From owner-chemistry@ccl.net Thu Feb 22 00:46:01 2018 From: "Jalal L jzalchem[-]gmail.com" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53201-180222000716-9345-GCUTlXm1ZnD3BSNkVcy55A]=[server.ccl.net> X-Original-From: Jalal L Content-Type: multipart/alternative; boundary="001a11352ed20e339d0565c604de" Date: Thu, 22 Feb 2018 09:07:09 +0400 MIME-Version: 1.0 Sent to CCL by: Jalal L [jzalchem*gmail.com] --001a11352ed20e339d0565c604de Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Dear Cesar, Thank you very much for your interest in ExcelAutomat and the positive feedback. Kindly refer to the setup instructions on t= he website. You may wish to post your specific compatibility and configuration issues in the forum section of the ExcelAutomat website . Do not hesitate should you need further assistance. Kind regards, Jalal Laloo On Wed, Feb 21, 2018 at 12:38 PM, C=C3=A9sar Alejandro Urbina Blanco c.alejandro.ub+/-gmail.com wrote: > 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 hav= e > 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 wit= h >>> varying basis sets. My approach has been to create a database file wit= h >>> names such as atom_basis_set and another template file with the startin= g >>> geometry. I then call the database file, read the template, and write t= he >>> appropriate atom_basis_set and save as a new file. This so far gets th= e >>> job done, but still requires some manual changes. Ideally I want someth= ing >>> 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_03_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 ki= nd >>> 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 = what >>> 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/ >>> >> --001a11352ed20e339d0565c604de Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear Cesar,

Thank you very much for your in= terest in ExcelAutomat and the positive feedback.

Kindly ref= er to the=C2=A0setup instructions=C2=A0on the website.

<= /div>
You may wish to post your specific compatibility and configuration iss= ues in the=C2=A0forum=C2=A0section of the=C2=A0ExcelAutomat website.

Do not hesitate should you need further assistance.

Kind re= gards,
Jalal Laloo


On Wed, Feb 21, 2018 at 12:38 PM, C=C3=A9sar Alejandr= o Urbina Blanco c.alejandro.ub+/-gmail.com= <owner-chemistry .. ccl.net> wrote:
Dear Jalal,=C2=A0

I just = saw your tool Excel Automat and I think it's super awesome. However, I = am running gaussian=C2=A016 and it seems it that it is not really compatibl= e.
I'm also having some troubles configuring the upload funct= ion. Do you have 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. Che= ck Orca Input Library.

Em 20 de fev de 2018 12:32 PM, "Geoffrey Hutchison geoff.hutchison*|= *gmail.com" <owner-chemistry= :_:ccl.net> escreveu:
=
I find myself using bash, a= wk/sed, Python, and the fantastic egrep utility for the bulk of the work (f= inding frequencies, enthalpies,=C2=A0 termination instances) for the bulk o= f the work.

Oh, please, p= lease 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.=C2=A0

<= div dir=3D"ltr">
Suppose I have 1 geometry, and want to generate severa= l 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 fil= e with the starting geometry. I then call the database file, read the templ= ate, 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. Ide= ally I want something where I can use the terminal for user input of the te= mplate file, and atom/basis set descriptors.=C2=A0 This seems doable, but I= cant quite figure out a Pythonic way of doing this.
<= /blockquote>
Someone mentioned Ope= n Babel, which allows specifying keywords from the command-line (-xk "= #n wB97/def2-SVP Opt") or a file (-xf atom_basis_set) for batch writin= g input files. Obviously, we do this in my group over hundreds or thousands= of files (e.g., for Gaussian=C2=A0= https://open-babel.readthedocs.io/en/latest/FileFormats/Gaussian_= 98_or_03_Input.html)

You might also want to check ou= t 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 "calculat= or" to write each basis set.

Again, the main = thing is that you'll be more productive if you take a little time and c= heck for existing community packages that probably do what you want.
<= div>
Cheers,
-Geoff

-= --
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
twitter: [a]ghutchis

--001a11352ed20e339d0565c604de-- From owner-chemistry@ccl.net Thu Feb 22 13:31:01 2018 From: "=?UTF-8?Q?=C5=81ukasz_Mentel?= lmmentel:gmail.com" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks - Recap List Message-Id: <-53202-180222132925-13827-vcTZEDKhWLqd55fr9YW1UQ[a]server.ccl.net> X-Original-From: =?UTF-8?Q?=C5=81ukasz_Mentel?= Content-Type: multipart/alternative; boundary="94eb2c0961cc884a9b0565d13838" Date: Thu, 22 Feb 2018 18:29:14 +0000 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?=C5=81ukasz_Mentel?= [lmmentel__gmail.com] --94eb2c0961cc884a9b0565d13838 Content-Type: text/plain; charset="UTF-8" Dear All, Thank you for sharing the list of very valuable tools. As an additional resource I would also like to add a list of chemistry related utilities for python fans: https://github.com/lmmentel/awesome-python-chemistry. Next to a considerable list of computational chemistry related tools it contains also ones for general chemistry applications. Please let me know if you feel the list could be updated with tools/scripts/libraries that I missed. Best, Lukasz 2018-02-21 20:39 GMT+01:00 Guzman, Francisco fg58 . njit.edu < owner-chemistry%ccl.net>: > 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 > --94eb2c0961cc884a9b0565d13838 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Dear All,

Thank you for sharing the lis= t of very valuable tools. As an additional resource I would also like to ad= d a list of chemistry related utilities for python fans:=C2=A0https://github.com/lmme= ntel/awesome-python-chemistry. Next to a considerable list of computati= onal chemistry related tools it contains also ones for general chemistry ap= plications. Please let me know if you feel the list could be updated with t= ools/scripts/libraries that I missed.

Best,
<= div>Lukasz

2018-02-21 20:39 GMT+01:00 Guzman, Francisco fg58 . njit.edu <owner-chemistry%ccl.net>:
<= blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px= #ccc solid;padding-left:1ex">
Thank you all for your = responses and participation in this discussion. I have compiled a copy/past= a of the mentioned programs.=C2=A0 I hope it is of some use to all of you. = Please keep posting any useful libraries/scripts/programs that may be missi= ng.

Happy scripting.
=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
PhD Candidate
Otto H. York Department of Chemi= cal, Biological and Pharmaceutical Engineering
New Jersey Institute of T= echnology

--94eb2c0961cc884a9b0565d13838-- From owner-chemistry@ccl.net Thu Feb 22 18:03:00 2018 From: "Guzman, Francisco fg58_-_njit.edu" To: CCL Subject: CCL: Use cclib functionality as part of Python script? Message-Id: <-53203-180222172130-12898-ooX9pXsZdwhepGX8GG+huA{}server.ccl.net> X-Original-From: "Guzman, Francisco" Content-Type: multipart/alternative; boundary="001a11477a3a396d9d0565d476be" Date: Thu, 22 Feb 2018 17:21:13 -0500 MIME-Version: 1.0 Sent to CCL by: "Guzman, Francisco" [fg58%x%njit.edu] --001a11477a3a396d9d0565d476be Content-Type: text/plain; charset="UTF-8" Hello CCL'ers Does anyone have experience using/importing parts cclib as part of a Python script? I want to be able to extract the CCSD(T) energies, convert from eV to Hartrees, and use plug these energies into an equation extrapolation to the CBS limit. This is straight forward enough to do in bash, but I can't extract these energies the same way I would using a terminal using a Python script. Using a terminal, I can extract the energies executing: ccget ccenergies filname.out However, I want to be able to store this ouput as a new variable as part of a larger Python script I am making for my own post processing. I've tried to "import cclib" in my script, but I don't know how to repeat the output of "ccget ccenergies" as I would using a terminal. Thanks, /python novice -- 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 --001a11477a3a396d9d0565d476be Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello CCL'ers

Does anyone = have experience using/importing parts cclib as part of a Python script?
I want to be able to extract the CCSD(T) energies, convert from eV to = Hartrees, and use plug these energies into an equation extrapolation to the= CBS limit. This is straight forward enough to do in bash, but I can't = extract these energies the same way I would using a terminal using a Python= script.

Using a terminal, I can extract the energies executin= g:
ccget ccenergies filname.out

However, I want to be able to store this ouput as a = new variable as part of a larger Python script I am making for my own post = processing.

I've tried to "import cclib" i= n my script, but I don't know how to repeat the output of "ccget c= cenergies" as I would using a terminal.

Thanks,
<= br>
/python novice

--
Francisco Guzman<= /span>
PhD Candidate
Otto H. York Department of Che= mical, Biological and Pharmaceutical Engineering
New Jersey Institute of= Technology
<= /div>
--001a11477a3a396d9d0565d476be--