ChemApps - A C++ Chemistry Toolkit

ChemApps provides a suite of utility tools and programs for thermochemistry and chemical kinetics.

Features

• Conversion of Cartesian coordinates to Z matrix
• Conversion of Z matrix to Cartesian coordinates
• Rotational analysis of molecules
• Vibrational analysis of molecules [1]
• Calculation of thermochemical properties for molecules [2]
• Calculation of reduced moment of inertia for torsional modes by using the curvilinear scheme [3]
• Calculation of partition function for torsional modes by using the CT-Cw scheme [4]
• Calculation of reaction rate coefficients using conventional Transition State Theory
• Calculation of Wigner [5] and Eckart tunneling corrections [6-8]
• Conformer search using an internal coordinate Monte Carlo Multiple Minima (MCMM) technique with uniform usage scheme [9,10]
• Conformer search using a genetic algorithm [11]
• Interface to MOPAC 7, MOPAC 5.022mn, and Gaussian

Code of Conduct

This project has adopted the Covenant Code of Conduct.

Licensing

ChemApps is released under the MIT license.

Usage of Third Party Libraries

This project makes use of code from the following third-party libraries:

• Catch2
• qcl
• cxxopts

Please see the ThirdPartyNotices.txt file for details regarding the licensing of these libraries

The user of this software needs to obtain separate licenses for MOPAC, MOPAC 5.022mn or Gaussian.

Quick Start

Requirements

• CMake 3.4.3
• Numlib
• Stdutils
• OpenBLAS 0.3.3 (Intel MKL is recommended)

Supported Compilers

Compiler	Versions Currently Tested
GCC	8
Clang	10
Visual Studio	VS2019 & VS2017
XCode	11.4 & 10.3

Obtaining the Source Code

The source code can be obtained from

    git clone git@github.com:stigrs/chemapps.git

Building the Software

These steps assumes that the source code of this repository has been cloned into a directory called chemapps.

1. Create a directory to contain the build outputs:

    cd chemapps
    mkdir build
    cd build
   

2. Configure CMake to use the compiler of your choice (you can see a list by running cmake --help):

    cmake -G "Visual Studio 15 2017" ..
   

3. Build the software (in this case in the Release configuration):

    cmake --build . --config Release
   

4. Run the test suite:

    ctest -C Release
   

5. Install the software:

    cmake --build . --config Release --target install
   

All tests should pass, indicating that your platform is fully supported.

NOTE: Test cases involving MOPAC could fail because of numerical roundoff errors in MOPAC on different platforms.

Notes and References

1. Vibrational analysis of molecules is computed in accordance with the methods implemented in Gaussian (see the Vibrational Analysis Whitepaper available at http://www.gaussian.com)
2. The thermochemical values are computed in accordance with the methods implemented in Gaussian (see the Thermochemistry Whitepaper available at http://www.gaussian.com)
3. Pitzer, K. S. J. Chem. Phys. 1946, vol. 14, p. 239.
4. Chuang, Y. Y.; Truhlar, D. G. J. Chem. Phys. 2000, vol. 112, p. 1221.
5. Wigner, E. Z. Physik. Chem. (Leipzig), 1932, vol. B19, p. 203.;
6. Eckart, E. Phys. Rev., 1962, vol. 35, p. 1303.
7. Brown, R. L. J. Research NIST, 1981, vol. 86, p. 357.
8. Johnston, H. S.; Heicklen, J. J. Phys. Chem., 1962, vol. 66, p. 532.
9. Li, Z.; Scheraga, H. A. Proc. Natl. Acad. Sci., 1987, vol. 84, p. 6611.
10. Chang, G.; Guida, W. C.; Still, C. J. Am. Chem. Soc., 1989, vol. 111, p. 4379.
11. Sudapy, A.; Blum, V.; Baldauf, C. J. Chem. Inf. Model, 2015, vol. 55, p. 2338.