Supporting Information

ExcelAutomat – A Tool for Systematic

Processing of Files as Applied to Quantum

Chemical Calculations

Jalal Z. A. Laloo1, Nassirah Laloo2, Lydia Rhyman1,3,4 and Ponnadurai Ramasami*1,3

1Computational Chemistry Group, Department of Chemistry, Faculty of Science,

University of Mauritius, Réduit 80837, Mauritius

2Department of Industrial Systems Engineering, School of Innovative Technologies &

Engineering, University of Technology, Mauritius, La Tour Koenig, Pointe-aux-Sables

11129, Mauritius

3Department of Applied Chemistry, University of Johannesburg, Doornfontein Campus,

Johannesburg 2028, South Africa

4Department of Chemistry, University of Johannesburg, PO Box 524, Auckland Park,

Johannesburg, 2006, South Africa

*E-mail: p.ramasami@uom.ac.mu

Contents

Figure S1. Task processing in ExcelAutomat........................................................................4

Worksheets.............................................................................................................................4

Figure S2. “ParseFile” worksheet......................................................................................4

Figure S3. “GetTemplate” worksheet................................................................................5

Figure S4. “Routes” worksheet.........................................................................................5

Figure S5. “FileID” worksheet..........................................................................................6

Figure S7. Workflow to handle output files......................................................................8

Figure S8. Worksheet “ProcessFiles” showing optimised and error lists.........................9

Figure S9. “WinSCP” worksheet.......................................................................................9

Examples..............................................................................................................................10

Join files directly.............................................................................................................10

Join files and add filenames to title section.....................................................................10

Join files for batch processing.........................................................................................10

Split files as per last word................................................................................................10

Split files with numbered jobname..................................................................................10

Split files as per title section............................................................................................11

Generate file for intrinsic reaction coordinates computation from a transition

state file using the worksheet “GetTemplate”.................................................................11

Parse files.........................................................................................................................11

Generate FileID...............................................................................................................11

Process files with workflow............................................................................................11

Table S1. List of selected extracted parameters with their descriptions, data type

and routines. The units are according to the output files of the software package..............12

Figure S10. Sample VBA script to extract and display electronic energy...........................13

2

Figure S11. Result of running sample VBA code................................................................14

Figure S12. ExcelAutomat add-in (a) in MS Excel tab and (b) with numbered

parts in “(a)” magnified........................................................................................................14

Complete reference to Gaussian software package [reference (22)]....................................15

Complete reference to Gaussian software package [reference (56)]....................................16

Complete reference to Gaussian software package [reference (57)]....................................17

Complete reference to Amsterdam density functional program package [reference

(23)]......................................................................................................................................18

3

Figure S1. Task processing in ExcelAutomat.

Worksheets

Figure S2. “ParseFile” worksheet.

User selects worksheet

The required button is clicked

The prompts are followed

4

Figure S3. “GetTemplate” worksheet.

Figure S4. “Routes” worksheet.

5

Figure S5. “FileID” worksheet.

6

Newfilecode = 0

Get initials from “FileID” worksheet

For each folder

For each file with the initial and “.out” as

Extension. ‘Loop through the output files

Get filename

Get filecode from the filename

If filecode > newfilecode Then

filecode = newfilecode

End If

End For

End For

newfilecode = newfilecode + 1

Add initials to filecode for new fileID

Close file and display new fileID

Figure S6. Pseudocode for generating the fileID

7

Figure S7. Workflow to handle output files.

Error = l9999.exe?

8

Figure S8. Worksheet “ProcessFiles” showing optimised and error lists.

Figure S9. “WinSCP” worksheet.

9

Examples

Samples files are provided in the download folder of ExcelAutomat.

Join files directly

1. Select worksheet “JoinSplit”.2. Click on button “Direct”.3. Enter “mergedfile” as filename in input box and click the button “Okay”.4. Select all files in the folder “Join input” and click the button “Okay”..

The merged file is generated in the folder “Join input”.

Join files and add filenames to title section

1. Select worksheet “JoinSplit”.2. Click on button “Add filename to title section”.3. Enter “mergedfile2” as filename in input box and click the button “Okay”.4. Select all files in the folder “Join input” and click the button “Okay”..

The merged file is generated in the folder “Join input” with the filename appended to the title section.

Join files for batch processing

1. Select worksheet “JoinSplit”.2. Click on button “Batch”.3. Enter “mergedfilebatch” as filename in input box and click the button “Okay”.4. Select all files in the folder “Join input” and click the button “Okay”..

The batch file is generated in the folder “Join input”.

Split files as per last word

1. Select worksheet “JoinSplit”.2. Click on button “As per last word in title section”.3. Select files in folder “Split” and click the button “Okay”..

The split files are generated in the folder “Split”.

Split files with numbered jobname

1. Select worksheet “JoinSplit”.2. Click on button “With numbered jobname”.3. Select files in folder “Split” and click the button “Okay”..

The split files are generated with a sequential jobname in the folder “Split”.

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Split files as per title section

1. Select worksheet “JoinSplit”.2. Click on button “As per title section”.3. Select files in folder “Split” and click the button “Okay”..

The split files are generated as per the title section in the folder “Split”.

Generate file for intrinsic reaction coordinates computation from a transition state file using the worksheet “GetTemplate”

1. Select worksheet “GetTemplate”2. Click on button “Get new template from output file”.3. Select file “TS” in folder “Gaussian|” of folder “Get template” and click okay.4. Select a checkbox for route containing the keyword “IRC” in worksheet “Routes”.5. In worksheet “GetTemplate”, click on button “Cycle through checked routes” until the

route containing the keyword “IRC” is reached.6. Amend the third line by writing “IRC” in the cell.7. Click on button “Print to Custom Folder”.8. Enter “IRC” as filename as click okay.9. Select a folder and click the button “Okay”..

Parse files

1. Select the worksheet “ParseFile”.2. Clear all checkboxes.3. Select the checkboxes for the parameters “Routes”, “Title” and “Atom coordinates”.4. Click on “Extract selected parameters” button.5. Select files in folder “ParseFile” and click the button “Okay”..

The selected parameters are displayed.

Generate FileID

1. Select the worksheet “FileID”2. Update the folder location with path to real folders.3. Click on “Get new fileID”.

Process files with workflow

1. Select the worksheet “ProcessFiles”2. Click on process files.3. Select all files in folder “ProcessFiles” and click the button “Okay”..

The files are processed and listed.

11

Table S1. List of selected extracted parameters with their descriptions, data type and routines. The units are according to the output files of the software package.

Parameter name Description Data type

Routine Default parser

Atomcoordinate Atomic numbers and coordinates

1D Array

Getatomlistandcoordinates Gaussian, Gamess

Atomlist List of atoms 1D Array

Getatomlistandcoordinates Gaussian, Gamess

Charge Charge of structure Integer Getchargeandmultiplicity Gaussian

Errorcode Error description upon error termination

String Getjobterminationstatus Gaussian

Fouryestatus Check for 4 consecutive yes (value=1 if true)

Integer Get4yestatus Gaussian

Freqnum Vibrational frequencies 1D Array

GetnimagfreqIR Gaussian, Gamess

Ircpointotal Total number of points in IRC computation

Integer GetIRCpointotal Gaussian,

Irnum Infrared intensities ID Array

GetnimagfreqIR Gaussian, Gamess

Jobtype Type of job. Value = “Opt+freq” when route section includes optimisation and a frequency computation, “Optimisation” when no frequency computation included, “Freq” when no optimisation included, “NBO” or “IRC”

String Getjobtype Gaussian

Modetotal Total number of modes of frequencies or IR intensities

Integer GetnimagfreqIR Gaussian

Multiplicity Multiplicity of structure Integer Getchargeandmultiplicity Gaussian

Natom Number of atoms Integer Getnumberatoms Gaussian, Gamess

Nimag Number of imaginary frequencies

Integer GetnimagfreqIR Gaussian

Njob Number of jobs in file Integer jobtermination

Pointgroup Point group of structure String Getpointgroup Gaussian, Gamess

Revision Revision of Gaussian String Getrevision Gaussian, Gamess

Route Route section String Getroute Gaussian, Gamess

Tenergy Sum of electronic and zero-point energies

String Gethermodata Gaussian

Tenthalpy Sum of electronic and thermal enthalpies

String Gethermodata Gaussian

Tentropy Entropy String Gethermodata Gaussian

12

Terminationstatus Check for normal and error termination. Value = 1 for normal termination, 2 for error termination and 3 if job not completed

Integer Getjobterminationstatus Gaussian

Tgibbs Sum of electronic and thermal free energies

String Gethermodata Gaussian

Title Title section String Getitle Gaussian, Gamess

Scfenergy Last SCF energy String Getscfenergy Gaussian, Gamess

1: Option vbasupport 1 'Do not include this line in MS Excel

2: Sub customscript()

3: 'The variables are declared.

4: Dim mainsheet,filepath,filepathlist,extractionfile As Variant

5: 'The user is prompted to select the output file

6: filepathlist = selectfilesfd

7: For Each filepath in filepathlist

8: If filepath <> "" 'check if no files are selected

9:

10:

11:

12:

13:

14:

15:

16:

17:

18:

'The file is opened in MS Excel

Call openwrkbk(filepath)

extractionfile = ActiveWorkbook.Name

'The thermodata is extracted

Call gethermodata

'The file is closed

Workbooks(extractionfile).Close Savechanges:=False

'The values are displayed in excel worksheet

Cells(1, 1).Value = "Sum of electronic and zero-point energies"

Cells(1, 2).Value = Tenergy

19: End if

20: Next

13

21: End Sub

Figure S10. Sample VBA script to extract and display electronic energy.

Figure S11. Result of running sample VBA code.

(a)

(b)

Figure S12. ExcelAutomat add-in (a) in MS Excel tab and (b) with numbered parts in “(a)”

magnified.

1

2

3

4

1

2 3 4

14

Complete reference to Gaussian software package [reference (22)]

Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.;

Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.;

Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, D. J.; Hada, M.; Ehara, M.;

Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.;

Vreven, T.; Montgomery, J. A., Jr.; Peralta, E.; Ogliaro, F.; Bearpark, M.; Heyd, J.; Brothers, E.;

Kudin, N.; Staroverov, N.; Keith, T.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell,

A.; Burant, C.; Iyengar, S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, M.; Klene, M.; Knox, E.;

Cross, B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, E.; Yazyev, O.;

Austin, J.; Cammi, R.; Pomelli, C.; Ochterski, W.; Martin, L.; Morokuma, K.; Zakrzewski, G.;

Voth, A.; Salvador, P.; Dannenberg, J.; Dapprich, S.; Daniels, D.; Farkas, Ö.; Foresman, B.;

Ortiz, V.; Cioslowski, J.; Fox, J. D. Gaussian 09, Revision D.01, Gaussian, Inc., Wallingford CT,

2009.

15

Complete reference to Gaussian software package [reference (56)]

Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.;

Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.;

Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, D. J.; Hada, M.; Ehara, M.;

Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.;

Vreven, T.; Montgomery, J. A., Jr.; Peralta, E.; Ogliaro, F.; Bearpark, M.; Heyd, J.; Brothers, E.;

Kudin, N.; Staroverov, N.; Keith, T.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell,

A.; Burant, C.; Iyengar, S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, M.; Klene, M.; Knox, E.;

Cross, B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, E.; Yazyev, O.;

Austin, J.; Cammi, R.; Pomelli, C.; Ochterski, W.; Martin, L.; Morokuma, K.; Zakrzewski, G.;

Voth, A.; Salvador, P.; Dannenberg, J.; Dapprich, S.; Daniels, D.; Farkas, Ö.; Foresman, B.;

Ortiz, V.; Cioslowski, J.; Fox, J. D. Gaussian 09, Revision C.01, Gaussian, Inc., Wallingford CT,

2009.

16

Complete reference to Gaussian software package [reference (57)]

Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.;

Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li,

X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.;

Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.;

Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.;

Petrone, A.; Henderson, T.; Ranasinghe, D.; Zakrzewski, V. G.; Gao, J.; Rega,

N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.;

Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven,

T.; Throssell, K.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.

J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.;

Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.;

Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.;

Cammi, R.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Farkas, O.;

Foresman, J. B.; Fox, D. J. Gaussian 16, Revision A.03, Gaussian, Inc., Wallingford

CT, 2016.

17

Complete reference to Amsterdam density functional program package

[reference (23)]

Baerends, E. J.; Ziegler, T.; Autschbach, J.; Bashford, D.; Bérces, A.; Bickelhaupt, F. M.; Bo, C.;

Boerrigter, P.M.; Cavallo, L.; Chong, D. P.; Deng, L.; Dickson, R. M.; Ellis, D. E.; van Faassen,

M.; Fan, L.; Fischer, T. H.; Fonseca Guerra, C.; Ghysels, A.; Giammona, A.; van Gisbergen, S.

J. A.; Götz, A.W.; Groeneveld, J. A.; Gritsenko, O. V.; Grüning, M.; Gusarov, S.; Harris, F. E.;

van den Hoek, P.; Jacob, C. R.; Jacobsen, H.; Jensen, L.; Kaminski, J. W.; van Kessel, G.;

Kootstra, F.; Kovalenko, A.; Krykunov, M. V.; van Lenthe, E.; McCormack, D. A.; Michalak,

A.; Mitoraj, M.; Neugebauer, J.; Nicu, V. P.; Noodleman, L.; Osinga, V. P.; Patchkovskii, S.;

Philipsen, P. H. T.; Post, D.; Pye, C. C.; Ravenek, W.; Rodríguez, J. I.; Ros, P.; Schipper, P. R.

T.; Schreckenbach, G.; Seldenthuis, J. S.; Seth, M.; Snijders, J. G.; Solà, M.; Swart, M.; Swer-

hone, D.; te Velde, G.; Vernooijs, P.; Versluis, L.; Visscher, L.; Visser, O.;Wang,

F.;Wesolowski, T. A.; vanWezenbeek, E. M.;Wiesenekker, G.;Wolff, S. K.;Woo, T. K.;

Yakovlev, A. L. ADF, Amsterdam density functional program, 2010. Available at:

http://www.scm.com.

18