0.061470 0.095310 + 0.116244 0.120151 0.122578 0.204959 0.275560 0.373010 + Highest eigenvalues + 0.691328 0.882781 1.216378 1.553964 1.815825 2.150343 + + +........................................................................ +.............................. CYCLE 1 .............................. +........................................................................ + 1 -12.6269689 -0.126270E+02 0.166E-05 2.80 0.0 T + 2 -12.6269689 -0.866862E-12 0.100E-05 2.80 3529.0 T + 3 -12.6269689 -0.481393E-12 0.392E-06 2.80 9012.5 T + SCC iter. ... 0 min, 0.097 sec + gradient ... 0 min, 0.075 sec + * total energy : -12.4608006 Eh change -0.1592024E-09 Eh + gradient norm : 0.0492276 Eh/α predicted 0.0000000E+00 (-100.00%) + displ. norm : 0.0681358 α lambda -0.2083977E-02 + maximum displ.: 0.0428669 α in ANC's #12, #10, #7, ... + +........................................................................ +.............................. CYCLE 2 .............................. +........................................................................ + 1 -12.6386519 -0.126387E+02 0.168E-01 2.83 0.0 T + 2 -12.6386762 -0.243236E-04 0.967E-02 2.84 1.0 T + 3 -12.6386751 0.112803E-05 0.340E-02 2.84 1.0 T + 4 -12.6386757 -0.622004E-06 0.173E-02 2.84 2.0 T + 5 -12.6386777 -0.198798E-05 0.428E-03 2.84 8.3 T + 6 -12.6386778 -0.545412E-07 0.143E-03 2.84 24.7 T + 7 -12.6386778 -0.687682E-08 0.596E-04 2.84 59.3 T + 8 -12.6386778 -0.184372E-09 0.106E-04 2.84 335.0 T + SCC iter. ... 0 min, 0.244 sec + gradient ... 0 min, 0.089 sec + * total energy : -12.4621329 Eh change -0.1332321E-02 Eh + gradient norm : 0.0160161 Eh/α predicted -0.1046825E-02 ( -21.43%) + displ. norm : 0.0426717 α lambda -0.3126434E-03 + maximum displ.: 0.0297874 α in ANC's #3, #7, #10, ... + +........................................................................ +.............................. CYCLE 3 .............................. +........................................................................ + 1 -12.6413473 -0.126413E+02 0.919E-02 2.84 0.0 T + 2 -12.6413511 -0.379125E-05 0.534E-02 2.85 1.0 T + 3 -12.6413511 -0.144316E-07 0.122E-02 2.84 2.9 T + 4 -12.6413512 -0.707960E-07 0.590E-03 2.84 6.0 T + 5 -12.6413514 -0.174490E-06 0.214E-03 2.84 16.5 T + 6 -12.6413514 -0.198041E-07 0.456E-04 2.84 77.5 T + 7 -12.6413514 -0.126256E-09 0.240E-04 2.84 147.2 T + SCC iter. ... 0 min, 0.227 sec + gradient ... 0 min, 0.089 sec + * total energy : -12.4623098 Eh change -0.1768535E-03 Eh + gradient norm : 0.0030405 Eh/α predicted -0.1566056E-03 ( -11.45%) + displ. norm : 0.0223827 α lambda -0.2441481E-04 + maximum displ.: 0.0206479 α in ANC's #3, #8, #6, ... + +........................................................................ +.............................. CYCLE 4 .............................. +........................................................................ + 1 -12.6409333 -0.126409E+02 0.192E-02 2.84 0.0 T + 2 -12.6409334 -0.543306E-07 0.114E-02 2.84 3.1 T + 3 -12.6409332 0.131372E-06 0.481E-03 2.84 7.4 T + 4 -12.6409334 -0.155889E-06 0.115E-03 2.84 30.7 T + 5 -12.6409334 -0.275147E-08 0.225E-04 2.84 157.3 T + 6 -12.6409334 -0.573408E-11 0.791E-05 2.84 447.2 T + SCC iter. ... 0 min, 0.185 sec + gradient ... 0 min, 0.080 sec + * total energy : -12.4623254 Eh change -0.1567032E-04 Eh + gradient norm : 0.0009347 Eh/α predicted -0.1221273E-04 ( -22.06%) + displ. norm : 0.0204727 α lambda -0.4591387E-05 + maximum displ.: 0.0196940 α in ANC's #3, #8, #6, ... + +........................................................................ +.............................. CYCLE 5 .............................. +........................................................................ + 1 -12.6404761 -0.126405E+02 0.116E-02 2.84 0.0 T + 2 -12.6404762 -0.276402E-07 0.687E-03 2.84 5.1 T + 3 -12.6404762 0.173422E-08 0.136E-03 2.84 26.0 T + 4 -12.6404762 -0.536354E-08 0.586E-04 2.84 60.3 T + 5 -12.6404762 -0.942974E-09 0.278E-04 2.84 127.3 T + SCC iter. ... 0 min, 0.152 sec + gradient ... 0 min, 0.079 sec + * total energy : -12.4623278 Eh change -0.2334995E-05 Eh + gradient norm : 0.0006904 Eh/α predicted -0.2295773E-05 ( -1.68%) + displ. norm : 0.0034964 α lambda -0.5910528E-06 + maximum displ.: 0.0030268 α in ANC's #3, #8, #12, ... + +........................................................................ +.............................. CYCLE 6 .............................. +........................................................................ + 1 -12.6406433 -0.126406E+02 0.349E-03 2.84 0.0 T + 2 -12.6406433 -0.286860E-08 0.210E-03 2.84 16.8 T + 3 -12.6406433 0.733069E-08 0.115E-03 2.84 30.7 T + 4 -12.6406433 -0.880051E-08 0.240E-04 2.84 147.2 T + 5 -12.6406433 -0.121268E-09 0.680E-05 2.84 520.2 T + SCC iter. ... 0 min, 0.146 sec + gradient ... 0 min, 0.085 sec + * total energy : -12.4623282 Eh change -0.4543308E-06 Eh + gradient norm : 0.0000695 Eh/α predicted -0.2944292E-06 ( -35.19%) + displ. norm : 0.0006683 α lambda -0.1341700E-07 + maximum displ.: 0.0006020 α in ANC's #3, #7, #10, ... + +........................................................................ +.............................. CYCLE 7 .............................. +........................................................................ + 1 -12.6406617 -0.126407E+02 0.640E-04 2.84 0.0 T + 2 -12.6406617 -0.350422E-10 0.382E-04 2.84 92.6 T + 3 -12.6406617 0.134213E-09 0.145E-04 2.84 243.8 T + SCC iter. ... 0 min, 0.086 sec + gradient ... 0 min, 0.072 sec + * total energy : -12.4623282 Eh change -0.7892329E-08 Eh + gradient norm : 0.0000280 Eh/α predicted -0.5663934E-08 ( -28.23%) + displ. norm : 0.0006019 α lambda -0.4580349E-08 + maximum displ.: 0.0003958 α in ANC's #3, #1, #5, ... + + *** GEOMETRY OPTIMIZATION CONVERGED AFTER 7 ITERATIONS *** + +------------------------------------------------------------------------ + total energy gain : -0.0015276 Eh -0.9586 kcal/mol + total RMSD : 0.0466515 a0 0.0247 Å + total power (kW/mol): -0.5729750 (step) -2.1392 (real) +------------------------------------------------------------------------ + + ANCopt (total) 0 d, 0 h, 0 min, 1.875 sec + optimizer setup ... 0 min, 0.000 sec ( 0.004%) + model hessian ... 0 min, 0.005 sec ( 0.244%) + ANC generation ... 0 min, 0.000 sec ( 0.018%) + coordinate transformation ... 0 min, 0.000 sec ( 0.002%) + single point calculation ... 0 min, 1.852 sec ( 98.767%) + optimization log ... 0 min, 0.005 sec ( 0.263%) + hessian update ... 0 min, 0.012 sec ( 0.663%) + rational function ... 0 min, 0.000 sec ( 0.024%) + +================ + final structure: +================ +$coord + -2.19083616836090E+00 -8.75055545944093E-02 -7.12358508847116E-01 c + -1.70663821576948E-01 -7.21009080780027E-01 6.33951435929200E-01 c + 2.27150340995404E+00 5.39200343733434E-01 3.05747355748416E-01 c + 4.16185183882216E+00 4.56870795397582E-02 1.46958543963615E+00 o + -2.10906550336131E+00 1.39281538085596E+00 -2.11159862590894E+00 h + -3.98822887666127E+00 -1.01150815322938E+00 -4.74092464462499E-01 h + -2.30883305078883E-01 -2.20128348308961E+00 2.04098984698359E+00 h + 2.25632242626311E+00 2.04360346756428E+00 -1.15222446018155E+00 h +$eht charge=0 unpaired=0 +$periodic 0 +$end + + Bond Distances (Angstroems) + --------------------------- +C1-C2=1.3277 C1-H5=1.0788 C1-H6=1.0769 C2-C1=1.3277 C2-C3=1.4646 C2-H7=1.0812 +C3-C2=1.4646 C3-O4=1.2034 C3-H8=1.1086 O4-C3=1.2034 H5-C1=1.0788 H6-C1=1.0769 +H7-C2=1.0812 H8-C3=1.1086 + C H Rav=1.0864 sigma=0.0129 Rmin=1.0769 Rmax=1.1086 4 + C C Rav=1.3961 sigma=0.0684 Rmin=1.3277 Rmax=1.4646 2 + O C Rav=1.2034 sigma=0.0000 Rmin=1.2034 Rmax=1.2034 1 + + selected bond angles (degree) + -------------------- +H5-C1-C2=121.29 H6-C1-C2=122.26 H6-C1-H5=116.46 C3-C2-C1=122.13 +H7-C2-C1=121.92 H7-C2-C3=115.95 O4-C3-C2=125.03 H8-C3-C2=113.77 +H8-C3-O4=121.20 + + selected dihedral angles (degree) + --------------------------------- +C3-C2-C1-H5= 0.00 C3-C2-C1-H6=180.00 H7-C2-C1-H5=180.00 H7-C2-C1-H6= 0.00 +O4-C3-C2-C1=180.00 O4-C3-C2-H7= 0.00 H8-C3-C2-C1= 0.00 H8-C3-C2-H7=180.00 + ------------------------------------------------- + | Final Singlepoint | + ------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : # basis functions 20 : + : # atomic orbitals 20 : + : # shells 12 : + : # electrons 22 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -12.6406617 -0.126407E+02 0.236E-05 2.84 0.0 T + 2 -12.6406617 -0.268230E-12 0.173E-05 2.84 2046.9 T + 3 -12.6406617 -0.164846E-11 0.789E-06 2.84 4481.0 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.7184412 -19.5498 + ... ... ... ... + 5 2.0000 -0.5461831 -14.8624 + 6 2.0000 -0.5438191 -14.7981 + 7 2.0000 -0.5413599 -14.7312 + 8 2.0000 -0.4966851 -13.5155 + 9 2.0000 -0.4767594 -12.9733 + 10 2.0000 -0.4509688 -12.2715 + 11 2.0000 -0.4071929 -11.0803 (HOMO) + 12 -0.3027498 -8.2382 (LUMO) + 13 -0.1874306 -5.1002 + 14 0.0852857 2.3207 + 15 0.1253890 3.4120 + 16 0.1526653 4.1542 + ... ... ... + 20 0.6705004 18.2452 + ------------------------------------------------------------- + HL-Gap 0.1044431 Eh 2.8420 eV + Fermi-level -0.3549713 Eh -9.6593 eV + + SCC (total) 0 d, 0 h, 0 min, 0.181 sec + SCC setup ... 0 min, 0.000 sec ( 0.027%) + Dispersion ... 0 min, 0.000 sec ( 0.024%) + classical contributions ... 0 min, 0.000 sec ( 0.011%) + integral evaluation ... 0 min, 0.000 sec ( 0.094%) + iterations ... 0 min, 0.091 sec ( 50.144%) + molecular gradient ... 0 min, 0.090 sec ( 49.570%) + printout ... 0 min, 0.000 sec ( 0.120%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -12.462328236846 Eh :: + :: gradient norm 0.000028105045 Eh/a0 :: + :: HOMO-LUMO gap 2.842040266862 eV :: + ::.................................................:: + :: SCC energy -12.640661718123 Eh :: + :: -> isotropic ES 0.021865290434 Eh :: + :: -> anisotropic ES 0.000684189274 Eh :: + :: -> anisotropic XC 0.007134499414 Eh :: + :: -> dispersion -0.003195397865 Eh :: + :: repulsion energy 0.178333216781 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.7184412 -19.5498 + 2 2.0000 -0.6579346 -17.9033 + 3 2.0000 -0.6163375 -16.7714 + 4 2.0000 -0.5907356 -16.0747 + 5 2.0000 -0.5461831 -14.8624 + 6 2.0000 -0.5438191 -14.7981 + 7 2.0000 -0.5413599 -14.7312 + 8 2.0000 -0.4966851 -13.5155 + 9 2.0000 -0.4767594 -12.9733 + 10 2.0000 -0.4509688 -12.2715 + 11 2.0000 -0.4071929 -11.0803 (HOMO) + 12 -0.3027498 -8.2382 (LUMO) + 13 -0.1874306 -5.1002 + 14 0.0852857 2.3207 + 15 0.1253890 3.4120 + 16 0.1526653 4.1542 + 17 0.2277756 6.1981 + 18 0.3864171 10.5149 + 19 0.5019278 13.6582 + 20 0.6705004 18.2452 + ------------------------------------------------------------- + HL-Gap 0.1044431 Eh 2.8420 eV + Fermi-level -0.3549713 Eh -9.6593 eV + + # Z covCN q C6AA α(0) + 1 6 c 2.841 -0.062 29.538 8.907 + 2 6 c 2.886 -0.047 29.153 8.852 + 3 6 c 2.765 0.212 23.512 7.941 + 4 8 o 0.856 -0.322 20.178 6.023 + 5 1 h 0.926 0.062 2.175 2.306 + 6 1 h 0.926 0.065 2.137 2.286 + 7 1 h 0.926 0.072 2.062 2.245 + 8 1 h 0.922 0.019 2.753 2.595 + + Mol. C6AA /au·bohr⁶ : 683.380955 + Mol. C8AA /au·bohr⁸ : 15676.006174 + Mol. α(0) /au : 41.154406 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + + --------------------------------------------------------------------------- + # Z sym total # sym WBO # sym WBO # sym WBO + --------------------------------------------------------------------------- + 1 6 c 3.983 -- 2 c 1.902 6 h 0.976 5 h 0.972 + 4 o 0.103 + 2 6 c 3.988 -- 1 c 1.902 3 c 1.067 7 h 0.961 + 3 6 c 3.925 -- 4 o 1.882 2 c 1.067 8 h 0.929 + 4 8 o 2.089 -- 3 c 1.882 1 c 0.103 + 5 1 h 0.996 -- 1 c 0.972 + 6 1 h 0.996 -- 1 c 0.976 + 7 1 h 0.995 -- 2 c 0.961 + 8 1 h 1.000 -- 3 c 0.929 + --------------------------------------------------------------------------- + +Topologies differ in total number of bonds +Writing topology from bond orders to xtbtopo.mol + +molecular dipole: + x y z tot (Debye) + q only: -1.079 0.038 -0.429 + full: -1.243 0.100 -0.549 3.463 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: -3.634 0.578 2.387 -2.393 -0.733 1.247 + q+dip: -4.530 1.216 3.107 -2.925 -2.284 1.423 + full: -5.187 0.809 3.411 -3.503 -0.782 1.777 + + ------------------------------------------------- + | Geometry Summary | + ------------------------------------------------- + + molecular mass/u : 56.0633756 + center of mass at/Å : 0.5795684 -0.0215046 0.2315612 + moments of inertia/u·Å² : 0.1023246E+02 0.1083647E+03 0.1185971E+03 +rotational constants/cm⁻¹ : 0.1647466E+01 0.1555639E+00 0.1421420E+00 + + * 5 selected distances + + # Z # Z value/Å + 1 6 c 2 6 c 1.3276944 (max) + 3 6 c 4 8 o 1.2033974 + 1 6 c 5 1 h 1.0787833 + 1 6 c 6 1 h 1.0768688 (min) + 2 6 c 7 1 h 1.0812059 + + * 3 distinct bonds (by element types) + + Z Z # av. dist./Å max./Å min./Å + 1 H 6 C 3 1.0789527 1.0812059 1.0768688 + 6 C 6 C 1 1.3276944 1.3276944 1.3276944 + 6 C 8 O 1 1.2033974 1.2033974 1.2033974 + + +optimized geometry written to: xtbopt.in + + + ------------------------------------------------- + | TOTAL ENERGY -12.462328236846 Eh | + | GRADIENT NORM 0.000028105045 Eh/α | + | HOMO-LUMO GAP 2.842040266862 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/25 at 06:22:20.233 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 2.644 sec + * cpu-time: 0 d, 0 h, 1 min, 1.192 sec + * ratio c/w: 23.142 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.497 sec + * cpu-time: 0 d, 0 h, 0 min, 11.606 sec + * ratio c/w: 23.352 speedup + ANC optimizer: + * wall-time: 0 d, 0 h, 0 min, 2.057 sec + * cpu-time: 0 d, 0 h, 0 min, 47.500 sec + * ratio c/w: 23.091 speedup + diff --git a/arkane/data/xTB/xtb_opt_2.out b/arkane/data/xTB/xtb_opt_2.out new file mode 100644 index 00000000000..6441b296eea --- /dev/null +++ b/arkane/data/xTB/xtb_opt_2.out @@ -0,0 +1,581 @@ + ----------------------------------------------------------- + | ===================== | + | x T B | + | ===================== | + | S. Grimme | + | Mulliken Center for Theoretical Chemistry | + | University of Bonn | + ----------------------------------------------------------- + + * xtb version 6.3.3 (4ae9cef) compiled by 'conda@95abc7406d43' on 2020-10-14 + + xtb is free software: you can redistribute it and/or modify it under + the terms of the GNU Lesser General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + xtb is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Lesser General Public License for more details. + + Cite this work as: + * C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht, + J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, + e01493. DOI: 10.1002/wcms.1493 + + for GFN2-xTB: + * S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017, + 13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118 + for GFN1-xTB: + * C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, + 15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176 + for GFN0-xTB: + * P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint. + DOI: 10.26434/chemrxiv.8326202.v1 + for GFN-FF: + * S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673. + DOI: 10.1002/anie.202004239 + + for DFT-D4: + * E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017, + 147, 034112. DOI: 10.1063/1.4993215 + * E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher, + C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122. + DOI: 10.1063/1.5090222 + * E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys. + 2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A + + for sTDA-xTB: + * S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103. + DOI: 10.1063/1.4959605 + + in the mass-spec context: + * V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879. + DOI: 10.1039/c7sc00601b + * J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133. + DOI: 10.1021/acsomega.9b02011 + + for metadynamics refer to: + * S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862 + DOI: 10.1021/acs.jctc.9b00143 + + with help from (in alphabetical order) + C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher, M. Checinski, + S. Dohm, S. Ehlert, S. Ehrlich, F. März, H. Neugebauer, J. Pisarek, + P. Pracht, P. Shushkov, and S. Spicher. + + * started run on 2022/07/27 at 14:05:02.400 + + ------------------------------------------------- + | Calculation Setup | + ------------------------------------------------- + + program call : /home/alon/anaconda3/envs/arc_env/bin/xtb mol.sdf --opt tight --gfn2 --uhf 0 --chrg 0 + coordinate file : mol.sdf + omp threads : 24 + number of atoms : 11 + number of electrons : 20 + charge : 0 + spin : 0.0 + first test random number : 0.42084347216098 + + ID Z sym. atoms + 1 6 C 1-3 + 2 1 H 4-11 + + ------------------------------------------------- + | G F N 2 - x T B | + ------------------------------------------------- + + Reference 10.1021/acs.jctc.8b01176 + * Hamiltonian: + H0-scaling (s, p, d) 1.850000 2.230000 2.230000 + zeta-weighting 0.500000 + * Dispersion: + s8 2.700000 + a1 0.520000 + a2 5.000000 + s9 5.000000 + * Repulsion: + kExp 1.500000 1.000000 + rExp 1.000000 + * Coulomb: + alpha 2.000000 + third order shell-resolved + anisotropic true + a3 3.000000 + a5 4.000000 + cn-shift 1.200000 + cn-exp 4.000000 + max-rad 5.000000 + + + ................................................... + : SETUP : + :.................................................: + : # basis functions 20 : + : # atomic orbitals 20 : + : # shells 14 : + : # electrons 20 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -10.6257535 -0.106258E+02 0.262E+00 15.04 0.0 T + 2 -10.6592586 -0.335051E-01 0.136E+00 14.70 1.0 T + 3 -10.6595797 -0.321137E-03 0.727E-01 14.66 1.0 T + 4 -10.6596716 -0.918270E-04 0.975E-02 14.65 1.0 T + 5 -10.6596808 -0.927928E-05 0.548E-02 14.65 1.0 T + 6 -10.6596811 -0.270781E-06 0.248E-03 14.65 12.2 T + 7 -10.6596811 -0.645330E-08 0.776E-04 14.65 38.9 T + 8 -10.6596811 -0.600750E-09 0.158E-04 14.65 190.7 T + + *** convergence criteria satisfied after 8 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6141157 -16.7109 + ... ... ... ... + 4 2.0000 -0.5075529 -13.8112 + 5 2.0000 -0.4966123 -13.5135 + 6 2.0000 -0.4758975 -12.9498 + 7 2.0000 -0.4590074 -12.4902 + 8 2.0000 -0.4363473 -11.8736 + 9 2.0000 -0.4355067 -11.8507 + 10 2.0000 -0.4235531 -11.5255 (HOMO) + 11 0.1148616 3.1255 (LUMO) + 12 0.1332450 3.6258 + 13 0.1353284 3.6825 + 14 0.1550471 4.2190 + 15 0.1641699 4.4673 + ... ... ... + 20 0.2958208 8.0497 + ------------------------------------------------------------- + HL-Gap 0.5384146 Eh 14.6510 eV + Fermi-level -0.1543458 Eh -4.2000 eV + + SCC (total) 0 d, 0 h, 0 min, 0.126 sec + SCC setup ... 0 min, 0.006 sec ( 4.788%) + Dispersion ... 0 min, 0.005 sec ( 4.002%) + classical contributions ... 0 min, 0.010 sec ( 7.862%) + integral evaluation ... 0 min, 0.020 sec ( 15.738%) + iterations ... 0 min, 0.002 sec ( 1.196%) + molecular gradient ... 0 min, 0.084 sec ( 66.241%) + printout ... 0 min, 0.000 sec ( 0.158%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -10.500602584535 Eh :: + :: gradient norm 0.014504141544 Eh/a0 :: + :: HOMO-LUMO gap 14.651008068562 eV :: + ::.................................................:: + :: SCC energy -10.659681120107 Eh :: + :: -> isotropic ES 0.002421663158 Eh :: + :: -> anisotropic ES 0.004136237416 Eh :: + :: -> anisotropic XC 0.007405219779 Eh :: + :: -> dispersion -0.003960516702 Eh :: + :: repulsion energy 0.159077129515 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge -0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ----------------------------------------------------------- + | ===================== | + | A N C O P T | + | ===================== | + | Approximate Normal Coordinate | + | Rational Function Optimizer | + ----------------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : optimization level tight : + : max. optcycles 200 : + : ANC micro-cycles 20 : + : degrees of freedom 27 : + :.................................................: + : RF solver davidson : + : write xtbopt.log true : + : linear? false : + : energy convergence 0.1000000E-05 Eh : + : grad. convergence 0.8000000E-03 Eh/α : + : maximium RF displ. 1.0000000 : + : Hlow (freq-cutoff) 0.1000000E-01 : + : Hmax (freq-cutoff) 5.0000000 : + : S6 in model hess. 20.0000000 : + ................................................... + +generating ANC from model Hessian ... +Using Lindh-Hessian (1995) + Shifting diagonal of input Hessian by 1.0542808446694953E-003 + Lowest eigenvalues of input Hessian + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.010000 0.012412 0.013676 0.039432 0.050560 0.052472 + 0.056109 0.059606 0.069906 0.078238 0.102829 0.122909 + Highest eigenvalues + 1.079294 1.090462 1.096031 1.169699 1.218667 1.266731 + + +........................................................................ +.............................. CYCLE 1 .............................. +........................................................................ + 1 -10.6596811 -0.106597E+02 0.183E-05 14.65 0.0 T + 2 -10.6596811 -0.186873E-11 0.642E-06 14.65 4697.8 T + 3 -10.6596811 -0.888178E-14 0.354E-06 14.65 8510.9 T + SCC iter. ... 0 min, 0.001 sec + gradient ... 0 min, 0.093 sec + * total energy : -10.5006026 Eh change -0.5696776E-11 Eh + gradient norm : 0.0145036 Eh/α predicted 0.0000000E+00 (-100.00%) + displ. norm : 0.0410783 α lambda -0.3613972E-03 + maximum displ.: 0.0229545 α in ANC's #7, #18, #10, ... + +........................................................................ +.............................. CYCLE 2 .............................. +........................................................................ + 1 -10.6639670 -0.106640E+02 0.792E-02 14.54 0.0 T + 2 -10.6639706 -0.360924E-05 0.461E-02 14.55 1.0 T + 3 -10.6639708 -0.119603E-06 0.835E-03 14.55 3.6 T + 4 -10.6639708 -0.367680E-08 0.167E-03 14.55 18.0 T + 5 -10.6639708 -0.461146E-09 0.202E-04 14.55 148.9 T + 6 -10.6639708 -0.530154E-10 0.967E-05 14.55 311.8 T + SCC iter. ... 0 min, 0.001 sec + gradient ... 0 min, 0.073 sec + * total energy : -10.5008063 Eh change -0.2037127E-03 Eh + gradient norm : 0.0048232 Eh/α predicted -0.1810025E-03 ( -11.15%) + displ. norm : 0.0265167 α lambda -0.4226909E-04 + maximum displ.: 0.0240501 α in ANC's #3, #7, #26, ... + +........................................................................ +.............................. CYCLE 3 .............................. +........................................................................ + 1 -10.6653153 -0.106653E+02 0.238E-02 14.60 0.0 T + 2 -10.6653157 -0.477935E-06 0.131E-02 14.61 2.3 T + 3 -10.6653157 -0.529422E-08 0.346E-03 14.61 8.7 T + 4 -10.6653157 -0.570763E-09 0.338E-04 14.61 89.3 T + 5 -10.6653157 -0.408473E-10 0.143E-04 14.61 210.6 T + SCC iter. ... 0 min, 0.001 sec + gradient ... 0 min, 0.002 sec + * total energy : -10.5008271 Eh change -0.2077954E-04 Eh + gradient norm : 0.0008332 Eh/α predicted -0.2114876E-04 ( 1.78%) + displ. norm : 0.0043735 α lambda -0.1734380E-05 + maximum displ.: 0.0023370 α in ANC's #10, #18, #16, ... + +........................................................................ +.............................. CYCLE 4 .............................. +........................................................................ + 1 -10.6650453 -0.106650E+02 0.769E-03 14.58 0.0 T + 2 -10.6650453 -0.198656E-07 0.451E-03 14.58 6.7 T + 3 -10.6650453 0.365032E-09 0.902E-04 14.58 33.4 T + 4 -10.6650453 -0.244372E-08 0.174E-04 14.58 172.8 T + SCC iter. ... 0 min, 0.001 sec + gradient ... 0 min, 0.001 sec + * total energy : -10.5008281 Eh change -0.9891214E-06 Eh + gradient norm : 0.0002078 Eh/α predicted -0.8676407E-06 ( -12.28%) + displ. norm : 0.0013168 α lambda -0.1396974E-06 + maximum displ.: 0.0009773 α in ANC's #10, #16, #3, ... + + *** GEOMETRY OPTIMIZATION CONVERGED AFTER 4 ITERATIONS *** + +------------------------------------------------------------------------ + total energy gain : -0.0002255 Eh -0.1415 kcal/mol + total RMSD : 0.0156873 a0 0.0083 Å + total power (kW/mol): -0.1480003 (step) -1.8617 (real) +------------------------------------------------------------------------ + + ANCopt (total) 0 d, 0 h, 0 min, 0.318 sec + optimizer setup ... 0 min, 0.000 sec ( 0.031%) + model hessian ... 0 min, 0.001 sec ( 0.417%) + ANC generation ... 0 min, 0.000 sec ( 0.056%) + coordinate transformation ... 0 min, 0.000 sec ( 0.005%) + single point calculation ... 0 min, 0.305 sec ( 96.010%) + optimization log ... 0 min, 0.000 sec ( 0.146%) + hessian update ... 0 min, 0.010 sec ( 3.123%) + rational function ... 0 min, 0.000 sec ( 0.069%) + +================ + final structure: +================ + + xtb 07272214053D +xtb: 6.3.3 (4ae9cef) + 11 10 0 0 0 999 V2000 + 1.2769 -0.0581 -0.1002 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1342 -0.6020 0.0867 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1766 0.5082 0.0354 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3672 0.4420 -1.0623 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0080 -0.8624 -0.0611 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5140 0.6603 0.6818 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1997 -1.1163 1.0482 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3465 -1.3346 -0.6954 H 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1394 1.0205 -0.9237 H 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9926 1.2388 0.8204 H 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1772 0.1036 0.1703 H 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 4 1 0 0 0 0 + 1 5 1 0 0 0 0 + 1 6 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 7 1 0 0 0 0 + 2 8 1 0 0 0 0 + 3 9 1 0 0 0 0 + 3 10 1 0 0 0 0 + 3 11 1 0 0 0 0 +M END +$$$$ + + Bond Distances (Angstroems) + --------------------------- +C1-C2=1.5238 C1-H4=1.0881 C1-H5=1.0877 C1-H6=1.0881 C2-C1=1.5238 C2-C3=1.5238 +C2-H7=1.0924 C2-H8=1.0924 C3-C2=1.5238 C3-H9=1.0881 C3-H10=1.0881 C3-H11=1.0877 +H4-C1=1.0881 H5-C1=1.0877 H6-C1=1.0881 H7-C2=1.0924 H8-C2=1.0924 H9-C3=1.0881 +H10-C3=1.0881 H11-C3=1.0877 + C H Rav=1.0890 sigma=0.0019 Rmin=1.0877 Rmax=1.0924 8 + C C Rav=1.5238 sigma=0.0000 Rmin=1.5238 Rmax=1.5238 2 + + selected bond angles (degree) + -------------------- +H4-C1-C2=110.45 H5-C1-C2=110.74 H5-C1-H4=108.42 H6-C1-C2=110.45 +H6-C1-H4=108.30 H6-C1-H5=108.42 C3-C2-C1=111.67 H7-C2-C1=109.36 +H7-C2-C3=109.36 H8-C2-C1=109.36 H8-C2-C3=109.36 H8-C2-H7=107.62 +H9-C3-C2=110.45 H10-C3-C2=110.45 H10-C3-H9=108.30 H11-C3-C2=110.74 +H11-C3-H9=108.42 H11-C3-H10=108.42 + + selected dihedral angles (degree) + --------------------------------- +C3-C2-C1-H4=300.11 C3-C2-C1-H5=180.00 C3-C2-C1-H6= 59.89 H7-C2-C1-H4=178.92 +H7-C2-C1-H5= 58.81 H7-C2-C1-H6=298.70 H8-C2-C1-H4= 61.30 H8-C2-C1-H5=301.19 +H8-C2-C1-H6=181.08 H9-C3-C2-C1= 59.89 H9-C3-C2-H7=181.08 H9-C3-C2-H8=298.70 +H10-C3-C2-C1=300.11 H10-C3-C2-H7= 61.30 H10-C3-C2-H8=178.92 H11-C3-C2-C1=180.00 +H11-C3-C2-H7=301.19 H11-C3-C2-H8= 58.81 + ------------------------------------------------- + | Final Singlepoint | + ------------------------------------------------- + + ................................................... + : SETUP : + :.................................................: + : # basis functions 20 : + : # atomic orbitals 20 : + : # shells 14 : + : # electrons 20 : + : max. iterations 250 : + : Hamiltonian GFN2-xTB : + : restarted? false : + : GBSA solvation false : + : PC potential false : + : electronic temp. 300.0000000 K : + : accuracy 1.0000000 : + : -> integral cutoff 0.2500000E+02 : + : -> integral neglect 0.1000000E-07 : + : -> SCF convergence 0.1000000E-05 Eh : + : -> wf. convergence 0.1000000E-03 e : + : Broyden damping 0.4000000 : + ................................................... + + iter E dE RMSdq gap omega full diag + 1 -10.6650453 -0.106650E+02 0.159E-05 14.58 0.0 T + 2 -10.6650453 -0.103029E-12 0.839E-06 14.58 3592.6 T + 3 -10.6650453 -0.319744E-13 0.138E-06 14.58 21857.7 T + + *** convergence criteria satisfied after 3 iterations *** + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6139733 -16.7071 + ... ... ... ... + 4 2.0000 -0.5076449 -13.8137 + 5 2.0000 -0.4966410 -13.5143 + 6 2.0000 -0.4754813 -12.9385 + 7 2.0000 -0.4592433 -12.4966 + 8 2.0000 -0.4372767 -11.8989 + 9 2.0000 -0.4351047 -11.8398 + 10 2.0000 -0.4239161 -11.5353 (HOMO) + 11 0.1118565 3.0438 (LUMO) + 12 0.1369565 3.7268 + 13 0.1421186 3.8672 + 14 0.1615191 4.3952 + 15 0.1721476 4.6844 + ... ... ... + 20 0.3019726 8.2171 + ------------------------------------------------------------- + HL-Gap 0.5357725 Eh 14.5791 eV + Fermi-level -0.1560298 Eh -4.2458 eV + + SCC (total) 0 d, 0 h, 0 min, 0.003 sec + SCC setup ... 0 min, 0.000 sec ( 3.294%) + Dispersion ... 0 min, 0.000 sec ( 2.217%) + classical contributions ... 0 min, 0.000 sec ( 8.298%) + integral evaluation ... 0 min, 0.001 sec ( 17.199%) + iterations ... 0 min, 0.001 sec ( 16.169%) + molecular gradient ... 0 min, 0.002 sec ( 48.964%) + printout ... 0 min, 0.000 sec ( 3.463%) + + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: SUMMARY :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + :: total energy -10.500828065933 Eh :: + :: gradient norm 0.000207649002 Eh/a0 :: + :: HOMO-LUMO gap 14.579112365988 eV :: + ::.................................................:: + :: SCC energy -10.665045349979 Eh :: + :: -> isotropic ES 0.002528651431 Eh :: + :: -> anisotropic ES 0.003983113400 Eh :: + :: -> anisotropic XC 0.007221858086 Eh :: + :: -> dispersion -0.003957748634 Eh :: + :: repulsion energy 0.164215907898 Eh :: + :: add. restraining 0.000000000000 Eh :: + :: total charge 0.000000000000 e :: + ::::::::::::::::::::::::::::::::::::::::::::::::::::: + + ------------------------------------------------- + | Property Printout | + ------------------------------------------------- + + * Orbital Energies and Occupations + + # Occupation Energy/Eh Energy/eV + ------------------------------------------------------------- + 1 2.0000 -0.6139733 -16.7071 + 2 2.0000 -0.5841211 -15.8947 + 3 2.0000 -0.5539146 -15.0728 + 4 2.0000 -0.5076449 -13.8137 + 5 2.0000 -0.4966410 -13.5143 + 6 2.0000 -0.4754813 -12.9385 + 7 2.0000 -0.4592433 -12.4966 + 8 2.0000 -0.4372767 -11.8989 + 9 2.0000 -0.4351047 -11.8398 + 10 2.0000 -0.4239161 -11.5353 (HOMO) + 11 0.1118565 3.0438 (LUMO) + 12 0.1369565 3.7268 + 13 0.1421186 3.8672 + 14 0.1615191 4.3952 + 15 0.1721476 4.6844 + 16 0.2031947 5.5292 + 17 0.2316279 6.3029 + 18 0.2598538 7.0710 + 19 0.2690539 7.3213 + 20 0.3019726 8.2171 + ------------------------------------------------------------- + HL-Gap 0.5357725 Eh 14.5791 eV + Fermi-level -0.1560298 Eh -4.2458 eV + + # Z covCN q C6AA α(0) + 1 6 C 3.752 -0.102 22.510 6.766 + 2 6 C 3.799 -0.047 21.425 6.591 + 3 6 C 3.752 -0.102 22.510 6.766 + 4 1 H 0.925 0.034 2.536 2.490 + 5 1 H 0.925 0.031 2.575 2.509 + 6 1 H 0.925 0.034 2.536 2.490 + 7 1 H 0.924 0.028 2.619 2.531 + 8 1 H 0.924 0.028 2.619 2.531 + 9 1 H 0.925 0.034 2.536 2.490 + 10 1 H 0.925 0.034 2.536 2.490 + 11 1 H 0.925 0.031 2.575 2.509 + + Mol. C6AA /au·bohr⁶ : 723.105058 + Mol. C8AA /au·bohr⁸ : 14472.819828 + Mol. α(0) /au : 40.162759 + + +Wiberg/Mayer (AO) data. +largest (>0.10) Wiberg bond orders for each atom + + --------------------------------------------------------------------------- + # Z sym total # sym WBO # sym WBO # sym WBO + --------------------------------------------------------------------------- + 1 6 C 3.997 -- 2 C 1.020 6 H 0.988 4 H 0.988 + 5 H 0.988 + 2 6 C 3.998 -- 3 C 1.020 1 C 1.020 7 H 0.980 + 8 H 0.980 + 3 6 C 3.997 -- 2 C 1.020 10 H 0.988 9 H 0.988 + 11 H 0.988 + 4 1 H 0.999 -- 1 C 0.988 + 5 1 H 0.999 -- 1 C 0.988 + 6 1 H 0.999 -- 1 C 0.988 + 7 1 H 0.999 -- 2 C 0.980 + 8 1 H 0.999 -- 2 C 0.980 + 9 1 H 0.999 -- 3 C 0.988 + 10 1 H 0.999 -- 3 C 0.988 + 11 1 H 0.999 -- 3 C 0.988 + --------------------------------------------------------------------------- + + +molecular dipole: + x y z tot (Debye) + q only: 0.002 0.008 -0.001 + full: 0.002 0.008 -0.001 0.022 +molecular quadrupole (traceless): + xx xy yy xz yz zz + q only: 0.082 -0.016 0.020 -0.014 -0.014 -0.103 + q+dip: -0.632 0.159 -0.003 0.088 0.069 0.635 + full: -0.283 0.071 -0.003 0.040 0.031 0.286 + + ------------------------------------------------- + | Geometry Summary | + ------------------------------------------------- + + molecular mass/u : 44.0957337 + center of mass at/Å : -0.0084579 -0.0379007 0.0054656 + moments of inertia/u·Å² : 0.1719555E+02 0.5890379E+02 0.6669384E+02 +rotational constants/cm⁻¹ : 0.9803483E+00 0.2861893E+00 0.2527615E+00 + + * 10 selected distances + + # Z # Z value/Å + 1 6 C 2 6 C 1.5237754 (max) + 2 6 C 3 6 C 1.5237752 + 1 6 C 4 1 H 1.0880501 + 1 6 C 5 1 H 1.0876612 (min) + 1 6 C 6 1 H 1.0880512 + 2 6 C 7 1 H 1.0923587 + 2 6 C 8 1 H 1.0923585 + 3 6 C 9 1 H 1.0880513 + 3 6 C 10 1 H 1.0880515 + 3 6 C 11 1 H 1.0876616 + + * 2 distinct bonds (by element types) + + Z Z # av. dist./Å max./Å min./Å + 1 H 6 C 8 1.0890305 1.0923587 1.0876612 + 6 C 6 C 2 1.5237753 1.5237754 1.5237752 + + +optimized geometry written to: xtbopt.sdf + + + ------------------------------------------------- + | TOTAL ENERGY -10.500828065933 Eh | + | GRADIENT NORM 0.000207649002 Eh/α | + | HOMO-LUMO GAP 14.579112365988 eV | + ------------------------------------------------- + +------------------------------------------------------------------------ + * finished run on 2022/07/27 at 14:05:02.907 +------------------------------------------------------------------------ + total: + * wall-time: 0 d, 0 h, 0 min, 0.506 sec + * cpu-time: 0 d, 0 h, 0 min, 10.210 sec + * ratio c/w: 20.159 speedup + SCF: + * wall-time: 0 d, 0 h, 0 min, 0.126 sec + * cpu-time: 0 d, 0 h, 0 min, 2.633 sec + * ratio c/w: 20.855 speedup + ANC optimizer: + * wall-time: 0 d, 0 h, 0 min, 0.322 sec + * cpu-time: 0 d, 0 h, 0 min, 6.501 sec + * ratio c/w: 20.186 speedup + diff --git a/test/arkane/ess/xtbTest.py b/test/arkane/ess/xtbTest.py new file mode 100644 index 00000000000..5a11e499a7e --- /dev/null +++ b/test/arkane/ess/xtbTest.py @@ -0,0 +1,348 @@ +#!/usr/bin/env python3 + +############################################################################### +# # +# RMG - Reaction Mechanism Generator # +# # +# Copyright (c) 2002-2023 Prof. William H. Green (whgreen@mit.edu), # +# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu) # +# # +# Permission is hereby granted, free of charge, to any person obtaining a # +# copy of this software and associated documentation files (the 'Software'), # +# to deal in the Software without restriction, including without limitation # +# the rights to use, copy, modify, merge, publish, distribute, sublicense, # +# and/or sell copies of the Software, and to permit persons to whom the # +# Software is furnished to do so, subject to the following conditions: # +# # +# The above copyright notice and this permission notice shall be included in # +# all copies or substantial portions of the Software. # +# # +# THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER # +# DEALINGS IN THE SOFTWARE. # +# # +############################################################################### + +"""Tests for the xTB ESS adapter.""" + +import os + +import numpy as np +import pytest + +import rmgpy.constants as constants +from arkane.exceptions import LogError +from arkane.ess.factory import ess_factory +from arkane.ess.xtb import XTBLog + +DATA_PATH = os.path.join(os.path.dirname(os.path.dirname(__file__)), '..', '..', 'arkane', 'data', 'xTB') + + +class TestFactory: + + def test_detects_freq(self): + assert isinstance(ess_factory(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False), XTBLog) + + def test_detects_opt(self): + assert isinstance(ess_factory(os.path.join(DATA_PATH, 'output.out'), check_for_errors=False), XTBLog) + + def test_detects_co2(self): + assert isinstance(ess_factory(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False), XTBLog) + + def test_detects_ts(self): + assert isinstance(ess_factory(os.path.join(DATA_PATH, 'TS_NH2+N2H3_xtb.out'), check_for_errors=False), XTBLog) + + def test_detects_sp(self): + assert isinstance(ess_factory(os.path.join(DATA_PATH, 'NCC_xTB.out'), check_for_errors=False), XTBLog) + + +class TestGetNumberOfAtoms: + + def test_freq_c3h7(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + assert log.get_number_of_atoms() == 10 + + def test_opt_c3h7(self): + log = XTBLog(os.path.join(DATA_PATH, 'output.out'), check_for_errors=False) + assert log.get_number_of_atoms() == 10 + + def test_co2(self): + """CO2 opt+freq output (Turbomol $coord format).""" + log = XTBLog(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False) + assert log.get_number_of_atoms() == 3 + + def test_opt2_c3h11(self): + log = XTBLog(os.path.join(DATA_PATH, 'xtb_opt_2.out'), check_for_errors=False) + assert log.get_number_of_atoms() == 11 + + +class TestGeometryV2000: + + def test_opt_c3h7_shape(self): + log = XTBLog(os.path.join(DATA_PATH, 'output.out'), check_for_errors=False) + coord, number, mass = log.load_geometry() + assert coord.shape == (10, 3) + assert len(number) == 10 + + def test_opt_c3h7_atoms(self): + log = XTBLog(os.path.join(DATA_PATH, 'output.out'), check_for_errors=False) + _, number, _ = log.load_geometry() + assert list(number[:3]) == [6, 6, 6] + assert all(n == 1 for n in number[3:]) + + def test_opt_c3h7_coords(self): + log = XTBLog(os.path.join(DATA_PATH, 'output.out'), check_for_errors=False) + coord, _, _ = log.load_geometry() + np.testing.assert_allclose(coord[0], [-1.2948, 0.0509, -0.1043], atol=1e-4) + + def test_opt2_v2000(self): + """xtb_opt_2.out uses V2000 format with 11 atoms.""" + log = XTBLog(os.path.join(DATA_PATH, 'xtb_opt_2.out'), check_for_errors=False) + coord, number, mass = log.load_geometry() + assert coord.shape == (11, 3) + assert sum(number == 6) == 3 # 3 carbons + assert sum(number == 1) == 8 # 8 hydrogens + + +class TestGeometryTurbomol: + + def test_co2_shape(self): + """CO2 opt output uses $coord (Bohr) format.""" + log = XTBLog(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False) + coord, number, mass = log.load_geometry() + assert coord.shape == (3, 3) + + def test_co2_atoms(self): + log = XTBLog(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False) + _, number, _ = log.load_geometry() + assert list(number) == [8, 6, 8] # O, C, O + + def test_co2_linearity(self): + """CO2 should be linear — central C at ~origin, O atoms symmetric.""" + log = XTBLog(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False) + coord, _, _ = log.load_geometry() + # Central carbon should be near origin + assert abs(coord[1, 0]) < 0.01 + # O atoms should be roughly symmetric about C + np.testing.assert_allclose(coord[0, 0], -coord[2, 0], atol=0.01) + + def test_opt1_turbomol(self): + """xtb_opt_1.out uses $coord Turbomol format with 8 atoms.""" + log = XTBLog(os.path.join(DATA_PATH, 'xtb_opt_1.out'), check_for_errors=False) + coord, number, mass = log.load_geometry() + assert coord.shape == (8, 3) + assert sum(number == 6) == 3 # 3 C + assert sum(number == 8) == 1 # 1 O + assert sum(number == 1) == 4 # 4 H + + def test_opt1_units_are_angstrom(self): + """Verify Bohr→Angstrom conversion: C-O bond ~1.14 Å, not ~2.16 Bohr.""" + log = XTBLog(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False) + coord, _, _ = log.load_geometry() + co_dist = np.linalg.norm(coord[0] - coord[1]) + assert 1.0 < co_dist < 1.3 # C=O bond is ~1.14 Å + + +class TestGeometryFreqOnly: + + def test_freq_only_raises(self): + """Freq-only (--hess) output has no embedded geometry.""" + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + with pytest.raises(LogError): + log.load_geometry() + + +class TestEnergy: + + def test_freq_c3h7(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + energy = log.load_energy() + expected = -9.907945789911 * constants.E_h * constants.Na + assert abs(energy - expected) < abs(expected) * 1e-6 + + def test_opt_c3h7(self): + log = XTBLog(os.path.join(DATA_PATH, 'output.out'), check_for_errors=False) + energy = log.load_energy() + expected = -9.907945789911 * constants.E_h * constants.Na + assert abs(energy - expected) < abs(expected) * 1e-6 + + def test_co2(self): + """CO2: total energy -10.308452243026 Eh.""" + log = XTBLog(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False) + energy = log.load_energy() + expected = -10.308452243026 * constants.E_h * constants.Na + assert abs(energy - expected) < abs(expected) * 1e-6 + + def test_sp_ncc(self): + """Single point NCC: -10.752192838993 Eh.""" + log = XTBLog(os.path.join(DATA_PATH, 'NCC_xTB.out'), check_for_errors=False) + energy = log.load_energy() + expected = -10.752192838993 * constants.E_h * constants.Na + assert abs(energy - expected) < abs(expected) * 1e-6 + + def test_ts(self): + log = XTBLog(os.path.join(DATA_PATH, 'TS_NH2+N2H3_xtb.out'), check_for_errors=False) + energy = log.load_energy() + assert energy < 0 # should be negative + + def test_units_j_per_mol(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + energy = log.load_energy() + assert energy < 0 + assert abs(energy) > 1e6 # millions of J/mol + + +class TestZPE: + + def test_freq_c3h7(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + zpe = log.load_zero_point_energy() + expected = 0.086665171024 * constants.E_h * constants.Na + assert abs(zpe - expected) < abs(expected) * 1e-6 + assert zpe > 0 + + def test_ts_zpe(self): + """TS_NH2+N2H3: ZPE = 0.056690417480 Eh.""" + log = XTBLog(os.path.join(DATA_PATH, 'TS_NH2+N2H3_xtb.out'), check_for_errors=False) + zpe = log.load_zero_point_energy() + expected = 0.056690417480 * constants.E_h * constants.Na + assert abs(zpe - expected) < abs(expected) * 1e-6 + + def test_opt_only_raises(self): + log = XTBLog(os.path.join(DATA_PATH, 'output.out'), check_for_errors=False) + with pytest.raises(LogError): + log.load_zero_point_energy() + + def test_sp_raises(self): + log = XTBLog(os.path.join(DATA_PATH, 'NCC_xTB.out'), check_for_errors=False) + with pytest.raises(LogError): + log.load_zero_point_energy() + + +class TestFrequencies: + + def test_c3h7_count(self): + """C3H7 (10 atoms): 3*10 - 6 = 24 real vibrational modes.""" + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + freqs = log._load_frequencies() + assert len(freqs) == 24 + + def test_c3h7_values(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + freqs = log._load_frequencies() + assert abs(freqs[0] - 63.60) < 0.1 + assert abs(freqs[-1] - 3104.88) < 0.1 + assert all(f > 0 for f in freqs) + + def test_co2_frequencies(self): + """CO2 (3 atoms, linear): 3*3 - 5 = 4 real modes.""" + log = XTBLog(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False) + freqs = log._load_frequencies() + np.testing.assert_allclose(freqs, [600.70, 600.70, 1424.29, 2592.18], atol=0.01) + + def test_ts_frequencies(self): + """TS should have real frequencies (imaginary excluded by _load_frequencies).""" + log = XTBLog(os.path.join(DATA_PATH, 'TS_NH2+N2H3_xtb.out'), check_for_errors=False) + freqs = log._load_frequencies() + assert all(f > 0 for f in freqs) + # TS has 8 atoms, 3*8 - 6 - 1(imaginary) = 17 real modes + assert len(freqs) == 17 + + def test_opt_only_no_freqs(self): + """Optimization-only output without --hess should have no frequencies.""" + log = XTBLog(os.path.join(DATA_PATH, 'NCC_xTB.out'), check_for_errors=False) + freqs = log._load_frequencies() + assert freqs == [] + + +class TestNegativeFrequency: + + def test_ts_imaginary(self): + """TS_NH2+N2H3 should have one imaginary frequency at ~-781.89 cm^-1.""" + log = XTBLog(os.path.join(DATA_PATH, 'TS_NH2+N2H3_xtb.out'), check_for_errors=False) + neg_freq = log.load_negative_frequency() + assert abs(neg_freq - (-781.89)) < 0.1 + + def test_stable_molecule_raises(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + with pytest.raises(LogError): + log.load_negative_frequency() + + +class TestSpinMultiplicity: + + def test_c3h7_doublet(self): + """C3H7 radical: spin=0.5, multiplicity=2.""" + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + assert log._load_spin_multiplicity() == 2 + + def test_co2_singlet(self): + """CO2 closed-shell: should default to singlet.""" + log = XTBLog(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False) + mult = log._load_spin_multiplicity() + assert mult == 1 + + +class TestConformer: + + def test_opt_c3h7(self): + """Conformer from optimization output (has geometry, no freqs).""" + log = XTBLog(os.path.join(DATA_PATH, 'output.out'), check_for_errors=False) + conformer, unscaled_freqs = log.load_conformer( + symmetry=1, spin_multiplicity=2, optical_isomers=1, label='C3H7') + assert conformer.spin_multiplicity == 2 + assert conformer.optical_isomers == 1 + mode_types = [type(m).__name__ for m in conformer.modes] + assert 'IdealGasTranslation' in mode_types + assert 'NonlinearRotor' in mode_types + + def test_co2_linear_rotor(self): + """CO2 is linear — conformer should have LinearRotor.""" + log = XTBLog(os.path.join(DATA_PATH, 'CO2_xtb.out'), check_for_errors=False) + conformer, freqs = log.load_conformer( + symmetry=2, spin_multiplicity=1, optical_isomers=1, label='CO2') + mode_types = [type(m).__name__ for m in conformer.modes] + assert 'LinearRotor' in mode_types + assert 'HarmonicOscillator' in mode_types + assert len(freqs) == 4 # CO2: 4 real modes + + def test_opt1_turbomol(self): + """Conformer from Turbomol $coord geometry.""" + log = XTBLog(os.path.join(DATA_PATH, 'xtb_opt_1.out'), check_for_errors=False) + conformer, freqs = log.load_conformer( + symmetry=1, spin_multiplicity=1, optical_isomers=1, label='test') + assert conformer is not None + mode_types = [type(m).__name__ for m in conformer.modes] + assert 'IdealGasTranslation' in mode_types + + def test_freq_only_raises(self): + """Freq-only output can't build conformer (no geometry).""" + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + with pytest.raises(LogError): + log.load_conformer(symmetry=1, spin_multiplicity=2, optical_isomers=1) + + +class TestUnsupported: + + def test_force_constant_matrix(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + assert log.load_force_constant_matrix() is None + + def test_scan_energies(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + with pytest.raises(NotImplementedError): + log.load_scan_energies() + + def test_scan_pivot_atoms(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + with pytest.raises(NotImplementedError): + log.load_scan_pivot_atoms() + + def test_scan_frozen_atoms(self): + log = XTBLog(os.path.join(DATA_PATH, 'freq.out'), check_for_errors=False) + with pytest.raises(NotImplementedError): + log.load_scan_frozen_atoms() From 3cb793b9c9b2fbe7704449978126946316044e82 Mon Sep 17 00:00:00 2001 From: Jackson Burns <33505528+JacksonBurns@users.noreply.github.com> Date: Thu, 9 Apr 2026 14:20:47 -0400 Subject: [PATCH 3/3] only run python 3.9 conda build on PRs --- .github/workflows/conda_build.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/conda_build.yml b/.github/workflows/conda_build.yml index 8df959e3822..9ec44a364ed 100644 --- a/.github/workflows/conda_build.yml +++ b/.github/workflows/conda_build.yml @@ -23,19 +23,19 @@ jobs: # for PRs just run a single build per platform to save time and resources - is_pr: true os: ubuntu-latest - python-version: "3.9" + python-version: "3.11" - is_pr: true os: ubuntu-latest python-version: "3.10" - is_pr: true os: macos-15-intel - python-version: "3.9" + python-version: "3.11" - is_pr: true os: macos-15-intel python-version: "3.10" - is_pr: true os: macos-latest - python-version: "3.9" + python-version: "3.11" - is_pr: true os: macos-latest python-version: "3.10"