MSTor version 2013: A new version of the computer code for the multi-structural torsional anharmonicity, now with a coupled torsional potential

Jingjing Zheng, Rubén Meana-Pañeda, Donald G. Truhlar

Research output: Contribution to journalArticlepeer-review

56 Scopus citations

Abstract

We present an improved version of the MSTor program package, which calculates partition functions and thermodynamic functions of complex molecules involving multiple torsions; the method is based on either a coupled torsional potential or an uncoupled torsional potential. The program can also carry out calculations in the multiple-structure local harmonic approximation. The program package also includes seven utility codes that can be used as stand-alone programs to calculate reduced moment of inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes for torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files for the MSTor calculation and Voronoi calculation, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. New version program summary Program title: MSTor Catalogue identifier: AEMF_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMF_v2_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 487256 No. of bytes in distributed program, including test data, etc.: 14766898 Distribution format: tar.gz Programming language: Fortran 90, C, and perl. Computer: Itasca (HP Linux cluster, each node has two-socket, quad-core 2.8 GHz Intel Xeon X5560 “Nehalem EP” processors), Calhoun (SGI Altix XE 1300 cluster, each node containing two quad-core 2.66 GHz Intel Xeon “Clovertown”-class processors sharing 16 GB of main memory), Koronis (Altix UV 1000 server with 190 6-core Intel Xeon X7542 “Westmere” processors at 2.66 GHz), and Mac Pro (two 2.8 GHz Quad-core intel Xeon processors). Operating system: Linux/Unix/Mac OS. Has the code been vectorized or parallelized?: No RAM: 2 Mbytes Catalogue identifier of previous version: AEMF_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 1803 Classification: 16.3, 16.12, 23. Does the new version supercede the previous version?: Yes Nature of problem: Calculation of the partition functions and thermodynamic functions (standard-state energy, enthalpy, entropy, and free energy as functions of temperature) of complex molecules involving multiple torsional motions. Solution method: The multi-structural approximation with torsional anharmonicity (MS-T). The program also provides results for the multi-structural local harmonic approximation. Reasons for new version: We implemented the newly developed MS-T method based on a coupled torsional potential, which is called the MS-T(C) method. It has been shown to be more accurate than the original MS-T method, i.e., the MS-T(U) method, based on an uncoupled torsional potential. We simplified the input files and improved our utility codes to make the MSTor package easier to use. Summary of revisions: 1. We added the MS-T method based on a coupled torsional potential, which is called MS-T(C), where C denotes coupled. The original method that is based on an uncoupled potential is called MS-T(U).2. The capability of treating linear bending motions is added.3. Definitions of frames and frame chains are no longer needed in the input file.4. The code symmetry is added to determine the group symmetry of a structure.5. The mvinput.exe utility program is added to generate the input file for the vorm.exe and/or mcvorm.exe codes. The msinput.exe utility code had been modified to write the local periodicities taken from the mvorm.out file. Both mvinput.exe and msinput.exe use the symmetry.exe program to determine the point group of each structure.6. The ConfGen.exe has been completely rewritten in Fortran 90, and it reads new fields corresponding to the Gaussian input keywords.7. We corrected a bug in which an array was not initialized.Restrictions: There is no limit on the number of torsions that can be included in either the Voronoi calculation or the full MS-T calculation. In practice, the range of problems that can be addressed with the present method consists of all multitorsional problems for which one can afford to calculate all the conformational structures and their frequencies. Unusual features: The method can be applied to transition states as well as stable molecules. The program package also includes the hull program for the calculation of Voronoi volumes, the symmetry program for determining point group symmetry of a molecule, and seven utility codes that can be used as stand-alone programs to calculate reduced moment-of-inertia matrices by the method of Kilpatrick and Pitzer, to generate conformational structures, to calculate, either analytically or by Monte Carlo sampling, volumes of the torsional subdomains defined by Voronoi tessellation of the conformational subspace, to generate template input files, and to calculate one-dimensional torsional partition functions using the torsional eigenvalue summation method. Additional comments: The program package includes a manual, installation script, and input and output files for a test suite. Running time: There are 26 test runs. The running time of the test runs on a single processor of the Itasca computer is less than 2 s. References: [1] MS-T(C) method: Quantum Thermochemistry: Multi-Structural Method with Torsional Anharmonicity Based on a Coupled Torsional Potential, J. Zheng and D.G. Truhlar, Journal of Chemical Theory and Computation 9 (2013) 1356–1367, DOI: http://dx.doi.org/10.1021/ct3010722. [2] MS-T(U) method: Practical Methods for Including Torsional Anharmonicity in Thermochemical Calculations of Complex Molecules: The Internal-Coordinate Multi-Structural Approximation, J. Zheng, T. Yu, E. Papajak, I, M. Alecu, S.L. Mielke, and D.G. Truhlar, Physical Chemistry Chemical Physics 13 (2011) 10885–10907.

Original languageEnglish (US)
Pages (from-to)2032-2033
Number of pages2
JournalComputer Physics Communications
Volume184
Issue number8
DOIs
StatePublished - Aug 2013

Bibliographical note

Funding Information:
The authors are grateful to Serguei Patchkovskii for providing the symmetry code. This work was supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Science through the Combustion Energy Frontier Research Center under Award Number DE-SC0001198 and through grant no. DE-FG02-86ER13579 .

Publisher Copyright:
© 2013 Elsevier B.V.

Keywords

  • Anharmonicity
  • Molecular vibrations
  • Thermochemistry
  • Torsions

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