From owner-chemistry@ccl.net Wed Feb 21 10:51:00 2018 From: "=?UTF-8?Q?C=C3=A9sar_Alejandro_Urbina_Blanco?= c.alejandro.ub+/-gmail.com" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53199-180221033819-29431-steYR7b9dvBMAW9QR5Mn3g..server.ccl.net> X-Original-From: =?UTF-8?Q?C=C3=A9sar_Alejandro_Urbina_Blanco?= Content-Type: multipart/alternative; boundary="001a113cfd060baff00565b4d95b" Date: Wed, 21 Feb 2018 08:38:02 +0000 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?C=C3=A9sar_Alejandro_Urbina_Blanco?= [c.alejandro.ub(~)gmail.com] --001a113cfd060baff00565b4d95b Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Jalal, I just saw your tool Excel Automat and I think it's super awesome. However, I am running gaussian 16 and it seems it that it is not really compatible. I'm also having some troubles configuring the upload function. Do you have a setup manual? I am sure I'm missing something. Cheers Cesar *Dr. C=C3=A9sar A. Urbina-Blanco* *Postdoctoral Research Fellow* *Laboratory for Chemical Technology (LCT) * Department of Materials, Textiles and Chemical Engineering Technologiepark 914, 9052 Ghent, Belgium T: +32 9 331 17 14 M: +32 480 44 87 13 http://www.lct.ugent.be/ http://helpdesk.UGent.be/e-maildisclaimer.php On Tue, Feb 20, 2018 at 7:53 PM Marcos Verissimo Alves marcos_verissimo%x% id.uff.br wrote: > There is an Orca interface for ASE. Check Orca Input Library. > > Em 20 de fev de 2018 12:32 PM, "Geoffrey Hutchison geoff.hutchison*|* > gmail.com" escreveu: > >> I find myself using bash, awk/sed, Python, and the fantastic egrep >> utility for the bulk of the work (finding frequencies, enthalpies, >> termination instances) for the bulk of the work. >> >> >> Oh, please, please use a package like cclib or Open Babel ( >> http://cclib.github.io) for parsing. The whole point of these community >> projects is that they easily handle reading output files and grab >> attributes. >> >> Suppose I have 1 geometry, and want to generate several input files with >> varying basis sets. My approach has been to create a database file with >> names such as atom_basis_set and another template file with the starting >> geometry. I then call the database file, read the template, and write th= e >> appropriate atom_basis_set and save as a new file. This so far gets the >> job done, but still requires some manual changes. Ideally I want somethi= ng >> where I can use the terminal for user input of the template file, and >> atom/basis set descriptors. This seems doable, but I cant quite figure = out >> a Pythonic way of doing this. >> >> Someone mentioned Open Babel, which allows specifying keywords from the >> command-line (-xk "#n wB97/def2-SVP Opt") or a file (-xf atom_basis_set) >> for batch writing input files. Obviously, we do this in my group over >> hundreds or thousands of files (e.g., for Gaussian >> https://open-babel.readthedocs.io/en/latest/FileFormats/Gaussian_98_or_0= 3_Input.html >> ) >> >> You might also want to check out ASE (https://wiki.fysik.dtu.dk/ase/). >> It's largely for solid-state codes, but definitely has code for this kin= d >> of task - you set up a "calculator" to write each basis set. >> >> Again, the main thing is that you'll be more productive if you take a >> little time and check for existing community packages that probably do w= hat >> you want. >> >> Cheers, >> -Geoff >> >> --- >> Prof. Geoffrey Hutchison >> Department of Chemistry >> University of Pittsburgh >> tel: (412) 648-0492 >> email: geoffh[a]pitt.edu >> twitter: [a]ghutchis >> web: https://hutchison.chem.pitt.edu/ >> > --001a113cfd060baff00565b4d95b Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Jalal,=C2=A0

I just saw your tool = Excel Automat and I think it's super awesome. However, I am running gau= ssian=C2=A016 and it seems it that it is not really compatible.
I= 'm also having some troubles configuring the upload function. Do you ha= ve a setup manual? I am sure I'm missing something.=C2=A0
Cheers
Cesar=C2=A0

Dr. C=C3=A9sar A. Urbina-Blanco

Postdoctoral Research Fellow

Laboratory for Chemical Technology (LCT)

Department of Materials, Textiles and Chemical Engineering

Technologiepark 914, 9052 Ghent, Belgium

T: +32 9 331 17 14=C2=A0 M: +32 480 44 87 13

http://www.lct.ugent.be/=C2=A0 http://helpdesk.UGent.be/e-maildisclaimer.php

=C2=A0

On Tue, Feb 20, 2018 at 7:53 PM Marcos Ve= rissimo Alves marcos_verissimo%x%id.uff.br= <owner-chemistry],[ccl.net= > wrote:
There= is an Orca interface for ASE. Check Orca Input Library.

Em 20 de fev de 2018 12:32 PM, "Ge= offrey Hutchison geoff.hutchison*|*gmail.com" <owner-chemistry:_:ccl.net> escreveu:
I find myself using bash, awk/sed, Python, and the fantastic egrep u= tility for the bulk of the work (finding frequencies, enthalpies,=C2=A0 ter= mination instances) for the bulk of the work.

Oh, please, please use a package like cclib or Open Ba= bel (http://cclib.gith= ub.io) for parsing. The whole point of these community projects is that= they easily handle reading output files and grab attributes.=C2=A0
Suppose I have 1 geo= metry, and want to generate several input files with varying basis sets.=C2= =A0 My approach has been to create a database file with names such as atom_= basis_set and another template file with the starting geometry. I then call= the database file, read the template, and write the appropriate atom_basis= _set and save as a new file.=C2=A0 This so far gets the job done, but still= requires some manual changes. Ideally I want something where I can use the= terminal for user input of the template file, and atom/basis set descripto= rs.=C2=A0 This seems doable, but I cant quite figure out a Pythonic way of = doing this.
Someone mentioned Open Babel, which allows specifying keywords= from the command-line (-xk "#n wB97/def2-SVP Opt") or a file (-x= f atom_basis_set) for batch writing input files. Obviously, we do this in m= y group over hundreds or thousands of files (e.g., for Gaussian=C2=A0https://open-babel.readthedocs.io/en/late= st/FileFormats/Gaussian_98_or_03_Input.html)

You might al= so want to check out ASE (https://wiki.fysik.dtu.dk/ase/). It's largely for solid= -state codes, but definitely has code for this kind of task - you set up a = "calculator" to write each basis set.

Ag= ain, the main thing is that you'll be more productive if you take a lit= tle time and check for existing community packages that probably do what yo= u want.

Cheers,
-Geoff

---
Prof. Geoffrey Hutchison
Department of= Chemistry
University of Pittsburgh
twitter: [a]ghutchis
<= /div> --001a113cfd060baff00565b4d95b-- From owner-chemistry@ccl.net Wed Feb 21 15:41:00 2018 From: "Guzman, Francisco fg58 . njit.edu" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks - Recap List Message-Id: <-53200-180221143945-31943-jnXYRpyx88igNz9tEkJccQ::server.ccl.net> X-Original-From: "Guzman, Francisco" Content-Type: multipart/alternative; boundary="001a114901ca787a300565be16fe" Date: Wed, 21 Feb 2018 14:39:38 -0500 MIME-Version: 1.0 Sent to CCL by: "Guzman, Francisco" [fg58~~njit.edu] --001a114901ca787a300565be16fe Content-Type: text/plain; charset="UTF-8" Thank you all for your responses and participation in this discussion. I have compiled a copy/pasta of the mentioned programs. I hope it is of some use to all of you. Please keep posting any useful libraries/scripts/programs that may be missing. Happy scripting. *Some interesting links/scripts:* *Vladislav Vasilyev Homepage (**several tools**; **CBS exptrapolation calculator**)* http://sf.anu.edu.au/~vvv900/ *Look4bas (basis set builder)*https://github.com/mfherbst/lo *Gaussian Tools (Some Gaussian post processing scripts)* https://github.com/chauncey-ga *cclib (Python library for parsing and interpreting results)* https://cclib.github.io/ *ESIgen **(create supporting information)*: https://github.com/insilichem/ Meant to create automated "Supporting Information" reports ready for publication attachment, but it also works in the command-line for more day-to-day tasks. It can be used in two ways: with a webserver (public demo here: http://esi.insilichem.com/), or from the command-line with the `esigen` executable. *Cauchian **(**Chimera GUI extension to create Gaussian input files**)*: https://github.com/insilichem/ UCSF Chimera extension that provides a GUI to create Gaussian input files. Created to deal with QM/MM, it also supports standard QM jobs. The dialog includes a fast Basis Set explorer like the one in BSE thanks to the included ebsel fork. *Pnictogen* (input file builder based on Jinja) https://github.com/dudektria/pnictogen *ExcelAutomat (Excel/LibreOffice VBA input/output processing)* ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations . https://sites.google.com/view/excelautomat/home *Launchanew (**tools for managing Gaussian calculations; **might be outdated)* https://github.com/esmuigors/ -- Francisco Guzman PhD Candidate Otto H. York Department of Chemical, Biological and Pharmaceutical Engineering New Jersey Institute of Technology Email: fg58-#-njit.edu, guzman.research-#-gmail.com --001a114901ca787a300565be16fe Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Thank you all for your responses and participation in= this discussion. I have compiled a copy/pasta of the mentioned programs.= =C2=A0 I hope it is of some use to all of you. Please keep posting any usef= ul libraries/scripts/programs that may be missing.

Happy scrip= ting.
=09 =09 =09 =09

Some interesti= ng links/scripts:


Vladislav Vasilyev Homepage (several tools; CBS exptrapolation calculator)
http://sf.anu.edu.au/~vvv900/

Look4bas (basis set builder)
https://github.com/mfherbst/lo

Gaussian Tools (Some Gaussian post processing scripts)

https://github.com/ch= auncey-ga

cclib (Python library for parsing and interpreting results)

https://cclib.github.io/

ESIgen (create supporting information):=20

https://github.com/insilichem/

Meant to create automated "Supporting Information" reports ready for publication attachment, but it also works in the command-line for more day-to-day tasks. It can be used in two ways: with a webserver (public demo here: http://esi.insilichem.com/), or from the command-line with the `esigen` executable.=20

Cauchian (= Chimera GUI extension to create Gaussian input files):=20

https://github.com/insilich= em/

UCSF Chimera extension that provides a GUI to create Gaussian input files. Created to deal with QM/MM, it also supports standard QM jobs. The dialog includes a fast Basis Set explorer like the one in BSE thanks to the included ebsel fork.

Pnictogen (input file builder based on Jinja)

https://github.com/dudektria/pnictogen

ExcelAutomat (Excel/LibreOffice VBA input/output processing)

=C2=A0ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations.

https://sites.google.com/view/excelautomat= /home

Launchanew (tools for managing Gaussian calculations; might be outdated)

https://github.com/esmuigors/




--
Francisco Guzman
P= hD Candidate
Otto H. York Department of Chemical, Biological and P= harmaceutical Engineering
New Jersey Institute of Technology
<= /div>
--001a114901ca787a300565be16fe--