From owner-chemistry@ccl.net Fri Jan 10 09:46:01 2020 From: "Fleurat-Lessard Paul Paul.Fleurat-Lessard^u-bourgogne.fr" To: CCL Subject: CCL:G: Recomputing Free energy at different temperature from Gaussian output Message-Id: <-53937-200110085457-8115-YAdytCI983/r/Rr7y42Rzw]|[server.ccl.net> X-Original-From: "Fleurat-Lessard Paul" Date: Fri, 10 Jan 2020 08:54:55 -0500 Sent to CCL by: "Fleurat-Lessard Paul" [Paul.Fleurat-Lessard^u-bourgogne.fr] Dear colleagues, In one project using Gaussian09, one student computed the free energies at room temperature instead of T=110C. I usually use a small script based on Freqchk to correct for this... but, to save some disk space in archiving, the student has deleted many CheckPoint files. I am thus looking for some codes/scripts that would parse the Gaussian output file to compute the thermochemical functions from it and not from the chk file. I have tens of files so I need something that can be used in command line with no graphical user interface. Could you help me in finding such a tool? Best regards, Paul. From owner-chemistry@ccl.net Fri Jan 10 11:34:00 2020 From: "Mariusz Radon mariusz.radon]![gmail.com" To: CCL Subject: CCL:G: Recomputing Free energy at different temperature from Gaussian output Message-Id: <-53938-200110113310-17049-UI6tqm9BNCzcdESD3ZqyzQ++server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Fri, 10 Jan 2020 17:33:03 +0100 Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.11\)) Sent to CCL by: Mariusz Radon [mariusz.radon##gmail.com] > On 10 Jan 2020, at 14:54, Fleurat-Lessard Paul Paul.Fleurat-Lessard^u-bourgogne.fr wrote: > > > Sent to CCL by: "Fleurat-Lessard Paul" [Paul.Fleurat-Lessard^u-bourgogne.fr] > Dear colleagues, > > In one project using Gaussian09, one student computed the free energies at room > temperature instead of T=110C. I usually use a small script based on Freqchk > to correct for this... but, to save some disk space in archiving, the student > has deleted many CheckPoint files. > I am thus looking for some codes/scripts that would parse the Gaussian output > file to compute the thermochemical functions from it and not from the chk file. > I have tens of files so I need something that can be used in command line with > no graphical user interface. > > Could you help me in finding such a tool? > > Best regards, > Paul. Dear Paul: “cclib" (https://cclib.github.io) is a Python library which can parse G09 output files, so you can easily access the frequencies. Best wishes, Mariusz -- Mariusz Radon, Ph.D., D.Sc. Jagiellonian University in Krakow Faculty of Chemistry Department of Inorganic Chemistry Gronostajowa 2, 30-387 Krakow, Poland room: C1-06 phone: 48-12-686-24-89 e-mail: mradon..chemia.uj.edu.pl; mariusz.radon..uj.edu.pl web: http://www.chemia.uj.edu.pl/~mradon ORCID: https://orcid.org/0000-0002-1901-8521 From owner-chemistry@ccl.net Fri Jan 10 12:09:00 2020 From: "Grant Hill grant.hill _ sheffield.ac.uk" To: CCL Subject: CCL:G: Recomputing Free energy at different temperature from Gaussian output Message-Id: <-53939-200110114140-20059-HRt02wi6rU1oYmJTjOJirw++server.ccl.net> X-Original-From: Grant Hill Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 10 Jan 2020 16:41:32 +0000 Mime-Version: 1.0 (Mac OS X Mail 13.0 \(3608.40.2.2.4\)) Sent to CCL by: Grant Hill [grant.hill]-[sheffield.ac.uk] If I understand what you want correctly, this can be done on the NIST website: https://www.nist.gov/mml/csd/chemical-informatics-research-group/thermodynamics-functions-gaussian-output-files You can also download the underlying perl script for command line automation. Hope this helps, Grant > On 10 Jan 2020, at 13:54, Fleurat-Lessard Paul Paul.Fleurat-Lessard^u-bourgogne.fr wrote: > > > Sent to CCL by: "Fleurat-Lessard Paul" [Paul.Fleurat-Lessard^u-bourgogne.fr] > Dear colleagues, > > In one project using Gaussian09, one student computed the free energies at room > temperature instead of T=110C. I usually use a small script based on Freqchk > to correct for this... but, to save some disk space in archiving, the student > has deleted many CheckPoint files. > I am thus looking for some codes/scripts that would parse the Gaussian output > file to compute the thermochemical functions from it and not from the chk file. > I have tens of files so I need something that can be used in command line with > no graphical user interface. > > Could you help me in finding such a tool? > > Best regards, > Paul.> > From owner-chemistry@ccl.net Fri Jan 10 12:44:00 2020 From: "Andrew Rosen rosen]![u.northwestern.edu" To: CCL Subject: CCL:G: Recomputing Free energy at different temperature from Gaussian output Message-Id: <-53940-200110121605-5776-6jNyYKey9ac9CeyzS7ZOTw---server.ccl.net> X-Original-From: Andrew Rosen Content-Type: multipart/alternative; boundary="00000000000077e44a059bcc4766" Date: Fri, 10 Jan 2020 11:15:48 -0600 MIME-Version: 1.0 Sent to CCL by: Andrew Rosen [rosen _ u.northwestern.edu] --00000000000077e44a059bcc4766 Content-Type: text/plain; charset="UTF-8" You will very much appreciate the program GoodVibes then, available on GitHub at https://github.com/bobbypaton/GoodVibes On Fri, Jan 10, 2020 at 10:23 AM Fleurat-Lessard Paul Paul.Fleurat-Lessard^ u-bourgogne.fr wrote: > > Sent to CCL by: "Fleurat-Lessard Paul" [Paul.Fleurat-Lessard^ > u-bourgogne.fr] > Dear colleagues, > > In one project using Gaussian09, one student computed the free energies at > room > temperature instead of T=110C. I usually use a small script based on > Freqchk > to correct for this... but, to save some disk space in archiving, the > student > has deleted many CheckPoint files. > I am thus looking for some codes/scripts that would parse the Gaussian > output > file to compute the thermochemical functions from it and not from the chk > file. > I have tens of files so I need something that can be used in command line > with > no graphical user interface. > > Could you help me in finding such a tool? > > Best regards, > Paul.> > > --00000000000077e44a059bcc4766 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
You will very much appreciate the program GoodVibes then, = available on GitHub at=C2=A0https://github.com/bobbypaton/GoodVibes

On Fri, Jan 10, 2020 at 10:= 23 AM Fleurat-Lessard Paul Paul.Fleurat-Lessard^u-bourgogne.fr <ow= ner-chemistry * ccl.net> wrote:

Sent to CCL by: "Fleurat-Lessard=C2=A0 Paul" [Paul.Fleurat-Lessar= d^u-= bourgogne.fr]
Dear colleagues,

In one project using Gaussian09, one student computed the free energies at = room
temperature instead of T=3D110C. I usually use a small script based on Freq= chk
to correct for this... but, to save some disk space in archiving, the stude= nt
has deleted many CheckPoint files.
I am thus looking for some codes/scripts that would parse the Gaussian outp= ut
file to compute the thermochemical functions from it and not from the chk f= ile.
I have tens of files so I need something that can be used in command line w= ith
no graphical user interface.

Could you help me in finding such a tool?

Best regards,
Paul.



-=3D This is automatically added to each message by the mailing script =3D-=
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--00000000000077e44a059bcc4766-- From owner-chemistry@ccl.net Fri Jan 10 14:49:00 2020 From: "John Keller jwkeller:alaska.edu" To: CCL Subject: CCL:G: Recomputing Free energy at different temperature from Gaussian output Message-Id: <-53941-200110143133-16041-rFs87X2J9f343LLgePeG2Q]*[server.ccl.net> X-Original-From: John Keller Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset="utf-8" Date: Fri, 10 Jan 2020 10:31:18 -0900 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller++alaska.edu]

HI,

I tried = the NIST website as suggested, but I got the following message:

=E2=80=9CThe requested URL "https:= //www.nist.gov/cgi-bin/thermo_cgi.pl" was not found on this server.=E2= =80=9D

One= can also upload Gaussian (and several other program) .log files to the fre= e WebMO demo site, which will parse them completely, including a table of f= requencies that can be animated.

=  

https://www.webmo.net/demoserver/cgi-bin/webmo/login.cgi<= o:p>

 = ;

Best,

John K= eller

University of Alaska Fairbanks

 

 

Sent from Mail for Windows 10

 <= /o:p>

From: Grant Hill grant.hill _ sheffield.ac.uk
Sent: Friday, = January 10, 2020 9:07 AM
To: Keller, John W
Subject: CCL:G: Recomputing Free e= nergy at different temperature from Gaussian output

 

 

Sent to CCL by: Grant Hill [grant.hill]-[sheffield.ac.uk]

If I understand what you want correctly, this can be= done on the NIST website: https://www.nist.gov/mml/csd/chemical-informatic= s-research-group/thermodynamics-functions-gaussian-output-files

 

You can also downloa= d the underlying perl script for command line automation.

 

Hope this helps,

Grant

 

 

 

> On 10 Jan 2020, at 13:54, Fleurat-Lessard Paul P= aul.Fleurat-Lessard^u-bourgogne.fr <owner-chemistry__ccl.net> wrote:<= /p>

>

>

> Sent to CCL by: "Fleurat-Lessard=C2=A0 Paul" [Paul.= Fleurat-Lessard^u-bourgogne.fr]

> Dear colleague= s,

>

> In one projec= t using Gaussian09, one student computed the free energies at room

> temperature instead of T=3D110C. I usually use a smal= l script based on Freqchk

> to correct for this= .. but, to save some disk space in archiving, the student

> has deleted many CheckPoint files.

&g= t; I am thus looking for some codes/scripts that would parse the Gaussian o= utput

> file to compute the thermochemical func= tions from it and not from the chk file.

> I hav= e tens of files so I need something that can be used in command line with <= /p>

> no graphical user interface.

>

> Could you help me in finding such= a tool?

>

> Best re= gards,

> Paul.>

>=  

 

 

 

-=3D This is automatically added to each message by the m= ailing script =3D-

To recover the email address of = the author of the message, please change

the strang= e characters on the top line to the * sign. You can also

 

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= From owner-chemistry@ccl.net Fri Jan 10 15:23:00 2020 From: "Gabriel Merino gabriel.merino2=-=gmail.com" To: CCL Subject: CCL:G: Recomputing Free energy at different temperature from Gaussian output Message-Id: <-53942-200110141417-8692-2oUbksw4S4pITttNE5IrdQ~~server.ccl.net> X-Original-From: Gabriel Merino Content-Type: multipart/alternative; boundary="000000000000347518059bcdee19" Date: Fri, 10 Jan 2020 13:13:59 -0600 MIME-Version: 1.0 Sent to CCL by: Gabriel Merino [gabriel.merino2|a|gmail.com] --000000000000347518059bcdee19 Content-Type: text/plain; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hi Paul, About your question in CCL, Eyringpy could help you. This program uses just the frequency output file and recomputes the partition function. So, it is possible to obtain G or H to any temperature. https://www.theochemmerida.org/eyringpy-1-0 Cheers Gabriel *************************************************************** Prof. Gabriel Merino Departamento de Fisica Aplicada Centro de Investigacion y de Estudios Avanzados Unidad Merida Km. 6 Antigua carretera a Progreso Apdo. Postal 73, Cordemex, 97310, M=C3=A9rida, Yuc., M=C3=A9xico e-mail: gmerino++cinvestav.mx Gabriel.Merino2++gmail.com Web page: https://www.theochemmerida.org twitter: ++theochemmerida *************************************************************** El vie., 10 ene. 2020 a las 10:23, Fleurat-Lessard Paul Paul.Fleurat-Lessard^u-bourgogne.fr () escribi=C3= =B3: > > Sent to CCL by: "Fleurat-Lessard Paul" [Paul.Fleurat-Lessard^ > u-bourgogne.fr] > Dear colleagues, > > In one project using Gaussian09, one student computed the free energies a= t > room > temperature instead of T=3D110C. I usually use a small script based on > Freqchk > to correct for this... but, to save some disk space in archiving, the > student > has deleted many CheckPoint files. > I am thus looking for some codes/scripts that would parse the Gaussian > output > file to compute the thermochemical functions from it and not from the chk > file. > I have tens of files so I need something that can be used in command line > with > no graphical user interface. > > Could you help me in finding such a tool? > > Best regards, > Paul. > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --000000000000347518059bcdee19 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable

Hi Paul,


About your question in CCL, Eyringpy could help you. This program uses= just the frequency output file and recomputes the partition function. So, = it is possible to obtain G or H to any temperature.


https://www.theochemmerida.org/eyringpy-1-0


Cheers


Gabriel

******= *********************************************************
Prof. Gabriel = Merino
Departamento de Fisica Aplicada
Centro de Investigacion y de E= studios Avanzados
Unidad Merida
Km. 6 Antigua carretera a ProgresoApdo. Postal 73, Cordemex, 97310, M=C3=A9rida, Yuc., M=C3=A9xico
e-mail= : gmerino++cinvest= av.mx
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Gabriel.Merino2++gmail.com
=
Web page: = https://www.theochemmerida.org
twitter: ++theochemmerida
*********= ******************************************************


El vie., 10 ene. 2020 a las 10:23, Fleurat-Lessard Paul Paul.Fleurat= -Lessard^u-bourgogne.fr (<owner-chemistry++ccl.net>) escrib= i=C3=B3:

Sent to CCL by: "Fleurat-Lessard=C2=A0 Paul" [Paul.Fleurat-Lessar= d^u-= bourgogne.fr]
Dear colleagues,

In one project using Gaussian09, one student computed the free energies at = room
temperature instead of T=3D110C. I usually use a small script based on Freq= chk
to correct for this... but, to save some disk space in archiving, the stude= nt
has deleted many CheckPoint files.
I am thus looking for some codes/scripts that would parse the Gaussian outp= ut
file to compute the thermochemical functions from it and not from the chk f= ile.
I have tens of files so I need something that can be used in command line w= ith
no graphical user interface.

Could you help me in finding such a tool?

Best regards,
Paul.



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY++ccl.net or use:
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Before posting, check wait time at: http://www.ccl.net

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RTFI: http://www.ccl.net/chemistry/aboutccl/ins= tructions/


--000000000000347518059bcdee19-- From owner-chemistry@ccl.net Fri Jan 10 15:58:00 2020 From: "Uche Anene uche _ uconn.edu" To: CCL Subject: CCL:G: Recomputing Free energy at different temperature from Gaussian output Message-Id: <-53943-200110152053-32377-5i7/x4uYWhIfaTPgLwENxQ]=[server.ccl.net> X-Original-From: Uche Anene Content-Type: multipart/alternative; boundary="Apple-Mail=_0551FA95-D896-489B-AECD-BA56187C66BB" Date: Fri, 10 Jan 2020 15:20:45 -0500 Mime-Version: 1.0 (Mac OS X Mail 12.4 \(3445.104.11\)) Sent to CCL by: Uche Anene [uche..uconn.edu] --Apple-Mail=_0551FA95-D896-489B-AECD-BA56187C66BB Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hi, The correct NIST website for "Using the output file from a Gaussian frequency calculation to compute = ideal-gas thermodynamic functions=E2=80=9D = https://www.nist.gov/mml/csd/chemical-informatics-research-group/products-= and-services/program-computing-ideal-gas I have tried the link and used the script and it works. Happy computing, Uche --- Uchenna A. Anene Ph.D. Student, Chemical Engineering =20 University of Connecticut Innovation Partnership Building=20 159 Discovery Drive Storrs, CT 06269 uche{}uconn.edu https://alpay.ims.uconn.edu/uche-anene/# www.linkedin.com/in/uche-anene =20= https://www.researchgate.net/profile/Uchenna_Anene = > On Jan 10, 2020, at 2:31 PM, John Keller jwkeller:alaska.edu = wrote: >=20 > Sent to CCL by: John Keller [jwkeller++alaska.edu = ] > HI, > I tried the NIST website as suggested, but I got the following = message: > =E2=80=9CThe requested URL "https://www.nist.gov/cgi-bin/thermo_cgi.pl = " was not found on this = server.=E2=80=9D > One can also upload Gaussian (and several other program) .log files to = the free WebMO demo site, which will parse them completely, including a = table of frequencies that can be animated. > =20 > https://www.webmo.net/demoserver/cgi-bin/webmo/login.cgi = > =20 > Best, > John Keller > University of Alaska Fairbanks > =20 > =20 > Sent from Mail for = Windows 10 > =20 > From: Grant Hill grant.hill _ sheffield.ac.uk = > Sent: Friday, January 10, 2020 9:07 AM > To: Keller, John W=C2=A0 > Subject: CCL:G: Recomputing Free energy at different temperature from = Gaussian output > =20 > =20 > Sent to CCL by: Grant Hill [grant.hill]-[sheffield.ac.uk = ] > If I understand what you want correctly, this can be done on the NIST = website: = https://www.nist.gov/mml/csd/chemical-informatics-research-group/thermodyn= amics-functions-gaussian-output-files = > =20 > You can also download the underlying perl script for command line = automation. > =20 > Hope this helps, > Grant > =20 > =20 > =20 > > On 10 Jan 2020, at 13:54, Fleurat-Lessard Paul = Paul.Fleurat-Lessard^u-bourgogne.fr = wrote: > > > > > > Sent to CCL by: "Fleurat-Lessard Paul" = [Paul.Fleurat-Lessard^u-bourgogne.fr ] > > Dear colleagues, > > > > In one project using Gaussian09, one student computed the free = energies at room > > temperature instead of T=3D110C. I usually use a small script based = on Freqchk > > to correct for this.. but, to save some disk space in archiving, the = student > > has deleted many CheckPoint files. > > I am thus looking for some codes/scripts that would parse the = Gaussian output > > file to compute the thermochemical functions from it and not from = the chk file. > > I have tens of files so I need something that can be used in command = line with > > no graphical user interface. > > > > Could you help me in finding such a tool? > > > > Best regards, > > Paul.> > >=20 > =20 > =20 > =20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change > the strange characters on the top line to the _+_ sign. You can also >=20 > =20 > E-mail to subscribers: CHEMISTRY_+_ccl.net or use: > =20 > =20 > E-mail to administrators: CHEMISTRY-REQUEST_+_ccl.net = or use > =20 > =20 >=20= > =20 >=20 > =20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ = > =20= > =20 >=20= > =20= > =20 > =20 > =20 > - This is automatically added to each message by the mailing script =3D-= To recover the email address of the author of the message, please = change the strange characters on the top line to the {} sign. You can = alsoE-mail to = subscribers: CHEMISTRY{}ccl.net or use: == E-mail to = administrators: CHEMISTRY-REQUEST{}ccl.net = or use == = Subscribe/Unsubscribe:http://www.ccl.net/chemistry/sub_unsub.shtml = Before posting, check = wait time at: http://www.ccl.net Job: = http://www.ccl.net/jobs Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ = Search = Messages: http://www.ccl.net/chemistry/searchccl/index.shtml = If your mail = bounces from CCL with 5.7.1 error, check: = RTFI: = http://www.ccl.net/chemistry/aboutccl/instructions/ = --Apple-Mail=_0551FA95-D896-489B-AECD-BA56187C66BB Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8
Hi,
The correct NIST website for

"Using the output file = > from a Gaussian frequency calculation to compute = ideal-gas thermodynamic functions=E2=80=9D

https://www.nist.gov/mml/csd/chemical-informatics-research-grou= p/products-and-services/program-computing-ideal-gas

I have tried the link = and used the script and it works.

Happy computing,
Uche



---
Uchenna A. Anene
Ph.D. Student, Chemical Engineering =  
University of = Connecticut
Innovation Partnership = Building 
159 Discovery = Drive
Storrs, CT = 06269
uche{}uconn.edu
https://alpay.ims.uconn.edu/uche-anene/#
www.linkedin.com/in/uche-anene 
https://www.researchgate.net/profile/Uchenna_Anene









On Jan 10, 2020, at 2:31 PM, John Keller jwkeller:alaska.edu <owner-chemistry{}ccl.net> wrote:

Sent to CCL by: John Keller = [jwkeller++alaska.edu]
HI,
I tried the NIST = website as suggested, but I got the following message:
=E2=80=9CThe requested URL "https://www.nist.gov/cgi-bin/thermo_cgi.pl" was not found = on this server.=E2=80=9D
One can also upload Gaussian (and several other = program) .log files to the free WebMO demo site, which will parse them = completely, including a table of frequencies that can be animated.
 
 
Best,
John = Keller
University of Alaska = Fairbanks
 
 
Sent = > from Mail for Windows 10
 
From: Grant Hill grant.hill _ = sheffield.ac.uk
Sent: Friday, January 10, = 2020 9:07 AM
To: Keller, John W 
Subject: CCL:G: Recomputing Free = energy at different temperature from Gaussian output
 
 
Sent to CCL by: Grant Hill = [grant.hill]-[sheffield.ac.uk]
If I understand what you want = correctly, this can be done on the NIST website: https://www.nist.gov/mml/csd/chemical-informatics-research-grou= p/thermodynamics-functions-gaussian-output-files
 
You can also download the underlying = perl script for command line automation.
 
Hope this helps,
Grant
 
 
 
> On = 10 Jan 2020, at 13:54, Fleurat-Lessard Paul Paul.Fleurat-Lessard^u-bourgogne.fr <owner-chemistry__ccl.net&= gt; wrote:
>
>
> Sent to CCL by: "Fleurat-Lessard  Paul" = [Paul.Fleurat-Lessard^u-bourgogne.fr]
> Dear colleagues,
>
> In one project = using Gaussian09, one student computed the free energies at = room
> temperature instead = of T=3D110C. I usually use a small script based on Freqchk
> to correct for this.. but, to save = some disk space in archiving, the student
> has deleted many CheckPoint files.
> I am thus looking for some = codes/scripts that would parse the Gaussian output
> file to compute the thermochemical = functions from it and not from the chk file.
> I have tens of files so I need something that can be = used in command line with
> no = graphical user interface.
>
> Could you help = me in finding such a tool?
>
> Best = regards,
> Paul.>
> 
 
 
 
-=3D This = is automatically added to each message by the mailing script = =3D-
To recover the email = address of the author of the message, please change
the strange characters on the top line = to the _+_ sign. You can also

 
E-mail to subscribers: CHEMISTRY_+_ccl.net or use:

     

 
E-mail to administrators: CHEMISTRY-REQUEST_+_ccl.net or use

     

 

 

 
Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= /div>
 
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