From 76f4ca0ca916aae0baa50989942f94ed58a60149 Mon Sep 17 00:00:00 2001 From: Yu Zhai Date: Wed, 19 Aug 2020 22:07:54 +0800 Subject: [PATCH 1/4] Signed-off-by: Yu Zhai I can already use this version. --- tamkin/io/__init__.py | 1 + tamkin/io/molpro.py | 132 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 133 insertions(+) create mode 100644 tamkin/io/molpro.py diff --git a/tamkin/io/__init__.py b/tamkin/io/__init__.py index dfde848..86c8579 100644 --- a/tamkin/io/__init__.py +++ b/tamkin/io/__init__.py @@ -44,3 +44,4 @@ from tamkin.io.qchem import * from tamkin.io.trajectory import * from tamkin.io.vasp import * +from tamkin.io.molpro import * diff --git a/tamkin/io/molpro.py b/tamkin/io/molpro.py new file mode 100644 index 0000000..42053ff --- /dev/null +++ b/tamkin/io/molpro.py @@ -0,0 +1,132 @@ +# -*- coding: utf-8 -*- +# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry +# and reaction kinetics. +# Copyright (C) 2008-2012 Toon Verstraelen , An Ghysels +# and Matthias Vandichel +# Center for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all +# rights reserved unless otherwise stated. +# +# This file is part of TAMkin. +# +# TAMkin is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License +# as published by the Free Software Foundation; either version 3 +# of the License, or (at your option) any later version. +# +# In addition to the regulations of the GNU General Public License, +# publications and communications based in parts on this program or on +# parts of this program are required to cite the following article: +# +# "TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics", +# An Ghysels, Toon Verstraelen, Karen Hemelsoet, Michel Waroquier and Veronique +# Van Speybroeck, Journal of Chemical Information and Modeling, 2010, 50, +# 1736-1750W +# http://dx.doi.org/10.1021/ci100099g +# +# TAMkin is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, see +# +# -- + + +from __future__ import print_function, division + +from tamkin.data import Molecule, RotScan + +from molmod.io import FCHKFile +from molmod import dihed_angle, amu, angstrom + +import numpy as np + + +__all__ = [ + "load_molecule_molpro", +] + +def load_molecule_molpro(filename): + """Load a molecule from Molpro 2012 output file. + + Argument: + | ``filename`` -- the molpro 2012 output + + """ + + lines = open(filename,"r").read().splitlines() + # locate positions + for lineno, line in enumerate(lines): + if "Current geometry" in line: + beginxyz = lineno + 2 + if "FREQUENCIES * CALCULATION OF NORMAL MODES" in line: + begincoordinate = lineno + 7 + if "Atomic Masses" in line: + beginmass = lineno + if "Force Constants" in line: + beginhessian = lineno + # xyz read, only meta data and energy + atomnumber = int(lines[beginxyz].split()[0]) + title = lines[beginxyz+1].split()[0] + energy = float(lines[beginxyz+1].split("=")[1]) + # print(atomnumber, title, energy) + + # coordinate read + numbers=[] + coordinates=[] + + for line in lines[begincoordinate : begincoordinate+atomnumber]: + words = line.split() + charge = int(float(words[2])) + x = float(words[3]) + y = float(words[4]) + z = float(words[5]) + numbers.append(charge) + coordinates.append([x, y, z]) + # print(charge, x, y, z) + + # masses + masses = [] + for line in lines[beginmass+1:]: + if len(line) > 8: + words = line[8:].split() + for word in words: + masses.append(float(word)*amu) + else: + break + # print(masses) + + # hessian + hessian = np.ndarray((3*atomnumber, 3*atomnumber), dtype= float) + headerline = beginhessian+1 + rowbegin = 0 + while rowbegin < 3*atomnumber: + for r, line in zip(\ + range(rowbegin, 3*atomnumber),\ + lines[headerline+1 : headerline+1+3*atomnumber-rowbegin]\ + ): + words = line[16:].split() + # print(words) + for c in range(rowbegin, rowbegin+min(5, 3*atomnumber-rowbegin, len(words))): + # print(r,c) + hessian[r,c] = float(words[c-rowbegin]) + hessian[c,r]=hessian[r,c] + headerline += 3*atomnumber-rowbegin+1 + rowbegin += 5 + + # print(hessian) + + return Molecule( + np.array(numbers), + np.array(coordinates), + np.array(masses), + energy, + np.zeros((atomnumber, 3)), + hessian, + title=title, + multiplicity=1, + ) + + From 2b0b481450f58bcb712edb5b34802c8bf8a3082a Mon Sep 17 00:00:00 2001 From: Yu Zhai Date: Thu, 20 Aug 2020 16:18:52 +0800 Subject: [PATCH 2/4] Add unit test Signed-off-by: Yu Zhai --- tamkin/data/test/molpro/ch3oh.out | 749 ++++++++++++++++++++++++++++++ tamkin/io/ch3oh.out | 749 ++++++++++++++++++++++++++++++ tamkin/io/molpro.py | 20 +- tamkin/test/test_io.py | 9 + 4 files changed, 1521 insertions(+), 6 deletions(-) create mode 100644 tamkin/data/test/molpro/ch3oh.out create mode 100644 tamkin/io/ch3oh.out diff --git a/tamkin/data/test/molpro/ch3oh.out b/tamkin/data/test/molpro/ch3oh.out new file mode 100644 index 0000000..80ae287 --- /dev/null +++ b/tamkin/data/test/molpro/ch3oh.out @@ -0,0 +1,749 @@ + + Primary working directories : /tmp/yuzhai + Secondary working directories : /tmp/yuzhai + Wavefunction directory : /home/yuzhai/wfu/ + Main file repository : /tmp/yuzhai/ + + SHA1 : 2c68d29c09da70e1723824271fadde4bcd5f07a0 + ARCHNAME : Linux/x86_64 + FC : /opt/intel/compilerpro-12.0.2.137/bin/intel64/ifort + FCVERSION : 12.0.2 + BLASLIB : + id : mailjlu + + Nodes nprocs + master 1 + + Using customized tuning parameters: mindgm=4; mindgv=4; mindgc=1; mindgr=1; noblas=0; minvec=7 + default implementation of scratch files=df + + ***,formaldehyde freqency calculation + memory,8,m + + basis=vtz + gthresh,energy=1.d-8 + + geomtyp=xyz + symmetry,nosym + geometry={ + 6 + HF-SCF000/VTZ ENERGY=-115.09019866 + C 0.6584121935 -0.0189169352 -0.0000050689 + H 1.0769852853 0.9771062764 -0.0000898996 + H 1.0177528792 -0.5399854299 0.8825905783 + H 1.0177611577 -0.5401385993 -0.8825068758 + O -0.7335133044 0.1126188517 -0.0000227984 + H -1.1354002112 -0.7362311637 0.0000300645 + } + + hf; + optg; + force; + {frequencies,analytic + print,hessian} + + + Variables initialized (766), CPU time= 0.00 sec + Commands initialized (545), CPU time= 0.01 sec, 513 directives. + Default parameters read. Elapsed time= 0.03 sec + + Checking input... + Passed +1 + + + *** PROGRAM SYSTEM MOLPRO *** + Copyright, University College Cardiff Consultants Limited, 2008 + + Version 2012.1 linked 30 Aug 2012 10:17:55 + + + ********************************************************************************************************************************** + LABEL * formaldehyde freqency calculation + Linux-2.6.32-642.el6.x86_64/master(x86_64) 64 bit serial version DATE: 20-Aug-20 TIME: 15:07:05 + ********************************************************************************************************************************** + + SHA1: 2c68d29c09da70e1723824271fadde4bcd5f07a0 + ********************************************************************************************************************************** + + Variable memory set to 8000000 words, buffer space 230000 words + + SETTING BASIS = VTZ + + THRESHOLDS: + + ZERO = 1.00D-12 ONEINT = 1.00D-12 TWOINT = 1.00D-11 PREFAC = 1.00D-14 LOCALI = 1.00D-09 EORDER = 1.00D-04 + ENERGY = 1.00D-08 ETEST = 0.00D+00 EDENS = 0.00D+00 THRDEDEF= 1.00D-06 GRADIENT= 1.00D-02 STEP = 1.00D-03 + ORBITAL = 1.00D-05 CIVEC = 1.00D-05 COEFF = 1.00D-04 PRINTCI = 5.00D-02 PUNCHCI = 9.90D+01 OPTGRAD = 3.00D-04 + OPTENERG= 1.00D-06 OPTSTEP = 3.00D-04 THRGRAD = 1.00D-10 COMPRESS= 1.00D-11 VARMIN = 1.00D-07 VARMAX = 1.00D-03 + THRDOUB = 0.00D+00 THRDIV = 1.00D-05 THRRED = 1.00D-07 THRPSP = 1.00D+00 THRDC = 1.00D-10 THRCS = 1.00D-10 + THRNRM = 1.00D-08 THREQ = 0.00D+00 THRDE = 1.00D+00 THRREF = 1.00D-05 SPARFAC = 1.00D+00 THRDLP = 1.00D-07 + THRDIA = 1.00D-10 THRDLS = 1.00D-07 THRGPS = 0.00D+00 THRKEX = 0.00D+00 THRDIS = 2.00D-01 THRVAR = 1.00D-10 + THRLOC = 1.00D-06 THRGAP = 1.00D-06 THRLOCT = -1.00D+00 THRGAPT = -1.00D+00 THRORB = 1.00D-06 THRMLTP = 0.00D+00 + THRCPQCI= 1.00D-10 KEXTA = 0.00D+00 THRCOARS= 0.00D+00 SYMTOL = 1.00D-06 GRADTOL = 1.00D-06 THROVL = 1.00D-08 + THRORTH = 1.00D-08 GRID = 1.00D-06 GRIDMAX = 1.00D-03 DTMAX = 0.00D+00 THROCCDE= 1.00D-01 THROCCDE= 1.00D-01 + + + SETTING GEOMTYP = XYZ + ZSYMEL=NOSYM + + + + Recomputing integrals since basis changed + + + Using spherical harmonics + + Library entry C S cc-pVTZ selected for orbital group 1 + Library entry C P cc-pVTZ selected for orbital group 1 + Library entry C D cc-pVTZ selected for orbital group 1 + Library entry C F cc-pVTZ selected for orbital group 1 + Library entry H S cc-pVTZ selected for orbital group 2 + Library entry H P cc-pVTZ selected for orbital group 2 + Library entry H D cc-pVTZ selected for orbital group 2 + Library entry O S cc-pVTZ selected for orbital group 3 + Library entry O P cc-pVTZ selected for orbital group 3 + Library entry O D cc-pVTZ selected for orbital group 3 + Library entry O F cc-pVTZ selected for orbital group 3 + +1PROGRAM * SEWARD (Integral evaluation for generally contracted gaussian basis sets) Author: Roland Lindh, 1990 + + Geometry written to block 1 of record 700 + + + Point group C1 + + + + ATOMIC COORDINATES + + NR ATOM CHARGE X Y Z + + 1 C 6.00 1.244218727 -0.035747827 -0.000009579 + 2 H 1.00 2.035207237 1.846463264 -0.000169886 + 3 H 1.00 1.923274211 -1.020424577 1.667854479 + 4 H 1.00 1.923289855 -1.020714026 -1.667696304 + 5 O 8.00 -1.386139259 0.212818787 -0.000043083 + 6 H 1.00 -2.145595449 -1.391275269 0.000056814 + + Bond lengths in Bohr (Angstrom) + + 1-2 2.041661440 1-3 2.052431526 1-4 2.052431491 1-5 2.642076551 5-6 1.774793355 + ( 1.080400703) ( 1.086099987) ( 1.086099968) ( 1.398126695) ( 0.939180194) + + Bond angles + + 1-5-6 109.93678065 2-1-3 108.31104810 2-1-4 108.31101554 2-1-5 107.39593209 + + 3-1-4 108.69856723 3-1-5 111.99544778 4-1-5 111.99546348 + + NUCLEAR CHARGE: 18 + NUMBER OF PRIMITIVE AOS: 162 + NUMBER OF SYMMETRY AOS: 148 + NUMBER OF CONTRACTIONS: 116 ( 116A ) + NUMBER OF CORE ORBITALS: 2 ( 2A ) + NUMBER OF VALENCE ORBITALS: 12 ( 12A ) + + + NUCLEAR REPULSION ENERGY 40.85541015 + + + Eigenvalues of metric + + 1 0.130E-02 0.176E-02 0.186E-02 0.220E-02 0.322E-02 0.439E-02 0.661E-02 0.949E-02 + + + Contracted 2-electron integrals neglected if value below 1.0D-12 + AO integral compression algorithm 1 Integral accuracy 1.0D-12 + + 126.878 MB (compressed) written to integral file ( 58.8%) + + + NUMBER OF SORTED TWO-ELECTRON INTEGRALS: 23028291. BUFFER LENGTH: 32768 + NUMBER OF SEGMENTS: 4 SEGMENT LENGTH: 7305795 RECORD LENGTH: 524288 + + Memory used in sort: 7.86 MW + + SORT1 READ 26927007. AND WROTE 22764038. INTEGRALS IN 67 RECORDS. CPU TIME: 0.31 SEC, REAL TIME: 0.49 SEC + SORT2 READ 22764038. AND WROTE 23028291. INTEGRALS IN 484 RECORDS. CPU TIME: 0.42 SEC, REAL TIME: 0.55 SEC + + FILE SIZES: FILE 1: 135.0 MBYTE, FILE 4: 281.1 MBYTE, TOTAL: 416.0 MBYTE + + OPERATOR DM FOR CENTER 0 COORDINATES: 0.000000 0.000000 0.000000 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.66 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + PROGRAMS * TOTAL INT + CPU TIMES * 1.97 1.89 + REAL TIME * 2.42 SEC + DISK USED * 416.42 MB + ********************************************************************************************************************************** + +1PROGRAM * RHF-SCF (CLOSED SHELL) Authors: W. Meyer, H.-J. Werner + + + NUMBER OF ELECTRONS: 9+ 9- SPACE SYMMETRY=1 SPIN SYMMETRY: Singlet + CONVERGENCE THRESHOLDS: 1.00E-06 (Density) 1.00E-09 (Energy) + MAX. NUMBER OF ITERATIONS: 60 + INTERPOLATION TYPE: DIIS + INTERPOLATION STEPS: 2 (START) 1 (STEP) + LEVEL SHIFTS: 0.00 (CLOSED) 0.00 (OPEN) + + + + Orbital guess generated from atomic densities. Full valence occupancy: 14 + + Molecular orbital dump at record 2100.2 + + ITERATION DDIFF GRAD ENERGY 2-EL.EN. DIPOLE MOMENTS DIIS ORB. + 1 0.000D+00 0.000D+00 -115.05488102 165.484264 0.39242 -0.88861 0.00006 0 start + 2 0.000D+00 0.628D-02 -115.08304967 162.991257 0.24119 -0.50614 0.00003 1 diag + 3 0.790D-02 0.328D-02 -115.08968087 164.161015 0.32168 -0.60010 0.00004 2 diag + 4 0.251D-02 0.651D-03 -115.09016974 164.006128 0.31588 -0.59495 0.00004 3 diag + 5 0.690D-03 0.125D-03 -115.09019745 164.011963 0.31951 -0.59079 0.00004 4 diag + 6 0.179D-03 0.232D-04 -115.09019861 164.011411 0.31984 -0.59089 0.00004 5 diag + 7 0.463D-04 0.492D-05 -115.09019865 164.010264 0.32001 -0.59071 0.00004 6 diag + 8 0.839D-05 0.159D-05 -115.09019866 164.010723 0.32004 -0.59068 0.00004 7 diag + 9 0.239D-05 0.395D-06 -115.09019866 164.010645 0.32005 -0.59067 0.00004 8 diag + 10 0.706D-06 0.745D-07 -115.09019866 164.010654 0.32005 -0.59067 0.00004 0 orth + + Final occupancy: 9 + + !RHF STATE 1.1 Energy -115.090198659041 + Nuclear energy 40.85541015 + One-electron energy -237.95093593 + Two-electron energy 82.00532711 + Virial quotient -1.00024091 + !RHF STATE 1.1 Dipole moment 0.32004761 -0.59066898 0.00003966 + Dipole moment /Debye 0.81342660 -1.50123246 0.00010080 + + Orbital energies: + + 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 + -20.548581 -11.264461 -1.364798 -0.927891 -0.696836 -0.622626 -0.598218 -0.499566 -0.447163 0.139721 + + 11.1 + 0.180053 + + HOMO 9.1 -0.447163 = -12.1679eV + LUMO 10.1 0.139721 = 3.8020eV + LUMO-HOMO 0.586884 = 15.9699eV + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.66 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 4 0.66 700 1000 520 2100 + GEOM BASIS MCVARS RHF + + PROGRAMS * TOTAL HF INT + CPU TIMES * 4.23 2.26 1.89 + REAL TIME * 4.89 SEC + DISK USED * 416.42 MB + ********************************************************************************************************************************** + + + PROGRAM * OPT (Geometry optimization) Authors: F. Eckert and H.-J. Werner + + + BFGS update of hessian + + *** Long output written to logfile /home/yuzhai/test/tamkinmolpro/ch3oh.log *** + + + Geometry optimization using default procedure for command HF-SCF + + Geometry written to block 1 of record 700 + + Making model hessian for cartesian coordinates + + Quadratic Steepest Descent - Minimum Search + + ITER. ENERGY(OLD) ENERGY(NEW) DE GRADMAX GRADNORM GRADRMS STEPMAX STEPLEN STEPRMS CPU-time + 1 -115.09019866 -115.09019866 0.00000000 0.00001754 0.00002865 0.00000239 0.00013819 0.00019448 0.00007939 6.47 + + END OF GEOMETRY OPTIMIZATION. + + Current geometry (xyz format, in Angstrom) + + 6 + HF-SCF000/VTZ ENERGY=-115.09019866 + C 0.6584186125 -0.0189608765 -0.0000054018 + H 1.0769283180 0.9770813808 -0.0000893840 + H 1.0177771339 -0.5399731259 0.8826204506 + H 1.0177868289 -0.5401255186 -0.8825373095 + O -0.7335034745 0.1126297556 -0.0000242360 + H -1.1354094186 -0.7361986153 0.0000318809 + + ********************************************************************************************************************************** + + Geometry written to block 1 of record 700 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.70 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 4 0.66 700 1000 520 2100 + GEOM BASIS MCVARS RHF + + PROGRAMS * TOTAL OPTG HF INT + CPU TIMES * 10.70 6.47 2.26 1.89 + REAL TIME * 11.89 SEC + DISK USED * 416.75 MB + ********************************************************************************************************************************** + +1PROGRAM * ALASKA (Gradient of the energy) Author: R. Lindh + + Orbitals from record 2100.2 + + Number of closed-shell orbitals: 9 ( 9 ) + Number of occupied orbitals: 9 ( 9 ) + + Number of electrons= 18 Singlet Space symmetry=1 Wavefunction type: CLOSED + + + SCF GRADIENT FOR STATE 1.1 + + Atom dE/dx dE/dy dE/dz + + 1 -0.000004039 -0.000009122 0.000000005 + 2 -0.000001708 0.000000871 -0.000000036 + 3 0.000001284 0.000002048 0.000001342 + 4 0.000001282 0.000002021 -0.000001325 + 5 0.000002549 0.000006186 0.000000090 + 6 0.000000631 -0.000002005 -0.000000076 + + Nuclear force contribution to virial = -0.000002116 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.70 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 4 0.66 700 1000 520 2100 + GEOM BASIS MCVARS RHF + + PROGRAMS * TOTAL FORCE OPTG HF INT + CPU TIMES * 14.23 3.53 6.47 2.26 1.89 + REAL TIME * 15.42 SEC + DISK USED * 416.75 MB + ********************************************************************************************************************************** + + + PROGRAM * HESSIAN + + PROGRAM * MCKINLEY (Hessian of the energy) Author: A. Bernhardsson, R. Lindh + + Orbitals from record 2100.2 + + Number of closed-shell orbitals: 9 ( 9 ) + Number of occupied orbitals: 9 ( 9 ) + + Number of electrons= 18 Singlet Space symmetry=1 Wavefunction type: CLOSED + + + McKinley needed 22.76 seconds of CPU time + + Entering CPHF calculation + + CPHF needed 145 iterations for 18 perturbations. Total CPU time: 31.89 sec + + + HF-SCF hessian saved to record 5300.2 + + FREQUENCIES * CALCULATION OF HARMONIC VIBRATIONAL SPECTRA FOR HF-SCF + + + Permanent Dipole Moment [debye] + 1- 3 0.000000 0.000000 0.000000 + + Dipole Moment Norm 0.0000000 [debye] + + Dipole Moment Derivatives [debye/ang] + 1 2 3 4 5 6 7 8 + 1 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 2 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 3 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 9 10 11 12 13 14 15 16 + 1 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 2 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 3 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 17 18 + 1 0.0000000 0.0000000 + 2 0.0000000 0.0000000 + 3 0.0000000 0.0000000 + + Projecting out rotations and translations + + Force Constants (Second Derivatives of the Energy) in [a.u.] + GX1 GY1 GZ1 GX2 GY2 + GX1 0.5630578 + GY1 0.0211212 0.6710883 + GZ1 -0.0000019 -0.0000035 0.6223391 + GX2 -0.0883848 -0.0819220 0.0000070 0.1141265 + GY2 -0.0983405 -0.3099913 0.0000209 0.1057671 0.3273558 + GZ2 0.0000084 0.0000211 -0.0617507 -0.0000088 -0.0000230 + GX3 -0.0788762 0.0304769 -0.0565174 0.0062356 -0.0046534 + GY3 0.0355120 -0.1262916 0.1037656 0.0092538 -0.0147660 + GZ3 -0.0615996 0.1052620 -0.2439117 0.0013291 -0.0000072 + GX4 -0.0788777 0.0304878 0.0565139 0.0062357 -0.0046553 + GY4 0.0355240 -0.1263277 -0.1037855 0.0092540 -0.0147712 + GZ4 0.0615954 -0.1052820 -0.2438743 -0.0013307 0.0000100 + GX5 -0.2936508 0.0482428 -0.0000049 -0.0300439 -0.0005342 + GY5 -0.0026464 -0.1153801 0.0000030 -0.0443077 0.0095660 + GZ5 -0.0000016 0.0000032 -0.0727000 0.0000034 -0.0000006 + GX6 -0.0232683 -0.0484067 0.0000032 -0.0081691 0.0024164 + GY6 0.0088296 0.0069025 -0.0000004 0.0019548 0.0026067 + GZ6 -0.0000007 -0.0000007 -0.0001025 0.0000000 -0.0000001 + GZ2 GX3 GY3 GZ3 GX4 + GZ2 0.0549592 + GX3 0.0110621 0.0985819 + GY3 0.0301051 -0.0446662 0.1251402 + GZ3 0.0017352 0.0729317 -0.1180408 0.2570558 + GX4 -0.0110613 0.0062259 -0.0054232 -0.0069623 0.0985835 + GY4 -0.0301022 -0.0054222 0.0111875 0.0155951 -0.0446801 + GZ4 0.0017403 0.0069636 -0.0156014 -0.0247392 -0.0729257 + GX5 -0.0000002 -0.0340348 0.0052968 -0.0046663 -0.0340352 + GY5 -0.0000009 0.0230400 0.0041473 -0.0028387 0.0230458 + GZ5 0.0030459 -0.0338477 0.0009405 0.0099321 0.0338433 + GX6 -0.0000003 0.0018677 0.0000267 -0.0010326 0.0018678 + GY6 -0.0000002 0.0012249 0.0005826 0.0000296 0.0012251 + GZ6 0.0002701 -0.0005923 -0.0011691 -0.0000722 0.0005921 + GY4 GZ4 GX5 GY5 GZ5 + GY4 0.1251810 + GZ4 0.1180631 0.2570134 + GX5 0.0052975 0.0046648 0.5364913 + GY5 0.0041475 0.0028400 0.1785918 0.6239575 + GZ5 -0.0009395 0.0099321 -0.0000088 -0.0000382 0.0526463 + GX6 0.0000269 0.0010326 -0.1447266 -0.1777235 0.0000113 + GY6 0.0005829 -0.0000297 -0.2368947 -0.5264383 0.0000346 + GZ6 0.0011690 -0.0000723 0.0000153 0.0000349 -0.0028563 + GX6 GY6 GZ6 + GX6 0.1724285 + GY6 0.2236602 0.5157636 + GZ6 -0.0000144 -0.0000340 0.0028332 + + + Atomic Masses + 1- 6 12.011000 1.007940 1.007940 1.007940 15.999400 1.007940 + + Mass weighted Second Derivative Matrix + GX1 GY1 GZ1 GX2 GY2 + GX1 0.0468785 + GY1 0.0017585 0.0558728 + GZ1 -0.0000002 -0.0000003 0.0518141 + GX2 -0.0254021 -0.0235447 0.0000020 0.1132275 + GY2 -0.0282635 -0.0890928 0.0000060 0.1049339 0.3247771 + GZ2 0.0000024 0.0000061 -0.0177474 -0.0000087 -0.0000228 + GX3 -0.0226694 0.0087592 -0.0162433 0.0061864 -0.0046168 + GY3 0.0102063 -0.0362967 0.0298227 0.0091809 -0.0146497 + GZ3 -0.0177040 0.0302527 -0.0701012 0.0013186 -0.0000071 + GX4 -0.0226698 0.0087623 0.0162423 0.0061866 -0.0046187 + GY4 0.0102097 -0.0363071 -0.0298284 0.0091811 -0.0146548 + GZ4 0.0177028 -0.0302585 -0.0700905 -0.0013202 0.0000099 + GX5 -0.0211831 0.0034801 -0.0000004 -0.0074815 -0.0001330 + GY5 -0.0001909 -0.0083232 0.0000002 -0.0110334 0.0023821 + GZ5 -0.0000001 0.0000002 -0.0052444 0.0000008 -0.0000002 + GX6 -0.0066874 -0.0139123 0.0000009 -0.0081048 0.0023973 + GY6 0.0025377 0.0019838 -0.0000001 0.0019394 0.0025862 + GZ6 -0.0000002 -0.0000002 -0.0000295 0.0000000 -0.0000001 + GZ2 GX3 GY3 GZ3 GX4 + GZ2 0.0545262 + GX3 0.0109750 0.0978053 + GY3 0.0298680 -0.0443143 0.1241544 + GZ3 0.0017215 0.0723572 -0.1171109 0.2550308 + GX4 -0.0109742 0.0061769 -0.0053805 -0.0069074 0.0978069 + GY4 -0.0298650 -0.0053795 0.0110994 0.0154722 -0.0443282 + GZ4 0.0017266 0.0069087 -0.0154785 -0.0245443 -0.0723513 + GX5 0.0000000 -0.0084753 0.0013190 -0.0011620 -0.0084754 + GY5 -0.0000002 0.0057374 0.0010328 -0.0007069 0.0057388 + GZ5 0.0007585 -0.0084287 0.0002342 0.0024733 0.0084276 + GX6 -0.0000003 0.0018530 0.0000265 -0.0010244 0.0018531 + GY6 -0.0000002 0.0012153 0.0005780 0.0000294 0.0012154 + GZ6 0.0002680 -0.0005876 -0.0011599 -0.0000716 0.0005874 + GY4 GZ4 GX5 GY5 GZ5 + GY4 0.1241949 + GZ4 0.1171331 0.2549888 + GX5 0.0013192 0.0011616 0.0335320 + GY5 0.0010328 0.0007072 0.0111624 0.0389988 + GZ5 -0.0002339 0.0024733 -0.0000005 -0.0000024 0.0032905 + GX6 0.0000267 0.0010245 -0.0360395 -0.0442564 0.0000028 + GY6 0.0005783 -0.0000294 -0.0589911 -0.1310926 0.0000086 + GZ6 0.0011598 -0.0000717 0.0000038 0.0000087 -0.0007113 + GX6 GY6 GZ6 + GX6 0.1710702 + GY6 0.2218984 0.5117007 + GZ6 -0.0000143 -0.0000337 0.0028109 + + + Mass Weighted 2nd Derivative Matrix Eigenvalues + 1- 10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003761 0.050499 0.052175 0.061924 + 11- 18 0.083324 0.098062 0.099381 0.100702 0.372430 0.382546 0.398043 0.659634 + + Mass Weighted 2nd Derivative Matrix Eigenvectors + 1 2 3 4 5 6 7 8 + 1 0.6017565 -0.0239548 0.0202968 -0.0184620 -0.0970973 0.0547754 -0.0000009 0.1111732 + 2 -0.0394960 0.0356013 0.1998306 0.0839239 0.0379152 0.7892503 0.0000001 0.2197573 + 3 0.1421767 0.2805713 -0.0970174 0.1588553 0.7425444 -0.0335392 0.0160951 -0.0000151 + 4 0.1777737 -0.0888839 0.1035427 0.0066474 0.0044055 -0.1607235 -0.0000029 0.5359546 + 5 -0.0128919 0.0447434 0.0168576 0.0192296 -0.0026722 0.3028363 0.0000243 -0.1518800 + 6 0.0474139 0.0733774 0.0278301 -0.4493853 0.3791964 0.0215828 0.2817942 0.0000132 + 7 0.1482039 0.1094619 0.0377452 -0.0058494 -0.2080577 0.0899153 -0.0559362 -0.2438691 + 8 -0.0079896 0.0159758 -0.0617713 0.4565510 -0.0777006 0.2723122 -0.2092273 -0.1799411 + 9 0.0538576 0.0372278 -0.1117133 0.3013723 0.2360128 -0.0140815 -0.0969342 -0.0324171 + 10 0.1968239 -0.0376001 -0.1281717 -0.0173980 0.1177610 0.1265904 0.0559374 -0.2438819 + 11 -0.0173829 0.0637728 0.1070611 -0.4165375 0.0761952 0.3123819 0.2092106 -0.1799323 + 12 0.0538587 0.0372229 -0.1117288 0.3014476 0.2360013 -0.0140848 -0.0969703 0.0324403 + 13 0.6963357 -0.0707822 0.0748284 -0.0149941 -0.0949350 -0.0297306 0.0000026 -0.2453683 + 14 -0.0263715 -0.4151079 0.7744386 0.1636137 0.2248135 -0.0722922 -0.0000170 0.0113063 + 15 0.0085517 0.8000827 0.4593888 -0.0396995 -0.1209264 -0.1419461 -0.2524987 -0.0000025 + 16 0.1718346 0.0520659 -0.0644484 -0.0139862 -0.0515502 0.1430293 -0.0000056 0.5456067 + 17 -0.0052264 -0.1372537 0.2337855 0.0459345 0.0695432 -0.0894020 0.0000598 -0.2918972 + 18 -0.0044069 0.2113199 0.0718898 0.4125151 -0.1785438 -0.0632400 0.8625398 0.0000257 + 9 10 11 12 13 14 15 16 + 1 0.6657247 -0.0000001 -0.0583024 -0.3622108 -0.0000084 0.1014707 -0.1378286 0.0000023 + 2 -0.1003744 0.0000298 -0.3754847 -0.0411953 -0.0000136 -0.1680182 0.1071814 -0.0000268 + 3 0.0000101 0.4196946 0.0000266 0.0000053 -0.2032828 0.0000099 -0.0000109 -0.3101525 + 4 0.0430442 -0.0000078 -0.4009594 0.5455268 0.0000009 0.2162754 0.1030178 -0.0000006 + 5 0.0296647 -0.0000187 0.0470346 -0.2679633 0.0000594 -0.1064189 0.2609238 -0.0000039 + 6 -0.0000006 -0.2417919 -0.0000049 0.0000128 0.7119833 0.0000299 -0.0000222 -0.0244699 + 7 0.2077070 0.5666907 0.1640474 0.4436119 0.3035593 -0.2849542 0.2058749 0.2093115 + 8 0.0215580 -0.1011205 0.1530850 0.2138296 0.3595321 0.4539889 -0.3140611 -0.3348047 + 9 0.0107916 -0.1658110 0.0838327 -0.0730178 0.0626220 0.3985241 0.5516726 0.5437770 + 10 0.2077148 -0.5666773 0.1640580 0.4436231 -0.3035276 -0.2849671 0.2058798 -0.2093186 + 11 0.0215554 0.1010984 0.1530677 0.2138561 -0.3595383 0.4539005 -0.3141543 0.3349003 + 12 -0.0107909 -0.1658366 -0.0838552 0.0729834 0.0627054 -0.3986023 -0.5516127 0.5437199 + 13 -0.6410595 -0.0000011 -0.0929685 -0.0428380 -0.0000014 0.0205907 -0.0083611 -0.0000001 + 14 0.0615961 -0.0000154 0.3000796 -0.0037302 -0.0000011 -0.0620676 -0.0003424 0.0000002 + 15 -0.0000081 -0.2183100 -0.0000213 0.0000007 -0.0314806 0.0000042 0.0000000 0.0016131 + 16 -0.2024852 -0.0000008 0.6445142 -0.0117334 0.0000021 -0.0786684 -0.0056748 0.0000000 + 17 0.0283080 -0.0000004 -0.2525687 -0.0026540 -0.0000016 0.0258161 -0.0013355 -0.0000001 + 18 -0.0000026 -0.0055737 0.0000203 0.0000007 -0.0101529 -0.0000025 0.0000000 0.0011963 + 17 18 + 1 -0.0685027 0.0019935 + 2 -0.2915984 -0.0064690 + 3 0.0000245 0.0000005 + 4 0.3449599 0.0051191 + 5 0.8532070 0.0113300 + 6 -0.0000720 -0.0000010 + 7 -0.0555741 0.0024444 + 8 0.0716526 0.0004263 + 9 -0.1526834 -0.0006181 + 10 -0.0555763 0.0024444 + 11 0.0716798 0.0004266 + 12 0.1526717 0.0006183 + 13 0.0002247 -0.1106833 + 14 0.0061387 -0.2163893 + 15 -0.0000005 0.0000142 + 16 0.0017670 0.4240881 + 17 -0.0143956 0.8722733 + 18 0.0000012 -0.0000575 + + Low Vibration Wavenumber + Nr [1/cm] + 1 0.00 + 2 0.00 + 3 0.00 + 4 0.00 + 5 0.00 + 6 0.00 + + Vibration Wavenumber + Nr [1/cm] + 1 315.25 + 2 1155.16 + 3 1174.17 + 4 1279.17 + 5 1483.83 + 6 1609.72 + 7 1620.51 + 8 1631.25 + 9 3137.06 + 10 3179.38 + 11 3243.14 + 12 4174.96 + + FREQUENCIES * CALCULATION OF NORMAL MODES FOR HF-SCF + + + Atomic Coordinates + + Nr Atom Charge X Y Z + + 1 C 6.00 1.244230857 -0.035830864 -0.000010208 + 2 H 1.00 2.035099584 1.846416218 -0.000168911 + 3 H 1.00 1.923320046 -1.020401326 1.667910930 + 4 H 1.00 1.923338367 -1.020689307 -1.667753816 + 5 O 8.00 -1.386120683 0.212839392 -0.000045799 + 6 H 1.00 -2.145612848 -1.391213761 0.000060246 + + Frequencies dumped to record 5400.2 + + Gradient norm at reference geometry: 0.12943D-04 + + Molecule is not in standard orientation! + Symmetry information for normal modes not available! + + Normal Modes + + 1 A 2 A 3 A 4 A 5 A + Wavenumbers [cm-1] 315.25 1155.16 1174.17 1279.17 1483.83 + Intensities [km/mol] 0.00 0.00 0.00 0.00 0.00 + Intensities [relative] 0.00 0.00 0.00 0.00 0.00 + GX1 0.00000 0.03208 0.19209 0.00000 -0.01682 + GY1 0.00000 0.06341 -0.02896 0.00001 -0.10834 + GZ1 0.00464 0.00000 0.00000 0.12110 0.00001 + GX2 0.00000 0.53384 0.04287 -0.00001 -0.39938 + GY2 0.00002 -0.15128 0.02955 -0.00002 0.04685 + GZ2 0.28068 0.00001 0.00000 -0.24084 0.00000 + GX3 -0.05572 -0.24291 0.20689 0.56445 0.16340 + GY3 -0.20840 -0.17923 0.02147 -0.10072 0.15248 + GZ3 -0.09655 -0.03229 0.01075 -0.16516 0.08350 + GX4 0.05572 -0.24292 0.20690 -0.56444 0.16341 + GY4 0.20838 -0.17922 0.02147 0.10070 0.15246 + GZ4 -0.09659 0.03231 -0.01075 -0.16518 -0.08352 + GX5 0.00000 -0.06134 -0.16027 0.00000 -0.02324 + GY5 0.00000 0.00283 0.01540 0.00000 0.07502 + GZ5 -0.06313 0.00000 0.00000 -0.05458 -0.00001 + GX6 -0.00001 0.54345 -0.20169 0.00000 0.64197 + GY6 0.00006 -0.29075 0.02820 0.00000 -0.25157 + GZ6 0.85914 0.00003 0.00000 -0.00555 0.00002 + + 6 A 7 A 8 A 9 A 10 A + Wavenumbers [cm-1] 1609.72 1620.51 1631.25 3137.06 3179.38 + Intensities [km/mol] 0.00 0.00 0.00 0.00 0.00 + Intensities [relative] 0.00 0.00 0.00 0.00 0.00 + GX1 -0.10451 0.00000 0.02928 -0.03977 0.00000 + GY1 -0.01189 0.00000 -0.04848 0.03093 -0.00001 + GZ1 0.00000 -0.05866 0.00000 0.00000 -0.08949 + GX2 0.54337 0.00000 0.21542 0.10261 0.00000 + GY2 -0.26691 0.00006 -0.10600 0.25989 0.00000 + GZ2 0.00001 0.70917 0.00003 -0.00002 -0.02437 + GX3 0.44186 0.30236 -0.28383 0.20506 0.20849 + GY3 0.21299 0.35811 0.45220 -0.31282 -0.33348 + GZ3 -0.07273 0.06237 0.39695 0.54950 0.54163 + GX4 0.44187 -0.30233 -0.28384 0.20507 -0.20849 + GY4 0.21301 -0.35812 0.45211 -0.31291 0.33358 + GZ4 0.07270 0.06246 -0.39703 -0.54944 0.54157 + GX5 -0.01071 0.00000 0.00515 -0.00209 0.00000 + GY5 -0.00093 0.00000 -0.01552 -0.00009 0.00000 + GZ5 0.00000 -0.00787 0.00000 0.00000 0.00040 + GX6 -0.01169 0.00000 -0.07836 -0.00565 0.00000 + GY6 -0.00264 0.00000 0.02571 -0.00133 0.00000 + GZ6 0.00000 -0.01011 0.00000 0.00000 0.00119 + + 11 A 12 A + Wavenumbers [cm-1] 3243.14 4174.96 + Intensities [km/mol] 0.00 0.00 + Intensities [relative] 0.00 0.00 + GX1 -0.01977 0.00058 + GY1 -0.08414 -0.00187 + GZ1 0.00001 0.00000 + GX2 0.34360 0.00510 + GY2 0.84984 0.01129 + GZ2 -0.00007 0.00000 + GX3 -0.05535 0.00243 + GY3 0.07137 0.00042 + GZ3 -0.15208 -0.00062 + GX4 -0.05536 0.00243 + GY4 0.07140 0.00042 + GZ4 0.15207 0.00062 + GX5 0.00006 -0.02767 + GY5 0.00153 -0.05410 + GZ5 0.00000 0.00000 + GX6 0.00176 0.42241 + GY6 -0.01434 0.86883 + GZ6 0.00000 -0.00006 + + + Normal Modes of low/zero frequencies + + 1 2 3 4 5 + Wavenumbers [cm-1] 0.00 0.00 0.00 0.00 0.00 + Intensities [km/mol] 0.00 0.00 0.00 0.00 0.00 + Intensities [relative] 0.00 0.00 0.00 0.00 0.00 + GX1 0.17363 -0.00691 0.00586 -0.00533 -0.02802 + GY1 -0.01140 0.01027 0.05766 0.02422 0.01094 + GZ1 0.04102 0.08096 -0.02799 0.04584 0.21426 + GX2 0.17707 -0.08853 0.10313 0.00662 0.00439 + GY2 -0.01284 0.04457 0.01679 0.01915 -0.00266 + GZ2 0.04723 0.07309 0.02772 -0.44761 0.37770 + GX3 0.14762 0.10903 0.03760 -0.00583 -0.20724 + GY3 -0.00796 0.01591 -0.06153 0.45475 -0.07739 + GZ3 0.05365 0.03708 -0.11127 0.30018 0.23508 + GX4 0.19605 -0.03745 -0.12767 -0.01733 0.11730 + GY4 -0.01731 0.06352 0.10664 -0.41489 0.07589 + GZ4 0.05365 0.03708 -0.11129 0.30026 0.23507 + GX5 0.17409 -0.01770 0.01871 -0.00375 -0.02373 + GY5 -0.00659 -0.10378 0.19361 0.04090 0.05620 + GZ5 0.00214 0.20002 0.11485 -0.00993 -0.03023 + GX6 0.17116 0.05186 -0.06419 -0.01393 -0.05135 + GY6 -0.00521 -0.13671 0.23286 0.04575 0.06927 + GZ6 -0.00439 0.21049 0.07161 0.41089 -0.17784 + + 6 + Wavenumbers [cm-1] 0.00 + Intensities [km/mol] 0.00 + Intensities [relative] 0.00 + GX1 0.01581 + GY1 0.22773 + GZ1 -0.00968 + GX2 -0.16009 + GY2 0.30164 + GZ2 0.02150 + GX3 0.08956 + GY3 0.27124 + GZ3 -0.01403 + GX4 0.12609 + GY4 0.31115 + GZ4 -0.01403 + GX5 -0.00743 + GY5 -0.01807 + GZ5 -0.03549 + GX6 0.14246 + GY6 -0.08905 + GZ6 -0.06299 + + + Zero point energy: 0.05468429 [H] 12001.81 [1/CM] 143.57 [KJ/MOL] + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.70 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 7 0.94 700 1000 520 2100 5300 5400 5450 + GEOM BASIS MCVARS RHF HESS FREQ NMOD + + 4 5 4.02 4100 4000 4200 4300 4400 + + PROGRAMS * TOTAL FREQ FORCE OPTG HF INT + CPU TIMES * 68.88 54.65 3.53 6.47 2.26 1.89 + REAL TIME * 74.60 SEC + DISK USED * 416.75 MB + ********************************************************************************************************************************** + + OPTG(HF) HF-SCF + -115.09019866 -115.09019866 + ********************************************************************************************************************************** + Variable memory released diff --git a/tamkin/io/ch3oh.out b/tamkin/io/ch3oh.out new file mode 100644 index 0000000..80ae287 --- /dev/null +++ b/tamkin/io/ch3oh.out @@ -0,0 +1,749 @@ + + Primary working directories : /tmp/yuzhai + Secondary working directories : /tmp/yuzhai + Wavefunction directory : /home/yuzhai/wfu/ + Main file repository : /tmp/yuzhai/ + + SHA1 : 2c68d29c09da70e1723824271fadde4bcd5f07a0 + ARCHNAME : Linux/x86_64 + FC : /opt/intel/compilerpro-12.0.2.137/bin/intel64/ifort + FCVERSION : 12.0.2 + BLASLIB : + id : mailjlu + + Nodes nprocs + master 1 + + Using customized tuning parameters: mindgm=4; mindgv=4; mindgc=1; mindgr=1; noblas=0; minvec=7 + default implementation of scratch files=df + + ***,formaldehyde freqency calculation + memory,8,m + + basis=vtz + gthresh,energy=1.d-8 + + geomtyp=xyz + symmetry,nosym + geometry={ + 6 + HF-SCF000/VTZ ENERGY=-115.09019866 + C 0.6584121935 -0.0189169352 -0.0000050689 + H 1.0769852853 0.9771062764 -0.0000898996 + H 1.0177528792 -0.5399854299 0.8825905783 + H 1.0177611577 -0.5401385993 -0.8825068758 + O -0.7335133044 0.1126188517 -0.0000227984 + H -1.1354002112 -0.7362311637 0.0000300645 + } + + hf; + optg; + force; + {frequencies,analytic + print,hessian} + + + Variables initialized (766), CPU time= 0.00 sec + Commands initialized (545), CPU time= 0.01 sec, 513 directives. + Default parameters read. Elapsed time= 0.03 sec + + Checking input... + Passed +1 + + + *** PROGRAM SYSTEM MOLPRO *** + Copyright, University College Cardiff Consultants Limited, 2008 + + Version 2012.1 linked 30 Aug 2012 10:17:55 + + + ********************************************************************************************************************************** + LABEL * formaldehyde freqency calculation + Linux-2.6.32-642.el6.x86_64/master(x86_64) 64 bit serial version DATE: 20-Aug-20 TIME: 15:07:05 + ********************************************************************************************************************************** + + SHA1: 2c68d29c09da70e1723824271fadde4bcd5f07a0 + ********************************************************************************************************************************** + + Variable memory set to 8000000 words, buffer space 230000 words + + SETTING BASIS = VTZ + + THRESHOLDS: + + ZERO = 1.00D-12 ONEINT = 1.00D-12 TWOINT = 1.00D-11 PREFAC = 1.00D-14 LOCALI = 1.00D-09 EORDER = 1.00D-04 + ENERGY = 1.00D-08 ETEST = 0.00D+00 EDENS = 0.00D+00 THRDEDEF= 1.00D-06 GRADIENT= 1.00D-02 STEP = 1.00D-03 + ORBITAL = 1.00D-05 CIVEC = 1.00D-05 COEFF = 1.00D-04 PRINTCI = 5.00D-02 PUNCHCI = 9.90D+01 OPTGRAD = 3.00D-04 + OPTENERG= 1.00D-06 OPTSTEP = 3.00D-04 THRGRAD = 1.00D-10 COMPRESS= 1.00D-11 VARMIN = 1.00D-07 VARMAX = 1.00D-03 + THRDOUB = 0.00D+00 THRDIV = 1.00D-05 THRRED = 1.00D-07 THRPSP = 1.00D+00 THRDC = 1.00D-10 THRCS = 1.00D-10 + THRNRM = 1.00D-08 THREQ = 0.00D+00 THRDE = 1.00D+00 THRREF = 1.00D-05 SPARFAC = 1.00D+00 THRDLP = 1.00D-07 + THRDIA = 1.00D-10 THRDLS = 1.00D-07 THRGPS = 0.00D+00 THRKEX = 0.00D+00 THRDIS = 2.00D-01 THRVAR = 1.00D-10 + THRLOC = 1.00D-06 THRGAP = 1.00D-06 THRLOCT = -1.00D+00 THRGAPT = -1.00D+00 THRORB = 1.00D-06 THRMLTP = 0.00D+00 + THRCPQCI= 1.00D-10 KEXTA = 0.00D+00 THRCOARS= 0.00D+00 SYMTOL = 1.00D-06 GRADTOL = 1.00D-06 THROVL = 1.00D-08 + THRORTH = 1.00D-08 GRID = 1.00D-06 GRIDMAX = 1.00D-03 DTMAX = 0.00D+00 THROCCDE= 1.00D-01 THROCCDE= 1.00D-01 + + + SETTING GEOMTYP = XYZ + ZSYMEL=NOSYM + + + + Recomputing integrals since basis changed + + + Using spherical harmonics + + Library entry C S cc-pVTZ selected for orbital group 1 + Library entry C P cc-pVTZ selected for orbital group 1 + Library entry C D cc-pVTZ selected for orbital group 1 + Library entry C F cc-pVTZ selected for orbital group 1 + Library entry H S cc-pVTZ selected for orbital group 2 + Library entry H P cc-pVTZ selected for orbital group 2 + Library entry H D cc-pVTZ selected for orbital group 2 + Library entry O S cc-pVTZ selected for orbital group 3 + Library entry O P cc-pVTZ selected for orbital group 3 + Library entry O D cc-pVTZ selected for orbital group 3 + Library entry O F cc-pVTZ selected for orbital group 3 + +1PROGRAM * SEWARD (Integral evaluation for generally contracted gaussian basis sets) Author: Roland Lindh, 1990 + + Geometry written to block 1 of record 700 + + + Point group C1 + + + + ATOMIC COORDINATES + + NR ATOM CHARGE X Y Z + + 1 C 6.00 1.244218727 -0.035747827 -0.000009579 + 2 H 1.00 2.035207237 1.846463264 -0.000169886 + 3 H 1.00 1.923274211 -1.020424577 1.667854479 + 4 H 1.00 1.923289855 -1.020714026 -1.667696304 + 5 O 8.00 -1.386139259 0.212818787 -0.000043083 + 6 H 1.00 -2.145595449 -1.391275269 0.000056814 + + Bond lengths in Bohr (Angstrom) + + 1-2 2.041661440 1-3 2.052431526 1-4 2.052431491 1-5 2.642076551 5-6 1.774793355 + ( 1.080400703) ( 1.086099987) ( 1.086099968) ( 1.398126695) ( 0.939180194) + + Bond angles + + 1-5-6 109.93678065 2-1-3 108.31104810 2-1-4 108.31101554 2-1-5 107.39593209 + + 3-1-4 108.69856723 3-1-5 111.99544778 4-1-5 111.99546348 + + NUCLEAR CHARGE: 18 + NUMBER OF PRIMITIVE AOS: 162 + NUMBER OF SYMMETRY AOS: 148 + NUMBER OF CONTRACTIONS: 116 ( 116A ) + NUMBER OF CORE ORBITALS: 2 ( 2A ) + NUMBER OF VALENCE ORBITALS: 12 ( 12A ) + + + NUCLEAR REPULSION ENERGY 40.85541015 + + + Eigenvalues of metric + + 1 0.130E-02 0.176E-02 0.186E-02 0.220E-02 0.322E-02 0.439E-02 0.661E-02 0.949E-02 + + + Contracted 2-electron integrals neglected if value below 1.0D-12 + AO integral compression algorithm 1 Integral accuracy 1.0D-12 + + 126.878 MB (compressed) written to integral file ( 58.8%) + + + NUMBER OF SORTED TWO-ELECTRON INTEGRALS: 23028291. BUFFER LENGTH: 32768 + NUMBER OF SEGMENTS: 4 SEGMENT LENGTH: 7305795 RECORD LENGTH: 524288 + + Memory used in sort: 7.86 MW + + SORT1 READ 26927007. AND WROTE 22764038. INTEGRALS IN 67 RECORDS. CPU TIME: 0.31 SEC, REAL TIME: 0.49 SEC + SORT2 READ 22764038. AND WROTE 23028291. INTEGRALS IN 484 RECORDS. CPU TIME: 0.42 SEC, REAL TIME: 0.55 SEC + + FILE SIZES: FILE 1: 135.0 MBYTE, FILE 4: 281.1 MBYTE, TOTAL: 416.0 MBYTE + + OPERATOR DM FOR CENTER 0 COORDINATES: 0.000000 0.000000 0.000000 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.66 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + PROGRAMS * TOTAL INT + CPU TIMES * 1.97 1.89 + REAL TIME * 2.42 SEC + DISK USED * 416.42 MB + ********************************************************************************************************************************** + +1PROGRAM * RHF-SCF (CLOSED SHELL) Authors: W. Meyer, H.-J. Werner + + + NUMBER OF ELECTRONS: 9+ 9- SPACE SYMMETRY=1 SPIN SYMMETRY: Singlet + CONVERGENCE THRESHOLDS: 1.00E-06 (Density) 1.00E-09 (Energy) + MAX. NUMBER OF ITERATIONS: 60 + INTERPOLATION TYPE: DIIS + INTERPOLATION STEPS: 2 (START) 1 (STEP) + LEVEL SHIFTS: 0.00 (CLOSED) 0.00 (OPEN) + + + + Orbital guess generated from atomic densities. Full valence occupancy: 14 + + Molecular orbital dump at record 2100.2 + + ITERATION DDIFF GRAD ENERGY 2-EL.EN. DIPOLE MOMENTS DIIS ORB. + 1 0.000D+00 0.000D+00 -115.05488102 165.484264 0.39242 -0.88861 0.00006 0 start + 2 0.000D+00 0.628D-02 -115.08304967 162.991257 0.24119 -0.50614 0.00003 1 diag + 3 0.790D-02 0.328D-02 -115.08968087 164.161015 0.32168 -0.60010 0.00004 2 diag + 4 0.251D-02 0.651D-03 -115.09016974 164.006128 0.31588 -0.59495 0.00004 3 diag + 5 0.690D-03 0.125D-03 -115.09019745 164.011963 0.31951 -0.59079 0.00004 4 diag + 6 0.179D-03 0.232D-04 -115.09019861 164.011411 0.31984 -0.59089 0.00004 5 diag + 7 0.463D-04 0.492D-05 -115.09019865 164.010264 0.32001 -0.59071 0.00004 6 diag + 8 0.839D-05 0.159D-05 -115.09019866 164.010723 0.32004 -0.59068 0.00004 7 diag + 9 0.239D-05 0.395D-06 -115.09019866 164.010645 0.32005 -0.59067 0.00004 8 diag + 10 0.706D-06 0.745D-07 -115.09019866 164.010654 0.32005 -0.59067 0.00004 0 orth + + Final occupancy: 9 + + !RHF STATE 1.1 Energy -115.090198659041 + Nuclear energy 40.85541015 + One-electron energy -237.95093593 + Two-electron energy 82.00532711 + Virial quotient -1.00024091 + !RHF STATE 1.1 Dipole moment 0.32004761 -0.59066898 0.00003966 + Dipole moment /Debye 0.81342660 -1.50123246 0.00010080 + + Orbital energies: + + 1.1 2.1 3.1 4.1 5.1 6.1 7.1 8.1 9.1 10.1 + -20.548581 -11.264461 -1.364798 -0.927891 -0.696836 -0.622626 -0.598218 -0.499566 -0.447163 0.139721 + + 11.1 + 0.180053 + + HOMO 9.1 -0.447163 = -12.1679eV + LUMO 10.1 0.139721 = 3.8020eV + LUMO-HOMO 0.586884 = 15.9699eV + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.66 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 4 0.66 700 1000 520 2100 + GEOM BASIS MCVARS RHF + + PROGRAMS * TOTAL HF INT + CPU TIMES * 4.23 2.26 1.89 + REAL TIME * 4.89 SEC + DISK USED * 416.42 MB + ********************************************************************************************************************************** + + + PROGRAM * OPT (Geometry optimization) Authors: F. Eckert and H.-J. Werner + + + BFGS update of hessian + + *** Long output written to logfile /home/yuzhai/test/tamkinmolpro/ch3oh.log *** + + + Geometry optimization using default procedure for command HF-SCF + + Geometry written to block 1 of record 700 + + Making model hessian for cartesian coordinates + + Quadratic Steepest Descent - Minimum Search + + ITER. ENERGY(OLD) ENERGY(NEW) DE GRADMAX GRADNORM GRADRMS STEPMAX STEPLEN STEPRMS CPU-time + 1 -115.09019866 -115.09019866 0.00000000 0.00001754 0.00002865 0.00000239 0.00013819 0.00019448 0.00007939 6.47 + + END OF GEOMETRY OPTIMIZATION. + + Current geometry (xyz format, in Angstrom) + + 6 + HF-SCF000/VTZ ENERGY=-115.09019866 + C 0.6584186125 -0.0189608765 -0.0000054018 + H 1.0769283180 0.9770813808 -0.0000893840 + H 1.0177771339 -0.5399731259 0.8826204506 + H 1.0177868289 -0.5401255186 -0.8825373095 + O -0.7335034745 0.1126297556 -0.0000242360 + H -1.1354094186 -0.7361986153 0.0000318809 + + ********************************************************************************************************************************** + + Geometry written to block 1 of record 700 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.70 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 4 0.66 700 1000 520 2100 + GEOM BASIS MCVARS RHF + + PROGRAMS * TOTAL OPTG HF INT + CPU TIMES * 10.70 6.47 2.26 1.89 + REAL TIME * 11.89 SEC + DISK USED * 416.75 MB + ********************************************************************************************************************************** + +1PROGRAM * ALASKA (Gradient of the energy) Author: R. Lindh + + Orbitals from record 2100.2 + + Number of closed-shell orbitals: 9 ( 9 ) + Number of occupied orbitals: 9 ( 9 ) + + Number of electrons= 18 Singlet Space symmetry=1 Wavefunction type: CLOSED + + + SCF GRADIENT FOR STATE 1.1 + + Atom dE/dx dE/dy dE/dz + + 1 -0.000004039 -0.000009122 0.000000005 + 2 -0.000001708 0.000000871 -0.000000036 + 3 0.000001284 0.000002048 0.000001342 + 4 0.000001282 0.000002021 -0.000001325 + 5 0.000002549 0.000006186 0.000000090 + 6 0.000000631 -0.000002005 -0.000000076 + + Nuclear force contribution to virial = -0.000002116 + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.70 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 4 0.66 700 1000 520 2100 + GEOM BASIS MCVARS RHF + + PROGRAMS * TOTAL FORCE OPTG HF INT + CPU TIMES * 14.23 3.53 6.47 2.26 1.89 + REAL TIME * 15.42 SEC + DISK USED * 416.75 MB + ********************************************************************************************************************************** + + + PROGRAM * HESSIAN + + PROGRAM * MCKINLEY (Hessian of the energy) Author: A. Bernhardsson, R. Lindh + + Orbitals from record 2100.2 + + Number of closed-shell orbitals: 9 ( 9 ) + Number of occupied orbitals: 9 ( 9 ) + + Number of electrons= 18 Singlet Space symmetry=1 Wavefunction type: CLOSED + + + McKinley needed 22.76 seconds of CPU time + + Entering CPHF calculation + + CPHF needed 145 iterations for 18 perturbations. Total CPU time: 31.89 sec + + + HF-SCF hessian saved to record 5300.2 + + FREQUENCIES * CALCULATION OF HARMONIC VIBRATIONAL SPECTRA FOR HF-SCF + + + Permanent Dipole Moment [debye] + 1- 3 0.000000 0.000000 0.000000 + + Dipole Moment Norm 0.0000000 [debye] + + Dipole Moment Derivatives [debye/ang] + 1 2 3 4 5 6 7 8 + 1 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 2 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 3 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 9 10 11 12 13 14 15 16 + 1 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 2 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 3 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 + 17 18 + 1 0.0000000 0.0000000 + 2 0.0000000 0.0000000 + 3 0.0000000 0.0000000 + + Projecting out rotations and translations + + Force Constants (Second Derivatives of the Energy) in [a.u.] + GX1 GY1 GZ1 GX2 GY2 + GX1 0.5630578 + GY1 0.0211212 0.6710883 + GZ1 -0.0000019 -0.0000035 0.6223391 + GX2 -0.0883848 -0.0819220 0.0000070 0.1141265 + GY2 -0.0983405 -0.3099913 0.0000209 0.1057671 0.3273558 + GZ2 0.0000084 0.0000211 -0.0617507 -0.0000088 -0.0000230 + GX3 -0.0788762 0.0304769 -0.0565174 0.0062356 -0.0046534 + GY3 0.0355120 -0.1262916 0.1037656 0.0092538 -0.0147660 + GZ3 -0.0615996 0.1052620 -0.2439117 0.0013291 -0.0000072 + GX4 -0.0788777 0.0304878 0.0565139 0.0062357 -0.0046553 + GY4 0.0355240 -0.1263277 -0.1037855 0.0092540 -0.0147712 + GZ4 0.0615954 -0.1052820 -0.2438743 -0.0013307 0.0000100 + GX5 -0.2936508 0.0482428 -0.0000049 -0.0300439 -0.0005342 + GY5 -0.0026464 -0.1153801 0.0000030 -0.0443077 0.0095660 + GZ5 -0.0000016 0.0000032 -0.0727000 0.0000034 -0.0000006 + GX6 -0.0232683 -0.0484067 0.0000032 -0.0081691 0.0024164 + GY6 0.0088296 0.0069025 -0.0000004 0.0019548 0.0026067 + GZ6 -0.0000007 -0.0000007 -0.0001025 0.0000000 -0.0000001 + GZ2 GX3 GY3 GZ3 GX4 + GZ2 0.0549592 + GX3 0.0110621 0.0985819 + GY3 0.0301051 -0.0446662 0.1251402 + GZ3 0.0017352 0.0729317 -0.1180408 0.2570558 + GX4 -0.0110613 0.0062259 -0.0054232 -0.0069623 0.0985835 + GY4 -0.0301022 -0.0054222 0.0111875 0.0155951 -0.0446801 + GZ4 0.0017403 0.0069636 -0.0156014 -0.0247392 -0.0729257 + GX5 -0.0000002 -0.0340348 0.0052968 -0.0046663 -0.0340352 + GY5 -0.0000009 0.0230400 0.0041473 -0.0028387 0.0230458 + GZ5 0.0030459 -0.0338477 0.0009405 0.0099321 0.0338433 + GX6 -0.0000003 0.0018677 0.0000267 -0.0010326 0.0018678 + GY6 -0.0000002 0.0012249 0.0005826 0.0000296 0.0012251 + GZ6 0.0002701 -0.0005923 -0.0011691 -0.0000722 0.0005921 + GY4 GZ4 GX5 GY5 GZ5 + GY4 0.1251810 + GZ4 0.1180631 0.2570134 + GX5 0.0052975 0.0046648 0.5364913 + GY5 0.0041475 0.0028400 0.1785918 0.6239575 + GZ5 -0.0009395 0.0099321 -0.0000088 -0.0000382 0.0526463 + GX6 0.0000269 0.0010326 -0.1447266 -0.1777235 0.0000113 + GY6 0.0005829 -0.0000297 -0.2368947 -0.5264383 0.0000346 + GZ6 0.0011690 -0.0000723 0.0000153 0.0000349 -0.0028563 + GX6 GY6 GZ6 + GX6 0.1724285 + GY6 0.2236602 0.5157636 + GZ6 -0.0000144 -0.0000340 0.0028332 + + + Atomic Masses + 1- 6 12.011000 1.007940 1.007940 1.007940 15.999400 1.007940 + + Mass weighted Second Derivative Matrix + GX1 GY1 GZ1 GX2 GY2 + GX1 0.0468785 + GY1 0.0017585 0.0558728 + GZ1 -0.0000002 -0.0000003 0.0518141 + GX2 -0.0254021 -0.0235447 0.0000020 0.1132275 + GY2 -0.0282635 -0.0890928 0.0000060 0.1049339 0.3247771 + GZ2 0.0000024 0.0000061 -0.0177474 -0.0000087 -0.0000228 + GX3 -0.0226694 0.0087592 -0.0162433 0.0061864 -0.0046168 + GY3 0.0102063 -0.0362967 0.0298227 0.0091809 -0.0146497 + GZ3 -0.0177040 0.0302527 -0.0701012 0.0013186 -0.0000071 + GX4 -0.0226698 0.0087623 0.0162423 0.0061866 -0.0046187 + GY4 0.0102097 -0.0363071 -0.0298284 0.0091811 -0.0146548 + GZ4 0.0177028 -0.0302585 -0.0700905 -0.0013202 0.0000099 + GX5 -0.0211831 0.0034801 -0.0000004 -0.0074815 -0.0001330 + GY5 -0.0001909 -0.0083232 0.0000002 -0.0110334 0.0023821 + GZ5 -0.0000001 0.0000002 -0.0052444 0.0000008 -0.0000002 + GX6 -0.0066874 -0.0139123 0.0000009 -0.0081048 0.0023973 + GY6 0.0025377 0.0019838 -0.0000001 0.0019394 0.0025862 + GZ6 -0.0000002 -0.0000002 -0.0000295 0.0000000 -0.0000001 + GZ2 GX3 GY3 GZ3 GX4 + GZ2 0.0545262 + GX3 0.0109750 0.0978053 + GY3 0.0298680 -0.0443143 0.1241544 + GZ3 0.0017215 0.0723572 -0.1171109 0.2550308 + GX4 -0.0109742 0.0061769 -0.0053805 -0.0069074 0.0978069 + GY4 -0.0298650 -0.0053795 0.0110994 0.0154722 -0.0443282 + GZ4 0.0017266 0.0069087 -0.0154785 -0.0245443 -0.0723513 + GX5 0.0000000 -0.0084753 0.0013190 -0.0011620 -0.0084754 + GY5 -0.0000002 0.0057374 0.0010328 -0.0007069 0.0057388 + GZ5 0.0007585 -0.0084287 0.0002342 0.0024733 0.0084276 + GX6 -0.0000003 0.0018530 0.0000265 -0.0010244 0.0018531 + GY6 -0.0000002 0.0012153 0.0005780 0.0000294 0.0012154 + GZ6 0.0002680 -0.0005876 -0.0011599 -0.0000716 0.0005874 + GY4 GZ4 GX5 GY5 GZ5 + GY4 0.1241949 + GZ4 0.1171331 0.2549888 + GX5 0.0013192 0.0011616 0.0335320 + GY5 0.0010328 0.0007072 0.0111624 0.0389988 + GZ5 -0.0002339 0.0024733 -0.0000005 -0.0000024 0.0032905 + GX6 0.0000267 0.0010245 -0.0360395 -0.0442564 0.0000028 + GY6 0.0005783 -0.0000294 -0.0589911 -0.1310926 0.0000086 + GZ6 0.0011598 -0.0000717 0.0000038 0.0000087 -0.0007113 + GX6 GY6 GZ6 + GX6 0.1710702 + GY6 0.2218984 0.5117007 + GZ6 -0.0000143 -0.0000337 0.0028109 + + + Mass Weighted 2nd Derivative Matrix Eigenvalues + 1- 10 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.003761 0.050499 0.052175 0.061924 + 11- 18 0.083324 0.098062 0.099381 0.100702 0.372430 0.382546 0.398043 0.659634 + + Mass Weighted 2nd Derivative Matrix Eigenvectors + 1 2 3 4 5 6 7 8 + 1 0.6017565 -0.0239548 0.0202968 -0.0184620 -0.0970973 0.0547754 -0.0000009 0.1111732 + 2 -0.0394960 0.0356013 0.1998306 0.0839239 0.0379152 0.7892503 0.0000001 0.2197573 + 3 0.1421767 0.2805713 -0.0970174 0.1588553 0.7425444 -0.0335392 0.0160951 -0.0000151 + 4 0.1777737 -0.0888839 0.1035427 0.0066474 0.0044055 -0.1607235 -0.0000029 0.5359546 + 5 -0.0128919 0.0447434 0.0168576 0.0192296 -0.0026722 0.3028363 0.0000243 -0.1518800 + 6 0.0474139 0.0733774 0.0278301 -0.4493853 0.3791964 0.0215828 0.2817942 0.0000132 + 7 0.1482039 0.1094619 0.0377452 -0.0058494 -0.2080577 0.0899153 -0.0559362 -0.2438691 + 8 -0.0079896 0.0159758 -0.0617713 0.4565510 -0.0777006 0.2723122 -0.2092273 -0.1799411 + 9 0.0538576 0.0372278 -0.1117133 0.3013723 0.2360128 -0.0140815 -0.0969342 -0.0324171 + 10 0.1968239 -0.0376001 -0.1281717 -0.0173980 0.1177610 0.1265904 0.0559374 -0.2438819 + 11 -0.0173829 0.0637728 0.1070611 -0.4165375 0.0761952 0.3123819 0.2092106 -0.1799323 + 12 0.0538587 0.0372229 -0.1117288 0.3014476 0.2360013 -0.0140848 -0.0969703 0.0324403 + 13 0.6963357 -0.0707822 0.0748284 -0.0149941 -0.0949350 -0.0297306 0.0000026 -0.2453683 + 14 -0.0263715 -0.4151079 0.7744386 0.1636137 0.2248135 -0.0722922 -0.0000170 0.0113063 + 15 0.0085517 0.8000827 0.4593888 -0.0396995 -0.1209264 -0.1419461 -0.2524987 -0.0000025 + 16 0.1718346 0.0520659 -0.0644484 -0.0139862 -0.0515502 0.1430293 -0.0000056 0.5456067 + 17 -0.0052264 -0.1372537 0.2337855 0.0459345 0.0695432 -0.0894020 0.0000598 -0.2918972 + 18 -0.0044069 0.2113199 0.0718898 0.4125151 -0.1785438 -0.0632400 0.8625398 0.0000257 + 9 10 11 12 13 14 15 16 + 1 0.6657247 -0.0000001 -0.0583024 -0.3622108 -0.0000084 0.1014707 -0.1378286 0.0000023 + 2 -0.1003744 0.0000298 -0.3754847 -0.0411953 -0.0000136 -0.1680182 0.1071814 -0.0000268 + 3 0.0000101 0.4196946 0.0000266 0.0000053 -0.2032828 0.0000099 -0.0000109 -0.3101525 + 4 0.0430442 -0.0000078 -0.4009594 0.5455268 0.0000009 0.2162754 0.1030178 -0.0000006 + 5 0.0296647 -0.0000187 0.0470346 -0.2679633 0.0000594 -0.1064189 0.2609238 -0.0000039 + 6 -0.0000006 -0.2417919 -0.0000049 0.0000128 0.7119833 0.0000299 -0.0000222 -0.0244699 + 7 0.2077070 0.5666907 0.1640474 0.4436119 0.3035593 -0.2849542 0.2058749 0.2093115 + 8 0.0215580 -0.1011205 0.1530850 0.2138296 0.3595321 0.4539889 -0.3140611 -0.3348047 + 9 0.0107916 -0.1658110 0.0838327 -0.0730178 0.0626220 0.3985241 0.5516726 0.5437770 + 10 0.2077148 -0.5666773 0.1640580 0.4436231 -0.3035276 -0.2849671 0.2058798 -0.2093186 + 11 0.0215554 0.1010984 0.1530677 0.2138561 -0.3595383 0.4539005 -0.3141543 0.3349003 + 12 -0.0107909 -0.1658366 -0.0838552 0.0729834 0.0627054 -0.3986023 -0.5516127 0.5437199 + 13 -0.6410595 -0.0000011 -0.0929685 -0.0428380 -0.0000014 0.0205907 -0.0083611 -0.0000001 + 14 0.0615961 -0.0000154 0.3000796 -0.0037302 -0.0000011 -0.0620676 -0.0003424 0.0000002 + 15 -0.0000081 -0.2183100 -0.0000213 0.0000007 -0.0314806 0.0000042 0.0000000 0.0016131 + 16 -0.2024852 -0.0000008 0.6445142 -0.0117334 0.0000021 -0.0786684 -0.0056748 0.0000000 + 17 0.0283080 -0.0000004 -0.2525687 -0.0026540 -0.0000016 0.0258161 -0.0013355 -0.0000001 + 18 -0.0000026 -0.0055737 0.0000203 0.0000007 -0.0101529 -0.0000025 0.0000000 0.0011963 + 17 18 + 1 -0.0685027 0.0019935 + 2 -0.2915984 -0.0064690 + 3 0.0000245 0.0000005 + 4 0.3449599 0.0051191 + 5 0.8532070 0.0113300 + 6 -0.0000720 -0.0000010 + 7 -0.0555741 0.0024444 + 8 0.0716526 0.0004263 + 9 -0.1526834 -0.0006181 + 10 -0.0555763 0.0024444 + 11 0.0716798 0.0004266 + 12 0.1526717 0.0006183 + 13 0.0002247 -0.1106833 + 14 0.0061387 -0.2163893 + 15 -0.0000005 0.0000142 + 16 0.0017670 0.4240881 + 17 -0.0143956 0.8722733 + 18 0.0000012 -0.0000575 + + Low Vibration Wavenumber + Nr [1/cm] + 1 0.00 + 2 0.00 + 3 0.00 + 4 0.00 + 5 0.00 + 6 0.00 + + Vibration Wavenumber + Nr [1/cm] + 1 315.25 + 2 1155.16 + 3 1174.17 + 4 1279.17 + 5 1483.83 + 6 1609.72 + 7 1620.51 + 8 1631.25 + 9 3137.06 + 10 3179.38 + 11 3243.14 + 12 4174.96 + + FREQUENCIES * CALCULATION OF NORMAL MODES FOR HF-SCF + + + Atomic Coordinates + + Nr Atom Charge X Y Z + + 1 C 6.00 1.244230857 -0.035830864 -0.000010208 + 2 H 1.00 2.035099584 1.846416218 -0.000168911 + 3 H 1.00 1.923320046 -1.020401326 1.667910930 + 4 H 1.00 1.923338367 -1.020689307 -1.667753816 + 5 O 8.00 -1.386120683 0.212839392 -0.000045799 + 6 H 1.00 -2.145612848 -1.391213761 0.000060246 + + Frequencies dumped to record 5400.2 + + Gradient norm at reference geometry: 0.12943D-04 + + Molecule is not in standard orientation! + Symmetry information for normal modes not available! + + Normal Modes + + 1 A 2 A 3 A 4 A 5 A + Wavenumbers [cm-1] 315.25 1155.16 1174.17 1279.17 1483.83 + Intensities [km/mol] 0.00 0.00 0.00 0.00 0.00 + Intensities [relative] 0.00 0.00 0.00 0.00 0.00 + GX1 0.00000 0.03208 0.19209 0.00000 -0.01682 + GY1 0.00000 0.06341 -0.02896 0.00001 -0.10834 + GZ1 0.00464 0.00000 0.00000 0.12110 0.00001 + GX2 0.00000 0.53384 0.04287 -0.00001 -0.39938 + GY2 0.00002 -0.15128 0.02955 -0.00002 0.04685 + GZ2 0.28068 0.00001 0.00000 -0.24084 0.00000 + GX3 -0.05572 -0.24291 0.20689 0.56445 0.16340 + GY3 -0.20840 -0.17923 0.02147 -0.10072 0.15248 + GZ3 -0.09655 -0.03229 0.01075 -0.16516 0.08350 + GX4 0.05572 -0.24292 0.20690 -0.56444 0.16341 + GY4 0.20838 -0.17922 0.02147 0.10070 0.15246 + GZ4 -0.09659 0.03231 -0.01075 -0.16518 -0.08352 + GX5 0.00000 -0.06134 -0.16027 0.00000 -0.02324 + GY5 0.00000 0.00283 0.01540 0.00000 0.07502 + GZ5 -0.06313 0.00000 0.00000 -0.05458 -0.00001 + GX6 -0.00001 0.54345 -0.20169 0.00000 0.64197 + GY6 0.00006 -0.29075 0.02820 0.00000 -0.25157 + GZ6 0.85914 0.00003 0.00000 -0.00555 0.00002 + + 6 A 7 A 8 A 9 A 10 A + Wavenumbers [cm-1] 1609.72 1620.51 1631.25 3137.06 3179.38 + Intensities [km/mol] 0.00 0.00 0.00 0.00 0.00 + Intensities [relative] 0.00 0.00 0.00 0.00 0.00 + GX1 -0.10451 0.00000 0.02928 -0.03977 0.00000 + GY1 -0.01189 0.00000 -0.04848 0.03093 -0.00001 + GZ1 0.00000 -0.05866 0.00000 0.00000 -0.08949 + GX2 0.54337 0.00000 0.21542 0.10261 0.00000 + GY2 -0.26691 0.00006 -0.10600 0.25989 0.00000 + GZ2 0.00001 0.70917 0.00003 -0.00002 -0.02437 + GX3 0.44186 0.30236 -0.28383 0.20506 0.20849 + GY3 0.21299 0.35811 0.45220 -0.31282 -0.33348 + GZ3 -0.07273 0.06237 0.39695 0.54950 0.54163 + GX4 0.44187 -0.30233 -0.28384 0.20507 -0.20849 + GY4 0.21301 -0.35812 0.45211 -0.31291 0.33358 + GZ4 0.07270 0.06246 -0.39703 -0.54944 0.54157 + GX5 -0.01071 0.00000 0.00515 -0.00209 0.00000 + GY5 -0.00093 0.00000 -0.01552 -0.00009 0.00000 + GZ5 0.00000 -0.00787 0.00000 0.00000 0.00040 + GX6 -0.01169 0.00000 -0.07836 -0.00565 0.00000 + GY6 -0.00264 0.00000 0.02571 -0.00133 0.00000 + GZ6 0.00000 -0.01011 0.00000 0.00000 0.00119 + + 11 A 12 A + Wavenumbers [cm-1] 3243.14 4174.96 + Intensities [km/mol] 0.00 0.00 + Intensities [relative] 0.00 0.00 + GX1 -0.01977 0.00058 + GY1 -0.08414 -0.00187 + GZ1 0.00001 0.00000 + GX2 0.34360 0.00510 + GY2 0.84984 0.01129 + GZ2 -0.00007 0.00000 + GX3 -0.05535 0.00243 + GY3 0.07137 0.00042 + GZ3 -0.15208 -0.00062 + GX4 -0.05536 0.00243 + GY4 0.07140 0.00042 + GZ4 0.15207 0.00062 + GX5 0.00006 -0.02767 + GY5 0.00153 -0.05410 + GZ5 0.00000 0.00000 + GX6 0.00176 0.42241 + GY6 -0.01434 0.86883 + GZ6 0.00000 -0.00006 + + + Normal Modes of low/zero frequencies + + 1 2 3 4 5 + Wavenumbers [cm-1] 0.00 0.00 0.00 0.00 0.00 + Intensities [km/mol] 0.00 0.00 0.00 0.00 0.00 + Intensities [relative] 0.00 0.00 0.00 0.00 0.00 + GX1 0.17363 -0.00691 0.00586 -0.00533 -0.02802 + GY1 -0.01140 0.01027 0.05766 0.02422 0.01094 + GZ1 0.04102 0.08096 -0.02799 0.04584 0.21426 + GX2 0.17707 -0.08853 0.10313 0.00662 0.00439 + GY2 -0.01284 0.04457 0.01679 0.01915 -0.00266 + GZ2 0.04723 0.07309 0.02772 -0.44761 0.37770 + GX3 0.14762 0.10903 0.03760 -0.00583 -0.20724 + GY3 -0.00796 0.01591 -0.06153 0.45475 -0.07739 + GZ3 0.05365 0.03708 -0.11127 0.30018 0.23508 + GX4 0.19605 -0.03745 -0.12767 -0.01733 0.11730 + GY4 -0.01731 0.06352 0.10664 -0.41489 0.07589 + GZ4 0.05365 0.03708 -0.11129 0.30026 0.23507 + GX5 0.17409 -0.01770 0.01871 -0.00375 -0.02373 + GY5 -0.00659 -0.10378 0.19361 0.04090 0.05620 + GZ5 0.00214 0.20002 0.11485 -0.00993 -0.03023 + GX6 0.17116 0.05186 -0.06419 -0.01393 -0.05135 + GY6 -0.00521 -0.13671 0.23286 0.04575 0.06927 + GZ6 -0.00439 0.21049 0.07161 0.41089 -0.17784 + + 6 + Wavenumbers [cm-1] 0.00 + Intensities [km/mol] 0.00 + Intensities [relative] 0.00 + GX1 0.01581 + GY1 0.22773 + GZ1 -0.00968 + GX2 -0.16009 + GY2 0.30164 + GZ2 0.02150 + GX3 0.08956 + GY3 0.27124 + GZ3 -0.01403 + GX4 0.12609 + GY4 0.31115 + GZ4 -0.01403 + GX5 -0.00743 + GY5 -0.01807 + GZ5 -0.03549 + GX6 0.14246 + GY6 -0.08905 + GZ6 -0.06299 + + + Zero point energy: 0.05468429 [H] 12001.81 [1/CM] 143.57 [KJ/MOL] + + + ********************************************************************************************************************************** + DATASETS * FILE NREC LENGTH (MB) RECORD NAMES + 1 19 118.70 500 610 700 900 950 970 1000 129 960 1100 + VAR BASINP GEOM SYMINP ZMAT AOBASIS BASIS P2S ABASIS S + 1400 1410 1200 1210 1080 1600 1650 1300 1700 + T V H0 H01 AOSYM SMH MOLCAS ERIS OPER + + 2 7 0.94 700 1000 520 2100 5300 5400 5450 + GEOM BASIS MCVARS RHF HESS FREQ NMOD + + 4 5 4.02 4100 4000 4200 4300 4400 + + PROGRAMS * TOTAL FREQ FORCE OPTG HF INT + CPU TIMES * 68.88 54.65 3.53 6.47 2.26 1.89 + REAL TIME * 74.60 SEC + DISK USED * 416.75 MB + ********************************************************************************************************************************** + + OPTG(HF) HF-SCF + -115.09019866 -115.09019866 + ********************************************************************************************************************************** + Variable memory released diff --git a/tamkin/io/molpro.py b/tamkin/io/molpro.py index 42053ff..9195b39 100644 --- a/tamkin/io/molpro.py +++ b/tamkin/io/molpro.py @@ -36,10 +36,9 @@ from __future__ import print_function, division -from tamkin.data import Molecule, RotScan +from tamkin.data import Molecule -from molmod.io import FCHKFile -from molmod import dihed_angle, amu, angstrom +from molmod import amu import numpy as np @@ -67,6 +66,8 @@ def load_molecule_molpro(filename): beginmass = lineno if "Force Constants" in line: beginhessian = lineno + if "GRADIENT FOR STATE" in line: + begingradient = lineno + 4 # xyz read, only meta data and energy atomnumber = int(lines[beginxyz].split()[0]) title = lines[beginxyz+1].split()[0] @@ -98,6 +99,15 @@ def load_molecule_molpro(filename): break # print(masses) + # gradient + gradient = np.zeros((atomnumber, 3)) + for i, line in enumerate(lines[begingradient: begingradient + atomnumber]): + words = line.split() + gradient[i,0] = float(words[1]) + gradient[i,1] = float(words[2]) + gradient[i,2] = float(words[3]) + # print(gradient) + # hessian hessian = np.ndarray((3*atomnumber, 3*atomnumber), dtype= float) headerline = beginhessian+1 @@ -123,10 +133,8 @@ def load_molecule_molpro(filename): np.array(coordinates), np.array(masses), energy, - np.zeros((atomnumber, 3)), + gradient, hessian, title=title, multiplicity=1, ) - - diff --git a/tamkin/test/test_io.py b/tamkin/test/test_io.py index 448196f..b149356 100644 --- a/tamkin/test/test_io.py +++ b/tamkin/test/test_io.py @@ -525,3 +525,12 @@ def test_dftd3(self): def test_dftd_orca(self): assert load_dftd_orca( pkg_resources.resource_filename("tamkin", "data/test/matvdw/R_b3lyp-d.out")) == -0.404083275 + + def test_load_molecule_molpro(self): + molecule = load_molecule_molpro( + pkg_resources.resource_filename("tamkin", "data/test/molpro/ch3oh.out") + ) + nma1 = NMA(molecule) + self.assertAlmostEqual(molecule.energy, -115.09019866) + self.assertAlmostEqual(nma1.freqs[-1], 0.003027552791107755, 5) + From 370318b3bbf64d527330ae07e65464c387062336 Mon Sep 17 00:00:00 2001 From: Yu Zhai Date: Mon, 14 Sep 2020 14:57:43 +0800 Subject: [PATCH 3/4] Signed-off-by: Yu Zhai --- doc/tutorial/data.rst | 24 ++++++++++++++++++++++++ tamkin/io/molpro.py | 24 +++++++++++++++++------- 2 files changed, 41 insertions(+), 7 deletions(-) diff --git a/doc/tutorial/data.rst b/doc/tutorial/data.rst index 729d042..26662e2 100644 --- a/doc/tutorial/data.rst +++ b/doc/tutorial/data.rst @@ -179,6 +179,18 @@ VASP **TODO** +Molpro 2012/2015 +~~~~~~~~~~~~~~~~ + +See https://www.molpro.net/ + +By default Molpro will print all need information but the mass weighted Hessian. +Use the following input card to get mass-weighted Hessian:: + + {frequencies,analytic + print,hessian} + +The output file ``*.out`` can then be used for TAMkin analysing. Loading data into TAMkin ======================== @@ -270,6 +282,18 @@ internal units, i.e. Hartree):: molecule = load_molecule_g03fchk("freq.fchk", energy=-135.12597) +Molpro 2012/2015 +~~~~~~~~~~~~~~~~ + +For the details, see :func:`tamkin.io.molpro.load_molecule_molpro`. + +Given a Molpro output file, it is loaded as follows:: + + molecule = load_molecule_molpro("ch3oh.out") + +where ``"ch3oh.out"`` is the name of the Molpro file of a +frequency computation. + Torsional potentials -------------------- diff --git a/tamkin/io/molpro.py b/tamkin/io/molpro.py index 9195b39..13668d5 100644 --- a/tamkin/io/molpro.py +++ b/tamkin/io/molpro.py @@ -57,6 +57,11 @@ def load_molecule_molpro(filename): lines = open(filename,"r").read().splitlines() # locate positions + beginxyz = None + begincoordinate = None + beginmass = None + beginhessian = None + begingradient = None for lineno, line in enumerate(lines): if "Current geometry" in line: beginxyz = lineno + 2 @@ -66,8 +71,8 @@ def load_molecule_molpro(filename): beginmass = lineno if "Force Constants" in line: beginhessian = lineno - if "GRADIENT FOR STATE" in line: - begingradient = lineno + 4 + # if "GRADIENT FOR" in line: + # begingradient = lineno + 4 # xyz read, only meta data and energy atomnumber = int(lines[beginxyz].split()[0]) title = lines[beginxyz+1].split()[0] @@ -101,11 +106,16 @@ def load_molecule_molpro(filename): # gradient gradient = np.zeros((atomnumber, 3)) - for i, line in enumerate(lines[begingradient: begingradient + atomnumber]): - words = line.split() - gradient[i,0] = float(words[1]) - gradient[i,1] = float(words[2]) - gradient[i,2] = float(words[3]) + # TODO, Gradient is more difficult than I thought... + # format of gradient from CCSD(T)-F12 is different from DFT + ''' + if begingradient != None: + for i, line in enumerate(lines[begingradient: begingradient + atomnumber]): + words = line.split() + gradient[i,0] = float(words[1]) + gradient[i,1] = float(words[2]) + gradient[i,2] = float(words[3]) + ''' # print(gradient) # hessian From ae28447484b7ad77615d17acffda91bb0f7ae77b Mon Sep 17 00:00:00 2001 From: Yu Zhai Date: Fri, 18 Sep 2020 16:22:59 +0800 Subject: [PATCH 4/4] remove trailing whitespaces --- doc/tutorial/data.rst | 2 +- tamkin/io/molpro.py | 32 ++++++++++++++++---------------- tamkin/test/test_io.py | 3 +-- 3 files changed, 18 insertions(+), 19 deletions(-) diff --git a/doc/tutorial/data.rst b/doc/tutorial/data.rst index 26662e2..fe6ae19 100644 --- a/doc/tutorial/data.rst +++ b/doc/tutorial/data.rst @@ -292,7 +292,7 @@ Given a Molpro output file, it is loaded as follows:: molecule = load_molecule_molpro("ch3oh.out") where ``"ch3oh.out"`` is the name of the Molpro file of a -frequency computation. +frequency computation. Torsional potentials -------------------- diff --git a/tamkin/io/molpro.py b/tamkin/io/molpro.py index 13668d5..1592c65 100644 --- a/tamkin/io/molpro.py +++ b/tamkin/io/molpro.py @@ -49,14 +49,14 @@ def load_molecule_molpro(filename): """Load a molecule from Molpro 2012 output file. - + Argument: | ``filename`` -- the molpro 2012 output - + """ - + lines = open(filename,"r").read().splitlines() - # locate positions + # locate positions beginxyz = None begincoordinate = None beginmass = None @@ -78,21 +78,21 @@ def load_molecule_molpro(filename): title = lines[beginxyz+1].split()[0] energy = float(lines[beginxyz+1].split("=")[1]) # print(atomnumber, title, energy) - + # coordinate read numbers=[] coordinates=[] - + for line in lines[begincoordinate : begincoordinate+atomnumber]: words = line.split() - charge = int(float(words[2])) - x = float(words[3]) - y = float(words[4]) - z = float(words[5]) + charge = int(float(words[2])) + x = float(words[3]) + y = float(words[4]) + z = float(words[5]) numbers.append(charge) coordinates.append([x, y, z]) # print(charge, x, y, z) - + # masses masses = [] for line in lines[beginmass+1:]: @@ -103,13 +103,13 @@ def load_molecule_molpro(filename): else: break # print(masses) - + # gradient gradient = np.zeros((atomnumber, 3)) - # TODO, Gradient is more difficult than I thought... + # TODO, Gradient is more difficult than I thought... # format of gradient from CCSD(T)-F12 is different from DFT ''' - if begingradient != None: + if begingradient != None: for i, line in enumerate(lines[begingradient: begingradient + atomnumber]): words = line.split() gradient[i,0] = float(words[1]) @@ -117,7 +117,7 @@ def load_molecule_molpro(filename): gradient[i,2] = float(words[3]) ''' # print(gradient) - + # hessian hessian = np.ndarray((3*atomnumber, 3*atomnumber), dtype= float) headerline = beginhessian+1 @@ -135,7 +135,7 @@ def load_molecule_molpro(filename): hessian[c,r]=hessian[r,c] headerline += 3*atomnumber-rowbegin+1 rowbegin += 5 - + # print(hessian) return Molecule( diff --git a/tamkin/test/test_io.py b/tamkin/test/test_io.py index b149356..9224921 100644 --- a/tamkin/test/test_io.py +++ b/tamkin/test/test_io.py @@ -525,7 +525,7 @@ def test_dftd3(self): def test_dftd_orca(self): assert load_dftd_orca( pkg_resources.resource_filename("tamkin", "data/test/matvdw/R_b3lyp-d.out")) == -0.404083275 - + def test_load_molecule_molpro(self): molecule = load_molecule_molpro( pkg_resources.resource_filename("tamkin", "data/test/molpro/ch3oh.out") @@ -533,4 +533,3 @@ def test_load_molecule_molpro(self): nma1 = NMA(molecule) self.assertAlmostEqual(molecule.energy, -115.09019866) self.assertAlmostEqual(nma1.freqs[-1], 0.003027552791107755, 5) -