├── .gitattributes ├── .travis-install.sh ├── .travis.yml ├── LICENSE ├── MANIFEST.in ├── README.md ├── SUPPORT.md ├── pyQRC_banner.png ├── pyqrc ├── __init__.py ├── __main__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── __main__.cpython-37.pyc │ └── pyQRC.cpython-37.pyc ├── examples │ ├── Gaussian │ │ ├── acetaldehyde.com │ │ ├── acetaldehyde.log │ │ ├── acetaldehyde_QRC.com │ │ ├── acetaldehyde_QRC.log │ │ ├── acetaldehyde_QRC.qrc │ │ ├── claisen_ts.com │ │ ├── claisen_ts.log │ │ ├── claisen_ts_IRCF.log │ │ ├── claisen_ts_IRCR.log │ │ ├── claisen_ts_QRCF.com │ │ ├── claisen_ts_QRCF.log │ │ ├── claisen_ts_QRCF.qrc │ │ ├── claisen_ts_QRCR.com │ │ ├── claisen_ts_QRCR.log │ │ ├── claisen_ts_QRCR.qrc │ │ ├── planar_chex.log │ │ ├── planar_chex_mode1.com │ │ ├── planar_chex_mode1.log │ │ ├── planar_chex_mode1.qrc │ │ ├── planar_chex_mode3.com │ │ ├── planar_chex_mode3.log │ │ └── planar_chex_mode3.qrc │ ├── Orca │ │ ├── acetaldehyde.out │ │ ├── acetaldehyde_QRC.inp │ │ ├── acetaldehyde_QRC.out │ │ ├── acetaldehyde_QRC.qrc │ │ ├── claisen_ts.out │ │ ├── claisen_ts_QRCF.inp │ │ ├── claisen_ts_QRCF.out │ │ ├── claisen_ts_QRCF.qrc │ │ ├── claisen_ts_QRCR.inp │ │ ├── claisen_ts_QRCR.out │ │ └── claisen_ts_QRCR.qrc │ └── QChem │ │ ├── acetaldehyde.inp │ │ ├── acetaldehyde.out │ │ ├── acetaldehyde_QRC.inp │ │ ├── acetaldehyde_QRC.out │ │ └── acetaldehyde_QRC.qrc ├── pyQRC.py ├── run_g16.sh └── test.py ├── setup.cfg ├── setup.py └── tests ├── __init__.py ├── conftest.py └── test_pyqrc.py /.gitattributes: -------------------------------------------------------------------------------- 1 | # Auto detect text files and perform LF normalization 2 | * text=auto 3 | -------------------------------------------------------------------------------- /.travis-install.sh: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env bash 2 | 3 | if [[$TRAVIS_OS_NAME == 'osx']]; then 4 | brew update 5 | brew install pyenv-virtualenv 6 | case "${TOXENV}" in 7 | py26) 8 | pyenv install 2.6.9 9 | export PYENV_VERSION=2.6.9 10 | ;; 11 | py27) 12 | pyenv install 2.7.12 13 | export PYENV_VERSION=2.7.12 14 | ;; 15 | py35) 16 | pyenv install 3.5.2 17 | export PYENV_VERSION=3.5.2 18 | ;; 19 | py36) 20 | pyenv install 3.6.7 21 | export PYENV_VERSION=3.6.7 22 | ;; 23 | py37) 24 | pyenv install 3.7.2 25 | export PYENV_VERSION=3.7.2 26 | ;; 27 | esac 28 | export PATH="/Users/travis/.pyenv/shims:${PATH}" 29 | pyenv-virtualenv venv 30 | source venv/bin/activate 31 | python --version 32 | fi 33 | 34 | -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 1 | language: python 2 | osx_image: xcode9.4 3 | dist: trusty 4 | 5 | matrix: 6 | include: 7 | - os: linux 8 | python: 3.6 9 | env: TOXENV=py36 10 | install: 11 | - ./.travis-install.sh 12 | - pip install pytest 13 | - pip install --upgrade numpy 14 | - python -m pip install . 15 | script: 16 | - pytest -v 17 | - os: linux 18 | python: 3.7 19 | env: TOXENV=py37 20 | dist: xenial 21 | install: 22 | - ./.travis-install.sh 23 | - pip install pytest 24 | - python -m pip install . 25 | script: 26 | - pytest -v 27 | - os: linux 28 | python: 3.8 29 | env: TOXENV=py38 30 | dist: xenial 31 | install: 32 | - ./.travis-install.sh 33 | - pip install pytest 34 | - python -m pip install . 35 | script: 36 | - pytest -v 37 | - os: osx 38 | language: generic 39 | env: TOXENV=py36 40 | install: 41 | - ./.travis-install.sh 42 | - pip3 install pytest 43 | - python3 -m pip install . 44 | script: 45 | - pytest -v 46 | - os: osx 47 | language: generic 48 | env: TOXENV=py37 49 | dist: xenial 50 | install: 51 | - ./.travis-install.sh 52 | - pip3 install pytest 53 | - python3 -m pip install . 54 | script: 55 | - pytest -v 56 | - os: osx 57 | language: generic 58 | env: TOXENV=py38 59 | dist: xenial 60 | install: 61 | - ./.travis-install.sh 62 | - pip3 install pytest 63 | - python3 -m pip install . 64 | script: 65 | - pytest -v 66 | - os: windows 67 | language: shell 68 | before_install: 69 | - choco install python --version=3.6 70 | - python --version 71 | - python -m pip install --upgrade pip 72 | - pip install --upgrade pytest 73 | - pip install codecov 74 | - pip install numpy 75 | - pip install cython 76 | env: PATH=/c/Python36:/c/Python36/Scripts:$PATH 77 | install: 78 | - ./.travis-install.sh 79 | - pip install pytest 80 | - python -m pip install . 81 | script: 82 | - pytest -v 83 | - os: windows 84 | language: shell 85 | before_install: 86 | - choco install python --version=3.7 87 | - python --version 88 | - python -m pip install --upgrade pip 89 | - pip install --upgrade pytest 90 | - pip install codecov 91 | - pip install numpy 92 | - pip install cython 93 | env: PATH=/c/Python37:/c/Python37/Scripts:$PATH 94 | install: 95 | - ./.travis-install.sh 96 | - pip install pytest 97 | - python -m pip install . 98 | script: 99 | - pytest -v 100 | - os: windows 101 | language: shell 102 | before_install: 103 | - choco install python --version=3.8 104 | - python --version 105 | - python -m pip install --upgrade pip 106 | - pip install --upgrade pytest 107 | - pip install codecov 108 | - pip install numpy 109 | - pip install cython 110 | env: PATH=/c/Python38:/c/Python38/Scripts:$PATH 111 | install: 112 | - ./.travis-install.sh 113 | - pip install pytest 114 | - python -m pip install . 115 | script: 116 | - pytest -v 117 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) 2018 Robert Paton 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include README.md 2 | include LICENSE.txt 3 | recursive-include pyqrc/examples * 4 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ![pyQRC](pyQRC_banner.png) 2 | 3 | [![DOI](https://zenodo.org/badge/138228684.svg)](https://zenodo.org/badge/latestdoi/138228684) 4 | [![Build Status](https://app.travis-ci.com/patonlab/pyQRC.svg?branch=master)](https://travis-ci.com/github/patonlab/pyQRC) 5 | [![PyPI version](https://badge.fury.io/py/pyqrc.svg)](https://badge.fury.io/py/pyqrc) 6 | 7 | ### Introduction 8 | QRC is an abbreviation of **Quick Reaction Coordinate**. This provides a quick alternative to IRC (intrisic reaction coordinate) calculations. This was first described by Silva and Goodman.1 The [original code](http://www-jmg.ch.cam.ac.uk/software/QRC/) was developed in java for Jaguar output files. This Python version uses [cclib](https://cclib.github.io/) to process a variety of compchem outputs. 9 | 10 | The program will read a Gaussian frequency calculation and will create a new input file which has been projcted from the final coordinates along the Hessian eigenvector with a negative force constant. The magnitude of displacement can be adjusted on the command line. By default the projection will be in a positive sense (in relation to the imaginary normal mode) and the level of theory in the new input file will match that of the frequency calculation. In addition to the new input file(s) a summary is output to a text file ending in '.qrc' 11 | 12 | In addition to a pound-shop (dollar store) IRC calculation, a common application for pyQRC is in distorting ground state structures to remove annoying imaginary frequencies after reoptimization. This code has, in some form or other, been in use since around 2010. 13 | 14 | ### Installation 15 | Easy: 16 | Pypi installation: `pip install pyqrc` 17 | 18 | Alternatively: Clone the repository https://github.com/patonlab/pyQRC.git and add to your PYTHONPATH variable 19 | 20 | Then run the script as a python module with your Gaussian output files (the program expects log or out extensions) and can accept wildcard arguments. 21 | 22 | ### Usage 23 | 24 | ```python 25 | python -m pyqrc [--amp AMPLITUDE] [--nproc N] [--mem NGB] [--name APPEND] [--route 'B3LYP/6-31G*'] [-v] [--auto] [--freqnum INT] 26 | ``` 27 | 28 | * The `--amp` multiplies the imaginary normal mode vector by this amount. It defaults to 0.2. Increase for larger displacements, and change the sign for displacement in the reverse direction. 29 | * The `--nproc ` option selects the number of processors requested in the new input file. It defatuls to 1. 30 | * The `--mem` option specifies the memory requested in the new input file. It defatuls to 4GB. The correct format of input is XGB or X000MB where X can take any integer value. 31 | * The `--route` option specifies the route line for the new calculation to be performed. 32 | * The `--name` option is appended to the existing filename to create the new input file(s). This defaults to 'QRC'. 33 | * The `-v` option requests verbose output to be printed. 34 | * The `--auto` option will only process files with an imaginary frequency. Given any number of files it will ignore those that have no imaginary frequencies. 35 | * The `-f` or `--freq` option allows you to request motion along a particular frequency (in cm-1). 36 | * The `--freqnum` option allows you to request motion along a particular frequency (by number from the lowest). 37 | 38 | 39 | ### Dependencies 40 | * [Python](https://www.python.org/) >= v. 3.6 41 | * [cclib]([https://www.python.org/](https://cclib.github.io/)) 42 | * One of: 43 | * [ORCA](https://sites.google.com/site/orcainputlibrary/home/) > v. 4.0 44 | * [Gaussian09](https://gaussian.com/glossary/g09/) 45 | * [Gaussian16](https://gaussian.com/gaussian16/) 46 | * [QChem](https://www.q-chem.com/) > 5.4 47 | 48 | ### Example 1 49 | 50 | ```python 51 | python -m pyqrc acetaldehyde.log --nproc 4 --mem 8GB 52 | ``` 53 | 54 | This initial optimization inadvertently produced a transition structure. The code displaces along the normal mode and creates a new input file. A subsequent optimization then fixes the problem since the imaginary frequency disappears. Note that by default this displacement occurs along all imaginary modes - if there is more than one imaginary frequency, and displacement is only desired along one of these (e.g. the lowest) then the use of `--freqnum 1` is necessary. 55 | 56 | 57 | ### Example 2 58 | 59 | ```python 60 | python -m pyqrc claisen_ts.log --nproc 4 --mem 8GB --amp 0.3 --name QRCF 61 | python -m pyqrc claisen_ts.log --nproc 4 --mem 8GB --amp -0.3 --name QRCR 62 | ``` 63 | 64 | The initial optimization located a transition structure. The quick reaction coordinate (QRC) is obtained from two optmizations, started from twp points displaced along the reaction coordinate in either direction. 65 | 66 | 67 | ### Example 3 68 | 69 | ```python 70 | python -m pyqrc planar_chex.log --nproc 4 --freqnum 1 --name mode1 71 | python -m pyqrc planar_chex.log --nproc 4 --freqnum 3 --name mode3 72 | ``` 73 | 74 | In this example, the initial optimization located a (3rd order) saddle point - planar cyclohexane - with three imaginary frequencies. Two new inputs are created by displacing along (i) only the first (i.e., lowest) normal mode and (ii) only the third normal mode. This contrasts from the `auto` function of pyQRC which displaces along all imaginary modes. Subsequent optimizations of these new inputs results in different minima, producing (i) chair-shaped cyclohexane and (ii) twist-boat cyclohexane. This example illustrates that displacement along particular normal modes could be used for e.g. conformational sampling. 75 | 76 | 77 | ### References for the underlying theory 78 | 1. (a) Goodman, J. M.; Silva, M. A. *Tetrahedron Lett.* **2003**, *44*, 8233-8236 [**DOI:** 10.1016/j.tetlet.2003.09.074](http://dx.doi.org/10.1016/j.tetlet.2003.09.074); (b) Goodman, J. M.; Silva, M. A. *Tetrahedron Lett.* **2005**, *46*, 2067-2069 [**DOI:** 10.1016/j.tetlet.2005.01.142](http://dx.doi.org/10.1016/j.tetlet.2005.01.142) 79 | 80 | 81 | ### Contributors 82 | 83 | - Robert Paton ([@bobbypaton](https://github.com/bobbypaton)) 84 | - Guilian Luchini ([@luchini18](https://github.com/luchini18)) 85 | - Shree Sowndarya ([@shreesowndarya](https://github.com/shreesowndarya)) 86 | - Alister Goodfellow ([@aligfellow](https://github.com/aligfellow)) 87 | 88 | --- 89 | License: [MIT](https://opensource.org/licenses/MIT) 90 | -------------------------------------------------------------------------------- /SUPPORT.md: -------------------------------------------------------------------------------- 1 | # Getting Support 2 | 3 | pyQRC offers the following support channels: 4 | 5 | - For detailed questions (e.g., those requiring examples) send us an 6 | [email](mailto:patonlab@colostate.edu?subject=[pyQRC]) 7 | - To report issues, use this repository's 8 | [issue tracker](https://github.com/bobbypaton/pyQRC/issues/new) 9 | - You can also find us on [![Twitter][1.2]][1] 10 | 11 | When reporting an issue, please include the following details: 12 | 13 | - A narrative description of what you are trying to accomplish. 14 | - The minimum code necessary to reproduce the issue. 15 | - The expected results of exercising that code. 16 | - The actual results received. 17 | 18 | You may also submit a failing test case as a pull request. 19 | 20 | [1.2]: http://i.imgur.com/wWzX9uB.png (twitter icon without padding) 21 | [1]: https://twitter.com/bobbypaton 22 | -------------------------------------------------------------------------------- /pyQRC_banner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patonlab/pyQRC/5c738c8b132fe9f8892ff351e81112b93cfa901a/pyQRC_banner.png -------------------------------------------------------------------------------- /pyqrc/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patonlab/pyQRC/5c738c8b132fe9f8892ff351e81112b93cfa901a/pyqrc/__init__.py -------------------------------------------------------------------------------- /pyqrc/__main__.py: -------------------------------------------------------------------------------- 1 | # Copied from __main__.py in pip 2 | from __future__ import absolute_import 3 | 4 | import os 5 | import sys 6 | 7 | # If we are running from a wheel, add the wheel to sys.path 8 | # This allows the usage python pip-*.whl/pip install pip-*.whl 9 | 10 | if __package__ == '': 11 | path = os.path.dirname(os.path.dirname(__file__)) 12 | sys.path.insert(0, path) 13 | 14 | from pyqrc import pyQRC # noqa 15 | 16 | if __name__ == '__main__': 17 | sys.exit(pyQRC.main()) 18 | -------------------------------------------------------------------------------- /pyqrc/__pycache__/__init__.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patonlab/pyQRC/5c738c8b132fe9f8892ff351e81112b93cfa901a/pyqrc/__pycache__/__init__.cpython-37.pyc -------------------------------------------------------------------------------- /pyqrc/__pycache__/__main__.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patonlab/pyQRC/5c738c8b132fe9f8892ff351e81112b93cfa901a/pyqrc/__pycache__/__main__.cpython-37.pyc -------------------------------------------------------------------------------- /pyqrc/__pycache__/pyQRC.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patonlab/pyQRC/5c738c8b132fe9f8892ff351e81112b93cfa901a/pyqrc/__pycache__/pyQRC.cpython-37.pyc -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/acetaldehyde.com: -------------------------------------------------------------------------------- 1 | %chk=acetaldehyde.chk 2 | %nproc=4 3 | %mem=8GB 4 | #opt freq B3LYP/def2tzvp empiricaldispersion=GD3BJ 5 | 6 | acetaldehyde = [H]C(C)[D=O 7 | 8 | 0 1 9 | H 1.02598 0.12223 0.06942 10 | C 2.12749 0.06671 0.05614 11 | C 2.85038 1.34175 0.36112 12 | O 2.70357 -0.98671 -0.19583 13 | H 2.11900 2.13190 0.55012 14 | H 3.46686 1.62591 -0.49461 15 | H 3.46687 1.20794 1.25280 16 | 17 | -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/acetaldehyde_QRC.com: -------------------------------------------------------------------------------- 1 | 2 | %chk=acetaldehyde_QRC.chk 3 | %nproc=1 4 | %mem=4GB 5 | # opt freq B3LYP/def2tzvp empiricaldispersion=GD3BJ 6 | 7 | acetaldehyde_QRC 8 | 9 | 0 1 10 | H 0.33785000 1.51500900 -0.12297600 11 | C 0.23858600 0.40899400 -0.02701200 12 | C -1.16763100 -0.13495700 0.00900100 13 | O 1.22090300 -0.28556300 0.02100300 14 | H -1.91311300 0.65951400 0.15300400 15 | H -1.25183700 -0.89311600 0.80424400 16 | H -1.36585000 -0.64112400 -0.95423300 17 | 18 | -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/acetaldehyde_QRC.qrc: -------------------------------------------------------------------------------- 1 | 2 | pyQRC - a quick alternative to IRC calculations 3 | version: 2.0 / author: Robert Paton / email: robert.paton@colostate.edu 4 | Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069. 5 | 6 | -----ORIGINAL GEOMETRY------ 7 | X Y Z 8 | H 0.337850 1.515009 0.000024 9 | C 0.238586 0.408994 -0.000012 10 | C -1.167631 -0.134957 0.000001 11 | O 1.220903 -0.285563 0.000003 12 | H -1.913113 0.659514 0.000004 13 | H -1.308837 -0.767116 0.879244 14 | H -1.308850 -0.767124 -0.879233 15 | 16 | ----HARMONIC FREQUENCIES---- 17 | Freq Red mass F const 18 | -175.8807 1.1941 0.0218 19 | 513.0858 2.6929 0.4177 20 | 751.3821 1.1766 0.3914 21 | 929.7926 2.3136 1.1785 22 | 1098.3728 1.9654 1.3970 23 | 1136.2547 1.7190 1.3076 24 | 1374.0088 1.2059 1.3413 25 | 1428.3721 1.1977 1.4398 26 | 1467.0223 1.0637 1.3488 27 | 1475.3487 1.0469 1.3427 28 | 1808.1767 10.0298 19.3207 29 | 2874.8396 1.0827 5.2722 30 | 3038.8301 1.0347 5.6296 31 | 3101.7183 1.0994 6.2319 32 | 3125.7552 1.1037 6.3535 33 | 34 | -SHIFTING ALONG NORMAL MODE- 35 | -AMPLIFIER = 0.3 36 | X Y Z 37 | H 0.000000 0.000000 -0.410000 38 | C 0.000000 -0.000000 -0.090000 39 | C 0.000000 -0.000000 0.030000 40 | O -0.000000 0.000000 0.070000 41 | H 0.000000 0.000000 0.510000 42 | H 0.190000 -0.420000 -0.250000 43 | H -0.190000 0.420000 -0.250000 44 | 45 | STRUCTURE MOVED BY 1.395 Bohr amu^1/2 46 | -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/claisen_ts.com: -------------------------------------------------------------------------------- 1 | %chk=claisen_ts.chk 2 | %nprocshared=4 3 | %mem=8GB 4 | # opt(ts,calcfc,noeigentest) freq b3lyp/6-31g(d) 5 | 6 | transition structure 7 | 8 | 0 1 9 | C -1.46630900 0.78416700 -0.28998400 10 | C -1.29105700 -0.47205600 0.26183900 11 | O -0.51102600 -1.35845600 -0.25222100 12 | C 1.28557000 -0.90028400 0.18203400 13 | C 1.37470200 0.41270400 -0.30179600 14 | C 0.66867800 1.42529500 0.32223600 15 | H -2.14589700 1.49239700 0.17879400 16 | H -1.22540000 0.95368900 -1.33299400 17 | H -1.67666300 -0.64615200 1.28181200 18 | H 1.76639500 -1.71190500 -0.35332000 19 | H 1.17354000 -1.06949500 1.24881600 20 | H 1.69249600 0.55703400 -1.33267500 21 | H 0.62902600 2.42494500 -0.10169800 22 | H 0.44520400 1.36817500 1.38305600 23 | 24 | -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/claisen_ts_QRCF.com: -------------------------------------------------------------------------------- 1 | 2 | %chk=claisen_ts_QRCF.chk 3 | %nproc=1 4 | %mem=4GB 5 | # opt(ts,calcfc,noeigentest) freq b3lyp/6-31g(d) 6 | 7 | claisen_ts_QRCF 8 | 9 | 0 1 10 | C -1.36430900 0.83516800 -0.26898400 11 | C -1.29105700 -0.49305500 0.25883900 12 | O -0.61602600 -1.38245600 -0.26722100 13 | C 1.42657000 -0.86128400 0.20303400 14 | C 1.38070200 0.39770400 -0.30179600 15 | C 0.55767900 1.40129500 0.30423600 16 | H -2.04389600 1.54639800 0.19979400 17 | H -1.24640000 0.93868900 -1.35399400 18 | H -1.68566300 -0.62815100 1.29081200 19 | H 1.85339400 -1.69390600 -0.34732000 20 | H 1.16154000 -1.06649500 1.24581600 21 | H 1.68349600 0.55403400 -1.33567500 22 | H 0.55702700 2.40694500 -0.11069800 23 | H 0.45720500 1.38017500 1.39505600 24 | 25 | -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/claisen_ts_QRCF.qrc: -------------------------------------------------------------------------------- 1 | 2 | pyQRC - a quick alternative to IRC calculations 3 | version: 2.0 / author: Robert Paton / email: robert.paton@colostate.edu 4 | Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069. 5 | 6 | -----ORIGINAL GEOMETRY------ 7 | X Y Z 8 | C -1.466309 0.784168 -0.289984 9 | C -1.291057 -0.472055 0.261839 10 | O -0.511026 -1.358456 -0.252221 11 | C 1.285570 -0.900284 0.182034 12 | C 1.374702 0.412704 -0.301796 13 | C 0.668679 1.425295 0.322236 14 | H -2.145896 1.492398 0.178794 15 | H -1.225400 0.953689 -1.332994 16 | H -1.676663 -0.646151 1.281812 17 | H 1.766394 -1.711906 -0.353320 18 | H 1.173540 -1.069495 1.248816 19 | H 1.692496 0.557034 -1.332675 20 | H 0.629027 2.424945 -0.101698 21 | H 0.445205 1.368175 1.383056 22 | 23 | ----HARMONIC FREQUENCIES---- 24 | Freq Red mass F const 25 | -483.4122 8.9495 1.2322 26 | 169.3112 2.9041 0.0490 27 | 269.6219 6.5566 0.2808 28 | 311.1570 3.2449 0.1851 29 | 379.3617 2.2174 0.1880 30 | 427.0425 2.2786 0.2448 31 | 464.1935 1.9450 0.2469 32 | 530.3299 2.3236 0.3850 33 | 737.0433 1.3824 0.4425 34 | 808.2233 1.2281 0.4727 35 | 875.1398 1.1489 0.5184 36 | 897.8114 1.2509 0.5941 37 | 962.2433 1.0712 0.5844 38 | 995.2676 1.4079 0.8217 39 | 1001.6875 1.4378 0.8500 40 | 1010.8771 1.3077 0.7873 41 | 1037.5116 1.3673 0.8671 42 | 1057.4665 1.5371 1.0127 43 | 1091.2083 1.2098 0.8488 44 | 1267.4636 1.5916 1.5064 45 | 1277.3162 2.1980 2.1129 46 | 1302.3846 1.8160 1.8148 47 | 1359.0854 1.5928 1.7335 48 | 1449.9030 1.3296 1.6469 49 | 1490.1065 1.4090 1.8433 50 | 1550.8654 1.3756 1.9494 51 | 1565.3557 1.6940 2.4457 52 | 1638.5863 3.4295 5.4253 53 | 2991.3641 1.0848 5.7191 54 | 3166.8889 1.0608 6.2682 55 | 3168.7916 1.0698 6.3290 56 | 3173.2625 1.0662 6.3259 57 | 3176.5564 1.0696 6.3589 58 | 3251.6095 1.1165 6.9553 59 | 3261.6672 1.1162 6.9966 60 | 3264.3300 1.1147 6.9982 61 | 62 | -SHIFTING ALONG NORMAL MODE- 63 | -AMPLIFIER = 0.3 64 | X Y Z 65 | C 0.340000 0.170000 0.070000 66 | C -0.000000 -0.070000 -0.010000 67 | O -0.350000 -0.080000 -0.050000 68 | C 0.470000 0.130000 0.070000 69 | C 0.020000 -0.050000 -0.000000 70 | C -0.370000 -0.080000 -0.060000 71 | H 0.340000 0.180000 0.070000 72 | H -0.070000 -0.050000 -0.070000 73 | H -0.030000 0.060000 0.030000 74 | H 0.290000 0.060000 0.020000 75 | H -0.040000 0.010000 -0.010000 76 | H -0.030000 -0.010000 -0.010000 77 | H -0.240000 -0.060000 -0.030000 78 | H 0.040000 0.040000 0.040000 79 | 80 | STRUCTURE MOVED BY 1.701 Bohr amu^1/2 81 | -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/claisen_ts_QRCR.com: -------------------------------------------------------------------------------- 1 | 2 | %chk=claisen_ts_QRCR.chk 3 | %nproc=4 4 | %mem=8GB 5 | # opt freq b3lyp/6-31g(d) 6 | 7 | claisen_ts_QRCR 8 | 9 | 0 1 10 | C -1.56830900 0.73316800 -0.31098400 11 | C -1.29105700 -0.45105500 0.26483900 12 | O -0.40602600 -1.33445600 -0.23722100 13 | C 1.14457000 -0.93928400 0.16103400 14 | C 1.36870200 0.42770400 -0.30179600 15 | C 0.77967900 1.44929500 0.34023600 16 | H -2.24789600 1.43839800 0.15779400 17 | H -1.20440000 0.96868900 -1.31199400 18 | H -1.66766300 -0.66415100 1.27281200 19 | H 1.67939400 -1.72990600 -0.35932000 20 | H 1.18554000 -1.07249500 1.25181600 21 | H 1.70149600 0.56003400 -1.32967500 22 | H 0.70102700 2.44294500 -0.09269800 23 | H 0.43320500 1.35617500 1.37105600 24 | 25 | -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/claisen_ts_QRCR.qrc: -------------------------------------------------------------------------------- 1 | 2 | pyQRC - a quick alternative to IRC calculations 3 | version: 1.0.1 / author: Rob Paton / email: robert.paton@colostate.edu 4 | Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069. 5 | 6 | -----ORIGINAL GEOMETRY------ 7 | X Y Z 8 | C -1.466309 0.784168 -0.289984 9 | C -1.291057 -0.472055 0.261839 10 | O -0.511026 -1.358456 -0.252221 11 | C 1.285570 -0.900284 0.182034 12 | C 1.374702 0.412704 -0.301796 13 | C 0.668679 1.425295 0.322236 14 | H -2.145896 1.492398 0.178794 15 | H -1.225400 0.953689 -1.332994 16 | H -1.676663 -0.646151 1.281812 17 | H 1.766394 -1.711906 -0.353320 18 | H 1.173540 -1.069495 1.248816 19 | H 1.692496 0.557034 -1.332675 20 | H 0.629027 2.424945 -0.101698 21 | H 0.445205 1.368175 1.383056 22 | 23 | ----HARMONIC FREQUENCIES---- 24 | Freq Red mass F const 25 | -483.4122 8.9495 1.2322 26 | 169.3112 2.9041 0.0490 27 | 269.6219 6.5566 0.2808 28 | 311.1570 3.2449 0.1851 29 | 379.3617 2.2174 0.1880 30 | 427.0425 2.2786 0.2448 31 | 464.1935 1.9450 0.2469 32 | 530.3299 2.3236 0.3850 33 | 737.0433 1.3824 0.4425 34 | 808.2233 1.2281 0.4727 35 | 875.1398 1.1489 0.5184 36 | 897.8114 1.2509 0.5941 37 | 962.2433 1.0712 0.5844 38 | 995.2676 1.4079 0.8217 39 | 1001.6875 1.4378 0.8500 40 | 1010.8771 1.3077 0.7873 41 | 1037.5116 1.3673 0.8671 42 | 1057.4665 1.5371 1.0127 43 | 1091.2083 1.2098 0.8488 44 | 1267.4636 1.5916 1.5064 45 | 1277.3162 2.1980 2.1129 46 | 1302.3846 1.8160 1.8148 47 | 1359.0854 1.5928 1.7335 48 | 1449.9030 1.3296 1.6469 49 | 1490.1065 1.4090 1.8433 50 | 1550.8654 1.3756 1.9494 51 | 1565.3557 1.6940 2.4457 52 | 1638.5863 3.4295 5.4253 53 | 2991.3641 1.0848 5.7191 54 | 3166.8889 1.0608 6.2682 55 | 3168.7916 1.0698 6.3290 56 | 3173.2625 1.0662 6.3259 57 | 3176.5564 1.0696 6.3589 58 | 3251.6095 1.1165 6.9553 59 | 3261.6672 1.1162 6.9966 60 | 3264.3300 1.1147 6.9982 61 | 62 | -SHIFTING ALONG NORMAL MODE- 63 | -AMPLIFIER = -0.3 64 | X Y Z 65 | C 0.340000 0.170000 0.070000 66 | C -0.000000 -0.070000 -0.010000 67 | O -0.350000 -0.080000 -0.050000 68 | C 0.470000 0.130000 0.070000 69 | C 0.020000 -0.050000 -0.000000 70 | C -0.370000 -0.080000 -0.060000 71 | H 0.340000 0.180000 0.070000 72 | H -0.070000 -0.050000 -0.070000 73 | H -0.030000 0.060000 0.030000 74 | H 0.290000 0.060000 0.020000 75 | H -0.040000 0.010000 -0.010000 76 | H -0.030000 -0.010000 -0.010000 77 | H -0.240000 -0.060000 -0.030000 78 | H 0.040000 0.040000 0.040000 -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/planar_chex_mode1.com: -------------------------------------------------------------------------------- 1 | 2 | %chk=planar_chex_mode1.chk 3 | %nproc=4 4 | %mem=4GB 5 | # symm=loose opt b3lyp/6-31G* freq 6 | 7 | planar_chex_mode1 8 | 9 | 0 1 10 | C 0.16785800 1.54628900 0.02756000 11 | C 1.42312500 0.62775100 -0.02526900 12 | C 1.25523200 -0.91851600 0.02656700 13 | C -0.16787900 -1.54628900 -0.02752600 14 | C -1.42311900 -0.62776900 0.02661000 15 | C -1.25521700 0.91853300 -0.02794300 16 | H 0.23306600 2.15643200 0.93474800 17 | H 1.98786500 0.87744800 -0.93097700 18 | H 1.83606300 -1.34190800 -0.80323100 19 | H -0.23387700 -2.15639500 -0.93467500 20 | H -2.08265200 -0.91869700 -0.80219100 21 | H -1.83746700 1.34341500 0.80029500 22 | H -1.75141400 1.28270400 -0.93578000 23 | H -1.98623800 -0.87625100 0.93384200 24 | H 0.24677200 2.26467500 -0.80130100 25 | H 2.08101200 0.91752000 0.80505100 26 | H 1.75280800 -1.28422500 0.93284500 27 | H -0.24593800 -2.26471400 0.80137600 28 | 29 | -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/planar_chex_mode1.qrc: -------------------------------------------------------------------------------- 1 | 2 | pyQRC - a quick alternative to IRC calculations 3 | version: 1.0 / author: Rob Paton / email: robert.paton@colostate.edu 4 | Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069. 5 | 6 | -----ORIGINAL GEOMETRY------ 7 | X Y Z 8 | C 0.167858 1.546289 0.000560 9 | C 1.423125 0.627751 0.001731 10 | C 1.255232 -0.918516 -0.000433 11 | C -0.167879 -1.546289 -0.000526 12 | C -1.423119 -0.627769 -0.000390 13 | C -1.255217 0.918533 -0.000943 14 | H 0.239066 2.210432 0.868748 15 | H 2.035865 0.898448 -0.864977 16 | H 1.794063 -1.311908 -0.869231 17 | H -0.239877 -2.210395 -0.868675 18 | H -2.034652 -0.897697 -0.868191 19 | H -1.795467 1.313415 0.866295 20 | H -1.793414 1.312704 -0.869780 21 | H -2.034238 -0.897251 0.867842 22 | H 0.240772 2.210675 -0.867301 23 | H 2.033012 0.896520 0.871051 24 | H 1.794808 -1.314225 0.866845 25 | H -0.239938 -2.210714 0.867376 26 | 27 | ----HARMONIC FREQUENCIES---- 28 | Freq Red mass F const 29 | -347.7647 1.4852 0.1058 30 | -243.5383 1.6265 0.0568 31 | -243.1500 1.6267 0.0567 32 | 480.4020 5.5814 0.7589 33 | 480.5318 5.5813 0.7593 34 | 718.5307 1.0543 0.3207 35 | 737.5801 4.9110 1.5741 36 | 749.0044 1.1642 0.3848 37 | 749.4799 1.1642 0.3853 38 | 852.6468 5.3095 2.2743 39 | 870.5836 3.0557 1.3645 40 | 871.1743 3.0523 1.3649 41 | 957.5711 1.4925 0.8063 42 | 957.7726 1.4925 0.8067 43 | 1130.8020 3.1130 2.3453 44 | 1131.1730 3.1088 2.3437 45 | 1132.4624 2.0383 1.5401 46 | 1143.7208 11.9396 9.2020 47 | 1260.9902 1.0078 0.9442 48 | 1320.8683 1.0080 1.0361 49 | 1323.3735 1.1482 1.1847 50 | 1323.5168 1.1479 1.1847 51 | 1337.0381 1.0731 1.1302 52 | 1337.1379 1.0731 1.1304 53 | 1343.6147 1.0084 1.0725 54 | 1379.1413 1.3159 1.4746 55 | 1395.3979 1.3041 1.4961 56 | 1395.5746 1.3046 1.4971 57 | 1420.3225 1.3610 1.6176 58 | 1420.4127 1.3614 1.6183 59 | 1517.3686 1.0664 1.4465 60 | 1528.1130 1.0713 1.4739 61 | 1528.2168 1.0713 1.4741 62 | 1551.5497 1.0813 1.5337 63 | 1551.8161 1.0812 1.5341 64 | 1570.2196 1.0835 1.5740 65 | 3034.2067 1.0619 5.7601 66 | 3042.0933 1.0608 5.7842 67 | 3042.1493 1.0608 5.7844 68 | 3047.1106 1.1063 6.0522 69 | 3059.7523 1.0611 5.8531 70 | 3059.7790 1.0611 5.8532 71 | 3062.1615 1.1059 6.1098 72 | 3062.2294 1.1059 6.1100 73 | 3073.1306 1.0624 5.9118 74 | 3092.1750 1.1053 6.2266 75 | 3092.2214 1.1053 6.2269 76 | 3109.7927 1.1047 6.2943 77 | 78 | -SHIFTING ALONG NORMAL MODE- 79 | -AMPLIFIER = 0.3 80 | X Y Z 81 | C -0.000000 0.000000 0.090000 82 | C 0.000000 0.000000 -0.090000 83 | C 0.000000 -0.000000 0.090000 84 | C -0.000000 0.000000 -0.090000 85 | C -0.000000 0.000000 0.090000 86 | C 0.000000 -0.000000 -0.090000 87 | H -0.020000 -0.180000 0.220000 88 | H -0.160000 -0.070000 -0.220000 89 | H 0.140000 -0.100000 0.220000 90 | H 0.020000 0.180000 -0.220000 91 | H -0.160000 -0.070000 0.220000 92 | H -0.140000 0.100000 -0.220000 93 | H 0.140000 -0.100000 -0.220000 94 | H 0.160000 0.070000 0.220000 95 | H 0.020000 0.180000 0.220000 96 | H 0.160000 0.070000 -0.220000 97 | H -0.140000 0.100000 0.220000 98 | H -0.020000 -0.180000 -0.220000 -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/planar_chex_mode3.com: -------------------------------------------------------------------------------- 1 | 2 | %chk=planar_chex_mode3.chk 3 | %nproc=4 4 | %mem=4GB 5 | # symm=loose opt b3lyp/6-31G* freq 6 | 7 | planar_chex_mode3 8 | 9 | 0 1 10 | C 0.16785800 1.54628900 0.03956000 11 | C 1.42312500 0.62775100 -0.02826900 12 | C 1.25523200 -0.91851600 -0.00943300 13 | C -0.16787900 -1.54628900 0.03847400 14 | C -1.42311900 -0.62776900 -0.03039000 15 | C -1.25521700 0.91853300 -0.00994300 16 | H 0.23606600 2.14443200 0.95874800 17 | H 1.98486500 0.88944800 -0.93697700 18 | H 1.77306300 -1.31790800 -0.88723100 19 | H -0.24287700 -2.27639500 -0.77867500 20 | H -1.98365200 -0.88869700 -0.94019100 21 | H -1.81646700 1.30741500 0.84829500 22 | H -1.77241400 1.31870400 -0.88778000 23 | H -2.08523800 -0.90625100 0.79584200 24 | H 0.24077200 2.27667500 -0.77730100 25 | H 2.08701200 0.90552000 0.79905100 26 | H 1.81580800 -1.30822500 0.84884500 27 | H -0.23693800 -2.14471400 0.95737600 28 | 29 | -------------------------------------------------------------------------------- /pyqrc/examples/Gaussian/planar_chex_mode3.qrc: -------------------------------------------------------------------------------- 1 | 2 | pyQRC - a quick alternative to IRC calculations 3 | version: 1.0 / author: Rob Paton / email: robert.paton@colostate.edu 4 | Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069. 5 | 6 | -----ORIGINAL GEOMETRY------ 7 | X Y Z 8 | C 0.167858 1.546289 0.000560 9 | C 1.423125 0.627751 0.001731 10 | C 1.255232 -0.918516 -0.000433 11 | C -0.167879 -1.546289 -0.000526 12 | C -1.423119 -0.627769 -0.000390 13 | C -1.255217 0.918533 -0.000943 14 | H 0.239066 2.210432 0.868748 15 | H 2.035865 0.898448 -0.864977 16 | H 1.794063 -1.311908 -0.869231 17 | H -0.239877 -2.210395 -0.868675 18 | H -2.034652 -0.897697 -0.868191 19 | H -1.795467 1.313415 0.866295 20 | H -1.793414 1.312704 -0.869780 21 | H -2.034238 -0.897251 0.867842 22 | H 0.240772 2.210675 -0.867301 23 | H 2.033012 0.896520 0.871051 24 | H 1.794808 -1.314225 0.866845 25 | H -0.239938 -2.210714 0.867376 26 | 27 | ----HARMONIC FREQUENCIES---- 28 | Freq Red mass F const 29 | -347.7647 1.4852 0.1058 30 | -243.5383 1.6265 0.0568 31 | -243.1500 1.6267 0.0567 32 | 480.4020 5.5814 0.7589 33 | 480.5318 5.5813 0.7593 34 | 718.5307 1.0543 0.3207 35 | 737.5801 4.9110 1.5741 36 | 749.0044 1.1642 0.3848 37 | 749.4799 1.1642 0.3853 38 | 852.6468 5.3095 2.2743 39 | 870.5836 3.0557 1.3645 40 | 871.1743 3.0523 1.3649 41 | 957.5711 1.4925 0.8063 42 | 957.7726 1.4925 0.8067 43 | 1130.8020 3.1130 2.3453 44 | 1131.1730 3.1088 2.3437 45 | 1132.4624 2.0383 1.5401 46 | 1143.7208 11.9396 9.2020 47 | 1260.9902 1.0078 0.9442 48 | 1320.8683 1.0080 1.0361 49 | 1323.3735 1.1482 1.1847 50 | 1323.5168 1.1479 1.1847 51 | 1337.0381 1.0731 1.1302 52 | 1337.1379 1.0731 1.1304 53 | 1343.6147 1.0084 1.0725 54 | 1379.1413 1.3159 1.4746 55 | 1395.3979 1.3041 1.4961 56 | 1395.5746 1.3046 1.4971 57 | 1420.3225 1.3610 1.6176 58 | 1420.4127 1.3614 1.6183 59 | 1517.3686 1.0664 1.4465 60 | 1528.1130 1.0713 1.4739 61 | 1528.2168 1.0713 1.4741 62 | 1551.5497 1.0813 1.5337 63 | 1551.8161 1.0812 1.5341 64 | 1570.2196 1.0835 1.5740 65 | 3034.2067 1.0619 5.7601 66 | 3042.0933 1.0608 5.7842 67 | 3042.1493 1.0608 5.7844 68 | 3047.1106 1.1063 6.0522 69 | 3059.7523 1.0611 5.8531 70 | 3059.7790 1.0611 5.8532 71 | 3062.1615 1.1059 6.1098 72 | 3062.2294 1.1059 6.1100 73 | 3073.1306 1.0624 5.9118 74 | 3092.1750 1.1053 6.2266 75 | 3092.2214 1.1053 6.2269 76 | 3109.7927 1.1047 6.2943 77 | 78 | -SHIFTING ALONG NORMAL MODE- 79 | -AMPLIFIER = 0.3 80 | X Y Z 81 | C -0.000000 -0.000000 0.130000 82 | C 0.000000 0.000000 -0.100000 83 | C -0.000000 -0.000000 -0.030000 84 | C -0.000000 -0.000000 0.130000 85 | C -0.000000 -0.000000 -0.100000 86 | C 0.000000 0.000000 -0.030000 87 | H -0.010000 -0.220000 0.300000 88 | H -0.170000 -0.030000 -0.240000 89 | H -0.070000 -0.020000 -0.060000 90 | H -0.010000 -0.220000 0.300000 91 | H 0.170000 0.030000 -0.240000 92 | H -0.070000 -0.020000 -0.060000 93 | H 0.070000 0.020000 -0.060000 94 | H -0.170000 -0.030000 -0.240000 95 | H 0.000000 0.220000 0.300000 96 | H 0.180000 0.030000 -0.240000 97 | H 0.070000 0.020000 -0.060000 98 | H 0.010000 0.220000 0.300000 -------------------------------------------------------------------------------- /pyqrc/examples/Orca/acetaldehyde_QRC.inp: -------------------------------------------------------------------------------- 1 | 2 | ! pal8 B3LYP def2-tzvp D3BJ Opt Freq 3 | 4 | # acetaldehyde_QRC 5 | 6 | * xyz 0 1 7 | H 0.33790250 1.51535410 -0.12376920 8 | C 0.23874870 0.40902130 -0.02782630 9 | C -1.16778430 -0.13504270 0.00820120 10 | O 1.22128130 -0.28562010 0.02235700 11 | H -1.91317700 0.65972730 0.15322360 12 | H -1.25080050 -0.89343340 0.80434940 13 | H -1.36725980 -0.64125450 -0.95454620 14 | * -------------------------------------------------------------------------------- /pyqrc/examples/Orca/acetaldehyde_QRC.qrc: -------------------------------------------------------------------------------- 1 | 2 | pyQRC - a quick alternative to IRC calculations 3 | version: 2.0 / author: Robert Paton / email: robert.paton@colostate.edu 4 | Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069. 5 | 6 | -----ORIGINAL GEOMETRY------ 7 | X Y Z 8 | H 0.337904 1.515355 -0.000012 9 | C 0.238749 0.409018 0.000056 10 | C -1.167784 -0.135043 0.000013 11 | O 1.221281 -0.285618 -0.000035 12 | H -1.913168 0.659733 0.000001 13 | H -1.309059 -0.767350 0.879452 14 | H -1.309016 -0.767337 -0.879443 15 | 16 | ----HARMONIC FREQUENCIES---- 17 | Freq Red mass F const 18 | -175.6900 0.0000 0.0000 19 | 512.7600 0.0000 0.0000 20 | 750.6800 0.0000 0.0000 21 | 928.9400 0.0000 0.0000 22 | 1097.6900 0.0000 0.0000 23 | 1135.7600 0.0000 0.0000 24 | 1373.3700 0.0000 0.0000 25 | 1427.4900 0.0000 0.0000 26 | 1466.3000 0.0000 0.0000 27 | 1474.7000 0.0000 0.0000 28 | 1806.5800 0.0000 0.0000 29 | 2870.4400 0.0000 0.0000 30 | 3036.1800 0.0000 0.0000 31 | 3098.5500 0.0000 0.0000 32 | 3123.3300 0.0000 0.0000 33 | 34 | -SHIFTING ALONG NORMAL MODE- 35 | -AMPLIFIER = 0.3 36 | X Y Z 37 | H -0.000005 -0.000003 -0.412524 38 | C -0.000001 0.000011 -0.092941 39 | C -0.000001 0.000001 0.027294 40 | O 0.000001 -0.000007 0.074640 41 | H -0.000030 -0.000019 0.510742 42 | H 0.194195 -0.420278 -0.250342 43 | H -0.194146 0.420275 -0.250344 44 | 45 | STRUCTURE MOVED BY 1.407 Bohr amu^1/2 46 | -------------------------------------------------------------------------------- /pyqrc/examples/Orca/claisen_ts_QRCF.inp: -------------------------------------------------------------------------------- 1 | 2 | ! pal8 opt freq b3lyp 6-31G(d) 3 | 4 | # claisen_ts_QRCF 5 | 6 | * xyz 0 1 7 | C -1.56584310 0.73334610 -0.31113370 8 | C -1.29059370 -0.45088390 0.26549730 9 | O -0.40659150 -1.33514620 -0.23288450 10 | C 1.14611610 -0.93967340 0.16020250 11 | C 1.36978850 0.42933060 -0.30232580 12 | C 0.77988430 1.45082070 0.34221670 13 | H -2.24695090 1.43954550 0.15583870 14 | H -1.20223800 0.96828930 -1.31375980 15 | H -1.67192470 -0.66439710 1.27264540 16 | H 1.67997550 -1.73129690 -0.36178140 17 | H 1.18966540 -1.07168970 1.25225580 18 | H 1.69900280 0.56097630 -1.33142000 19 | H 0.69730660 2.44465560 -0.09116450 20 | H 0.43415730 1.35409650 1.37393050 21 | * -------------------------------------------------------------------------------- /pyqrc/examples/Orca/claisen_ts_QRCF.qrc: -------------------------------------------------------------------------------- 1 | 2 | pyQRC - a quick alternative to IRC calculations 3 | version: 2.0 / author: Robert Paton / email: robert.paton@colostate.edu 4 | Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069. 5 | 6 | -----ORIGINAL GEOMETRY------ 7 | X Y Z 8 | C -1.464657 0.784530 -0.290326 9 | C -1.291941 -0.472408 0.262803 10 | O -0.510690 -1.359778 -0.248159 11 | C 1.285752 -0.900638 0.181144 12 | C 1.374668 0.413094 -0.302531 13 | C 0.667510 1.425318 0.322732 14 | H -2.145217 1.493481 0.176599 15 | H -1.223070 0.952659 -1.333684 16 | H -1.680343 -0.645069 1.282279 17 | H 1.766104 -1.712135 -0.355410 18 | H 1.176850 -1.069848 1.248513 19 | H 1.691081 0.557970 -1.334006 20 | H 0.627301 2.425611 -0.100310 21 | H 0.445911 1.367271 1.384255 22 | 23 | ----HARMONIC FREQUENCIES---- 24 | Freq Red mass F const 25 | -484.3000 0.0000 0.0000 26 | 169.3400 0.0000 0.0000 27 | 269.7300 0.0000 0.0000 28 | 311.6000 0.0000 0.0000 29 | 379.4100 0.0000 0.0000 30 | 426.8700 0.0000 0.0000 31 | 464.4000 0.0000 0.0000 32 | 529.8300 0.0000 0.0000 33 | 737.7100 0.0000 0.0000 34 | 808.2800 0.0000 0.0000 35 | 875.6800 0.0000 0.0000 36 | 898.1600 0.0000 0.0000 37 | 962.5900 0.0000 0.0000 38 | 995.4900 0.0000 0.0000 39 | 1001.9600 0.0000 0.0000 40 | 1011.6900 0.0000 0.0000 41 | 1037.4000 0.0000 0.0000 42 | 1057.2100 0.0000 0.0000 43 | 1091.1200 0.0000 0.0000 44 | 1266.3300 0.0000 0.0000 45 | 1276.0600 0.0000 0.0000 46 | 1301.4300 0.0000 0.0000 47 | 1357.9600 0.0000 0.0000 48 | 1449.5900 0.0000 0.0000 49 | 1490.4900 0.0000 0.0000 50 | 1550.4000 0.0000 0.0000 51 | 1564.2100 0.0000 0.0000 52 | 1637.0700 0.0000 0.0000 53 | 2990.5800 0.0000 0.0000 54 | 3165.5500 0.0000 0.0000 55 | 3167.8000 0.0000 0.0000 56 | 3172.1300 0.0000 0.0000 57 | 3175.3300 0.0000 0.0000 58 | 3250.0500 0.0000 0.0000 59 | 3260.0500 0.0000 0.0000 60 | 3262.8800 0.0000 0.0000 61 | 62 | -SHIFTING ALONG NORMAL MODE- 63 | -AMPLIFIER = 0.3 64 | X Y Z 65 | C -0.337287 -0.170613 -0.069359 66 | C 0.004491 0.071747 0.008981 67 | O 0.346995 0.082106 0.050915 68 | C -0.465453 -0.130118 -0.069805 69 | C -0.016265 0.054122 0.000684 70 | C 0.374581 0.085009 0.064949 71 | H -0.339113 -0.179785 -0.069201 72 | H 0.069440 0.052101 0.066414 73 | H 0.028061 -0.064427 -0.032112 74 | H -0.287095 -0.063873 -0.021238 75 | H 0.042718 -0.006139 0.012476 76 | H 0.026406 0.010021 0.008620 77 | H 0.233352 0.063482 0.030485 78 | H -0.039179 -0.043915 -0.034415 79 | 80 | STRUCTURE MOVED BY 3.222 Bohr amu^1/2 -------------------------------------------------------------------------------- /pyqrc/examples/Orca/claisen_ts_QRCR.inp: -------------------------------------------------------------------------------- 1 | 2 | ! pal8 opt freq b3lyp 6-31G(d) 3 | 4 | # claisen_ts_QRCR 5 | 6 | * xyz 0 1 7 | C -1.36347090 0.83571390 -0.26951830 8 | C -1.29328830 -0.49393210 0.26010870 9 | O -0.61478850 -1.38440980 -0.26343350 10 | C 1.42538790 -0.86160260 0.20208550 11 | C 1.37954750 0.39685740 -0.30273620 12 | C 0.55513570 1.39981530 0.30324730 13 | H -2.04348310 1.54741650 0.19735930 14 | H -1.24390200 0.93702870 -1.35360820 15 | H -1.68876130 -0.62574090 1.29191260 16 | H 1.85223250 -1.69297310 -0.34903860 17 | H 1.16403460 -1.06800630 1.24477020 18 | H 1.68315920 0.55496370 -1.33659200 19 | H 0.55729540 2.40656640 -0.10945550 20 | H 0.45766470 1.38044550 1.39457950 21 | * -------------------------------------------------------------------------------- /pyqrc/examples/Orca/claisen_ts_QRCR.qrc: -------------------------------------------------------------------------------- 1 | 2 | pyQRC - a quick alternative to IRC calculations 3 | version: 2.0 / author: Robert Paton / email: robert.paton@colostate.edu 4 | Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069. 5 | 6 | -----ORIGINAL GEOMETRY------ 7 | X Y Z 8 | C -1.464657 0.784530 -0.290326 9 | C -1.291941 -0.472408 0.262803 10 | O -0.510690 -1.359778 -0.248159 11 | C 1.285752 -0.900638 0.181144 12 | C 1.374668 0.413094 -0.302531 13 | C 0.667510 1.425318 0.322732 14 | H -2.145217 1.493481 0.176599 15 | H -1.223070 0.952659 -1.333684 16 | H -1.680343 -0.645069 1.282279 17 | H 1.766104 -1.712135 -0.355410 18 | H 1.176850 -1.069848 1.248513 19 | H 1.691081 0.557970 -1.334006 20 | H 0.627301 2.425611 -0.100310 21 | H 0.445911 1.367271 1.384255 22 | 23 | ----HARMONIC FREQUENCIES---- 24 | Freq Red mass F const 25 | -484.3000 0.0000 0.0000 26 | 169.3400 0.0000 0.0000 27 | 269.7300 0.0000 0.0000 28 | 311.6000 0.0000 0.0000 29 | 379.4100 0.0000 0.0000 30 | 426.8700 0.0000 0.0000 31 | 464.4000 0.0000 0.0000 32 | 529.8300 0.0000 0.0000 33 | 737.7100 0.0000 0.0000 34 | 808.2800 0.0000 0.0000 35 | 875.6800 0.0000 0.0000 36 | 898.1600 0.0000 0.0000 37 | 962.5900 0.0000 0.0000 38 | 995.4900 0.0000 0.0000 39 | 1001.9600 0.0000 0.0000 40 | 1011.6900 0.0000 0.0000 41 | 1037.4000 0.0000 0.0000 42 | 1057.2100 0.0000 0.0000 43 | 1091.1200 0.0000 0.0000 44 | 1266.3300 0.0000 0.0000 45 | 1276.0600 0.0000 0.0000 46 | 1301.4300 0.0000 0.0000 47 | 1357.9600 0.0000 0.0000 48 | 1449.5900 0.0000 0.0000 49 | 1490.4900 0.0000 0.0000 50 | 1550.4000 0.0000 0.0000 51 | 1564.2100 0.0000 0.0000 52 | 1637.0700 0.0000 0.0000 53 | 2990.5800 0.0000 0.0000 54 | 3165.5500 0.0000 0.0000 55 | 3167.8000 0.0000 0.0000 56 | 3172.1300 0.0000 0.0000 57 | 3175.3300 0.0000 0.0000 58 | 3250.0500 0.0000 0.0000 59 | 3260.0500 0.0000 0.0000 60 | 3262.8800 0.0000 0.0000 61 | 62 | -SHIFTING ALONG NORMAL MODE- 63 | -AMPLIFIER = -0.3 64 | X Y Z 65 | C -0.337287 -0.170613 -0.069359 66 | C 0.004491 0.071747 0.008981 67 | O 0.346995 0.082106 0.050915 68 | C -0.465453 -0.130118 -0.069805 69 | C -0.016265 0.054122 0.000684 70 | C 0.374581 0.085009 0.064949 71 | H -0.339113 -0.179785 -0.069201 72 | H 0.069440 0.052101 0.066414 73 | H 0.028061 -0.064427 -0.032112 74 | H -0.287095 -0.063873 -0.021238 75 | H 0.042718 -0.006139 0.012476 76 | H 0.026406 0.010021 0.008620 77 | H 0.233352 0.063482 0.030485 78 | H -0.039179 -0.043915 -0.034415 79 | 80 | STRUCTURE MOVED BY 3.222 Bohr amu^1/2 81 | -------------------------------------------------------------------------------- /pyqrc/examples/QChem/acetaldehyde.inp: -------------------------------------------------------------------------------- 1 | $molecule 2 | 0 1 3 | H 1.02598 0.12223 0.06942 4 | C 2.12749 0.06671 0.05614 5 | C 2.85038 1.34175 0.36112 6 | O 2.70357 -0.98671 -0.19583 7 | H 2.11900 2.13190 0.55012 8 | H 3.46686 1.62591 -0.49461 9 | H 3.46687 1.20794 1.25280 10 | $end 11 | 12 | $rem 13 | JOBTYPE opt 14 | METHOD b3lyp 15 | BASIS def2tzvp 16 | $end 17 | 18 | @@@ 19 | 20 | $molecule 21 | read 22 | $end 23 | 24 | $rem 25 | JOBTYPE freq 26 | METHOD b3lyp 27 | BASIS def2tzvp 28 | $end 29 | -------------------------------------------------------------------------------- /pyqrc/examples/QChem/acetaldehyde.out: -------------------------------------------------------------------------------- 1 | You are running Q-Chem version: 5.4.0 2 | 3 | # 4 | # job setting 5 | # 6 | local host: dynamo.chem.colostate.edu 7 | current dir: /home/rpaton 8 | input file: acetaldehyde.inp 9 | output file: 10 | nprocs : 0 11 | nthreads : 24 12 | # 13 | # qchem installation setting 14 | # 15 | QC: /usr/local/qchem 16 | QCAUX: /usr/local/qchem/qcaux 17 | QCPROG: /usr/local/qchem/exe/qcprog.exe_s 18 | QCPROG_S: /usr/local/qchem/exe/qcprog.exe_s 19 | PARALLEL: -DSERIAL 20 | QCMPI: seq 21 | # 22 | # qchem directory setting 23 | # 24 | qcrun: qchem3962149 25 | QCSCRATCH: /scratch 26 | QCLOCALSCR: 27 | QCTMPDIR: /scratch 28 | QCFILEPREF: /scratch/qchem3962149 29 | QCSAVEDIR: 30 | workdirs: /scratch/qchem3962149 31 | workdir0: /scratch/qchem3962149 32 | partmpdirs = 33 | # 34 | # parallel setting 35 | # 36 | QCRSH: ssh 37 | QCMPI: seq 38 | QCMPIRUN: 39 | QCMACHINEFILE: /usr/local/qchem/bin/mpi/machines 40 | 41 | # 42 | # env setting 43 | # 44 | exported envs: QC QCAUX QCSCRATCH QCRUNNAME QCFILEPREF QCPROG QCPROG_S GUIFILE 45 | 46 | Running Job 1 of 2 acetaldehyde.inp 47 | qchem acetaldehyde.inp_3962149.0 /scratch/qchem3962149/ 0 48 | /usr/local/qchem/exe/qcprog.exe_s acetaldehyde.inp_3962149.0 /scratch/qchem3962149/ 49 | Welcome to Q-Chem 50 | A Quantum Leap Into The Future Of Chemistry 51 | 52 | 53 | Q-Chem 5.4, Q-Chem, Inc., Pleasanton, CA (2021) 54 | 55 | E. Epifanovsky, A. T. B. Gilbert, Xintian Feng, Joonho Lee, Yuezhi Mao, 56 | N. Mardirossian, P. Pokhilko, A. White, M. Wormit, M. P. Coons, 57 | A. L. Dempwolff, Zhengting Gan, D. Hait, P. R. Horn, L. D. Jacobson, 58 | I. Kaliman, J. Kussmann, A. W. Lange, Ka Un Lao, D. S. Levine, Jie Liu, 59 | S. C. McKenzie, A. F. Morrison, K. Nanda, F. Plasser, D. R. Rehn, 60 | M. L. Vidal, Zhi-Qiang You, Ying Zhu, B. Alam, B. Albrecht, 61 | A. Aldossary, E. Alguire, J. H. Andersen, D. Barton, K. Begam, A. Behn, 62 | Y. A. Bernard, E. J. Berquist, H. Burton, A. Carreras, K. Carter-Fenk, 63 | R. Chakraborty, A. D. Chien, K. D. Closser, V. Cofer-Shabica, 64 | S. Dasgupta, Jia Deng, M. de Wergifosse, M. Diedenhofen, Hainam Do, 65 | S. Ehlert, Po-Tung Fang, S. Fatehi, Qingguo Feng, J. Gayvert, 66 | Qinghui Ge, G. Gidofalvi, M. Goldey, J. Gomes, C. Gonzalez-Espinoza, 67 | S. Gulania, A. Gunina, M. W. D. Hanson-Heine, P. H. P. Harbach, 68 | A. W. Hauser, M. F. Herbst, M. Hernandez Vera, M. Hodecker, 69 | Z. C. Holden, S. Houck, Xunkun Huang, Kerwin Hui, B. C. Huynh, 70 | M. Ivanov, Hyunjun Ji, Hanjie Jiang, B. Kaduk, S. Kaehler, 71 | K. Khistyaev, Jaehoon Kim, P. Klunzinger, Z. Koczor-Benda, 72 | Joong Hoon Koh, D. Kosenkov, L. Koulias, T. Kowalczyk, C. M. Krauter, 73 | K. Kue, A. Kunitsa, T. Kus, A. Landau, K. V. Lawler, D. Lefrancois, 74 | S. Lehtola, Rain Li, Yi-Pei Li, Jiashu Liang, M. Liebenthal, 75 | Hung-Hsuan Lin, You-Sheng Lin, Fenglai Liu, Kuan-Yu Liu, 76 | M. Loipersberger, A. Luenser, A. Manjanath, P. Manohar, E. Mansoor, 77 | S. F. Manzer, Shan-Ping Mao, A. V. Marenich, T. Markovich, S. Mason, 78 | S. A. Maurer, P. F. McLaughlin, M. F. S. J. Menger, J.-M. Mewes, 79 | S. A. Mewes, P. Morgante, J. W. Mullinax, T. S. Nguyen-Beck, 80 | K. J. Oosterbaan, G. Paran, Alexander C. Paul, Suranjan K. Paul, 81 | F. Pavosevic, Zheng Pei, S. Prager, E. I. Proynov, E. Ramos, B. Rana, 82 | A. E. Rask, A. Rettig, R. M. Richard, F. Rob, E. Rossomme, T. Scheele, 83 | M. Scheurer, M. Schneider, N. Sergueev, S. M. Sharada, W. Skomorowski, 84 | D. W. Small, C. J. Stein, Yu-Chuan Su, E. J. Sundstrom, Zhen Tao, 85 | J. Thirman, T. Tsuchimochi, N. M. Tubman, S. P. Veccham, O. Vydrov, 86 | J. Wenzel, J. Witte, A. Yamada, Kun Yao, S. Yeganeh, S. R. Yost, 87 | A. Zech, Igor Ying Zhang, Xing Zhang, Yu Zhang, D. Zuev, 88 | A. Aspuru-Guzik, A. T. Bell, N. A. Besley, K. B. Bravaya, B. R. Brooks, 89 | D. Casanova, Jeng-Da Chai, S. Coriani, C. J. Cramer, 90 | A. E. DePrince, III, R. A. DiStasio Jr., A. Dreuw, B. D. Dunietz, 91 | T. R. Furlani, W. A. Goddard III, S. Grimme, S. Hammes-Schiffer, 92 | T. Head-Gordon, W. J. Hehre, Chao-Ping Hsu, T.-C. Jagau, Yousung Jung, 93 | A. Klamt, Jing Kong, D. S. Lambrecht, WanZhen Liang, N. J. Mayhall, 94 | C. W. McCurdy, J. B. Neaton, C. Ochsenfeld, J. A. Parkhill, R. Peverati, 95 | V. A. Rassolov, Yihan Shao, L. V. Slipchenko, T. Stauch, R. P. Steele, 96 | J. E. Subotnik, A. J. W. Thom, A. Tkatchenko, D. G. Truhlar, 97 | T. Van Voorhis, T. A. Wesolowski, K. B. Whaley, H. L. Woodcock III, 98 | P. M. Zimmerman, S. Faraji, P. M. W. Gill, M. Head-Gordon, 99 | J. M. Herbert, A. I. Krylov 100 | 101 | Contributors to earlier versions of Q-Chem not listed above: 102 | R. D. Adamson, B. Austin, R. Baer, J. Baker, G. J. O. Beran, 103 | K. Brandhorst, S. T. Brown, E. F. C. Byrd, A. K. Chakraborty, 104 | G. K. L. Chan, Chun-Min Chang, Yunqing Chen, C.-L. Cheng, 105 | Siu Hung Chien, D. M. Chipman, D. L. Crittenden, H. Dachsel, 106 | R. J. Doerksen, A. D. Dutoi, R. G. Edgar, J. Fosso-Tande, 107 | L. Fusti-Molnar, D. Ghosh, A. Ghysels, A. Golubeva-Zadorozhnaya, 108 | J. Gonthier, M. S. Gordon, S. R. Gwaltney, G. Hawkins, J. E. Herr, 109 | A. Heyden, S. Hirata, E. G. Hohenstein, G. Kedziora, F. J. Keil, 110 | C. Kelley, Jihan Kim, R. A. King, R. Z. Khaliullin, P. P. Korambath, 111 | W. Kurlancheek, A. Laurent, A. M. Lee, M. S. Lee, S. V. Levchenko, 112 | Ching Yeh Lin, D. Liotard, E. Livshits, R. C. Lochan, I. Lotan, 113 | L. A. Martinez-Martinez, P. E. Maslen, N. Nair, D. P. O'Neill, 114 | D. Neuhauser, E. Neuscamman, C. M. Oana, R. Olivares-Amaya, R. Olson, 115 | T. M. Perrine, B. Peters, P. A. Pieniazek, A. Prociuk, Y. M. Rhee, 116 | J. Ritchie, M. A. Rohrdanz, E. Rosta, N. J. Russ, H. F. Schaefer III, 117 | M. W. Schmidt, N. E. Schultz, S. Sharma, N. Shenvi, C. D. Sherrill, 118 | A. C. Simmonett, A. Sodt, T. Stein, D. Stuck, K. S. Thanthiriwatte, 119 | V. Vanovschi, L. Vogt, Tao Wang, A. Warshel, M. A. Watson, 120 | C. F. Williams, Q. Wu, X. Xu, Jun Yang, W. Zhang, Yan Zhao 121 | 122 | Please cite Q-Chem as follows: 123 | Y. Shao et al., Mol. Phys. 113, 184-215 (2015) 124 | DOI: 10.1080/00268976.2014.952696 125 | 126 | Q-Chem 5.4.0 for Intel X86 EM64T Linux 127 | 128 | Parts of Q-Chem use Armadillo 9.800.1 (Horizon Scraper). 129 | http://arma.sourceforge.net/ 130 | 131 | Q-Chem begins on Thu Jan 13 13:54:47 2022 132 | 133 | Host: 134 | 0 135 | 136 | Scratch files written to /scratch/qchem3962149// 137 | May1621 |scratch|qcdevops|jenkins|workspace|build_RNUM 7542 138 | Processing $rem in /usr/local/qchem/config/preferences: 139 | Processing $rem in /home/rpaton/.qchemrc: 140 | 141 | Checking the input file for inconsistencies... ...done. 142 | 143 | -------------------------------------------------------------- 144 | User input: 145 | -------------------------------------------------------------- 146 | $molecule 147 | 0 1 148 | H 1.02598 0.12223 0.06942 149 | C 2.12749 0.06671 0.05614 150 | C 2.85038 1.34175 0.36112 151 | O 2.70357 -0.98671 -0.19583 152 | H 2.11900 2.13190 0.55012 153 | H 3.46686 1.62591 -0.49461 154 | H 3.46687 1.20794 1.25280 155 | $end 156 | 157 | $rem 158 | JOBTYPE opt 159 | METHOD b3lyp 160 | BASIS def2-tzvp 161 | $end 162 | 163 | -------------------------------------------------------------- 164 | ---------------------------------------------------------------- 165 | Standard Nuclear Orientation (Angstroms) 166 | I Atom X Y Z 167 | ---------------------------------------------------------------- 168 | 1 H -0.2927524203 -1.5159921714 0.0000001692 169 | 2 C -0.2225693528 -0.4152390447 -0.0000001342 170 | 3 C 1.1629840074 0.1518161910 -0.0000010891 171 | 4 O -1.2321323302 0.2817784143 0.0000001099 172 | 5 H 1.8857631883 -0.6682844019 -0.0000032818 173 | 6 H 1.3107811935 0.7552883162 0.8983561420 174 | 7 H 1.3107787528 0.7552980648 -0.8983465682 175 | ---------------------------------------------------------------- 176 | Molecular Point Group C1 NOp = 1 177 | Largest Abelian Subgroup C1 NOp = 1 178 | Nuclear Repulsion Energy = 69.48546556 hartrees 179 | There are 12 alpha and 12 beta electrons 180 | Requested basis set is def2-TZVP 181 | There are 49 shells and 117 basis functions 182 | 183 | Total QAlloc Memory Limit 8000 MB 184 | Mega-Array Size 188 MB 185 | MEM_STATIC part 192 MB 186 | A cutoff of 1.0D-11 yielded 1208 shell pairs 187 | There are 7034 function pairs ( 9009 Cartesian) 188 | Smallest overlap matrix eigenvalue = 5.26E-04 189 | 190 | Scale SEOQF with 1.000000e-01/1.000000e-01/1.000000e+00 191 | 192 | Standard Electronic Orientation quadrupole field applied 193 | Nucleus-field energy = -0.0000000003 hartrees 194 | Guess from superposition of atomic densities 195 | Warning: Energy on first SCF cycle will be non-variational 196 | SAD guess density has 24.000000 electrons 197 | 198 | ----------------------------------------------------------------------- 199 | General SCF calculation program by 200 | Eric Jon Sundstrom, Paul Horn, Yuezhi Mao, Dmitri Zuev, Alec White, 201 | David Stuck, Shaama M.S., Shane Yost, Joonho Lee, David Small, 202 | Daniel Levine, Susi Lehtola, Hugh Burton, Evgeny Epifanovsky, 203 | Bang C. Huynh 204 | ----------------------------------------------------------------------- 205 | Exchange: 0.2000 Hartree-Fock + 0.0800 Slater + 0.7200 B88 206 | Correlation: 0.1900 VWN1RPA + 0.8100 LYP 207 | Using SG-1 standard quadrature grid 208 | using 24 threads for integral computing 209 | ------------------------------------------------------- 210 | OpenMP Integral computing Module 211 | Release: version 1.0, May 2013, Q-Chem Inc. Pittsburgh 212 | ------------------------------------------------------- 213 | A restricted SCF calculation will be 214 | performed using DIIS 215 | SCF converges when DIIS error is below 1.0e-08 216 | --------------------------------------- 217 | Cycle Energy DIIS error 218 | --------------------------------------- 219 | 1 -154.2039871003 4.83e-02 220 | 2 -153.7946308445 8.31e-03 221 | 3 -153.5812457989 1.53e-02 222 | 4 -153.8812746542 3.04e-03 223 | 5 -153.8949426998 4.64e-04 224 | 6 -153.8952394218 9.29e-05 225 | 7 -153.8952518961 2.60e-05 226 | 8 -153.8952528721 6.76e-06 227 | 9 -153.8952529347 1.10e-06 228 | 10 -153.8952529367 1.47e-07 229 | 11 -153.8952529369 3.86e-08 230 | 12 -153.8952529368 5.59e-09 Convergence criterion met 231 | --------------------------------------- 232 | SCF time: CPU 24.80s wall 2.00s 233 | SCF energy in the final basis set = -153.8952529368 234 | Total energy in the final basis set = -153.8952529368 235 | 236 | -------------------------------------------------------------- 237 | 238 | Orbital Energies (a.u.) 239 | -------------------------------------------------------------- 240 | 241 | Alpha MOs 242 | -- Occupied -- 243 | -19.1319 -10.2716 -10.1872 -1.0457 -0.7632 -0.5913 -0.4847 -0.4576 244 | -0.4433 -0.4034 -0.3693 -0.2681 245 | -- Virtual -- 246 | -0.0488 0.0402 0.0633 0.1085 0.1116 0.1402 0.1578 0.2033 247 | 0.2061 0.2438 0.2747 0.3141 0.3785 0.3905 0.3942 0.4243 248 | 0.4329 0.4524 0.5008 0.5239 0.5307 0.5810 0.6274 0.7524 249 | 0.7882 0.8587 0.8724 0.9124 0.9423 1.0368 1.0596 1.1096 250 | 1.1965 1.3670 1.3804 1.4725 1.4896 1.4977 1.5233 1.5295 251 | 1.5431 1.6321 1.6828 1.8112 1.8417 1.8991 1.9093 1.9485 252 | 2.0320 2.1022 2.1441 2.2037 2.2744 2.3147 2.3300 2.3571 253 | 2.4991 2.5122 2.5275 2.6697 2.6726 2.7217 2.8236 2.8518 254 | 2.8837 2.8953 2.9257 2.9899 3.0386 3.0502 3.1120 3.1343 255 | 3.1790 3.2816 3.3043 3.3889 3.4463 3.4980 3.6681 3.7434 256 | 3.8091 3.8435 3.8842 3.9418 4.1271 4.2690 4.2925 4.4392 257 | 4.5563 4.6521 5.1727 5.1763 5.5126 5.6100 6.0193 6.2400 258 | 6.3178 6.3202 6.4069 6.7688 6.8874 7.0041 22.2495 22.6449 259 | 43.6211 260 | -------------------------------------------------------------- 261 | 262 | Ground-State Mulliken Net Atomic Charges 263 | 264 | Atom Charge (a.u.) 265 | ---------------------------------------- 266 | 1 H 0.076858 267 | 2 C 0.120066 268 | 3 C -0.264839 269 | 4 O -0.292467 270 | 5 H 0.096631 271 | 6 H 0.131875 272 | 7 H 0.131876 273 | ---------------------------------------- 274 | Sum of atomic charges = 0.000000 275 | 276 | ----------------------------------------------------------------- 277 | Cartesian Multipole Moments 278 | ----------------------------------------------------------------- 279 | Charge (ESU x 10^10) 280 | -0.0000 281 | Dipole Moment (Debye) 282 | X 2.6019 Y -1.1157 Z 0.0000 283 | Tot 2.8310 284 | Quadrupole Moments (Debye-Ang) 285 | XX -21.4595 XY 1.1501 YY -18.0806 286 | XZ 0.0000 YZ -0.0000 ZZ -17.8496 287 | Octopole Moments (Debye-Ang^2) 288 | XXX 0.9808 XXY -0.5873 XYY -0.5858 289 | YYY -0.5084 XXZ 0.0000 XYZ -0.0000 290 | YYZ -0.0000 XZZ -0.7313 YZZ 1.2339 291 | ZZZ 0.0000 292 | Hexadecapole Moments (Debye-Ang^3) 293 | XXXX -154.0817 XXXY -1.8727 XXYY -31.2612 294 | XYYY -0.2958 YYYY -44.7043 XXXZ 0.0000 295 | XXYZ -0.0000 XYYZ -0.0000 YYYZ -0.0000 296 | XXZZ -27.8382 XYZZ 0.8709 YYZZ -11.0979 297 | XZZZ 0.0000 YZZZ 0.0000 ZZZZ -23.9747 298 | ----------------------------------------------------------------- 299 | Calculating analytic gradient of the SCF energy 300 | Gradient of SCF Energy 301 | 1 2 3 4 5 6 302 | 1 0.0033563 0.0297664 -0.0046388 -0.0263263 -0.0018028 -0.0001772 303 | 2 0.0024543 -0.0245487 0.0088046 0.0217489 -0.0030560 -0.0027009 304 | 3 -0.0000001 0.0000001 -0.0000026 0.0000000 0.0000003 0.0027883 305 | 7 306 | 1 -0.0001776 307 | 2 -0.0027022 308 | 3 -0.0027860 309 | Max gradient component = 2.977E-02 310 | RMS gradient = 1.158E-02 311 | Gradient time: CPU 10.26 s wall 0.44 s 312 | Geometry Optimization Parameters 313 | NAtoms, NIC, NZ, NCons, NDum, NFix, NCnnct, MaxDiis 314 | 7 35 0 0 0 0 0 0 315 | 316 | 317 | ** GEOMETRY OPTIMIZATION IN DELOCALIZED INTERNAL COORDINATES ** 318 | Searching for a Minimum 319 | 320 | Optimization Cycle: 1 321 | 322 | Coordinates (Angstroms) 323 | ATOM X Y Z 324 | 1 H -0.2927524203 -1.5159921714 0.0000001692 325 | 2 C -0.2225693528 -0.4152390447 -0.0000001342 326 | 3 C 1.1629840074 0.1518161910 -0.0000010891 327 | 4 O -1.2321323302 0.2817784143 0.0000001099 328 | 5 H 1.8857631883 -0.6682844019 -0.0000032818 329 | 6 H 1.3107811935 0.7552883162 0.8983561420 330 | 7 H 1.3107787528 0.7552980648 -0.8983465682 331 | Point Group: c1 Number of degrees of freedom: 15 332 | 333 | 334 | Energy is -153.895252937 335 | 336 | 337 | Attempting to generate delocalized internal coordinates 338 | Initial Hessian constructed with Jon Baker's OPTIMIZE code 339 | 340 | 15 Hessian modes will be used to form the next step 341 | Hessian Eigenvalues: 342 | 0.009562 0.009562 0.075880 0.077193 0.160000 0.160000 343 | 0.160000 0.160000 0.220000 0.326834 0.333538 0.344513 344 | 0.345509 0.345514 0.924306 345 | 346 | Minimum search - taking simple RFO step 347 | Searching for Lamda that Minimizes Along All modes 348 | Value Taken Lamda = -0.00225427 349 | Step Taken. Stepsize is 0.100344 350 | 351 | Maximum Tolerance Cnvgd? 352 | Gradient 0.020607 0.000300 NO 353 | Displacement 0.064954 0.001200 NO 354 | Energy change ********* 0.000001 NO 355 | 356 | 357 | New Cartesian Coordinates Obtained by Inverse Iteration 358 | 359 | Displacement from previous Coordinates is: 0.115969 360 | ---------------------------------------------------------------- 361 | Standard Nuclear Orientation (Angstroms) 362 | I Atom X Y Z 363 | ---------------------------------------------------------------- 364 | 1 H -0.3313982265 -1.5190928009 0.0000018625 365 | 2 C -0.2317383743 -0.4164048855 -0.0000003452 366 | 3 C 1.1692566282 0.1388202100 -0.0000000135 367 | 4 O -1.2248211267 0.2702848522 -0.0000008821 368 | 5 H 1.9180089128 -0.6553330805 -0.0000042381 369 | 6 H 1.3117735512 0.7631893730 0.8833666818 370 | 7 H 1.3117716740 0.7632016999 -0.8833577176 371 | ---------------------------------------------------------------- 372 | Molecular Point Group C1 NOp = 1 373 | Largest Abelian Subgroup C1 NOp = 1 374 | Nuclear Repulsion Energy = 69.71556213 hartrees 375 | There are 12 alpha and 12 beta electrons 376 | Applying Cartesian multipole field 377 | Component Value 378 | --------- ----- 379 | (2,0,0) 1.00000E-11 380 | (0,2,0) 2.00000E-11 381 | (0,0,2) -3.00000E-10 382 | Nucleus-field energy = -0.0000000003 hartrees 383 | Requested basis set is def2-TZVP 384 | There are 49 shells and 117 basis functions 385 | A cutoff of 1.0D-11 yielded 1208 shell pairs 386 | There are 7034 function pairs ( 9009 Cartesian) 387 | Smallest overlap matrix eigenvalue = 5.58E-04 388 | Guess MOs from SCF MO coefficient file 389 | 390 | ----------------------------------------------------------------------- 391 | General SCF calculation program by 392 | Eric Jon Sundstrom, Paul Horn, Yuezhi Mao, Dmitri Zuev, Alec White, 393 | David Stuck, Shaama M.S., Shane Yost, Joonho Lee, David Small, 394 | Daniel Levine, Susi Lehtola, Hugh Burton, Evgeny Epifanovsky, 395 | Bang C. Huynh 396 | ----------------------------------------------------------------------- 397 | Exchange: 0.2000 Hartree-Fock + 0.0800 Slater + 0.7200 B88 398 | Correlation: 0.1900 VWN1RPA + 0.8100 LYP 399 | Using SG-1 standard quadrature grid 400 | A restricted SCF calculation will be 401 | performed using DIIS 402 | SCF converges when DIIS error is below 1.0e-08 403 | --------------------------------------- 404 | Cycle Energy DIIS error 405 | --------------------------------------- 406 | 1 -153.8960702016 5.58e-04 407 | 2 -153.8964717331 2.37e-04 408 | 3 -153.8964127477 3.15e-04 409 | 4 -153.8965305397 5.17e-05 410 | 5 -153.8965340146 9.67e-06 411 | 6 -153.8965341741 1.20e-06 412 | 7 -153.8965341764 2.87e-07 413 | 8 -153.8965341766 1.10e-07 414 | 9 -153.8965341766 1.53e-08 415 | 10 -153.8965341765 2.38e-09 Convergence criterion met 416 | --------------------------------------- 417 | SCF time: CPU 18.49s wall 1.00s 418 | SCF energy in the final basis set = -153.8965341765 419 | Total energy in the final basis set = -153.8965341765 420 | 421 | -------------------------------------------------------------- 422 | 423 | Orbital Energies (a.u.) 424 | -------------------------------------------------------------- 425 | 426 | Alpha MOs 427 | -- Occupied -- 428 | -19.1315 -10.2701 -10.1864 -1.0566 -0.7597 -0.5898 -0.4868 -0.4550 429 | -0.4459 -0.4062 -0.3734 -0.2674 430 | -- Virtual -- 431 | -0.0438 0.0414 0.0646 0.1078 0.1127 0.1405 0.1584 0.2048 432 | 0.2057 0.2429 0.2773 0.3144 0.3767 0.3859 0.3946 0.4237 433 | 0.4311 0.4635 0.5101 0.5271 0.5315 0.5808 0.6310 0.7473 434 | 0.7899 0.8570 0.8711 0.9115 0.9432 1.0420 1.0608 1.1188 435 | 1.2082 1.3654 1.3780 1.4737 1.4812 1.5021 1.5176 1.5285 436 | 1.5441 1.6322 1.6815 1.8085 1.8382 1.9073 1.9092 1.9594 437 | 2.0206 2.0942 2.1568 2.2140 2.2786 2.3266 2.3353 2.3595 438 | 2.5095 2.5119 2.5336 2.6731 2.6748 2.7355 2.8207 2.8282 439 | 2.8783 2.8987 2.9258 2.9852 3.0329 3.0595 3.1108 3.1340 440 | 3.1778 3.2876 3.3033 3.3873 3.4472 3.5001 3.6605 3.7569 441 | 3.7977 3.8534 3.8848 3.9543 4.1028 4.2584 4.3087 4.4221 442 | 4.5503 4.6530 5.1742 5.1789 5.5357 5.6379 6.0639 6.2941 443 | 6.3243 6.3544 6.4267 6.7708 6.8901 7.0269 22.2519 22.6649 444 | 43.6370 445 | -------------------------------------------------------------- 446 | 447 | Ground-State Mulliken Net Atomic Charges 448 | 449 | Atom Charge (a.u.) 450 | ---------------------------------------- 451 | 1 H 0.070989 452 | 2 C 0.111915 453 | 3 C -0.275471 454 | 4 O -0.270919 455 | 5 H 0.100695 456 | 6 H 0.131395 457 | 7 H 0.131395 458 | ---------------------------------------- 459 | Sum of atomic charges = 0.000000 460 | 461 | ----------------------------------------------------------------- 462 | Cartesian Multipole Moments 463 | ----------------------------------------------------------------- 464 | Charge (ESU x 10^10) 465 | -0.0000 466 | Dipole Moment (Debye) 467 | X 2.5232 Y -1.0527 Z 0.0000 468 | Tot 2.7340 469 | Quadrupole Moments (Debye-Ang) 470 | XX -21.2599 XY 1.1642 YY -18.1160 471 | XZ 0.0000 YZ -0.0000 ZZ -17.9079 472 | Octopole Moments (Debye-Ang^2) 473 | XXX 0.9500 XXY -0.5433 XYY -0.6817 474 | YYY 0.1197 XXZ 0.0000 XYZ -0.0000 475 | YYZ -0.0000 XZZ -0.9518 YZZ 1.3181 476 | ZZZ 0.0000 477 | Hexadecapole Moments (Debye-Ang^3) 478 | XXXX -153.4436 XXXY -2.3613 XXYY -31.2007 479 | XYYY -0.5003 YYYY -44.8697 XXXZ -0.0000 480 | XXYZ 0.0000 XYYZ -0.0000 YYYZ -0.0000 481 | XXZZ -28.0284 XYZZ 0.7007 YYZZ -11.0749 482 | XZZZ -0.0000 YZZZ 0.0000 ZZZZ -23.9341 483 | ----------------------------------------------------------------- 484 | Calculating analytic gradient of the SCF energy 485 | Gradient of SCF Energy 486 | 1 2 3 4 5 6 487 | 1 -0.0010273 0.0067685 -0.0014405 -0.0053754 0.0006649 0.0002050 488 | 2 0.0016611 -0.0043964 0.0033852 0.0024856 -0.0005921 -0.0012717 489 | 3 0.0000000 -0.0000001 -0.0000003 0.0000001 0.0000001 0.0001546 490 | 7 491 | 1 0.0002049 492 | 2 -0.0012717 493 | 3 -0.0001544 494 | Max gradient component = 6.769E-03 495 | RMS gradient = 2.408E-03 496 | Gradient time: CPU 8.21 s wall 0.35 s 497 | Geometry Optimization Parameters 498 | NAtoms, NIC, NZ, NCons, NDum, NFix, NCnnct, MaxDiis 499 | 7 35 0 0 0 0 0 0 500 | 501 | Cartesian Hessian Update 502 | Hessian updated using BFGS update 503 | 504 | 505 | ** GEOMETRY OPTIMIZATION IN DELOCALIZED INTERNAL COORDINATES ** 506 | Searching for a Minimum 507 | 508 | Optimization Cycle: 2 509 | 510 | Coordinates (Angstroms) 511 | ATOM X Y Z 512 | 1 H -0.3313982265 -1.5190928009 0.0000018625 513 | 2 C -0.2317383743 -0.4164048855 -0.0000003452 514 | 3 C 1.1692566282 0.1388202100 -0.0000000135 515 | 4 O -1.2248211267 0.2702848522 -0.0000008821 516 | 5 H 1.9180089128 -0.6553330805 -0.0000042381 517 | 6 H 1.3117735512 0.7631893730 0.8833666818 518 | 7 H 1.3117716740 0.7632016999 -0.8833577176 519 | Point Group: c1 Number of degrees of freedom: 15 520 | 521 | 522 | Energy is -153.896534176 523 | 524 | Hessian updated using BFGS update 525 | 526 | 13 Hessian modes will be used to form the next step 527 | Hessian Eigenvalues: 528 | 0.009562 0.009562 0.069415 0.077193 0.158117 0.173961 529 | 0.224229 0.323889 0.333350 0.344105 0.345511 0.347387 530 | 0.816516 531 | 532 | Minimum search - taking simple RFO step 533 | Searching for Lamda that Minimizes Along All modes 534 | Value Taken Lamda = -0.00013019 535 | Step Taken. Stepsize is 0.031259 536 | 537 | Maximum Tolerance Cnvgd? 538 | Gradient 0.003588 0.000300 NO 539 | Displacement 0.024682 0.001200 NO 540 | Energy change -0.001281 0.000001 NO 541 | 542 | 543 | New Cartesian Coordinates Obtained by Inverse Iteration 544 | 545 | Displacement from previous Coordinates is: 0.023932 546 | ---------------------------------------------------------------- 547 | Standard Nuclear Orientation (Angstroms) 548 | I Atom X Y Z 549 | ---------------------------------------------------------------- 550 | 1 H -0.3308303470 -1.5226667376 0.0000018342 551 | 2 C -0.2341324525 -0.4167102453 0.0000019434 552 | 3 C 1.1694807203 0.1341452729 0.0000008908 553 | 4 O -1.2187777588 0.2740924624 -0.0000035681 554 | 5 H 1.9193484264 -0.6567228189 -0.0000056256 555 | 6 H 1.3088845135 0.7662576195 0.8795410179 556 | 7 H 1.3088799367 0.7662698153 -0.8795311450 557 | ---------------------------------------------------------------- 558 | Molecular Point Group C1 NOp = 1 559 | Largest Abelian Subgroup C1 NOp = 1 560 | Nuclear Repulsion Energy = 69.80946597 hartrees 561 | There are 12 alpha and 12 beta electrons 562 | Applying Cartesian multipole field 563 | Component Value 564 | --------- ----- 565 | (2,0,0) 1.00000E-11 566 | (0,2,0) 2.00000E-11 567 | (0,0,2) -3.00000E-10 568 | Nucleus-field energy = -0.0000000003 hartrees 569 | Requested basis set is def2-TZVP 570 | There are 49 shells and 117 basis functions 571 | A cutoff of 1.0D-11 yielded 1208 shell pairs 572 | There are 7034 function pairs ( 9009 Cartesian) 573 | Smallest overlap matrix eigenvalue = 5.61E-04 574 | Guess MOs from SCF MO coefficient file 575 | 576 | ----------------------------------------------------------------------- 577 | General SCF calculation program by 578 | Eric Jon Sundstrom, Paul Horn, Yuezhi Mao, Dmitri Zuev, Alec White, 579 | David Stuck, Shaama M.S., Shane Yost, Joonho Lee, David Small, 580 | Daniel Levine, Susi Lehtola, Hugh Burton, Evgeny Epifanovsky, 581 | Bang C. Huynh 582 | ----------------------------------------------------------------------- 583 | Exchange: 0.2000 Hartree-Fock + 0.0800 Slater + 0.7200 B88 584 | Correlation: 0.1900 VWN1RPA + 0.8100 LYP 585 | Using SG-1 standard quadrature grid 586 | A restricted SCF calculation will be 587 | performed using DIIS 588 | SCF converges when DIIS error is below 1.0e-08 589 | --------------------------------------- 590 | Cycle Energy DIIS error 591 | --------------------------------------- 592 | 1 -153.8965464552 1.84e-04 593 | 2 -153.8965927303 8.54e-05 594 | 3 -153.8965837307 1.19e-04 595 | 4 -153.8966008771 1.39e-05 596 | 5 -153.8966011316 2.87e-06 597 | 6 -153.8966011458 3.05e-07 598 | 7 -153.8966011459 9.08e-08 599 | 8 -153.8966011459 2.36e-08 600 | 9 -153.8966011460 3.30e-09 Convergence criterion met 601 | --------------------------------------- 602 | SCF time: CPU 15.68s wall 1.00s 603 | SCF energy in the final basis set = -153.8966011460 604 | Total energy in the final basis set = -153.8966011460 605 | 606 | -------------------------------------------------------------- 607 | 608 | Orbital Energies (a.u.) 609 | -------------------------------------------------------------- 610 | 611 | Alpha MOs 612 | -- Occupied -- 613 | -19.1316 -10.2699 -10.1859 -1.0593 -0.7591 -0.5893 -0.4873 -0.4542 614 | -0.4465 -0.4072 -0.3739 -0.2675 615 | -- Virtual -- 616 | -0.0428 0.0418 0.0645 0.1079 0.1129 0.1403 0.1588 0.2041 617 | 0.2061 0.2427 0.2786 0.3140 0.3768 0.3865 0.3950 0.4225 618 | 0.4300 0.4638 0.5132 0.5271 0.5315 0.5816 0.6310 0.7473 619 | 0.7901 0.8574 0.8716 0.9119 0.9442 1.0423 1.0613 1.1215 620 | 1.2087 1.3650 1.3774 1.4729 1.4811 1.5009 1.5183 1.5288 621 | 1.5460 1.6325 1.6811 1.8101 1.8387 1.9057 1.9079 1.9654 622 | 2.0189 2.0935 2.1552 2.2167 2.2771 2.3228 2.3416 2.3617 623 | 2.5086 2.5126 2.5362 2.6737 2.6768 2.7354 2.8204 2.8243 624 | 2.8783 2.8994 2.9255 2.9875 3.0325 3.0637 3.1118 3.1374 625 | 3.1777 3.2845 3.3009 3.3896 3.4505 3.5042 3.6607 3.7584 626 | 3.7952 3.8534 3.8843 3.9554 4.0952 4.2565 4.3141 4.4246 627 | 4.5487 4.6523 5.1745 5.1792 5.5422 5.6472 6.0737 6.3079 628 | 6.3249 6.3616 6.4286 6.7710 6.8918 7.0323 22.2523 22.6641 629 | 43.6424 630 | -------------------------------------------------------------- 631 | 632 | Ground-State Mulliken Net Atomic Charges 633 | 634 | Atom Charge (a.u.) 635 | ---------------------------------------- 636 | 1 H 0.069217 637 | 2 C 0.111079 638 | 3 C -0.277567 639 | 4 O -0.265713 640 | 5 H 0.100771 641 | 6 H 0.131106 642 | 7 H 0.131106 643 | ---------------------------------------- 644 | Sum of atomic charges = 0.000000 645 | 646 | ----------------------------------------------------------------- 647 | Cartesian Multipole Moments 648 | ----------------------------------------------------------------- 649 | Charge (ESU x 10^10) 650 | -0.0000 651 | Dipole Moment (Debye) 652 | X 2.4919 Y -1.0481 Z 0.0000 653 | Tot 2.7033 654 | Quadrupole Moments (Debye-Ang) 655 | XX -21.2365 XY 1.1605 YY -18.1118 656 | XZ -0.0000 YZ 0.0000 ZZ -17.9276 657 | Octopole Moments (Debye-Ang^2) 658 | XXX 0.7852 XXY -0.5560 XYY -0.6800 659 | YYY 0.1964 XXZ 0.0000 XYZ 0.0000 660 | YYZ -0.0000 XZZ -1.0316 YZZ 1.3176 661 | ZZZ 0.0000 662 | Hexadecapole Moments (Debye-Ang^3) 663 | XXXX -152.8508 XXXY -2.2901 XXYY -31.1226 664 | XYYY -0.4212 YYYY -45.0862 XXXZ -0.0001 665 | XXYZ 0.0000 XYYZ -0.0000 YYYZ 0.0000 666 | XXZZ -28.0020 XYZZ 0.7142 YYZZ -11.1004 667 | XZZZ -0.0001 YZZZ 0.0000 ZZZZ -23.9442 668 | ----------------------------------------------------------------- 669 | Calculating analytic gradient of the SCF energy 670 | Gradient of SCF Energy 671 | 1 2 3 4 5 6 672 | 1 -0.0002386 -0.0000450 -0.0006445 0.0006853 0.0001216 0.0000606 673 | 2 0.0002248 0.0000286 0.0005309 -0.0003760 -0.0000337 -0.0001873 674 | 3 -0.0000003 0.0000008 -0.0000002 -0.0000003 0.0000000 -0.0000300 675 | 7 676 | 1 0.0000607 677 | 2 -0.0001873 678 | 3 0.0000300 679 | Max gradient component = 6.853E-04 680 | RMS gradient = 2.685E-04 681 | Gradient time: CPU 7.60 s wall 0.32 s 682 | Geometry Optimization Parameters 683 | NAtoms, NIC, NZ, NCons, NDum, NFix, NCnnct, MaxDiis 684 | 7 35 0 0 0 0 0 0 685 | 686 | Cartesian Hessian Update 687 | Hessian updated using BFGS update 688 | 689 | 690 | ** GEOMETRY OPTIMIZATION IN DELOCALIZED INTERNAL COORDINATES ** 691 | Searching for a Minimum 692 | 693 | Optimization Cycle: 3 694 | 695 | Coordinates (Angstroms) 696 | ATOM X Y Z 697 | 1 H -0.3308303470 -1.5226667376 0.0000018342 698 | 2 C -0.2341324525 -0.4167102453 0.0000019434 699 | 3 C 1.1694807203 0.1341452729 0.0000008908 700 | 4 O -1.2187777588 0.2740924624 -0.0000035681 701 | 5 H 1.9193484264 -0.6567228189 -0.0000056256 702 | 6 H 1.3088845135 0.7662576195 0.8795410179 703 | 7 H 1.3088799367 0.7662698153 -0.8795311450 704 | Point Group: c1 Number of degrees of freedom: 15 705 | 706 | 707 | Energy is -153.896601146 708 | 709 | Hessian updated using BFGS update 710 | 711 | 14 Hessian modes will be used to form the next step 712 | Hessian Eigenvalues: 713 | 0.009562 0.009562 0.064176 0.077193 0.156069 0.160025 714 | 0.167514 0.230160 0.316376 0.335238 0.344241 0.345511 715 | 0.346386 0.900549 716 | 717 | Minimum search - taking simple RFO step 718 | Searching for Lamda that Minimizes Along All modes 719 | Value Taken Lamda = -0.00000337 720 | Step Taken. Stepsize is 0.004798 721 | 722 | Maximum Tolerance Cnvgd? 723 | Gradient 0.000577 0.000300 NO 724 | Displacement 0.003665 0.001200 NO 725 | Energy change -0.000067 0.000001 NO 726 | 727 | 728 | New Cartesian Coordinates Obtained by Inverse Iteration 729 | 730 | Displacement from previous Coordinates is: 0.004201 731 | ---------------------------------------------------------------- 732 | Standard Nuclear Orientation (Angstroms) 733 | I Atom X Y Z 734 | ---------------------------------------------------------------- 735 | 1 H -0.3296886168 -1.5227382927 0.0000083676 736 | 2 C -0.2346989861 -0.4162428165 -0.0000081073 737 | 3 C 1.1699384130 0.1336160593 -0.0000007420 738 | 4 O -1.2199402533 0.2742748432 0.0000008445 739 | 5 H 1.9192240282 -0.6575290181 -0.0000059858 740 | 6 H 1.3090079001 0.7666340978 0.8791986702 741 | 7 H 1.3090105534 0.7666504952 -0.8791876995 742 | ---------------------------------------------------------------- 743 | Molecular Point Group C1 NOp = 1 744 | Largest Abelian Subgroup C1 NOp = 1 745 | Nuclear Repulsion Energy = 69.78653475 hartrees 746 | There are 12 alpha and 12 beta electrons 747 | Applying Cartesian multipole field 748 | Component Value 749 | --------- ----- 750 | (2,0,0) 1.00000E-11 751 | (0,2,0) 2.00000E-11 752 | (0,0,2) -3.00000E-10 753 | Nucleus-field energy = -0.0000000003 hartrees 754 | Requested basis set is def2-TZVP 755 | There are 49 shells and 117 basis functions 756 | A cutoff of 1.0D-11 yielded 1208 shell pairs 757 | There are 7034 function pairs ( 9009 Cartesian) 758 | Smallest overlap matrix eigenvalue = 5.63E-04 759 | Guess MOs from SCF MO coefficient file 760 | 761 | ----------------------------------------------------------------------- 762 | General SCF calculation program by 763 | Eric Jon Sundstrom, Paul Horn, Yuezhi Mao, Dmitri Zuev, Alec White, 764 | David Stuck, Shaama M.S., Shane Yost, Joonho Lee, David Small, 765 | Daniel Levine, Susi Lehtola, Hugh Burton, Evgeny Epifanovsky, 766 | Bang C. Huynh 767 | ----------------------------------------------------------------------- 768 | Exchange: 0.2000 Hartree-Fock + 0.0800 Slater + 0.7200 B88 769 | Correlation: 0.1900 VWN1RPA + 0.8100 LYP 770 | Using SG-1 standard quadrature grid 771 | A restricted SCF calculation will be 772 | performed using DIIS 773 | SCF converges when DIIS error is below 1.0e-08 774 | --------------------------------------- 775 | Cycle Energy DIIS error 776 | --------------------------------------- 777 | 1 -153.8966022834 1.93e-05 778 | 2 -153.8966028129 9.83e-06 779 | 3 -153.8966026975 1.39e-05 780 | 4 -153.8966029386 1.53e-06 781 | 5 -153.8966029420 1.56e-07 782 | 6 -153.8966029420 3.53e-08 783 | 7 -153.8966029420 9.97e-09 Convergence criterion met 784 | --------------------------------------- 785 | SCF time: CPU 12.17s wall 1.00s 786 | SCF energy in the final basis set = -153.8966029420 787 | Total energy in the final basis set = -153.8966029420 788 | 789 | -------------------------------------------------------------- 790 | 791 | Orbital Energies (a.u.) 792 | -------------------------------------------------------------- 793 | 794 | Alpha MOs 795 | -- Occupied -- 796 | -19.1317 -10.2701 -10.1859 -1.0591 -0.7590 -0.5893 -0.4872 -0.4540 797 | -0.4465 -0.4074 -0.3739 -0.2675 798 | -- Virtual -- 799 | -0.0429 0.0417 0.0645 0.1079 0.1129 0.1402 0.1588 0.2040 800 | 0.2061 0.2427 0.2787 0.3140 0.3766 0.3863 0.3949 0.4225 801 | 0.4299 0.4635 0.5131 0.5270 0.5315 0.5816 0.6308 0.7471 802 | 0.7898 0.8574 0.8715 0.9120 0.9442 1.0423 1.0610 1.1212 803 | 1.2085 1.3652 1.3774 1.4730 1.4813 1.5004 1.5183 1.5288 804 | 1.5459 1.6324 1.6810 1.8098 1.8384 1.9052 1.9076 1.9655 805 | 2.0189 2.0931 2.1549 2.2163 2.2763 2.3220 2.3421 2.3620 806 | 2.5080 2.5127 2.5363 2.6736 2.6766 2.7353 2.8206 2.8238 807 | 2.8780 2.8995 2.9252 2.9874 3.0324 3.0634 3.1120 3.1372 808 | 3.1781 3.2840 3.3003 3.3894 3.4491 3.5035 3.6606 3.7583 809 | 3.7941 3.8529 3.8838 3.9552 4.0947 4.2551 4.3141 4.4244 810 | 4.5478 4.6522 5.1743 5.1790 5.5418 5.6465 6.0730 6.3068 811 | 6.3247 6.3610 6.4280 6.7709 6.8912 7.0318 22.2513 22.6625 812 | 43.6424 813 | -------------------------------------------------------------- 814 | 815 | Ground-State Mulliken Net Atomic Charges 816 | 817 | Atom Charge (a.u.) 818 | ---------------------------------------- 819 | 1 H 0.069103 820 | 2 C 0.111509 821 | 3 C -0.277723 822 | 4 O -0.266026 823 | 5 H 0.100933 824 | 6 H 0.131103 825 | 7 H 0.131102 826 | ---------------------------------------- 827 | Sum of atomic charges = 0.000000 828 | 829 | ----------------------------------------------------------------- 830 | Cartesian Multipole Moments 831 | ----------------------------------------------------------------- 832 | Charge (ESU x 10^10) 833 | -0.0000 834 | Dipole Moment (Debye) 835 | X 2.4941 Y -1.0472 Z -0.0000 836 | Tot 2.7050 837 | Quadrupole Moments (Debye-Ang) 838 | XX -21.2406 XY 1.1569 YY -18.1118 839 | XZ 0.0000 YZ -0.0000 ZZ -17.9324 840 | Octopole Moments (Debye-Ang^2) 841 | XXX 0.8137 XXY -0.5606 XYY -0.6647 842 | YYY 0.1987 XXZ 0.0000 XYZ 0.0000 843 | YYZ 0.0000 XZZ -1.0297 YZZ 1.3170 844 | ZZZ 0.0001 845 | Hexadecapole Moments (Debye-Ang^3) 846 | XXXX -152.9906 XXXY -2.2861 XXYY -31.1434 847 | XYYY -0.4115 YYYY -45.0877 XXXZ 0.0000 848 | XXYZ 0.0000 XYYZ -0.0000 YYYZ -0.0001 849 | XXZZ -28.0310 XYZZ 0.7185 YYZZ -11.1015 850 | XZZZ 0.0000 YZZZ 0.0000 ZZZZ -23.9520 851 | ----------------------------------------------------------------- 852 | Calculating analytic gradient of the SCF energy 853 | Gradient of SCF Energy 854 | 1 2 3 4 5 6 855 | 1 -0.0000216 -0.0000064 -0.0000996 0.0000280 0.0000790 0.0000105 856 | 2 -0.0000077 0.0000564 0.0000047 -0.0000027 0.0000125 -0.0000315 857 | 3 0.0000012 -0.0000037 0.0000011 0.0000013 0.0000001 -0.0000004 858 | 7 859 | 1 0.0000100 860 | 2 -0.0000317 861 | 3 0.0000004 862 | Max gradient component = 9.956E-05 863 | RMS gradient = 3.317E-05 864 | Gradient time: CPU 7.64 s wall 0.32 s 865 | Geometry Optimization Parameters 866 | NAtoms, NIC, NZ, NCons, NDum, NFix, NCnnct, MaxDiis 867 | 7 35 0 0 0 0 0 0 868 | 869 | Cartesian Hessian Update 870 | Hessian updated using BFGS update 871 | 872 | 873 | ** GEOMETRY OPTIMIZATION IN DELOCALIZED INTERNAL COORDINATES ** 874 | Searching for a Minimum 875 | 876 | Optimization Cycle: 4 877 | 878 | Coordinates (Angstroms) 879 | ATOM X Y Z 880 | 1 H -0.3296886168 -1.5227382927 0.0000083676 881 | 2 C -0.2346989861 -0.4162428165 -0.0000081073 882 | 3 C 1.1699384130 0.1336160593 -0.0000007420 883 | 4 O -1.2199402533 0.2742748432 0.0000008445 884 | 5 H 1.9192240282 -0.6575290181 -0.0000059858 885 | 6 H 1.3090079001 0.7666340978 0.8791986702 886 | 7 H 1.3090105534 0.7666504952 -0.8791876995 887 | Point Group: c1 Number of degrees of freedom: 15 888 | 889 | 890 | Energy is -153.896602942 891 | 892 | Hessian updated using BFGS update 893 | 894 | 15 Hessian modes will be used to form the next step 895 | Hessian Eigenvalues: 896 | 0.009562 0.009563 0.064042 0.077193 0.146505 0.159072 897 | 0.160000 0.168102 0.230689 0.316025 0.334125 0.345511 898 | 0.345583 0.346055 0.900219 899 | 900 | Minimum search - taking simple RFO step 901 | Searching for Lamda that Minimizes Along All modes 902 | Value Taken Lamda = -0.00000012 903 | Step Taken. Stepsize is 0.000923 904 | 905 | Maximum Tolerance Cnvgd? 906 | Gradient 0.000098 0.000300 YES 907 | Displacement 0.000623 0.001200 YES 908 | Energy change -0.000002 0.000001 NO 909 | 910 | 911 | Distance Matrix (Angstroms) 912 | H ( 1) C ( 2) C ( 3) O ( 4) H ( 5) H ( 6) 913 | C ( 2) 1.110565 914 | C ( 3) 2.234366 1.508427 915 | O ( 4) 2.005444 1.203127 2.394014 916 | H ( 5) 2.409605 2.167396 1.089651 3.274540 917 | H ( 6) 2.949496 2.134299 1.092265 2.722312 1.781462 918 | H ( 7) 2.949512 2.134299 1.092265 2.722315 1.781462 1.758386 919 | 920 | 921 | Final energy is -153.896602942043 922 | 923 | 924 | ****************************** 925 | ** OPTIMIZATION CONVERGED ** 926 | ****************************** 927 | 928 | Coordinates (Angstroms) 929 | ATOM X Y Z 930 | 1 H -0.3296886168 -1.5227382927 0.0000083676 931 | 2 C -0.2346989861 -0.4162428165 -0.0000081073 932 | 3 C 1.1699384130 0.1336160593 -0.0000007420 933 | 4 O -1.2199402533 0.2742748432 0.0000008445 934 | 5 H 1.9192240282 -0.6575290181 -0.0000059858 935 | 6 H 1.3090079001 0.7666340978 0.8791986702 936 | 7 H 1.3090105534 0.7666504952 -0.8791876995 937 | 938 | Z-matrix Print: 939 | $molecule 940 | 0 1 941 | C 942 | H 1 1.110565 943 | O 1 1.203127 2 120.118477 944 | C 1 1.508427 2 116.284996 3 179.998282 0 945 | H 4 1.089651 1 112.065096 2 0.001497 0 946 | H 4 1.092265 1 109.258107 2 121.501792 0 947 | H 4 1.092265 1 109.258111 2 -121.498683 0 948 | $end 949 | 950 | 951 | -------------------------------------------------------------- 952 | 953 | Orbital Energies (a.u.) 954 | -------------------------------------------------------------- 955 | 956 | Alpha MOs 957 | -- Occupied -- 958 | -19.1317 -10.2701 -10.1859 -1.0591 -0.7590 -0.5893 -0.4872 -0.4540 959 | -0.4465 -0.4074 -0.3739 -0.2675 960 | -- Virtual -- 961 | -0.0429 0.0417 0.0645 0.1079 0.1129 0.1402 0.1588 0.2040 962 | 0.2061 0.2427 0.2787 0.3140 0.3766 0.3863 0.3949 0.4225 963 | 0.4299 0.4635 0.5131 0.5270 0.5315 0.5816 0.6308 0.7471 964 | 0.7898 0.8574 0.8715 0.9120 0.9442 1.0423 1.0610 1.1212 965 | 1.2085 1.3652 1.3774 1.4730 1.4813 1.5004 1.5183 1.5288 966 | 1.5459 1.6324 1.6810 1.8098 1.8384 1.9052 1.9076 1.9655 967 | 2.0189 2.0931 2.1549 2.2163 2.2763 2.3220 2.3421 2.3620 968 | 2.5080 2.5127 2.5363 2.6736 2.6766 2.7353 2.8206 2.8238 969 | 2.8780 2.8995 2.9252 2.9874 3.0324 3.0634 3.1120 3.1372 970 | 3.1781 3.2840 3.3003 3.3894 3.4491 3.5035 3.6606 3.7583 971 | 3.7941 3.8529 3.8838 3.9552 4.0947 4.2551 4.3141 4.4244 972 | 4.5478 4.6522 5.1743 5.1790 5.5418 5.6465 6.0730 6.3068 973 | 6.3247 6.3610 6.4280 6.7709 6.8912 7.0318 22.2513 22.6625 974 | 43.6424 975 | -------------------------------------------------------------- 976 | 977 | Ground-State Mulliken Net Atomic Charges 978 | 979 | Atom Charge (a.u.) 980 | ---------------------------------------- 981 | 1 H 0.069103 982 | 2 C 0.111509 983 | 3 C -0.277723 984 | 4 O -0.266026 985 | 5 H 0.100933 986 | 6 H 0.131103 987 | 7 H 0.131102 988 | ---------------------------------------- 989 | Sum of atomic charges = 0.000000 990 | 991 | ----------------------------------------------------------------- 992 | Cartesian Multipole Moments 993 | ----------------------------------------------------------------- 994 | Charge (ESU x 10^10) 995 | -0.0000 996 | Dipole Moment (Debye) 997 | X 2.4941 Y -1.0472 Z -0.0000 998 | Tot 2.7050 999 | Quadrupole Moments (Debye-Ang) 1000 | XX -21.2406 XY 1.1569 YY -18.1118 1001 | XZ 0.0000 YZ -0.0000 ZZ -17.9324 1002 | Octopole Moments (Debye-Ang^2) 1003 | XXX 0.8137 XXY -0.5606 XYY -0.6647 1004 | YYY 0.1987 XXZ 0.0000 XYZ 0.0000 1005 | YYZ 0.0000 XZZ -1.0297 YZZ 1.3170 1006 | ZZZ 0.0001 1007 | Hexadecapole Moments (Debye-Ang^3) 1008 | XXXX -152.9906 XXXY -2.2861 XXYY -31.1434 1009 | XYYY -0.4115 YYYY -45.0877 XXXZ 0.0000 1010 | XXYZ 0.0000 XYYZ -0.0000 YYYZ -0.0001 1011 | XXZZ -28.0310 XYZZ 0.7185 YYZZ -11.1015 1012 | XZZZ 0.0000 YZZZ 0.0000 ZZZZ -23.9520 1013 | ----------------------------------------------------------------- 1014 | Total job time: 5.05s(wall), 112.84s(cpu) 1015 | Thu Jan 13 13:54:52 2022 1016 | 1017 | ************************************************************* 1018 | * * 1019 | * Thank you very much for using Q-Chem. Have a nice day. * 1020 | * * 1021 | ************************************************************* 1022 | 1023 | 1024 | 1025 | Running Job 2 of 2 acetaldehyde.inp 1026 | qchem acetaldehyde.inp_3962149.1 /scratch/qchem3962149/ 0 1027 | /usr/local/qchem/exe/qcprog.exe_s acetaldehyde.inp_3962149.1 /scratch/qchem3962149/ 1028 | Welcome to Q-Chem 1029 | A Quantum Leap Into The Future Of Chemistry 1030 | 1031 | 1032 | Q-Chem 5.4, Q-Chem, Inc., Pleasanton, CA (2021) 1033 | 1034 | E. Epifanovsky, A. T. B. Gilbert, Xintian Feng, Joonho Lee, Yuezhi Mao, 1035 | N. Mardirossian, P. Pokhilko, A. White, M. Wormit, M. P. Coons, 1036 | A. L. Dempwolff, Zhengting Gan, D. Hait, P. R. Horn, L. D. Jacobson, 1037 | I. Kaliman, J. Kussmann, A. W. Lange, Ka Un Lao, D. S. Levine, Jie Liu, 1038 | S. C. McKenzie, A. F. Morrison, K. Nanda, F. Plasser, D. R. Rehn, 1039 | M. L. Vidal, Zhi-Qiang You, Ying Zhu, B. Alam, B. Albrecht, 1040 | A. Aldossary, E. Alguire, J. H. Andersen, D. Barton, K. Begam, A. Behn, 1041 | Y. A. Bernard, E. J. Berquist, H. Burton, A. Carreras, K. Carter-Fenk, 1042 | R. Chakraborty, A. D. Chien, K. D. Closser, V. Cofer-Shabica, 1043 | S. Dasgupta, Jia Deng, M. de Wergifosse, M. Diedenhofen, Hainam Do, 1044 | S. Ehlert, Po-Tung Fang, S. Fatehi, Qingguo Feng, J. Gayvert, 1045 | Qinghui Ge, G. Gidofalvi, M. Goldey, J. Gomes, C. Gonzalez-Espinoza, 1046 | S. Gulania, A. Gunina, M. W. D. Hanson-Heine, P. H. P. Harbach, 1047 | A. W. Hauser, M. F. Herbst, M. Hernandez Vera, M. Hodecker, 1048 | Z. C. Holden, S. Houck, Xunkun Huang, Kerwin Hui, B. C. Huynh, 1049 | M. Ivanov, Hyunjun Ji, Hanjie Jiang, B. Kaduk, S. Kaehler, 1050 | K. Khistyaev, Jaehoon Kim, P. Klunzinger, Z. Koczor-Benda, 1051 | Joong Hoon Koh, D. Kosenkov, L. Koulias, T. Kowalczyk, C. M. Krauter, 1052 | K. Kue, A. Kunitsa, T. Kus, A. Landau, K. V. Lawler, D. Lefrancois, 1053 | S. Lehtola, Rain Li, Yi-Pei Li, Jiashu Liang, M. Liebenthal, 1054 | Hung-Hsuan Lin, You-Sheng Lin, Fenglai Liu, Kuan-Yu Liu, 1055 | M. Loipersberger, A. Luenser, A. Manjanath, P. Manohar, E. Mansoor, 1056 | S. F. Manzer, Shan-Ping Mao, A. V. Marenich, T. Markovich, S. Mason, 1057 | S. A. Maurer, P. F. McLaughlin, M. F. S. J. Menger, J.-M. Mewes, 1058 | S. A. Mewes, P. Morgante, J. W. Mullinax, T. S. Nguyen-Beck, 1059 | K. J. Oosterbaan, G. Paran, Alexander C. Paul, Suranjan K. Paul, 1060 | F. Pavosevic, Zheng Pei, S. Prager, E. I. Proynov, E. Ramos, B. Rana, 1061 | A. E. Rask, A. Rettig, R. M. Richard, F. Rob, E. Rossomme, T. Scheele, 1062 | M. Scheurer, M. Schneider, N. Sergueev, S. M. Sharada, W. Skomorowski, 1063 | D. W. Small, C. J. Stein, Yu-Chuan Su, E. J. Sundstrom, Zhen Tao, 1064 | J. Thirman, T. Tsuchimochi, N. M. Tubman, S. P. Veccham, O. Vydrov, 1065 | J. Wenzel, J. Witte, A. Yamada, Kun Yao, S. Yeganeh, S. R. Yost, 1066 | A. Zech, Igor Ying Zhang, Xing Zhang, Yu Zhang, D. Zuev, 1067 | A. Aspuru-Guzik, A. T. Bell, N. A. Besley, K. B. Bravaya, B. R. Brooks, 1068 | D. Casanova, Jeng-Da Chai, S. Coriani, C. J. Cramer, 1069 | A. E. DePrince, III, R. A. DiStasio Jr., A. Dreuw, B. D. Dunietz, 1070 | T. R. Furlani, W. A. Goddard III, S. Grimme, S. Hammes-Schiffer, 1071 | T. Head-Gordon, W. J. Hehre, Chao-Ping Hsu, T.-C. Jagau, Yousung Jung, 1072 | A. Klamt, Jing Kong, D. S. Lambrecht, WanZhen Liang, N. J. Mayhall, 1073 | C. W. McCurdy, J. B. Neaton, C. Ochsenfeld, J. A. Parkhill, R. Peverati, 1074 | V. A. Rassolov, Yihan Shao, L. V. Slipchenko, T. Stauch, R. P. Steele, 1075 | J. E. Subotnik, A. J. W. Thom, A. Tkatchenko, D. G. Truhlar, 1076 | T. Van Voorhis, T. A. Wesolowski, K. B. Whaley, H. L. Woodcock III, 1077 | P. M. Zimmerman, S. Faraji, P. M. W. Gill, M. Head-Gordon, 1078 | J. M. Herbert, A. I. Krylov 1079 | 1080 | Contributors to earlier versions of Q-Chem not listed above: 1081 | R. D. Adamson, B. Austin, R. Baer, J. Baker, G. J. O. Beran, 1082 | K. Brandhorst, S. T. Brown, E. F. C. Byrd, A. K. Chakraborty, 1083 | G. K. L. Chan, Chun-Min Chang, Yunqing Chen, C.-L. Cheng, 1084 | Siu Hung Chien, D. M. Chipman, D. L. Crittenden, H. Dachsel, 1085 | R. J. Doerksen, A. D. Dutoi, R. G. Edgar, J. Fosso-Tande, 1086 | L. Fusti-Molnar, D. Ghosh, A. Ghysels, A. Golubeva-Zadorozhnaya, 1087 | J. Gonthier, M. S. Gordon, S. R. Gwaltney, G. Hawkins, J. E. Herr, 1088 | A. Heyden, S. Hirata, E. G. Hohenstein, G. Kedziora, F. J. Keil, 1089 | C. Kelley, Jihan Kim, R. A. King, R. Z. Khaliullin, P. P. Korambath, 1090 | W. Kurlancheek, A. Laurent, A. M. Lee, M. S. Lee, S. V. Levchenko, 1091 | Ching Yeh Lin, D. Liotard, E. Livshits, R. C. Lochan, I. Lotan, 1092 | L. A. Martinez-Martinez, P. E. Maslen, N. Nair, D. P. O'Neill, 1093 | D. Neuhauser, E. Neuscamman, C. M. Oana, R. Olivares-Amaya, R. Olson, 1094 | T. M. Perrine, B. Peters, P. A. Pieniazek, A. Prociuk, Y. M. Rhee, 1095 | J. Ritchie, M. A. Rohrdanz, E. Rosta, N. J. Russ, H. F. Schaefer III, 1096 | M. W. Schmidt, N. E. Schultz, S. Sharma, N. Shenvi, C. D. Sherrill, 1097 | A. C. Simmonett, A. Sodt, T. Stein, D. Stuck, K. S. Thanthiriwatte, 1098 | V. Vanovschi, L. Vogt, Tao Wang, A. Warshel, M. A. Watson, 1099 | C. F. Williams, Q. Wu, X. Xu, Jun Yang, W. Zhang, Yan Zhao 1100 | 1101 | Please cite Q-Chem as follows: 1102 | Y. Shao et al., Mol. Phys. 113, 184-215 (2015) 1103 | DOI: 10.1080/00268976.2014.952696 1104 | 1105 | Q-Chem 5.4.0 for Intel X86 EM64T Linux 1106 | 1107 | Parts of Q-Chem use Armadillo 9.800.1 (Horizon Scraper). 1108 | http://arma.sourceforge.net/ 1109 | 1110 | Q-Chem begins on Thu Jan 13 13:54:52 2022 1111 | 1112 | Host: 1113 | 0 1114 | 1115 | Scratch files written to /scratch/qchem3962149// 1116 | May1621 |scratch|qcdevops|jenkins|workspace|build_RNUM 7542 1117 | Processing $rem in /usr/local/qchem/config/preferences: 1118 | Processing $rem in /home/rpaton/.qchemrc: 1119 | The previous job contains 0 fragments, simply inherited here 1120 | 1121 | Checking the input file for inconsistencies... ...done. 1122 | 1123 | -------------------------------------------------------------- 1124 | User input: 1125 | -------------------------------------------------------------- 1126 | 1127 | $molecule 1128 | read 1129 | $end 1130 | 1131 | $rem 1132 | JOBTYPE freq 1133 | METHOD b3lyp 1134 | BASIS def2-tzvp 1135 | $end 1136 | -------------------------------------------------------------- 1137 | ---------------------------------------------------------------- 1138 | Standard Nuclear Orientation (Angstroms) 1139 | I Atom X Y Z 1140 | ---------------------------------------------------------------- 1141 | 1 H -0.3387020393 -1.5151026933 0.0000120770 1142 | 2 C -0.2389425931 -0.4090270532 -0.0000061259 1143 | 3 C 1.1680524883 0.1347705629 0.0000006052 1144 | 4 O -1.2211975089 0.2857320945 0.0000015748 1145 | 5 H 1.9139200862 -0.6595977353 -0.0000032679 1146 | 6 H 1.3098498253 0.7671845002 0.8791990429 1147 | 7 H 1.3098528282 0.7671981139 -0.8791873268 1148 | ---------------------------------------------------------------- 1149 | Molecular Point Group C1 NOp = 1 1150 | Largest Abelian Subgroup C1 NOp = 1 1151 | Nuclear Repulsion Energy = 69.78653475 hartrees 1152 | There are 12 alpha and 12 beta electrons 1153 | Requested basis set is def2-TZVP 1154 | There are 49 shells and 117 basis functions 1155 | 1156 | Total QAlloc Memory Limit 8000 MB 1157 | Mega-Array Size 188 MB 1158 | MEM_STATIC part 192 MB 1159 | 1160 | Distance Matrix (Angstroms) 1161 | H ( 1) C ( 2) C ( 3) O ( 4) H ( 5) H ( 6) 1162 | C ( 2) 1.110565 1163 | C ( 3) 2.234366 1.508427 1164 | O ( 4) 2.005444 1.203127 2.394014 1165 | H ( 5) 2.409605 2.167396 1.089651 3.274540 1166 | H ( 6) 2.949496 2.134299 1.092265 2.722312 1.781462 1167 | H ( 7) 2.949512 2.134299 1.092265 2.722315 1.781462 1.758386 1168 | 1169 | 1170 | A cutoff of 1.0D-11 yielded 1208 shell pairs 1171 | There are 7034 function pairs ( 9009 Cartesian) 1172 | Smallest overlap matrix eigenvalue = 5.63E-04 1173 | Guess from superposition of atomic densities 1174 | Warning: Energy on first SCF cycle will be non-variational 1175 | SAD guess density has 24.000000 electrons 1176 | 1177 | ----------------------------------------------------------------------- 1178 | General SCF calculation program by 1179 | Eric Jon Sundstrom, Paul Horn, Yuezhi Mao, Dmitri Zuev, Alec White, 1180 | David Stuck, Shaama M.S., Shane Yost, Joonho Lee, David Small, 1181 | Daniel Levine, Susi Lehtola, Hugh Burton, Evgeny Epifanovsky, 1182 | Bang C. Huynh 1183 | ----------------------------------------------------------------------- 1184 | Exchange: 0.2000 Hartree-Fock + 0.0800 Slater + 0.7200 B88 1185 | Correlation: 0.1900 VWN1RPA + 0.8100 LYP 1186 | Using SG-1 standard quadrature grid 1187 | using 24 threads for integral computing 1188 | ------------------------------------------------------- 1189 | OpenMP Integral computing Module 1190 | Release: version 1.0, May 2013, Q-Chem Inc. Pittsburgh 1191 | ------------------------------------------------------- 1192 | A restricted SCF calculation will be 1193 | performed using DIIS 1194 | SCF converges when DIIS error is below 1.0e-08 1195 | --------------------------------------- 1196 | Cycle Energy DIIS error 1197 | --------------------------------------- 1198 | 1 -154.2315336670 4.91e-02 1199 | 2 -153.7970286262 8.30e-03 1200 | 3 -153.6095856875 1.47e-02 1201 | 4 -153.8841445373 2.88e-03 1202 | 5 -153.8963183939 4.41e-04 1203 | 6 -153.8965913008 8.51e-05 1204 | 7 -153.8966015685 2.45e-05 1205 | 8 -153.8966024526 5.96e-06 1206 | 9 -153.8966025017 9.70e-07 1207 | 10 -153.8966025032 1.36e-07 1208 | 11 -153.8966025034 3.66e-08 1209 | 12 -153.8966025033 5.30e-09 Convergence criterion met 1210 | --------------------------------------- 1211 | SCF time: CPU 23.71s wall 1.00s 1212 | SCF energy in the final basis set = -153.8966025033 1213 | Total energy in the final basis set = -153.8966025033 1214 | 1215 | -------------------------------------------------------------- 1216 | 1217 | Orbital Energies (a.u.) 1218 | -------------------------------------------------------------- 1219 | 1220 | Alpha MOs 1221 | -- Occupied -- 1222 | -19.1317 -10.2701 -10.1859 -1.0591 -0.7590 -0.5893 -0.4872 -0.4540 1223 | -0.4465 -0.4074 -0.3739 -0.2675 1224 | -- Virtual -- 1225 | -0.0429 0.0417 0.0645 0.1079 0.1129 0.1402 0.1588 0.2040 1226 | 0.2061 0.2427 0.2787 0.3140 0.3766 0.3863 0.3949 0.4225 1227 | 0.4299 0.4635 0.5131 0.5270 0.5315 0.5816 0.6308 0.7471 1228 | 0.7898 0.8574 0.8715 0.9120 0.9442 1.0423 1.0610 1.1212 1229 | 1.2085 1.3652 1.3774 1.4730 1.4813 1.5004 1.5183 1.5288 1230 | 1.5459 1.6324 1.6810 1.8098 1.8384 1.9052 1.9076 1.9655 1231 | 2.0189 2.0931 2.1549 2.2163 2.2763 2.3220 2.3421 2.3620 1232 | 2.5080 2.5127 2.5363 2.6736 2.6766 2.7353 2.8206 2.8238 1233 | 2.8780 2.8995 2.9252 2.9874 3.0324 3.0634 3.1120 3.1372 1234 | 3.1781 3.2841 3.3003 3.3894 3.4491 3.5035 3.6606 3.7583 1235 | 3.7941 3.8529 3.8838 3.9552 4.0947 4.2551 4.3141 4.4244 1236 | 4.5478 4.6522 5.1743 5.1790 5.5418 5.6465 6.0730 6.3068 1237 | 6.3247 6.3610 6.4280 6.7709 6.8912 7.0318 22.2513 22.6625 1238 | 43.6424 1239 | -------------------------------------------------------------- 1240 | 1241 | Ground-State Mulliken Net Atomic Charges 1242 | 1243 | Atom Charge (a.u.) 1244 | ---------------------------------------- 1245 | 1 H 0.069106 1246 | 2 C 0.111505 1247 | 3 C -0.277717 1248 | 4 O -0.266027 1249 | 5 H 0.100933 1250 | 6 H 0.131101 1251 | 7 H 0.131100 1252 | ---------------------------------------- 1253 | Sum of atomic charges = 0.000000 1254 | 1255 | ----------------------------------------------------------------- 1256 | Cartesian Multipole Moments 1257 | ----------------------------------------------------------------- 1258 | Charge (ESU x 10^10) 1259 | -0.0000 1260 | Dipole Moment (Debye) 1261 | X 2.4896 Y -1.0579 Z 0.0000 1262 | Tot 2.7050 1263 | Quadrupole Moments (Debye-Ang) 1264 | XX -21.2428 XY 1.1884 YY -18.1349 1265 | XZ 0.0000 YZ -0.0000 ZZ -17.9324 1266 | Octopole Moments (Debye-Ang^2) 1267 | XXX 0.9626 XXY -0.7072 XYY -0.5999 1268 | YYY -0.1299 XXZ 0.0000 XYZ 0.0000 1269 | YYZ 0.0000 XZZ -0.9801 YZZ 1.2103 1270 | ZZZ 0.0000 1271 | Hexadecapole Moments (Debye-Ang^3) 1272 | XXXX -153.0365 XXXY -2.0190 XXYY -31.1323 1273 | XYYY -0.2150 YYYY -45.0815 XXXZ 0.0000 1274 | XXYZ 0.0000 XYYZ -0.0000 YYYZ -0.0000 1275 | XXZZ -28.0195 XYZZ 0.7821 YYZZ -11.0923 1276 | XZZZ 0.0000 YZZZ 0.0000 ZZZZ -23.9520 1277 | ----------------------------------------------------------------- 1278 | Calculating MO derivatives via CPSCF 1279 | 1 0 24 0.0441504 1280 | 2 0 24 0.0090942 1281 | 3 0 24 0.0007024 1282 | 4 1 23 0.0000478 1283 | 5 22 2 0.0000023 1284 | 6 24 0 0.0000001 Converged 1285 | Time for AOints: 7.3 s (CPU) 0.3 s (wall) 1286 | ------------------------------------------------------------------------------ 1287 | AOints : Timing summary (seconds) 1288 | ------------------------------------------------------------------------------ 1289 | job step cpu (% of tot) sys (% of tot) wall (% of tot) 1290 | ------------------------------------------------------------------------------ 1291 | AOints 0.7274E+01 ( 8.2) 0.1500E-04 ( 5.0) 0.3042E+00 ( 8.0) 1292 | ------------------------------------------------------------------------------ 1293 | Grand Totals 0.8862E+02 0.3020E-03 0.3822E+01 1294 | ------------------------------------------------------------------------------ 1295 | Polarizability Matrix (a.u.) 1296 | 1 2 3 1297 | 1 -32.9418629 1.3361958 0.0000262 1298 | 2 1.3361958 -29.3076907 0.0000401 1299 | 3 0.0000262 0.0000401 -21.6301370 1300 | Calculating analytic Hessian of the SCF energy 1301 | 1302 | Direct stationary perturbation theory relativistic correction: 1303 | 1304 | rels = 0.047463576425 1305 | relv = -0.196844522807 1306 | rel2e = 0.069571896858 1307 | E_rel = -0.079809049524 1308 | 1309 | ********************************************************************** 1310 | ** ** 1311 | ** VIBRATIONAL ANALYSIS ** 1312 | ** -------------------- ** 1313 | ** ** 1314 | ** VIBRATIONAL FREQUENCIES (CM**-1) AND NORMAL MODES ** 1315 | ** FORCE CONSTANTS (mDYN/ANGSTROM) AND REDUCED MASSES (AMU) ** 1316 | ** INFRARED INTENSITIES (KM/MOL) ** 1317 | ** ** 1318 | ********************************************************************** 1319 | 1320 | 1321 | Mode: 1 2 3 1322 | Frequency: -188.22 511.33 750.64 1323 | Force Cnst: 0.0249 0.4141 0.3905 1324 | Red. Mass: 1.1940 2.6884 1.1763 1325 | IR Active: YES YES YES 1326 | IR Intens: 6.659 12.382 1.569 1327 | Raman Active: YES YES YES 1328 | X Y Z X Y Z X Y Z 1329 | H -0.000 -0.000 -0.412 -0.202 -0.181 -0.000 0.000 0.000 0.574 1330 | C -0.000 0.000 -0.093 -0.012 -0.205 -0.000 -0.000 -0.000 -0.087 1331 | C 0.000 0.000 0.027 -0.184 0.026 0.000 -0.000 0.000 -0.071 1332 | O 0.000 -0.000 0.075 0.213 0.104 0.000 0.000 -0.000 0.045 1333 | H -0.000 -0.000 0.512 0.212 0.402 0.000 -0.000 -0.000 0.297 1334 | H -0.197 0.419 -0.250 -0.527 0.124 -0.016 -0.477 -0.183 0.151 1335 | H 0.197 -0.419 -0.250 -0.527 0.124 0.016 0.477 0.183 0.151 1336 | TransDip -0.000 -0.000 -0.083 -0.084 -0.075 -0.000 -0.000 0.000 0.040 1337 | 1338 | Mode: 4 5 6 1339 | Frequency: 927.45 1096.53 1134.93 1340 | Force Cnst: 1.1754 1.3927 1.3055 1341 | Red. Mass: 2.3192 1.9659 1.7202 1342 | IR Active: YES YES YES 1343 | IR Intens: 13.277 40.545 0.353 1344 | Raman Active: YES YES YES 1345 | X Y Z X Y Z X Y Z 1346 | H -0.401 -0.088 0.000 -0.150 -0.178 0.000 -0.000 -0.000 -0.698 1347 | C -0.155 -0.117 -0.000 -0.119 -0.173 -0.000 -0.000 -0.000 0.210 1348 | C 0.260 0.008 0.000 0.004 0.195 0.000 0.000 0.000 -0.135 1349 | O -0.092 0.043 0.000 0.057 0.020 0.000 0.000 0.000 -0.042 1350 | H 0.700 0.419 0.000 -0.441 -0.250 -0.000 -0.000 -0.000 0.282 1351 | H -0.047 0.145 -0.043 0.533 -0.081 0.104 -0.349 -0.229 0.102 1352 | H -0.047 0.145 0.043 0.533 -0.081 -0.104 0.349 0.229 0.102 1353 | TransDip -0.088 -0.077 0.000 -0.179 -0.098 -0.000 -0.000 -0.000 0.019 1354 | 1355 | Mode: 7 8 9 1356 | Frequency: 1375.48 1428.83 1466.41 1357 | Force Cnst: 1.3436 1.4420 1.3466 1358 | Red. Mass: 1.2053 1.1988 1.0629 1359 | IR Active: YES YES YES 1360 | IR Intens: 15.022 15.382 13.530 1361 | Raman Active: YES YES YES 1362 | X Y Z X Y Z X Y Z 1363 | H 0.300 -0.040 0.000 0.935 -0.172 -0.000 -0.055 -0.022 0.000 1364 | C -0.012 -0.015 -0.000 -0.059 -0.061 -0.000 -0.019 -0.016 0.000 1365 | C -0.108 -0.074 -0.000 0.052 0.002 0.000 0.060 -0.022 0.000 1366 | O -0.004 0.019 -0.000 -0.030 0.068 -0.000 0.014 -0.006 -0.000 1367 | H 0.304 0.304 0.000 -0.049 -0.096 -0.000 -0.366 -0.395 -0.000 1368 | H 0.447 0.248 -0.302 -0.160 -0.058 0.075 -0.143 0.479 -0.318 1369 | H 0.447 0.248 0.302 -0.160 -0.058 -0.075 -0.143 0.479 0.318 1370 | TransDip 0.106 0.065 0.000 -0.077 -0.099 -0.000 -0.073 0.092 -0.000 1371 | 1372 | Mode: 10 11 12 1373 | Frequency: 1474.84 1806.54 2877.91 1374 | Force Cnst: 1.3418 19.2476 5.2837 1375 | Red. Mass: 1.0470 10.0100 1.0828 1376 | IR Active: YES YES YES 1377 | IR Intens: 8.444 178.066 127.653 1378 | Raman Active: YES YES YES 1379 | X Y Z X Y Z X Y Z 1380 | H 0.000 0.000 0.038 -0.364 -0.211 -0.000 0.109 0.989 -0.000 1381 | C -0.000 -0.000 -0.028 0.602 -0.374 -0.000 -0.013 -0.081 0.000 1382 | C 0.000 0.000 -0.052 -0.041 0.029 -0.000 -0.001 0.003 0.000 1383 | O -0.000 0.000 0.005 -0.393 0.276 0.000 0.003 -0.001 0.000 1384 | H -0.000 -0.000 0.726 -0.226 -0.145 -0.000 0.025 -0.042 -0.000 1385 | H 0.430 -0.216 0.052 0.067 0.045 -0.036 -0.003 -0.000 -0.002 1386 | H -0.430 0.216 0.052 0.067 0.045 0.036 -0.003 -0.000 0.002 1387 | TransDip -0.000 -0.000 0.093 0.393 -0.168 0.000 -0.065 -0.356 0.000 1388 | 1389 | Mode: 13 14 15 1390 | Frequency: 3039.77 3102.42 3126.29 1391 | Force Cnst: 5.6335 6.2339 6.3555 1392 | Red. Mass: 1.0348 1.0993 1.1037 1393 | IR Active: YES YES YES 1394 | IR Intens: 1.587 3.655 17.474 1395 | Raman Active: YES YES YES 1396 | X Y Z X Y Z X Y Z 1397 | H -0.006 -0.019 0.000 0.000 0.000 -0.003 0.006 0.041 -0.000 1398 | C 0.001 0.002 -0.000 -0.000 -0.000 -0.001 -0.001 -0.005 0.000 1399 | C -0.041 -0.027 -0.000 0.000 -0.000 -0.091 0.041 -0.084 0.000 1400 | O 0.000 -0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1401 | H 0.336 -0.372 -0.000 -0.000 0.000 -0.018 -0.589 0.631 0.000 1402 | H 0.070 0.349 0.496 0.092 0.418 0.559 0.052 0.189 0.290 1403 | H 0.070 0.349 -0.496 -0.092 -0.418 0.559 0.052 0.189 -0.290 1404 | TransDip -0.037 0.016 0.000 0.000 0.000 -0.061 0.093 -0.096 0.000 1405 | 1406 | STANDARD THERMODYNAMIC QUANTITIES AT 298.15 K AND 1.00 ATM 1407 | 1408 | This Molecule has 1 Imaginary Frequencies 1409 | Zero point vibrational energy: 34.480 kcal/mol 1410 | 1411 | Atom 1 Element H Has Mass 1.00783 1412 | Atom 2 Element C Has Mass 12.00000 1413 | Atom 3 Element C Has Mass 12.00000 1414 | Atom 4 Element O Has Mass 15.99491 1415 | Atom 5 Element H Has Mass 1.00783 1416 | Atom 6 Element H Has Mass 1.00783 1417 | Atom 7 Element H Has Mass 1.00783 1418 | Molecular Mass: 44.026230 amu 1419 | Principal axes and moments of inertia in amu*Bohr^2: 1420 | 1 2 3 1421 | Eigenvalues -- 32.08152 176.32972 197.28333 1422 | X 0.99957 0.02945 0.00000 1423 | Y -0.02945 0.99957 -0.00000 1424 | Z -0.00000 0.00000 1.00000 1425 | Rotational Symmetry Number is 1 1426 | The Molecule is an Asymmetric Top 1427 | Translational Enthalpy: 0.889 kcal/mol 1428 | Rotational Enthalpy: 0.889 kcal/mol 1429 | Vibrational Enthalpy: 34.752 kcal/mol 1430 | gas constant (RT): 0.592 kcal/mol 1431 | Translational Entropy: 37.272 cal/mol.K 1432 | Rotational Entropy: 21.639 cal/mol.K 1433 | Vibrational Entropy: 1.190 cal/mol.K 1434 | 1435 | Total Enthalpy: 37.122 kcal/mol 1436 | Total Entropy: 60.101 cal/mol.K 1437 | Total job time: 7.02s(wall), 161.50s(cpu) 1438 | Thu Jan 13 13:54:59 2022 1439 | 1440 | ************************************************************* 1441 | * * 1442 | * Thank you very much for using Q-Chem. Have a nice day. * 1443 | * * 1444 | ************************************************************* 1445 | 1446 | 1447 | remove work dirs /scratch/qchem3962149.0 -- /scratch/qchem3962149.-1 1448 | rm -rf /scratch/qchem3962149 1449 | -------------------------------------------------------------------------------- /pyqrc/examples/QChem/acetaldehyde_QRC.inp: -------------------------------------------------------------------------------- 1 | 2 | $molecule 3 | 0 1 4 | H -0.33870204 -1.51510269 -0.12358792 5 | C -0.23894259 -0.40902705 -0.02790613 6 | C 1.16805249 0.13477056 0.00810061 7 | O -1.22119751 0.28573209 0.02250157 8 | H 1.91392009 -0.65959774 0.15359673 9 | H 1.25074983 0.89288450 0.80419904 10 | H 1.36895283 0.64149811 -0.95418733 11 | $end 12 | 13 | $rem 14 | JOBTYPE opt 15 | METHOD B3LYP 16 | BASIS def2-TZVP 17 | $end 18 | 19 | @@@ 20 | 21 | $molecule 22 | read 23 | $end 24 | 25 | $rem 26 | JOBTYPE freq 27 | METHOD B3LYP 28 | BASIS def2-TZVP 29 | $end 30 | -------------------------------------------------------------------------------- /pyqrc/examples/QChem/acetaldehyde_QRC.qrc: -------------------------------------------------------------------------------- 1 | 2 | pyQRC - a quick alternative to IRC calculations 3 | version: 2.0 / author: Robert Paton / email: robert.paton@colostate.edu 4 | Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069. 5 | 6 | -----ORIGINAL GEOMETRY------ 7 | X Y Z 8 | H -0.338702 -1.515103 0.000012 9 | C -0.238943 -0.409027 -0.000006 10 | C 1.168052 0.134771 0.000001 11 | O -1.221198 0.285732 0.000002 12 | H 1.913920 -0.659598 -0.000003 13 | H 1.309850 0.767185 0.879199 14 | H 1.309853 0.767198 -0.879187 15 | 16 | ----HARMONIC FREQUENCIES---- 17 | Freq Red mass F const 18 | -188.2200 1.1940 0.0249 19 | 511.3300 2.6884 0.4141 20 | 750.6400 1.1763 0.3905 21 | 927.4500 2.3192 1.1754 22 | 1096.5300 1.9659 1.3927 23 | 1134.9300 1.7202 1.3055 24 | 1375.4800 1.2053 1.3436 25 | 1428.8300 1.1988 1.4420 26 | 1466.4100 1.0629 1.3466 27 | 1474.8400 1.0470 1.3418 28 | 1806.5400 10.0100 19.2476 29 | 2877.9100 1.0828 5.2837 30 | 3039.7700 1.0348 5.6335 31 | 3102.4200 1.0993 6.2339 32 | 3126.2900 1.1037 6.3555 33 | 34 | -SHIFTING ALONG NORMAL MODE- 35 | -AMPLIFIER = 0.3 36 | X Y Z 37 | H -0.000000 -0.000000 -0.412000 38 | C -0.000000 0.000000 -0.093000 39 | C 0.000000 0.000000 0.027000 40 | O 0.000000 -0.000000 0.075000 41 | H -0.000000 -0.000000 0.512000 42 | H -0.197000 0.419000 -0.250000 43 | H 0.197000 -0.419000 -0.250000 44 | 45 | STRUCTURE MOVED BY 1.407 Bohr amu^1/2 46 | -------------------------------------------------------------------------------- /pyqrc/pyQRC.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/python 2 | from __future__ import print_function, absolute_import 3 | 4 | ####################################################################### 5 | # pyQRC.py # 6 | # A Python implementation of Silva and Goodman's QRC approach # 7 | # From a Gaussian frequency calculation it is possible to create # 8 | # new input files which are displaced along any normal modes which # 9 | # have an imaginary frequency. # 10 | ####################################################################### 11 | __version__ = '2.0' # last modified May 5 2018 12 | __author__ = 'Robert Paton' 13 | __email__= 'robert.paton@colostate.edu' 14 | ####################################################################### 15 | 16 | #Python Libraries 17 | import sys, os, re 18 | from glob import glob 19 | from optparse import OptionParser 20 | import cclib 21 | import numpy as np 22 | import shutil 23 | import subprocess 24 | 25 | #Some useful arrays 26 | periodictable = ["","H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar","K","Ca","Sc","Ti","V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr","Rb","Sr","Y","Zr", 27 | "Nb","Mo","Tc","Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te","I","Xe","Cs","Ba","La","Ce","Pr","Nd","Pm","Sm","Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu","Hf","Ta","W","Re","Os","Ir","Pt","Au","Hg","Tl", 28 | "Pb","Bi","Po","At","Rn","Fr","Ra","Ac","Th","Pa","U","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr","Rf","Db","Sg","Bh","Hs","Mt","Ds","Rg","Uub","Uut","Uuq","Uup","Uuh","Uus","Uuo"] 29 | 30 | atomic_masses = [0.0, 1.007825, 4.00, 7.00, 9.00,\ 31 | 11.00, 12.01, 14.0067, 15.9994,\ 32 | 19.00, 20.180, 22.990, 24.305,\ 33 | 26.982, 28.086, 30.973762, 31.972071,\ 34 | 35.453, 39.948, 39.098, 40.078,\ 35 | 44.956, 47.867, 50.942, 51.996,\ 36 | 54.938, 55.845,58.933, 58.693,\ 37 | 63.546, 65.38, 69.723, 72.631,\ 38 | 74.922, 78.971, 79.904, 84.798,\ 39 | 84.468, 87.62, 88.906, 91.224,\ 40 | 92.906, 95.95, 98.907, 101.07,\ 41 | 102.906, 106.42, 107.868, 112.414,\ 42 | 114.818, 118.711, 121.760, 126.7,\ 43 | 126.904, 131.294, 132.905, 137.328,\ 44 | 138.905, 140.116, 140.908, 144.243,\ 45 | 144.913, 150.36, 151.964, 157.25,\ 46 | 158.925, 162.500, 164.930, 167.259,\ 47 | 168.934, 173.055, 174.967, 178.49,\ 48 | 180.948, 183.84, 186.207, 190.23,\ 49 | 192.217, 195.085, 196.967, 200.592,\ 50 | 204.383, 207.2, 208.980, 208.982,\ 51 | 209.987, 222.081, 223.020, 226.025,\ 52 | 227.028, 232.038, 231.036, 238.029,\ 53 | 237, 244, 243, 247, 247,\ 54 | 251, 252, 257, 258, 259,\ 55 | 262, 261, 262, 266, 264,\ 56 | 269, 268, 271, 272, 285,\ 57 | 284, 289, 288, 292, 294,\ 58 | 294] 59 | 60 | rcov = {"H": 0.32,"He": 0.46, 61 | "Li":1.33,"Be":1.02,"B":0.85,"C":0.75,"N":0.71,"O":0.63,"F":0.64,"Ne":0.67, 62 | "Na":1.55,"Mg":1.39,"Al":1.26, "Si":1.16,"P":1.11,"S":1.03,"Cl":0.99, "Ar":0.96, 63 | "K":1.96,"Ca":1.71,"Sc": 1.48, "Ti": 1.36, "V": 1.34, "Cr": 1.22, "Mn":1.19, "Fe":1.16, "Co":1.11, "Ni":1.10,"Zn":1.18, "Ga":1.24, "Ge":1.21, "As":1.21, "Se":1.16, "Br":1.14, "Kr":1.17, 64 | "Rb":2.10, "Sr":1.85,"Y":1.63, "Zr":1.54, "Nb":1.47, "Mo":1.38, "Tc":1.28, "Ru":1.25,"Rh":1.25,"Pd":1.20,"Ag":1.28,"Cd":1.36, "In":1.42, "Sn":1.40,"Sb":1.40,"Te":1.36,"I":1.33,"Xe":1.31} 65 | 66 | def elementID(massno): 67 | if massno < len(periodictable): return periodictable[massno] 68 | else: return "XX" 69 | 70 | # Enables output to terminal and to text file 71 | class Logger: 72 | # Designated initializer 73 | def __init__(self,filein,suffix,append): 74 | # Create the log file at the input path 75 | self.log = open(filein+"_"+append+"."+suffix,'w') 76 | # Write a message only to the log and not to the terminal 77 | def Writeonlyfile(self, message): 78 | self.log.write(message+"\n") 79 | 80 | #Read data from an output file - data not currently provided by cclib 81 | class getoutData: 82 | def __init__(self, file): 83 | if not os.path.exists(file): 84 | print(("\nFATAL ERROR: Output file [ %s ] does not exist"%file)) 85 | 86 | def getFORMAT(self, outlines): 87 | for i in range(0,len(outlines)): 88 | if outlines[i].find('Gaussian, Inc.') > -1: self.format = "Gaussian" 89 | if outlines[i].find('* O R C A *') > -1: self.format = "ORCA" 90 | if outlines[i].find('Q-Chem, Inc.') > -1: self.format = "QChem" 91 | 92 | def level_of_theory(file): 93 | """Read output for the level of theory and basis set used.""" 94 | repeated_theory = 0 95 | with open(file) as f: 96 | data = f.readlines() 97 | level, bs = 'none', 'none' 98 | 99 | for line in data: 100 | if line.strip().find('External calculation') > -1: 101 | level, bs = 'ext', 'ext' 102 | break 103 | if '\\Freq\\' in line.strip() and repeated_theory == 0: 104 | try: 105 | level, bs = (line.strip().split("\\")[4:6]) 106 | repeated_theory = 1 107 | except IndexError: 108 | pass 109 | elif '|Freq|' in line.strip() and repeated_theory == 0: 110 | try: 111 | level, bs = (line.strip().split("|")[4:6]) 112 | repeated_theory = 1 113 | except IndexError: 114 | pass 115 | if '\\SP\\' in line.strip() and repeated_theory == 0: 116 | try: 117 | level, bs = (line.strip().split("\\")[4:6]) 118 | repeated_theory = 1 119 | except IndexError: 120 | pass 121 | elif '|SP|' in line.strip() and repeated_theory == 0: 122 | try: 123 | level, bs = (line.strip().split("|")[4:6]) 124 | repeated_theory = 1 125 | except IndexError: 126 | pass 127 | if 'DLPNO BASED TRIPLES CORRECTION' in line.strip(): 128 | level = 'DLPNO-CCSD(T)' 129 | if 'Estimated CBS total energy' in line.strip(): 130 | try: 131 | bs = ("Extrapol." + line.strip().split()[4]) 132 | except IndexError: 133 | pass 134 | # Remove the restricted R or unrestricted U label 135 | if level[0] in ('R', 'U'): 136 | level = level[1:] 137 | level_of_theory = '/'.join([level, bs]) 138 | return level_of_theory 139 | 140 | def getJOBTYPE(self, outlines): 141 | if self.format == "Gaussian": 142 | level = "none"; bs = "none" 143 | for i in range(0,len(outlines)): 144 | if outlines[i].strip().find('----------') > -1: 145 | if outlines[i+1].strip().find('#') > -1: 146 | self.JOBTYPE = '' 147 | for j in range(i+1,len(outlines)): 148 | if outlines[j].strip().find('----------') > -1: 149 | break 150 | else: 151 | self.JOBTYPE = self.JOBTYPE+re.sub('#','',outlines[j].strip()) 152 | self.JOBTYPE = re.sub(r' geom=\S+','',self.JOBTYPE) 153 | self.LEVELOFTHEORY = level_of_theory(file) 154 | break 155 | if self.format == "ORCA": 156 | level = "none"; bs = "none" 157 | for i in range(0,len(outlines)): 158 | if outlines[i].strip().find('> !') > -1: 159 | self.JOBTYPE = outlines[i].strip().split('> !')[1].lstrip() 160 | self.LEVELOFTHEORY = level_of_theory(file) 161 | break 162 | 163 | def getTERMINATION(self, outlines): 164 | if self.format == "Gaussian": 165 | for i in range(0,len(outlines)): 166 | if outlines[i].find("Normal termination") > -1: 167 | self.TERMINATION = "normal" 168 | 169 | outfile = open(file,"r") 170 | outlines = outfile.readlines() 171 | getFORMAT(self, outlines) 172 | getJOBTYPE(self, outlines) 173 | getTERMINATION(self, outlines) 174 | 175 | 176 | # compute mass-weighted Cartesian displacment between two structures (bohr amu^1/2) 177 | def mwdist(coords1, coords2, elements): 178 | dist = 0 179 | 180 | for n, atom in enumerate(elements): 181 | 182 | dist += atomic_masses[atom] * (np.linalg.norm(coords1[n] - coords2[n])) ** 2 183 | #print(coords1[n], coords2[n], atomic_masses[atom] ** 0.5, (np.linalg.norm(coords1[n] - coords2[n]))) 184 | #print(atomic_masses[atom] ** 0.5 * (np.linalg.norm(coords1[n] - coords2[n]))) 185 | #print((np.linalg.norm(coords1[n] - coords2[n])), dist) 186 | 187 | dist = 1.88972612456506 * dist ** 0.5 188 | 189 | return dist 190 | 191 | class gen_qrc: 192 | def __init__(self, file, amplitude, nproc, mem, route, verbose, suffix, val, num): 193 | 194 | # parse compchem output with cclib 195 | parser = cclib.io.ccopen(file) 196 | data = parser.parse() 197 | 198 | #try: 199 | nat, charge, atomnos = data.natom, data.charge, data.atomnos 200 | try: 201 | mult = data.mult 202 | except: 203 | AttributeError 204 | mult = '1' # surface level workaround to set default value of multiplicity to 1 if not parsed properly by cclib 205 | print('Warning - multiplicity not parsed from input: defaulted to 1 in input files') 206 | elements = [periodictable[z] for z in atomnos] 207 | cartesians = data.atomcoords[-1] 208 | freq, disps = data.vibfreqs, data.vibdisps 209 | nmodes = len(freq) 210 | if hasattr(data, 'vibrmasses'): rmass = data.vibrmasses 211 | else: rmass = [0.0] * nmodes 212 | if hasattr(data, 'vibfconsts'): fconst = data.vibfconsts 213 | else: fconst = [0.0] * nmodes 214 | 215 | self.CARTESIAN = [] 216 | for atom in range(0,nat): 217 | self.CARTESIAN.append([cartesians[atom][0], cartesians[atom][1], cartesians[atom][2]]) 218 | 219 | # Write an output file 220 | if verbose: log = Logger(file.split(".")[0],"qrc", suffix) 221 | 222 | # The molecular data as read in from the frequency calculation, including atomic masses 223 | if verbose: 224 | log.Writeonlyfile(' pyQRC - a quick alternative to IRC calculations') 225 | log.Writeonlyfile(' version: '+__version__+' / author: '+__author__+' / email: '+__email__) 226 | log.Writeonlyfile(' Based on: Goodman, J. M.; Silva, M. A. Tet. Lett. 2003, 44, 8233-8236; Tet. Lett. 2005, 46, 2067-2069.\n') 227 | log.Writeonlyfile(' -----ORIGINAL GEOMETRY------') 228 | log.Writeonlyfile('{0:>4} {1:>9} {2:>9} {3:>9} {4:>9}'.format('', '', 'X', 'Y', 'Z')) 229 | for atom in range(0,nat): 230 | log.Writeonlyfile('{0:>4} {1:>9} {2:9.6f} {3:9.6f} {4:9.6f}'.format(elements[atom], '', cartesians[atom][0], cartesians[atom][1], cartesians[atom][2])) 231 | log.Writeonlyfile('\n ----HARMONIC FREQUENCIES----') 232 | log.Writeonlyfile('{0:>24} {1:>9} {2:>9}'.format('Freq', 'Red mass', 'F const')) 233 | for mode in range(0,nmodes): 234 | log.Writeonlyfile('{0:24.4f} {1:9.4f} {2:9.4f}'.format(freq[mode], rmass[mode], fconst[mode])) 235 | 236 | shift = [] 237 | 238 | # Save the original Cartesian coordinates before they are altered 239 | orig_carts = [] 240 | for atom in range(0,nat): 241 | orig_carts.append([cartesians[atom][0], cartesians[atom][1], cartesians[atom][2]]) 242 | 243 | # Based on user input select the appropriate displacements 244 | for mode, wn in enumerate(freq): 245 | 246 | # Either moves along any and all imaginary freqs, or a specific mode requested by the user 247 | if wn < 0.0 and val == None and num == None: 248 | shift.append(amplitude) 249 | if verbose: 250 | log.Writeonlyfile('\n -SHIFTING ALONG NORMAL MODE-') 251 | log.Writeonlyfile(' -AMPLIFIER = '+str(shift[mode])) 252 | 253 | log.Writeonlyfile('{0:>4} {1:>9} {2:>9} {3:>9} {4:>9}'.format('', '', 'X', 'Y', 'Z')) 254 | for atom in range(0,nat): 255 | log.Writeonlyfile('{0:>4} {1:>9} {2:9.6f} {3:9.6f} {4:9.6f}'.format(elements[atom], '', disps[mode][atom][0], disps[mode][atom][1], disps[mode][atom][2])) 256 | 257 | elif wn == val or mode+1 == num: 258 | # print(wn, num) 259 | shift.append(amplitude) 260 | if verbose: 261 | log.Writeonlyfile('\n -SHIFTING ALONG NORMAL MODE-') 262 | log.Writeonlyfile(' -AMPLIFIER = '+str(shift[mode])) 263 | 264 | log.Writeonlyfile('{0:>4} {1:>9} {2:>9} {3:>9} {4:>9}'.format('', '', 'X', 'Y', 'Z')) 265 | for atom in range(0,nat): 266 | log.Writeonlyfile('{0:>4} {1:>9} {2:9.6f} {3:9.6f} {4:9.6f}'.format(elements[atom], '', disps[mode][atom][0], disps[mode][atom][1], disps[mode][atom][2])) 267 | else: shift.append(0.0) 268 | 269 | # This is where a perturbed structure is generated 270 | # The starting geometry is displaced along the each normal mode multipled by a user-specified amplitude 271 | for atom in range(0,nat): 272 | for coord in range(0,3): 273 | cartesians[atom][coord] = cartesians[atom][coord] + disps[mode][atom][coord] * shift[mode] 274 | 275 | # useful information 276 | self.NEW_CARTESIAN = cartesians 277 | self.ATOMTYPES = elements 278 | 279 | # Record by how much the structure has been altered 280 | mw_distance = mwdist(self.NEW_CARTESIAN, self.CARTESIAN, atomnos) 281 | log.Writeonlyfile('\n STRUCTURE MOVED BY {:.3f} Bohr amu^1/2 \n'.format(mw_distance)) 282 | 283 | # Create a new compchem input file 284 | if hasattr(data, 'metadata'): 285 | try: format = data.metadata['package'] 286 | except: format = None 287 | try: func = data.metadata['functional'] 288 | except: func = None 289 | try: basis = data.metadata['basis_set'] 290 | except: basis = None 291 | 292 | # if not specified, the job specification will be cloned from the previous calculation 293 | # In practice this works better than cclib metadata so is the default for now 294 | gdata = getoutData(file) 295 | 296 | if format == None: format = gdata.format 297 | if route == None: route = gdata.JOBTYPE 298 | 299 | if format == "Gaussian": input = "com" 300 | elif format == "ORCA" or format == "QChem": input = "inp" 301 | 302 | new_input = Logger(file.split(".")[0],input, suffix) 303 | 304 | if format == "Gaussian": 305 | new_input.Writeonlyfile('%chk='+file.split(".")[0]+"_"+suffix+".chk") 306 | new_input.Writeonlyfile('%nproc='+str(nproc)+'\n%mem='+mem+'\n#'+route+'\n\n'+file.split(".")[0]+'_'+suffix+'\n\n'+str(charge)+" "+str(mult)) 307 | elif format == "ORCA": 308 | 309 | ## split maxcore string for ORCA 310 | memory_number = re.findall(r'\d+',mem) 311 | unit = re.findall(r'GB',mem) 312 | if len(unit) > 0: 313 | mem = int(memory_number[0])*1024 314 | 315 | else: 316 | ## assuming memory is given in MB 317 | mem = memory_number[0] 318 | 319 | new_input.Writeonlyfile('! '+route+'\n %pal nprocs '+str(nproc) + ' end\n %maxcore '+ str(mem)+ '\n\n# '+file.split(".")[0]+'_'+suffix+'\n\n* xyz '+str(charge)+" "+str(mult)) 320 | elif format == "QChem": 321 | new_input.Writeonlyfile('$molecule\n'+str(charge)+" "+str(mult)) 322 | # Save the new Cartesian coordinates 323 | for atom in range(0,nat): 324 | new_input.Writeonlyfile('{0:>2} {1:12.8f} {2:12.8f} {3:12.8f}'.format(elements[atom], cartesians[atom][0], cartesians[atom][1], cartesians[atom][2])) 325 | if format == "Gaussian": new_input.Writeonlyfile("") 326 | elif format == "ORCA": new_input.Writeonlyfile("*") 327 | elif format == "QChem": 328 | new_input.Writeonlyfile("$end\n\n$rem") 329 | new_input.Writeonlyfile(" JOBTYPE opt\n METHOD "+func+"\n BASIS "+basis) 330 | new_input.Writeonlyfile("$end\n\n@@@\n\n$molecule\n read\n$end\n\n$rem") 331 | new_input.Writeonlyfile(" JOBTYPE freq\n METHOD "+func+"\n BASIS "+basis) 332 | new_input.Writeonlyfile("$end\n") 333 | 334 | 335 | 336 | def gen_overlap(mol_atoms, coords, covfrac): 337 | ## Use VDW radii to infer a connectivity matrix 338 | over_mat = np.zeros((len(mol_atoms), len(mol_atoms))) 339 | for i, atom_no_i in enumerate(mol_atoms): 340 | for j, atom_no_j in enumerate(mol_atoms): 341 | if j > i: 342 | rcov_ij = rcov[atom_no_i] + rcov[atom_no_j] 343 | dist_ij = np.linalg.norm(np.array(coords[i])-np.array(coords[j])) 344 | if dist_ij / rcov_ij < covfrac: 345 | #print((i+1), (j+1), dist_ij, vdw_ij, rcov_ij) 346 | over_mat[i][j] = 1 347 | else: pass 348 | return over_mat 349 | 350 | def check_overlap(self, covfrac=0.8): 351 | overlapped = None 352 | over_mat = gen_overlap(self.ATOMTYPES, self.NEW_CARTESIAN, covfrac) 353 | overlapped = np.any(over_mat) 354 | return overlapped 355 | 356 | self.OVERLAPPED = check_overlap(self) 357 | 358 | #except: 359 | # print('o Unable to parse information from {} with cclib ...'.format(file)) 360 | 361 | 362 | def g16_opt( comfile): 363 | ''' run g16 using shell script and args ''' 364 | # check whether job has already been run 365 | logfile = os.path.splitext(comfile)[0] + '.log' 366 | command = [os.path.abspath(os.path.dirname(__file__))+'/run_g16.sh', str(comfile)] 367 | g16_result = subprocess.run(command) 368 | 369 | 370 | def run_irc(file,options,num,amp,lot_bs,suffix,charge,mult,log_output): 371 | #checking amplitutes energy for a given node and creating the single point file 372 | qrc = gen_qrc(file, amp, options.nproc, options.mem, lot_bs, options.verbose, suffix, None, num) 373 | #do check of GEOMETRY if its valid and no atoms overlappins 374 | if not qrc.OVERLAPPED: 375 | g16_opt(file.split('.')[0]+'_'+suffix+'.com') 376 | else: 377 | log_output.Writeonlyfile('x Skipping {} due to overlap in atoms'.format(file.split('.')[0]+'_'+suffix+'.com')) 378 | 379 | def main(): 380 | # get command line inputs. Use -h to list all possible arguments and default values 381 | parser = OptionParser(usage="Usage: %prog [options] .log .log ...") 382 | parser.add_option("--amp", dest="amplitude", action="store", help="amplitude (default 0.2)", default="0.2", type="float", metavar="AMPLITUDE") 383 | parser.add_option("--nproc", dest="nproc", action="store", help="number of processors (default 1)", default="1", type="int", metavar="NPROC") 384 | parser.add_option("--mem", dest="mem", action="store", help="memory (default 4GB)", default="4GB", type="string", metavar="MEM") 385 | parser.add_option("--route", dest="route", action="store", help="calculation route (defaults to same as original file)", default=None, type="string", metavar="ROUTE") 386 | parser.add_option("-v", dest="verbose", action="store_true", help="verbose output", default=True, metavar="VERBOSE") 387 | parser.add_option("--auto", dest="auto", action="store_true", help="turn on automatic batch processing", default=False, metavar="AUTO") 388 | parser.add_option("--name", dest="suffix", action="store", help="append to file name (defaults to QRC)", default="QRC", type="string", metavar="SUFFIX") 389 | parser.add_option("-f", "--freq", dest="freq", action="store", help="request motion along a particular frequency (cm-1)", default=None, type="float", metavar="FREQ") 390 | parser.add_option("--freqnum", dest="freqnum", action="store", help="request motion along a particular frequency (number)", default=None, type="int", metavar="FREQNUM") 391 | 392 | #arguments for running calcs 393 | parser.add_option("--qcoord", dest="qcoord", action="store_true", help="request automatic single point calculation along a particular normal mode (number)", default=False, metavar="QCOORD") 394 | parser.add_option("--nummodes", dest="nummodes", action="store", help="number of modes for automatic single point calculation", default='all', type='string',metavar="NUMMODES") 395 | 396 | (options, args) = parser.parse_args() 397 | 398 | files = [] 399 | if len(sys.argv) > 1: 400 | for elem in sys.argv[1:]: 401 | try: 402 | if os.path.splitext(elem)[1] in [".out", ".log"]: 403 | for file in glob(elem): files.append(file) 404 | except IndexError: pass 405 | 406 | 407 | for file in files: 408 | # parse compchem output with cclib & count imaginary frequencies 409 | parser = cclib.io.ccopen(file) 410 | data = parser.parse() 411 | 412 | #for i in range(1,len(data.atomcoords)): 413 | # mw_distance = mwdist(data.atomcoords[i], data.atomcoords[1], data.atomnos) 414 | # print(mw_distance) 415 | 416 | if hasattr(data, 'vibfreqs'): 417 | im_freq = len([val for val in data.vibfreqs if val < 0]) 418 | else: print('o {} has no frequency information: exiting'.format(file)); sys.exit() 419 | 420 | if not options.qcoord: 421 | if im_freq == 0 and options.auto != False: 422 | print('x {} has no imaginary frequencies: skipping'.format(file)) 423 | else: 424 | if options.freq == None and options.freqnum == None: 425 | print('o {} has {} imaginary frequencies: processing'.format(file, im_freq)) 426 | elif options.freq != None: 427 | print('o {} will be distorted along the frequency of {} cm-1: processing'.format(file, options.freq)) 428 | elif options.freqnum != None: 429 | print('o {} will be distorted along the frequency number {}: processing'.format(file, options.freqnum)) 430 | qrc = gen_qrc(file, options.amplitude, options.nproc, options.mem, options.route, options.verbose, options.suffix, options.freq, options.freqnum) 431 | 432 | #doing automatic calcualtions (single points for stability check) 433 | else: 434 | log_output = Logger("RUNIRC",'dat',options.nummodes) 435 | if im_freq == 0: 436 | log_output.Writeonlyfile('o {} has no imaginary frequencies: check for stability'.format(file)) 437 | amp_base = [round(elem, 2) for elem in np.arange(0,1,0.1) ] 438 | # amp_base_backward = [round(elem, 2) for elem in np.arange(-1,0,0.1) ] 439 | energy_base = [] 440 | root_dir = os.getcwd() 441 | parent_dir = os.getcwd()+'/'+file.split('.')[0] 442 | if not os.path.exists(parent_dir): 443 | os.makedirs(parent_dir) 444 | log_output.Writeonlyfile('o Entering directory {}'.format(parent_dir)) 445 | 446 | # getting energetics of the current molecule 447 | energy_base.append(data.freeenergy) 448 | #creating folders for number of normal modes 449 | if options.nummodes=='all': 450 | freq_range = range(1,len(data.vibfreqs)+1) 451 | else: 452 | freq_range = range(1,len(data.vibfreqs)+1) 453 | freq_range = freq_range[:int(options.nummodes)] 454 | for num in freq_range: 455 | num_dir = parent_dir +'/'+ 'num_'+str(num) 456 | if not os.path.exists(num_dir): 457 | os.makedirs(num_dir) 458 | log_output.Writeonlyfile('o Entering directory {}'.format(num_dir)) 459 | shutil.copyfile(root_dir+'/'+file, num_dir+'/'+file) 460 | os.chdir(num_dir) 461 | for amp in amp_base: 462 | suffix = 'num_'+str(num)+'_amp_'+str(amp).split('.')[0]+str(amp).split('.')[1] 463 | run_irc(file,options,num,amp,freq.LEVELOFTHEORY,suffix,freq.CHARGE,freq.MULT,log_output) 464 | log_output.Writeonlyfile('o Writing to file {}'.format(file.split('.')[0]+'_'+suffix)) 465 | os.chdir(parent_dir) 466 | 467 | if __name__ == "__main__": 468 | main() 469 | -------------------------------------------------------------------------------- /pyqrc/run_g16.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # default variables 4 | rung16=g16 5 | input=$1 6 | 7 | echo -e $"- RUNNING $input WITH G16 \n" 8 | 9 | # run gaussian if com file supplied 10 | if [ -z "$input" ] 11 | then 12 | echo "NO INPUT!" 13 | else 14 | $rung16 $input 15 | fi 16 | -------------------------------------------------------------------------------- /pyqrc/test.py: -------------------------------------------------------------------------------- 1 | import os 2 | 3 | a = os.path.dirname(os.path.abspath(__file__)) 4 | print(a) 5 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | description-file = README.md 3 | 4 | [bdist_wheel] 5 | universal=1 6 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | import io 3 | 4 | # read the contents of your README file 5 | from os import path 6 | this_directory = path.abspath(path.dirname(__file__)) 7 | with io.open(path.join(this_directory, 'README.md'), encoding='utf-8') as f: 8 | long_description = f.read() 9 | 10 | setup( 11 | name='pyqrc', 12 | packages=['pyqrc'], 13 | version='1.0.3', 14 | description='A python program to project computed structures along computed normal modes and perform a Quick Reaction Coordinate calculation', 15 | long_description=long_description, 16 | long_description_content_type='text/markdown', 17 | author='Paton Research Group & pyQRC contributors', 18 | author_email='patonlab@colostate.edu', 19 | url='https://github.com/patonlab/pyQRC', 20 | download_url='https://github.com/patonlab/pyQRC/archive/v1.0.3.zip', 21 | keywords=['compchem', 'thermochemistry', 'gaussian', 'imaginary frequencies', 'intrinsic reaction coordinate', 'normal modes'], 22 | classifiers=[], 23 | install_requires=["cclib"], 24 | python_requires='>=3.6', 25 | include_package_data=True, 26 | ) 27 | -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/patonlab/pyQRC/5c738c8b132fe9f8892ff351e81112b93cfa901a/tests/__init__.py -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # -*- coding: utf-8 -*- 3 | 4 | import os 5 | import pytest 6 | 7 | try: 8 | import pyqrc 9 | BASEPATH = os.path.join(pyqrc.__path__[0]) 10 | except ImportError: 11 | here = os.path.dirname(os.path.abspath(__file__)) 12 | BASEPATH = os.path.normpath(os.path.join(here, '..', 'pyqrc')) 13 | 14 | 15 | def datapath(path): 16 | return os.path.join(BASEPATH, 'examples', path) 17 | -------------------------------------------------------------------------------- /tests/test_pyqrc.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | # -*- coding: utf-8 -*- 3 | 4 | import os 5 | import pytest 6 | import math 7 | from pyqrc import pyQRC as QRC 8 | from .conftest import datapath 9 | 10 | @pytest.mark.parametrize("path, nproc, mem", [ 11 | ('Gaussian/acetaldehyde.log', 4, '8GB'), 12 | ]) 13 | def test_QRC(path, nproc, mem): 14 | path = datapath(path) 15 | amplitude = 0.2 16 | route = None 17 | verbose = True 18 | suffix = 'QRC' 19 | freq, freq_num = None, None 20 | qrc = QRC.gen_qrc(path, amplitude, nproc, mem, route, verbose, suffix, freq, freq_num) 21 | --------------------------------------------------------------------------------