Computational WorkFlow From the initial structures to their computed thermodynamical properties

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

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

HORIZONT_02_sdf4CHNOFS.x 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 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!

HORIZONT_03_RUN4.x HORIZONT_03_RUN4.x Automatically finds files with.com extension (Gaussian input files) in the subfolders and submits all of them into the queue using 4 CPUs for each calculations Check your calculation using qstat and qhost commands AFTER all your Gaussian calculations are terminated!

HORIZONT_04_CheckRUN HORIZONT_04_CheckRUN Automatically finds files with.com and.log extensions (Gaussian input and output files) in the subfolders It runs automatically the HORIZONT_04_Check.x This script decides whether your calulations are terminated in a proper way: (a) normal termination? (b) geometry fully optimized? (c) imaginary frequencies? (d) G3MP2 Enthalpy? If yes Files with proper calculations move to the MinCheck folder If no It automatically resubmits the job into the queue using 8 CPUs for each calculation Previous calulation is stored in files with cold (input) and lold (output) extension

The worst case If after resubmission, no proper calculations are obtained, then try the followings: – Online help (find the error message in the output): CCL: google e.g „ccl.net gaussian SCF not converged” – Check the structure Restart form the minimum energy structure Break the symmetry (Structure modification & NoSymm ) Obtain structure from vibrational analysis (imaginary frequency)

HORIZONT_05_DigestRUN WARNING!!! Only after all calculations are fine! It runs HORIZONT_05_Digest.x automatically HORIZONT_05_Digest.x does: – Evaluates and collects all of the data you need for discussing thermodynamical properties of the species – Information is stored in.sdf files WARNING!!! Use the standard name of the file!!!

Generate the QM database Command: cat *.sdf > database.txt mv database.txt C2_H4_N0_O3_F0_S0_G3MP2B3.sdf (Gaussview can open this 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 ) containing thermodynamical properties (Excel can open this file)

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