From dda14dbbb0af8c551a5368e10c1e80d13a13b880 Mon Sep 17 00:00:00 2001 From: Alex Epstein Date: Thu, 10 Jun 2021 18:41:17 -0700 Subject: [PATCH 01/25] Linear molecules + units Tried to use more built-in units. Added functionality for checking if linear and adjusting rotational entropy accordingly. Added testing for linear molecule --- pymatgen/analysis/quasirrho.py | 139 +- pymatgen/analysis/tests/test_quasirrho.py | 37 +- test_files/molecules/co2.log | 2025 +++++++++++++++++++++ 3 files changed, 2123 insertions(+), 78 deletions(-) create mode 100644 test_files/molecules/co2.log diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 5862f2ccde8..0f6e26a5fb8 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -15,26 +15,25 @@ __maintainer__ = "Alex Epstein" __email__ = "aepstein@lbl.gov" __date__ = "January 5, 2021" -__credits__ = "Steven Wheeler, Trevor Seguin" +__credits__ = "Steven Wheeler, Trevor Seguin, Evan Spotte-Smith" from typing import Union import numpy as np from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.qchem.outputs import QCOutput +from math import isclose +from pymatgen.core.units import amu_to_kg, kb as kb_ev +import scipy.constants as const # Define useful constants -kb = 1.380662E-23 # J/K -c = 29979245800 # cm/s -h = 6.62606957E-34 # J.s -R = 1.987204 # kcal/mol +kb = kb_ev * const.eV # pymatgen kb from ev/K to J/K +c = const.speed_of_light * 100 # cm/s +h = const.h # Planck's constant J.s +R = const.R / const.calorie # Ideal gas constant cal/mol # Define useful conversion factors -cm2kcal = 0.0028591459 -cm2hartree = 4.5563352812122E-06 -kcal2hartree = 0.0015936 -amu2kg = 1.66053886E-27 -bohr2angs = 0.52917721092 +kcal2hartree = 0.0015936 # kcal/mol to hartree/mol class QuasiRRHO: @@ -43,9 +42,9 @@ class QuasiRRHO: All outputs are in atomic units. """ - def __init__(self, output: Union[GaussianOutput, QCOutput, dict], - sigma_r=1, temp=298.15, press=101317, conc=1, - v0=100): + def __init__( + self, output: Union[GaussianOutput, QCOutput, dict], sigma_r=1, temp=298.15, press=101317, conc=1, v0=100 + ): """ :param output: Requires input of a Gaussian output file, @@ -53,11 +52,11 @@ def __init__(self, output: Union[GaussianOutput, QCOutput, dict], {"mol": Molecule, "mult": spin multiplicity (int), "frequencies": list of vibrational frequencies [a.u.], elec_energy": electronic energy [a.u.]} - :param sigma_r: Rotational symmetry number - :param temp: Temperature [K] - :param press: Pressure [Pa] - :param conc: Solvent concentration [M] - :param v0: Cutoff frequency for Quasi-RRHO method [cm^1] + :param sigma_r (int): Rotational symmetry number + :param temp (float): Temperature [K] + :param press (float): Pressure [Pa] + :param conc (float): Solvent concentration [M] + :param v0 (float): Cutoff frequency for Quasi-RRHO method [cm^1] """ # TO-DO: calculate sigma_r with PointGroupAnalyzer @@ -73,38 +72,40 @@ def __init__(self, output: Union[GaussianOutput, QCOutput, dict], self.free_energy_quasiRRHO = None # Ha self.concentration_corrected_g_quasiRRHO = None # Ha + self.entropy_ho = None # Ha/K + self.free_energy_ho = None # Ha + if isinstance(output, GaussianOutput): mult = output.spin_multiplicity sigma_r = self.sigma_r elec_e = output.final_energy mol = output.final_structure - vib_freqs = [f['frequency'] for f in output.frequencies[-1]] + vib_freqs = [f["frequency"] for f in output.frequencies[-1]] - self._get_quasirrho_thermo(mol=mol, mult=mult, sigma_r=sigma_r, - frequencies=vib_freqs, - elec_energy=elec_e) + self._get_quasirrho_thermo(mol=mol, mult=mult, sigma_r=sigma_r, frequencies=vib_freqs, elec_energy=elec_e) if isinstance(output, QCOutput): - mult = output.data['multiplicity'] + mult = output.data["multiplicity"] elec_e = output.data["SCF_energy_in_the_final_basis_set"] if output.data["optimization"]: mol = output.data["molecule_from_last_geometry"] else: mol = output.data["initial_molecule"] - frequencies = output.data['frequencies'] + frequencies = output.data["frequencies"] - self._get_quasirrho_thermo(mol=mol, mult=mult, - sigma_r=self.sigma_r, - frequencies=frequencies, - elec_energy=elec_e) + self._get_quasirrho_thermo( + mol=mol, mult=mult, sigma_r=self.sigma_r, frequencies=frequencies, elec_energy=elec_e + ) if isinstance(output, dict): - self._get_quasirrho_thermo(mol=output["mol"], - mult=output["mult"], - sigma_r=self.sigma_r, - frequencies=output["frequencies"], - elec_energy=output["elec_energy"]) + self._get_quasirrho_thermo( + mol=output["mol"], + mult=output["mult"], + sigma_r=self.sigma_r, + frequencies=output["frequencies"], + elec_energy=output["elec_energy"], + ) def get_avg_mom_inertia(self, mol): """ @@ -118,37 +119,34 @@ def get_avg_mom_inertia(self, mol): c = site.coords wt = site.specie.atomic_mass for i in range(3): - inertia_tensor[i, i] += wt * ( - c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2 - ) + inertia_tensor[i, i] += wt * (c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2) for i, j in [(0, 1), (1, 2), (0, 2)]: inertia_tensor[i, j] += -wt * c[i] * c[j] inertia_tensor[j, i] += -wt * c[j] * c[i] inertia_eigenvals = np.multiply( - np.linalg.eig(inertia_tensor)[0], - amu2kg * 1E-20).tolist() # amuangs^2 to kg m^2 + np.linalg.eig(inertia_tensor)[0], amu_to_kg * 1e-20 + ).tolist() # amuangs^2 to kg m^2 iav = np.average(inertia_eigenvals) return iav, inertia_eigenvals - def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, - elec_energy): + def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): """ Caclulate Quasi-RRHO thermochemistry :param mol: Molecule :param mult: Spin multiplicity :param sigma_r: Rotational symmetry number :param frequencies: List of frequencies [a.u.] - :param elec_energy: Electornic energy [a.u.] + :param elec_energy: Electronic energy [a.u.] """ # Calculate mass in kg mass = 0 for site in mol.sites: mass += site.specie.atomic_mass - mass *= amu2kg + mass *= amu_to_kg # Calculate vibrational temperatures vib_temps = [] @@ -156,51 +154,66 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, if f > 0: vib_temps.append(f * c * h / kb) - # Get properties related to rotational symmetry. Bav is average moment of inertia - Bav, i_eigen = self.get_avg_mom_inertia(mol) - rot_temps = [h ** 2 / (np.pi ** 2 * kb * 8 * i) for i in i_eigen] - # Translational component of entropy and energy - qt = (2 * np.pi * mass * kb * self.temp / (h * h)) ** ( - 3 / 2) * kb * self.temp / self.press + qt = (2 * np.pi * mass * kb * self.temp / (h * h)) ** (3 / 2) * kb * self.temp / self.press st = R * (np.log(qt) + 5 / 2) et = 3 * R * self.temp / 2 # Electronic component of Entropy se = R * np.log(mult) + # Get properties related to rotational symmetry. Bav is average moment of inertia + Bav, i_eigen = self.get_avg_mom_inertia(mol) + + # Check if linear + coords = mol.cart_coords + v0 = coords[1] - coords[0] + linear = True + for coord in coords[1:]: + theta = abs(np.dot(coord - coords[0], v0) / np.linalg.norm(coord - coords[0]) / np.linalg.norm(v0)) + if not isclose(theta, 1, abs_tol=1e-4): + linear = False + # Rotational component of Entropy and Energy - qr = np.sqrt(np.pi) / sigma_r * self.temp ** (3 / 2) / np.sqrt( - rot_temps[0] * rot_temps[1] * rot_temps[2]) - sr = R * (np.log(qr) + 3 / 2) - er = 3 * R * self.temp / 2 + if linear: + i = np.amax(i_eigen) + qr = 8 * np.pi ** 2 * i * kb * self.temp / (sigma_r * (h * h)) + sr = R * (np.log(qr) + 1) + er = R * self.temp + else: + rot_temps = [h ** 2 / (np.pi ** 2 * kb * 8 * i) for i in i_eigen] + qr = np.sqrt(np.pi) / sigma_r * self.temp ** (3 / 2) / np.sqrt(rot_temps[0] * rot_temps[1] * rot_temps[2]) + sr = R * (np.log(qr) + 3 / 2) + er = 3 * R * self.temp / 2 # Vibrational component of Entropy and Energy ev = 0 sv_quasiRRHO = 0 + sv = 0 for vt in vib_temps: ev += vt * (1 / 2 + 1 / (np.exp(vt / self.temp) - 1)) - sv_temp = vt / (self.temp * (np.exp(vt / self.temp) - 1)) - np.log( - 1 - np.exp(-vt / self.temp)) + sv_temp = vt / (self.temp * (np.exp(vt / self.temp) - 1)) - np.log(1 - np.exp(-vt / self.temp)) + sv += sv_temp + mu = h / (8 * np.pi ** 2 * vt * c) mu_prime = mu * Bav / (mu + Bav) - srotor = 1 / 2 + np.log( - np.sqrt(8 * np.pi ** 3 * mu_prime * kb * self.temp / h ** 2)) + srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi ** 3 * mu_prime * kb * self.temp / h ** 2)) weight = 1 / (1 + (self.v0 / vt) ** 4) sv_quasiRRHO += weight * sv_temp + (1 - weight) * srotor sv_quasiRRHO *= R + sv *= R ev *= R etot = (et + er + ev) * kcal2hartree / 1000 h_corrected = etot + R * self.temp * kcal2hartree / 1000 - molarity_corr = 0.000003166488448771253 * self.temp * np.log( - 0.082057338 * self.temp * self.conc) + molarity_corr = 0.000003166488448771253 * self.temp * np.log(0.082057338 * self.temp * self.conc) + self.entropy_ho = st + sr + sv + se + self.free_energy_ho = elec_energy + h_corrected - (self.temp * self.entropy_ho * kcal2hartree / 1000) self.entropy_quasiRRHO = st + sr + sv_quasiRRHO + se - self.free_energy_quasiRRHO = (elec_energy + h_corrected - - (self.temp * self.entropy_quasiRRHO - * kcal2hartree / 1000)) + self.free_energy_quasiRRHO = ( + elec_energy + h_corrected - (self.temp * self.entropy_quasiRRHO * kcal2hartree / 1000) + ) - self.concentration_corrected_g_quasiRRHO = ( - self.free_energy_quasiRRHO + molarity_corr) + self.concentration_corrected_g_quasiRRHO = self.free_energy_quasiRRHO + molarity_corr diff --git a/pymatgen/analysis/tests/test_quasirrho.py b/pymatgen/analysis/tests/test_quasirrho.py index 96119a02313..be271f7bc25 100644 --- a/pymatgen/analysis/tests/test_quasirrho.py +++ b/pymatgen/analysis/tests/test_quasirrho.py @@ -6,7 +6,6 @@ """ import os -import unittest from pymatgen.analysis.quasirrho import QuasiRRHO from pymatgen.io.gaussian import GaussianOutput @@ -21,12 +20,9 @@ class TestQuasiRRHO(PymatgenTest): def setUp(self): test_dir = self.TEST_FILES_DIR - self.gout = GaussianOutput( - os.path.join(test_dir, "molecules", "quasirrho_gaufreq.log")) - self.qout = QCOutput(os.path.join(test_dir, - "molecules", - "new_qchem_files", - "Frequency_no_equal.qout")) + self.gout = GaussianOutput(os.path.join(test_dir, "molecules", "quasirrho_gaufreq.log")) + self.linear_gout = GaussianOutput(os.path.join(test_dir, "molecules", "co2.log")) + self.qout = QCOutput(os.path.join(test_dir, "molecules", "new_qchem_files", "Frequency_no_equal.qout")) def test_qrrho_gaussian(self): """ @@ -40,8 +36,7 @@ def test_qrrho_gaussian(self): qrrho = QuasiRRHO(self.gout, conc=m) self.assertAlmostEqual(correct_stot, qrrho.entropy_quasiRRHO, 0) self.assertAlmostEqual(correct_g, qrrho.free_energy_quasiRRHO, 3) - self.assertAlmostEqual(correct_g_conc, - qrrho.concentration_corrected_g_quasiRRHO, 3) + self.assertAlmostEqual(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO, 3) def test_qrrho_qchem(self): """ @@ -58,8 +53,7 @@ def test_qrrho_qchem(self): qrrho = QuasiRRHO(self.qout, conc=m) self.assertAlmostEqual(correct_stot, qrrho.entropy_quasiRRHO, 0) self.assertAlmostEqual(correct_g, qrrho.free_energy_quasiRRHO, 3) - self.assertAlmostEqual(correct_g_conc, - qrrho.concentration_corrected_g_quasiRRHO, 3) + self.assertAlmostEqual(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO, 3) def test_rrho_manual(self): """ @@ -69,8 +63,8 @@ def test_rrho_manual(self): rrho_in["mult"] = self.gout.spin_multiplicity rrho_in["elec_energy"] = self.gout.final_energy rrho_in["mol"] = self.gout.final_structure - vib_freqs = [f['frequency'] for f in self.gout.frequencies[-1]] - rrho_in['frequencies'] = vib_freqs + vib_freqs = [f["frequency"] for f in self.gout.frequencies[-1]] + rrho_in["frequencies"] = vib_freqs m = 55 correct_g_conc = -884.770084 @@ -79,5 +73,18 @@ def test_rrho_manual(self): qrrho = QuasiRRHO(rrho_in, conc=m) self.assertAlmostEqual(correct_stot, qrrho.entropy_quasiRRHO, 0) self.assertAlmostEqual(correct_g, qrrho.free_energy_quasiRRHO, 3) - self.assertAlmostEqual(correct_g_conc, - qrrho.concentration_corrected_g_quasiRRHO, 3) + self.assertAlmostEqual(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO, 3) + + def test_rrho_linear(self): + """ + Testing on a linear CO2 molecule from Gaussian Output file. + Correct free_energy_ho is checked with Gaussian's internal calculation. + Correct free_energy_quasirrho is compared internally in the hope of + preventing future errors. + . + """ + correct_g_ho = -187.642070 + correct_g_qrrho = -187.642725 + qrrho = QuasiRRHO(self.linear_gout) + self.assertAlmostEqual(correct_g_ho, qrrho.free_energy_ho, 2) + self.assertAlmostEqual(correct_g_qrrho, qrrho.free_energy_quasiRRHO, 2) diff --git a/test_files/molecules/co2.log b/test_files/molecules/co2.log new file mode 100644 index 00000000000..f996a83090d --- /dev/null +++ b/test_files/molecules/co2.log @@ -0,0 +1,2025 @@ + Entering Gaussian System, Link 0=g16 + Initial command: + /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1.exe "/global/scratch/alex_epstein/line_c2o/Gau-207402.inp" -scrdir="/global/scratch/alex_epstein/line_c2o/" + Default is to use a total of 32 processors: + 32 via shared-memory + 1 via Linda + Entering Link 1 = /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1.exe PID= 207403. + + Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2016, + Gaussian, Inc. All Rights Reserved. + + This is part of the Gaussian(R) 16 program. It is based on + the Gaussian(R) 09 system (copyright 2009, Gaussian, Inc.), + the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.), + the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), + the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), + the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), + the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), + the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), + the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon + University), and the Gaussian 82(TM) system (copyright 1983, + Carnegie Mellon University). Gaussian is a federally registered + trademark of Gaussian, Inc. + + This software contains proprietary and confidential information, + including trade secrets, belonging to Gaussian, Inc. + + This software is provided under written license and may be + used, copied, transmitted, or stored only in accord with that + written license. + + The following legend is applicable only to US Government + contracts under FAR: + + RESTRICTED RIGHTS LEGEND + + Use, reproduction and disclosure by the US Government is + subject to restrictions as set forth in subparagraphs (a) + and (c) of the Commercial Computer Software - Restricted + Rights clause in FAR 52.227-19. + + Gaussian, Inc. + 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 + + + --------------------------------------------------------------- + Warning -- This program may not be used in any manner that + competes with the business of Gaussian, Inc. or will provide + assistance to any competitor of Gaussian, Inc. The licensee + of this program is prohibited from giving any competitor of + Gaussian, Inc. access to this program. By using this program, + the user acknowledges that Gaussian, Inc. is engaged in the + business of creating and licensing software in the field of + computational chemistry and represents and warrants to the + licensee that it is not a competitor of Gaussian, Inc. and that + it will not use this program in any manner prohibited above. + --------------------------------------------------------------- + + + Cite this work as: + Gaussian 16, Revision A.03, + M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, + M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, + G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, + J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, + J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, + F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, + T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, + G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, + J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, + T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, + F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin, + V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, + K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, + J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, + J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, + J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016. + + ****************************************** + Gaussian 16: ES64L-G16RevA.03 25-Dec-2016 + 10-Jun-2021 + ****************************************** + ------------------------------------------------- + #P HF/6-31g(d) freq=noraman opt=(noeigen, calcfc) + ------------------------------------------------- + 1/10=4,11=1,18=20,19=15,38=1/1,3; + 2/9=110,12=2,17=6,18=5,40=1/2; + 3/5=1,6=6,7=1,11=9,25=1,30=1,71=2,140=1/1,2,3; + 4//1; + 5/5=2,38=5/2; + 8/6=4,10=90,11=11/1; + 11/6=1,8=1,9=11,15=111,16=1/1,2,10; + 10/6=1,13=1/2; + 6/7=2,8=2,9=2,10=2,28=1/1; + 7/10=1,18=20,25=1/1,2,3,16; + 1/10=4,11=1,18=20,19=15/3(2); + 2/9=110/2; + 99//99; + 2/9=110/2; + 3/5=1,6=6,7=1,11=9,25=1,30=1,71=1/1,2,3; + 4/5=5,16=3,69=1/1; + 5/5=2,38=5/2; + 7//1,2,3,16; + 1/11=1,18=20,19=15/3(-5); + 2/9=110/2; + 6/7=2,8=2,9=2,10=2,19=2,28=1/1; + 99/9=1/99; + Leave Link 1 at Thu Jun 10 18:05:48 2021, MaxMem= 0 cpu: 6.0 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l101.exe) + ------------------- + co2 for linear test + ------------------- + Symbolic Z-matrix: + Charge = 0 Multiplicity = 1 + O -0.81185 -0.38536 3.24234 + O 1.18899 0. 1.98561 + C 0.18857 -0.19268 2.61398 + + ITRead= 0 0 0 + MicOpt= -1 -1 -1 + NAtoms= 3 NQM= 3 NQMF= 0 NMMI= 0 NMMIF= 0 + NMic= 0 NMicF= 0. + Isotopes and Nuclear Properties: + (Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM) + in nuclear magnetons) + + Atom 1 2 3 + IAtWgt= 16 16 12 + AtmWgt= 15.9949146 15.9949146 12.0000000 + NucSpn= 0 0 0 + AtZEff= -0.0000000 -0.0000000 -0.0000000 + NQMom= 0.0000000 0.0000000 0.0000000 + NMagM= 0.0000000 0.0000000 0.0000000 + AtZNuc= 8.0000000 8.0000000 6.0000000 + Leave Link 101 at Thu Jun 10 18:05:49 2021, MaxMem= 4800000000 cpu: 11.2 elap: 0.4 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Initialization pass. + ---------------------------- + ! Initial Parameters ! + ! (Angstroms and Degrees) ! + -------------------------- -------------------------- + ! Name Definition Value Derivative Info. ! + -------------------------------------------------------------------------------- + ! R1 R(1,3) 1.197 calculate D2E/DX2 analytically ! + ! R2 R(2,3) 1.197 calculate D2E/DX2 analytically ! + ! A1 L(1,3,2,-2,-1) 180.0 calculate D2E/DX2 analytically ! + ! A2 L(1,3,2,-3,-2) 180.0 calculate D2E/DX2 analytically ! + -------------------------------------------------------------------------------- + Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 EigMax=2.50D+02 EigMin=1.00D-04 + Number of steps in this run= 20 maximum allowed number of steps= 100. + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Thu Jun 10 18:05:49 2021, MaxMem= 4800000000 cpu: 2.2 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 -0.811852 -0.385361 3.242336 + 2 8 0 1.188993 0.000000 1.985615 + 3 6 0 0.188571 -0.192681 2.613975 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 O 2.394000 0.000000 + 3 C 1.197000 1.197000 0.000000 + Stoichiometry CO2 + Framework group D*H[O(C),C*(O.O)] + Deg. of freedom 1 + Full point group D*H NOp 8 + Largest Abelian subgroup D2H NOp 8 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 0.000000 0.000000 1.197000 + 2 8 0 0.000000 0.000000 -1.197000 + 3 6 0 0.000000 0.000000 0.000000 + --------------------------------------------------------------------- + Rotational constants (GHZ): 0.0000000 11.0259743 11.0259743 + Leave Link 202 at Thu Jun 10 18:05:50 2021, MaxMem= 4800000000 cpu: 0.7 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l301.exe) + Standard basis: 6-31G(d) (6D, 7F) + Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. + There are 14 symmetry adapted cartesian basis functions of AG symmetry. + There are 2 symmetry adapted cartesian basis functions of B1G symmetry. + There are 4 symmetry adapted cartesian basis functions of B2G symmetry. + There are 4 symmetry adapted cartesian basis functions of B3G symmetry. + There are 1 symmetry adapted cartesian basis functions of AU symmetry. + There are 10 symmetry adapted cartesian basis functions of B1U symmetry. + There are 5 symmetry adapted cartesian basis functions of B2U symmetry. + There are 5 symmetry adapted cartesian basis functions of B3U symmetry. + There are 14 symmetry adapted basis functions of AG symmetry. + There are 2 symmetry adapted basis functions of B1G symmetry. + There are 4 symmetry adapted basis functions of B2G symmetry. + There are 4 symmetry adapted basis functions of B3G symmetry. + There are 1 symmetry adapted basis functions of AU symmetry. + There are 10 symmetry adapted basis functions of B1U symmetry. + There are 5 symmetry adapted basis functions of B2U symmetry. + There are 5 symmetry adapted basis functions of B3U symmetry. + 45 basis functions, 84 primitive gaussians, 45 cartesian basis functions + 11 alpha electrons 11 beta electrons + nuclear repulsion energy 56.5870367581 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 + IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 + NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F + Integral buffers will be 131072 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned on. + Leave Link 301 at Thu Jun 10 18:05:50 2021, MaxMem= 4800000000 cpu: 5.0 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l302.exe) + NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 + NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. + One-electron integrals computed using PRISM. + One-electron integral symmetry used in STVInt + NBasis= 45 RedAO= T EigKep= 2.89D-03 NBF= 14 2 4 4 1 10 5 5 + NBsUse= 45 1.00D-06 EigRej= -1.00D+00 NBFU= 14 2 4 4 1 10 5 5 + Leave Link 302 at Thu Jun 10 18:05:51 2021, MaxMem= 4800000000 cpu: 4.8 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l303.exe) + DipDrv: MaxL=1. + Leave Link 303 at Thu Jun 10 18:05:51 2021, MaxMem= 4800000000 cpu: 1.5 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l401.exe) + ExpMin= 1.69D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=3 IRadAn= 5 AccDes= 0.00D+00 + Harris functional with IExCor= 205 and IRadAn= 5 diagonalized for initial guess. + HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 5 IDoV= 1 UseB2=F ITyADJ=14 + ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000 + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 + NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T + wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Harris En= -187.643581197863 + JPrj=0 DoOrth=F DoCkMO=F. + Initial guess orbital symmetries: + Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) + (PIU) (PIG) (PIG) + Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) + (SGG) (PIG) (PIG) (SGU) (PIU) (PIU) (SGG) (PIG) + (PIG) (DLTG) (DLTG) (DLTU) (DLTU) (SGU) (DLTG) + (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) + (SGG) (SGG) (SGU) + The electronic state of the initial guess is 1-SGG. + Leave Link 401 at Thu Jun 10 18:05:52 2021, MaxMem= 4800000000 cpu: 11.4 elap: 0.4 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l502.exe) + Keep R1 ints in memory in symmetry-blocked form, NReq=7134157. + FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Closed shell SCF: + Using DIIS extrapolation, IDIIS= 1040. + NGot= 4800000000 LenX= 4799912550 LenY= 4799910084 + Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. + Requested convergence on MAX density matrix=1.00D-06. + Requested convergence on energy=1.00D-06. + No special actions if energy rises. + + Cycle 1 Pass 1 IDiag 1: + E= -187.546707470472 + DIIS: error= 6.33D-02 at cycle 1 NSaved= 1. + NSaved= 1 IEnMin= 1 EnMin= -187.546707470472 IErMin= 1 ErrMin= 6.33D-02 + ErrMax= 6.33D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.94D-01 BMatP= 1.94D-01 + IDIUse=3 WtCom= 3.67D-01 WtEn= 6.33D-01 + Coeff-Com: 0.100D+01 + Coeff-En: 0.100D+01 + Coeff: 0.100D+01 + Gap= 0.676 Goal= None Shift= 0.000 + GapD= 0.676 DampG=2.000 DampE=0.500 DampFc=1.0000 IDamp=-1. + RMSDP=6.43D-03 MaxDP=7.26D-02 OVMax= 6.99D-02 + + Cycle 2 Pass 1 IDiag 1: + E= -187.595924288405 Delta-E= -0.049216817934 Rises=F Damp=F + DIIS: error= 2.63D-02 at cycle 2 NSaved= 2. + NSaved= 2 IEnMin= 2 EnMin= -187.595924288405 IErMin= 2 ErrMin= 2.63D-02 + ErrMax= 2.63D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.59D-02 BMatP= 1.94D-01 + IDIUse=3 WtCom= 7.37D-01 WtEn= 2.63D-01 + Coeff-Com: 0.238D+00 0.762D+00 + Coeff-En: 0.344D-01 0.966D+00 + Coeff: 0.184D+00 0.816D+00 + Gap= 0.740 Goal= None Shift= 0.000 + RMSDP=3.36D-03 MaxDP=3.52D-02 DE=-4.92D-02 OVMax= 6.26D-02 + + Cycle 3 Pass 1 IDiag 1: + E= -187.616366824535 Delta-E= -0.020442536129 Rises=F Damp=F + DIIS: error= 1.34D-02 at cycle 3 NSaved= 3. + NSaved= 3 IEnMin= 3 EnMin= -187.616366824535 IErMin= 3 ErrMin= 1.34D-02 + ErrMax= 1.34D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 7.66D-03 BMatP= 3.59D-02 + IDIUse=3 WtCom= 8.66D-01 WtEn= 1.34D-01 + Coeff-Com: -0.360D-01 0.293D+00 0.743D+00 + Coeff-En: 0.000D+00 0.334D-01 0.967D+00 + Coeff: -0.311D-01 0.258D+00 0.773D+00 + Gap= 0.721 Goal= None Shift= 0.000 + RMSDP=1.06D-03 MaxDP=1.47D-02 DE=-2.04D-02 OVMax= 1.60D-02 + + Cycle 4 Pass 1 IDiag 1: + E= -187.621353362497 Delta-E= -0.004986537963 Rises=F Damp=F + DIIS: error= 1.58D-03 at cycle 4 NSaved= 4. + NSaved= 4 IEnMin= 4 EnMin= -187.621353362497 IErMin= 4 ErrMin= 1.58D-03 + ErrMax= 1.58D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.04D-05 BMatP= 7.66D-03 + IDIUse=3 WtCom= 9.84D-01 WtEn= 1.58D-02 + Coeff-Com: 0.207D-02-0.487D-01-0.427D-01 0.109D+01 + Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.100D+01 + Coeff: 0.203D-02-0.479D-01-0.420D-01 0.109D+01 + Gap= 0.725 Goal= None Shift= 0.000 + RMSDP=1.58D-04 MaxDP=2.13D-03 DE=-4.99D-03 OVMax= 3.68D-03 + + Cycle 5 Pass 1 IDiag 1: + E= -187.621425151085 Delta-E= -0.000071788588 Rises=F Damp=F + DIIS: error= 5.17D-04 at cycle 5 NSaved= 5. + NSaved= 5 IEnMin= 5 EnMin= -187.621425151085 IErMin= 5 ErrMin= 5.17D-04 + ErrMax= 5.17D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 4.47D-06 BMatP= 5.04D-05 + IDIUse=3 WtCom= 9.95D-01 WtEn= 5.17D-03 + Coeff-Com: 0.253D-02-0.216D-01-0.716D-01-0.281D-01 0.112D+01 + Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.100D+01 + Coeff: 0.252D-02-0.215D-01-0.712D-01-0.280D-01 0.112D+01 + Gap= 0.725 Goal= None Shift= 0.000 + RMSDP=6.56D-05 MaxDP=9.16D-04 DE=-7.18D-05 OVMax= 9.83D-04 + + Cycle 6 Pass 1 IDiag 1: + E= -187.621431407661 Delta-E= -0.000006256576 Rises=F Damp=F + DIIS: error= 7.99D-05 at cycle 6 NSaved= 6. + NSaved= 6 IEnMin= 6 EnMin= -187.621431407661 IErMin= 6 ErrMin= 7.99D-05 + ErrMax= 7.99D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.39D-07 BMatP= 4.47D-06 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.876D-03 0.101D-01 0.248D-01-0.543D-01-0.344D+00 0.136D+01 + Coeff: -0.876D-03 0.101D-01 0.248D-01-0.543D-01-0.344D+00 0.136D+01 + Gap= 0.725 Goal= None Shift= 0.000 + RMSDP=1.64D-05 MaxDP=1.76D-04 DE=-6.26D-06 OVMax= 2.85D-04 + + Cycle 7 Pass 1 IDiag 1: + E= -187.621431721890 Delta-E= -0.000000314229 Rises=F Damp=F + DIIS: error= 1.03D-05 at cycle 7 NSaved= 7. + NSaved= 7 IEnMin= 7 EnMin= -187.621431721890 IErMin= 7 ErrMin= 1.03D-05 + ErrMax= 1.03D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.17D-09 BMatP= 1.39D-07 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.122D-03-0.158D-02-0.362D-02 0.120D-01 0.499D-01-0.305D+00 + Coeff-Com: 0.125D+01 + Coeff: 0.122D-03-0.158D-02-0.362D-02 0.120D-01 0.499D-01-0.305D+00 + Coeff: 0.125D+01 + Gap= 0.725 Goal= None Shift= 0.000 + RMSDP=2.05D-06 MaxDP=2.19D-05 DE=-3.14D-07 OVMax= 3.28D-05 + + Cycle 8 Pass 1 IDiag 1: + E= -187.621431725649 Delta-E= -0.000000003760 Rises=F Damp=F + DIIS: error= 8.83D-07 at cycle 8 NSaved= 8. + NSaved= 8 IEnMin= 8 EnMin= -187.621431725649 IErMin= 8 ErrMin= 8.83D-07 + ErrMax= 8.83D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.90D-11 BMatP= 2.17D-09 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.880D-05 0.120D-03 0.258D-03-0.128D-02-0.328D-02 0.277D-01 + Coeff-Com: -0.175D+00 0.115D+01 + Coeff: -0.880D-05 0.120D-03 0.258D-03-0.128D-02-0.328D-02 0.277D-01 + Coeff: -0.175D+00 0.115D+01 + Gap= 0.725 Goal= None Shift= 0.000 + RMSDP=1.51D-07 MaxDP=1.58D-06 DE=-3.76D-09 OVMax= 2.29D-06 + + Cycle 9 Pass 1 IDiag 1: + E= -187.621431725679 Delta-E= -0.000000000030 Rises=F Damp=F + DIIS: error= 1.00D-07 at cycle 9 NSaved= 9. + NSaved= 9 IEnMin= 9 EnMin= -187.621431725679 IErMin= 9 ErrMin= 1.00D-07 + ErrMax= 1.00D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.42D-13 BMatP= 1.90D-11 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.353D-06 0.381D-05 0.104D-04-0.648D-05-0.199D-03 0.118D-02 + Coeff-Com: -0.417D-02-0.101D+00 0.110D+01 + Coeff: -0.353D-06 0.381D-05 0.104D-04-0.648D-05-0.199D-03 0.118D-02 + Coeff: -0.417D-02-0.101D+00 0.110D+01 + Gap= 0.725 Goal= None Shift= 0.000 + RMSDP=1.45D-08 MaxDP=1.29D-07 DE=-2.96D-11 OVMax= 2.57D-07 + + Cycle 10 Pass 1 IDiag 1: + E= -187.621431725679 Delta-E= -0.000000000000 Rises=F Damp=F + DIIS: error= 1.28D-08 at cycle 10 NSaved= 10. + NSaved=10 IEnMin=10 EnMin= -187.621431725679 IErMin=10 ErrMin= 1.28D-08 + ErrMax= 1.28D-08 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.78D-15 BMatP= 2.42D-13 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.960D-07-0.116D-05-0.278D-05 0.745D-05 0.528D-04-0.399D-03 + Coeff-Com: 0.221D-02 0.986D-02-0.221D+00 0.121D+01 + Coeff: 0.960D-07-0.116D-05-0.278D-05 0.745D-05 0.528D-04-0.399D-03 + Coeff: 0.221D-02 0.986D-02-0.221D+00 0.121D+01 + Gap= 0.725 Goal= None Shift= 0.000 + RMSDP=3.14D-09 MaxDP=3.10D-08 DE=-2.27D-13 OVMax= 3.54D-08 + + SCF Done: E(RHF) = -187.621431726 A.U. after 10 cycles + NFock= 10 Conv=0.31D-08 -V/T= 2.0055 + KE= 1.865922906646D+02 PE=-5.554229239539D+02 EE= 1.246221648055D+02 + Leave Link 502 at Thu Jun 10 18:05:53 2021, MaxMem= 4800000000 cpu: 7.3 elap: 0.3 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l801.exe) + Range of M.O.s used for correlation: 1 45 + NBasis= 45 NAE= 11 NBE= 11 NFC= 0 NFV= 0 + NROrb= 45 NOA= 11 NOB= 11 NVA= 34 NVB= 34 + Leave Link 801 at Thu Jun 10 18:05:54 2021, MaxMem= 4800000000 cpu: 1.9 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1101.exe) + Using compressed storage, NAtomX= 3. + Will process 4 centers per pass. + Leave Link 1101 at Thu Jun 10 18:05:54 2021, MaxMem= 4800000000 cpu: 5.6 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1102.exe) + Symmetrizing basis deriv contribution to polar: + IMax=3 JMax=2 DiffMx= 0.00D+00 + Leave Link 1102 at Thu Jun 10 18:05:55 2021, MaxMem= 4800000000 cpu: 2.4 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1110.exe) + Forming Gx(P) for the SCF density, NAtomX= 3. + Integral derivatives from FoFJK, PRISM(SPDF). + Do as many integral derivatives as possible in FoFJK. + G2DrvN: MDV= 4799999660. + G2DrvN: will do 4 centers at a time, making 1 passes. + Calling FoFCou, ICntrl= 3107 FMM=F I1Cent= 0 AccDes= 0.00D+00. + FoFJK: IHMeth= 1 ICntrl= 3107 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 3107 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + End of G2Drv F.D. properties file 721 does not exist. + End of G2Drv F.D. properties file 722 does not exist. + End of G2Drv F.D. properties file 788 does not exist. + Leave Link 1110 at Thu Jun 10 18:05:55 2021, MaxMem= 4800000000 cpu: 5.8 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1002.exe) + Minotr: Closed shell wavefunction. + IDoAtm=111 + Direct CPHF calculation. + Differentiating once with respect to nuclear coordinates. + Using symmetry in CPHF. + Requested convergence is 1.0D-08 RMS, and 1.0D-07 maximum. + Secondary convergence is 1.0D-12 RMS, and 1.0D-12 maximum. + NewPWx=T KeepS1=F KeepF1=F KeepIn=T MapXYZ=F SortEE=F KeepMc=T. + Keep R1 ints in memory in symmetry-blocked form, NReq=7134362. + FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + MDV= 4800000000 using IRadAn= 1. + Solving linear equations simultaneously, MaxMat= 0. + There are 9 degrees of freedom in the 1st order CPHF. IDoFFX=4 NUNeed= 9. + 6 vectors produced by pass 0 Test12= 4.16D-15 1.11D-08 XBig12= 6.90D-02 1.06D-01. + AX will form 6 AO Fock derivatives at one time. + 6 vectors produced by pass 1 Test12= 4.16D-15 1.11D-08 XBig12= 1.67D-02 7.48D-02. + 6 vectors produced by pass 2 Test12= 4.16D-15 1.11D-08 XBig12= 1.51D-03 2.09D-02. + 6 vectors produced by pass 3 Test12= 4.16D-15 1.11D-08 XBig12= 9.09D-05 4.01D-03. + 6 vectors produced by pass 4 Test12= 4.16D-15 1.11D-08 XBig12= 1.09D-06 3.95D-04. + 6 vectors produced by pass 5 Test12= 4.16D-15 1.11D-08 XBig12= 7.27D-09 2.77D-05. + 6 vectors produced by pass 6 Test12= 4.16D-15 1.11D-08 XBig12= 3.31D-11 1.52D-06. + 6 vectors produced by pass 7 Test12= 4.16D-15 1.11D-08 XBig12= 1.89D-13 1.38D-07. + 1 vectors produced by pass 8 Test12= 4.16D-15 1.11D-08 XBig12= 1.15D-15 1.24D-08. + InvSVY: IOpt=1 It= 1 EMax= 4.44D-16 + Solved reduced A of dimension 49 with 6 vectors. + FullF1: Do perturbations 4 to 9. + End of Minotr F.D. properties file 721 does not exist. + End of Minotr F.D. properties file 722 does not exist. + End of Minotr F.D. properties file 788 does not exist. + Leave Link 1002 at Thu Jun 10 18:05:56 2021, MaxMem= 4800000000 cpu: 6.8 elap: 0.3 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l601.exe) + Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0. + + ********************************************************************** + + Population analysis using the SCF density. + + ********************************************************************** + + Orbital symmetries: + Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) + (PIU) (PIG) (PIG) + Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) + (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (PIG) + (PIG) (DLTG) (DLTG) (DLTU) (DLTU) (SGU) (DLTG) + (DLTG) (PIU) (PIU) (SGG) (PIG) (PIG) (SGU) (SGG) + (SGG) (SGG) (SGU) + The electronic state is 1-SGG. + Alpha occ. eigenvalues -- -20.67031 -20.67029 -11.48878 -1.51161 -1.45747 + Alpha occ. eigenvalues -- -0.79885 -0.72959 -0.69633 -0.69633 -0.53680 + Alpha occ. eigenvalues -- -0.53680 + Alpha virt. eigenvalues -- 0.18784 0.18784 0.24518 0.51387 0.67053 + Alpha virt. eigenvalues -- 0.67053 0.78559 0.94979 0.99832 1.14995 + Alpha virt. eigenvalues -- 1.14995 1.31539 1.31539 1.33343 1.58692 + Alpha virt. eigenvalues -- 1.65218 1.65218 1.65329 1.65329 2.01750 + Alpha virt. eigenvalues -- 2.01750 2.08060 2.30593 2.30593 2.40379 + Alpha virt. eigenvalues -- 2.40379 2.96934 3.25089 3.25089 3.25688 + Alpha virt. eigenvalues -- 3.38018 4.10539 4.76452 4.83832 + Condensed to atoms (all electrons): + 1 2 3 + 1 O 7.909034 -0.027930 0.584117 + 2 O -0.027930 7.909034 0.584117 + 3 C 0.584117 0.584117 3.901325 + Mulliken charges: + 1 + 1 O -0.465221 + 2 O -0.465221 + 3 C 0.930442 + Sum of Mulliken charges = -0.00000 + Mulliken charges with hydrogens summed into heavy atoms: + 1 + 1 O -0.465221 + 2 O -0.465221 + 3 C 0.930442 + APT charges: + 1 + 1 O -0.222397 + 2 O -0.222397 + 3 C 0.444794 + Sum of APT charges = -0.00000 + APT charges with hydrogens summed into heavy atoms: + 1 + 1 O -0.222397 + 2 O -0.222397 + 3 C 0.444794 + Electronic spatial extent (au): = 118.8759 + Charge= 0.0000 electrons + Dipole moment (field-independent basis, Debye): + X= 0.0000 Y= 0.0000 Z= -0.0000 Tot= 0.0000 + Quadrupole moment (field-independent basis, Debye-Ang): + XX= -14.7300 YY= -14.7300 ZZ= -20.3189 + XY= -0.0000 XZ= 0.0000 YZ= 0.0000 + Traceless Quadrupole moment (field-independent basis, Debye-Ang): + XX= 1.8629 YY= 1.8629 ZZ= -3.7259 + XY= -0.0000 XZ= 0.0000 YZ= 0.0000 + Octapole moment (field-independent basis, Debye-Ang**2): + XXX= 0.0000 YYY= 0.0000 ZZZ= 0.0000 XYY= 0.0000 + XXY= 0.0000 XXZ= 0.0000 XZZ= 0.0000 YZZ= 0.0000 + YYZ= 0.0000 XYZ= 0.0000 + Hexadecapole moment (field-independent basis, Debye-Ang**3): + XXXX= -10.6612 YYYY= -10.6612 ZZZZ= -108.1601 XXXY= -0.0000 + XXXZ= 0.0000 YYYX= -0.0000 YYYZ= 0.0000 ZZZX= 0.0000 + ZZZY= 0.0000 XXYY= -3.5537 XXZZ= -19.5713 YYZZ= -19.5713 + XXYZ= 0.0000 YYXZ= 0.0000 ZZXY= -0.0000 + N-N= 5.658703675808D+01 E-N=-5.554229240023D+02 KE= 1.865922906646D+02 + Symmetry AG KE= 1.010224941329D+02 + Symmetry B1G KE= 1.206473085192D-32 + Symmetry B2G KE= 4.663694725369D+00 + Symmetry B3G KE= 4.663694725369D+00 + Symmetry AU KE= 6.793861401711D-33 + Symmetry B1U KE= 6.894203292220D+01 + Symmetry B2U KE= 3.650187079387D+00 + Symmetry B3U KE= 3.650187079387D+00 + Exact polarizability: 0.000 0.000 0.000 0.000 0.000 0.000 + Approx polarizability: 7.074 0.000 7.074 -0.000 -0.000 24.413 + No NMR shielding tensors so no spin-rotation constants. + Leave Link 601 at Thu Jun 10 18:05:57 2021, MaxMem= 4800000000 cpu: 5.3 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l701.exe) + ... and contract with generalized density number 0. + Compute integral second derivatives. + Leave Link 701 at Thu Jun 10 18:05:57 2021, MaxMem= 4800000000 cpu: 8.8 elap: 0.3 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l702.exe) + L702 exits ... SP integral derivatives will be done elsewhere. + Leave Link 702 at Thu Jun 10 18:05:58 2021, MaxMem= 4800000000 cpu: 0.9 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l703.exe) + Integral derivatives from FoFJK, PRISM(SPDF). + Compute integral second derivatives, UseDBF=F ICtDFT= 0. + Calling FoFJK, ICntrl= 100147 FMM=F ISym2X=1 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0. + FoFJK: IHMeth= 1 ICntrl= 100147 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 800 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 100147 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Leave Link 703 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 9.9 elap: 0.3 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l716.exe) + Dipole = 2.67876454D-16 3.07397010D-17-1.27007489D-16 + Polarizability= 0.00000000D+00 0.00000000D+00 0.00000000D+00 + 0.00000000D+00 0.00000000D+00 0.00000000D+00 + ***** Axes restored to original set ***** + ------------------------------------------------------------------- + Center Atomic Forces (Hartrees/Bohr) + Number Number X Y Z + ------------------------------------------------------------------- + 1 8 0.098554123 0.018981445 -0.061901374 + 2 8 -0.098554123 -0.018981445 0.061901374 + 3 6 -0.000000000 -0.000000000 -0.000000000 + ------------------------------------------------------------------- + Cartesian Forces: Max 0.098554123 RMS 0.055587750 + Force constants in Cartesian coordinates: + 1 2 3 4 5 + 1 0.598086D+00 + 2 0.982942D-01 0.106661D+00 + 3 -0.320552D+00 -0.617381D-01 0.289067D+00 + 4 -0.798254D-01 -0.222307D-01 0.724977D-01 0.598086D+00 + 5 -0.222307D-01 0.313177D-01 0.139630D-01 0.982942D-01 0.106661D+00 + 6 0.724977D-01 0.139630D-01 -0.993618D-02 -0.320552D+00 -0.617381D-01 + 7 -0.518261D+00 -0.760635D-01 0.248055D+00 -0.518261D+00 -0.760635D-01 + 8 -0.760635D-01 -0.137979D+00 0.477751D-01 -0.760635D-01 -0.137979D+00 + 9 0.248055D+00 0.477751D-01 -0.279131D+00 0.248055D+00 0.477751D-01 + 6 7 8 9 + 6 0.289067D+00 + 7 0.248055D+00 0.103652D+01 + 8 0.477751D-01 0.152127D+00 0.275958D+00 + 9 -0.279131D+00 -0.496109D+00 -0.955502D-01 0.558262D+00 + FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. + Force constants in internal coordinates: + 1 2 3 4 + 1 0.818355D+00 + 2 0.129642D+00 0.818355D+00 + 3 0.000000D+00 0.000000D+00 0.179243D+00 + 4 0.000000D+00 0.000000D+00 -0.155490D-01 0.133303D+00 + Leave Link 716 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 2.3 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Red2BG is reusing G-inverse. + Internal Forces: Max 0.117919424 RMS 0.083381624 + Search for a local minimum. + Step number 1 out of a maximum of 20 + All quantities printed in internal units (Hartrees-Bohrs-Radians) + RMS Force = .83382D-01 SwitMx=.10000D-02 MixMth= 1 + Mixed Optimization -- RFO/linear search + Second derivative matrix not updated -- analytic derivatives used. + The second derivative matrix: + R1 R2 A1 A2 + R1 0.81835 + R2 0.12964 0.81835 + A1 0.00000 -0.00000 0.17924 + A2 -0.00000 0.00000 -0.01555 0.13330 + ITU= 0 + Eigenvalues --- 0.12854 0.18401 0.68871 0.94800 + RFO step: Lambda=-2.84799103D-02 EMin= 1.28535469D-01 + Linear search not attempted -- first point. + Iteration 1 RMS(Cart)= 0.08539025 RMS(Int)= 0.00000002 + SLEqS3 Cycle: 91 Max:0.329680E-07 RMS:0.210049E-07 Conv:0.459712E-13 + SLEqS3 Cycle: 91 Max:0.408456E-07 RMS:0.253351E-07 Conv:0.459712E-13 + Iteration 2 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000003 + ITry= 1 IFail=0 DXMaxC= 1.01D-01 DCOld= 1.00D+10 DXMaxT= 3.00D-01 DXLimC= 3.00D+00 Rises=F + ClnCor: largest displacement from symmetrization is 2.56D-08 for atom 3. + Variable Old X -DE/DX Delta X Delta X Delta X New X + (Linear) (Quad) (Total) + R1 2.26200 -0.11792 0.00000 -0.12076 -0.12076 2.14124 + R2 2.26200 -0.11792 0.00000 -0.12076 -0.12076 2.14124 + A1 3.14159 0.00000 0.00000 0.00000 0.00000 3.14159 + A2 3.14159 -0.00000 0.00000 0.00000 0.00000 3.14159 + Item Value Threshold Converged? + Maximum Force 0.117919 0.000450 NO + RMS Force 0.083382 0.000300 NO + Maximum Displacement 0.100928 0.001800 NO + RMS Displacement 0.085390 0.001200 NO + Predicted change in Energy=-1.465528D-02 + Lowest energy point so far. Saving SCF results. + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 0.7 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 -0.758443 -0.375075 3.208790 + 2 8 0 1.135585 -0.010287 2.019161 + 3 6 0 0.188571 -0.192681 2.613975 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 O 2.266193 0.000000 + 3 C 1.133097 1.133097 0.000000 + Stoichiometry CO2 + Framework group D*H[O(C),C*(O.O)] + Deg. of freedom 1 + Full point group D*H NOp 8 + RotChk: IX=0 Diff= 3.51D-16 + Largest Abelian subgroup D2H NOp 8 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 -0.000000 -0.000000 1.133097 + 2 8 0 0.000000 -0.000000 -1.133097 + 3 6 0 0.000000 0.000000 0.000000 + --------------------------------------------------------------------- + Rotational constants (GHZ): 0.0000000 12.3047121 12.3047121 + Leave Link 202 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 1.6 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l301.exe) + Standard basis: 6-31G(d) (6D, 7F) + Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. + There are 14 symmetry adapted cartesian basis functions of AG symmetry. + There are 2 symmetry adapted cartesian basis functions of B1G symmetry. + There are 4 symmetry adapted cartesian basis functions of B2G symmetry. + There are 4 symmetry adapted cartesian basis functions of B3G symmetry. + There are 1 symmetry adapted cartesian basis functions of AU symmetry. + There are 10 symmetry adapted cartesian basis functions of B1U symmetry. + There are 5 symmetry adapted cartesian basis functions of B2U symmetry. + There are 5 symmetry adapted cartesian basis functions of B3U symmetry. + There are 14 symmetry adapted basis functions of AG symmetry. + There are 2 symmetry adapted basis functions of B1G symmetry. + There are 4 symmetry adapted basis functions of B2G symmetry. + There are 4 symmetry adapted basis functions of B3G symmetry. + There are 1 symmetry adapted basis functions of AU symmetry. + There are 10 symmetry adapted basis functions of B1U symmetry. + There are 5 symmetry adapted basis functions of B2U symmetry. + There are 5 symmetry adapted basis functions of B3U symmetry. + 45 basis functions, 84 primitive gaussians, 45 cartesian basis functions + 11 alpha electrons 11 beta electrons + nuclear repulsion energy 59.7783870222 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 + IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 + NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F + Integral buffers will be 131072 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned on. + Leave Link 301 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 1.8 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l302.exe) + NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 + NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. + One-electron integrals computed using PRISM. + One-electron integral symmetry used in STVInt + NBasis= 45 RedAO= T EigKep= 2.75D-03 NBF= 14 2 4 4 1 10 5 5 + NBsUse= 45 1.00D-06 EigRej= -1.00D+00 NBFU= 14 2 4 4 1 10 5 5 + Leave Link 302 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 5.3 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l303.exe) + DipDrv: MaxL=1. + Leave Link 303 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 0.9 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l401.exe) + Initial guess from the checkpoint file: "/global/scratch/alex_epstein/line_c2o/Gau-207403.chk" + B after Tr= 0.000000 -0.000000 0.000000 + Rot= 1.000000 0.000000 0.000000 0.000000 Ang= 0.00 deg. + Guess basis will be translated and rotated to current coordinates. + JPrj=2 DoOrth=T DoCkMO=T. + Initial guess orbital symmetries: + Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) + (PIU) (PIG) (PIG) + Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) + (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (PIG) + (PIG) (DLTG) (DLTG) (DLTU) (DLTU) (SGU) (DLTG) + (DLTG) (PIU) (PIU) (SGG) (PIG) (PIG) (SGU) (SGG) + (SGG) (SGG) (SGU) + The electronic state of the initial guess is 1-SGG. + Generating alternative initial guess. + ExpMin= 1.69D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=2 IRadAn= 4 AccDes= 0.00D+00 + Harris functional with IExCor= 205 and IRadAn= 4 diagonalized for initial guess. + HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 4 IDoV= 1 UseB2=F ITyADJ=14 + ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000 + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 + NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T + wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Harris En= -187.647008958098 + Leave Link 401 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 6.4 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l502.exe) + Keep R1 ints in memory in symmetry-blocked form, NReq=7134369. + FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Closed shell SCF: + Using DIIS extrapolation, IDIIS= 1040. + NGot= 4800000000 LenX= 4799912550 LenY= 4799910084 + Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. + Requested convergence on MAX density matrix=1.00D-06. + Requested convergence on energy=1.00D-06. + No special actions if energy rises. + + Cycle 1 Pass 1 IDiag 1: + E= -187.627251532061 + DIIS: error= 1.09D-02 at cycle 1 NSaved= 1. + NSaved= 1 IEnMin= 1 EnMin= -187.627251532061 IErMin= 1 ErrMin= 1.09D-02 + ErrMax= 1.09D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.78D-03 BMatP= 5.78D-03 + IDIUse=3 WtCom= 8.91D-01 WtEn= 1.09D-01 + Coeff-Com: 0.100D+01 + Coeff-En: 0.100D+01 + Coeff: 0.100D+01 + Recover alternate guess density for next cycle. + RMSDP=6.93D-03 MaxDP=6.80D-02 OVMax= 0.00D+00 + + Cycle 2 Pass 1 IDiag 1: + E= -187.556267240062 Delta-E= 0.070984291999 Rises=F Damp=F + Switch densities from cycles 1 and 2 for lowest energy. + DIIS: error= 6.05D-02 at cycle 2 NSaved= 2. + NSaved= 2 IEnMin= 1 EnMin= -187.627251532061 IErMin= 1 ErrMin= 1.09D-02 + ErrMax= 6.05D-02 0.00D+00 EMaxC= 1.00D+00 BMatC= 1.97D-01 BMatP= 5.78D-03 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.923D+00 0.766D-01 + Coeff: 0.923D+00 0.766D-01 + Gap= 0.782 Goal= None Shift= 0.000 + RMSDP=2.04D-03 MaxDP=1.36D-02 DE= 7.10D-02 OVMax= 2.15D-02 + + Cycle 3 Pass 1 IDiag 1: + E= -187.633231258904 Delta-E= -0.076964018842 Rises=F Damp=F + DIIS: error= 3.80D-03 at cycle 3 NSaved= 3. + NSaved= 3 IEnMin= 3 EnMin= -187.633231258904 IErMin= 3 ErrMin= 3.80D-03 + ErrMax= 3.80D-03 0.00D+00 EMaxC= 1.00D+00 BMatC= 2.94D-04 BMatP= 5.78D-03 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.251D-01 0.800D-02 0.967D+00 + Coeff: 0.251D-01 0.800D-02 0.967D+00 + Gap= 0.781 Goal= None Shift= 0.000 + RMSDP=5.34D-04 MaxDP=5.79D-03 DE=-7.70D-02 OVMax= 8.53D-03 + + Cycle 4 Pass 1 IDiag 1: + E= -187.633592700632 Delta-E= -0.000361441728 Rises=F Damp=F + DIIS: error= 9.49D-04 at cycle 4 NSaved= 4. + NSaved= 4 IEnMin= 4 EnMin= -187.633592700632 IErMin= 4 ErrMin= 9.49D-04 + ErrMax= 9.49D-04 0.00D+00 EMaxC= 1.00D+00 BMatC= 3.43D-05 BMatP= 2.94D-04 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.591D-01-0.632D-02 0.608D-02 0.106D+01 + Coeff: -0.591D-01-0.632D-02 0.608D-02 0.106D+01 + Gap= 0.779 Goal= None Shift= 0.000 + RMSDP=1.97D-04 MaxDP=1.82D-03 DE=-3.61D-04 OVMax= 2.99D-03 + + Cycle 5 Pass 1 IDiag 1: + E= -187.633644199040 Delta-E= -0.000051498408 Rises=F Damp=F + DIIS: error= 4.48D-04 at cycle 5 NSaved= 5. + NSaved= 5 IEnMin= 5 EnMin= -187.633644199040 IErMin= 5 ErrMin= 4.48D-04 + ErrMax= 4.48D-04 0.00D+00 EMaxC= 1.00D+00 BMatC= 5.04D-06 BMatP= 3.43D-05 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.111D-01 0.714D-03-0.654D-01 0.195D+00 0.881D+00 + Coeff: -0.111D-01 0.714D-03-0.654D-01 0.195D+00 0.881D+00 + Gap= 0.780 Goal= None Shift= 0.000 + RMSDP=5.62D-05 MaxDP=6.49D-04 DE=-5.15D-05 OVMax= 1.01D-03 + + Cycle 6 Pass 1 IDiag 1: + E= -187.633649185699 Delta-E= -0.000004986659 Rises=F Damp=F + DIIS: error= 7.74D-05 at cycle 6 NSaved= 6. + NSaved= 6 IEnMin= 6 EnMin= -187.633649185699 IErMin= 6 ErrMin= 7.74D-05 + ErrMax= 7.74D-05 0.00D+00 EMaxC= 1.00D+00 BMatC= 1.67D-07 BMatP= 5.04D-06 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.578D-02 0.172D-03-0.237D-02-0.891D-01-0.113D+00 0.120D+01 + Coeff: 0.578D-02 0.172D-03-0.237D-02-0.891D-01-0.113D+00 0.120D+01 + Gap= 0.780 Goal= None Shift= 0.000 + RMSDP=2.01D-05 MaxDP=1.73D-04 DE=-4.99D-06 OVMax= 2.92D-04 + + Cycle 7 Pass 1 IDiag 1: + E= -187.633649541865 Delta-E= -0.000000356166 Rises=F Damp=F + DIIS: error= 1.60D-05 at cycle 7 NSaved= 7. + NSaved= 7 IEnMin= 7 EnMin= -187.633649541865 IErMin= 7 ErrMin= 1.60D-05 + ErrMax= 1.60D-05 0.00D+00 EMaxC= 1.00D+00 BMatC= 5.78D-09 BMatP= 1.67D-07 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.110D-02-0.479D-04 0.211D-02 0.182D-01-0.179D-01-0.235D+00 + Coeff-Com: 0.123D+01 + Coeff: -0.110D-02-0.479D-04 0.211D-02 0.182D-01-0.179D-01-0.235D+00 + Coeff: 0.123D+01 + Gap= 0.780 Goal= None Shift= 0.000 + RMSDP=2.52D-06 MaxDP=2.84D-05 DE=-3.56D-07 OVMax= 2.87D-05 + + Cycle 8 Pass 1 IDiag 1: + E= -187.633649548981 Delta-E= -0.000000007115 Rises=F Damp=F + DIIS: error= 1.65D-06 at cycle 8 NSaved= 8. + NSaved= 8 IEnMin= 8 EnMin= -187.633649548981 IErMin= 8 ErrMin= 1.65D-06 + ErrMax= 1.65D-06 0.00D+00 EMaxC= 1.00D+00 BMatC= 6.65D-11 BMatP= 5.78D-09 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.121D-03 0.421D-05-0.326D-03-0.183D-02 0.282D-02 0.331D-01 + Coeff-Com: -0.256D+00 0.122D+01 + Coeff: 0.121D-03 0.421D-05-0.326D-03-0.183D-02 0.282D-02 0.331D-01 + Coeff: -0.256D+00 0.122D+01 + Gap= 0.780 Goal= None Shift= 0.000 + RMSDP=5.63D-07 MaxDP=5.53D-06 DE=-7.12D-09 OVMax= 4.70D-06 + + Cycle 9 Pass 1 IDiag 1: + E= -187.633649549076 Delta-E= -0.000000000095 Rises=F Damp=F + DIIS: error= 1.03D-07 at cycle 9 NSaved= 9. + NSaved= 9 IEnMin= 9 EnMin= -187.633649549076 IErMin= 9 ErrMin= 1.03D-07 + ErrMax= 1.03D-07 0.00D+00 EMaxC= 1.00D+00 BMatC= 2.75D-13 BMatP= 6.65D-11 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.322D-05-0.809D-07 0.112D-04 0.494D-04-0.543D-04-0.154D-02 + Coeff-Com: 0.154D-01-0.138D+00 0.112D+01 + Coeff: -0.322D-05-0.809D-07 0.112D-04 0.494D-04-0.543D-04-0.154D-02 + Coeff: 0.154D-01-0.138D+00 0.112D+01 + Gap= 0.780 Goal= None Shift= 0.000 + RMSDP=4.24D-08 MaxDP=5.22D-07 DE=-9.55D-11 OVMax= 4.11D-07 + + Cycle 10 Pass 1 IDiag 1: + E= -187.633649549076 Delta-E= 0.000000000000 Rises=F Damp=F + DIIS: error= 9.95D-09 at cycle 10 NSaved= 10. + NSaved=10 IEnMin= 9 EnMin= -187.633649549076 IErMin=10 ErrMin= 9.95D-09 + ErrMax= 9.95D-09 0.00D+00 EMaxC= 1.00D+00 BMatC= 2.67D-15 BMatP= 2.75D-13 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.156D-06 0.876D-09-0.696D-06-0.259D-05 0.830D-06 0.118D-03 + Coeff-Com: -0.139D-02 0.187D-01-0.207D+00 0.119D+01 + Coeff: 0.156D-06 0.876D-09-0.696D-06-0.259D-05 0.830D-06 0.118D-03 + Coeff: -0.139D-02 0.187D-01-0.207D+00 0.119D+01 + Gap= 0.780 Goal= None Shift= 0.000 + RMSDP=2.07D-09 MaxDP=2.23D-08 DE= 0.00D+00 OVMax= 1.82D-08 + + SCF Done: E(RHF) = -187.633649549 A.U. after 10 cycles + NFock= 10 Conv=0.21D-08 -V/T= 2.0022 + KE= 1.872219534074D+02 PE=-5.623087732485D+02 EE= 1.276747832698D+02 + Leave Link 502 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 4.8 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l701.exe) + ... and contract with generalized density number 0. + Compute integral first derivatives. + Leave Link 701 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 4.6 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l702.exe) + L702 exits ... SP integral derivatives will be done elsewhere. + Leave Link 702 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 0.7 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l703.exe) + Integral derivatives from FoFJK, PRISM(SPDF). + Compute integral first derivatives, UseDBF=F ICtDFT= 0. + Calling FoFJK, ICntrl= 2127 FMM=F ISym2X=1 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0. + FoFJK: IHMeth= 1 ICntrl= 2127 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 800 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 2127 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Leave Link 703 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 5.3 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l716.exe) + Dipole = 1.50340041D-16 3.00969273D-17 0.00000000D+00 + ***** Axes restored to original set ***** + ------------------------------------------------------------------- + Center Atomic Forces (Hartrees/Bohr) + Number Number X Y Z + ------------------------------------------------------------------- + 1 8 -0.023193813 -0.004467110 0.014567923 + 2 8 0.023193813 0.004467110 -0.014567923 + 3 6 -0.000000000 -0.000000000 -0.000000000 + ------------------------------------------------------------------- + Cartesian Forces: Max 0.023193813 RMS 0.013082069 + Leave Link 716 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Using GEDIIS/GDIIS optimizer. + Red2BG is reusing G-inverse. + Internal Forces: Max 0.027751260 RMS 0.019623104 + Search for a local minimum. + Step number 2 out of a maximum of 20 + All quantities printed in internal units (Hartrees-Bohrs-Radians) + RMS Force = .19623D-01 SwitMx=.10000D-02 MixMth= 1 + Mixed Optimization -- RFO/linear search + Update second derivatives using D2CorX and points 1 2 + DE= -1.22D-02 DEPred=-1.47D-02 R= 8.34D-01 + TightC=F SS= 1.41D+00 RLast= 1.71D-01 DXNew= 5.0454D-01 5.1234D-01 + Trust test= 8.34D-01 RLast= 1.71D-01 DXMaxT set to 5.05D-01 + The second derivative matrix: + R1 R2 A1 A2 + R1 0.94750 + R2 0.25878 0.94750 + A1 -0.00000 -0.00000 0.17924 + A2 0.00000 0.00000 -0.01555 0.13330 + ITU= 1 0 + Use linear search instead of GDIIS. + Eigenvalues --- 0.12854 0.18401 0.68871 1.20628 + RFO step: Lambda= 0.00000000D+00 EMin= 1.28535469D-01 + Quartic linear search produced a step of -0.15936. + Iteration 1 RMS(Cart)= 0.01360755 RMS(Int)= 0.00000000 + Iteration 2 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000001 + ITry= 1 IFail=0 DXMaxC= 1.61D-02 DCOld= 1.00D+10 DXMaxT= 5.05D-01 DXLimC= 3.00D+00 Rises=F + ClnCor: largest displacement from symmetrization is 4.25D-13 for atom 3. + Variable Old X -DE/DX Delta X Delta X Delta X New X + (Linear) (Quad) (Total) + R1 2.14124 0.02775 0.01924 -0.00000 0.01924 2.16049 + R2 2.14124 0.02775 0.01924 0.00000 0.01924 2.16049 + A1 3.14159 0.00000 0.00000 0.00000 -0.00000 3.14159 + A2 3.14159 0.00000 0.00000 0.00000 -0.00000 3.14159 + Item Value Threshold Converged? + Maximum Force 0.027751 0.000450 NO + RMS Force 0.019623 0.000300 NO + Maximum Displacement 0.016084 0.001800 NO + RMS Displacement 0.013608 0.001200 NO + Predicted change in Energy=-6.213660D-04 + Lowest energy point so far. Saving SCF results. + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 1.9 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 -0.766954 -0.376714 3.214136 + 2 8 0 1.144096 -0.008647 2.013815 + 3 6 0 0.188571 -0.192681 2.613975 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 O 2.286560 0.000000 + 3 C 1.143280 1.143280 0.000000 + Stoichiometry CO2 + Framework group D*H[O(C),C*(O.O)] + Deg. of freedom 1 + Full point group D*H NOp 8 + RotChk: IX=0 Diff= 3.70D-16 + Largest Abelian subgroup D2H NOp 8 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 -0.000000 0.000000 1.143280 + 2 8 0 0.000000 0.000000 -1.143280 + 3 6 0 0.000000 0.000000 0.000000 + --------------------------------------------------------------------- + Rotational constants (GHZ): 0.0000000 12.0864862 12.0864862 + Leave Link 202 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 0.4 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l301.exe) + Standard basis: 6-31G(d) (6D, 7F) + Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. + There are 14 symmetry adapted cartesian basis functions of AG symmetry. + There are 2 symmetry adapted cartesian basis functions of B1G symmetry. + There are 4 symmetry adapted cartesian basis functions of B2G symmetry. + There are 4 symmetry adapted cartesian basis functions of B3G symmetry. + There are 1 symmetry adapted cartesian basis functions of AU symmetry. + There are 10 symmetry adapted cartesian basis functions of B1U symmetry. + There are 5 symmetry adapted cartesian basis functions of B2U symmetry. + There are 5 symmetry adapted cartesian basis functions of B3U symmetry. + There are 14 symmetry adapted basis functions of AG symmetry. + There are 2 symmetry adapted basis functions of B1G symmetry. + There are 4 symmetry adapted basis functions of B2G symmetry. + There are 4 symmetry adapted basis functions of B3G symmetry. + There are 1 symmetry adapted basis functions of AU symmetry. + There are 10 symmetry adapted basis functions of B1U symmetry. + There are 5 symmetry adapted basis functions of B2U symmetry. + There are 5 symmetry adapted basis functions of B3U symmetry. + 45 basis functions, 84 primitive gaussians, 45 cartesian basis functions + 11 alpha electrons 11 beta electrons + nuclear repulsion energy 59.2459262762 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 + IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 + NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F + Integral buffers will be 131072 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned on. + Leave Link 301 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 3.4 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l302.exe) + NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 + NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. + One-electron integrals computed using PRISM. + One-electron integral symmetry used in STVInt + NBasis= 45 RedAO= T EigKep= 2.77D-03 NBF= 14 2 4 4 1 10 5 5 + NBsUse= 45 1.00D-06 EigRej= -1.00D+00 NBFU= 14 2 4 4 1 10 5 5 + Leave Link 302 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 3.7 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l303.exe) + DipDrv: MaxL=1. + Leave Link 303 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l401.exe) + Initial guess from the checkpoint file: "/global/scratch/alex_epstein/line_c2o/Gau-207403.chk" + B after Tr= 0.000000 0.000000 0.000000 + Rot= 1.000000 -0.000000 0.000000 -0.000000 Ang= 0.00 deg. + Guess basis will be translated and rotated to current coordinates. + JPrj=2 DoOrth=T DoCkMO=T. + Initial guess orbital symmetries: + Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) + (PIU) (PIG) (PIG) + Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) + (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (DLTG) + (DLTG) (PIG) (PIG) (DLTU) (DLTU) (SGU) (DLTG) + (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) + (SGG) (SGU) (SGG) + The electronic state of the initial guess is 1-SGG. + Leave Link 401 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 2.8 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l502.exe) + Keep R1 ints in memory in symmetry-blocked form, NReq=7134369. + FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Closed shell SCF: + Using DIIS extrapolation, IDIIS= 1040. + NGot= 4800000000 LenX= 4799912550 LenY= 4799910084 + Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. + Requested convergence on MAX density matrix=1.00D-06. + Requested convergence on energy=1.00D-06. + No special actions if energy rises. + + Cycle 1 Pass 1 IDiag 1: + E= -187.634006821630 + DIIS: error= 1.79D-03 at cycle 1 NSaved= 1. + NSaved= 1 IEnMin= 1 EnMin= -187.634006821630 IErMin= 1 ErrMin= 1.79D-03 + ErrMax= 1.79D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.56D-04 BMatP= 1.56D-04 + IDIUse=3 WtCom= 9.82D-01 WtEn= 1.79D-02 + Coeff-Com: 0.100D+01 + Coeff-En: 0.100D+01 + Coeff: 0.100D+01 + Gap= 0.770 Goal= None Shift= 0.000 + GapD= 0.770 DampG=2.000 DampE=1.000 DampFc=2.0000 IDamp=-1. + RMSDP=3.32D-04 MaxDP=2.24D-03 OVMax= 3.40D-03 + + Cycle 2 Pass 1 IDiag 1: + E= -187.634161427579 Delta-E= -0.000154605949 Rises=F Damp=F + DIIS: error= 5.77D-04 at cycle 2 NSaved= 2. + NSaved= 2 IEnMin= 2 EnMin= -187.634161427579 IErMin= 2 ErrMin= 5.77D-04 + ErrMax= 5.77D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.25D-05 BMatP= 1.56D-04 + IDIUse=3 WtCom= 9.94D-01 WtEn= 5.77D-03 + Coeff-Com: 0.725D-01 0.927D+00 + Coeff-En: 0.000D+00 0.100D+01 + Coeff: 0.721D-01 0.928D+00 + Gap= 0.771 Goal= None Shift= 0.000 + RMSDP=9.96D-05 MaxDP=8.60D-04 DE=-1.55D-04 OVMax= 1.20D-03 + + Cycle 3 Pass 1 IDiag 1: + E= -187.634173995685 Delta-E= -0.000012568105 Rises=F Damp=F + DIIS: error= 2.79D-04 at cycle 3 NSaved= 3. + NSaved= 3 IEnMin= 3 EnMin= -187.634173995685 IErMin= 3 ErrMin= 2.79D-04 + ErrMax= 2.79D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.48D-06 BMatP= 1.25D-05 + IDIUse=3 WtCom= 9.97D-01 WtEn= 2.79D-03 + Coeff-Com: -0.583D-01 0.421D-01 0.102D+01 + Coeff-En: 0.000D+00 0.000D+00 0.100D+01 + Coeff: -0.581D-01 0.419D-01 0.102D+01 + Gap= 0.770 Goal= None Shift= 0.000 + RMSDP=3.71D-05 MaxDP=4.08D-04 DE=-1.26D-05 OVMax= 7.08D-04 + + Cycle 4 Pass 1 IDiag 1: + E= -187.634175927579 Delta-E= -0.000001931894 Rises=F Damp=F + DIIS: error= 8.29D-05 at cycle 4 NSaved= 4. + NSaved= 4 IEnMin= 4 EnMin= -187.634175927579 IErMin= 4 ErrMin= 8.29D-05 + ErrMax= 8.29D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.90D-07 BMatP= 1.48D-06 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.183D-01-0.611D-01 0.208D+00 0.872D+00 + Coeff: -0.183D-01-0.611D-01 0.208D+00 0.872D+00 + Gap= 0.771 Goal= None Shift= 0.000 + RMSDP=1.21D-05 MaxDP=1.05D-04 DE=-1.93D-06 OVMax= 1.79D-04 + + Cycle 5 Pass 1 IDiag 1: + E= -187.634176173131 Delta-E= -0.000000245552 Rises=F Damp=F + DIIS: error= 3.39D-05 at cycle 5 NSaved= 5. + NSaved= 5 IEnMin= 5 EnMin= -187.634176173131 IErMin= 5 ErrMin= 3.39D-05 + ErrMax= 3.39D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.43D-08 BMatP= 1.90D-07 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.851D-02-0.116D-02-0.161D+00 0.702D-01 0.108D+01 + Coeff: 0.851D-02-0.116D-02-0.161D+00 0.702D-01 0.108D+01 + Gap= 0.771 Goal= None Shift= 0.000 + RMSDP=5.14D-06 MaxDP=5.49D-05 DE=-2.46D-07 OVMax= 8.59D-05 + + Cycle 6 Pass 1 IDiag 1: + E= -187.634176201019 Delta-E= -0.000000027888 Rises=F Damp=F + DIIS: error= 3.64D-06 at cycle 6 NSaved= 6. + NSaved= 6 IEnMin= 6 EnMin= -187.634176201019 IErMin= 6 ErrMin= 3.64D-06 + ErrMax= 3.64D-06 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.01D-10 BMatP= 2.43D-08 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.140D-02 0.201D-02 0.281D-01-0.231D-01-0.288D+00 0.128D+01 + Coeff: -0.140D-02 0.201D-02 0.281D-01-0.231D-01-0.288D+00 0.128D+01 + Gap= 0.771 Goal= None Shift= 0.000 + RMSDP=6.25D-07 MaxDP=7.41D-06 DE=-2.79D-08 OVMax= 7.24D-06 + + Cycle 7 Pass 1 IDiag 1: + E= -187.634176201487 Delta-E= -0.000000000467 Rises=F Damp=F + DIIS: error= 4.22D-07 at cycle 7 NSaved= 7. + NSaved= 7 IEnMin= 7 EnMin= -187.634176201487 IErMin= 7 ErrMin= 4.22D-07 + ErrMax= 4.22D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 4.52D-12 BMatP= 3.01D-10 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.166D-03-0.268D-03-0.370D-02 0.548D-02 0.387D-01-0.261D+00 + Coeff-Com: 0.122D+01 + Coeff: 0.166D-03-0.268D-03-0.370D-02 0.548D-02 0.387D-01-0.261D+00 + Coeff: 0.122D+01 + Gap= 0.771 Goal= None Shift= 0.000 + RMSDP=1.37D-07 MaxDP=1.21D-06 DE=-4.67D-10 OVMax= 1.09D-06 + + Cycle 8 Pass 1 IDiag 1: + E= -187.634176201493 Delta-E= -0.000000000006 Rises=F Damp=F + DIIS: error= 2.73D-08 at cycle 8 NSaved= 8. + NSaved= 8 IEnMin= 8 EnMin= -187.634176201493 IErMin= 8 ErrMin= 2.73D-08 + ErrMax= 2.73D-08 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.11D-14 BMatP= 4.52D-12 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: -0.639D-05 0.763D-05 0.176D-03-0.323D-03-0.173D-02 0.173D-01 + Coeff-Com: -0.155D+00 0.114D+01 + Coeff: -0.639D-05 0.763D-05 0.176D-03-0.323D-03-0.173D-02 0.173D-01 + Coeff: -0.155D+00 0.114D+01 + Gap= 0.771 Goal= None Shift= 0.000 + RMSDP=1.27D-08 MaxDP=1.48D-07 DE=-6.11D-12 OVMax= 1.20D-07 + + Cycle 9 Pass 1 IDiag 1: + E= -187.634176201493 Delta-E= 0.000000000000 Rises=F Damp=F + DIIS: error= 2.66D-09 at cycle 9 NSaved= 9. + NSaved= 9 IEnMin= 8 EnMin= -187.634176201493 IErMin= 9 ErrMin= 2.66D-09 + ErrMax= 2.66D-09 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.49D-16 BMatP= 2.11D-14 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.697D-06-0.917D-06-0.174D-04 0.345D-04 0.164D-03-0.200D-02 + Coeff-Com: 0.242D-01-0.222D+00 0.120D+01 + Coeff: 0.697D-06-0.917D-06-0.174D-04 0.345D-04 0.164D-03-0.200D-02 + Coeff: 0.242D-01-0.222D+00 0.120D+01 + Gap= 0.771 Goal= None Shift= 0.000 + RMSDP=6.02D-10 MaxDP=6.56D-09 DE= 2.84D-13 OVMax= 5.28D-09 + + SCF Done: E(RHF) = -187.634176201 A.U. after 9 cycles + NFock= 9 Conv=0.60D-09 -V/T= 2.0028 + KE= 1.871094202810D+02 PE=-5.611564169403D+02 EE= 1.271668941815D+02 + Leave Link 502 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 4.9 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l701.exe) + ... and contract with generalized density number 0. + Compute integral first derivatives. + Leave Link 701 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 4.0 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l702.exe) + L702 exits ... SP integral derivatives will be done elsewhere. + Leave Link 702 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 0.7 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l703.exe) + Integral derivatives from FoFJK, PRISM(SPDF). + Compute integral first derivatives, UseDBF=F ICtDFT= 0. + Calling FoFJK, ICntrl= 2127 FMM=F ISym2X=1 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0. + FoFJK: IHMeth= 1 ICntrl= 2127 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 800 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 2127 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Leave Link 703 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 4.8 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l716.exe) + Dipole =-1.68515248D-16-1.40429373D-17 0.00000000D+00 + ***** Axes restored to original set ***** + ------------------------------------------------------------------- + Center Atomic Forces (Hartrees/Bohr) + Number Number X Y Z + ------------------------------------------------------------------- + 1 8 0.000051665 0.000009951 -0.000032451 + 2 8 -0.000051665 -0.000009951 0.000032451 + 3 6 0.000000000 0.000000000 -0.000000000 + ------------------------------------------------------------------- + Cartesian Forces: Max 0.000051665 RMS 0.000029141 + Leave Link 716 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Using GEDIIS/GDIIS optimizer. + Red2BG is reusing G-inverse. + Internal Forces: Max 0.000061817 RMS 0.000043711 + Search for a local minimum. + Step number 3 out of a maximum of 20 + All quantities printed in internal units (Hartrees-Bohrs-Radians) + RMS Force = .43711D-04 SwitMx=.10000D-02 MixMth= 2 + Mixed Optimization -- En-DIIS/RFO-DIIS + Update second derivatives using D2CorX and points 1 2 3 + DE= -5.27D-04 DEPred=-6.21D-04 R= 8.48D-01 + TightC=F SS= 1.41D+00 RLast= 2.72D-02 DXNew= 8.4853D-01 8.1645D-02 + Trust test= 8.48D-01 RLast= 2.72D-02 DXMaxT set to 5.05D-01 + The second derivative matrix: + R1 R2 A1 A2 + R1 1.06700 + R2 0.37829 1.06700 + A1 0.00000 0.00000 0.17924 + A2 -0.00000 -0.00000 -0.01555 0.13330 + ITU= 1 1 0 + Use linear search instead of GDIIS. + Eigenvalues --- 0.12854 0.18401 0.68871 1.44529 + RFO step: Lambda= 0.00000000D+00 EMin= 1.28535469D-01 + Quartic linear search produced a step of -0.00230. + Iteration 1 RMS(Cart)= 0.00003132 RMS(Int)= 0.00000000 + Iteration 2 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000001 + ITry= 1 IFail=0 DXMaxC= 3.70D-05 DCOld= 1.00D+10 DXMaxT= 5.05D-01 DXLimC= 3.00D+00 Rises=F + ClnCor: largest displacement from symmetrization is 4.13D-13 for atom 3. + Variable Old X -DE/DX Delta X Delta X Delta X New X + (Linear) (Quad) (Total) + R1 2.16049 -0.00006 -0.00004 0.00000 -0.00004 2.16044 + R2 2.16049 -0.00006 -0.00004 -0.00000 -0.00004 2.16044 + A1 3.14159 -0.00000 0.00000 -0.00000 0.00000 3.14159 + A2 3.14159 0.00000 0.00000 0.00000 0.00000 3.14159 + Item Value Threshold Converged? + Maximum Force 0.000062 0.000450 YES + RMS Force 0.000044 0.000300 YES + Maximum Displacement 0.000037 0.001800 YES + RMS Displacement 0.000031 0.001200 YES + Predicted change in Energy=-2.640612D-09 + Optimization completed. + -- Stationary point found. + ---------------------------- + ! Optimized Parameters ! + ! (Angstroms and Degrees) ! + -------------------------- -------------------------- + ! Name Definition Value Derivative Info. ! + -------------------------------------------------------------------------------- + ! R1 R(1,3) 1.1433 -DE/DX = -0.0001 ! + ! R2 R(2,3) 1.1433 -DE/DX = -0.0001 ! + ! A1 L(1,3,2,-2,-1) 180.0 -DE/DX = 0.0 ! + ! A2 L(1,3,2,-3,-2) 180.0 -DE/DX = 0.0 ! + -------------------------------------------------------------------------------- + Lowest energy point so far. Saving SCF results. + Largest change from initial coordinates is atom 1 0.000 Angstoms. + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 2.1 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 -0.766954 -0.376714 3.214136 + 2 8 0 1.144096 -0.008647 2.013815 + 3 6 0 0.188571 -0.192681 2.613975 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 O 2.286560 0.000000 + 3 C 1.143280 1.143280 0.000000 + Stoichiometry CO2 + Framework group D*H[O(C),C*(O.O)] + Deg. of freedom 1 + Full point group D*H NOp 8 + RotChk: IX=0 Diff= 4.01D-16 + Largest Abelian subgroup D2H NOp 8 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 0.000000 -0.000000 1.143280 + 2 8 0 0.000000 0.000000 -1.143280 + 3 6 0 0.000000 0.000000 0.000000 + --------------------------------------------------------------------- + Rotational constants (GHZ): 0.0000000 12.0864862 12.0864862 + Leave Link 202 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 0.4 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l601.exe) + Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0. + + ********************************************************************** + + Population analysis using the SCF density. + + ********************************************************************** + + Orbital symmetries: + Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) + (PIU) (PIG) (PIG) + Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) + (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (DLTG) + (DLTG) (PIG) (PIG) (DLTU) (DLTU) (SGU) (DLTG) + (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) + (SGG) (SGU) (SGG) + The electronic state is 1-SGG. + Alpha occ. eigenvalues -- -20.65784 -20.65782 -11.46212 -1.54200 -1.48690 + Alpha occ. eigenvalues -- -0.79261 -0.73924 -0.71908 -0.71908 -0.53995 + Alpha occ. eigenvalues -- -0.53995 + Alpha virt. eigenvalues -- 0.23058 0.23058 0.26636 0.51004 0.66340 + Alpha virt. eigenvalues -- 0.66340 0.84293 0.98303 0.99234 1.14705 + Alpha virt. eigenvalues -- 1.14705 1.33111 1.33111 1.45461 1.61575 + Alpha virt. eigenvalues -- 1.63482 1.63482 1.70440 1.70440 2.01268 + Alpha virt. eigenvalues -- 2.01268 2.08925 2.35732 2.35732 2.49060 + Alpha virt. eigenvalues -- 2.49060 3.14657 3.32784 3.35175 3.35175 + Alpha virt. eigenvalues -- 3.48917 4.18091 4.90146 4.90696 + Condensed to atoms (all electrons): + 1 2 3 + 1 O 7.841235 -0.025877 0.630900 + 2 O -0.025877 7.841235 0.630900 + 3 C 0.630900 0.630900 3.845681 + Mulliken charges: + 1 + 1 O -0.446259 + 2 O -0.446259 + 3 C 0.892518 + Sum of Mulliken charges = -0.00000 + Mulliken charges with hydrogens summed into heavy atoms: + 1 + 1 O -0.446259 + 2 O -0.446259 + 3 C 0.892518 + Electronic spatial extent (au): = 110.9843 + Charge= -0.0000 electrons + Dipole moment (field-independent basis, Debye): + X= 0.0000 Y= -0.0000 Z= -0.0000 Tot= 0.0000 + Quadrupole moment (field-independent basis, Debye-Ang): + XX= -14.4559 YY= -14.4559 ZZ= -19.9144 + XY= -0.0000 XZ= 0.0000 YZ= -0.0000 + Traceless Quadrupole moment (field-independent basis, Debye-Ang): + XX= 1.8195 YY= 1.8195 ZZ= -3.6391 + XY= -0.0000 XZ= 0.0000 YZ= -0.0000 + Octapole moment (field-independent basis, Debye-Ang**2): + XXX= -0.0000 YYY= -0.0000 ZZZ= -0.0000 XYY= -0.0000 + XXY= -0.0000 XXZ= 0.0000 XZZ= 0.0000 YZZ= -0.0000 + YYZ= 0.0000 XYZ= -0.0000 + Hexadecapole moment (field-independent basis, Debye-Ang**3): + XXXX= -10.2550 YYYY= -10.2550 ZZZZ= -99.4698 XXXY= -0.0000 + XXXZ= 0.0000 YYYX= -0.0000 YYYZ= 0.0000 ZZZX= 0.0000 + ZZZY= -0.0000 XXYY= -3.4183 XXZZ= -17.9582 YYZZ= -17.9582 + XXYZ= 0.0000 YYXZ= 0.0000 ZZXY= -0.0000 + N-N= 5.924592627624D+01 E-N=-5.611564169572D+02 KE= 1.871094202810D+02 + Symmetry AG KE= 1.012480411172D+02 + Symmetry B1G KE= 4.161560280064D-32 + Symmetry B2G KE= 4.700699095130D+00 + Symmetry B3G KE= 4.700699095129D+00 + Symmetry AU KE= 2.452413593718D-32 + Symmetry B1U KE= 6.913256481078D+01 + Symmetry B2U KE= 3.663708081395D+00 + Symmetry B3U KE= 3.663708081395D+00 + No NMR shielding tensors so no spin-rotation constants. + Leave Link 601 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 5.4 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l9999.exe) + 1\1\GINC-N0045\FOpt\RHF\6-31G(d)\C1O2\ALEX_EPSTEIN\10-Jun-2021\0\\#P H + F/6-31g(d) freq=noraman opt=(noeigen, calcfc)\\co2 for linear test\\0, + 1\O,-0.7669543606,-0.3767139767,3.2141361692\O,1.1440956549,-0.0086472 + 867,2.0138147763\C,0.1885706471,-0.1926806317,2.6139754728\\Version=ES + 64L-G16RevA.03\State=1-SGG\HF=-187.6341762\RMSD=6.023e-10\RMSF=2.914e- + 05\Dipole=0.,0.,0.\Quadrupole=-1.4820442,1.2476169,0.2344273,-0.545983 + 5,1.7805351,0.3429296\PG=D*H [O(C1),C*(O1.O1)]\\@ + + + STEINBACH'S GUIDELINES FOR SYSTEMS PROGRAMMING: + NEVER TEST FOR AN ERROR CONDITION YOU DON'T KNOW HOW + TO HANDLE. + Leave Link 9999 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 2.0 elap: 0.1 + Job cpu time: 0 days 0 hours 2 minutes 51.6 seconds. + Elapsed time: 0 days 0 hours 0 minutes 6.8 seconds. + File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 + Normal termination of Gaussian 16 at Thu Jun 10 18:06:03 2021. + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1.exe) + Link1: Proceeding to internal job step number 2. + ----------------------------------------------------------------- + #P Geom=AllCheck Guess=TCheck SCRF=Check GenChk RHF/6-31G(d) Freq + ----------------------------------------------------------------- + 1/10=4,11=1,29=7,30=1,38=1,40=1/1,3; + 2/12=2,40=1/2; + 3/5=1,6=6,7=1,11=1,14=-4,25=1,30=1,70=2,71=2,116=1,140=1/1,2,3; + 4/5=101/1; + 5/5=2,38=6,98=1/2; + 8/6=4,10=90,11=11/1; + 11/6=1,8=1,9=11,15=111,16=1/1,2,10; + 10/6=1/2; + 6/7=2,8=2,9=2,10=2,28=1/1; + 7/8=1,10=1,25=1/1,2,3,16; + 1/10=4,11=1,30=1/3; + 99//99; + Leave Link 1 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 1.4 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l101.exe) + Structure from the checkpoint file: "/global/scratch/alex_epstein/line_c2o/Gau-207403.chk" + ------------------- + co2 for linear test + ------------------- + Charge = 0 Multiplicity = 1 + Redundant internal coordinates found in file. (old form). + O,0,-0.7669543606,-0.3767139767,3.2141361692 + O,0,1.1440956549,-0.0086472867,2.0138147763 + C,0,0.1885706471,-0.1926806317,2.6139754728 + Recover connectivity data from disk. + ITRead= 0 0 0 + MicOpt= -1 -1 -1 + NAtoms= 3 NQM= 3 NQMF= 0 NMMI= 0 NMMIF= 0 + NMic= 0 NMicF= 0. + Isotopes and Nuclear Properties: + (Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM) + in nuclear magnetons) + + Atom 1 2 3 + IAtWgt= 16 16 12 + AtmWgt= 15.9949146 15.9949146 12.0000000 + NucSpn= 0 0 0 + AtZEff= 5.6000000 5.6000000 3.6000000 + NQMom= 0.0000000 0.0000000 0.0000000 + NMagM= 0.0000000 0.0000000 0.0000000 + AtZNuc= 8.0000000 8.0000000 6.0000000 + Leave Link 101 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 11.0 elap: 0.4 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Initialization pass. + ---------------------------- + ! Initial Parameters ! + ! (Angstroms and Degrees) ! + -------------------------- -------------------------- + ! Name Definition Value Derivative Info. ! + -------------------------------------------------------------------------------- + ! R1 R(1,3) 1.1433 calculate D2E/DX2 analytically ! + ! R2 R(2,3) 1.1433 calculate D2E/DX2 analytically ! + ! A1 L(1,3,2,-2,-1) 180.0 calculate D2E/DX2 analytically ! + ! A2 L(1,3,2,-3,-2) 180.0 calculate D2E/DX2 analytically ! + -------------------------------------------------------------------------------- + Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 EigMax=2.50D+02 EigMin=1.00D-04 + Number of steps in this run= 2 maximum allowed number of steps= 2. + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 0.4 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) + Input orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 -0.766954 -0.376714 3.214136 + 2 8 0 1.144096 -0.008647 2.013815 + 3 6 0 0.188571 -0.192681 2.613975 + --------------------------------------------------------------------- + Distance matrix (angstroms): + 1 2 3 + 1 O 0.000000 + 2 O 2.286560 0.000000 + 3 C 1.143280 1.143280 0.000000 + Stoichiometry CO2 + Framework group D*H[O(C),C*(O.O)] + Deg. of freedom 1 + Full point group D*H NOp 8 + RotChk: IX=0 Diff= 4.44D-16 + Largest Abelian subgroup D2H NOp 8 + Largest concise Abelian subgroup C2 NOp 2 + Standard orientation: + --------------------------------------------------------------------- + Center Atomic Atomic Coordinates (Angstroms) + Number Number Type X Y Z + --------------------------------------------------------------------- + 1 8 0 0.000000 -0.000000 1.143280 + 2 8 0 0.000000 -0.000000 -1.143280 + 3 6 0 0.000000 0.000000 0.000000 + --------------------------------------------------------------------- + Rotational constants (GHZ): 0.0000000 12.0864862 12.0864862 + Leave Link 202 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 0.4 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l301.exe) + Standard basis: 6-31G(d) (6D, 7F) + Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. + There are 14 symmetry adapted cartesian basis functions of AG symmetry. + There are 2 symmetry adapted cartesian basis functions of B1G symmetry. + There are 4 symmetry adapted cartesian basis functions of B2G symmetry. + There are 4 symmetry adapted cartesian basis functions of B3G symmetry. + There are 1 symmetry adapted cartesian basis functions of AU symmetry. + There are 10 symmetry adapted cartesian basis functions of B1U symmetry. + There are 5 symmetry adapted cartesian basis functions of B2U symmetry. + There are 5 symmetry adapted cartesian basis functions of B3U symmetry. + There are 14 symmetry adapted basis functions of AG symmetry. + There are 2 symmetry adapted basis functions of B1G symmetry. + There are 4 symmetry adapted basis functions of B2G symmetry. + There are 4 symmetry adapted basis functions of B3G symmetry. + There are 1 symmetry adapted basis functions of AU symmetry. + There are 10 symmetry adapted basis functions of B1U symmetry. + There are 5 symmetry adapted basis functions of B2U symmetry. + There are 5 symmetry adapted basis functions of B3U symmetry. + 45 basis functions, 84 primitive gaussians, 45 cartesian basis functions + 11 alpha electrons 11 beta electrons + nuclear repulsion energy 59.2459262762 Hartrees. + IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 + ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 + IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 + NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F + Integral buffers will be 131072 words long. + Raffenetti 1 integral format. + Two-electron integral symmetry is turned on. + Leave Link 301 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 3.3 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l302.exe) + NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 + NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. + One-electron integrals computed using PRISM. + One-electron integral symmetry used in STVInt + NBasis= 45 RedAO= T EigKep= 2.77D-03 NBF= 14 2 4 4 1 10 5 5 + NBsUse= 45 1.00D-06 EigRej= -1.00D+00 NBFU= 14 2 4 4 1 10 5 5 + Leave Link 302 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 3.7 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l303.exe) + DipDrv: MaxL=1. + Leave Link 303 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l401.exe) + Initial guess from the checkpoint file: "/global/scratch/alex_epstein/line_c2o/Gau-207403.chk" + B after Tr= 0.000000 -0.000000 0.000000 + Rot= 1.000000 -0.000000 -0.000000 -0.000000 Ang= 0.00 deg. + Guess basis will be translated and rotated to current coordinates. + JPrj=2 DoOrth=T DoCkMO=T. + Initial guess orbital symmetries: + Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) + (PIU) (PIG) (PIG) + Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) + (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (DLTG) + (DLTG) (PIG) (PIG) (DLTU) (DLTU) (SGU) (DLTG) + (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) + (SGG) (SGU) (SGG) + The electronic state of the initial guess is 1-SGG. + Leave Link 401 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 4.3 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l502.exe) + Keep R1 ints in memory in symmetry-blocked form, NReq=7134369. + FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Closed shell SCF: + Using DIIS extrapolation, IDIIS= 1040. + NGot= 4800000000 LenX= 4799912550 LenY= 4799910084 + Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. + Requested convergence on MAX density matrix=1.00D-06. + Requested convergence on energy=1.00D-06. + No special actions if energy rises. + + Cycle 1 Pass 1 IDiag 1: + E= -187.634176201493 + DIIS: error= 4.01D-10 at cycle 1 NSaved= 1. + NSaved= 1 IEnMin= 1 EnMin= -187.634176201493 IErMin= 1 ErrMin= 4.01D-10 + ErrMax= 4.01D-10 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.50D-18 BMatP= 2.50D-18 + IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 + Coeff-Com: 0.100D+01 + Coeff: 0.100D+01 + Gap= 0.771 Goal= None Shift= 0.000 + Skip diagonalization as Alpha Fock matrix is already diagonal. + RMSDP=0.00D+00 MaxDP=0.00D+00 OVMax= 0.00D+00 + + SCF Done: E(RHF) = -187.634176201 A.U. after 1 cycles + NFock= 1 Conv=0.00D+00 -V/T= 2.0028 + KE= 1.871094202810D+02 PE=-5.611564169572D+02 EE= 1.271668941984D+02 + Leave Link 502 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 4.1 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l801.exe) + Range of M.O.s used for correlation: 1 45 + NBasis= 45 NAE= 11 NBE= 11 NFC= 0 NFV= 0 + NROrb= 45 NOA= 11 NOB= 11 NVA= 34 NVB= 34 + Leave Link 801 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 1.0 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1101.exe) + Using compressed storage, NAtomX= 3. + Will process 4 centers per pass. + Leave Link 1101 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 3.9 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1102.exe) + Symmetrizing basis deriv contribution to polar: + IMax=3 JMax=2 DiffMx= 0.00D+00 + Leave Link 1102 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1110.exe) + Forming Gx(P) for the SCF density, NAtomX= 3. + Integral derivatives from FoFJK, PRISM(SPDF). + Do as many integral derivatives as possible in FoFJK. + G2DrvN: MDV= 4799999660. + G2DrvN: will do 4 centers at a time, making 1 passes. + Calling FoFCou, ICntrl= 3107 FMM=F I1Cent= 0 AccDes= 0.00D+00. + FoFJK: IHMeth= 1 ICntrl= 3107 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 3107 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + End of G2Drv F.D. properties file 721 does not exist. + End of G2Drv F.D. properties file 722 does not exist. + End of G2Drv F.D. properties file 788 does not exist. + Leave Link 1110 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 5.5 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1002.exe) + Minotr: Closed shell wavefunction. + IDoAtm=111 + Direct CPHF calculation. + Differentiating once with respect to electric field. + with respect to dipole field. + Differentiating once with respect to nuclear coordinates. + Using symmetry in CPHF. + Requested convergence is 1.0D-08 RMS, and 1.0D-07 maximum. + Secondary convergence is 1.0D-12 RMS, and 1.0D-12 maximum. + NewPWx=T KeepS1=F KeepF1=F KeepIn=T MapXYZ=F SortEE=F KeepMc=T. + Keep R1 ints in memory in symmetry-blocked form, NReq=7134647. + FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + MDV= 4800000000 using IRadAn= 1. + Solving linear equations simultaneously, MaxMat= 0. + There are 9 degrees of freedom in the 1st order CPHF. IDoFFX=4 NUNeed= 9. + 9 vectors produced by pass 0 Test12= 4.16D-15 1.11D-08 XBig12= 6.14D+00 1.61D+00. + AX will form 9 AO Fock derivatives at one time. + 9 vectors produced by pass 1 Test12= 4.16D-15 1.11D-08 XBig12= 5.51D-01 2.86D-01. + 9 vectors produced by pass 2 Test12= 4.16D-15 1.11D-08 XBig12= 8.52D-03 4.00D-02. + 9 vectors produced by pass 3 Test12= 4.16D-15 1.11D-08 XBig12= 4.40D-05 3.33D-03. + 9 vectors produced by pass 4 Test12= 4.16D-15 1.11D-08 XBig12= 4.02D-07 3.42D-04. + 9 vectors produced by pass 5 Test12= 4.16D-15 1.11D-08 XBig12= 3.91D-09 2.22D-05. + 7 vectors produced by pass 6 Test12= 4.16D-15 1.11D-08 XBig12= 1.58D-11 1.48D-06. + 4 vectors produced by pass 7 Test12= 4.16D-15 1.11D-08 XBig12= 6.52D-14 8.91D-08. + InvSVY: IOpt=1 It= 1 EMax= 2.22D-16 + Solved reduced A of dimension 65 with 9 vectors. + FullF1: Do perturbations 1 to 9. + Isotropic polarizability for W= 0.000000 11.53 Bohr**3. + End of Minotr F.D. properties file 721 does not exist. + End of Minotr F.D. properties file 722 does not exist. + End of Minotr F.D. properties file 788 does not exist. + Leave Link 1002 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 4.0 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l601.exe) + Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0. + + ********************************************************************** + + Population analysis using the SCF density. + + ********************************************************************** + + Orbital symmetries: + Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) + (PIU) (PIG) (PIG) + Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) + (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (DLTG) + (DLTG) (PIG) (PIG) (DLTU) (DLTU) (SGU) (DLTG) + (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) + (SGG) (SGU) (SGG) + The electronic state is 1-SGG. + Alpha occ. eigenvalues -- -20.65784 -20.65782 -11.46212 -1.54200 -1.48690 + Alpha occ. eigenvalues -- -0.79261 -0.73924 -0.71908 -0.71908 -0.53995 + Alpha occ. eigenvalues -- -0.53995 + Alpha virt. eigenvalues -- 0.23058 0.23058 0.26636 0.51004 0.66340 + Alpha virt. eigenvalues -- 0.66340 0.84293 0.98303 0.99234 1.14705 + Alpha virt. eigenvalues -- 1.14705 1.33111 1.33111 1.45461 1.61575 + Alpha virt. eigenvalues -- 1.63482 1.63482 1.70440 1.70440 2.01268 + Alpha virt. eigenvalues -- 2.01268 2.08925 2.35732 2.35732 2.49060 + Alpha virt. eigenvalues -- 2.49060 3.14657 3.32784 3.35175 3.35175 + Alpha virt. eigenvalues -- 3.48917 4.18091 4.90146 4.90696 + Condensed to atoms (all electrons): + 1 2 3 + 1 O 7.841235 -0.025877 0.630900 + 2 O -0.025877 7.841235 0.630900 + 3 C 0.630900 0.630900 3.845681 + Mulliken charges: + 1 + 1 O -0.446259 + 2 O -0.446259 + 3 C 0.892518 + Sum of Mulliken charges = -0.00000 + Mulliken charges with hydrogens summed into heavy atoms: + 1 + 1 O -0.446259 + 2 O -0.446259 + 3 C 0.892518 + APT charges: + 1 + 1 O -0.757618 + 2 O -0.757618 + 3 C 1.515236 + Sum of APT charges = 0.00000 + APT charges with hydrogens summed into heavy atoms: + 1 + 1 O -0.757618 + 2 O -0.757618 + 3 C 1.515236 + Electronic spatial extent (au): = 110.9843 + Charge= 0.0000 electrons + Dipole moment (field-independent basis, Debye): + X= -0.0000 Y= 0.0000 Z= -0.0000 Tot= 0.0000 + Quadrupole moment (field-independent basis, Debye-Ang): + XX= -14.4559 YY= -14.4559 ZZ= -19.9144 + XY= -0.0000 XZ= -0.0000 YZ= 0.0000 + Traceless Quadrupole moment (field-independent basis, Debye-Ang): + XX= 1.8195 YY= 1.8195 ZZ= -3.6391 + XY= -0.0000 XZ= -0.0000 YZ= 0.0000 + Octapole moment (field-independent basis, Debye-Ang**2): + XXX= -0.0000 YYY= 0.0000 ZZZ= -0.0000 XYY= -0.0000 + XXY= 0.0000 XXZ= 0.0000 XZZ= -0.0000 YZZ= 0.0000 + YYZ= -0.0000 XYZ= 0.0000 + Hexadecapole moment (field-independent basis, Debye-Ang**3): + XXXX= -10.2550 YYYY= -10.2550 ZZZZ= -99.4698 XXXY= -0.0000 + XXXZ= -0.0000 YYYX= -0.0000 YYYZ= -0.0000 ZZZX= -0.0000 + ZZZY= -0.0000 XXYY= -3.4183 XXZZ= -17.9582 YYZZ= -17.9582 + XXYZ= -0.0000 YYXZ= -0.0000 ZZXY= -0.0000 + N-N= 5.924592627624D+01 E-N=-5.611564169572D+02 KE= 1.871094202810D+02 + Symmetry AG KE= 1.012480411172D+02 + Symmetry B1G KE= 6.425625434594D-32 + Symmetry B2G KE= 4.700699095130D+00 + Symmetry B3G KE= 4.700699095130D+00 + Symmetry AU KE= 4.036962633852D-32 + Symmetry B1U KE= 6.913256481077D+01 + Symmetry B2U KE= 3.663708081395D+00 + Symmetry B3U KE= 3.663708081395D+00 + Exact polarizability: 7.265 0.000 7.265 0.000 -0.000 20.046 + Approx polarizability: 6.855 0.000 6.855 0.000 0.000 21.410 + No NMR shielding tensors so no spin-rotation constants. + Leave Link 601 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 4.6 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l701.exe) + ... and contract with generalized density number 0. + Compute integral second derivatives. + Leave Link 701 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 4.7 elap: 0.2 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l702.exe) + L702 exits ... SP integral derivatives will be done elsewhere. + Leave Link 702 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 0.6 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l703.exe) + Integral derivatives from FoFJK, PRISM(SPDF). + Compute integral second derivatives, UseDBF=F ICtDFT= 0. + Calling FoFJK, ICntrl= 100127 FMM=F ISym2X=1 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0. + FoFJK: IHMeth= 1 ICntrl= 100127 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F + IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. + FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 800 + NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T + wScrn= 0.000000 ICntrl= 100127 IOpCl= 0 I1Cent= 0 NGrid= 0 + NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 + Petite list used in FoFCou. + Leave Link 703 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 12.3 elap: 0.4 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l716.exe) + Dipole =-4.12474804D-16 5.96103206D-18-6.00536387D-17 + Polarizability= 7.26459359D+00 1.04356972D-15 7.26459359D+00 + 4.00195616D-16-8.24734058D-16 2.00463336D+01 + HyperPolar =-2.05313456D-14-8.23492026D-16-7.08130094D-15 + -2.48077388D-15 4.90831008D-09-4.13155815D-17 + 4.90830245D-09-9.49123619D-15-2.35777082D-15 + -1.28018861D-08 + Full mass-weighted force constant matrix: + Low frequencies --- -0.0015 0.0009 0.0009 6.8752 6.8752 745.8810 + Low frequencies --- 745.8810 1518.3734 2584.7877 + Diagonal vibrational polarizability: + 3.3342741 3.3342741 3.9818087 + Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering + activities (A**4/AMU), depolarization ratios for plane and unpolarized + incident light, reduced masses (AMU), force constants (mDyne/A), + and normal coordinates: + 1 2 3 + PIU PIU SGG + Frequencies -- 745.8810 745.8810 1518.3734 + Red. masses -- 12.8774 12.8774 15.9949 + Frc consts -- 4.2210 4.2210 21.7265 + IR Inten -- 68.9298 68.9298 0.0000 + Atom AN X Y Z X Y Z X Y Z + 1 8 -0.03 -0.33 -0.00 -0.33 0.03 -0.00 -0.00 0.00 0.71 + 2 8 -0.03 -0.33 0.00 -0.33 0.03 0.00 -0.00 0.00 -0.71 + 3 6 0.07 0.88 -0.00 0.88 -0.07 0.00 0.00 -0.00 -0.00 + 4 + SGU + Frequencies -- 2584.7877 + Red. masses -- 12.8774 + Frc consts -- 50.6906 + IR Inten -- 988.5463 + Atom AN X Y Z + 1 8 0.00 -0.00 -0.33 + 2 8 0.00 -0.00 -0.33 + 3 6 -0.00 0.00 0.88 + + ------------------- + - Thermochemistry - + ------------------- + Temperature 298.150 Kelvin. Pressure 1.00000 Atm. + Atom 1 has atomic number 8 and mass 15.99491 + Atom 2 has atomic number 8 and mass 15.99491 + Atom 3 has atomic number 6 and mass 12.00000 + Molecular mass: 43.98983 amu. + Principal axes and moments of inertia in atomic units: + 1 2 3 + Eigenvalues -- 0.00000 149.31893 149.31893 + X 0.00000 0.50717 0.86184 + Y 0.00000 0.86184 -0.50717 + Z 1.00000 -0.00000 -0.00000 + This molecule is a prolate symmetric top. + Rotational symmetry number 2. + Rotational temperature (Kelvin) 0.58006 + Rotational constant (GHZ): 12.086486 + Zero-point vibrational energy 33465.1 (Joules/Mol) + 7.99834 (Kcal/Mol) + Vibrational temperatures: 1073.16 1073.16 2184.60 3718.93 + (Kelvin) + + Zero-point correction= 0.012746 (Hartree/Particle) + Thermal correction to Energy= 0.015302 + Thermal correction to Enthalpy= 0.016246 + Thermal correction to Gibbs Free Energy= -0.007894 + Sum of electronic and zero-point Energies= -187.621430 + Sum of electronic and thermal Energies= -187.618874 + Sum of electronic and thermal Enthalpies= -187.617930 + Sum of electronic and thermal Free Energies= -187.642070 + + E (Thermal) CV S + KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin + Total 9.602 6.527 50.808 + Electronic 0.000 0.000 0.000 + Translational 0.889 2.981 37.270 + Rotational 0.592 1.987 13.014 + Vibrational 8.121 1.559 0.523 + Q Log10(Q) Ln(Q) + Total Bot 0.427516D+04 3.630953 8.360578 + Total V=0 0.311731D+10 9.493780 21.860236 + Vib (Bot) 0.145057D-05 -5.838461 -13.443554 + Vib (V=0) 0.105771D+01 0.024366 0.056104 + Electronic 0.100000D+01 0.000000 0.000000 + Translational 0.114679D+08 7.059482 16.255059 + Rotational 0.256999D+03 2.409932 5.549073 + + co2 for linear test + IR Spectrum + + 2 1 + 5 5 7 + 8 1 4 + 5 8 6 + + X X + X X + X X + X + X + X + X + X + X + X + X + X + X + X + X + X + X + X + X + X + + ***** Axes restored to original set ***** + ------------------------------------------------------------------- + Center Atomic Forces (Hartrees/Bohr) + Number Number X Y Z + ------------------------------------------------------------------- + 1 8 0.000051665 0.000009951 -0.000032450 + 2 8 -0.000051665 -0.000009951 0.000032450 + 3 6 0.000000000 -0.000000000 0.000000000 + ------------------------------------------------------------------- + Cartesian Forces: Max 0.000051665 RMS 0.000029141 + Force constants in Cartesian coordinates: + 1 2 3 4 5 + 1 0.886547D+00 + 2 0.161899D+00 0.771275D-01 + 3 -0.527977D+00 -0.101688D+00 0.377566D+00 + 4 -0.882483D-01 -0.258402D-01 0.842687D-01 0.886547D+00 + 5 -0.258402D-01 0.409405D-01 0.162301D-01 0.161899D+00 0.771275D-01 + 6 0.842687D-01 0.162301D-01 -0.701151D-02 -0.527977D+00 -0.101688D+00 + 7 -0.798298D+00 -0.136059D+00 0.443709D+00 -0.798298D+00 -0.136059D+00 + 8 -0.136059D+00 -0.118068D+00 0.854579D-01 -0.136059D+00 -0.118068D+00 + 9 0.443709D+00 0.854579D-01 -0.370554D+00 0.443709D+00 0.854579D-01 + 6 7 8 9 + 6 0.377566D+00 + 7 0.443709D+00 0.159660D+01 + 8 0.854579D-01 0.272118D+00 0.236136D+00 + 9 -0.370554D+00 -0.887417D+00 -0.170916D+00 0.741109D+00 + FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. + Force constants in internal coordinates: + 1 2 3 4 + 1 0.124935D+01 + 2 0.146154D+00 0.124935D+01 + 3 0.000000D+00 0.000000D+00 0.210909D+00 + 4 0.000000D+00 0.000000D+00 -0.182959D-01 0.156853D+00 + Leave Link 716 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 1.8 elap: 0.1 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) + + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + Berny optimization. + Red2BG is reusing G-inverse. + Internal Forces: Max 0.000061817 RMS 0.000043711 + Search for a local minimum. + Step number 1 out of a maximum of 2 + All quantities printed in internal units (Hartrees-Bohrs-Radians) + Second derivative matrix not updated -- analytic derivatives used. + The second derivative matrix: + R1 R2 A1 A2 + R1 1.24935 + R2 0.14615 1.24935 + A1 -0.00000 0.00000 0.21091 + A2 -0.00000 0.00000 -0.01830 0.15685 + ITU= 0 + Eigenvalues --- 0.15124 0.21652 1.10319 1.39550 + Angle between quadratic step and forces= 0.00 degrees. + Linear search not attempted -- first point. + Iteration 1 RMS(Cart)= 0.00003132 RMS(Int)= 0.00000000 + Iteration 2 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000000 + ITry= 1 IFail=0 DXMaxC= 3.70D-05 DCOld= 1.00D+10 DXMaxT= 3.00D-01 DXLimC= 3.00D+00 Rises=F + ClnCor: largest displacement from symmetrization is 1.20D-09 for atom 3. + Variable Old X -DE/DX Delta X Delta X Delta X New X + (Linear) (Quad) (Total) + R1 2.16049 -0.00006 0.00000 -0.00004 -0.00004 2.16044 + R2 2.16049 -0.00006 0.00000 -0.00004 -0.00004 2.16044 + A1 3.14159 -0.00000 0.00000 -0.00000 0.00000 3.14159 + A2 3.14159 -0.00000 0.00000 -0.00000 -0.00000 3.14159 + Item Value Threshold Converged? + Maximum Force 0.000062 0.000450 YES + RMS Force 0.000044 0.000300 YES + Maximum Displacement 0.000037 0.001800 YES + RMS Displacement 0.000031 0.001200 YES + Predicted change in Energy=-2.738298D-09 + Optimization completed. + -- Stationary point found. + ---------------------------- + ! Optimized Parameters ! + ! (Angstroms and Degrees) ! + -------------------------- -------------------------- + ! Name Definition Value Derivative Info. ! + -------------------------------------------------------------------------------- + ! R1 R(1,3) 1.1433 -DE/DX = -0.0001 ! + ! R2 R(2,3) 1.1433 -DE/DX = -0.0001 ! + ! A1 L(1,3,2,-2,-1) 180.0 -DE/DX = 0.0 ! + ! A2 L(1,3,2,-3,-2) 180.0 -DE/DX = 0.0 ! + -------------------------------------------------------------------------------- + GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad + + Leave Link 103 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 0.3 elap: 0.0 + (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l9999.exe) + Dipole is zero, so no output in dipole orientation. + + ---------------------------------------------------------------------- + + Electric dipole moment (input orientation): + (Debye = 10**-18 statcoulomb cm , SI units = C m) + (au) (Debye) (10**-30 SI) + Tot 0.000000D+00 0.000000D+00 0.000000D+00 + x 0.000000D+00 0.000000D+00 0.000000D+00 + y 0.000000D+00 0.000000D+00 0.000000D+00 + z 0.000000D+00 0.000000D+00 0.000000D+00 + + Dipole polarizability, Alpha (input orientation). + (esu units = cm**3 , SI units = C**2 m**2 J**-1) + Alpha(0;0): + (au) (10**-24 esu) (10**-40 SI) + iso 0.115252D+02 0.170785D+01 0.190024D+01 + aniso 0.127817D+02 0.189406D+01 0.210742D+01 + xx 0.161929D+02 0.239954D+01 0.266985D+01 + yx 0.171958D+01 0.254816D+00 0.283521D+00 + yy 0.759578D+01 0.112558D+01 0.125238D+01 + zx -0.560782D+01 -0.830994D+00 -0.924605D+00 + zy -0.108006D+01 -0.160049D+00 -0.178078D+00 + zz 0.107868D+02 0.159844D+01 0.177851D+01 + + ---------------------------------------------------------------------- + 1\1\GINC-N0045\Freq\RHF\6-31G(d)\C1O2\ALEX_EPSTEIN\10-Jun-2021\0\\#P G + eom=AllCheck Guess=TCheck SCRF=Check GenChk RHF/6-31G(d) Freq\\co2 for + linear test\\0,1\O,-0.7669543606,-0.3767139767,3.2141361692\O,1.14409 + 56549,-0.0086472867,2.0138147763\C,0.1885706471,-0.1926806317,2.613975 + 4728\\Version=ES64L-G16RevA.03\State=1-SGG\HF=-187.6341762\RMSD=0.000e + +00\RMSF=2.914e-05\ZeroPoint=0.0127462\Thermal=0.0153023\Dipole=0.,0., + 0.\DipoleDeriv=-1.1573511,-0.1472612,0.480241,-0.1472612,-0.4211144,0. + 092494,0.480241,0.092494,-0.6943891,-1.1573511,-0.1472612,0.480241,-0. + 1472612,-0.4211144,0.092494,0.480241,0.092494,-0.6943891,2.3147021,0.2 + 945223,-0.960482,0.2945223,0.8422288,-0.1849881,-0.960482,-0.1849881,1 + .3887782\Polar=16.1928957,1.7195838,7.595784,-5.6078239,-1.0800624,10. + 786841\HyperPolar=0.,0.,0.,0.,0.,0.,0.,0.,0.,0.\Quadrupole=-1.4820442, + 1.2476169,0.2344273,-0.5459835,1.7805351,0.3429296\PG=D*H [O(C1),C*(O1 + .O1)]\NImag=0\\0.88654668,0.16189903,0.07712751,-0.52797735,-0.1016880 + 1,0.37756594,-0.08824827,-0.02584017,0.08426874,0.88654668,-0.02584017 + ,0.04094048,0.01623009,0.16189903,0.07712751,0.08426874,0.01623009,-0. + 00701151,-0.52797735,-0.10168801,0.37756594,-0.79829842,-0.13605886,0. + 44370861,-0.79829842,-0.13605886,0.44370861,1.59659684,-0.13605886,-0. + 11806799,0.08545792,-0.13605886,-0.11806799,0.08545792,0.27211772,0.23 + 613597,0.44370861,0.08545792,-0.37055442,0.44370861,0.08545792,-0.3705 + 5442,-0.88741723,-0.17091584,0.74110884\\-0.00005166,-0.00000995,0.000 + 03245,0.00005166,0.00000995,-0.00003245,0.,0.,0.\\\@ + + + NEVER LISTEN TO CRITICISM + OR YOU'LL BE DOIN' EVERYBODY ELSE'S THING BUT BUT YOUR OWN. + + -- ANDY CAPP + Job cpu time: 0 days 0 hours 1 minutes 10.3 seconds. + Elapsed time: 0 days 0 hours 0 minutes 2.6 seconds. + File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 + Normal termination of Gaussian 16 at Thu Jun 10 18:06:05 2021. From 9bf5f12b47486fb8fb3d3fb8bebeab62252b2212 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 4 Mar 2022 17:33:56 +0000 Subject: [PATCH 02/25] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- pymatgen/analysis/quasirrho.py | 17 +++++++++-------- pymatgen/analysis/tests/test_quasirrho.py | 1 - 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 0f6e26a5fb8..1b869009c59 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -1,4 +1,3 @@ -# coding: utf-8 # Copyright (c) Pymatgen Development Team. # Distributed under the terms of the MIT License. @@ -17,14 +16,16 @@ __date__ = "January 5, 2021" __credits__ = "Steven Wheeler, Trevor Seguin, Evan Spotte-Smith" +from math import isclose from typing import Union import numpy as np +import scipy.constants as const + +from pymatgen.core.units import amu_to_kg +from pymatgen.core.units import kb as kb_ev from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.qchem.outputs import QCOutput -from math import isclose -from pymatgen.core.units import amu_to_kg, kb as kb_ev -import scipy.constants as const # Define useful constants kb = kb_ev * const.eV # pymatgen kb from ev/K to J/K @@ -177,11 +178,11 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): # Rotational component of Entropy and Energy if linear: i = np.amax(i_eigen) - qr = 8 * np.pi ** 2 * i * kb * self.temp / (sigma_r * (h * h)) + qr = 8 * np.pi**2 * i * kb * self.temp / (sigma_r * (h * h)) sr = R * (np.log(qr) + 1) er = R * self.temp else: - rot_temps = [h ** 2 / (np.pi ** 2 * kb * 8 * i) for i in i_eigen] + rot_temps = [h**2 / (np.pi**2 * kb * 8 * i) for i in i_eigen] qr = np.sqrt(np.pi) / sigma_r * self.temp ** (3 / 2) / np.sqrt(rot_temps[0] * rot_temps[1] * rot_temps[2]) sr = R * (np.log(qr) + 3 / 2) er = 3 * R * self.temp / 2 @@ -196,9 +197,9 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): sv_temp = vt / (self.temp * (np.exp(vt / self.temp) - 1)) - np.log(1 - np.exp(-vt / self.temp)) sv += sv_temp - mu = h / (8 * np.pi ** 2 * vt * c) + mu = h / (8 * np.pi**2 * vt * c) mu_prime = mu * Bav / (mu + Bav) - srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi ** 3 * mu_prime * kb * self.temp / h ** 2)) + srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi**3 * mu_prime * kb * self.temp / h**2)) weight = 1 / (1 + (self.v0 / vt) ** 4) sv_quasiRRHO += weight * sv_temp + (1 - weight) * srotor diff --git a/pymatgen/analysis/tests/test_quasirrho.py b/pymatgen/analysis/tests/test_quasirrho.py index be271f7bc25..b3c2a05ac9e 100644 --- a/pymatgen/analysis/tests/test_quasirrho.py +++ b/pymatgen/analysis/tests/test_quasirrho.py @@ -1,4 +1,3 @@ -# coding: utf-8 # Copyright (c) Pymatgen Development Team. # Distributed under the terms of the MIT License. """ From ed81ba288b5e343589bb4d7d46799c29b29f6ec8 Mon Sep 17 00:00:00 2001 From: Alex Epstein Date: Fri, 4 Mar 2022 09:46:30 -0800 Subject: [PATCH 03/25] pylint debugging Tried to make avg_mom_inertia an internal function --- pymatgen/analysis/quasirrho.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 0f6e26a5fb8..00d8661d9c6 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -107,7 +107,7 @@ def __init__( elec_energy=output["elec_energy"], ) - def get_avg_mom_inertia(self, mol): + def _get_avg_mom_inertia(self, mol): """ Caclulate the average moment of inertia of a molecule :param mol: Molecule @@ -163,7 +163,7 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): se = R * np.log(mult) # Get properties related to rotational symmetry. Bav is average moment of inertia - Bav, i_eigen = self.get_avg_mom_inertia(mol) + Bav, i_eigen = self._get_avg_mom_inertia(mol) # Check if linear coords = mol.cart_coords From ba4edbe9d1231132d6be83eef7e52c88bf547ad7 Mon Sep 17 00:00:00 2001 From: Alex Epstein Date: Fri, 4 Mar 2022 16:01:38 -0800 Subject: [PATCH 04/25] Pylint fixing Moved get_avg_mom_inertia outside the class --- pymatgen/analysis/quasirrho.py | 53 ++++++++++++++++++---------------- 1 file changed, 28 insertions(+), 25 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 8fc0163cb6b..39eb97b2cea 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -37,6 +37,33 @@ kcal2hartree = 0.0015936 # kcal/mol to hartree/mol +def get_avg_mom_inertia(mol): + """ + Caclulate the average moment of inertia of a molecule + :param mol: Molecule + :return: average moment of inertia, eigenvalues of inertia tensor + """ + centered_mol = mol.get_centered_molecule() + inertia_tensor = np.zeros((3, 3)) + for site in centered_mol: + c = site.coords + wt = site.specie.atomic_mass + for i in range(3): + inertia_tensor[i, i] += wt * ( + c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2) + for i, j in [(0, 1), (1, 2), (0, 2)]: + inertia_tensor[i, j] += -wt * c[i] * c[j] + inertia_tensor[j, i] += -wt * c[j] * c[i] + + inertia_eigenvals = np.multiply( + np.linalg.eig(inertia_tensor)[0], amu_to_kg * 1e-20 + ).tolist() # amuangs^2 to kg m^2 + + iav = np.average(inertia_eigenvals) + + return iav, inertia_eigenvals + + class QuasiRRHO: """ Class to calculate thermochemistry using Grimme's Quasi-RRHO approximation. @@ -108,30 +135,6 @@ def __init__( elec_energy=output["elec_energy"], ) - def _get_avg_mom_inertia(self, mol): - """ - Caclulate the average moment of inertia of a molecule - :param mol: Molecule - :return: average moment of inertia, eigenvalues of inertia tensor - """ - centered_mol = mol.get_centered_molecule() - inertia_tensor = np.zeros((3, 3)) - for site in centered_mol: - c = site.coords - wt = site.specie.atomic_mass - for i in range(3): - inertia_tensor[i, i] += wt * (c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2) - for i, j in [(0, 1), (1, 2), (0, 2)]: - inertia_tensor[i, j] += -wt * c[i] * c[j] - inertia_tensor[j, i] += -wt * c[j] * c[i] - - inertia_eigenvals = np.multiply( - np.linalg.eig(inertia_tensor)[0], amu_to_kg * 1e-20 - ).tolist() # amuangs^2 to kg m^2 - - iav = np.average(inertia_eigenvals) - - return iav, inertia_eigenvals def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): """ @@ -164,7 +167,7 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): se = R * np.log(mult) # Get properties related to rotational symmetry. Bav is average moment of inertia - Bav, i_eigen = self._get_avg_mom_inertia(mol) + Bav, i_eigen = get_avg_mom_inertia(mol) # Check if linear coords = mol.cart_coords From 793897a9c7f9e5619f5e25a31e0fcd098f661881 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Sat, 5 Mar 2022 00:04:26 +0000 Subject: [PATCH 05/25] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- pymatgen/analysis/quasirrho.py | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 39eb97b2cea..86fb9fef31a 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -49,15 +49,12 @@ def get_avg_mom_inertia(mol): c = site.coords wt = site.specie.atomic_mass for i in range(3): - inertia_tensor[i, i] += wt * ( - c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2) + inertia_tensor[i, i] += wt * (c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2) for i, j in [(0, 1), (1, 2), (0, 2)]: inertia_tensor[i, j] += -wt * c[i] * c[j] inertia_tensor[j, i] += -wt * c[j] * c[i] - inertia_eigenvals = np.multiply( - np.linalg.eig(inertia_tensor)[0], amu_to_kg * 1e-20 - ).tolist() # amuangs^2 to kg m^2 + inertia_eigenvals = np.multiply(np.linalg.eig(inertia_tensor)[0], amu_to_kg * 1e-20).tolist() # amuangs^2 to kg m^2 iav = np.average(inertia_eigenvals) @@ -135,7 +132,6 @@ def __init__( elec_energy=output["elec_energy"], ) - def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): """ Caclulate Quasi-RRHO thermochemistry From 023ba4883d3ef8897f68d76c37238469a8737c5d Mon Sep 17 00:00:00 2001 From: Alex Epstein Date: Mon, 7 Mar 2022 10:50:50 -0800 Subject: [PATCH 06/25] black --- pymatgen/analysis/quasirrho.py | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 39eb97b2cea..85f2eb34638 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -49,15 +49,12 @@ def get_avg_mom_inertia(mol): c = site.coords wt = site.specie.atomic_mass for i in range(3): - inertia_tensor[i, i] += wt * ( - c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2) + inertia_tensor[i, i] += wt * (c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2) for i, j in [(0, 1), (1, 2), (0, 2)]: inertia_tensor[i, j] += -wt * c[i] * c[j] inertia_tensor[j, i] += -wt * c[j] * c[i] - inertia_eigenvals = np.multiply( - np.linalg.eig(inertia_tensor)[0], amu_to_kg * 1e-20 - ).tolist() # amuangs^2 to kg m^2 + inertia_eigenvals = np.multiply(np.linalg.eig(inertia_tensor)[0], amu_to_kg * 1e-20).tolist() # amuangs^2 to kg m^2 iav = np.average(inertia_eigenvals) @@ -135,7 +132,6 @@ def __init__( elec_energy=output["elec_energy"], ) - def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): """ Caclulate Quasi-RRHO thermochemistry @@ -181,11 +177,11 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): # Rotational component of Entropy and Energy if linear: i = np.amax(i_eigen) - qr = 8 * np.pi**2 * i * kb * self.temp / (sigma_r * (h * h)) + qr = 8 * np.pi ** 2 * i * kb * self.temp / (sigma_r * (h * h)) sr = R * (np.log(qr) + 1) er = R * self.temp else: - rot_temps = [h**2 / (np.pi**2 * kb * 8 * i) for i in i_eigen] + rot_temps = [h ** 2 / (np.pi ** 2 * kb * 8 * i) for i in i_eigen] qr = np.sqrt(np.pi) / sigma_r * self.temp ** (3 / 2) / np.sqrt(rot_temps[0] * rot_temps[1] * rot_temps[2]) sr = R * (np.log(qr) + 3 / 2) er = 3 * R * self.temp / 2 @@ -200,9 +196,9 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): sv_temp = vt / (self.temp * (np.exp(vt / self.temp) - 1)) - np.log(1 - np.exp(-vt / self.temp)) sv += sv_temp - mu = h / (8 * np.pi**2 * vt * c) + mu = h / (8 * np.pi ** 2 * vt * c) mu_prime = mu * Bav / (mu + Bav) - srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi**3 * mu_prime * kb * self.temp / h**2)) + srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi ** 3 * mu_prime * kb * self.temp / h ** 2)) weight = 1 / (1 + (self.v0 / vt) ** 4) sv_quasiRRHO += weight * sv_temp + (1 - weight) * srotor From 80f2cc208fdddaa3ec574b5fb7dcefa25b82319d Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Mon, 7 Mar 2022 18:55:33 +0000 Subject: [PATCH 07/25] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- pymatgen/analysis/quasirrho.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 85f2eb34638..86fb9fef31a 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -177,11 +177,11 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): # Rotational component of Entropy and Energy if linear: i = np.amax(i_eigen) - qr = 8 * np.pi ** 2 * i * kb * self.temp / (sigma_r * (h * h)) + qr = 8 * np.pi**2 * i * kb * self.temp / (sigma_r * (h * h)) sr = R * (np.log(qr) + 1) er = R * self.temp else: - rot_temps = [h ** 2 / (np.pi ** 2 * kb * 8 * i) for i in i_eigen] + rot_temps = [h**2 / (np.pi**2 * kb * 8 * i) for i in i_eigen] qr = np.sqrt(np.pi) / sigma_r * self.temp ** (3 / 2) / np.sqrt(rot_temps[0] * rot_temps[1] * rot_temps[2]) sr = R * (np.log(qr) + 3 / 2) er = 3 * R * self.temp / 2 @@ -196,9 +196,9 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): sv_temp = vt / (self.temp * (np.exp(vt / self.temp) - 1)) - np.log(1 - np.exp(-vt / self.temp)) sv += sv_temp - mu = h / (8 * np.pi ** 2 * vt * c) + mu = h / (8 * np.pi**2 * vt * c) mu_prime = mu * Bav / (mu + Bav) - srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi ** 3 * mu_prime * kb * self.temp / h ** 2)) + srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi**3 * mu_prime * kb * self.temp / h**2)) weight = 1 / (1 + (self.v0 / vt) ** 4) sv_quasiRRHO += weight * sv_temp + (1 - weight) * srotor From 8e6e005aa1468a17963d57459aaf08be3ab73569 Mon Sep 17 00:00:00 2001 From: Alex Epstein Date: Mon, 7 Mar 2022 10:58:33 -0800 Subject: [PATCH 08/25] black 22.1.0 --- pymatgen/analysis/quasirrho.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 85f2eb34638..86fb9fef31a 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -177,11 +177,11 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): # Rotational component of Entropy and Energy if linear: i = np.amax(i_eigen) - qr = 8 * np.pi ** 2 * i * kb * self.temp / (sigma_r * (h * h)) + qr = 8 * np.pi**2 * i * kb * self.temp / (sigma_r * (h * h)) sr = R * (np.log(qr) + 1) er = R * self.temp else: - rot_temps = [h ** 2 / (np.pi ** 2 * kb * 8 * i) for i in i_eigen] + rot_temps = [h**2 / (np.pi**2 * kb * 8 * i) for i in i_eigen] qr = np.sqrt(np.pi) / sigma_r * self.temp ** (3 / 2) / np.sqrt(rot_temps[0] * rot_temps[1] * rot_temps[2]) sr = R * (np.log(qr) + 3 / 2) er = 3 * R * self.temp / 2 @@ -196,9 +196,9 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): sv_temp = vt / (self.temp * (np.exp(vt / self.temp) - 1)) - np.log(1 - np.exp(-vt / self.temp)) sv += sv_temp - mu = h / (8 * np.pi ** 2 * vt * c) + mu = h / (8 * np.pi**2 * vt * c) mu_prime = mu * Bav / (mu + Bav) - srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi ** 3 * mu_prime * kb * self.temp / h ** 2)) + srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi**3 * mu_prime * kb * self.temp / h**2)) weight = 1 / (1 + (self.v0 / vt) ** 4) sv_quasiRRHO += weight * sv_temp + (1 - weight) * srotor From e8a6a813e24a2d400a6124b05d9a5ca49d485211 Mon Sep 17 00:00:00 2001 From: Ryan Kingsbury Date: Sun, 5 Mar 2023 12:39:29 -0800 Subject: [PATCH 09/25] QuasiRRHO: edits --- pymatgen/analysis/quasirrho.py | 30 +++++++++++++++--------------- 1 file changed, 15 insertions(+), 15 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 86fb9fef31a..c114f85a08d 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -8,6 +8,8 @@ See: Grimme, S. Chem. Eur. J. 2012, 18, 9955 """ +from __future__ import annotations + __author__ = "Alex Epstein" __copyright__ = "Copyright 2020, The Materials Project" __version__ = "0.1" @@ -17,11 +19,11 @@ __credits__ = "Steven Wheeler, Trevor Seguin, Evan Spotte-Smith" from math import isclose -from typing import Union import numpy as np import scipy.constants as const +from pymatgen.core import Molecule from pymatgen.core.units import amu_to_kg from pymatgen.core.units import kb as kb_ev from pymatgen.io.gaussian import GaussianOutput @@ -39,7 +41,7 @@ def get_avg_mom_inertia(mol): """ - Caclulate the average moment of inertia of a molecule + Calculate the average moment of inertia of a molecule :param mol: Molecule :return: average moment of inertia, eigenvalues of inertia tensor """ @@ -67,9 +69,7 @@ class QuasiRRHO: All outputs are in atomic units. """ - def __init__( - self, output: Union[GaussianOutput, QCOutput, dict], sigma_r=1, temp=298.15, press=101317, conc=1, v0=100 - ): + def __init__(self, output: GaussianOutput | QCOutput | dict, sigma_r=1, temp=298.15, press=101317, conc=1, v0=100): """ :param output: Requires input of a Gaussian output file, @@ -83,7 +83,6 @@ def __init__( :param conc (float): Solvent concentration [M] :param v0 (float): Cutoff frequency for Quasi-RRHO method [cm^1] """ - # TO-DO: calculate sigma_r with PointGroupAnalyzer # and/or edit Gaussian and QChem io to parse for sigma_r @@ -96,6 +95,7 @@ def __init__( self.entropy_quasiRRHO = None # Ha/K self.free_energy_quasiRRHO = None # Ha self.concentration_corrected_g_quasiRRHO = None # Ha + self.h_corrected = None self.entropy_ho = None # Ha/K self.free_energy_ho = None # Ha @@ -124,24 +124,24 @@ def __init__( ) if isinstance(output, dict): + mol = Molecule.from_dict(output.get("optimized_molecule", output.get("initial_molecule"))) self._get_quasirrho_thermo( - mol=output["mol"], - mult=output["mult"], + mol=mol, + mult=mol.spin_multiplicity, sigma_r=self.sigma_r, - frequencies=output["frequencies"], - elec_energy=output["elec_energy"], + frequencies=output.get("frequencies", []), + elec_energy=output["final_energy"], ) def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): """ - Caclulate Quasi-RRHO thermochemistry + Calculate Quasi-RRHO thermochemistry :param mol: Molecule :param mult: Spin multiplicity :param sigma_r: Rotational symmetry number :param frequencies: List of frequencies [a.u.] :param elec_energy: Electronic energy [a.u.] """ - # Calculate mass in kg mass = 0 for site in mol.sites: @@ -206,14 +206,14 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): sv *= R ev *= R etot = (et + er + ev) * kcal2hartree / 1000 - h_corrected = etot + R * self.temp * kcal2hartree / 1000 + self.h_corrected = etot + R * self.temp * kcal2hartree / 1000 molarity_corr = 0.000003166488448771253 * self.temp * np.log(0.082057338 * self.temp * self.conc) self.entropy_ho = st + sr + sv + se - self.free_energy_ho = elec_energy + h_corrected - (self.temp * self.entropy_ho * kcal2hartree / 1000) + self.free_energy_ho = elec_energy + self.h_corrected - (self.temp * self.entropy_ho * kcal2hartree / 1000) self.entropy_quasiRRHO = st + sr + sv_quasiRRHO + se self.free_energy_quasiRRHO = ( - elec_energy + h_corrected - (self.temp * self.entropy_quasiRRHO * kcal2hartree / 1000) + elec_energy + self.h_corrected - (self.temp * self.entropy_quasiRRHO * kcal2hartree / 1000) ) self.concentration_corrected_g_quasiRRHO = self.free_energy_quasiRRHO + molarity_corr From dcb07ef2a183d5aaf041e83c62bbdbe0209bbc90 Mon Sep 17 00:00:00 2001 From: Ryan Kingsbury Date: Sun, 5 Mar 2023 12:42:55 -0800 Subject: [PATCH 10/25] QuasiRRHO: update tests --- pymatgen/analysis/tests/test_quasirrho.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/pymatgen/analysis/tests/test_quasirrho.py b/pymatgen/analysis/tests/test_quasirrho.py index b3c2a05ac9e..e239fd40440 100644 --- a/pymatgen/analysis/tests/test_quasirrho.py +++ b/pymatgen/analysis/tests/test_quasirrho.py @@ -59,9 +59,8 @@ def test_rrho_manual(self): Test manual input creation. Values from GaussianOutput """ rrho_in = {} - rrho_in["mult"] = self.gout.spin_multiplicity - rrho_in["elec_energy"] = self.gout.final_energy - rrho_in["mol"] = self.gout.final_structure + rrho_in["final_energy"] = self.gout.final_energy + rrho_in["optimized_molecule"] = self.gout.final_structure.as_dict() vib_freqs = [f["frequency"] for f in self.gout.frequencies[-1]] rrho_in["frequencies"] = vib_freqs From 8e8e256c2e4db7815d3e595dcf1117239f4d4987 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Tue, 1 Aug 2023 17:35:10 +0000 Subject: [PATCH 11/25] pre-commit auto-fixes --- pymatgen/analysis/tests/test_quasirrho.py | 1 + 1 file changed, 1 insertion(+) diff --git a/pymatgen/analysis/tests/test_quasirrho.py b/pymatgen/analysis/tests/test_quasirrho.py index e239fd40440..4350f89acce 100644 --- a/pymatgen/analysis/tests/test_quasirrho.py +++ b/pymatgen/analysis/tests/test_quasirrho.py @@ -3,6 +3,7 @@ """ Testing for quasirrho.py """ +from __future__ import annotations import os From aef77b1397173825b06c862b7ef2128d227dd1ce Mon Sep 17 00:00:00 2001 From: Alex Epstein Date: Tue, 1 Aug 2023 13:46:07 -0700 Subject: [PATCH 12/25] Incorporating comments - Cleaned up constants to use scipy.const - Created general __init__ and added functions from_GuassianOutput and from_QCOutput - Updated to google style docstrings --- pymatgen/analysis/quasirrho.py | 171 ++++++++++++++-------- pymatgen/analysis/tests/test_quasirrho.py | 58 +++++--- 2 files changed, 145 insertions(+), 84 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index c114f85a08d..70c87914bea 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -15,8 +15,8 @@ __version__ = "0.1" __maintainer__ = "Alex Epstein" __email__ = "aepstein@lbl.gov" -__date__ = "January 5, 2021" -__credits__ = "Steven Wheeler, Trevor Seguin, Evan Spotte-Smith" +__date__ = "August 1, 2023" +__credits__ = "Ryan Kingsbury, Steven Wheeler, Trevor Seguin, " "Evan Spotte-Smith" from math import isclose @@ -24,26 +24,34 @@ import scipy.constants as const from pymatgen.core import Molecule -from pymatgen.core.units import amu_to_kg from pymatgen.core.units import kb as kb_ev from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.qchem.outputs import QCOutput # Define useful constants -kb = kb_ev * const.eV # pymatgen kb from ev/K to J/K -c = const.speed_of_light * 100 # cm/s -h = const.h # Planck's constant J.s -R = const.R / const.calorie # Ideal gas constant cal/mol +kb = kb_ev * const.eV # Pymatgen kb [J/k] +c = const.speed_of_light * 100 # [cm/s] +h = const.h # Planck's constant [J.s] +R = const.R / const.calorie # Ideal gas constant [cal/mol/K] +R_ha = const.R / const.value("Hartree energy") / const.Avogadro # Ideal gas +# constant [Ha/K] +R_volume = const.R / const.atm * 1000 # Ideal gas constant [L.atm.K^−1.mol^−1] # Define useful conversion factors -kcal2hartree = 0.0015936 # kcal/mol to hartree/mol +amu_to_kg = const.value("atomic mass unit-kilogram relationship") # AMU to kg +# kcal2hartree = 0.0015936 # kcal/mol to hartree/mol +kcal2hartree = 1000 * const.calorie / const.value("Hartree energy") / const.Avogadro def get_avg_mom_inertia(mol): """ Calculate the average moment of inertia of a molecule - :param mol: Molecule - :return: average moment of inertia, eigenvalues of inertia tensor + + Args: + mol (Molecule): Pymatgen Molecule + + Returns: + int, list: average moment of inertia, eigenvalues of the inertia tensor """ centered_mol = mol.get_centered_molecule() inertia_tensor = np.zeros((3, 3)) @@ -66,27 +74,55 @@ def get_avg_mom_inertia(mol): class QuasiRRHO: """ Class to calculate thermochemistry using Grimme's Quasi-RRHO approximation. - All outputs are in atomic units. + All outputs are in atomic units, e.g. energy outpouts are in Hartrees. + Citation: Grimme, S. Chemistry - A European Journal 18, 9955–9964 (2012). + + Attributes: + temp (float): Temperature [K] + press (float): Pressure [Pa] + conc (float): Solvent concentration [M] + v0 (float): Cutoff frequency for Quasi-RRHO method [1/cm] + entropy_quasiRRHO (float): Quasi-RRHO entropy [Ha/K] + entropy_ho (float): Total entropy calculated with a harmonic + oscillator approximation for the vibrational entropy [Ha/K] + h_corrected (float): Thermal correction to the enthalpy [Ha] + free_energy_quasiRRHO (float): Quasi-RRHO free energy [Ha] + concentration_corrected_g_quasiRRHO (float): Quasi-RRHO free energy + with a standard state correction for the solvent concentration [Ha] + free_energy_ho (float): Free energy calculated without the Quasi-RRHO + method, i.e. with a harmonic oscillator approximation for the + vibrational entropy [Ha] + """ - def __init__(self, output: GaussianOutput | QCOutput | dict, sigma_r=1, temp=298.15, press=101317, conc=1, v0=100): - """ + def __init__( + self, + mol: Molecule, + frequencies: List, + energy: float, + mult: int, + sigma_r=1, + temp=298.15, + press=101317, + conc=1, + v0=100, + ): - :param output: Requires input of a Gaussian output file, - QChem output file, or dictionary of necessary inputs: - {"mol": Molecule, "mult": spin multiplicity (int), - "frequencies": list of vibrational frequencies [a.u.], - elec_energy": electronic energy [a.u.]} - :param sigma_r (int): Rotational symmetry number - :param temp (float): Temperature [K] - :param press (float): Pressure [Pa] - :param conc (float): Solvent concentration [M] - :param v0 (float): Cutoff frequency for Quasi-RRHO method [cm^1] + """ + Args: + mol (Molecule): Pymatgen molecule + frequencies (list): List of frequencies (float) [cm^-1] + energy (float): Electronic energy [Ha] + mult (int): Spin muliplicity + sigma_r (int): Rotational symmetry number + temp (float): Temperature [K] + press (float): Pressure [Pa] + conc (float): Solvent concentration [M] + v0 (float): Cutoff frequency for Quasi-RRHO method [cm^-1] """ # TO-DO: calculate sigma_r with PointGroupAnalyzer # and/or edit Gaussian and QChem io to parse for sigma_r - self.sigma_r = sigma_r self.temp = temp self.press = press self.conc = conc @@ -95,52 +131,59 @@ def __init__(self, output: GaussianOutput | QCOutput | dict, sigma_r=1, temp=298 self.entropy_quasiRRHO = None # Ha/K self.free_energy_quasiRRHO = None # Ha self.concentration_corrected_g_quasiRRHO = None # Ha - self.h_corrected = None + self.h_corrected = None # Ha self.entropy_ho = None # Ha/K self.free_energy_ho = None # Ha - if isinstance(output, GaussianOutput): - mult = output.spin_multiplicity - sigma_r = self.sigma_r - elec_e = output.final_energy - mol = output.final_structure - vib_freqs = [f["frequency"] for f in output.frequencies[-1]] - - self._get_quasirrho_thermo(mol=mol, mult=mult, sigma_r=sigma_r, frequencies=vib_freqs, elec_energy=elec_e) - - if isinstance(output, QCOutput): - mult = output.data["multiplicity"] - elec_e = output.data["SCF_energy_in_the_final_basis_set"] - - if output.data["optimization"]: - mol = output.data["molecule_from_last_geometry"] - else: - mol = output.data["initial_molecule"] - frequencies = output.data["frequencies"] - - self._get_quasirrho_thermo( - mol=mol, mult=mult, sigma_r=self.sigma_r, frequencies=frequencies, elec_energy=elec_e - ) - - if isinstance(output, dict): - mol = Molecule.from_dict(output.get("optimized_molecule", output.get("initial_molecule"))) - self._get_quasirrho_thermo( - mol=mol, - mult=mol.spin_multiplicity, - sigma_r=self.sigma_r, - frequencies=output.get("frequencies", []), - elec_energy=output["final_energy"], - ) + self._get_quasirrho_thermo(mol=mol, mult=mult, frequencies=frequencies, elec_energy=energy, sigma_r=sigma_r) + + @classmethod + def from_GaussianOutput(cls, output: GaussianOutput, **kwargs): + """ + + Args: + output (GaussianOutput): Pymatgen GaussianOutput object + + Returns: + QuasiRRHO: QuasiRRHO class instantiated from a Gaussian Output + """ + mult = output.spin_multiplicity + elec_e = output.final_energy + mol = output.final_structure + vib_freqs = [f["frequency"] for f in output.frequencies[-1]] + return cls(mol=mol, frequencies=vib_freqs, energy=elec_e, mult=mult, **kwargs) + + @classmethod + def from_QCOutput(cls, output: QCOutput, **kwargs): + """ + + Args: + output (QCOutput): Pymatgen QCOutput object + + Returns: + QuasiRRHO: QuasiRRHO class instantiated from a QChem Output + + """ + mult = output.data["multiplicity"] + elec_e = output.data["SCF_energy_in_the_final_basis_set"] + if output.data["optimization"]: + mol = output.data["molecule_from_last_geometry"] + else: + mol = output.data["initial_molecule"] + frequencies = output.data["frequencies"] + + return cls(mol=mol, frequencies=frequencies, energy=elec_e, mult=mult, **kwargs) def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): """ Calculate Quasi-RRHO thermochemistry - :param mol: Molecule - :param mult: Spin multiplicity - :param sigma_r: Rotational symmetry number - :param frequencies: List of frequencies [a.u.] - :param elec_energy: Electronic energy [a.u.] + Args: + mol (Molecule): Pymatgen molecule + mult (int): Spin multiplicity + sigma_r (int): Rotational symmetry number + frequencies (list): List of frequencies [cm^-1] + elec_energy (float): Electronic energy [Ha] """ # Calculate mass in kg mass = 0 @@ -207,13 +250,11 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): ev *= R etot = (et + er + ev) * kcal2hartree / 1000 self.h_corrected = etot + R * self.temp * kcal2hartree / 1000 - - molarity_corr = 0.000003166488448771253 * self.temp * np.log(0.082057338 * self.temp * self.conc) + molarity_corr = R_ha * self.temp * np.log(R_volume * self.temp * self.conc) self.entropy_ho = st + sr + sv + se self.free_energy_ho = elec_energy + self.h_corrected - (self.temp * self.entropy_ho * kcal2hartree / 1000) self.entropy_quasiRRHO = st + sr + sv_quasiRRHO + se self.free_energy_quasiRRHO = ( elec_energy + self.h_corrected - (self.temp * self.entropy_quasiRRHO * kcal2hartree / 1000) ) - self.concentration_corrected_g_quasiRRHO = self.free_energy_quasiRRHO + molarity_corr diff --git a/pymatgen/analysis/tests/test_quasirrho.py b/pymatgen/analysis/tests/test_quasirrho.py index e239fd40440..4b74b97a02c 100644 --- a/pymatgen/analysis/tests/test_quasirrho.py +++ b/pymatgen/analysis/tests/test_quasirrho.py @@ -10,6 +10,7 @@ from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.qchem.outputs import QCOutput from pymatgen.util.testing import PymatgenTest +import pytest class TestQuasiRRHO(PymatgenTest): @@ -32,11 +33,15 @@ def test_qrrho_gaussian(self): correct_g_conc = -884.770084 correct_g = -884.776886 correct_stot = 141.584080 - qrrho = QuasiRRHO(self.gout, conc=m) - self.assertAlmostEqual(correct_stot, qrrho.entropy_quasiRRHO, 0) - self.assertAlmostEqual(correct_g, qrrho.free_energy_quasiRRHO, 3) - self.assertAlmostEqual(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO, 3) - + qrrho = QuasiRRHO.from_GaussianOutput(self.gout, conc=m) + assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO,0.1), \ + 'Incorrect total entropy' + assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), \ + 'Incorrect Quasi-RRHO free energy' + assert correct_g_conc == \ + pytest.approx(qrrho.concentration_corrected_g_quasiRRHO), \ + 'Incorrect concentration corrected Quasi-RRHO free energy, ' \ + '{} != {}'.format(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO) def test_qrrho_qchem(self): """ Testing from a QChem output file. "Correct" values are from @@ -49,29 +54,40 @@ def test_qrrho_qchem(self): correct_stot = 103.41012732045324 # HO total entropy from QChem = 106.521 - qrrho = QuasiRRHO(self.qout, conc=m) - self.assertAlmostEqual(correct_stot, qrrho.entropy_quasiRRHO, 0) - self.assertAlmostEqual(correct_g, qrrho.free_energy_quasiRRHO, 3) - self.assertAlmostEqual(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO, 3) + qrrho = QuasiRRHO.from_QCOutput(self.qout, conc=m) + assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), \ + 'Incorrect total entropy' + assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), \ + 'Incorrect Quasi-RRHO free energy' + assert correct_g_conc == \ + pytest.approx(qrrho.concentration_corrected_g_quasiRRHO), \ + 'Incorrect concentration corrected Quasi-RRHO free energy' def test_rrho_manual(self): """ Test manual input creation. Values from GaussianOutput """ rrho_in = {} - rrho_in["final_energy"] = self.gout.final_energy - rrho_in["optimized_molecule"] = self.gout.final_structure.as_dict() + e = self.gout.final_energy + mol = self.gout.final_structure vib_freqs = [f["frequency"] for f in self.gout.frequencies[-1]] - rrho_in["frequencies"] = vib_freqs m = 55 correct_g_conc = -884.770084 correct_g = -884.776886 correct_stot = 141.584080 - qrrho = QuasiRRHO(rrho_in, conc=m) - self.assertAlmostEqual(correct_stot, qrrho.entropy_quasiRRHO, 0) - self.assertAlmostEqual(correct_g, qrrho.free_energy_quasiRRHO, 3) - self.assertAlmostEqual(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO, 3) + qrrho = QuasiRRHO(mol=mol, energy=e, frequencies=vib_freqs,mult=1, + conc=m) + # self.assertAlmostEqual(correct_stot, qrrho.entropy_quasiRRHO, 0) + # self.assertAlmostEqual(correct_g, qrrho.free_energy_quasiRRHO, 3) + # self.assertAlmostEqual(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO, 3) + assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), \ + 'Incorrect total entropy' + assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), \ + 'Incorrect Quasi-RRHO free energy' + assert correct_g_conc == \ + pytest.approx(qrrho.concentration_corrected_g_quasiRRHO), \ + 'Incorrect concentration corrected Quasi-RRHO free energy' def test_rrho_linear(self): """ @@ -83,6 +99,10 @@ def test_rrho_linear(self): """ correct_g_ho = -187.642070 correct_g_qrrho = -187.642725 - qrrho = QuasiRRHO(self.linear_gout) - self.assertAlmostEqual(correct_g_ho, qrrho.free_energy_ho, 2) - self.assertAlmostEqual(correct_g_qrrho, qrrho.free_energy_quasiRRHO, 2) + qrrho = QuasiRRHO.from_GaussianOutput(self.linear_gout) + assert correct_g_ho == pytest.approx(qrrho.free_energy_ho, 0.0001), \ + 'Incorrect harmonic oscillator free energy, {} != {}'.format( + correct_g_ho, qrrho.free_energy_ho) + assert correct_g_qrrho == \ + pytest.approx(qrrho.free_energy_quasiRRHO), \ + 'Incorrect Quasi-RRHO free energy' From b783de27e395962883ef590355d129614a204759 Mon Sep 17 00:00:00 2001 From: arepstein Date: Tue, 1 Aug 2023 14:14:20 -0700 Subject: [PATCH 13/25] pre-commit Running pre-commit --- pymatgen/analysis/quasirrho.py | 20 ++++---- pymatgen/analysis/tests/test_quasirrho.py | 57 ++++++++++------------- 2 files changed, 36 insertions(+), 41 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 70c87914bea..e4c2c93c948 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -16,17 +16,20 @@ __maintainer__ = "Alex Epstein" __email__ = "aepstein@lbl.gov" __date__ = "August 1, 2023" -__credits__ = "Ryan Kingsbury, Steven Wheeler, Trevor Seguin, " "Evan Spotte-Smith" +__credits__ = "Ryan Kingsbury, Steven Wheeler, Trevor Seguin, Evan Spotte-Smith" from math import isclose +from typing import TYPE_CHECKING import numpy as np import scipy.constants as const -from pymatgen.core import Molecule from pymatgen.core.units import kb as kb_ev -from pymatgen.io.gaussian import GaussianOutput -from pymatgen.io.qchem.outputs import QCOutput + +if TYPE_CHECKING: + from pymatgen.core import Molecule + from pymatgen.io.gaussian import GaussianOutput + from pymatgen.io.qchem.outputs import QCOutput # Define useful constants kb = kb_ev * const.eV # Pymatgen kb [J/k] @@ -35,7 +38,7 @@ R = const.R / const.calorie # Ideal gas constant [cal/mol/K] R_ha = const.R / const.value("Hartree energy") / const.Avogadro # Ideal gas # constant [Ha/K] -R_volume = const.R / const.atm * 1000 # Ideal gas constant [L.atm.K^−1.mol^−1] +R_volume = const.R / const.atm * 1000 # Ideal gas constant [L.atm.K^-1.mol^-1] # Define useful conversion factors amu_to_kg = const.value("atomic mass unit-kilogram relationship") # AMU to kg @@ -74,8 +77,8 @@ def get_avg_mom_inertia(mol): class QuasiRRHO: """ Class to calculate thermochemistry using Grimme's Quasi-RRHO approximation. - All outputs are in atomic units, e.g. energy outpouts are in Hartrees. - Citation: Grimme, S. Chemistry - A European Journal 18, 9955–9964 (2012). + All outputs are in atomic units, e.g. energy outputs are in Hartrees. + Citation: Grimme, S. Chemistry - A European Journal 18, 9955-9964 (2012). Attributes: temp (float): Temperature [K] @@ -98,7 +101,7 @@ class QuasiRRHO: def __init__( self, mol: Molecule, - frequencies: List, + frequencies: list, energy: float, mult: int, sigma_r=1, @@ -107,7 +110,6 @@ def __init__( conc=1, v0=100, ): - """ Args: mol (Molecule): Pymatgen molecule diff --git a/pymatgen/analysis/tests/test_quasirrho.py b/pymatgen/analysis/tests/test_quasirrho.py index c731c55d71b..f2a90fc35e1 100644 --- a/pymatgen/analysis/tests/test_quasirrho.py +++ b/pymatgen/analysis/tests/test_quasirrho.py @@ -7,11 +7,12 @@ import os +import pytest + from pymatgen.analysis.quasirrho import QuasiRRHO from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.qchem.outputs import QCOutput from pymatgen.util.testing import PymatgenTest -import pytest class TestQuasiRRHO(PymatgenTest): @@ -35,14 +36,14 @@ def test_qrrho_gaussian(self): correct_g = -884.776886 correct_stot = 141.584080 qrrho = QuasiRRHO.from_GaussianOutput(self.gout, conc=m) - assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO,0.1), \ - 'Incorrect total entropy' - assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), \ - 'Incorrect Quasi-RRHO free energy' - assert correct_g_conc == \ - pytest.approx(qrrho.concentration_corrected_g_quasiRRHO), \ - 'Incorrect concentration corrected Quasi-RRHO free energy, ' \ - '{} != {}'.format(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO) + assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy" + assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" + assert correct_g_conc == pytest.approx( + qrrho.concentration_corrected_g_quasiRRHO + ), "Incorrect concentration corrected Quasi-RRHO free energy, {} != {}".format( + correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO + ) + def test_qrrho_qchem(self): """ Testing from a QChem output file. "Correct" values are from @@ -56,19 +57,16 @@ def test_qrrho_qchem(self): # HO total entropy from QChem = 106.521 qrrho = QuasiRRHO.from_QCOutput(self.qout, conc=m) - assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), \ - 'Incorrect total entropy' - assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), \ - 'Incorrect Quasi-RRHO free energy' - assert correct_g_conc == \ - pytest.approx(qrrho.concentration_corrected_g_quasiRRHO), \ - 'Incorrect concentration corrected Quasi-RRHO free energy' + assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy" + assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" + assert correct_g_conc == pytest.approx( + qrrho.concentration_corrected_g_quasiRRHO + ), "Incorrect concentration corrected Quasi-RRHO free energy" def test_rrho_manual(self): """ Test manual input creation. Values from GaussianOutput """ - rrho_in = {} e = self.gout.final_energy mol = self.gout.final_structure vib_freqs = [f["frequency"] for f in self.gout.frequencies[-1]] @@ -77,18 +75,15 @@ def test_rrho_manual(self): correct_g_conc = -884.770084 correct_g = -884.776886 correct_stot = 141.584080 - qrrho = QuasiRRHO(mol=mol, energy=e, frequencies=vib_freqs,mult=1, - conc=m) + qrrho = QuasiRRHO(mol=mol, energy=e, frequencies=vib_freqs, mult=1, conc=m) # self.assertAlmostEqual(correct_stot, qrrho.entropy_quasiRRHO, 0) # self.assertAlmostEqual(correct_g, qrrho.free_energy_quasiRRHO, 3) # self.assertAlmostEqual(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO, 3) - assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), \ - 'Incorrect total entropy' - assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), \ - 'Incorrect Quasi-RRHO free energy' - assert correct_g_conc == \ - pytest.approx(qrrho.concentration_corrected_g_quasiRRHO), \ - 'Incorrect concentration corrected Quasi-RRHO free energy' + assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy" + assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" + assert correct_g_conc == pytest.approx( + qrrho.concentration_corrected_g_quasiRRHO + ), "Incorrect concentration corrected Quasi-RRHO free energy" def test_rrho_linear(self): """ @@ -101,9 +96,7 @@ def test_rrho_linear(self): correct_g_ho = -187.642070 correct_g_qrrho = -187.642725 qrrho = QuasiRRHO.from_GaussianOutput(self.linear_gout) - assert correct_g_ho == pytest.approx(qrrho.free_energy_ho, 0.0001), \ - 'Incorrect harmonic oscillator free energy, {} != {}'.format( - correct_g_ho, qrrho.free_energy_ho) - assert correct_g_qrrho == \ - pytest.approx(qrrho.free_energy_quasiRRHO), \ - 'Incorrect Quasi-RRHO free energy' + assert correct_g_ho == pytest.approx( + qrrho.free_energy_ho, 0.0001 + ), f"Incorrect harmonic oscillator free energy, {correct_g_ho} != {qrrho.free_energy_ho}" + assert correct_g_qrrho == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" From e6df7d9b92914cb1914d1a177fede1add9a43ed1 Mon Sep 17 00:00:00 2001 From: Alex Epstein Date: Wed, 2 Aug 2023 10:13:08 -0700 Subject: [PATCH 14/25] Typos and doi fixed typo in units added duecredit decorator --- pymatgen/analysis/quasirrho.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index e4c2c93c948..40aef4157c7 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -32,7 +32,7 @@ from pymatgen.io.qchem.outputs import QCOutput # Define useful constants -kb = kb_ev * const.eV # Pymatgen kb [J/k] +kb = kb_ev * const.eV # Pymatgen kb [J/K] c = const.speed_of_light * 100 # [cm/s] h = const.h # Planck's constant [J.s] R = const.R / const.calorie # Ideal gas constant [cal/mol/K] @@ -177,6 +177,10 @@ def from_QCOutput(cls, output: QCOutput, **kwargs): return cls(mol=mol, frequencies=frequencies, energy=elec_e, mult=mult, **kwargs) + @due.dcite( + Doi("10.1002/chem.201200497"), + description="Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory", + ) def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): """ Calculate Quasi-RRHO thermochemistry From 9420e6fd2e58b0188b0a671a13017fe3f9712619 Mon Sep 17 00:00:00 2001 From: Alex Epstein Date: Wed, 2 Aug 2023 10:14:35 -0700 Subject: [PATCH 15/25] docs update 1M in docs --- pymatgen/analysis/quasirrho.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 40aef4157c7..c5eccb02a7e 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -83,7 +83,7 @@ class QuasiRRHO: Attributes: temp (float): Temperature [K] press (float): Pressure [Pa] - conc (float): Solvent concentration [M] + conc (float): Solvent concentration. Assumes 1M unless specified [M] v0 (float): Cutoff frequency for Quasi-RRHO method [1/cm] entropy_quasiRRHO (float): Quasi-RRHO entropy [Ha/K] entropy_ho (float): Total entropy calculated with a harmonic From 54ed55769b2b12fe3dc5320530af549d69c27ec6 Mon Sep 17 00:00:00 2001 From: Alex Epstein Date: Wed, 2 Aug 2023 10:18:18 -0700 Subject: [PATCH 16/25] duecredit fixing bugs --- pymatgen/analysis/quasirrho.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index c5eccb02a7e..7569a3e2761 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -20,11 +20,12 @@ from math import isclose from typing import TYPE_CHECKING +from pymatgen.util.due import Doi, due +from pymatgen.core.units import kb as kb_ev import numpy as np import scipy.constants as const -from pymatgen.core.units import kb as kb_ev if TYPE_CHECKING: from pymatgen.core import Molecule From 0122859344e481bb39c70c68916c6551715e5b54 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 2 Aug 2023 17:19:56 +0000 Subject: [PATCH 17/25] pre-commit auto-fixes --- pymatgen/analysis/quasirrho.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 7569a3e2761..37056796860 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -20,12 +20,12 @@ from math import isclose from typing import TYPE_CHECKING -from pymatgen.util.due import Doi, due -from pymatgen.core.units import kb as kb_ev import numpy as np import scipy.constants as const +from pymatgen.core.units import kb as kb_ev +from pymatgen.util.due import Doi, due if TYPE_CHECKING: from pymatgen.core import Molecule From b6fa30017ffeda2456d099fa0cf6edcc9cdaff1d Mon Sep 17 00:00:00 2001 From: arepstein Date: Fri, 11 Aug 2023 12:08:20 -0700 Subject: [PATCH 18/25] Remove Concentration Correction Removed solvent concentration corrections from the code so the class only deals with QuasiRRHO corrections --- pymatgen/analysis/quasirrho.py | 11 ----------- pymatgen/analysis/tests/test_quasirrho.py | 24 +++-------------------- 2 files changed, 3 insertions(+), 32 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 37056796860..eb3b719c09f 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -38,8 +38,6 @@ h = const.h # Planck's constant [J.s] R = const.R / const.calorie # Ideal gas constant [cal/mol/K] R_ha = const.R / const.value("Hartree energy") / const.Avogadro # Ideal gas -# constant [Ha/K] -R_volume = const.R / const.atm * 1000 # Ideal gas constant [L.atm.K^-1.mol^-1] # Define useful conversion factors amu_to_kg = const.value("atomic mass unit-kilogram relationship") # AMU to kg @@ -84,15 +82,12 @@ class QuasiRRHO: Attributes: temp (float): Temperature [K] press (float): Pressure [Pa] - conc (float): Solvent concentration. Assumes 1M unless specified [M] v0 (float): Cutoff frequency for Quasi-RRHO method [1/cm] entropy_quasiRRHO (float): Quasi-RRHO entropy [Ha/K] entropy_ho (float): Total entropy calculated with a harmonic oscillator approximation for the vibrational entropy [Ha/K] h_corrected (float): Thermal correction to the enthalpy [Ha] free_energy_quasiRRHO (float): Quasi-RRHO free energy [Ha] - concentration_corrected_g_quasiRRHO (float): Quasi-RRHO free energy - with a standard state correction for the solvent concentration [Ha] free_energy_ho (float): Free energy calculated without the Quasi-RRHO method, i.e. with a harmonic oscillator approximation for the vibrational entropy [Ha] @@ -108,7 +103,6 @@ def __init__( sigma_r=1, temp=298.15, press=101317, - conc=1, v0=100, ): """ @@ -120,7 +114,6 @@ def __init__( sigma_r (int): Rotational symmetry number temp (float): Temperature [K] press (float): Pressure [Pa] - conc (float): Solvent concentration [M] v0 (float): Cutoff frequency for Quasi-RRHO method [cm^-1] """ # TO-DO: calculate sigma_r with PointGroupAnalyzer @@ -128,12 +121,10 @@ def __init__( self.temp = temp self.press = press - self.conc = conc self.v0 = v0 self.entropy_quasiRRHO = None # Ha/K self.free_energy_quasiRRHO = None # Ha - self.concentration_corrected_g_quasiRRHO = None # Ha self.h_corrected = None # Ha self.entropy_ho = None # Ha/K @@ -257,11 +248,9 @@ def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): ev *= R etot = (et + er + ev) * kcal2hartree / 1000 self.h_corrected = etot + R * self.temp * kcal2hartree / 1000 - molarity_corr = R_ha * self.temp * np.log(R_volume * self.temp * self.conc) self.entropy_ho = st + sr + sv + se self.free_energy_ho = elec_energy + self.h_corrected - (self.temp * self.entropy_ho * kcal2hartree / 1000) self.entropy_quasiRRHO = st + sr + sv_quasiRRHO + se self.free_energy_quasiRRHO = ( elec_energy + self.h_corrected - (self.temp * self.entropy_quasiRRHO * kcal2hartree / 1000) ) - self.concentration_corrected_g_quasiRRHO = self.free_energy_quasiRRHO + molarity_corr diff --git a/pymatgen/analysis/tests/test_quasirrho.py b/pymatgen/analysis/tests/test_quasirrho.py index f2a90fc35e1..2e906c17a5c 100644 --- a/pymatgen/analysis/tests/test_quasirrho.py +++ b/pymatgen/analysis/tests/test_quasirrho.py @@ -31,18 +31,12 @@ def test_qrrho_gaussian(self): Testing from a Gaussian Output file. Correct values are taken from Trevor Seguin's original bash script. """ - m = 55 correct_g_conc = -884.770084 correct_g = -884.776886 correct_stot = 141.584080 - qrrho = QuasiRRHO.from_GaussianOutput(self.gout, conc=m) + qrrho = QuasiRRHO.from_GaussianOutput(self.gout) assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy" assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" - assert correct_g_conc == pytest.approx( - qrrho.concentration_corrected_g_quasiRRHO - ), "Incorrect concentration corrected Quasi-RRHO free energy, {} != {}".format( - correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO - ) def test_qrrho_qchem(self): """ @@ -50,18 +44,13 @@ def test_qrrho_qchem(self): the version of QuasiRRHO that worked for Gaussian. initial run. """ - m = 55 - correct_g_conc = -428.60088006873156 correct_g = -428.60768184222934 correct_stot = 103.41012732045324 # HO total entropy from QChem = 106.521 - qrrho = QuasiRRHO.from_QCOutput(self.qout, conc=m) + qrrho = QuasiRRHO.from_QCOutput(self.qout) assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy" assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" - assert correct_g_conc == pytest.approx( - qrrho.concentration_corrected_g_quasiRRHO - ), "Incorrect concentration corrected Quasi-RRHO free energy" def test_rrho_manual(self): """ @@ -72,18 +61,11 @@ def test_rrho_manual(self): vib_freqs = [f["frequency"] for f in self.gout.frequencies[-1]] m = 55 - correct_g_conc = -884.770084 correct_g = -884.776886 correct_stot = 141.584080 - qrrho = QuasiRRHO(mol=mol, energy=e, frequencies=vib_freqs, mult=1, conc=m) - # self.assertAlmostEqual(correct_stot, qrrho.entropy_quasiRRHO, 0) - # self.assertAlmostEqual(correct_g, qrrho.free_energy_quasiRRHO, 3) - # self.assertAlmostEqual(correct_g_conc, qrrho.concentration_corrected_g_quasiRRHO, 3) + qrrho = QuasiRRHO(mol=mol, energy=e, frequencies=vib_freqs, mult=1) assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy" assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" - assert correct_g_conc == pytest.approx( - qrrho.concentration_corrected_g_quasiRRHO - ), "Incorrect concentration corrected Quasi-RRHO free energy" def test_rrho_linear(self): """ From 3e2a0cd13ffdeb20e0b619eb8a746cd03cc6f4a3 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Fri, 11 Aug 2023 19:09:52 +0000 Subject: [PATCH 19/25] pre-commit auto-fixes --- pymatgen/analysis/tests/test_quasirrho.py | 2 - test_files/molecules/co2.log | 192 +++++++++++----------- 2 files changed, 96 insertions(+), 98 deletions(-) diff --git a/pymatgen/analysis/tests/test_quasirrho.py b/pymatgen/analysis/tests/test_quasirrho.py index 2e906c17a5c..c10fbbfb8d3 100644 --- a/pymatgen/analysis/tests/test_quasirrho.py +++ b/pymatgen/analysis/tests/test_quasirrho.py @@ -31,7 +31,6 @@ def test_qrrho_gaussian(self): Testing from a Gaussian Output file. Correct values are taken from Trevor Seguin's original bash script. """ - correct_g_conc = -884.770084 correct_g = -884.776886 correct_stot = 141.584080 qrrho = QuasiRRHO.from_GaussianOutput(self.gout) @@ -60,7 +59,6 @@ def test_rrho_manual(self): mol = self.gout.final_structure vib_freqs = [f["frequency"] for f in self.gout.frequencies[-1]] - m = 55 correct_g = -884.776886 correct_stot = 141.584080 qrrho = QuasiRRHO(mol=mol, energy=e, frequencies=vib_freqs, mult=1) diff --git a/test_files/molecules/co2.log b/test_files/molecules/co2.log index f996a83090d..c44885dc9c3 100644 --- a/test_files/molecules/co2.log +++ b/test_files/molecules/co2.log @@ -5,10 +5,10 @@ 32 via shared-memory 1 via Linda Entering Link 1 = /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1.exe PID= 207403. - + Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2016, Gaussian, Inc. All Rights Reserved. - + This is part of the Gaussian(R) 16 program. It is based on the Gaussian(R) 09 system (copyright 2009, Gaussian, Inc.), the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.), @@ -21,28 +21,28 @@ University), and the Gaussian 82(TM) system (copyright 1983, Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. - + This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. - + This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. - + The following legend is applicable only to US Government contracts under FAR: - + RESTRICTED RIGHTS LEGEND - + Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraphs (a) and (c) of the Commercial Computer Software - Restricted Rights clause in FAR 52.227-19. - + Gaussian, Inc. 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 - - + + --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide @@ -55,30 +55,30 @@ licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- - + Cite this work as: Gaussian 16, Revision A.03, - M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, - M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, - G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, - J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, - J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, - F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, - T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, - G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, - J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, - T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, - F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin, - V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, - K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, - J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, - J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, + M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, + M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, + G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, + J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, + J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, + F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, + T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, + G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, + J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, + T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, + F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin, + V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, + K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, + J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, + J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016. - + ****************************************** Gaussian 16: ES64L-G16RevA.03 25-Dec-2016 - 10-Jun-2021 + 10-Jun-2021 ****************************************** ------------------------------------------------- #P HF/6-31g(d) freq=noraman opt=(noeigen, calcfc) @@ -112,10 +112,10 @@ ------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 - O -0.81185 -0.38536 3.24234 - O 1.18899 0. 1.98561 - C 0.18857 -0.19268 2.61398 - + O -0.81185 -0.38536 3.24234 + O 1.18899 0. 1.98561 + C 0.18857 -0.19268 2.61398 + ITRead= 0 0 0 MicOpt= -1 -1 -1 NAtoms= 3 NQM= 3 NQMF= 0 NMMI= 0 NMMIF= 0 @@ -155,7 +155,7 @@ Leave Link 103 at Thu Jun 10 18:05:49 2021, MaxMem= 4800000000 cpu: 2.2 elap: 0.1 (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: + Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -175,7 +175,7 @@ Full point group D*H NOp 8 Largest Abelian subgroup D2H NOp 8 Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: + Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -237,7 +237,7 @@ wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0 NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 Petite list used in FoFCou. - Harris En= -187.643581197863 + Harris En= -187.643581197863 JPrj=0 DoOrth=F DoCkMO=F. Initial guess orbital symmetries: Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) @@ -265,7 +265,7 @@ No special actions if energy rises. Cycle 1 Pass 1 IDiag 1: - E= -187.546707470472 + E= -187.546707470472 DIIS: error= 6.33D-02 at cycle 1 NSaved= 1. NSaved= 1 IEnMin= 1 EnMin= -187.546707470472 IErMin= 1 ErrMin= 6.33D-02 ErrMax= 6.33D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.94D-01 BMatP= 1.94D-01 @@ -578,8 +578,8 @@ 3 6 -0.000000000 -0.000000000 -0.000000000 ------------------------------------------------------------------- Cartesian Forces: Max 0.098554123 RMS 0.055587750 - Force constants in Cartesian coordinates: - 1 2 3 4 5 + Force constants in Cartesian coordinates: + 1 2 3 4 5 1 0.598086D+00 2 0.982942D-01 0.106661D+00 3 -0.320552D+00 -0.617381D-01 0.289067D+00 @@ -589,14 +589,14 @@ 7 -0.518261D+00 -0.760635D-01 0.248055D+00 -0.518261D+00 -0.760635D-01 8 -0.760635D-01 -0.137979D+00 0.477751D-01 -0.760635D-01 -0.137979D+00 9 0.248055D+00 0.477751D-01 -0.279131D+00 0.248055D+00 0.477751D-01 - 6 7 8 9 + 6 7 8 9 6 0.289067D+00 7 0.248055D+00 0.103652D+01 8 0.477751D-01 0.152127D+00 0.275958D+00 9 -0.279131D+00 -0.496109D+00 -0.955502D-01 0.558262D+00 FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. - Force constants in internal coordinates: - 1 2 3 4 + Force constants in internal coordinates: + 1 2 3 4 1 0.818355D+00 2 0.129642D+00 0.818355D+00 3 0.000000D+00 0.000000D+00 0.179243D+00 @@ -637,17 +637,17 @@ A1 3.14159 0.00000 0.00000 0.00000 0.00000 3.14159 A2 3.14159 -0.00000 0.00000 0.00000 0.00000 3.14159 Item Value Threshold Converged? - Maximum Force 0.117919 0.000450 NO - RMS Force 0.083382 0.000300 NO - Maximum Displacement 0.100928 0.001800 NO - RMS Displacement 0.085390 0.001200 NO + Maximum Force 0.117919 0.000450 NO + RMS Force 0.083382 0.000300 NO + Maximum Displacement 0.100928 0.001800 NO + RMS Displacement 0.085390 0.001200 NO Predicted change in Energy=-1.465528D-02 Lowest energy point so far. Saving SCF results. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Leave Link 103 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 0.7 elap: 0.0 (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: + Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -668,7 +668,7 @@ RotChk: IX=0 Diff= 3.51D-16 Largest Abelian subgroup D2H NOp 8 Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: + Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -745,7 +745,7 @@ wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0 NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 Petite list used in FoFCou. - Harris En= -187.647008958098 + Harris En= -187.647008958098 Leave Link 401 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 6.4 elap: 0.2 (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l502.exe) Keep R1 ints in memory in symmetry-blocked form, NReq=7134369. @@ -763,7 +763,7 @@ No special actions if energy rises. Cycle 1 Pass 1 IDiag 1: - E= -187.627251532061 + E= -187.627251532061 DIIS: error= 1.09D-02 at cycle 1 NSaved= 1. NSaved= 1 IEnMin= 1 EnMin= -187.627251532061 IErMin= 1 ErrMin= 1.09D-02 ErrMax= 1.09D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.78D-03 BMatP= 5.78D-03 @@ -956,17 +956,17 @@ A1 3.14159 0.00000 0.00000 0.00000 -0.00000 3.14159 A2 3.14159 0.00000 0.00000 0.00000 -0.00000 3.14159 Item Value Threshold Converged? - Maximum Force 0.027751 0.000450 NO - RMS Force 0.019623 0.000300 NO - Maximum Displacement 0.016084 0.001800 NO - RMS Displacement 0.013608 0.001200 NO + Maximum Force 0.027751 0.000450 NO + RMS Force 0.019623 0.000300 NO + Maximum Displacement 0.016084 0.001800 NO + RMS Displacement 0.013608 0.001200 NO Predicted change in Energy=-6.213660D-04 Lowest energy point so far. Saving SCF results. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Leave Link 103 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 1.9 elap: 0.1 (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: + Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -987,7 +987,7 @@ RotChk: IX=0 Diff= 3.70D-16 Largest Abelian subgroup D2H NOp 8 Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: + Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -1071,7 +1071,7 @@ No special actions if energy rises. Cycle 1 Pass 1 IDiag 1: - E= -187.634006821630 + E= -187.634006821630 DIIS: error= 1.79D-03 at cycle 1 NSaved= 1. NSaved= 1 IEnMin= 1 EnMin= -187.634006821630 IErMin= 1 ErrMin= 1.79D-03 ErrMax= 1.79D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.56D-04 BMatP= 1.56D-04 @@ -1277,7 +1277,7 @@ Leave Link 103 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 2.1 elap: 0.1 (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: + Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -1298,7 +1298,7 @@ RotChk: IX=0 Diff= 4.01D-16 Largest Abelian subgroup D2H NOp 8 Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: + Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -1469,7 +1469,7 @@ Leave Link 103 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 0.4 elap: 0.0 (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: + Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -1490,7 +1490,7 @@ RotChk: IX=0 Diff= 4.44D-16 Largest Abelian subgroup D2H NOp 8 Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: + Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z @@ -1574,7 +1574,7 @@ No special actions if energy rises. Cycle 1 Pass 1 IDiag 1: - E= -187.634176201493 + E= -187.634176201493 DIIS: error= 4.01D-10 at cycle 1 NSaved= 1. NSaved= 1 IEnMin= 1 EnMin= -187.634176201493 IErMin= 1 ErrMin= 4.01D-10 ErrMax= 4.01D-10 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.50D-18 BMatP= 2.50D-18 @@ -1823,7 +1823,7 @@ 7.99834 (Kcal/Mol) Vibrational temperatures: 1073.16 1073.16 2184.60 3718.93 (Kelvin) - + Zero-point correction= 0.012746 (Hartree/Particle) Thermal correction to Energy= 0.015302 Thermal correction to Enthalpy= 0.016246 @@ -1832,7 +1832,7 @@ Sum of electronic and thermal Energies= -187.618874 Sum of electronic and thermal Enthalpies= -187.617930 Sum of electronic and thermal Free Energies= -187.642070 - + E (Thermal) CV S KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin Total 9.602 6.527 50.808 @@ -1848,36 +1848,36 @@ Electronic 0.100000D+01 0.000000 0.000000 Translational 0.114679D+08 7.059482 16.255059 Rotational 0.256999D+03 2.409932 5.549073 - + co2 for linear test IR Spectrum - - 2 1 - 5 5 7 - 8 1 4 - 5 8 6 - - X X - X X - X X - X - X - X - X - X - X - X - X - X - X - X - X - X - X - X - X - X - + + 2 1 + 5 5 7 + 8 1 4 + 5 8 6 + + X X + X X + X X + X + X + X + X + X + X + X + X + X + X + X + X + X + X + X + X + X + ***** Axes restored to original set ***** ------------------------------------------------------------------- Center Atomic Forces (Hartrees/Bohr) @@ -1888,8 +1888,8 @@ 3 6 0.000000000 -0.000000000 0.000000000 ------------------------------------------------------------------- Cartesian Forces: Max 0.000051665 RMS 0.000029141 - Force constants in Cartesian coordinates: - 1 2 3 4 5 + Force constants in Cartesian coordinates: + 1 2 3 4 5 1 0.886547D+00 2 0.161899D+00 0.771275D-01 3 -0.527977D+00 -0.101688D+00 0.377566D+00 @@ -1899,14 +1899,14 @@ 7 -0.798298D+00 -0.136059D+00 0.443709D+00 -0.798298D+00 -0.136059D+00 8 -0.136059D+00 -0.118068D+00 0.854579D-01 -0.136059D+00 -0.118068D+00 9 0.443709D+00 0.854579D-01 -0.370554D+00 0.443709D+00 0.854579D-01 - 6 7 8 9 + 6 7 8 9 6 0.377566D+00 7 0.443709D+00 0.159660D+01 8 0.854579D-01 0.272118D+00 0.236136D+00 9 -0.370554D+00 -0.887417D+00 -0.170916D+00 0.741109D+00 FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. - Force constants in internal coordinates: - 1 2 3 4 + Force constants in internal coordinates: + 1 2 3 4 1 0.124935D+01 2 0.146154D+00 0.124935D+01 3 0.000000D+00 0.000000D+00 0.210909D+00 From e4cf61c25472ed664e0259974c350cb18810b0a6 Mon Sep 17 00:00:00 2001 From: arepstein Date: Mon, 21 Aug 2023 13:35:08 -0700 Subject: [PATCH 20/25] Changes to testing --- test_files/molecules/co2.log | 2025 ----------------- .../analysis}/test_quasirrho.py | 10 +- tests/files/molecules/co2.log.gz | Bin 0 -> 21852 bytes 3 files changed, 5 insertions(+), 2030 deletions(-) delete mode 100644 test_files/molecules/co2.log rename {pymatgen/analysis/tests => tests/analysis}/test_quasirrho.py (94%) create mode 100644 tests/files/molecules/co2.log.gz diff --git a/test_files/molecules/co2.log b/test_files/molecules/co2.log deleted file mode 100644 index c44885dc9c3..00000000000 --- a/test_files/molecules/co2.log +++ /dev/null @@ -1,2025 +0,0 @@ - Entering Gaussian System, Link 0=g16 - Initial command: - /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1.exe "/global/scratch/alex_epstein/line_c2o/Gau-207402.inp" -scrdir="/global/scratch/alex_epstein/line_c2o/" - Default is to use a total of 32 processors: - 32 via shared-memory - 1 via Linda - Entering Link 1 = /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1.exe PID= 207403. - - Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2009,2016, - Gaussian, Inc. All Rights Reserved. - - This is part of the Gaussian(R) 16 program. It is based on - the Gaussian(R) 09 system (copyright 2009, Gaussian, Inc.), - the Gaussian(R) 03 system (copyright 2003, Gaussian, Inc.), - the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), - the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), - the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), - the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), - the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), - the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon - University), and the Gaussian 82(TM) system (copyright 1983, - Carnegie Mellon University). Gaussian is a federally registered - trademark of Gaussian, Inc. - - This software contains proprietary and confidential information, - including trade secrets, belonging to Gaussian, Inc. - - This software is provided under written license and may be - used, copied, transmitted, or stored only in accord with that - written license. - - The following legend is applicable only to US Government - contracts under FAR: - - RESTRICTED RIGHTS LEGEND - - Use, reproduction and disclosure by the US Government is - subject to restrictions as set forth in subparagraphs (a) - and (c) of the Commercial Computer Software - Restricted - Rights clause in FAR 52.227-19. - - Gaussian, Inc. - 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 - - - --------------------------------------------------------------- - Warning -- This program may not be used in any manner that - competes with the business of Gaussian, Inc. or will provide - assistance to any competitor of Gaussian, Inc. The licensee - of this program is prohibited from giving any competitor of - Gaussian, Inc. access to this program. By using this program, - the user acknowledges that Gaussian, Inc. is engaged in the - business of creating and licensing software in the field of - computational chemistry and represents and warrants to the - licensee that it is not a competitor of Gaussian, Inc. and that - it will not use this program in any manner prohibited above. - --------------------------------------------------------------- - - - Cite this work as: - Gaussian 16, Revision A.03, - M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, - M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, - G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, - J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, - J. V. Ortiz, A. F. Izmaylov, J. L. Sonnenberg, D. Williams-Young, - F. Ding, F. Lipparini, F. Egidi, J. Goings, B. Peng, A. Petrone, - T. Henderson, D. Ranasinghe, V. G. Zakrzewski, J. Gao, N. Rega, - G. Zheng, W. Liang, M. Hada, M. Ehara, K. Toyota, R. Fukuda, - J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, - T. Vreven, K. Throssell, J. A. Montgomery, Jr., J. E. Peralta, - F. Ogliaro, M. J. Bearpark, J. J. Heyd, E. N. Brothers, K. N. Kudin, - V. N. Staroverov, T. A. Keith, R. Kobayashi, J. Normand, - K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, - J. Tomasi, M. Cossi, J. M. Millam, M. Klene, C. Adamo, R. Cammi, - J. W. Ochterski, R. L. Martin, K. Morokuma, O. Farkas, - J. B. Foresman, and D. J. Fox, Gaussian, Inc., Wallingford CT, 2016. - - ****************************************** - Gaussian 16: ES64L-G16RevA.03 25-Dec-2016 - 10-Jun-2021 - ****************************************** - ------------------------------------------------- - #P HF/6-31g(d) freq=noraman opt=(noeigen, calcfc) - ------------------------------------------------- - 1/10=4,11=1,18=20,19=15,38=1/1,3; - 2/9=110,12=2,17=6,18=5,40=1/2; - 3/5=1,6=6,7=1,11=9,25=1,30=1,71=2,140=1/1,2,3; - 4//1; - 5/5=2,38=5/2; - 8/6=4,10=90,11=11/1; - 11/6=1,8=1,9=11,15=111,16=1/1,2,10; - 10/6=1,13=1/2; - 6/7=2,8=2,9=2,10=2,28=1/1; - 7/10=1,18=20,25=1/1,2,3,16; - 1/10=4,11=1,18=20,19=15/3(2); - 2/9=110/2; - 99//99; - 2/9=110/2; - 3/5=1,6=6,7=1,11=9,25=1,30=1,71=1/1,2,3; - 4/5=5,16=3,69=1/1; - 5/5=2,38=5/2; - 7//1,2,3,16; - 1/11=1,18=20,19=15/3(-5); - 2/9=110/2; - 6/7=2,8=2,9=2,10=2,19=2,28=1/1; - 99/9=1/99; - Leave Link 1 at Thu Jun 10 18:05:48 2021, MaxMem= 0 cpu: 6.0 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l101.exe) - ------------------- - co2 for linear test - ------------------- - Symbolic Z-matrix: - Charge = 0 Multiplicity = 1 - O -0.81185 -0.38536 3.24234 - O 1.18899 0. 1.98561 - C 0.18857 -0.19268 2.61398 - - ITRead= 0 0 0 - MicOpt= -1 -1 -1 - NAtoms= 3 NQM= 3 NQMF= 0 NMMI= 0 NMMIF= 0 - NMic= 0 NMicF= 0. - Isotopes and Nuclear Properties: - (Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM) - in nuclear magnetons) - - Atom 1 2 3 - IAtWgt= 16 16 12 - AtmWgt= 15.9949146 15.9949146 12.0000000 - NucSpn= 0 0 0 - AtZEff= -0.0000000 -0.0000000 -0.0000000 - NQMom= 0.0000000 0.0000000 0.0000000 - NMagM= 0.0000000 0.0000000 0.0000000 - AtZNuc= 8.0000000 8.0000000 6.0000000 - Leave Link 101 at Thu Jun 10 18:05:49 2021, MaxMem= 4800000000 cpu: 11.2 elap: 0.4 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) - - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - Berny optimization. - Initialization pass. - ---------------------------- - ! Initial Parameters ! - ! (Angstroms and Degrees) ! - -------------------------- -------------------------- - ! Name Definition Value Derivative Info. ! - -------------------------------------------------------------------------------- - ! R1 R(1,3) 1.197 calculate D2E/DX2 analytically ! - ! R2 R(2,3) 1.197 calculate D2E/DX2 analytically ! - ! A1 L(1,3,2,-2,-1) 180.0 calculate D2E/DX2 analytically ! - ! A2 L(1,3,2,-3,-2) 180.0 calculate D2E/DX2 analytically ! - -------------------------------------------------------------------------------- - Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 EigMax=2.50D+02 EigMin=1.00D-04 - Number of steps in this run= 20 maximum allowed number of steps= 100. - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - - Leave Link 103 at Thu Jun 10 18:05:49 2021, MaxMem= 4800000000 cpu: 2.2 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 -0.811852 -0.385361 3.242336 - 2 8 0 1.188993 0.000000 1.985615 - 3 6 0 0.188571 -0.192681 2.613975 - --------------------------------------------------------------------- - Distance matrix (angstroms): - 1 2 3 - 1 O 0.000000 - 2 O 2.394000 0.000000 - 3 C 1.197000 1.197000 0.000000 - Stoichiometry CO2 - Framework group D*H[O(C),C*(O.O)] - Deg. of freedom 1 - Full point group D*H NOp 8 - Largest Abelian subgroup D2H NOp 8 - Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 0.000000 0.000000 1.197000 - 2 8 0 0.000000 0.000000 -1.197000 - 3 6 0 0.000000 0.000000 0.000000 - --------------------------------------------------------------------- - Rotational constants (GHZ): 0.0000000 11.0259743 11.0259743 - Leave Link 202 at Thu Jun 10 18:05:50 2021, MaxMem= 4800000000 cpu: 0.7 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l301.exe) - Standard basis: 6-31G(d) (6D, 7F) - Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. - There are 14 symmetry adapted cartesian basis functions of AG symmetry. - There are 2 symmetry adapted cartesian basis functions of B1G symmetry. - There are 4 symmetry adapted cartesian basis functions of B2G symmetry. - There are 4 symmetry adapted cartesian basis functions of B3G symmetry. - There are 1 symmetry adapted cartesian basis functions of AU symmetry. - There are 10 symmetry adapted cartesian basis functions of B1U symmetry. - There are 5 symmetry adapted cartesian basis functions of B2U symmetry. - There are 5 symmetry adapted cartesian basis functions of B3U symmetry. - There are 14 symmetry adapted basis functions of AG symmetry. - There are 2 symmetry adapted basis functions of B1G symmetry. - There are 4 symmetry adapted basis functions of B2G symmetry. - There are 4 symmetry adapted basis functions of B3G symmetry. - There are 1 symmetry adapted basis functions of AU symmetry. - There are 10 symmetry adapted basis functions of B1U symmetry. - There are 5 symmetry adapted basis functions of B2U symmetry. - There are 5 symmetry adapted basis functions of B3U symmetry. - 45 basis functions, 84 primitive gaussians, 45 cartesian basis functions - 11 alpha electrons 11 beta electrons - nuclear repulsion energy 56.5870367581 Hartrees. - IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 - ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 - IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 - NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F - Integral buffers will be 131072 words long. - Raffenetti 1 integral format. - Two-electron integral symmetry is turned on. - Leave Link 301 at Thu Jun 10 18:05:50 2021, MaxMem= 4800000000 cpu: 5.0 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l302.exe) - NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 - NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. - One-electron integrals computed using PRISM. - One-electron integral symmetry used in STVInt - NBasis= 45 RedAO= T EigKep= 2.89D-03 NBF= 14 2 4 4 1 10 5 5 - NBsUse= 45 1.00D-06 EigRej= -1.00D+00 NBFU= 14 2 4 4 1 10 5 5 - Leave Link 302 at Thu Jun 10 18:05:51 2021, MaxMem= 4800000000 cpu: 4.8 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l303.exe) - DipDrv: MaxL=1. - Leave Link 303 at Thu Jun 10 18:05:51 2021, MaxMem= 4800000000 cpu: 1.5 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l401.exe) - ExpMin= 1.69D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=3 IRadAn= 5 AccDes= 0.00D+00 - Harris functional with IExCor= 205 and IRadAn= 5 diagonalized for initial guess. - HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 5 IDoV= 1 UseB2=F ITyADJ=14 - ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000 - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 - NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T - wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Harris En= -187.643581197863 - JPrj=0 DoOrth=F DoCkMO=F. - Initial guess orbital symmetries: - Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) - (PIU) (PIG) (PIG) - Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) - (SGG) (PIG) (PIG) (SGU) (PIU) (PIU) (SGG) (PIG) - (PIG) (DLTG) (DLTG) (DLTU) (DLTU) (SGU) (DLTG) - (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) - (SGG) (SGG) (SGU) - The electronic state of the initial guess is 1-SGG. - Leave Link 401 at Thu Jun 10 18:05:52 2021, MaxMem= 4800000000 cpu: 11.4 elap: 0.4 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l502.exe) - Keep R1 ints in memory in symmetry-blocked form, NReq=7134157. - FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Closed shell SCF: - Using DIIS extrapolation, IDIIS= 1040. - NGot= 4800000000 LenX= 4799912550 LenY= 4799910084 - Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. - Requested convergence on MAX density matrix=1.00D-06. - Requested convergence on energy=1.00D-06. - No special actions if energy rises. - - Cycle 1 Pass 1 IDiag 1: - E= -187.546707470472 - DIIS: error= 6.33D-02 at cycle 1 NSaved= 1. - NSaved= 1 IEnMin= 1 EnMin= -187.546707470472 IErMin= 1 ErrMin= 6.33D-02 - ErrMax= 6.33D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.94D-01 BMatP= 1.94D-01 - IDIUse=3 WtCom= 3.67D-01 WtEn= 6.33D-01 - Coeff-Com: 0.100D+01 - Coeff-En: 0.100D+01 - Coeff: 0.100D+01 - Gap= 0.676 Goal= None Shift= 0.000 - GapD= 0.676 DampG=2.000 DampE=0.500 DampFc=1.0000 IDamp=-1. - RMSDP=6.43D-03 MaxDP=7.26D-02 OVMax= 6.99D-02 - - Cycle 2 Pass 1 IDiag 1: - E= -187.595924288405 Delta-E= -0.049216817934 Rises=F Damp=F - DIIS: error= 2.63D-02 at cycle 2 NSaved= 2. - NSaved= 2 IEnMin= 2 EnMin= -187.595924288405 IErMin= 2 ErrMin= 2.63D-02 - ErrMax= 2.63D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.59D-02 BMatP= 1.94D-01 - IDIUse=3 WtCom= 7.37D-01 WtEn= 2.63D-01 - Coeff-Com: 0.238D+00 0.762D+00 - Coeff-En: 0.344D-01 0.966D+00 - Coeff: 0.184D+00 0.816D+00 - Gap= 0.740 Goal= None Shift= 0.000 - RMSDP=3.36D-03 MaxDP=3.52D-02 DE=-4.92D-02 OVMax= 6.26D-02 - - Cycle 3 Pass 1 IDiag 1: - E= -187.616366824535 Delta-E= -0.020442536129 Rises=F Damp=F - DIIS: error= 1.34D-02 at cycle 3 NSaved= 3. - NSaved= 3 IEnMin= 3 EnMin= -187.616366824535 IErMin= 3 ErrMin= 1.34D-02 - ErrMax= 1.34D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 7.66D-03 BMatP= 3.59D-02 - IDIUse=3 WtCom= 8.66D-01 WtEn= 1.34D-01 - Coeff-Com: -0.360D-01 0.293D+00 0.743D+00 - Coeff-En: 0.000D+00 0.334D-01 0.967D+00 - Coeff: -0.311D-01 0.258D+00 0.773D+00 - Gap= 0.721 Goal= None Shift= 0.000 - RMSDP=1.06D-03 MaxDP=1.47D-02 DE=-2.04D-02 OVMax= 1.60D-02 - - Cycle 4 Pass 1 IDiag 1: - E= -187.621353362497 Delta-E= -0.004986537963 Rises=F Damp=F - DIIS: error= 1.58D-03 at cycle 4 NSaved= 4. - NSaved= 4 IEnMin= 4 EnMin= -187.621353362497 IErMin= 4 ErrMin= 1.58D-03 - ErrMax= 1.58D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.04D-05 BMatP= 7.66D-03 - IDIUse=3 WtCom= 9.84D-01 WtEn= 1.58D-02 - Coeff-Com: 0.207D-02-0.487D-01-0.427D-01 0.109D+01 - Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.100D+01 - Coeff: 0.203D-02-0.479D-01-0.420D-01 0.109D+01 - Gap= 0.725 Goal= None Shift= 0.000 - RMSDP=1.58D-04 MaxDP=2.13D-03 DE=-4.99D-03 OVMax= 3.68D-03 - - Cycle 5 Pass 1 IDiag 1: - E= -187.621425151085 Delta-E= -0.000071788588 Rises=F Damp=F - DIIS: error= 5.17D-04 at cycle 5 NSaved= 5. - NSaved= 5 IEnMin= 5 EnMin= -187.621425151085 IErMin= 5 ErrMin= 5.17D-04 - ErrMax= 5.17D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 4.47D-06 BMatP= 5.04D-05 - IDIUse=3 WtCom= 9.95D-01 WtEn= 5.17D-03 - Coeff-Com: 0.253D-02-0.216D-01-0.716D-01-0.281D-01 0.112D+01 - Coeff-En: 0.000D+00 0.000D+00 0.000D+00 0.000D+00 0.100D+01 - Coeff: 0.252D-02-0.215D-01-0.712D-01-0.280D-01 0.112D+01 - Gap= 0.725 Goal= None Shift= 0.000 - RMSDP=6.56D-05 MaxDP=9.16D-04 DE=-7.18D-05 OVMax= 9.83D-04 - - Cycle 6 Pass 1 IDiag 1: - E= -187.621431407661 Delta-E= -0.000006256576 Rises=F Damp=F - DIIS: error= 7.99D-05 at cycle 6 NSaved= 6. - NSaved= 6 IEnMin= 6 EnMin= -187.621431407661 IErMin= 6 ErrMin= 7.99D-05 - ErrMax= 7.99D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.39D-07 BMatP= 4.47D-06 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.876D-03 0.101D-01 0.248D-01-0.543D-01-0.344D+00 0.136D+01 - Coeff: -0.876D-03 0.101D-01 0.248D-01-0.543D-01-0.344D+00 0.136D+01 - Gap= 0.725 Goal= None Shift= 0.000 - RMSDP=1.64D-05 MaxDP=1.76D-04 DE=-6.26D-06 OVMax= 2.85D-04 - - Cycle 7 Pass 1 IDiag 1: - E= -187.621431721890 Delta-E= -0.000000314229 Rises=F Damp=F - DIIS: error= 1.03D-05 at cycle 7 NSaved= 7. - NSaved= 7 IEnMin= 7 EnMin= -187.621431721890 IErMin= 7 ErrMin= 1.03D-05 - ErrMax= 1.03D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.17D-09 BMatP= 1.39D-07 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.122D-03-0.158D-02-0.362D-02 0.120D-01 0.499D-01-0.305D+00 - Coeff-Com: 0.125D+01 - Coeff: 0.122D-03-0.158D-02-0.362D-02 0.120D-01 0.499D-01-0.305D+00 - Coeff: 0.125D+01 - Gap= 0.725 Goal= None Shift= 0.000 - RMSDP=2.05D-06 MaxDP=2.19D-05 DE=-3.14D-07 OVMax= 3.28D-05 - - Cycle 8 Pass 1 IDiag 1: - E= -187.621431725649 Delta-E= -0.000000003760 Rises=F Damp=F - DIIS: error= 8.83D-07 at cycle 8 NSaved= 8. - NSaved= 8 IEnMin= 8 EnMin= -187.621431725649 IErMin= 8 ErrMin= 8.83D-07 - ErrMax= 8.83D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.90D-11 BMatP= 2.17D-09 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.880D-05 0.120D-03 0.258D-03-0.128D-02-0.328D-02 0.277D-01 - Coeff-Com: -0.175D+00 0.115D+01 - Coeff: -0.880D-05 0.120D-03 0.258D-03-0.128D-02-0.328D-02 0.277D-01 - Coeff: -0.175D+00 0.115D+01 - Gap= 0.725 Goal= None Shift= 0.000 - RMSDP=1.51D-07 MaxDP=1.58D-06 DE=-3.76D-09 OVMax= 2.29D-06 - - Cycle 9 Pass 1 IDiag 1: - E= -187.621431725679 Delta-E= -0.000000000030 Rises=F Damp=F - DIIS: error= 1.00D-07 at cycle 9 NSaved= 9. - NSaved= 9 IEnMin= 9 EnMin= -187.621431725679 IErMin= 9 ErrMin= 1.00D-07 - ErrMax= 1.00D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.42D-13 BMatP= 1.90D-11 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.353D-06 0.381D-05 0.104D-04-0.648D-05-0.199D-03 0.118D-02 - Coeff-Com: -0.417D-02-0.101D+00 0.110D+01 - Coeff: -0.353D-06 0.381D-05 0.104D-04-0.648D-05-0.199D-03 0.118D-02 - Coeff: -0.417D-02-0.101D+00 0.110D+01 - Gap= 0.725 Goal= None Shift= 0.000 - RMSDP=1.45D-08 MaxDP=1.29D-07 DE=-2.96D-11 OVMax= 2.57D-07 - - Cycle 10 Pass 1 IDiag 1: - E= -187.621431725679 Delta-E= -0.000000000000 Rises=F Damp=F - DIIS: error= 1.28D-08 at cycle 10 NSaved= 10. - NSaved=10 IEnMin=10 EnMin= -187.621431725679 IErMin=10 ErrMin= 1.28D-08 - ErrMax= 1.28D-08 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.78D-15 BMatP= 2.42D-13 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.960D-07-0.116D-05-0.278D-05 0.745D-05 0.528D-04-0.399D-03 - Coeff-Com: 0.221D-02 0.986D-02-0.221D+00 0.121D+01 - Coeff: 0.960D-07-0.116D-05-0.278D-05 0.745D-05 0.528D-04-0.399D-03 - Coeff: 0.221D-02 0.986D-02-0.221D+00 0.121D+01 - Gap= 0.725 Goal= None Shift= 0.000 - RMSDP=3.14D-09 MaxDP=3.10D-08 DE=-2.27D-13 OVMax= 3.54D-08 - - SCF Done: E(RHF) = -187.621431726 A.U. after 10 cycles - NFock= 10 Conv=0.31D-08 -V/T= 2.0055 - KE= 1.865922906646D+02 PE=-5.554229239539D+02 EE= 1.246221648055D+02 - Leave Link 502 at Thu Jun 10 18:05:53 2021, MaxMem= 4800000000 cpu: 7.3 elap: 0.3 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l801.exe) - Range of M.O.s used for correlation: 1 45 - NBasis= 45 NAE= 11 NBE= 11 NFC= 0 NFV= 0 - NROrb= 45 NOA= 11 NOB= 11 NVA= 34 NVB= 34 - Leave Link 801 at Thu Jun 10 18:05:54 2021, MaxMem= 4800000000 cpu: 1.9 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1101.exe) - Using compressed storage, NAtomX= 3. - Will process 4 centers per pass. - Leave Link 1101 at Thu Jun 10 18:05:54 2021, MaxMem= 4800000000 cpu: 5.6 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1102.exe) - Symmetrizing basis deriv contribution to polar: - IMax=3 JMax=2 DiffMx= 0.00D+00 - Leave Link 1102 at Thu Jun 10 18:05:55 2021, MaxMem= 4800000000 cpu: 2.4 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1110.exe) - Forming Gx(P) for the SCF density, NAtomX= 3. - Integral derivatives from FoFJK, PRISM(SPDF). - Do as many integral derivatives as possible in FoFJK. - G2DrvN: MDV= 4799999660. - G2DrvN: will do 4 centers at a time, making 1 passes. - Calling FoFCou, ICntrl= 3107 FMM=F I1Cent= 0 AccDes= 0.00D+00. - FoFJK: IHMeth= 1 ICntrl= 3107 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F - IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 3107 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - End of G2Drv F.D. properties file 721 does not exist. - End of G2Drv F.D. properties file 722 does not exist. - End of G2Drv F.D. properties file 788 does not exist. - Leave Link 1110 at Thu Jun 10 18:05:55 2021, MaxMem= 4800000000 cpu: 5.8 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1002.exe) - Minotr: Closed shell wavefunction. - IDoAtm=111 - Direct CPHF calculation. - Differentiating once with respect to nuclear coordinates. - Using symmetry in CPHF. - Requested convergence is 1.0D-08 RMS, and 1.0D-07 maximum. - Secondary convergence is 1.0D-12 RMS, and 1.0D-12 maximum. - NewPWx=T KeepS1=F KeepF1=F KeepIn=T MapXYZ=F SortEE=F KeepMc=T. - Keep R1 ints in memory in symmetry-blocked form, NReq=7134362. - FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - MDV= 4800000000 using IRadAn= 1. - Solving linear equations simultaneously, MaxMat= 0. - There are 9 degrees of freedom in the 1st order CPHF. IDoFFX=4 NUNeed= 9. - 6 vectors produced by pass 0 Test12= 4.16D-15 1.11D-08 XBig12= 6.90D-02 1.06D-01. - AX will form 6 AO Fock derivatives at one time. - 6 vectors produced by pass 1 Test12= 4.16D-15 1.11D-08 XBig12= 1.67D-02 7.48D-02. - 6 vectors produced by pass 2 Test12= 4.16D-15 1.11D-08 XBig12= 1.51D-03 2.09D-02. - 6 vectors produced by pass 3 Test12= 4.16D-15 1.11D-08 XBig12= 9.09D-05 4.01D-03. - 6 vectors produced by pass 4 Test12= 4.16D-15 1.11D-08 XBig12= 1.09D-06 3.95D-04. - 6 vectors produced by pass 5 Test12= 4.16D-15 1.11D-08 XBig12= 7.27D-09 2.77D-05. - 6 vectors produced by pass 6 Test12= 4.16D-15 1.11D-08 XBig12= 3.31D-11 1.52D-06. - 6 vectors produced by pass 7 Test12= 4.16D-15 1.11D-08 XBig12= 1.89D-13 1.38D-07. - 1 vectors produced by pass 8 Test12= 4.16D-15 1.11D-08 XBig12= 1.15D-15 1.24D-08. - InvSVY: IOpt=1 It= 1 EMax= 4.44D-16 - Solved reduced A of dimension 49 with 6 vectors. - FullF1: Do perturbations 4 to 9. - End of Minotr F.D. properties file 721 does not exist. - End of Minotr F.D. properties file 722 does not exist. - End of Minotr F.D. properties file 788 does not exist. - Leave Link 1002 at Thu Jun 10 18:05:56 2021, MaxMem= 4800000000 cpu: 6.8 elap: 0.3 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l601.exe) - Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0. - - ********************************************************************** - - Population analysis using the SCF density. - - ********************************************************************** - - Orbital symmetries: - Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) - (PIU) (PIG) (PIG) - Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) - (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (PIG) - (PIG) (DLTG) (DLTG) (DLTU) (DLTU) (SGU) (DLTG) - (DLTG) (PIU) (PIU) (SGG) (PIG) (PIG) (SGU) (SGG) - (SGG) (SGG) (SGU) - The electronic state is 1-SGG. - Alpha occ. eigenvalues -- -20.67031 -20.67029 -11.48878 -1.51161 -1.45747 - Alpha occ. eigenvalues -- -0.79885 -0.72959 -0.69633 -0.69633 -0.53680 - Alpha occ. eigenvalues -- -0.53680 - Alpha virt. eigenvalues -- 0.18784 0.18784 0.24518 0.51387 0.67053 - Alpha virt. eigenvalues -- 0.67053 0.78559 0.94979 0.99832 1.14995 - Alpha virt. eigenvalues -- 1.14995 1.31539 1.31539 1.33343 1.58692 - Alpha virt. eigenvalues -- 1.65218 1.65218 1.65329 1.65329 2.01750 - Alpha virt. eigenvalues -- 2.01750 2.08060 2.30593 2.30593 2.40379 - Alpha virt. eigenvalues -- 2.40379 2.96934 3.25089 3.25089 3.25688 - Alpha virt. eigenvalues -- 3.38018 4.10539 4.76452 4.83832 - Condensed to atoms (all electrons): - 1 2 3 - 1 O 7.909034 -0.027930 0.584117 - 2 O -0.027930 7.909034 0.584117 - 3 C 0.584117 0.584117 3.901325 - Mulliken charges: - 1 - 1 O -0.465221 - 2 O -0.465221 - 3 C 0.930442 - Sum of Mulliken charges = -0.00000 - Mulliken charges with hydrogens summed into heavy atoms: - 1 - 1 O -0.465221 - 2 O -0.465221 - 3 C 0.930442 - APT charges: - 1 - 1 O -0.222397 - 2 O -0.222397 - 3 C 0.444794 - Sum of APT charges = -0.00000 - APT charges with hydrogens summed into heavy atoms: - 1 - 1 O -0.222397 - 2 O -0.222397 - 3 C 0.444794 - Electronic spatial extent (au): = 118.8759 - Charge= 0.0000 electrons - Dipole moment (field-independent basis, Debye): - X= 0.0000 Y= 0.0000 Z= -0.0000 Tot= 0.0000 - Quadrupole moment (field-independent basis, Debye-Ang): - XX= -14.7300 YY= -14.7300 ZZ= -20.3189 - XY= -0.0000 XZ= 0.0000 YZ= 0.0000 - Traceless Quadrupole moment (field-independent basis, Debye-Ang): - XX= 1.8629 YY= 1.8629 ZZ= -3.7259 - XY= -0.0000 XZ= 0.0000 YZ= 0.0000 - Octapole moment (field-independent basis, Debye-Ang**2): - XXX= 0.0000 YYY= 0.0000 ZZZ= 0.0000 XYY= 0.0000 - XXY= 0.0000 XXZ= 0.0000 XZZ= 0.0000 YZZ= 0.0000 - YYZ= 0.0000 XYZ= 0.0000 - Hexadecapole moment (field-independent basis, Debye-Ang**3): - XXXX= -10.6612 YYYY= -10.6612 ZZZZ= -108.1601 XXXY= -0.0000 - XXXZ= 0.0000 YYYX= -0.0000 YYYZ= 0.0000 ZZZX= 0.0000 - ZZZY= 0.0000 XXYY= -3.5537 XXZZ= -19.5713 YYZZ= -19.5713 - XXYZ= 0.0000 YYXZ= 0.0000 ZZXY= -0.0000 - N-N= 5.658703675808D+01 E-N=-5.554229240023D+02 KE= 1.865922906646D+02 - Symmetry AG KE= 1.010224941329D+02 - Symmetry B1G KE= 1.206473085192D-32 - Symmetry B2G KE= 4.663694725369D+00 - Symmetry B3G KE= 4.663694725369D+00 - Symmetry AU KE= 6.793861401711D-33 - Symmetry B1U KE= 6.894203292220D+01 - Symmetry B2U KE= 3.650187079387D+00 - Symmetry B3U KE= 3.650187079387D+00 - Exact polarizability: 0.000 0.000 0.000 0.000 0.000 0.000 - Approx polarizability: 7.074 0.000 7.074 -0.000 -0.000 24.413 - No NMR shielding tensors so no spin-rotation constants. - Leave Link 601 at Thu Jun 10 18:05:57 2021, MaxMem= 4800000000 cpu: 5.3 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l701.exe) - ... and contract with generalized density number 0. - Compute integral second derivatives. - Leave Link 701 at Thu Jun 10 18:05:57 2021, MaxMem= 4800000000 cpu: 8.8 elap: 0.3 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l702.exe) - L702 exits ... SP integral derivatives will be done elsewhere. - Leave Link 702 at Thu Jun 10 18:05:58 2021, MaxMem= 4800000000 cpu: 0.9 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l703.exe) - Integral derivatives from FoFJK, PRISM(SPDF). - Compute integral second derivatives, UseDBF=F ICtDFT= 0. - Calling FoFJK, ICntrl= 100147 FMM=F ISym2X=1 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0. - FoFJK: IHMeth= 1 ICntrl= 100147 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F - IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 800 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 100147 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Leave Link 703 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 9.9 elap: 0.3 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l716.exe) - Dipole = 2.67876454D-16 3.07397010D-17-1.27007489D-16 - Polarizability= 0.00000000D+00 0.00000000D+00 0.00000000D+00 - 0.00000000D+00 0.00000000D+00 0.00000000D+00 - ***** Axes restored to original set ***** - ------------------------------------------------------------------- - Center Atomic Forces (Hartrees/Bohr) - Number Number X Y Z - ------------------------------------------------------------------- - 1 8 0.098554123 0.018981445 -0.061901374 - 2 8 -0.098554123 -0.018981445 0.061901374 - 3 6 -0.000000000 -0.000000000 -0.000000000 - ------------------------------------------------------------------- - Cartesian Forces: Max 0.098554123 RMS 0.055587750 - Force constants in Cartesian coordinates: - 1 2 3 4 5 - 1 0.598086D+00 - 2 0.982942D-01 0.106661D+00 - 3 -0.320552D+00 -0.617381D-01 0.289067D+00 - 4 -0.798254D-01 -0.222307D-01 0.724977D-01 0.598086D+00 - 5 -0.222307D-01 0.313177D-01 0.139630D-01 0.982942D-01 0.106661D+00 - 6 0.724977D-01 0.139630D-01 -0.993618D-02 -0.320552D+00 -0.617381D-01 - 7 -0.518261D+00 -0.760635D-01 0.248055D+00 -0.518261D+00 -0.760635D-01 - 8 -0.760635D-01 -0.137979D+00 0.477751D-01 -0.760635D-01 -0.137979D+00 - 9 0.248055D+00 0.477751D-01 -0.279131D+00 0.248055D+00 0.477751D-01 - 6 7 8 9 - 6 0.289067D+00 - 7 0.248055D+00 0.103652D+01 - 8 0.477751D-01 0.152127D+00 0.275958D+00 - 9 -0.279131D+00 -0.496109D+00 -0.955502D-01 0.558262D+00 - FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. - Force constants in internal coordinates: - 1 2 3 4 - 1 0.818355D+00 - 2 0.129642D+00 0.818355D+00 - 3 0.000000D+00 0.000000D+00 0.179243D+00 - 4 0.000000D+00 0.000000D+00 -0.155490D-01 0.133303D+00 - Leave Link 716 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 2.3 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) - - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - Berny optimization. - Red2BG is reusing G-inverse. - Internal Forces: Max 0.117919424 RMS 0.083381624 - Search for a local minimum. - Step number 1 out of a maximum of 20 - All quantities printed in internal units (Hartrees-Bohrs-Radians) - RMS Force = .83382D-01 SwitMx=.10000D-02 MixMth= 1 - Mixed Optimization -- RFO/linear search - Second derivative matrix not updated -- analytic derivatives used. - The second derivative matrix: - R1 R2 A1 A2 - R1 0.81835 - R2 0.12964 0.81835 - A1 0.00000 -0.00000 0.17924 - A2 -0.00000 0.00000 -0.01555 0.13330 - ITU= 0 - Eigenvalues --- 0.12854 0.18401 0.68871 0.94800 - RFO step: Lambda=-2.84799103D-02 EMin= 1.28535469D-01 - Linear search not attempted -- first point. - Iteration 1 RMS(Cart)= 0.08539025 RMS(Int)= 0.00000002 - SLEqS3 Cycle: 91 Max:0.329680E-07 RMS:0.210049E-07 Conv:0.459712E-13 - SLEqS3 Cycle: 91 Max:0.408456E-07 RMS:0.253351E-07 Conv:0.459712E-13 - Iteration 2 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000003 - ITry= 1 IFail=0 DXMaxC= 1.01D-01 DCOld= 1.00D+10 DXMaxT= 3.00D-01 DXLimC= 3.00D+00 Rises=F - ClnCor: largest displacement from symmetrization is 2.56D-08 for atom 3. - Variable Old X -DE/DX Delta X Delta X Delta X New X - (Linear) (Quad) (Total) - R1 2.26200 -0.11792 0.00000 -0.12076 -0.12076 2.14124 - R2 2.26200 -0.11792 0.00000 -0.12076 -0.12076 2.14124 - A1 3.14159 0.00000 0.00000 0.00000 0.00000 3.14159 - A2 3.14159 -0.00000 0.00000 0.00000 0.00000 3.14159 - Item Value Threshold Converged? - Maximum Force 0.117919 0.000450 NO - RMS Force 0.083382 0.000300 NO - Maximum Displacement 0.100928 0.001800 NO - RMS Displacement 0.085390 0.001200 NO - Predicted change in Energy=-1.465528D-02 - Lowest energy point so far. Saving SCF results. - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - - Leave Link 103 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 0.7 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 -0.758443 -0.375075 3.208790 - 2 8 0 1.135585 -0.010287 2.019161 - 3 6 0 0.188571 -0.192681 2.613975 - --------------------------------------------------------------------- - Distance matrix (angstroms): - 1 2 3 - 1 O 0.000000 - 2 O 2.266193 0.000000 - 3 C 1.133097 1.133097 0.000000 - Stoichiometry CO2 - Framework group D*H[O(C),C*(O.O)] - Deg. of freedom 1 - Full point group D*H NOp 8 - RotChk: IX=0 Diff= 3.51D-16 - Largest Abelian subgroup D2H NOp 8 - Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 -0.000000 -0.000000 1.133097 - 2 8 0 0.000000 -0.000000 -1.133097 - 3 6 0 0.000000 0.000000 0.000000 - --------------------------------------------------------------------- - Rotational constants (GHZ): 0.0000000 12.3047121 12.3047121 - Leave Link 202 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 1.6 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l301.exe) - Standard basis: 6-31G(d) (6D, 7F) - Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. - There are 14 symmetry adapted cartesian basis functions of AG symmetry. - There are 2 symmetry adapted cartesian basis functions of B1G symmetry. - There are 4 symmetry adapted cartesian basis functions of B2G symmetry. - There are 4 symmetry adapted cartesian basis functions of B3G symmetry. - There are 1 symmetry adapted cartesian basis functions of AU symmetry. - There are 10 symmetry adapted cartesian basis functions of B1U symmetry. - There are 5 symmetry adapted cartesian basis functions of B2U symmetry. - There are 5 symmetry adapted cartesian basis functions of B3U symmetry. - There are 14 symmetry adapted basis functions of AG symmetry. - There are 2 symmetry adapted basis functions of B1G symmetry. - There are 4 symmetry adapted basis functions of B2G symmetry. - There are 4 symmetry adapted basis functions of B3G symmetry. - There are 1 symmetry adapted basis functions of AU symmetry. - There are 10 symmetry adapted basis functions of B1U symmetry. - There are 5 symmetry adapted basis functions of B2U symmetry. - There are 5 symmetry adapted basis functions of B3U symmetry. - 45 basis functions, 84 primitive gaussians, 45 cartesian basis functions - 11 alpha electrons 11 beta electrons - nuclear repulsion energy 59.7783870222 Hartrees. - IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 - ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 - IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 - NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F - Integral buffers will be 131072 words long. - Raffenetti 1 integral format. - Two-electron integral symmetry is turned on. - Leave Link 301 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 1.8 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l302.exe) - NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 - NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. - One-electron integrals computed using PRISM. - One-electron integral symmetry used in STVInt - NBasis= 45 RedAO= T EigKep= 2.75D-03 NBF= 14 2 4 4 1 10 5 5 - NBsUse= 45 1.00D-06 EigRej= -1.00D+00 NBFU= 14 2 4 4 1 10 5 5 - Leave Link 302 at Thu Jun 10 18:05:59 2021, MaxMem= 4800000000 cpu: 5.3 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l303.exe) - DipDrv: MaxL=1. - Leave Link 303 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 0.9 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l401.exe) - Initial guess from the checkpoint file: "/global/scratch/alex_epstein/line_c2o/Gau-207403.chk" - B after Tr= 0.000000 -0.000000 0.000000 - Rot= 1.000000 0.000000 0.000000 0.000000 Ang= 0.00 deg. - Guess basis will be translated and rotated to current coordinates. - JPrj=2 DoOrth=T DoCkMO=T. - Initial guess orbital symmetries: - Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) - (PIU) (PIG) (PIG) - Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) - (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (PIG) - (PIG) (DLTG) (DLTG) (DLTU) (DLTU) (SGU) (DLTG) - (DLTG) (PIU) (PIU) (SGG) (PIG) (PIG) (SGU) (SGG) - (SGG) (SGG) (SGU) - The electronic state of the initial guess is 1-SGG. - Generating alternative initial guess. - ExpMin= 1.69D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=2 IRadAn= 4 AccDes= 0.00D+00 - Harris functional with IExCor= 205 and IRadAn= 4 diagonalized for initial guess. - HarFok: IExCor= 205 AccDes= 0.00D+00 IRadAn= 4 IDoV= 1 UseB2=F ITyADJ=14 - ICtDFT= 3500011 ScaDFX= 1.000000 1.000000 1.000000 1.000000 - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 - NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T - wScrn= 0.000000 ICntrl= 500 IOpCl= 0 I1Cent= 200000004 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Harris En= -187.647008958098 - Leave Link 401 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 6.4 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l502.exe) - Keep R1 ints in memory in symmetry-blocked form, NReq=7134369. - FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Closed shell SCF: - Using DIIS extrapolation, IDIIS= 1040. - NGot= 4800000000 LenX= 4799912550 LenY= 4799910084 - Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. - Requested convergence on MAX density matrix=1.00D-06. - Requested convergence on energy=1.00D-06. - No special actions if energy rises. - - Cycle 1 Pass 1 IDiag 1: - E= -187.627251532061 - DIIS: error= 1.09D-02 at cycle 1 NSaved= 1. - NSaved= 1 IEnMin= 1 EnMin= -187.627251532061 IErMin= 1 ErrMin= 1.09D-02 - ErrMax= 1.09D-02 0.00D+00 EMaxC= 1.00D-01 BMatC= 5.78D-03 BMatP= 5.78D-03 - IDIUse=3 WtCom= 8.91D-01 WtEn= 1.09D-01 - Coeff-Com: 0.100D+01 - Coeff-En: 0.100D+01 - Coeff: 0.100D+01 - Recover alternate guess density for next cycle. - RMSDP=6.93D-03 MaxDP=6.80D-02 OVMax= 0.00D+00 - - Cycle 2 Pass 1 IDiag 1: - E= -187.556267240062 Delta-E= 0.070984291999 Rises=F Damp=F - Switch densities from cycles 1 and 2 for lowest energy. - DIIS: error= 6.05D-02 at cycle 2 NSaved= 2. - NSaved= 2 IEnMin= 1 EnMin= -187.627251532061 IErMin= 1 ErrMin= 1.09D-02 - ErrMax= 6.05D-02 0.00D+00 EMaxC= 1.00D+00 BMatC= 1.97D-01 BMatP= 5.78D-03 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.923D+00 0.766D-01 - Coeff: 0.923D+00 0.766D-01 - Gap= 0.782 Goal= None Shift= 0.000 - RMSDP=2.04D-03 MaxDP=1.36D-02 DE= 7.10D-02 OVMax= 2.15D-02 - - Cycle 3 Pass 1 IDiag 1: - E= -187.633231258904 Delta-E= -0.076964018842 Rises=F Damp=F - DIIS: error= 3.80D-03 at cycle 3 NSaved= 3. - NSaved= 3 IEnMin= 3 EnMin= -187.633231258904 IErMin= 3 ErrMin= 3.80D-03 - ErrMax= 3.80D-03 0.00D+00 EMaxC= 1.00D+00 BMatC= 2.94D-04 BMatP= 5.78D-03 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.251D-01 0.800D-02 0.967D+00 - Coeff: 0.251D-01 0.800D-02 0.967D+00 - Gap= 0.781 Goal= None Shift= 0.000 - RMSDP=5.34D-04 MaxDP=5.79D-03 DE=-7.70D-02 OVMax= 8.53D-03 - - Cycle 4 Pass 1 IDiag 1: - E= -187.633592700632 Delta-E= -0.000361441728 Rises=F Damp=F - DIIS: error= 9.49D-04 at cycle 4 NSaved= 4. - NSaved= 4 IEnMin= 4 EnMin= -187.633592700632 IErMin= 4 ErrMin= 9.49D-04 - ErrMax= 9.49D-04 0.00D+00 EMaxC= 1.00D+00 BMatC= 3.43D-05 BMatP= 2.94D-04 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.591D-01-0.632D-02 0.608D-02 0.106D+01 - Coeff: -0.591D-01-0.632D-02 0.608D-02 0.106D+01 - Gap= 0.779 Goal= None Shift= 0.000 - RMSDP=1.97D-04 MaxDP=1.82D-03 DE=-3.61D-04 OVMax= 2.99D-03 - - Cycle 5 Pass 1 IDiag 1: - E= -187.633644199040 Delta-E= -0.000051498408 Rises=F Damp=F - DIIS: error= 4.48D-04 at cycle 5 NSaved= 5. - NSaved= 5 IEnMin= 5 EnMin= -187.633644199040 IErMin= 5 ErrMin= 4.48D-04 - ErrMax= 4.48D-04 0.00D+00 EMaxC= 1.00D+00 BMatC= 5.04D-06 BMatP= 3.43D-05 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.111D-01 0.714D-03-0.654D-01 0.195D+00 0.881D+00 - Coeff: -0.111D-01 0.714D-03-0.654D-01 0.195D+00 0.881D+00 - Gap= 0.780 Goal= None Shift= 0.000 - RMSDP=5.62D-05 MaxDP=6.49D-04 DE=-5.15D-05 OVMax= 1.01D-03 - - Cycle 6 Pass 1 IDiag 1: - E= -187.633649185699 Delta-E= -0.000004986659 Rises=F Damp=F - DIIS: error= 7.74D-05 at cycle 6 NSaved= 6. - NSaved= 6 IEnMin= 6 EnMin= -187.633649185699 IErMin= 6 ErrMin= 7.74D-05 - ErrMax= 7.74D-05 0.00D+00 EMaxC= 1.00D+00 BMatC= 1.67D-07 BMatP= 5.04D-06 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.578D-02 0.172D-03-0.237D-02-0.891D-01-0.113D+00 0.120D+01 - Coeff: 0.578D-02 0.172D-03-0.237D-02-0.891D-01-0.113D+00 0.120D+01 - Gap= 0.780 Goal= None Shift= 0.000 - RMSDP=2.01D-05 MaxDP=1.73D-04 DE=-4.99D-06 OVMax= 2.92D-04 - - Cycle 7 Pass 1 IDiag 1: - E= -187.633649541865 Delta-E= -0.000000356166 Rises=F Damp=F - DIIS: error= 1.60D-05 at cycle 7 NSaved= 7. - NSaved= 7 IEnMin= 7 EnMin= -187.633649541865 IErMin= 7 ErrMin= 1.60D-05 - ErrMax= 1.60D-05 0.00D+00 EMaxC= 1.00D+00 BMatC= 5.78D-09 BMatP= 1.67D-07 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.110D-02-0.479D-04 0.211D-02 0.182D-01-0.179D-01-0.235D+00 - Coeff-Com: 0.123D+01 - Coeff: -0.110D-02-0.479D-04 0.211D-02 0.182D-01-0.179D-01-0.235D+00 - Coeff: 0.123D+01 - Gap= 0.780 Goal= None Shift= 0.000 - RMSDP=2.52D-06 MaxDP=2.84D-05 DE=-3.56D-07 OVMax= 2.87D-05 - - Cycle 8 Pass 1 IDiag 1: - E= -187.633649548981 Delta-E= -0.000000007115 Rises=F Damp=F - DIIS: error= 1.65D-06 at cycle 8 NSaved= 8. - NSaved= 8 IEnMin= 8 EnMin= -187.633649548981 IErMin= 8 ErrMin= 1.65D-06 - ErrMax= 1.65D-06 0.00D+00 EMaxC= 1.00D+00 BMatC= 6.65D-11 BMatP= 5.78D-09 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.121D-03 0.421D-05-0.326D-03-0.183D-02 0.282D-02 0.331D-01 - Coeff-Com: -0.256D+00 0.122D+01 - Coeff: 0.121D-03 0.421D-05-0.326D-03-0.183D-02 0.282D-02 0.331D-01 - Coeff: -0.256D+00 0.122D+01 - Gap= 0.780 Goal= None Shift= 0.000 - RMSDP=5.63D-07 MaxDP=5.53D-06 DE=-7.12D-09 OVMax= 4.70D-06 - - Cycle 9 Pass 1 IDiag 1: - E= -187.633649549076 Delta-E= -0.000000000095 Rises=F Damp=F - DIIS: error= 1.03D-07 at cycle 9 NSaved= 9. - NSaved= 9 IEnMin= 9 EnMin= -187.633649549076 IErMin= 9 ErrMin= 1.03D-07 - ErrMax= 1.03D-07 0.00D+00 EMaxC= 1.00D+00 BMatC= 2.75D-13 BMatP= 6.65D-11 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.322D-05-0.809D-07 0.112D-04 0.494D-04-0.543D-04-0.154D-02 - Coeff-Com: 0.154D-01-0.138D+00 0.112D+01 - Coeff: -0.322D-05-0.809D-07 0.112D-04 0.494D-04-0.543D-04-0.154D-02 - Coeff: 0.154D-01-0.138D+00 0.112D+01 - Gap= 0.780 Goal= None Shift= 0.000 - RMSDP=4.24D-08 MaxDP=5.22D-07 DE=-9.55D-11 OVMax= 4.11D-07 - - Cycle 10 Pass 1 IDiag 1: - E= -187.633649549076 Delta-E= 0.000000000000 Rises=F Damp=F - DIIS: error= 9.95D-09 at cycle 10 NSaved= 10. - NSaved=10 IEnMin= 9 EnMin= -187.633649549076 IErMin=10 ErrMin= 9.95D-09 - ErrMax= 9.95D-09 0.00D+00 EMaxC= 1.00D+00 BMatC= 2.67D-15 BMatP= 2.75D-13 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.156D-06 0.876D-09-0.696D-06-0.259D-05 0.830D-06 0.118D-03 - Coeff-Com: -0.139D-02 0.187D-01-0.207D+00 0.119D+01 - Coeff: 0.156D-06 0.876D-09-0.696D-06-0.259D-05 0.830D-06 0.118D-03 - Coeff: -0.139D-02 0.187D-01-0.207D+00 0.119D+01 - Gap= 0.780 Goal= None Shift= 0.000 - RMSDP=2.07D-09 MaxDP=2.23D-08 DE= 0.00D+00 OVMax= 1.82D-08 - - SCF Done: E(RHF) = -187.633649549 A.U. after 10 cycles - NFock= 10 Conv=0.21D-08 -V/T= 2.0022 - KE= 1.872219534074D+02 PE=-5.623087732485D+02 EE= 1.276747832698D+02 - Leave Link 502 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 4.8 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l701.exe) - ... and contract with generalized density number 0. - Compute integral first derivatives. - Leave Link 701 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 4.6 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l702.exe) - L702 exits ... SP integral derivatives will be done elsewhere. - Leave Link 702 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 0.7 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l703.exe) - Integral derivatives from FoFJK, PRISM(SPDF). - Compute integral first derivatives, UseDBF=F ICtDFT= 0. - Calling FoFJK, ICntrl= 2127 FMM=F ISym2X=1 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0. - FoFJK: IHMeth= 1 ICntrl= 2127 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F - IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 800 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 2127 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Leave Link 703 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 5.3 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l716.exe) - Dipole = 1.50340041D-16 3.00969273D-17 0.00000000D+00 - ***** Axes restored to original set ***** - ------------------------------------------------------------------- - Center Atomic Forces (Hartrees/Bohr) - Number Number X Y Z - ------------------------------------------------------------------- - 1 8 -0.023193813 -0.004467110 0.014567923 - 2 8 0.023193813 0.004467110 -0.014567923 - 3 6 -0.000000000 -0.000000000 -0.000000000 - ------------------------------------------------------------------- - Cartesian Forces: Max 0.023193813 RMS 0.013082069 - Leave Link 716 at Thu Jun 10 18:06:00 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) - - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - Berny optimization. - Using GEDIIS/GDIIS optimizer. - Red2BG is reusing G-inverse. - Internal Forces: Max 0.027751260 RMS 0.019623104 - Search for a local minimum. - Step number 2 out of a maximum of 20 - All quantities printed in internal units (Hartrees-Bohrs-Radians) - RMS Force = .19623D-01 SwitMx=.10000D-02 MixMth= 1 - Mixed Optimization -- RFO/linear search - Update second derivatives using D2CorX and points 1 2 - DE= -1.22D-02 DEPred=-1.47D-02 R= 8.34D-01 - TightC=F SS= 1.41D+00 RLast= 1.71D-01 DXNew= 5.0454D-01 5.1234D-01 - Trust test= 8.34D-01 RLast= 1.71D-01 DXMaxT set to 5.05D-01 - The second derivative matrix: - R1 R2 A1 A2 - R1 0.94750 - R2 0.25878 0.94750 - A1 -0.00000 -0.00000 0.17924 - A2 0.00000 0.00000 -0.01555 0.13330 - ITU= 1 0 - Use linear search instead of GDIIS. - Eigenvalues --- 0.12854 0.18401 0.68871 1.20628 - RFO step: Lambda= 0.00000000D+00 EMin= 1.28535469D-01 - Quartic linear search produced a step of -0.15936. - Iteration 1 RMS(Cart)= 0.01360755 RMS(Int)= 0.00000000 - Iteration 2 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000001 - ITry= 1 IFail=0 DXMaxC= 1.61D-02 DCOld= 1.00D+10 DXMaxT= 5.05D-01 DXLimC= 3.00D+00 Rises=F - ClnCor: largest displacement from symmetrization is 4.25D-13 for atom 3. - Variable Old X -DE/DX Delta X Delta X Delta X New X - (Linear) (Quad) (Total) - R1 2.14124 0.02775 0.01924 -0.00000 0.01924 2.16049 - R2 2.14124 0.02775 0.01924 0.00000 0.01924 2.16049 - A1 3.14159 0.00000 0.00000 0.00000 -0.00000 3.14159 - A2 3.14159 0.00000 0.00000 0.00000 -0.00000 3.14159 - Item Value Threshold Converged? - Maximum Force 0.027751 0.000450 NO - RMS Force 0.019623 0.000300 NO - Maximum Displacement 0.016084 0.001800 NO - RMS Displacement 0.013608 0.001200 NO - Predicted change in Energy=-6.213660D-04 - Lowest energy point so far. Saving SCF results. - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - - Leave Link 103 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 1.9 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 -0.766954 -0.376714 3.214136 - 2 8 0 1.144096 -0.008647 2.013815 - 3 6 0 0.188571 -0.192681 2.613975 - --------------------------------------------------------------------- - Distance matrix (angstroms): - 1 2 3 - 1 O 0.000000 - 2 O 2.286560 0.000000 - 3 C 1.143280 1.143280 0.000000 - Stoichiometry CO2 - Framework group D*H[O(C),C*(O.O)] - Deg. of freedom 1 - Full point group D*H NOp 8 - RotChk: IX=0 Diff= 3.70D-16 - Largest Abelian subgroup D2H NOp 8 - Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 -0.000000 0.000000 1.143280 - 2 8 0 0.000000 0.000000 -1.143280 - 3 6 0 0.000000 0.000000 0.000000 - --------------------------------------------------------------------- - Rotational constants (GHZ): 0.0000000 12.0864862 12.0864862 - Leave Link 202 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 0.4 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l301.exe) - Standard basis: 6-31G(d) (6D, 7F) - Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. - There are 14 symmetry adapted cartesian basis functions of AG symmetry. - There are 2 symmetry adapted cartesian basis functions of B1G symmetry. - There are 4 symmetry adapted cartesian basis functions of B2G symmetry. - There are 4 symmetry adapted cartesian basis functions of B3G symmetry. - There are 1 symmetry adapted cartesian basis functions of AU symmetry. - There are 10 symmetry adapted cartesian basis functions of B1U symmetry. - There are 5 symmetry adapted cartesian basis functions of B2U symmetry. - There are 5 symmetry adapted cartesian basis functions of B3U symmetry. - There are 14 symmetry adapted basis functions of AG symmetry. - There are 2 symmetry adapted basis functions of B1G symmetry. - There are 4 symmetry adapted basis functions of B2G symmetry. - There are 4 symmetry adapted basis functions of B3G symmetry. - There are 1 symmetry adapted basis functions of AU symmetry. - There are 10 symmetry adapted basis functions of B1U symmetry. - There are 5 symmetry adapted basis functions of B2U symmetry. - There are 5 symmetry adapted basis functions of B3U symmetry. - 45 basis functions, 84 primitive gaussians, 45 cartesian basis functions - 11 alpha electrons 11 beta electrons - nuclear repulsion energy 59.2459262762 Hartrees. - IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 - ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 - IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 - NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F - Integral buffers will be 131072 words long. - Raffenetti 1 integral format. - Two-electron integral symmetry is turned on. - Leave Link 301 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 3.4 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l302.exe) - NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 - NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. - One-electron integrals computed using PRISM. - One-electron integral symmetry used in STVInt - NBasis= 45 RedAO= T EigKep= 2.77D-03 NBF= 14 2 4 4 1 10 5 5 - NBsUse= 45 1.00D-06 EigRej= -1.00D+00 NBFU= 14 2 4 4 1 10 5 5 - Leave Link 302 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 3.7 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l303.exe) - DipDrv: MaxL=1. - Leave Link 303 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l401.exe) - Initial guess from the checkpoint file: "/global/scratch/alex_epstein/line_c2o/Gau-207403.chk" - B after Tr= 0.000000 0.000000 0.000000 - Rot= 1.000000 -0.000000 0.000000 -0.000000 Ang= 0.00 deg. - Guess basis will be translated and rotated to current coordinates. - JPrj=2 DoOrth=T DoCkMO=T. - Initial guess orbital symmetries: - Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) - (PIU) (PIG) (PIG) - Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) - (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (DLTG) - (DLTG) (PIG) (PIG) (DLTU) (DLTU) (SGU) (DLTG) - (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) - (SGG) (SGU) (SGG) - The electronic state of the initial guess is 1-SGG. - Leave Link 401 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 2.8 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l502.exe) - Keep R1 ints in memory in symmetry-blocked form, NReq=7134369. - FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Closed shell SCF: - Using DIIS extrapolation, IDIIS= 1040. - NGot= 4800000000 LenX= 4799912550 LenY= 4799910084 - Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. - Requested convergence on MAX density matrix=1.00D-06. - Requested convergence on energy=1.00D-06. - No special actions if energy rises. - - Cycle 1 Pass 1 IDiag 1: - E= -187.634006821630 - DIIS: error= 1.79D-03 at cycle 1 NSaved= 1. - NSaved= 1 IEnMin= 1 EnMin= -187.634006821630 IErMin= 1 ErrMin= 1.79D-03 - ErrMax= 1.79D-03 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.56D-04 BMatP= 1.56D-04 - IDIUse=3 WtCom= 9.82D-01 WtEn= 1.79D-02 - Coeff-Com: 0.100D+01 - Coeff-En: 0.100D+01 - Coeff: 0.100D+01 - Gap= 0.770 Goal= None Shift= 0.000 - GapD= 0.770 DampG=2.000 DampE=1.000 DampFc=2.0000 IDamp=-1. - RMSDP=3.32D-04 MaxDP=2.24D-03 OVMax= 3.40D-03 - - Cycle 2 Pass 1 IDiag 1: - E= -187.634161427579 Delta-E= -0.000154605949 Rises=F Damp=F - DIIS: error= 5.77D-04 at cycle 2 NSaved= 2. - NSaved= 2 IEnMin= 2 EnMin= -187.634161427579 IErMin= 2 ErrMin= 5.77D-04 - ErrMax= 5.77D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.25D-05 BMatP= 1.56D-04 - IDIUse=3 WtCom= 9.94D-01 WtEn= 5.77D-03 - Coeff-Com: 0.725D-01 0.927D+00 - Coeff-En: 0.000D+00 0.100D+01 - Coeff: 0.721D-01 0.928D+00 - Gap= 0.771 Goal= None Shift= 0.000 - RMSDP=9.96D-05 MaxDP=8.60D-04 DE=-1.55D-04 OVMax= 1.20D-03 - - Cycle 3 Pass 1 IDiag 1: - E= -187.634173995685 Delta-E= -0.000012568105 Rises=F Damp=F - DIIS: error= 2.79D-04 at cycle 3 NSaved= 3. - NSaved= 3 IEnMin= 3 EnMin= -187.634173995685 IErMin= 3 ErrMin= 2.79D-04 - ErrMax= 2.79D-04 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.48D-06 BMatP= 1.25D-05 - IDIUse=3 WtCom= 9.97D-01 WtEn= 2.79D-03 - Coeff-Com: -0.583D-01 0.421D-01 0.102D+01 - Coeff-En: 0.000D+00 0.000D+00 0.100D+01 - Coeff: -0.581D-01 0.419D-01 0.102D+01 - Gap= 0.770 Goal= None Shift= 0.000 - RMSDP=3.71D-05 MaxDP=4.08D-04 DE=-1.26D-05 OVMax= 7.08D-04 - - Cycle 4 Pass 1 IDiag 1: - E= -187.634175927579 Delta-E= -0.000001931894 Rises=F Damp=F - DIIS: error= 8.29D-05 at cycle 4 NSaved= 4. - NSaved= 4 IEnMin= 4 EnMin= -187.634175927579 IErMin= 4 ErrMin= 8.29D-05 - ErrMax= 8.29D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.90D-07 BMatP= 1.48D-06 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.183D-01-0.611D-01 0.208D+00 0.872D+00 - Coeff: -0.183D-01-0.611D-01 0.208D+00 0.872D+00 - Gap= 0.771 Goal= None Shift= 0.000 - RMSDP=1.21D-05 MaxDP=1.05D-04 DE=-1.93D-06 OVMax= 1.79D-04 - - Cycle 5 Pass 1 IDiag 1: - E= -187.634176173131 Delta-E= -0.000000245552 Rises=F Damp=F - DIIS: error= 3.39D-05 at cycle 5 NSaved= 5. - NSaved= 5 IEnMin= 5 EnMin= -187.634176173131 IErMin= 5 ErrMin= 3.39D-05 - ErrMax= 3.39D-05 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.43D-08 BMatP= 1.90D-07 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.851D-02-0.116D-02-0.161D+00 0.702D-01 0.108D+01 - Coeff: 0.851D-02-0.116D-02-0.161D+00 0.702D-01 0.108D+01 - Gap= 0.771 Goal= None Shift= 0.000 - RMSDP=5.14D-06 MaxDP=5.49D-05 DE=-2.46D-07 OVMax= 8.59D-05 - - Cycle 6 Pass 1 IDiag 1: - E= -187.634176201019 Delta-E= -0.000000027888 Rises=F Damp=F - DIIS: error= 3.64D-06 at cycle 6 NSaved= 6. - NSaved= 6 IEnMin= 6 EnMin= -187.634176201019 IErMin= 6 ErrMin= 3.64D-06 - ErrMax= 3.64D-06 0.00D+00 EMaxC= 1.00D-01 BMatC= 3.01D-10 BMatP= 2.43D-08 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.140D-02 0.201D-02 0.281D-01-0.231D-01-0.288D+00 0.128D+01 - Coeff: -0.140D-02 0.201D-02 0.281D-01-0.231D-01-0.288D+00 0.128D+01 - Gap= 0.771 Goal= None Shift= 0.000 - RMSDP=6.25D-07 MaxDP=7.41D-06 DE=-2.79D-08 OVMax= 7.24D-06 - - Cycle 7 Pass 1 IDiag 1: - E= -187.634176201487 Delta-E= -0.000000000467 Rises=F Damp=F - DIIS: error= 4.22D-07 at cycle 7 NSaved= 7. - NSaved= 7 IEnMin= 7 EnMin= -187.634176201487 IErMin= 7 ErrMin= 4.22D-07 - ErrMax= 4.22D-07 0.00D+00 EMaxC= 1.00D-01 BMatC= 4.52D-12 BMatP= 3.01D-10 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.166D-03-0.268D-03-0.370D-02 0.548D-02 0.387D-01-0.261D+00 - Coeff-Com: 0.122D+01 - Coeff: 0.166D-03-0.268D-03-0.370D-02 0.548D-02 0.387D-01-0.261D+00 - Coeff: 0.122D+01 - Gap= 0.771 Goal= None Shift= 0.000 - RMSDP=1.37D-07 MaxDP=1.21D-06 DE=-4.67D-10 OVMax= 1.09D-06 - - Cycle 8 Pass 1 IDiag 1: - E= -187.634176201493 Delta-E= -0.000000000006 Rises=F Damp=F - DIIS: error= 2.73D-08 at cycle 8 NSaved= 8. - NSaved= 8 IEnMin= 8 EnMin= -187.634176201493 IErMin= 8 ErrMin= 2.73D-08 - ErrMax= 2.73D-08 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.11D-14 BMatP= 4.52D-12 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: -0.639D-05 0.763D-05 0.176D-03-0.323D-03-0.173D-02 0.173D-01 - Coeff-Com: -0.155D+00 0.114D+01 - Coeff: -0.639D-05 0.763D-05 0.176D-03-0.323D-03-0.173D-02 0.173D-01 - Coeff: -0.155D+00 0.114D+01 - Gap= 0.771 Goal= None Shift= 0.000 - RMSDP=1.27D-08 MaxDP=1.48D-07 DE=-6.11D-12 OVMax= 1.20D-07 - - Cycle 9 Pass 1 IDiag 1: - E= -187.634176201493 Delta-E= 0.000000000000 Rises=F Damp=F - DIIS: error= 2.66D-09 at cycle 9 NSaved= 9. - NSaved= 9 IEnMin= 8 EnMin= -187.634176201493 IErMin= 9 ErrMin= 2.66D-09 - ErrMax= 2.66D-09 0.00D+00 EMaxC= 1.00D-01 BMatC= 1.49D-16 BMatP= 2.11D-14 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.697D-06-0.917D-06-0.174D-04 0.345D-04 0.164D-03-0.200D-02 - Coeff-Com: 0.242D-01-0.222D+00 0.120D+01 - Coeff: 0.697D-06-0.917D-06-0.174D-04 0.345D-04 0.164D-03-0.200D-02 - Coeff: 0.242D-01-0.222D+00 0.120D+01 - Gap= 0.771 Goal= None Shift= 0.000 - RMSDP=6.02D-10 MaxDP=6.56D-09 DE= 2.84D-13 OVMax= 5.28D-09 - - SCF Done: E(RHF) = -187.634176201 A.U. after 9 cycles - NFock= 9 Conv=0.60D-09 -V/T= 2.0028 - KE= 1.871094202810D+02 PE=-5.611564169403D+02 EE= 1.271668941815D+02 - Leave Link 502 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 4.9 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l701.exe) - ... and contract with generalized density number 0. - Compute integral first derivatives. - Leave Link 701 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 4.0 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l702.exe) - L702 exits ... SP integral derivatives will be done elsewhere. - Leave Link 702 at Thu Jun 10 18:06:01 2021, MaxMem= 4800000000 cpu: 0.7 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l703.exe) - Integral derivatives from FoFJK, PRISM(SPDF). - Compute integral first derivatives, UseDBF=F ICtDFT= 0. - Calling FoFJK, ICntrl= 2127 FMM=F ISym2X=1 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0. - FoFJK: IHMeth= 1 ICntrl= 2127 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F - IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 800 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 2127 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Leave Link 703 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 4.8 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l716.exe) - Dipole =-1.68515248D-16-1.40429373D-17 0.00000000D+00 - ***** Axes restored to original set ***** - ------------------------------------------------------------------- - Center Atomic Forces (Hartrees/Bohr) - Number Number X Y Z - ------------------------------------------------------------------- - 1 8 0.000051665 0.000009951 -0.000032451 - 2 8 -0.000051665 -0.000009951 0.000032451 - 3 6 0.000000000 0.000000000 -0.000000000 - ------------------------------------------------------------------- - Cartesian Forces: Max 0.000051665 RMS 0.000029141 - Leave Link 716 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) - - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - Berny optimization. - Using GEDIIS/GDIIS optimizer. - Red2BG is reusing G-inverse. - Internal Forces: Max 0.000061817 RMS 0.000043711 - Search for a local minimum. - Step number 3 out of a maximum of 20 - All quantities printed in internal units (Hartrees-Bohrs-Radians) - RMS Force = .43711D-04 SwitMx=.10000D-02 MixMth= 2 - Mixed Optimization -- En-DIIS/RFO-DIIS - Update second derivatives using D2CorX and points 1 2 3 - DE= -5.27D-04 DEPred=-6.21D-04 R= 8.48D-01 - TightC=F SS= 1.41D+00 RLast= 2.72D-02 DXNew= 8.4853D-01 8.1645D-02 - Trust test= 8.48D-01 RLast= 2.72D-02 DXMaxT set to 5.05D-01 - The second derivative matrix: - R1 R2 A1 A2 - R1 1.06700 - R2 0.37829 1.06700 - A1 0.00000 0.00000 0.17924 - A2 -0.00000 -0.00000 -0.01555 0.13330 - ITU= 1 1 0 - Use linear search instead of GDIIS. - Eigenvalues --- 0.12854 0.18401 0.68871 1.44529 - RFO step: Lambda= 0.00000000D+00 EMin= 1.28535469D-01 - Quartic linear search produced a step of -0.00230. - Iteration 1 RMS(Cart)= 0.00003132 RMS(Int)= 0.00000000 - Iteration 2 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000001 - ITry= 1 IFail=0 DXMaxC= 3.70D-05 DCOld= 1.00D+10 DXMaxT= 5.05D-01 DXLimC= 3.00D+00 Rises=F - ClnCor: largest displacement from symmetrization is 4.13D-13 for atom 3. - Variable Old X -DE/DX Delta X Delta X Delta X New X - (Linear) (Quad) (Total) - R1 2.16049 -0.00006 -0.00004 0.00000 -0.00004 2.16044 - R2 2.16049 -0.00006 -0.00004 -0.00000 -0.00004 2.16044 - A1 3.14159 -0.00000 0.00000 -0.00000 0.00000 3.14159 - A2 3.14159 0.00000 0.00000 0.00000 0.00000 3.14159 - Item Value Threshold Converged? - Maximum Force 0.000062 0.000450 YES - RMS Force 0.000044 0.000300 YES - Maximum Displacement 0.000037 0.001800 YES - RMS Displacement 0.000031 0.001200 YES - Predicted change in Energy=-2.640612D-09 - Optimization completed. - -- Stationary point found. - ---------------------------- - ! Optimized Parameters ! - ! (Angstroms and Degrees) ! - -------------------------- -------------------------- - ! Name Definition Value Derivative Info. ! - -------------------------------------------------------------------------------- - ! R1 R(1,3) 1.1433 -DE/DX = -0.0001 ! - ! R2 R(2,3) 1.1433 -DE/DX = -0.0001 ! - ! A1 L(1,3,2,-2,-1) 180.0 -DE/DX = 0.0 ! - ! A2 L(1,3,2,-3,-2) 180.0 -DE/DX = 0.0 ! - -------------------------------------------------------------------------------- - Lowest energy point so far. Saving SCF results. - Largest change from initial coordinates is atom 1 0.000 Angstoms. - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - - Leave Link 103 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 2.1 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 -0.766954 -0.376714 3.214136 - 2 8 0 1.144096 -0.008647 2.013815 - 3 6 0 0.188571 -0.192681 2.613975 - --------------------------------------------------------------------- - Distance matrix (angstroms): - 1 2 3 - 1 O 0.000000 - 2 O 2.286560 0.000000 - 3 C 1.143280 1.143280 0.000000 - Stoichiometry CO2 - Framework group D*H[O(C),C*(O.O)] - Deg. of freedom 1 - Full point group D*H NOp 8 - RotChk: IX=0 Diff= 4.01D-16 - Largest Abelian subgroup D2H NOp 8 - Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 0.000000 -0.000000 1.143280 - 2 8 0 0.000000 0.000000 -1.143280 - 3 6 0 0.000000 0.000000 0.000000 - --------------------------------------------------------------------- - Rotational constants (GHZ): 0.0000000 12.0864862 12.0864862 - Leave Link 202 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 0.4 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l601.exe) - Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0. - - ********************************************************************** - - Population analysis using the SCF density. - - ********************************************************************** - - Orbital symmetries: - Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) - (PIU) (PIG) (PIG) - Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) - (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (DLTG) - (DLTG) (PIG) (PIG) (DLTU) (DLTU) (SGU) (DLTG) - (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) - (SGG) (SGU) (SGG) - The electronic state is 1-SGG. - Alpha occ. eigenvalues -- -20.65784 -20.65782 -11.46212 -1.54200 -1.48690 - Alpha occ. eigenvalues -- -0.79261 -0.73924 -0.71908 -0.71908 -0.53995 - Alpha occ. eigenvalues -- -0.53995 - Alpha virt. eigenvalues -- 0.23058 0.23058 0.26636 0.51004 0.66340 - Alpha virt. eigenvalues -- 0.66340 0.84293 0.98303 0.99234 1.14705 - Alpha virt. eigenvalues -- 1.14705 1.33111 1.33111 1.45461 1.61575 - Alpha virt. eigenvalues -- 1.63482 1.63482 1.70440 1.70440 2.01268 - Alpha virt. eigenvalues -- 2.01268 2.08925 2.35732 2.35732 2.49060 - Alpha virt. eigenvalues -- 2.49060 3.14657 3.32784 3.35175 3.35175 - Alpha virt. eigenvalues -- 3.48917 4.18091 4.90146 4.90696 - Condensed to atoms (all electrons): - 1 2 3 - 1 O 7.841235 -0.025877 0.630900 - 2 O -0.025877 7.841235 0.630900 - 3 C 0.630900 0.630900 3.845681 - Mulliken charges: - 1 - 1 O -0.446259 - 2 O -0.446259 - 3 C 0.892518 - Sum of Mulliken charges = -0.00000 - Mulliken charges with hydrogens summed into heavy atoms: - 1 - 1 O -0.446259 - 2 O -0.446259 - 3 C 0.892518 - Electronic spatial extent (au): = 110.9843 - Charge= -0.0000 electrons - Dipole moment (field-independent basis, Debye): - X= 0.0000 Y= -0.0000 Z= -0.0000 Tot= 0.0000 - Quadrupole moment (field-independent basis, Debye-Ang): - XX= -14.4559 YY= -14.4559 ZZ= -19.9144 - XY= -0.0000 XZ= 0.0000 YZ= -0.0000 - Traceless Quadrupole moment (field-independent basis, Debye-Ang): - XX= 1.8195 YY= 1.8195 ZZ= -3.6391 - XY= -0.0000 XZ= 0.0000 YZ= -0.0000 - Octapole moment (field-independent basis, Debye-Ang**2): - XXX= -0.0000 YYY= -0.0000 ZZZ= -0.0000 XYY= -0.0000 - XXY= -0.0000 XXZ= 0.0000 XZZ= 0.0000 YZZ= -0.0000 - YYZ= 0.0000 XYZ= -0.0000 - Hexadecapole moment (field-independent basis, Debye-Ang**3): - XXXX= -10.2550 YYYY= -10.2550 ZZZZ= -99.4698 XXXY= -0.0000 - XXXZ= 0.0000 YYYX= -0.0000 YYYZ= 0.0000 ZZZX= 0.0000 - ZZZY= -0.0000 XXYY= -3.4183 XXZZ= -17.9582 YYZZ= -17.9582 - XXYZ= 0.0000 YYXZ= 0.0000 ZZXY= -0.0000 - N-N= 5.924592627624D+01 E-N=-5.611564169572D+02 KE= 1.871094202810D+02 - Symmetry AG KE= 1.012480411172D+02 - Symmetry B1G KE= 4.161560280064D-32 - Symmetry B2G KE= 4.700699095130D+00 - Symmetry B3G KE= 4.700699095129D+00 - Symmetry AU KE= 2.452413593718D-32 - Symmetry B1U KE= 6.913256481078D+01 - Symmetry B2U KE= 3.663708081395D+00 - Symmetry B3U KE= 3.663708081395D+00 - No NMR shielding tensors so no spin-rotation constants. - Leave Link 601 at Thu Jun 10 18:06:02 2021, MaxMem= 4800000000 cpu: 5.4 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l9999.exe) - 1\1\GINC-N0045\FOpt\RHF\6-31G(d)\C1O2\ALEX_EPSTEIN\10-Jun-2021\0\\#P H - F/6-31g(d) freq=noraman opt=(noeigen, calcfc)\\co2 for linear test\\0, - 1\O,-0.7669543606,-0.3767139767,3.2141361692\O,1.1440956549,-0.0086472 - 867,2.0138147763\C,0.1885706471,-0.1926806317,2.6139754728\\Version=ES - 64L-G16RevA.03\State=1-SGG\HF=-187.6341762\RMSD=6.023e-10\RMSF=2.914e- - 05\Dipole=0.,0.,0.\Quadrupole=-1.4820442,1.2476169,0.2344273,-0.545983 - 5,1.7805351,0.3429296\PG=D*H [O(C1),C*(O1.O1)]\\@ - - - STEINBACH'S GUIDELINES FOR SYSTEMS PROGRAMMING: - NEVER TEST FOR AN ERROR CONDITION YOU DON'T KNOW HOW - TO HANDLE. - Leave Link 9999 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 2.0 elap: 0.1 - Job cpu time: 0 days 0 hours 2 minutes 51.6 seconds. - Elapsed time: 0 days 0 hours 0 minutes 6.8 seconds. - File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 - Normal termination of Gaussian 16 at Thu Jun 10 18:06:03 2021. - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1.exe) - Link1: Proceeding to internal job step number 2. - ----------------------------------------------------------------- - #P Geom=AllCheck Guess=TCheck SCRF=Check GenChk RHF/6-31G(d) Freq - ----------------------------------------------------------------- - 1/10=4,11=1,29=7,30=1,38=1,40=1/1,3; - 2/12=2,40=1/2; - 3/5=1,6=6,7=1,11=1,14=-4,25=1,30=1,70=2,71=2,116=1,140=1/1,2,3; - 4/5=101/1; - 5/5=2,38=6,98=1/2; - 8/6=4,10=90,11=11/1; - 11/6=1,8=1,9=11,15=111,16=1/1,2,10; - 10/6=1/2; - 6/7=2,8=2,9=2,10=2,28=1/1; - 7/8=1,10=1,25=1/1,2,3,16; - 1/10=4,11=1,30=1/3; - 99//99; - Leave Link 1 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 1.4 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l101.exe) - Structure from the checkpoint file: "/global/scratch/alex_epstein/line_c2o/Gau-207403.chk" - ------------------- - co2 for linear test - ------------------- - Charge = 0 Multiplicity = 1 - Redundant internal coordinates found in file. (old form). - O,0,-0.7669543606,-0.3767139767,3.2141361692 - O,0,1.1440956549,-0.0086472867,2.0138147763 - C,0,0.1885706471,-0.1926806317,2.6139754728 - Recover connectivity data from disk. - ITRead= 0 0 0 - MicOpt= -1 -1 -1 - NAtoms= 3 NQM= 3 NQMF= 0 NMMI= 0 NMMIF= 0 - NMic= 0 NMicF= 0. - Isotopes and Nuclear Properties: - (Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM) - in nuclear magnetons) - - Atom 1 2 3 - IAtWgt= 16 16 12 - AtmWgt= 15.9949146 15.9949146 12.0000000 - NucSpn= 0 0 0 - AtZEff= 5.6000000 5.6000000 3.6000000 - NQMom= 0.0000000 0.0000000 0.0000000 - NMagM= 0.0000000 0.0000000 0.0000000 - AtZNuc= 8.0000000 8.0000000 6.0000000 - Leave Link 101 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 11.0 elap: 0.4 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) - - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - Berny optimization. - Initialization pass. - ---------------------------- - ! Initial Parameters ! - ! (Angstroms and Degrees) ! - -------------------------- -------------------------- - ! Name Definition Value Derivative Info. ! - -------------------------------------------------------------------------------- - ! R1 R(1,3) 1.1433 calculate D2E/DX2 analytically ! - ! R2 R(2,3) 1.1433 calculate D2E/DX2 analytically ! - ! A1 L(1,3,2,-2,-1) 180.0 calculate D2E/DX2 analytically ! - ! A2 L(1,3,2,-3,-2) 180.0 calculate D2E/DX2 analytically ! - -------------------------------------------------------------------------------- - Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 EigMax=2.50D+02 EigMin=1.00D-04 - Number of steps in this run= 2 maximum allowed number of steps= 2. - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - - Leave Link 103 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 0.4 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l202.exe) - Input orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 -0.766954 -0.376714 3.214136 - 2 8 0 1.144096 -0.008647 2.013815 - 3 6 0 0.188571 -0.192681 2.613975 - --------------------------------------------------------------------- - Distance matrix (angstroms): - 1 2 3 - 1 O 0.000000 - 2 O 2.286560 0.000000 - 3 C 1.143280 1.143280 0.000000 - Stoichiometry CO2 - Framework group D*H[O(C),C*(O.O)] - Deg. of freedom 1 - Full point group D*H NOp 8 - RotChk: IX=0 Diff= 4.44D-16 - Largest Abelian subgroup D2H NOp 8 - Largest concise Abelian subgroup C2 NOp 2 - Standard orientation: - --------------------------------------------------------------------- - Center Atomic Atomic Coordinates (Angstroms) - Number Number Type X Y Z - --------------------------------------------------------------------- - 1 8 0 0.000000 -0.000000 1.143280 - 2 8 0 0.000000 -0.000000 -1.143280 - 3 6 0 0.000000 0.000000 0.000000 - --------------------------------------------------------------------- - Rotational constants (GHZ): 0.0000000 12.0864862 12.0864862 - Leave Link 202 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 0.4 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l301.exe) - Standard basis: 6-31G(d) (6D, 7F) - Ernie: Thresh= 0.10000D-02 Tol= 0.10000D-05 Strict=F. - There are 14 symmetry adapted cartesian basis functions of AG symmetry. - There are 2 symmetry adapted cartesian basis functions of B1G symmetry. - There are 4 symmetry adapted cartesian basis functions of B2G symmetry. - There are 4 symmetry adapted cartesian basis functions of B3G symmetry. - There are 1 symmetry adapted cartesian basis functions of AU symmetry. - There are 10 symmetry adapted cartesian basis functions of B1U symmetry. - There are 5 symmetry adapted cartesian basis functions of B2U symmetry. - There are 5 symmetry adapted cartesian basis functions of B3U symmetry. - There are 14 symmetry adapted basis functions of AG symmetry. - There are 2 symmetry adapted basis functions of B1G symmetry. - There are 4 symmetry adapted basis functions of B2G symmetry. - There are 4 symmetry adapted basis functions of B3G symmetry. - There are 1 symmetry adapted basis functions of AU symmetry. - There are 10 symmetry adapted basis functions of B1U symmetry. - There are 5 symmetry adapted basis functions of B2U symmetry. - There are 5 symmetry adapted basis functions of B3U symmetry. - 45 basis functions, 84 primitive gaussians, 45 cartesian basis functions - 11 alpha electrons 11 beta electrons - nuclear repulsion energy 59.2459262762 Hartrees. - IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 - ScaDFX= 1.000000 1.000000 1.000000 1.000000 ScalE2= 1.000000 1.000000 - IRadAn= 5 IRanWt= -1 IRanGd= 0 ICorTp=0 IEmpDi= 4 - NAtoms= 3 NActive= 3 NUniq= 2 SFac= 2.25D+00 NAtFMM= 60 NAOKFM=F Big=F - Integral buffers will be 131072 words long. - Raffenetti 1 integral format. - Two-electron integral symmetry is turned on. - Leave Link 301 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 3.3 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l302.exe) - NPDir=0 NMtPBC= 1 NCelOv= 1 NCel= 1 NClECP= 1 NCelD= 1 - NCelK= 1 NCelE2= 1 NClLst= 1 CellRange= 0.0. - One-electron integrals computed using PRISM. - One-electron integral symmetry used in STVInt - NBasis= 45 RedAO= T EigKep= 2.77D-03 NBF= 14 2 4 4 1 10 5 5 - NBsUse= 45 1.00D-06 EigRej= -1.00D+00 NBFU= 14 2 4 4 1 10 5 5 - Leave Link 302 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 3.7 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l303.exe) - DipDrv: MaxL=1. - Leave Link 303 at Thu Jun 10 18:06:03 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l401.exe) - Initial guess from the checkpoint file: "/global/scratch/alex_epstein/line_c2o/Gau-207403.chk" - B after Tr= 0.000000 -0.000000 0.000000 - Rot= 1.000000 -0.000000 -0.000000 -0.000000 Ang= 0.00 deg. - Guess basis will be translated and rotated to current coordinates. - JPrj=2 DoOrth=T DoCkMO=T. - Initial guess orbital symmetries: - Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) - (PIU) (PIG) (PIG) - Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) - (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (DLTG) - (DLTG) (PIG) (PIG) (DLTU) (DLTU) (SGU) (DLTG) - (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) - (SGG) (SGU) (SGG) - The electronic state of the initial guess is 1-SGG. - Leave Link 401 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 4.3 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l502.exe) - Keep R1 ints in memory in symmetry-blocked form, NReq=7134369. - FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Closed shell SCF: - Using DIIS extrapolation, IDIIS= 1040. - NGot= 4800000000 LenX= 4799912550 LenY= 4799910084 - Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. - Requested convergence on MAX density matrix=1.00D-06. - Requested convergence on energy=1.00D-06. - No special actions if energy rises. - - Cycle 1 Pass 1 IDiag 1: - E= -187.634176201493 - DIIS: error= 4.01D-10 at cycle 1 NSaved= 1. - NSaved= 1 IEnMin= 1 EnMin= -187.634176201493 IErMin= 1 ErrMin= 4.01D-10 - ErrMax= 4.01D-10 0.00D+00 EMaxC= 1.00D-01 BMatC= 2.50D-18 BMatP= 2.50D-18 - IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 - Coeff-Com: 0.100D+01 - Coeff: 0.100D+01 - Gap= 0.771 Goal= None Shift= 0.000 - Skip diagonalization as Alpha Fock matrix is already diagonal. - RMSDP=0.00D+00 MaxDP=0.00D+00 OVMax= 0.00D+00 - - SCF Done: E(RHF) = -187.634176201 A.U. after 1 cycles - NFock= 1 Conv=0.00D+00 -V/T= 2.0028 - KE= 1.871094202810D+02 PE=-5.611564169572D+02 EE= 1.271668941984D+02 - Leave Link 502 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 4.1 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l801.exe) - Range of M.O.s used for correlation: 1 45 - NBasis= 45 NAE= 11 NBE= 11 NFC= 0 NFV= 0 - NROrb= 45 NOA= 11 NOB= 11 NVA= 34 NVB= 34 - Leave Link 801 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 1.0 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1101.exe) - Using compressed storage, NAtomX= 3. - Will process 4 centers per pass. - Leave Link 1101 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 3.9 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1102.exe) - Symmetrizing basis deriv contribution to polar: - IMax=3 JMax=2 DiffMx= 0.00D+00 - Leave Link 1102 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 0.8 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1110.exe) - Forming Gx(P) for the SCF density, NAtomX= 3. - Integral derivatives from FoFJK, PRISM(SPDF). - Do as many integral derivatives as possible in FoFJK. - G2DrvN: MDV= 4799999660. - G2DrvN: will do 4 centers at a time, making 1 passes. - Calling FoFCou, ICntrl= 3107 FMM=F I1Cent= 0 AccDes= 0.00D+00. - FoFJK: IHMeth= 1 ICntrl= 3107 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F - IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 0 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 3107 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - End of G2Drv F.D. properties file 721 does not exist. - End of G2Drv F.D. properties file 722 does not exist. - End of G2Drv F.D. properties file 788 does not exist. - Leave Link 1110 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 5.5 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l1002.exe) - Minotr: Closed shell wavefunction. - IDoAtm=111 - Direct CPHF calculation. - Differentiating once with respect to electric field. - with respect to dipole field. - Differentiating once with respect to nuclear coordinates. - Using symmetry in CPHF. - Requested convergence is 1.0D-08 RMS, and 1.0D-07 maximum. - Secondary convergence is 1.0D-12 RMS, and 1.0D-12 maximum. - NewPWx=T KeepS1=F KeepF1=F KeepIn=T MapXYZ=F SortEE=F KeepMc=T. - Keep R1 ints in memory in symmetry-blocked form, NReq=7134647. - FoFCou: FMM=F IPFlag= 0 FMFlag= 0 FMFlg1= 0 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 600 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1035 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - MDV= 4800000000 using IRadAn= 1. - Solving linear equations simultaneously, MaxMat= 0. - There are 9 degrees of freedom in the 1st order CPHF. IDoFFX=4 NUNeed= 9. - 9 vectors produced by pass 0 Test12= 4.16D-15 1.11D-08 XBig12= 6.14D+00 1.61D+00. - AX will form 9 AO Fock derivatives at one time. - 9 vectors produced by pass 1 Test12= 4.16D-15 1.11D-08 XBig12= 5.51D-01 2.86D-01. - 9 vectors produced by pass 2 Test12= 4.16D-15 1.11D-08 XBig12= 8.52D-03 4.00D-02. - 9 vectors produced by pass 3 Test12= 4.16D-15 1.11D-08 XBig12= 4.40D-05 3.33D-03. - 9 vectors produced by pass 4 Test12= 4.16D-15 1.11D-08 XBig12= 4.02D-07 3.42D-04. - 9 vectors produced by pass 5 Test12= 4.16D-15 1.11D-08 XBig12= 3.91D-09 2.22D-05. - 7 vectors produced by pass 6 Test12= 4.16D-15 1.11D-08 XBig12= 1.58D-11 1.48D-06. - 4 vectors produced by pass 7 Test12= 4.16D-15 1.11D-08 XBig12= 6.52D-14 8.91D-08. - InvSVY: IOpt=1 It= 1 EMax= 2.22D-16 - Solved reduced A of dimension 65 with 9 vectors. - FullF1: Do perturbations 1 to 9. - Isotropic polarizability for W= 0.000000 11.53 Bohr**3. - End of Minotr F.D. properties file 721 does not exist. - End of Minotr F.D. properties file 722 does not exist. - End of Minotr F.D. properties file 788 does not exist. - Leave Link 1002 at Thu Jun 10 18:06:04 2021, MaxMem= 4800000000 cpu: 4.0 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l601.exe) - Copying SCF densities to generalized density rwf, IOpCl= 0 IROHF=0. - - ********************************************************************** - - Population analysis using the SCF density. - - ********************************************************************** - - Orbital symmetries: - Occupied (SGU) (SGG) (SGG) (SGG) (SGU) (SGG) (SGU) (PIU) - (PIU) (PIG) (PIG) - Virtual (PIU) (PIU) (SGG) (SGU) (PIU) (PIU) (SGG) (SGU) - (SGG) (PIG) (PIG) (PIU) (PIU) (SGU) (SGG) (DLTG) - (DLTG) (PIG) (PIG) (DLTU) (DLTU) (SGU) (DLTG) - (DLTG) (PIU) (PIU) (SGG) (SGU) (PIG) (PIG) (SGG) - (SGG) (SGU) (SGG) - The electronic state is 1-SGG. - Alpha occ. eigenvalues -- -20.65784 -20.65782 -11.46212 -1.54200 -1.48690 - Alpha occ. eigenvalues -- -0.79261 -0.73924 -0.71908 -0.71908 -0.53995 - Alpha occ. eigenvalues -- -0.53995 - Alpha virt. eigenvalues -- 0.23058 0.23058 0.26636 0.51004 0.66340 - Alpha virt. eigenvalues -- 0.66340 0.84293 0.98303 0.99234 1.14705 - Alpha virt. eigenvalues -- 1.14705 1.33111 1.33111 1.45461 1.61575 - Alpha virt. eigenvalues -- 1.63482 1.63482 1.70440 1.70440 2.01268 - Alpha virt. eigenvalues -- 2.01268 2.08925 2.35732 2.35732 2.49060 - Alpha virt. eigenvalues -- 2.49060 3.14657 3.32784 3.35175 3.35175 - Alpha virt. eigenvalues -- 3.48917 4.18091 4.90146 4.90696 - Condensed to atoms (all electrons): - 1 2 3 - 1 O 7.841235 -0.025877 0.630900 - 2 O -0.025877 7.841235 0.630900 - 3 C 0.630900 0.630900 3.845681 - Mulliken charges: - 1 - 1 O -0.446259 - 2 O -0.446259 - 3 C 0.892518 - Sum of Mulliken charges = -0.00000 - Mulliken charges with hydrogens summed into heavy atoms: - 1 - 1 O -0.446259 - 2 O -0.446259 - 3 C 0.892518 - APT charges: - 1 - 1 O -0.757618 - 2 O -0.757618 - 3 C 1.515236 - Sum of APT charges = 0.00000 - APT charges with hydrogens summed into heavy atoms: - 1 - 1 O -0.757618 - 2 O -0.757618 - 3 C 1.515236 - Electronic spatial extent (au): = 110.9843 - Charge= 0.0000 electrons - Dipole moment (field-independent basis, Debye): - X= -0.0000 Y= 0.0000 Z= -0.0000 Tot= 0.0000 - Quadrupole moment (field-independent basis, Debye-Ang): - XX= -14.4559 YY= -14.4559 ZZ= -19.9144 - XY= -0.0000 XZ= -0.0000 YZ= 0.0000 - Traceless Quadrupole moment (field-independent basis, Debye-Ang): - XX= 1.8195 YY= 1.8195 ZZ= -3.6391 - XY= -0.0000 XZ= -0.0000 YZ= 0.0000 - Octapole moment (field-independent basis, Debye-Ang**2): - XXX= -0.0000 YYY= 0.0000 ZZZ= -0.0000 XYY= -0.0000 - XXY= 0.0000 XXZ= 0.0000 XZZ= -0.0000 YZZ= 0.0000 - YYZ= -0.0000 XYZ= 0.0000 - Hexadecapole moment (field-independent basis, Debye-Ang**3): - XXXX= -10.2550 YYYY= -10.2550 ZZZZ= -99.4698 XXXY= -0.0000 - XXXZ= -0.0000 YYYX= -0.0000 YYYZ= -0.0000 ZZZX= -0.0000 - ZZZY= -0.0000 XXYY= -3.4183 XXZZ= -17.9582 YYZZ= -17.9582 - XXYZ= -0.0000 YYXZ= -0.0000 ZZXY= -0.0000 - N-N= 5.924592627624D+01 E-N=-5.611564169572D+02 KE= 1.871094202810D+02 - Symmetry AG KE= 1.012480411172D+02 - Symmetry B1G KE= 6.425625434594D-32 - Symmetry B2G KE= 4.700699095130D+00 - Symmetry B3G KE= 4.700699095130D+00 - Symmetry AU KE= 4.036962633852D-32 - Symmetry B1U KE= 6.913256481077D+01 - Symmetry B2U KE= 3.663708081395D+00 - Symmetry B3U KE= 3.663708081395D+00 - Exact polarizability: 7.265 0.000 7.265 0.000 -0.000 20.046 - Approx polarizability: 6.855 0.000 6.855 0.000 0.000 21.410 - No NMR shielding tensors so no spin-rotation constants. - Leave Link 601 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 4.6 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l701.exe) - ... and contract with generalized density number 0. - Compute integral second derivatives. - Leave Link 701 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 4.7 elap: 0.2 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l702.exe) - L702 exits ... SP integral derivatives will be done elsewhere. - Leave Link 702 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 0.6 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l703.exe) - Integral derivatives from FoFJK, PRISM(SPDF). - Compute integral second derivatives, UseDBF=F ICtDFT= 0. - Calling FoFJK, ICntrl= 100127 FMM=F ISym2X=1 I1Cent= 0 IOpClX= 0 NMat=1 NMatS=1 NMatT=0. - FoFJK: IHMeth= 1 ICntrl= 100127 DoSepK=F KAlg= 0 I1Cent= 0 FoldK=F - IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 1 IDoP0=0 IntGTp=1. - FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 800 - NFxFlg= 0 DoJE=F BraDBF=F KetDBF=F FulRan=T - wScrn= 0.000000 ICntrl= 100127 IOpCl= 0 I1Cent= 0 NGrid= 0 - NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 - Petite list used in FoFCou. - Leave Link 703 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 12.3 elap: 0.4 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l716.exe) - Dipole =-4.12474804D-16 5.96103206D-18-6.00536387D-17 - Polarizability= 7.26459359D+00 1.04356972D-15 7.26459359D+00 - 4.00195616D-16-8.24734058D-16 2.00463336D+01 - HyperPolar =-2.05313456D-14-8.23492026D-16-7.08130094D-15 - -2.48077388D-15 4.90831008D-09-4.13155815D-17 - 4.90830245D-09-9.49123619D-15-2.35777082D-15 - -1.28018861D-08 - Full mass-weighted force constant matrix: - Low frequencies --- -0.0015 0.0009 0.0009 6.8752 6.8752 745.8810 - Low frequencies --- 745.8810 1518.3734 2584.7877 - Diagonal vibrational polarizability: - 3.3342741 3.3342741 3.9818087 - Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering - activities (A**4/AMU), depolarization ratios for plane and unpolarized - incident light, reduced masses (AMU), force constants (mDyne/A), - and normal coordinates: - 1 2 3 - PIU PIU SGG - Frequencies -- 745.8810 745.8810 1518.3734 - Red. masses -- 12.8774 12.8774 15.9949 - Frc consts -- 4.2210 4.2210 21.7265 - IR Inten -- 68.9298 68.9298 0.0000 - Atom AN X Y Z X Y Z X Y Z - 1 8 -0.03 -0.33 -0.00 -0.33 0.03 -0.00 -0.00 0.00 0.71 - 2 8 -0.03 -0.33 0.00 -0.33 0.03 0.00 -0.00 0.00 -0.71 - 3 6 0.07 0.88 -0.00 0.88 -0.07 0.00 0.00 -0.00 -0.00 - 4 - SGU - Frequencies -- 2584.7877 - Red. masses -- 12.8774 - Frc consts -- 50.6906 - IR Inten -- 988.5463 - Atom AN X Y Z - 1 8 0.00 -0.00 -0.33 - 2 8 0.00 -0.00 -0.33 - 3 6 -0.00 0.00 0.88 - - ------------------- - - Thermochemistry - - ------------------- - Temperature 298.150 Kelvin. Pressure 1.00000 Atm. - Atom 1 has atomic number 8 and mass 15.99491 - Atom 2 has atomic number 8 and mass 15.99491 - Atom 3 has atomic number 6 and mass 12.00000 - Molecular mass: 43.98983 amu. - Principal axes and moments of inertia in atomic units: - 1 2 3 - Eigenvalues -- 0.00000 149.31893 149.31893 - X 0.00000 0.50717 0.86184 - Y 0.00000 0.86184 -0.50717 - Z 1.00000 -0.00000 -0.00000 - This molecule is a prolate symmetric top. - Rotational symmetry number 2. - Rotational temperature (Kelvin) 0.58006 - Rotational constant (GHZ): 12.086486 - Zero-point vibrational energy 33465.1 (Joules/Mol) - 7.99834 (Kcal/Mol) - Vibrational temperatures: 1073.16 1073.16 2184.60 3718.93 - (Kelvin) - - Zero-point correction= 0.012746 (Hartree/Particle) - Thermal correction to Energy= 0.015302 - Thermal correction to Enthalpy= 0.016246 - Thermal correction to Gibbs Free Energy= -0.007894 - Sum of electronic and zero-point Energies= -187.621430 - Sum of electronic and thermal Energies= -187.618874 - Sum of electronic and thermal Enthalpies= -187.617930 - Sum of electronic and thermal Free Energies= -187.642070 - - E (Thermal) CV S - KCal/Mol Cal/Mol-Kelvin Cal/Mol-Kelvin - Total 9.602 6.527 50.808 - Electronic 0.000 0.000 0.000 - Translational 0.889 2.981 37.270 - Rotational 0.592 1.987 13.014 - Vibrational 8.121 1.559 0.523 - Q Log10(Q) Ln(Q) - Total Bot 0.427516D+04 3.630953 8.360578 - Total V=0 0.311731D+10 9.493780 21.860236 - Vib (Bot) 0.145057D-05 -5.838461 -13.443554 - Vib (V=0) 0.105771D+01 0.024366 0.056104 - Electronic 0.100000D+01 0.000000 0.000000 - Translational 0.114679D+08 7.059482 16.255059 - Rotational 0.256999D+03 2.409932 5.549073 - - co2 for linear test - IR Spectrum - - 2 1 - 5 5 7 - 8 1 4 - 5 8 6 - - X X - X X - X X - X - X - X - X - X - X - X - X - X - X - X - X - X - X - X - X - X - - ***** Axes restored to original set ***** - ------------------------------------------------------------------- - Center Atomic Forces (Hartrees/Bohr) - Number Number X Y Z - ------------------------------------------------------------------- - 1 8 0.000051665 0.000009951 -0.000032450 - 2 8 -0.000051665 -0.000009951 0.000032450 - 3 6 0.000000000 -0.000000000 0.000000000 - ------------------------------------------------------------------- - Cartesian Forces: Max 0.000051665 RMS 0.000029141 - Force constants in Cartesian coordinates: - 1 2 3 4 5 - 1 0.886547D+00 - 2 0.161899D+00 0.771275D-01 - 3 -0.527977D+00 -0.101688D+00 0.377566D+00 - 4 -0.882483D-01 -0.258402D-01 0.842687D-01 0.886547D+00 - 5 -0.258402D-01 0.409405D-01 0.162301D-01 0.161899D+00 0.771275D-01 - 6 0.842687D-01 0.162301D-01 -0.701151D-02 -0.527977D+00 -0.101688D+00 - 7 -0.798298D+00 -0.136059D+00 0.443709D+00 -0.798298D+00 -0.136059D+00 - 8 -0.136059D+00 -0.118068D+00 0.854579D-01 -0.136059D+00 -0.118068D+00 - 9 0.443709D+00 0.854579D-01 -0.370554D+00 0.443709D+00 0.854579D-01 - 6 7 8 9 - 6 0.377566D+00 - 7 0.443709D+00 0.159660D+01 - 8 0.854579D-01 0.272118D+00 0.236136D+00 - 9 -0.370554D+00 -0.887417D+00 -0.170916D+00 0.741109D+00 - FormGI is forming the generalized inverse of G from B-inverse, IUseBI=4. - Force constants in internal coordinates: - 1 2 3 4 - 1 0.124935D+01 - 2 0.146154D+00 0.124935D+01 - 3 0.000000D+00 0.000000D+00 0.210909D+00 - 4 0.000000D+00 0.000000D+00 -0.182959D-01 0.156853D+00 - Leave Link 716 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 1.8 elap: 0.1 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l103.exe) - - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - Berny optimization. - Red2BG is reusing G-inverse. - Internal Forces: Max 0.000061817 RMS 0.000043711 - Search for a local minimum. - Step number 1 out of a maximum of 2 - All quantities printed in internal units (Hartrees-Bohrs-Radians) - Second derivative matrix not updated -- analytic derivatives used. - The second derivative matrix: - R1 R2 A1 A2 - R1 1.24935 - R2 0.14615 1.24935 - A1 -0.00000 0.00000 0.21091 - A2 -0.00000 0.00000 -0.01830 0.15685 - ITU= 0 - Eigenvalues --- 0.15124 0.21652 1.10319 1.39550 - Angle between quadratic step and forces= 0.00 degrees. - Linear search not attempted -- first point. - Iteration 1 RMS(Cart)= 0.00003132 RMS(Int)= 0.00000000 - Iteration 2 RMS(Cart)= 0.00000000 RMS(Int)= 0.00000000 - ITry= 1 IFail=0 DXMaxC= 3.70D-05 DCOld= 1.00D+10 DXMaxT= 3.00D-01 DXLimC= 3.00D+00 Rises=F - ClnCor: largest displacement from symmetrization is 1.20D-09 for atom 3. - Variable Old X -DE/DX Delta X Delta X Delta X New X - (Linear) (Quad) (Total) - R1 2.16049 -0.00006 0.00000 -0.00004 -0.00004 2.16044 - R2 2.16049 -0.00006 0.00000 -0.00004 -0.00004 2.16044 - A1 3.14159 -0.00000 0.00000 -0.00000 0.00000 3.14159 - A2 3.14159 -0.00000 0.00000 -0.00000 -0.00000 3.14159 - Item Value Threshold Converged? - Maximum Force 0.000062 0.000450 YES - RMS Force 0.000044 0.000300 YES - Maximum Displacement 0.000037 0.001800 YES - RMS Displacement 0.000031 0.001200 YES - Predicted change in Energy=-2.738298D-09 - Optimization completed. - -- Stationary point found. - ---------------------------- - ! Optimized Parameters ! - ! (Angstroms and Degrees) ! - -------------------------- -------------------------- - ! Name Definition Value Derivative Info. ! - -------------------------------------------------------------------------------- - ! R1 R(1,3) 1.1433 -DE/DX = -0.0001 ! - ! R2 R(2,3) 1.1433 -DE/DX = -0.0001 ! - ! A1 L(1,3,2,-2,-1) 180.0 -DE/DX = 0.0 ! - ! A2 L(1,3,2,-3,-2) 180.0 -DE/DX = 0.0 ! - -------------------------------------------------------------------------------- - GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad - - Leave Link 103 at Thu Jun 10 18:06:05 2021, MaxMem= 4800000000 cpu: 0.3 elap: 0.0 - (Enter /clusterfs/cloudcuckoo/software/gaussian/G16_AVX2-enabled/tar/g16/l9999.exe) - Dipole is zero, so no output in dipole orientation. - - ---------------------------------------------------------------------- - - Electric dipole moment (input orientation): - (Debye = 10**-18 statcoulomb cm , SI units = C m) - (au) (Debye) (10**-30 SI) - Tot 0.000000D+00 0.000000D+00 0.000000D+00 - x 0.000000D+00 0.000000D+00 0.000000D+00 - y 0.000000D+00 0.000000D+00 0.000000D+00 - z 0.000000D+00 0.000000D+00 0.000000D+00 - - Dipole polarizability, Alpha (input orientation). - (esu units = cm**3 , SI units = C**2 m**2 J**-1) - Alpha(0;0): - (au) (10**-24 esu) (10**-40 SI) - iso 0.115252D+02 0.170785D+01 0.190024D+01 - aniso 0.127817D+02 0.189406D+01 0.210742D+01 - xx 0.161929D+02 0.239954D+01 0.266985D+01 - yx 0.171958D+01 0.254816D+00 0.283521D+00 - yy 0.759578D+01 0.112558D+01 0.125238D+01 - zx -0.560782D+01 -0.830994D+00 -0.924605D+00 - zy -0.108006D+01 -0.160049D+00 -0.178078D+00 - zz 0.107868D+02 0.159844D+01 0.177851D+01 - - ---------------------------------------------------------------------- - 1\1\GINC-N0045\Freq\RHF\6-31G(d)\C1O2\ALEX_EPSTEIN\10-Jun-2021\0\\#P G - eom=AllCheck Guess=TCheck SCRF=Check GenChk RHF/6-31G(d) Freq\\co2 for - linear test\\0,1\O,-0.7669543606,-0.3767139767,3.2141361692\O,1.14409 - 56549,-0.0086472867,2.0138147763\C,0.1885706471,-0.1926806317,2.613975 - 4728\\Version=ES64L-G16RevA.03\State=1-SGG\HF=-187.6341762\RMSD=0.000e - +00\RMSF=2.914e-05\ZeroPoint=0.0127462\Thermal=0.0153023\Dipole=0.,0., - 0.\DipoleDeriv=-1.1573511,-0.1472612,0.480241,-0.1472612,-0.4211144,0. - 092494,0.480241,0.092494,-0.6943891,-1.1573511,-0.1472612,0.480241,-0. - 1472612,-0.4211144,0.092494,0.480241,0.092494,-0.6943891,2.3147021,0.2 - 945223,-0.960482,0.2945223,0.8422288,-0.1849881,-0.960482,-0.1849881,1 - .3887782\Polar=16.1928957,1.7195838,7.595784,-5.6078239,-1.0800624,10. - 786841\HyperPolar=0.,0.,0.,0.,0.,0.,0.,0.,0.,0.\Quadrupole=-1.4820442, - 1.2476169,0.2344273,-0.5459835,1.7805351,0.3429296\PG=D*H [O(C1),C*(O1 - .O1)]\NImag=0\\0.88654668,0.16189903,0.07712751,-0.52797735,-0.1016880 - 1,0.37756594,-0.08824827,-0.02584017,0.08426874,0.88654668,-0.02584017 - ,0.04094048,0.01623009,0.16189903,0.07712751,0.08426874,0.01623009,-0. - 00701151,-0.52797735,-0.10168801,0.37756594,-0.79829842,-0.13605886,0. - 44370861,-0.79829842,-0.13605886,0.44370861,1.59659684,-0.13605886,-0. - 11806799,0.08545792,-0.13605886,-0.11806799,0.08545792,0.27211772,0.23 - 613597,0.44370861,0.08545792,-0.37055442,0.44370861,0.08545792,-0.3705 - 5442,-0.88741723,-0.17091584,0.74110884\\-0.00005166,-0.00000995,0.000 - 03245,0.00005166,0.00000995,-0.00003245,0.,0.,0.\\\@ - - - NEVER LISTEN TO CRITICISM - OR YOU'LL BE DOIN' EVERYBODY ELSE'S THING BUT BUT YOUR OWN. - - -- ANDY CAPP - Job cpu time: 0 days 0 hours 1 minutes 10.3 seconds. - Elapsed time: 0 days 0 hours 0 minutes 2.6 seconds. - File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 - Normal termination of Gaussian 16 at Thu Jun 10 18:06:05 2021. diff --git a/pymatgen/analysis/tests/test_quasirrho.py b/tests/analysis/test_quasirrho.py similarity index 94% rename from pymatgen/analysis/tests/test_quasirrho.py rename to tests/analysis/test_quasirrho.py index c10fbbfb8d3..2e433865454 100644 --- a/pymatgen/analysis/tests/test_quasirrho.py +++ b/tests/analysis/test_quasirrho.py @@ -6,24 +6,24 @@ from __future__ import annotations import os +import unittest import pytest from pymatgen.analysis.quasirrho import QuasiRRHO from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.qchem.outputs import QCOutput -from pymatgen.util.testing import PymatgenTest +from pymatgen.util.testing import TEST_FILES_DIR -class TestQuasiRRHO(PymatgenTest): +class TestQuasiRRHO(unittest.TestCase): """ Test class for QuasiRRHO """ - def setUp(self): - test_dir = self.TEST_FILES_DIR + test_dir = TEST_FILES_DIR self.gout = GaussianOutput(os.path.join(test_dir, "molecules", "quasirrho_gaufreq.log")) - self.linear_gout = GaussianOutput(os.path.join(test_dir, "molecules", "co2.log")) + self.linear_gout = GaussianOutput(os.path.join(test_dir, "molecules","co2.log.gz")) self.qout = QCOutput(os.path.join(test_dir, "molecules", "new_qchem_files", "Frequency_no_equal.qout")) def test_qrrho_gaussian(self): diff --git a/tests/files/molecules/co2.log.gz b/tests/files/molecules/co2.log.gz new file mode 100644 index 0000000000000000000000000000000000000000..03854efe27aad419b469e7860eb3678da4630fc9 GIT binary patch literal 21852 zcmYg%V{m3cw{<4A?M!S;Y}?7iwlT5&#J25;ZQC}U*fzg;-+Sw;TeW|5ozs1GuU)5V 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21/25] pre-commit auto-fixes --- tests/analysis/test_quasirrho.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tests/analysis/test_quasirrho.py b/tests/analysis/test_quasirrho.py index 2e433865454..76d0647d561 100644 --- a/tests/analysis/test_quasirrho.py +++ b/tests/analysis/test_quasirrho.py @@ -20,10 +20,11 @@ class TestQuasiRRHO(unittest.TestCase): """ Test class for QuasiRRHO """ + def setUp(self): test_dir = TEST_FILES_DIR self.gout = GaussianOutput(os.path.join(test_dir, "molecules", "quasirrho_gaufreq.log")) - self.linear_gout = GaussianOutput(os.path.join(test_dir, "molecules","co2.log.gz")) + self.linear_gout = GaussianOutput(os.path.join(test_dir, "molecules", "co2.log.gz")) self.qout = QCOutput(os.path.join(test_dir, "molecules", "new_qchem_files", "Frequency_no_equal.qout")) def test_qrrho_gaussian(self): From 9d2bcc942eed6ddd3801539c9f395ec903b3c4c6 Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Mon, 21 Aug 2023 14:55:34 -0700 Subject: [PATCH 22/25] add type hints and snake_case QuasiRRHO method names --- pymatgen/analysis/quasirrho.py | 29 ++++++++++++++++------------- 1 file changed, 16 insertions(+), 13 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index eb3b719c09f..9c210ff657c 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -97,24 +97,24 @@ class QuasiRRHO: def __init__( self, mol: Molecule, - frequencies: list, + frequencies: list[float], energy: float, mult: int, - sigma_r=1, - temp=298.15, - press=101317, - v0=100, - ): + sigma_r: float = 1, + temp: float = 298.15, + press: float = 101_317, + v0: float = 100, + ) -> None: """ Args: mol (Molecule): Pymatgen molecule frequencies (list): List of frequencies (float) [cm^-1] energy (float): Electronic energy [Ha] - mult (int): Spin muliplicity - sigma_r (int): Rotational symmetry number - temp (float): Temperature [K] - press (float): Pressure [Pa] - v0 (float): Cutoff frequency for Quasi-RRHO method [cm^-1] + mult (int): Spin multiplicity + sigma_r (int): Rotational symmetry number. Defaults to 1. + temp (float): Temperature [K]. Defaults to 298.15. + press (float): Pressure [Pa]. Defaults to 101_317. + v0 (float): Cutoff frequency for Quasi-RRHO method [cm^-1]. Defaults to 100. """ # TO-DO: calculate sigma_r with PointGroupAnalyzer # and/or edit Gaussian and QChem io to parse for sigma_r @@ -149,7 +149,7 @@ def from_GaussianOutput(cls, output: GaussianOutput, **kwargs): return cls(mol=mol, frequencies=vib_freqs, energy=elec_e, mult=mult, **kwargs) @classmethod - def from_QCOutput(cls, output: QCOutput, **kwargs): + def from_qc_output(cls, output: QCOutput, **kwargs) -> QuasiRRHO: """ Args: @@ -173,9 +173,12 @@ def from_QCOutput(cls, output: QCOutput, **kwargs): Doi("10.1002/chem.201200497"), description="Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory", ) - def _get_quasirrho_thermo(self, mol, mult, sigma_r, frequencies, elec_energy): + def _get_quasirrho_thermo( + self, mol: Molecule, mult: int, sigma_r: int, frequencies: list[float], elec_energy: float + ) -> None: """ Calculate Quasi-RRHO thermochemistry + Args: mol (Molecule): Pymatgen molecule mult (int): Spin multiplicity From 9232e5dc594c0e7c914d224c5386953e202ed847 Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Mon, 21 Aug 2023 14:56:28 -0700 Subject: [PATCH 23/25] rename single-letter module-scoped vars --- pymatgen/analysis/quasirrho.py | 59 ++++++++++++++++------------------ 1 file changed, 28 insertions(+), 31 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 9c210ff657c..0505f17be73 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -4,7 +4,7 @@ """ A module to calculate free energies using the Quasi-Rigid Rotor Harmonic - Oscillator approximation. Modified from a script by Steven Wheeler. +Oscillator approximation. Modified from a script by Steven Wheeler. See: Grimme, S. Chem. Eur. J. 2012, 18, 9955 """ @@ -34,15 +34,15 @@ # Define useful constants kb = kb_ev * const.eV # Pymatgen kb [J/K] -c = const.speed_of_light * 100 # [cm/s] -h = const.h # Planck's constant [J.s] -R = const.R / const.calorie # Ideal gas constant [cal/mol/K] +light_speed = const.speed_of_light * 100 # [cm/s] +h_plank = const.h # Planck's constant [J.s] +ideal_gas_const = const.R / const.calorie # Ideal gas constant [cal/mol/K] R_ha = const.R / const.value("Hartree energy") / const.Avogadro # Ideal gas # Define useful conversion factors amu_to_kg = const.value("atomic mass unit-kilogram relationship") # AMU to kg # kcal2hartree = 0.0015936 # kcal/mol to hartree/mol -kcal2hartree = 1000 * const.calorie / const.value("Hartree energy") / const.Avogadro +kcal_to_hartree = 1000 * const.calorie / const.value("Hartree energy") / const.Avogadro def get_avg_mom_inertia(mol): @@ -133,7 +133,7 @@ def __init__( self._get_quasirrho_thermo(mol=mol, mult=mult, frequencies=frequencies, elec_energy=energy, sigma_r=sigma_r) @classmethod - def from_GaussianOutput(cls, output: GaussianOutput, **kwargs): + def from_gaussian_output(cls, output: GaussianOutput, **kwargs) -> QuasiRRHO: """ Args: @@ -187,24 +187,21 @@ def _get_quasirrho_thermo( elec_energy (float): Electronic energy [Ha] """ # Calculate mass in kg - mass = 0 + mass: float = 0 for site in mol.sites: mass += site.specie.atomic_mass mass *= amu_to_kg # Calculate vibrational temperatures - vib_temps = [] - for f in frequencies: - if f > 0: - vib_temps.append(f * c * h / kb) + vib_temps = [freq * light_speed * h_plank / kb for freq in frequencies if freq > 0] # Translational component of entropy and energy - qt = (2 * np.pi * mass * kb * self.temp / (h * h)) ** (3 / 2) * kb * self.temp / self.press - st = R * (np.log(qt) + 5 / 2) - et = 3 * R * self.temp / 2 + qt = (2 * np.pi * mass * kb * self.temp / (h_plank * h_plank)) ** (3 / 2) * kb * self.temp / self.press + st = ideal_gas_const * (np.log(qt) + 5 / 2) + et = 3 * ideal_gas_const * self.temp / 2 # Electronic component of Entropy - se = R * np.log(mult) + se = ideal_gas_const * np.log(mult) # Get properties related to rotational symmetry. Bav is average moment of inertia Bav, i_eigen = get_avg_mom_inertia(mol) @@ -221,14 +218,14 @@ def _get_quasirrho_thermo( # Rotational component of Entropy and Energy if linear: i = np.amax(i_eigen) - qr = 8 * np.pi**2 * i * kb * self.temp / (sigma_r * (h * h)) - sr = R * (np.log(qr) + 1) - er = R * self.temp + qr = 8 * np.pi**2 * i * kb * self.temp / (sigma_r * (h_plank * h_plank)) + sr = ideal_gas_const * (np.log(qr) + 1) + er = ideal_gas_const * self.temp else: - rot_temps = [h**2 / (np.pi**2 * kb * 8 * i) for i in i_eigen] + rot_temps = [h_plank**2 / (np.pi**2 * kb * 8 * i) for i in i_eigen] qr = np.sqrt(np.pi) / sigma_r * self.temp ** (3 / 2) / np.sqrt(rot_temps[0] * rot_temps[1] * rot_temps[2]) - sr = R * (np.log(qr) + 3 / 2) - er = 3 * R * self.temp / 2 + sr = ideal_gas_const * (np.log(qr) + 3 / 2) + er = 3 * ideal_gas_const * self.temp / 2 # Vibrational component of Entropy and Energy ev = 0 @@ -240,20 +237,20 @@ def _get_quasirrho_thermo( sv_temp = vt / (self.temp * (np.exp(vt / self.temp) - 1)) - np.log(1 - np.exp(-vt / self.temp)) sv += sv_temp - mu = h / (8 * np.pi**2 * vt * c) + mu = h_plank / (8 * np.pi**2 * vt * light_speed) mu_prime = mu * Bav / (mu + Bav) - srotor = 1 / 2 + np.log(np.sqrt(8 * np.pi**3 * mu_prime * kb * self.temp / h**2)) + s_rotor = 1 / 2 + np.log(np.sqrt(8 * np.pi**3 * mu_prime * kb * self.temp / h_plank**2)) weight = 1 / (1 + (self.v0 / vt) ** 4) - sv_quasiRRHO += weight * sv_temp + (1 - weight) * srotor + sv_quasiRRHO += weight * sv_temp + (1 - weight) * s_rotor - sv_quasiRRHO *= R - sv *= R - ev *= R - etot = (et + er + ev) * kcal2hartree / 1000 - self.h_corrected = etot + R * self.temp * kcal2hartree / 1000 + sv_quasiRRHO *= ideal_gas_const + sv *= ideal_gas_const + ev *= ideal_gas_const + e_tot = (et + er + ev) * kcal_to_hartree / 1000 + self.h_corrected = e_tot + ideal_gas_const * self.temp * kcal_to_hartree / 1000 self.entropy_ho = st + sr + sv + se - self.free_energy_ho = elec_energy + self.h_corrected - (self.temp * self.entropy_ho * kcal2hartree / 1000) + self.free_energy_ho = elec_energy + self.h_corrected - (self.temp * self.entropy_ho * kcal_to_hartree / 1000) self.entropy_quasiRRHO = st + sr + sv_quasiRRHO + se self.free_energy_quasiRRHO = ( - elec_energy + self.h_corrected - (self.temp * self.entropy_quasiRRHO * kcal2hartree / 1000) + elec_energy + self.h_corrected - (self.temp * self.entropy_quasiRRHO * kcal_to_hartree / 1000) ) From 02ac2c75c99f91d32a692d2dac2f0177bf0bc223 Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Mon, 21 Aug 2023 14:56:47 -0700 Subject: [PATCH 24/25] fix tests following method renaming --- tests/analysis/test_quasirrho.py | 28 +++++++++------------------- 1 file changed, 9 insertions(+), 19 deletions(-) diff --git a/tests/analysis/test_quasirrho.py b/tests/analysis/test_quasirrho.py index 76d0647d561..5f48c799dc3 100644 --- a/tests/analysis/test_quasirrho.py +++ b/tests/analysis/test_quasirrho.py @@ -1,11 +1,5 @@ -# Copyright (c) Pymatgen Development Team. -# Distributed under the terms of the MIT License. -""" -Testing for quasirrho.py -""" from __future__ import annotations -import os import unittest import pytest @@ -17,15 +11,13 @@ class TestQuasiRRHO(unittest.TestCase): - """ - Test class for QuasiRRHO - """ + """Test class for QuasiRRHO""" def setUp(self): test_dir = TEST_FILES_DIR - self.gout = GaussianOutput(os.path.join(test_dir, "molecules", "quasirrho_gaufreq.log")) - self.linear_gout = GaussianOutput(os.path.join(test_dir, "molecules", "co2.log.gz")) - self.qout = QCOutput(os.path.join(test_dir, "molecules", "new_qchem_files", "Frequency_no_equal.qout")) + self.gout = GaussianOutput(f"{test_dir}/molecules/quasirrho_gaufreq.log") + self.linear_gout = GaussianOutput(f"{test_dir}/molecules/co2.log.gz") + self.qout = QCOutput(f"{test_dir}/molecules/new_qchem_files/Frequency_no_equal.qout") def test_qrrho_gaussian(self): """ @@ -34,7 +26,7 @@ def test_qrrho_gaussian(self): """ correct_g = -884.776886 correct_stot = 141.584080 - qrrho = QuasiRRHO.from_GaussianOutput(self.gout) + qrrho = QuasiRRHO.from_gaussian_output(self.gout) assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy" assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" @@ -48,7 +40,7 @@ def test_qrrho_qchem(self): correct_stot = 103.41012732045324 # HO total entropy from QChem = 106.521 - qrrho = QuasiRRHO.from_QCOutput(self.qout) + qrrho = QuasiRRHO.from_qc_output(self.qout) assert correct_stot == pytest.approx(qrrho.entropy_quasiRRHO, 0.1), "Incorrect total entropy" assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" @@ -67,17 +59,15 @@ def test_rrho_manual(self): assert correct_g == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" def test_rrho_linear(self): - """ - Testing on a linear CO2 molecule from Gaussian Output file. + """Test on a linear CO2 molecule from Gaussian Output file. Correct free_energy_ho is checked with Gaussian's internal calculation. Correct free_energy_quasirrho is compared internally in the hope of preventing future errors. - . """ correct_g_ho = -187.642070 correct_g_qrrho = -187.642725 - qrrho = QuasiRRHO.from_GaussianOutput(self.linear_gout) + qrrho = QuasiRRHO.from_gaussian_output(self.linear_gout) assert correct_g_ho == pytest.approx( - qrrho.free_energy_ho, 0.0001 + qrrho.free_energy_ho, rel=1e-5 ), f"Incorrect harmonic oscillator free energy, {correct_g_ho} != {qrrho.free_energy_ho}" assert correct_g_qrrho == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" From f7d3fa70909755e873c5913fee0a58aeba4eebeb Mon Sep 17 00:00:00 2001 From: Janosh Riebesell Date: Mon, 21 Aug 2023 15:00:45 -0700 Subject: [PATCH 25/25] add test_extreme_temperature_and_pressure() and test_get_avg_mom_inertia() --- pymatgen/analysis/quasirrho.py | 17 +++++++++-------- tests/analysis/test_quasirrho.py | 13 ++++++++++++- 2 files changed, 21 insertions(+), 9 deletions(-) diff --git a/pymatgen/analysis/quasirrho.py b/pymatgen/analysis/quasirrho.py index 0505f17be73..070c193095b 100644 --- a/pymatgen/analysis/quasirrho.py +++ b/pymatgen/analysis/quasirrho.py @@ -60,17 +60,18 @@ def get_avg_mom_inertia(mol): for site in centered_mol: c = site.coords wt = site.specie.atomic_mass - for i in range(3): - inertia_tensor[i, i] += wt * (c[(i + 1) % 3] ** 2 + c[(i + 2) % 3] ** 2) - for i, j in [(0, 1), (1, 2), (0, 2)]: - inertia_tensor[i, j] += -wt * c[i] * c[j] - inertia_tensor[j, i] += -wt * c[j] * c[i] + for dim in range(3): + inertia_tensor[dim, dim] += wt * (c[(dim + 1) % 3] ** 2 + c[(dim + 2) % 3] ** 2) + for ii, jj in [(0, 1), (1, 2), (0, 2)]: + inertia_tensor[ii, jj] += -wt * c[ii] * c[jj] + inertia_tensor[jj, ii] += -wt * c[jj] * c[ii] - inertia_eigenvals = np.multiply(np.linalg.eig(inertia_tensor)[0], amu_to_kg * 1e-20).tolist() # amuangs^2 to kg m^2 + # amuangs^2 to kg m^2 + inertia_eigen_vals = np.linalg.eig(inertia_tensor)[0] * amu_to_kg * 1e-20 - iav = np.average(inertia_eigenvals) + iav = np.average(inertia_eigen_vals) - return iav, inertia_eigenvals + return iav, inertia_eigen_vals class QuasiRRHO: diff --git a/tests/analysis/test_quasirrho.py b/tests/analysis/test_quasirrho.py index 5f48c799dc3..f06cf50d511 100644 --- a/tests/analysis/test_quasirrho.py +++ b/tests/analysis/test_quasirrho.py @@ -4,7 +4,7 @@ import pytest -from pymatgen.analysis.quasirrho import QuasiRRHO +from pymatgen.analysis.quasirrho import QuasiRRHO, get_avg_mom_inertia from pymatgen.io.gaussian import GaussianOutput from pymatgen.io.qchem.outputs import QCOutput from pymatgen.util.testing import TEST_FILES_DIR @@ -71,3 +71,14 @@ def test_rrho_linear(self): qrrho.free_energy_ho, rel=1e-5 ), f"Incorrect harmonic oscillator free energy, {correct_g_ho} != {qrrho.free_energy_ho}" assert correct_g_qrrho == pytest.approx(qrrho.free_energy_quasiRRHO), "Incorrect Quasi-RRHO free energy" + + def test_extreme_temperature_and_pressure(self): + qrrho = QuasiRRHO.from_gaussian_output(self.gout, temp=0.1, press=1e9) + assert qrrho.temp == 0.1 + assert qrrho.press == 1e9 + + def test_get_avg_mom_inertia(self): + mol = self.gout.final_structure + avg_mom_inertia, inertia_eigen_vals = get_avg_mom_inertia(mol) + assert avg_mom_inertia == pytest.approx(0) + assert inertia_eigen_vals == pytest.approx([0, 0, 0])