{"id":620,"date":"2016-10-20T14:55:58","date_gmt":"2016-10-20T18:55:58","guid":{"rendered":"https:\/\/scholarblogs.emory.edu\/bowman\/?page_id=620"},"modified":"2024-11-23T15:42:32","modified_gmt":"2024-11-23T20:42:32","slug":"msa","status":"publish","type":"page","link":"https:\/\/scholarblogs.emory.edu\/bowman\/msa\/","title":{"rendered":"MSA"},"content":{"rendered":"

Monomial Symmetrization for Creating Permutationally Invariant Polynomials and Potential Energy Surface (PES) Fitting<\/strong><\/p>\n

MSA 2.0.1 https:\/\/github.com\/szquchen\/MSA-2.0\/releases\/tag\/v2.0.1<\/a>
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The Software<\/strong>
\nMSA is software that produces polynomials and their gradient of a desired maximum order that are invariant with respect to permutations of like atoms. These are called permutationally invariant polynomials (PIPs).\u00a0 Optionally these PIPs and gradients are used in linear regression to fit electronic energies and gradients given in standard format at nuclear configurations in Cartesian coordinates. There is an option to weight the energies and also to change the Morse range parameter.\u00a0 Default values are in the file param.inp and they can be used as is, or changed in the interactive script shown in the video below. We suggest that the user experiment with both parameters to achieve an optimum precision of the fit.<\/p>\n

A\u00a0 data set for CH4<\/sub> is provided as part of the download of MSA.zip folder. This is not needed if you are just generating PIPs.\u00a0 \u00a0Below is a sample:\u00a0 no. of atoms, energy in hartree<\/strong>, atom label followed by cartesian coords in angstroms<\/strong> and cartesian components of grad (if inputed) in hartree\/bohr<\/strong>\u00a0blank otherwise. Based on the order of atoms the symmetry label is 4 1.\u00a0 This indicates that the full permutation group of the 4 H atoms will be used.\u00a0 A reduced symmetry, for example, 2 2 1 could also be used, but that is not done in this case.<\/p>\n

5
\n-40.48132472
\nH -0.10095840 -0.41955010 -1.31205540 0.00475800 -0.00753200 0.00876200
\nH -0.33382290 -1.64227710 -0.08089010 0.00501000 -0.01045300 -0.00392400
\nH 0.27898620 0.01183520 0.37889600 0.00242100 0.01037400 0.00814600
\nH -1.41320490 -0.14046190 -0.03074290 -0.00415000 0.00917100 0.01147400
\nC -0.41724430 -0.55439810 -0.28616510 -0.00804000 -0.00155500 -0.02444600<\/p>\n

A Short Video on Creating a PIP Basis and Fitting\u00a0<\/strong>
\nIn the video we take you through the process of using this MSA software and provide an example for a fit of the H3<\/sub>O2<\/sub>–<\/sup> potential.4<\/sup>\u00a0 We assume the MSA folder has been downloaded and unzipped. The driver is “msa.py”. \u00a0 Note the default value of the Morse range parameter used in the fit in the video is 2 bohr.\u00a0 A value of 3 bohr was used in ref. 4 and this gave smaller fitting root mean square errors. The wall clock time to generate the basis is about 2 minutes and also several minutes to do the fit.\u00a0 This is on a single 2018 Intel. <\/span>CoreTM <\/span>i7-8750H processor.<\/p>\n

https:\/\/scholarblogs.emory.edu\/bowman\/files\/2024\/01\/Msa201_short_video.mp4<\/a><\/video><\/div>\n

What is Needed in Order to Run the Codes
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