From owner-chemistry@ccl.net Mon Feb 19 21:11:00 2018 From: "Guzman, Francisco fg58[a]njit.edu" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53188-180219210734-19303-763VW/z8BJu3HgeDuhs1oA[#]server.ccl.net> X-Original-From: "Guzman, Francisco" Content-Type: multipart/alternative; boundary="001a114901cac29c5805659b455d" Date: Mon, 19 Feb 2018 21:07:27 -0500 MIME-Version: 1.0 Sent to CCL by: "Guzman, Francisco" [fg58^^njit.edu] --001a114901cac29c5805659b455d Content-Type: text/plain; charset="UTF-8" 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^^^njit.edu, guzman.research^^^gmail.com --001a114901cac29c5805659b455d Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Hello Fellow CCL'ers,

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

I find myself using = bash, awk/sed, Python, and the fantastic 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 inpu= t 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 sev= eral input files with varying basis sets.=C2=A0 My approach has been to cre= ate 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 te= mplate, 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 descriptors.=C2=A0 This seems doable, bu= t I cant quite figure out a Pythonic way of doing this.

<= br>


Some interesting links/scrip= ts:

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

=
Look4bas (basis set builder)
https://github.com/mfherbst/look4b= as

Gaussian Tools (Some Gaussian post= processing scripts)
https://github.com/chauncey-gar= rett/gaussian-tools



= --
Francisco Guzman
PhD Candidate
Otto= H. York Department of Chemical, Biological and Pharmaceutical Engineering<= br>New Jersey Institute of Technology
--001a114901cac29c5805659b455d-- From owner-chemistry@ccl.net Mon Feb 19 23:12:01 2018 From: "Jing Trerayapiwat jingsk129.:.gmail.com" To: CCL Subject: CCL:G: Tools for scripting repetitive tasks Message-Id: <-53189-180219225918-20503-/Ru5lG+YaTcSchHHS50Vdw.@.server.ccl.net> X-Original-From: Jing Trerayapiwat Content-Type: multipart/alternative; boundary="Apple-Mail=_7292E349-2FA9-4C1E-BA6A-A3EFDE6C65E2" Date: Mon, 19 Feb 2018 22:59:06 -0500 Mime-Version: 1.0 (Mac OS X Mail 11.2 \(3445.5.20\)) Sent to CCL by: Jing Trerayapiwat [jingsk129*gmail.com] --Apple-Mail=_7292E349-2FA9-4C1E-BA6A-A3EFDE6C65E2 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Hi, I guess you can create a library of basis sets inside your python script = and call one forth from command line using sys.argv (See = https://www.tutorialspoint.com/python/python_command_line_arguments.htm). I wonder if there is already a library published somewhere online. Jing Trerayapiwat Thayer School of Engineering=20 Email: kasidet.trerayapiwat at dartmouth.edu > On Feb 19, 2018, at 9:07 PM, Guzman, Francisco fg58[a]njit.edu = wrote: >=20 > Hello Fellow CCL'ers, >=20 > 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. =20 >=20 > 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.=20 >=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. >=20 >=20 >=20 >=20 > Some interesting links/scripts: >=20 > Vladislav Vasilyev Homepage (great resource) > http://sf.anu.edu.au/~vvv900/ >=20 > Look4bas (basis set builder) > https://github.com/mfherbst/look4bas = >=20 > Gaussian Tools (Some Gaussian post processing scripts) > https://github.com/chauncey-garrett/gaussian-tools = >=20 >=20 >=20 > --=20 > 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 --Apple-Mail=_7292E349-2FA9-4C1E-BA6A-A3EFDE6C65E2 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=us-ascii Hi,

I guess you can create a library of basis sets inside your = python script and call one forth from command line using sys.argv (See = https://www.tutorialspoint.com/python/python_command_line_argum= ents.htm).

I= wonder if there is already a library published somewhere = online.

Jing = Trerayapiwat
Thayer School of = Engineering 
Email: kasidet.trerayapiwat at dartmouth.edu

On Feb 19, 2018, at 9:07 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

= --Apple-Mail=_7292E349-2FA9-4C1E-BA6A-A3EFDE6C65E2--