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Computational WorkFlow

This document outlines the computational workflow for analyzing the thermodynamic properties of molecular structures derived from initial SDF files. It details the process from input preparation using scripts like HORIZONT_02_sdf4CHNOFS.x, to automatic submission of Gaussian calculations via HORIZONT_03_RUN4.x. The workflow includes error checking and resubmission of jobs using HORIZONT_04_CheckRUN, as well as data collection for thermodynamic properties with HORIZONT_05_DigestRUN. Finally, the gathered data is formatted into CSV files for analysis.

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Computational WorkFlow

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  1. Computational WorkFlow From the initial structures to their computed thermodynamical properties

  2. Workflow of the HORIZONT Terminated output (.log) Initial input (.sdf) Runnable input (.com) Input preparation Output with no error termination Normal term. Conv. Crit. Freq G3MP2 Enthalpy Output with Error termination Normal termination? Modified input Manipulation of the input (By hand) Calculation and collection of molecular properties ComputationalKnow How Database Methodology Know How Chemical Know How

  3. Scripts • HORIZONT_02_sdf4CHNOFS.x • HORIZONT_03_RUN4.x • HORIZONT_04_CheckRUN • HORIZONT_04_Check.x • HORIZONT_05_DigestRUN • HORIZONT_05_Digest.x • HORIZONT_06_sdf2csv.x

  4. HORIZONT_02_sdf4CHNOFS.x szorim@cluster:~/SummerSchool_2014$ HORIZONT_02_sdf4CHNOFS.x C2_H4_N0_O3_F0_S0.sdf ********************************************RUN**************************************************** This script generates standard Cartesian Gaussian inputs from a sdf file generated by MolGen using Babel environment. ONLY FOR CxHyOzFwSv species!!! ********************************************RUN**************************************************** InPutName: C2_H4_N0_O3_F0_S0.sdf Temp0Name: C2_H4_N0_O3_F0_S0_.tmp0 DirName: C2_H4_N0_O3_F0_S0 nC: 2 nH: 4 nN: 0 nO: 3 nF: 0 nS: 0 45 molecules converted 45 files output. The first is C2_H4_N0_O3_F0_S0_1.tmp0 900 audit log messages ********************************************END**************************************************** Thu May 15 07:51:37 UTC 2014 szorim@cluster:~/SummerSchool_2014$ Generates gaussian input files in the folder from SDF database file SDF contains all the structures which can be obtained by valence rule WARNING! Do not modify the initial file name!

  5. HORIZONT_03_RUN4.x szorim@cluster:~/SummerSchool_2014$ HORIZONT_03_RUN4.x Automaticallyfindsfileswith .comextension (Gaussian input files) inthesubfolders and submitsall of themintothequeueusing 4 CPUsforeachcalculations Checkyourcalculationusingqstat and qhostcommands AFTER allyour Gaussian calculationsareterminated!

  6. HORIZONT_04_CheckRUN szorim@cluster:~/SummerSchool_2014$ HORIZONT_04_CheckRUN Automaticallyfindsfileswith .com and .log extensions (Gaussian input and output files) inthesubfolders ItrunsautomaticallytheHORIZONT_04_Check.x This script decideswhetheryourcalulationsareterminatedin a properway: (a) normaltermination? (b) geometryfullyoptimized? (c) imaginaryfrequencies? (d) G3MP2 Enthalpy? Ifyes FileswithpropercalculationsmovetotheMinCheckfolder Ifno Itautomaticallyresubmitsthejobintothequeueusing8 CPUsforeachcalculation Previouscalulation is storedinfileswithcold (input) and lold (output) extension

  7. The worstcase • Ifafterresubmission, no propercalculationsareobtained, thentrythefollowings: • Online help(findtheerrormessageinthe output): • CCL: googlee.g „ccl.net gaussianSCF not converged” • http://www.ace-net.ca/wiki/Gaussian_Error_Messages • Checkthestructure • Restartformthe minimum energystructure • Breakthesymmetry (Structuremodification & NoSymm) • Obtainstructurefromvibrationalanalysis (imaginaryfrequency)

  8. HORIZONT_05_DigestRUN • WARNING!!! Onlyafterallcalculationsarefine! • ItrunsHORIZONT_05_Digest.xautomatically • HORIZONT_05_Digest.xdoes: • Evaluates and collectsall of thedatayouneedfordiscussingthermodynamicalproperties of the species • Information is storedin .sdffiles WARNING!!! Usethe standard name of the file!!!

  9. Generatethe QM database • Command: cat *.sdf > database.txt mvdatabase.txtC2_H4_N0_O3_F0_S0_G3MP2B3.sdf (Gaussviewcanopenthis file) • Command: HORIZONT_06_sdf2csv.x C2_H4_N0_O3_F0_S0_G3MP2B3 This script creates an Excel readable file (C2_H4_N0_O3_F0_S0_G3MP2B3.csv) containingthermodynamicalproperties (Excel canopenthis file)

  10. Vielen Dank fürIhreAufmerksamkeit! Köszönöm a figyelmet! Dekujevám! Thank for your attention!

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