%0 Journal Article %1 Barnett2007944 %A Barnett, Michael P. %A Capitani, Joseph F. %D 2007 %J Computer Physics Communications %K chemistry data parser quantum software %N 12 %P 944 - 950 %R 10.1016/j.cpc.2007.07.009 %T The MATHSCOUT Mathematica package to postprocess the output of other scientific programs %U http://www.sciencedirect.com/science/article/pii/S0010465507003670 %V 177 %X mathscout is a mathematica1 package to postprocess the output of other programs for scientific calculations. We wrote mathscout to import data from a major program for ab initio computational chemistry into mathematica, so that we could postprocess the chemical results. It can be used to import the output of many other packages that are used, e.g. in molecular dynamics, crystallography, spectroscopic analysis, metabolic and physiological modeling, meteorology and other areas of environmental science, cosmology and particle physics. mathscout assigns a name to each table and non-tabular datum that it extracts. This name is constructed mechanically from the identifier or phrase that precedes or follows or embeds the item in the output that mathscout processes. A selection of non-contiguous items, or all the items in a section of the file, or in the entire file are extracted using simple commands. So far, we have focused on our immediate needs to postprocess the output of the Gaussian2 program. Calculations on several molecules that illustrate the usage of the package are presented here and in the Supplementary Information. mathscout is shortened to msct in the software.Program summary Program title: msct.m Catalogue identifier: ADZQ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZQ_v1_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.: 30thin space396 No. of bytes in distributed program, including test data, etc.: 1thin space799thin space469 Distribution format: tar.gz Programming language: Mathematica Computer: Any computer running unix and Mathematica Operating system: Unix Supplementary material: The Development guide Classification: 4.14, 5, 16.1, 20 Nature of problem: Import data from output files of scientific computing packages, such as Gaussian, into Mathematica for symbolic calculation and production of publication quality tables and plots. Solution method: Provision of mnemonic top-down parsing procedures, functional programming. Running time: The complete extraction of data from a small basis density functional calculation on the water molecule, and from a larger basis density functional calculation on the zinc hydrate ion, that ran to 33 iterations, took 1 second and 23 seconds, respectively, on a Dell Poweredge 1750.

@article{Barnett2007944, abstract = {mathscout is a mathematica1 package to postprocess the output of other programs for scientific calculations. We wrote mathscout to import data from a major program for ab initio computational chemistry into mathematica, so that we could postprocess the chemical results. It can be used to import the output of many other packages that are used, e.g. in molecular dynamics, crystallography, spectroscopic analysis, metabolic and physiological modeling, meteorology and other areas of environmental science, cosmology and particle physics. mathscout assigns a name to each table and non-tabular datum that it extracts. This name is constructed mechanically from the identifier or phrase that precedes or follows or embeds the item in the output that mathscout processes. A selection of non-contiguous items, or all the items in a section of the file, or in the entire file are extracted using simple commands. So far, we have focused on our immediate needs to postprocess the output of the Gaussian2 program. Calculations on several molecules that illustrate the usage of the package are presented here and in the Supplementary Information. mathscout is shortened to msct in the software.Program summary Program title: msct.m Catalogue identifier: ADZQ_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADZQ_v1_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.: 30[thin space]396 No. of bytes in distributed program, including test data, etc.: 1[thin space]799[thin space]469 Distribution format: tar.gz Programming language: Mathematica Computer: Any computer running unix and Mathematica Operating system: Unix Supplementary material: The Development guide Classification: 4.14, 5, 16.1, 20 Nature of problem: Import data from output files of scientific computing packages, such as Gaussian, into Mathematica for symbolic calculation and production of publication quality tables and plots. Solution method: Provision of mnemonic top-down parsing procedures, functional programming. Running time: The complete extraction of data from a small basis density functional calculation on the water molecule, and from a larger basis density functional calculation on the zinc hydrate ion, that ran to 33 iterations, took 1 second and 23 seconds, respectively, on a Dell Poweredge 1750.}, added-at = {2011-07-06T17:10:39.000+0200}, author = {Barnett, Michael P. and Capitani, Joseph F.}, biburl = {https://www.bibsonomy.org/bibtex/2640ca9e3f08f96f8588864c80f8bf32c/drmatusek}, description = {ScienceDirect - Computer Physics Communications : The MATHSCOUT Mathematica package to postprocess the output of other scientific programs}, doi = {10.1016/j.cpc.2007.07.009}, interhash = {fcdd63c5c1b6a6c803a1490e336370e3}, intrahash = {640ca9e3f08f96f8588864c80f8bf32c}, issn = {0010-4655}, journal = {Computer Physics Communications}, keywords = {chemistry data parser quantum software}, number = 12, pages = {944 - 950}, timestamp = {2012-08-20T03:26:47.000+0200}, title = {The MATHSCOUT Mathematica package to postprocess the output of other scientific programs}, url = {http://www.sciencedirect.com/science/article/pii/S0010465507003670}, volume = 177, year = 2007 }