From owner-chemistry@ccl.net Tue Feb 20 00:50:00 2018 From: "dipankar roy theodip::gmail.com" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53190-180220004823-23525-uykGs2U+HJPQbM0P8nFjfQ-*-server.ccl.net> X-Original-From: dipankar roy Content-Type: multipart/alternative; boundary="94eb2c1c1b7c500a3805659e5bb9" Date: Mon, 19 Feb 2018 22:48:13 -0700 MIME-Version: 1.0 Sent to CCL by: dipankar roy [theodip%x%gmail.com] --94eb2c1c1b7c500a3805659e5bb9 Content-Type: text/plain; charset="UTF-8" Hi, Input file format is code/software specific so generalization may be an issue. Open babel can make input file with -xk option to add job specific sections. An interesting perl script for QM calculation setup is described for RESP charge generation in REDDB. One can get a starting point from there I guess. best, Dipankar On Feb 19, 2018 8:29 PM, "Guzman, Francisco fg58[a]njit.edu" < owner-chemistry-*-ccl.net> wrote: > Hello Fellow CCL'ers, > > I would like to start a discussion as to some of the tools/scripts some of > you use to build input files and analyze results. > > 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. However, as of late I want to start > streamlining an input file generation script and here is where I can't > quite figure out the best approach. > > 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 the > 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 something > 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. > > > > > *Some interesting links/scripts:* > > *Vladislav Vasilyev Homepage (great resource)* > http://sf.anu.edu.au/~vvv900/ > > > *Look4bas (basis set builder)*https://github.com/mfherbst/look4bas > > *Gaussian Tools (Some Gaussian post processing scripts)* > https://github.com/chauncey-garrett/gaussian-tools > > > > -- > Francisco Guzman > PhD Candidate > Otto H. York Department of Chemical, Biological and Pharmaceutical > Engineering > New Jersey Institute of Technology > Email: fg58|a|njit.edu, guzman.research|a|gmail.com > --94eb2c1c1b7c500a3805659e5bb9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi,
Input file format is code/software s= pecific so generalization may be an issue. Open babel can make input file w= ith -xk option to add job specific sections.=C2=A0
A= n interesting perl script for QM calculation setup is described for RESP ch= arge generation in REDDB. One can get a starting point from there I guess.<= /div>

best,
Dipankar

On Feb 19, 2018 8:29 PM, "Guzman, Francisco fg58[a]njit.edu" <owner-chemistry-*-ccl.net> wrote:
Hello Fellow CCL'ers,<= br>
I would like to start a discussion as to some of the tool= s/scripts some of you use to build input files and analyze results.=C2=A0 <= br>
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. However, as of late I want to= start streamlining an input file generation script and here is where I can= 't quite figure out the best approach.

Suppose I have 1 geometr= y, 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_basi= s_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 req= uires some manual changes. Ideally I want something where I can use the ter= minal for user input of the template file, and atom/basis set descriptors.= =C2=A0 This seems doable, but I cant quite figure out a Pythonic way of doi= ng this.




= Some interesting links/scripts:

Vladislav Vasil= yev Homepage (great resource)
http://sf.anu.edu.a= u/~vvv900/

Look4bas (basis set builder)
https://git= hub.com/mfherbst/look4bas

Gaussi= an Tools (Some Gaussian post processing scripts)
https://= github.com/chauncey-garrett/gaussian-tools



--
Franc= isco Guzman
PhD Candidate
Otto H. York Department of C= hemical, Biological and Pharmaceutical Engineering
New Jersey Institute = of Technology
--94eb2c1c1b7c500a3805659e5bb9-- From owner-chemistry@ccl.net Tue Feb 20 03:49:01 2018 From: "=?UTF-8?Q?Jaime_Rodr=C3=ADguez=2DGuerra?= jaime.rodriguezguerra:-:uab.cat" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53191-180220034633-6708-QYz9EfEQswUHZnTkqbt9iw]^[server.ccl.net> X-Original-From: =?UTF-8?Q?Jaime_Rodr=C3=ADguez=2DGuerra?= Content-Type: multipart/alternative; boundary="f403043e8a3cdfa71e0565a0d7ee" Date: Tue, 20 Feb 2018 09:45:54 +0100 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?Q?Jaime_Rodr=C3=ADguez=2DGuerra?= [jaime.rodriguezguerra,uab.cat] --f403043e8a3cdfa71e0565a0d7ee Content-Type: text/plain; charset="UTF-8" Hi! I am so glad you are asking this. I have developed some tools that might be helpful! Indeed, that same frustration you mention is what led me to create some of these in the first place. - *ESIgen*: https://github.com/insilichem/esigen 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. Source code is available in GitHub if you want to take a look in how this is implemented (hint: cclib+jinja), and a manuscript is already under revision. - *Cauchian*: https://github.com/insilichem/plume_cauchian 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. Check the code of the pygaussian module and use that in your scripts, but maybe it's too specific. I think a simpler approach using Jinja templates would be enough. In fact, if there's enough interest, we can start something! Feel free to ask any questions. I'd be happy to answer :) 2018-02-20 3:07 GMT+01:00 Guzman, Francisco fg58[a]njit.edu < owner-chemistry###ccl.net>: > Hello Fellow CCL'ers, > > I would like to start a discussion as to some of the tools/scripts some of > you use to build input files and analyze results. > > 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. However, as of late I want to start > streamlining an input file generation script and here is where I can't > quite figure out the best approach. > > 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 the > 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 something > 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. > > > > > *Some interesting links/scripts:* > > *Vladislav Vasilyev Homepage (great resource)* > http://sf.anu.edu.au/~vvv900/ > > > *Look4bas (basis set builder)*https://github.com/mfherbst/look4bas > > *Gaussian Tools (Some Gaussian post processing scripts)* > https://github.com/chauncey-garrett/gaussian-tools > > > > -- > Francisco Guzman > PhD Candidate > Otto H. York Department of Chemical, Biological and Pharmaceutical > Engineering > New Jersey Institute of Technology > Email: fg58|a|njit.edu, guzman.research|a|gmail.com > --f403043e8a3cdfa71e0565a0d7ee Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi!

I am so glad you are = asking this. I have developed some tools that might be helpful! Indeed, tha= t same frustration you mention is what led me to create some of these in th= e first place.

- ESIgen: https://github.com/insilichem/esigen

Meant to= create automated "Supporting Information" reports ready for publ= ication attachment, but it also works in the command-line for more day-to-d= ay tasks. It can be used in two ways: with a webserver (public demo here: <= a href=3D"http://esi.insilichem.com/">http://esi.insilichem.com/), or f= rom the command-line with the `esigen` executable. Source code is available= in GitHub if you want to take a look in how this is implemented (hint: ccl= ib+jinja), and a manuscript is already under revision.

- C= auchian: https= ://github.com/insilichem/plume_cauchian

UCSF Chimera extension t= hat 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. Check the = code of the pygaussian module and use that in your scr= ipts, but maybe it's too specific. I think a simpler approach using Jin= ja templates would be enough. In fact, if there's enough interest, we c= an start something!

Feel free to ask any questions. I'd be= happy to answer :)

2018-02-20 3:07 GMT+01:00 Guzman, Francisco fg58[a]njit.edu <owner-chemistry###ccl.net>= :
Hello Fellow CCL&= #39;ers,

I would like to start a discussion as to some of= the tools/scripts some of you use to build input files and analyze results= .=C2=A0

I find myself using bash, awk/sed, Python, and the fantasti= c egrep utility for the bulk of the work (finding frequencies, enthalpies,= =C2=A0 termination instances) for the bulk of the work. However, as of late= I want to start streamlining an input file generation script and here is w= here I can't quite figure out the best approach.

Suppose I have= 1 geometry, and want to generate several input files with varying basis se= ts.=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 the= n 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 u= se the terminal for user input of the template file, and atom/basis set des= criptors.=C2=A0 This seems doable, but I cant quite figure out a Pythonic w= ay of doing this.




Some interesting links/scripts:

Vladis= lav Vasilyev Homepage (great resource)
<= /b>http://sf.= anu.edu.au/~vvv900/

Look4bas (basis set builder)ht= tps://github.com/mfherbst/look4bas

= Gaussian Tools (Some Gaussian post processing scripts)
<= span class=3D"HOEnZb">


--
Francisco Guzman
PhD Candid= ate
= <= /font>Otto H. York Department of Chemical, Biological and Pharmaceut= ical Engineering
New Jersey Institute of Technology

--f403043e8a3cdfa71e0565a0d7ee-- From owner-chemistry@ccl.net Tue Feb 20 09:32:00 2018 From: "Geoffrey Hutchison geoff.hutchison*|*gmail.com" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53192-180220091659-18020-HOJV7llBnpjLB91k3jRRRA~!~server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Type: multipart/alternative; boundary="Apple-Mail=_20B9F0CD-5779-4093-ABE4-2111262BCE2A" Date: Tue, 20 Feb 2018 09:16:50 -0500 Mime-Version: 1.0 (Mac OS X Mail 11.2 \(3445.5.20\)) Sent to CCL by: Geoffrey Hutchison [geoff.hutchison,+,gmail.com] --Apple-Mail=_20B9F0CD-5779-4093-ABE4-2111262BCE2A Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii > 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.=20 > 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 the 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 something 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 kind 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**pitt.edu twitter: **ghutchis web: https://hutchison.chem.pitt.edu/= --Apple-Mail=_20B9F0CD-5779-4093-ABE4-2111262BCE2A Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii
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 the 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 something 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/Gaussia= n_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 kind 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**pitt.edu
twitter: = **ghutchis
web: https://hutchison.chem.pitt.edu/
= --Apple-Mail=_20B9F0CD-5779-4093-ABE4-2111262BCE2A-- From owner-chemistry@ccl.net Tue Feb 20 10:12:00 2018 From: "Jalal L jzalchem]|[gmail.com" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53193-180220025044-32163-uzlduPO5zokyq9rb93Gyew-x-server.ccl.net> X-Original-From: Jalal L Content-Type: multipart/alternative; boundary="94eb2c1c0e84f62ecb0565a0109d" Date: Tue, 20 Feb 2018 11:50:36 +0400 MIME-Version: 1.0 Sent to CCL by: Jalal L [jzalchem[A]gmail.com] --94eb2c1c0e84f62ecb0565a0109d Content-Type: text/plain; charset="UTF-8" Dear Francisco, Greetings from Mauritius. You may wish to refer to a tool we developed: ExcelAutomat. Link to article: ExcelAutomat: a tool for systematic processing of files as applied to quantum chemical calculations . Link to website: https://sites.google.com/view/excelautomat/home. Kind regards, Jalal Laloo Virus-free. www.avg.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On Tue, Feb 20, 2018 at 6:07 AM, Guzman, Francisco fg58[a]njit.edu < owner-chemistry++ccl.net> wrote: > Hello Fellow CCL'ers, > > I would like to start a discussion as to some of the tools/scripts some of > you use to build input files and analyze results. > > 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. However, as of late I want to start > streamlining an input file generation script and here is where I can't > quite figure out the best approach. > > 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 the > 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 something > 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. > > > > > *Some interesting links/scripts:* > > *Vladislav Vasilyev Homepage (great resource)* > http://sf.anu.edu.au/~vvv900/ > > > *Look4bas (basis set builder)*https://github.com/mfherbst/look4bas > > *Gaussian Tools (Some Gaussian post processing scripts)* > https://github.com/chauncey-garrett/gaussian-tools > > > > -- > Francisco Guzman > PhD Candidate > Otto H. York Department of Chemical, Biological and Pharmaceutical > Engineering > New Jersey Institute of Technology > Email: fg58|a|njit.edu, guzman.research|a|gmail.com > --94eb2c1c0e84f62ecb0565a0109d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
=
Dear=C2=A0Franc= isco,

Greetings from Ma= uritius.

You may wish t= o refer to a tool we developed: ExcelAutomat.

Link to article:=C2=A0ExcelAutomat: a tool for system= atic processing of files as applied to quantum chemical calculations.

Li= nk to website: https://sites.google.com/view/excelaut= omat/home.

Kind regards,
Jalal Laloo

= Virus-free. www.avg.com

On Tue, Feb 20, 2018 at 6:07 AM, Guzman, Francisco fg58[a]njit.edu <owner-chemistry++ccl.net> wro= te:
Hello Fellow CC= L'ers,

I would like to start a discussion as to some = of the tools/scripts some of you use to build input files and analyze resul= ts.=C2=A0

I find myself using bash, awk/sed, Python, and the fantas= tic egrep utility for the bulk of the work (finding frequencies, enthalpies= ,=C2=A0 termination instances) for the bulk of the work. However, as of lat= e I want to start streamlining an input file generation script and here is = where I can't quite figure out the best approach.

Suppose I hav= e 1 geometry, and want to generate several input files with varying basis s= ets.=C2=A0 My approach has been to create a database file with names such a= s atom_basis_set and another template file with the starting geometry. I th= en call the database file, read the template, and write the appropriate ato= m_basis_set and save as a new file.=C2=A0 This so far gets the job done, bu= t 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 de= scriptors.=C2=A0 This seems doable, but I cant quite figure out a Pythonic = way of doing this.




Some interesting links/scripts:

Vladi= slav Vasilyev Homepage (great resource)
= http://sf= .anu.edu.au/~vvv900/

Look4bas (basis set builder)<= br>h= ttps://github.com/mfherbst/look4bas

Gaussian Tools (Some Gaussian post processing scripts)
=


-- <= br>
Francisco Guzman
PhD Candid= ate
= <= /font>Otto H. York Department of Chemical, Biological and Pharmaceut= ical Engineering
New Jersey Institute of Technology

--94eb2c1c0e84f62ecb0565a0109d-- From owner-chemistry@ccl.net Tue Feb 20 10:47:01 2018 From: "Felipe Schneider schneider.felipe.5 .. gmail.com" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53194-180220070422-9792-RT4871EC6WCohx0qHJ0UNQ=-=server.ccl.net> X-Original-From: Felipe Schneider Content-Type: multipart/alternative; boundary="94eb2c1a0958ee2e6c0565a39bb9" Date: Tue, 20 Feb 2018 12:04:02 +0000 MIME-Version: 1.0 Sent to CCL by: Felipe Schneider [schneider.felipe.5_._gmail.com] --94eb2c1a0958ee2e6c0565a39bb9 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi all, I developed a very simple software that uses Jinja templates to create input files for computational chemistry packages ( https://github.com/dudektria/pnictogen). Templates look like the following (for Gaussian as an example): %nproc=3D16 %mem=3D{{ 250 * (molecules[0].atoms|count) }}MB %chk=3Dcheckfile #p wB97XD/6-311++G** opt=3D(calcfc,ts,redundant,maxcycles=3D{{ 20 * (molecules[0].atoms|count) }}) freq=3Dnoraman scrf=3D(solvent=3Dwater,smd) pop=3D(full,nbo) scf=3D(tight,maxcycle=3D{{ 10 * (molecules[0].atoms|count)= }}) integral=3D(acc2e=3D12,grid=3Dultrafine) {{ molecules[0].title }} {{ molecules[0].charge }} {{ molecules[0].spin }} {{ xyz(molecules[0]) }} There are many examples in the GitHub page. You can either install it from GitHub or using pip: $ pip install -U pnictogen Please check it out, report bugs and contribute! All the best, Felipe On Tue, 20 Feb 2018 at 07:42 Jaime Rodr=C3=ADguez-Guerra jaime.rodriguezgue= rra:-: uab.cat wrote: > Hi! > > I am so glad you are asking this. I have developed some tools that might > be helpful! Indeed, that same frustration you mention is what led me to > create some of these in the first place. > > - *ESIgen*: https://github.com/insilichem/esigen > > 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 de= mo > here: http://esi.insilichem.com/), or from the command-line with the > `esigen` executable. Source code is available in GitHub if you want to ta= ke > a look in how this is implemented (hint: cclib+jinja), and a manuscript i= s > already under revision. > > - *Cauchian*: https://github.com/insilichem/plume_cauchian > > 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. Check the code of the pygaussian > > module and use that in your scripts, but maybe it's too specific. I think= a > simpler approach using Jinja templates would be enough. In fact, if there= 's > enough interest, we can start something! > > Feel free to ask any questions. I'd be happy to answer :) > > 2018-02-20 3:07 GMT+01:00 Guzman, Francisco fg58[a]njit.edu a ccl.net>: > >> Hello Fellow CCL'ers, >> >> I would like to start a discussion as to some of the tools/scripts some >> of you use to build input files and analyze results. >> >> 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. However, as of late I w= ant >> to start streamlining an input file generation script and here is where = I >> can't quite figure out the best approach. >> >> 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. >> >> >> >> >> *Some interesting links/scripts:* >> >> *Vladislav Vasilyev Homepage (great resource)* >> http://sf.anu.edu.au/~vvv900/ >> >> >> *Look4bas (basis set builder)*https://github.com/mfherbst/look4bas >> >> *Gaussian Tools (Some Gaussian post processing scripts)* >> https://github.com/chauncey-garrett/gaussian-tools >> >> >> >> -- >> Francisco Guzman >> PhD Candidate >> Otto H. York Department of Chemical, Biological and Pharmaceutical >> Engineering >> New Jersey Institute of Technology >> Email: fg58|a|njit.edu, guzman.research|a|gmail.com >> > > -- Felipe S. S. Schneider, M.Sc. Molecular Electronic Structure Group Departamento de Qu=C3=ADmica, UFSC https://dudektria.github.io/ +55 (48) 3721-6839 --94eb2c1a0958ee2e6c0565a39bb9 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hi all,

I developed a ver= y simple software that uses Jinja templates to create input files for compu= tational chemistry packages (https://github.com/dudektria/pnictogen). Templates look like the f= ollowing (for Gaussian as an example):

%nproc=3D16
%mem=3D{{ 250 * (molecules[0].atoms|count) }}MB
= %chk=3Dcheckfile

#p wB97XD/6-311++G** opt=3D(calcfc,ts,redundant,max= cycles=3D{{ 20 * (molecules[0].atoms|count) }}) freq=3Dnoraman scrf=3D(solv= ent=3Dwater,smd) pop=3D(full,nbo) scf=3D(tight,maxcycle=3D{{ 10 * (molecule= s[0].atoms|count) }}) integral=3D(acc2e=3D12,grid=3Dultrafine)

=C2= =A0{{ molecules[0].title }}

{{ molecules[0].charge }}=C2=A0 {{ molec= ules[0].spin }}
{{ xyz(molecules[0]) }}

There are ma= ny examples in the GitHub page. You can either install it from GitHub or us= ing pip:

$ pip install -U pnictogen

Please check it out, report bugs and contribute!

A= ll the best,
Felipe

On Tue, 20 Feb 2018 at 07:42 Jaime Rodr=C3=ADguez-Guerra jaime.r= odriguezguerra:-:uab.cat <owner-chemistry!A!ccl.net> wrote:
Hi!
I am so glad you are asking this. I have developed some tools th= at might be helpful! Indeed, that same frustration you mention is what led = me to create some of these in the first place.

- ESIgen= : https:= //github.com/insilichem/esigen

Meant to create automated "S= upporting Information" reports ready for publication attachment, but i= t 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. Source code is available in Git= Hub if you want to take a look in how this is implemented (hint: cclib+jinj= a), and a manuscript is already under revision.

- Cauchian= : https://github.com/insilichem/plume_cauchian

UCSF Chimera = extension that provides a GUI to create Gaussian input files. Created to de= al with QM/MM, it also supports standard QM jobs. The dialog includes a fas= t Basis Set explorer like the one in BSE thanks to the included ebsel fork.= Check the code of the pygaussian mo= dule and use that in your scripts, but maybe it's too specific. I think= a simpler approach using Jinja templates would be enough. In fact, if ther= e's enough interest, we can start something!

Feel free to = ask any questions. I'd be happy to answer :)

2018-02-20 3:07 GMT+01:00 Guzman, = Francisco fg58[a]njit.edu= <owner-chemistry a ccl.net>:
Hello Fellow CCL'ers,

=
I would like to start a discussion as to some of the tools/scripts som= e of you use to build input files and analyze results.=C2=A0

I find= myself using bash, awk/sed, Python, and the fantastic egrep utility for th= e bulk of the work (finding frequencies, enthalpies,=C2=A0 termination inst= ances) for the bulk of the work. However, as of late I want to start stream= lining an input file generation script and here is where I can't quite = figure out the best approach.

Suppose I have 1 geometry, and want t= o generate several input files with varying basis sets.=C2=A0 My approach h= as been to create a database file with names such as atom_basis_set and ano= ther template file with the starting geometry. I then call the database fil= e, 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 ma= nual changes. Ideally I want something where I can use the terminal for use= r input of the template file, and atom/basis set descriptors.=C2=A0 This se= ems doable, but I cant quite figure out a Pythonic way of doing this.



Some interesti= ng links/scripts:

Vladislav Vasilyev Homepa= ge (great resource)
http://sf.anu.edu.au/~vvv900/=

Look4bas (basis set builder)
https://github.com/mfherb= st/look4bas

Gaussian Tools (Some Gaus= sian post processing scripts)


--
Franc= isco Guzman
PhD Candidate
Otto H. York Department of C= hemical, Biological and Pharmaceutical Engineering
New Jersey Institute = of Technology

--
--94eb2c1a0958ee2e6c0565a39bb9-- From owner-chemistry@ccl.net Tue Feb 20 11:22:01 2018 From: "Igors Mihailovs igorsm()cfi.lu.lv" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53195-180220081811-14858-bdq0JDAV4heSV8GMhZU1Bw^server.ccl.net> X-Original-From: Igors Mihailovs Content-Language: lv-LV Content-Type: multipart/alternative; boundary="------------EA28D40A5A3658240525EA00" Date: Tue, 20 Feb 2018 15:17:58 +0200 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm(_)cfi.lu.lv] This is a multi-part message in MIME format. --------------EA28D40A5A3658240525EA00 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit If anyone is interested, maybe they can find something useful at https://github.com/esmuigors/launchanew. The script is intended for managing running Gaussian calculations: preventing accidental overwrites of CHK and OUT files, printing out short description of errors, solving SCF convergence problems by sequentially adding various keywords to the Route section, attempts to do the same for geometry optimizations and so on. Developed haphazardly, possibly some parts are defunct now (?), but as I have said, maybe somebody founds some pieces of the code interesting. With best wishes (not deeds) Igors Mihailovs 2018-02-20 3:07 GMT+01:00 Guzman, Francisco fg58[a]njit.edu >: > > Hello Fellow CCL'ers, > > I would like to start a discussion as to some of the tools/scripts > some of you use to build input files and analyze results. > > 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. > However, as of late I want to start streamlining an input file > generation script and here is where I can't quite figure out the > best approach. > > 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 the 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 something 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. > > > > > *Some interesting links/scripts:* > > **Vladislav Vasilyev *Homepage (great resource)* > http://sf.anu.edu.au/~vvv900/ > > *Look4bas (basis set builder) > *https://github.com/mfherbst/look4bas > * > * > > *Gaussian Tools (Some Gaussian post processing scripts)* > https://github.com/chauncey-garrett/gaussian-tools > > > > > -- > Francisco Guzman > PhD Candidate > Otto H. York Department of Chemical, Biological and Pharmaceutical > Engineering > New Jersey Institute of Technology > Email: fg58|a|njit.edu > ,guzman.research|a|gmail.com > > > -- Ar cieņu, Igors Mihailovs Organisko materiālu laboratorija LU CFI --------------EA28D40A5A3658240525EA00 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit If anyone is interested, maybe they can find something useful at https://github.com/esmuigors/launchanew. The script is intended for managing running Gaussian calculations: preventing accidental overwrites of CHK and OUT files, printing out short description of errors, solving SCF convergence problems by sequentially adding various keywords to the Route section, attempts to do the same for geometry optimizations and so on. Developed haphazardly, possibly some parts are defunct now (?), but as I have said, maybe somebody founds some pieces of the code interesting.

With best wishes (not deeds)
Igors Mihailovs

2018-02-20 3:07 GMT+01:00 Guzman, Francisco fg58[a]njit.edu <owner-chemistry a ccl.net>:
Hello Fellow CCL'ers,

I would like to start a discussion as to some of the tools/scripts some of you use to build input files and analyze results. 

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. However, as of late I want to start streamlining an input file generation script and here is where I can't quite figure out the best approach.

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 the 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 something 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.




Some interesting links/scripts:

Vladislav Vasilyev Homepage (great resource)
http://sf.anu.edu.au/~vvv900/

Look4bas (basis set builder)
https://github.com/mfherbst/look4bas

Gaussian Tools (Some Gaussian post processing scripts)


--
Francisco Guzman
PhD Candidate
Otto H. York Department of Chemical, Biological and Pharmaceutical Engineering
New Jersey Institute of Technology


--
Ar cieņu,
Igors Mihailovs
Organisko materiālu laboratorija
LU CFI
--------------EA28D40A5A3658240525EA00-- From owner-chemistry@ccl.net Tue Feb 20 11:56:00 2018 From: "Marcos Verissimo Alves marcos_verissimo%x%id.uff.br" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53196-180220103520-17384-uUTIwfHHz+mWAaeW8BGycg=server.ccl.net> X-Original-From: Marcos Verissimo Alves Content-Type: multipart/alternative; boundary="089e08e5861d81705a0565a68e4f" Date: Tue, 20 Feb 2018 12:35:12 -0300 MIME-Version: 1.0 Sent to CCL by: Marcos Verissimo Alves [marcos_verissimo^-^id.uff.br] --089e08e5861d81705a0565a68e4f Content-Type: text/plain; charset="UTF-8" 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 the > 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 something > 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 kind > 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/ > --089e08e5861d81705a0565a68e4f Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
There is an Orca interface for ASE. Check Orca Input Libr= ary.

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

Oh, please, please use a package like cclib or Open = Babel (http://cclib.gi= thub.io) for parsing. The whole point of these community projects is th= at they easily handle reading output files and grab attributes.=C2=A0
=
Suppose I have 1 g= eometry, 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 at= om_basis_set and another template file with the starting geometry. I then c= all the database file, read the template, and write the appropriate atom_ba= sis_set and save as a new file.=C2=A0 This so far gets the job done, but st= ill 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 descri= ptors.=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 com= mand-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=C2=A0https://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 fo= r solid-state codes, but definitely has code for this kind of task - you se= t up a "calculator" to write each basis set.

=
Again, the main thing is that you'll be more productive if you tak= e a little time and check for existing community packages that probably do = what you want.

Cheers,
-Geoff
=
---
Prof. Geoffrey Hutchison
Depart= ment of Chemistry
University of Pittsburgh
twitter: [a]ghutchis
--089e08e5861d81705a0565a68e4f-- From owner-chemistry@ccl.net Tue Feb 20 12:32:00 2018 From: "Fedor Goumans goumans-,-scm.com" To: CCL Subject: CCL: Tools for scripting repetitive tasks Message-Id: <-53197-180220104252-21744-XZRDMublr/wV0SdRz5ONvw,server.ccl.net> X-Original-From: "Fedor Goumans" Date: Tue, 20 Feb 2018 10:42:51 -0500 Sent to CCL by: "Fedor Goumans" [goumans__scm.com] Dear Francisco, The Python Library for Automating Molecular Simulations (PLAMS) does essentially just that, and much more (job scheduler integration, advanced molecular coordinates manipulation etc.). It is available as LGPL from github: https://github.com/SCM-NV/PLAMS PLAMS is shipped with the ADF Modeling Suite, and is very suitable for making your workflows and high-throughput screening with the codes in that software, but you can tailor it to your own needs and software packages. For more documentation and examples see here: https://www.scm.com/doc/plams/index.html Best wishes, Fedor goumans(!)scm.com From owner-chemistry@ccl.net Tue Feb 20 19:14:00 2018 From: "Dave.Winkler]_[csiro.au" To: CCL Subject: CCL: "We the people of the CCL" as research subjects in IEEE Paper Message-Id: <-53198-180220175357-4615-lVxufW0G9ZfGnlSWNjmB+A|server.ccl.net> X-Original-From: Content-Language: en-AU Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 20 Feb 2018 22:53:28 +0000 MIME-Version: 1.0 Sent to CCL by: [Dave.Winkler^^csiro.au] Very interesting paper. I there a list of the original 100 subscribers to CCL? I think I was probably one of them? Prof. Dave Winkler Fellow CSIRO Manufacturing Clayton 3168, Australia The call for Pacifichem 2020 symposia has now opened. Please see http://www.pacifichem.org. ________________________________________ > From: owner-chemistry+dave.winkler==csiro.au]|[ccl.net [owner-chemistry+dave.winkler==csiro.au]|[ccl.net] on behalf of Alexandre Hocquet alexandre.hocquet-x-univ-lorraine.fr [owner-chemistry]|[ccl.net] Sent: Monday, 19 February 2018 12:34 PM To: Winkler, Dave (Manufacturing, Clayton) Subject: CCL: "We the people of the CCL" as research subjects in IEEE Paper Sent to CCL by: Alexandre Hocquet [alexandre.hocquet[]univ-lorraine.fr] On 18/02/2018 03:01, Alejandro Pisanty apisan*servidor.unam.mx wrote: > in http://ieeexplore.ieee.org.pbidi.unam.mx:8080/document/8268025/ > Alexandre Hocquet and Frederic Wieber have published a very interesting > and thought-provoking paper about the CCL, Computational Chemistry List, > titled "Only the Initiates Will Have the Secrets Revealed: > Computational Chemists and the Openness of Scientific Software". Estimado Alejandro, Thank you very much for your kind post. Though I first subscribed to the CCL a few years later than you, some people may remember that I once was a computational chemist before I metamorphosed into a historian of science. Our work, Frdric Wieber and I, is threefold. The first paper you mention has just been released and depicts the relationships of computational chemists with software from a social history viewpoint. In a second paper, the epistemological issues at stake are discussed in a chemistry oriented journal, and in a third, we methodologically highlight the characteristics of the CCL mailing list (and flame wars!) as a corpus for historians. Both the second and third are still under review. You are right that the CCL is pivotal to our work and we also argue that the CCL is pivotal to computational chemistry. As a matter of fact, this paper was supposed to be dedicated to Jan Labanowski, but for some reason, it did not appear on the final manuscript. To all members of the list, if you email me or DM me on twitter, I can provide a #Icanhazpdf author version if your library does not provide the IEEE Annals of the history of computing. I'd be happy to discuss the topics adressed in the paper in this list, this would be a beautiful "mise en abyme". Likewise, if CCLers have complaints about inacurracies or misinterpretations, feel free to discuss it here too. Best regards, -- *********************************************** Alexandre Hocquet Universit de Lorraine & Archives Henri Poincar Alexandre.Hocquet-x-univ-lorraine.fr http://poincare.univ-lorraine.fr/fr/membre-titulaire/alexandre-hocquet -x-osvaldopiazzoll ***********************************************http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt