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

ComputationalKnow 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.xszorim@cluster:~/SummerSchool_2014$ HORIZONT_02_sdf4CHNOFS.x C2_H4_N0_O3_F0_S0.sdf********************************************RUN****************************************************This script generates standard Cartesian Gaussian inputsfrom 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_S0nC: 2 nH: 4 nN: 0 nO: 3 nF: 0 nS: 045 molecules converted45 files output. The first is C2_H4_N0_O3_F0_S0_1.tmp0900 audit log messages********************************************END****************************************************Thu May 15 07:51:37 UTC 2014szorim@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!

HORIZONT_03_RUN4.xszorim@cluster:~/SummerSchool_2014$ 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_CheckRUNszorim@cluster:~/SummerSchool_2014$ 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 yesFiles with proper calculations move to the MinCheck folder

If noIt automatically resubmits the job into the queue using 8 CPUs for each calculationPrevious 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”• http://www.ace-net.ca/wiki/Gaussian_Error_Messages

– 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 filesWARNING!!! 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_G3MP2B3This script creates an Excel readable file (C2_H4_N0_O3_F0_S0_G3MP2B3.csv) containing thermodynamical properties (Excel can open this file)

Vielen Dank für Ihre Aufmerksamkeit!Köszönöm a figyelmet!Dekuje vám!Thank for your attention!