From owner-chemistry@ccl.net Tue Oct  2 09:04:00 2018
From: "Grigoriy Zhurko reg_zhurko_._chemcraftprog.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL:G: Interaction of QC software components via text files
Message-Id: <-53483-181002053207-1676-fDIgmMx8v+7DrvWylEWtug .. server.ccl.net>
X-Original-From: Grigoriy Zhurko <reg_zhurko_._chemcraftprog.com>
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Date: Tue, 2 Oct 2018 12:35:01 +0400
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Sent to CCL by: Grigoriy Zhurko [reg_zhurko#%#chemcraftprog.com]
> the ORCA optimizer is robust and efficient. ORCA's optimizer can be used
> as an external optimizer and can be used for the described scenario.
> Besides that, ORCA by itself provides plenty of density functionals and
> efficient Post-HF methods. Using ORCA's optimizer as external optimizer
> is well documented in the manual. ORCA is free of charge for academic
> use (https://orcaforum.cec.mpg.de/).

ORCA seems to be an interesting choice (as far as I know, it provides 90% of features provided by Gaussian). I am thinking of switching from Gaussian to Orca in my research work, and in this case implementing the external use of ORCA will be easy for me. However, the main problem for me is that ORCA is a freeware code (state-funded). I greatly dislike socialism in any form, and I think that state-funded codes can provide good quality only if they compete with the commercial codes like Gaussian (and steal their algorithms). If the commercial codes disappear, the computation chemistry will go into stagnation.

> The likewise freely available open source Psi4 program also has a 
> variety of ab initio and DFT methods implemented, and also supports a 
> variety of CBS extrapolations for energies and geometry optimizations 
> out of the box.

As far as I understand, the Psi program is state-funded too?

I’ve heard that the ADF program offers the external interaction. But ADF uses Slater functions instead of Gaussian ones; sorry for my profanity, but I can’t understand why such approach has not been rejected yet by the chemical community.



> What you describe can be achieved by using the Atomic Simulation
> Environment (ASE). The peer-reviewed article for ASE can be found
> here and main webpage found here. ASE is a Python-based code meant
> to manipulate, run, and analyse quantum-chemical calculations. ASE
> has a built-in set of optimization routines (described here), and
> the quantum-chemical program of your choice can be used just to
> calculate the energies and forces required for ASE to update the
> atomic positions. You then do not have to rely on the optimizers
> built into Gaussian, and it operates using the exact same workflow
> you proposed. ASE does support Gaussian as a calculator (as listed
> here), but it is currently lacking documentation and would probably
> require some modifications to suit all your needs.

So, if using Gaussian as an external calculator is in principle possible, I’d like to clarify some more points. I’ve heard that Gaussian authors even prohibit such manipulations, do they not?
The Gaussian package contains two exe files: e.g., g09w.exe (a GUI) and g09.exe. The first one evidently can be run to handle a gjf file only manually (not by another program). Maybe running the g09.exe file by my program would be a good choice, but as far as I remember, in previous version of Gaussian (G98) the g98w.exe and g98.exe files sometimes produced different outputs from the same gjf input (sorry for not sufficiently reliable information, I tried to reproduce this error with g09.exe but found difficult to run it).

One more question is, how high (low) is the speed of Windows QC codes if they are run from Linux via Wine.


> But please, be aware that any serious quantum chemistry code is written by
> professionals and it will be very challenging to "beat" built in
> optimizers. Sometimes, slow optimization is rather a consequence of
> chemical system at hand (too shallow PES minimum, noisy
> energy/gradients, etc).

I have some experience of implementing a non-gradient optimization (e.g. Chemcraft performs it for setting a point group). Besides that, I suppose it can be a good approach to perform an optimization and frequencies computation in curvilinear coordinates specified manually by the user (using a GUI).

> Could you be a bit more specific about DFT functionals and neural networks?

  Currently, this is just an idea; neural networks are powerful paradigms for some tasks, and implementing by me a NN for processing multiple single point DFT computations to obtain a single point energy is in principle possible.
  Grigoriy Zhurko


From owner-chemistry@ccl.net Tue Oct  2 11:26:01 2018
From: "Fco. Javier Modrego modrego[a]unizar.es" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: Interaction of QC software components via text files
Message-Id: <-53484-181002103918-30158-QZj2CAHtZ3QKbWW4Mo7tqQ^server.ccl.net>
X-Original-From: "Fco. Javier Modrego" <modrego#%#unizar.es>
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	charset=utf-8
Date: Tue, 2 Oct 2018 16:39:10 +0200
Mime-Version: 1.0 (Mac OS X Mail 11.5 \(3445.9.1\))


Sent to CCL by: "Fco. Javier Modrego" [modrego[a]unizar.es]
This is probably an ideological issue not properly addresses in this forum, but here are my two cents:
Probably you should stop doing research based on previous research right now. Most of it is state funded. And stop reading papers coming from public funded research centers. Also disregard any code inside Gaussian designed and done by researchers of public centers based on public funded research projects. Do what you can with what is left…


> El 2 oct 2018, a las 10:35, Grigoriy Zhurko reg_zhurko_._chemcraftprog.com <owner-chemistry.^.ccl.net> escribió:
> 
> 
> Sent to CCL by: Grigoriy Zhurko [reg_zhurko#%#chemcraftprog.com]
>> the ORCA optimizer is robust and efficient. ORCA's optimizer can be used
>> as an external optimizer and can be used for the described scenario.
>> Besides that, ORCA by itself provides plenty of density functionals and
>> efficient Post-HF methods. Using ORCA's optimizer as external optimizer
>> is well documented in the manual. ORCA is free of charge for academic
>> use (https://orcaforum.cec.mpg.de/).
> 
> ORCA seems to be an interesting choice (as far as I know, it provides 90% of features provided by Gaussian). I am thinking of switching from Gaussian to Orca in my research work, and in this case implementing the external use of ORCA will be easy for me. However, the main problem for me is that ORCA is a freeware code (state-funded). I greatly dislike socialism in any form, and I think that state-funded codes can provide good quality only if they compete with the commercial codes like Gaussian (and steal their algorithms). If the commercial codes disappear, the computation chemistry will go into stagnation.
> 
>> The likewise freely available open source Psi4 program also has a 
>> variety of ab initio and DFT methods implemented, and also supports a 
>> variety of CBS extrapolations for energies and geometry optimizations 
>> out of the box.
> 
> As far as I understand, the Psi program is state-funded too?
> 
> I’ve heard that the ADF program offers the external interaction. But ADF uses Slater functions instead of Gaussian ones; sorry for my profanity, but I can’t understand why such approach has not been rejected yet by the chemical community.
> 
> 
> 
>> What you describe can be achieved by using the Atomic Simulation
>> Environment (ASE). The peer-reviewed article for ASE can be found
>> here and main webpage found here. ASE is a Python-based code meant
>> to manipulate, run, and analyse quantum-chemical calculations. ASE
>> has a built-in set of optimization routines (described here), and
>> the quantum-chemical program of your choice can be used just to
>> calculate the energies and forces required for ASE to update the
>> atomic positions. You then do not have to rely on the optimizers
>> built into Gaussian, and it operates using the exact same workflow
>> you proposed. ASE does support Gaussian as a calculator (as listed
>> here), but it is currently lacking documentation and would probably
>> require some modifications to suit all your needs.
> 
> So, if using Gaussian as an external calculator is in principle possible, I’d like to clarify some more points. I’ve heard that Gaussian authors even prohibit such manipulations, do they not?
> The Gaussian package contains two exe files: e.g., g09w.exe (a GUI) and g09.exe. The first one evidently can be run to handle a gjf file only manually (not by another program). Maybe running the g09.exe file by my program would be a good choice, but as far as I remember, in previous version of Gaussian (G98) the g98w.exe and g98.exe files sometimes produced different outputs from the same gjf input (sorry for not sufficiently reliable information, I tried to reproduce this error with g09.exe but found difficult to run it).
> 
> One more question is, how high (low) is the speed of Windows QC codes if they are run from Linux via Wine.
> 
> 
>> But please, be aware that any serious quantum chemistry code is written by
>> professionals and it will be very challenging to "beat" built in
>> optimizers. Sometimes, slow optimization is rather a consequence of
>> chemical system at hand (too shallow PES minimum, noisy
>> energy/gradients, etc).
> 
> I have some experience of implementing a non-gradient optimization (e.g. Chemcraft performs it for setting a point group). Besides that, I suppose it can be a good approach to perform an optimization and frequencies computation in curvilinear coordinates specified manually by the user (using a GUI).
> 
>> Could you be a bit more specific about DFT functionals and neural networks?
> 
>  Currently, this is just an idea; neural networks are powerful paradigms for some tasks, and implementing by me a NN for processing multiple single point DFT computations to obtain a single point energy is in principle possible.
>  Grigoriy Zhurko> 
> 

Dr. F.J. Modrego
Department of Inorganic Chemistry
Facultad de Ciencias
University of Zaragoza
50009 ZARAGOZA
SPAIN
Tel <34>-976-762288
Fax <34>-976-761187
E-mail:  modrego.^.unizar.es


From owner-chemistry@ccl.net Tue Oct  2 12:01:00 2018
From: "Dr.N Sukumar n.sukumar _ snu.edu.in" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL:G: Interaction of QC software components via text files
Message-Id: <-53485-181002111558-13749-ba9XX8qOLg4KvgDYv6LqJw[-]server.ccl.net>
X-Original-From: "Dr.N Sukumar" <n.sukumar^-^snu.edu.in>
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Date: Tue, 2 Oct 2018 20:45:36 +0530
MIME-Version: 1.0


Sent to CCL by: "Dr.N Sukumar" [n.sukumar+*+snu.edu.in]
--000000000000a420530577406539
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oh dear, I fear we may be returning to the Great Annual Gaussian Wars!
Gaussian may be commercial software today, but it did not originate thus.
The bulk of the core code was written at a state university with government
grants and was thus "state-funded." So for that matter is the internet you
are using for this communication, as well as most of the original search
engines, computer hardware,...

And I don't see why you feel that using Slater functions (actual solutions
of the Schrodinger equation for one-electron atoms) instead of Gaussians
should be "rejected by the chemical community." In the end, they are both
(as well as plane waves) just mathematical functions (basis sets) for
expansion of the many-electron molecular wavefunction.




*N. SukumarProfessor of ChemistryDirector, Center for Informatics**Shiv
Nadar University, India*
<http://as.wiley.com/WileyCDA/WileyTitle/productCd-0470769009.html>

=E2=80=9CBe a nuisance where it counts=E2=80=9D - Marjory Stoneman Douglas


On Tue, Oct 2, 2018 at 8:29 PM Grigoriy Zhurko reg_zhurko_._
chemcraftprog.com <owner-chemistry]*[ccl.net> wrote:

>
> Sent to CCL by: Grigoriy Zhurko [reg_zhurko#%#chemcraftprog.com]
> > the ORCA optimizer is robust and efficient. ORCA's optimizer can be use=
d
> > as an external optimizer and can be used for the described scenario.
> > Besides that, ORCA by itself provides plenty of density functionals and
> > efficient Post-HF methods. Using ORCA's optimizer as external optimizer
> > is well documented in the manual. ORCA is free of charge for academic
> > use (https://orcaforum.cec.mpg.de/).
>
> ORCA seems to be an interesting choice (as far as I know, it provides 90%
> of features provided by Gaussian). I am thinking of switching from Gaussi=
an
> to Orca in my research work, and in this case implementing the external u=
se
> of ORCA will be easy for me. However, the main problem for me is that ORC=
A
> is a freeware code (state-funded). I greatly dislike socialism in any for=
m,
> and I think that state-funded codes can provide good quality only if they
> compete with the commercial codes like Gaussian (and steal their
> algorithms). If the commercial codes disappear, the computation chemistry
> will go into stagnation.
>
> > The likewise freely available open source Psi4 program also has a
> > variety of ab initio and DFT methods implemented, and also supports a
> > variety of CBS extrapolations for energies and geometry optimizations
> > out of the box.
>
> As far as I understand, the Psi program is state-funded too?
>
> I=E2=80=99ve heard that the ADF program offers the external interaction. =
But ADF
> uses Slater functions instead of Gaussian ones; sorry for my profanity, b=
ut
> I can=E2=80=99t understand why such approach has not been rejected yet by=
 the
> chemical community.
>
>
>
> > What you describe can be achieved by using the Atomic Simulation
> > Environment (ASE). The peer-reviewed article for ASE can be found
> > here and main webpage found here. ASE is a Python-based code meant
> > to manipulate, run, and analyse quantum-chemical calculations. ASE
> > has a built-in set of optimization routines (described here), and
> > the quantum-chemical program of your choice can be used just to
> > calculate the energies and forces required for ASE to update the
> > atomic positions. You then do not have to rely on the optimizers
> > built into Gaussian, and it operates using the exact same workflow
> > you proposed. ASE does support Gaussian as a calculator (as listed
> > here), but it is currently lacking documentation and would probably
> > require some modifications to suit all your needs.
>
> So, if using Gaussian as an external calculator is in principle possible,
> I=E2=80=99d like to clarify some more points. I=E2=80=99ve heard that Gau=
ssian authors even
> prohibit such manipulations, do they not?
> The Gaussian package contains two exe files: e.g., g09w.exe (a GUI) and
> g09.exe. The first one evidently can be run to handle a gjf file only
> manually (not by another program). Maybe running the g09.exe file by my
> program would be a good choice, but as far as I remember, in previous
> version of Gaussian (G98) the g98w.exe and g98.exe files sometimes produc=
ed
> different outputs from the same gjf input (sorry for not sufficiently
> reliable information, I tried to reproduce this error with g09.exe but
> found difficult to run it).
>
> One more question is, how high (low) is the speed of Windows QC codes if
> they are run from Linux via Wine.
>
>
> > But please, be aware that any serious quantum chemistry code is written
> by
> > professionals and it will be very challenging to "beat" built in
> > optimizers. Sometimes, slow optimization is rather a consequence of
> > chemical system at hand (too shallow PES minimum, noisy
> > energy/gradients, etc).
>
> I have some experience of implementing a non-gradient optimization (e.g.
> Chemcraft performs it for setting a point group). Besides that, I suppose
> it can be a good approach to perform an optimization and frequencies
> computation in curvilinear coordinates specified manually by the user
> (using a GUI).
>
> > Could you be a bit more specific about DFT functionals and neural
> networks?
>
>   Currently, this is just an idea; neural networks are powerful paradigms
> for some tasks, and implementing by me a NN for processing multiple singl=
e
> point DFT computations to obtain a single point energy is in principle
> possible.
>   Grigoriy Zhurko
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D->
>
>

--000000000000a420530577406539
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><div>oh dear, I fear we may be returning to the Great Annu=
al Gaussian Wars!=20
Gaussian may be commercial software today, but it did not originate thus. T=
he bulk of the core code was written at a state university with government =
grants and was thus &quot;state-funded.&quot; So for that matter is the int=
ernet you are using for this communication, as well as most of the original=
 search engines, computer hardware,...<br></div><div><br></div><div>And I d=
on&#39;t see why you feel that using=20
Slater functions (actual solutions of the Schrodinger equation for one-elec=
tron atoms) instead of Gaussians should be &quot;rejected by the=20
chemical community.&quot; In the end, they are both (as well as plane waves=
) just mathematical functions (basis sets) for expansion of the many-electr=
on molecular wavefunction.<br></div><div><br></div><div><div><div dir=3D"lt=
r" class=3D"gmail_signature" data-smartmail=3D"gmail_signature"><div dir=3D=
"ltr"><div><div dir=3D"ltr"><div><div dir=3D"ltr"><div><div dir=3D"ltr"><di=
v><div dir=3D"ltr"><div><span style=3D"color:rgb(51,51,255)"><i>N. Sukumar<=
br>Professor of Chemistry<br>Director, Center for Informatics<br></i><i>Shi=
v Nadar University, India</i></span><br><a href=3D"http://as.wiley.com/Wile=
yCDA/WileyTitle/productCd-0470769009.html" target=3D"_blank"><img src=3D"ht=
tp://media.wiley.com/product_data/coverImage300/09/04707690/0470769009.jpg"=
 width=3D"110" height=3D"175"></a><br><br>=E2=80=9CBe a nuisance where it c=
ounts=E2=80=9D - Marjory Stoneman Douglas<br></div></div></div></div></div>=
</div></div></div></div></div></div></div><br></div></div><br><div class=3D=
"gmail_quote"><div dir=3D"ltr">On Tue, Oct 2, 2018 at 8:29 PM Grigoriy Zhur=
ko reg_zhurko_._<a href=3D"http://chemcraftprog.com">chemcraftprog.com</a> =
&lt;<a href=3D"mailto:owner-chemistry]*[ccl.net">owner-chemistry]*[ccl.net</a>&=
gt; wrote:<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0=
 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
Sent to CCL by: Grigoriy Zhurko [reg_zhurko#%#<a href=3D"http://chemcraftpr=
og.com" rel=3D"noreferrer" target=3D"_blank">chemcraftprog.com</a>]<br>
&gt; the ORCA optimizer is robust and efficient. ORCA&#39;s optimizer can b=
e used<br>
&gt; as an external optimizer and can be used for the described scenario.<b=
r>
&gt; Besides that, ORCA by itself provides plenty of density functionals an=
d<br>
&gt; efficient Post-HF methods. Using ORCA&#39;s optimizer as external opti=
mizer<br>
&gt; is well documented in the manual. ORCA is free of charge for academic<=
br>
&gt; use (<a href=3D"https://orcaforum.cec.mpg.de/" rel=3D"noreferrer" targ=
et=3D"_blank">https://orcaforum.cec.mpg.de/</a>).<br>
<br>
ORCA seems to be an interesting choice (as far as I know, it provides 90% o=
f features provided by Gaussian). I am thinking of switching from Gaussian =
to Orca in my research work, and in this case implementing the external use=
 of ORCA will be easy for me. However, the main problem for me is that ORCA=
 is a freeware code (state-funded). I greatly dislike socialism in any form=
, and I think that state-funded codes can provide good quality only if they=
 compete with the commercial codes like Gaussian (and steal their algorithm=
s). If the commercial codes disappear, the computation chemistry will go in=
to stagnation.<br>
<br>
&gt; The likewise freely available open source Psi4 program also has a <br>
&gt; variety of ab initio and DFT methods implemented, and also supports a =
<br>
&gt; variety of CBS extrapolations for energies and geometry optimizations =
<br>
&gt; out of the box.<br>
<br>
As far as I understand, the Psi program is state-funded too?<br>
<br>
I=E2=80=99ve heard that the ADF program offers the external interaction. Bu=
t ADF uses Slater functions instead of Gaussian ones; sorry for my profanit=
y, but I can=E2=80=99t understand why such approach has not been rejected y=
et by the chemical community.<br>
<br>
<br>
<br>
&gt; What you describe can be achieved by using the Atomic Simulation<br>
&gt; Environment (ASE). The peer-reviewed article for ASE can be found<br>
&gt; here and main webpage found here. ASE is a Python-based code meant<br>
&gt; to manipulate, run, and analyse quantum-chemical calculations. ASE<br>
&gt; has a built-in set of optimization routines (described here), and<br>
&gt; the quantum-chemical program of your choice can be used just to<br>
&gt; calculate the energies and forces required for ASE to update the<br>
&gt; atomic positions. You then do not have to rely on the optimizers<br>
&gt; built into Gaussian, and it operates using the exact same workflow<br>
&gt; you proposed. ASE does support Gaussian as a calculator (as listed<br>
&gt; here), but it is currently lacking documentation and would probably<br=
>
&gt; require some modifications to suit all your needs.<br>
<br>
So, if using Gaussian as an external calculator is in principle possible, I=
=E2=80=99d like to clarify some more points. I=E2=80=99ve heard that Gaussi=
an authors even prohibit such manipulations, do they not?<br>
The Gaussian package contains two exe files: e.g., g09w.exe (a GUI) and g09=
.exe. The first one evidently can be run to handle a gjf file only manually=
 (not by another program). Maybe running the g09.exe file by my program wou=
ld be a good choice, but as far as I remember, in previous version of Gauss=
ian (G98) the g98w.exe and g98.exe files sometimes produced different outpu=
ts from the same gjf input (sorry for not sufficiently reliable information=
, I tried to reproduce this error with g09.exe but found difficult to run i=
t).<br>
<br>
One more question is, how high (low) is the speed of Windows QC codes if th=
ey are run from Linux via Wine.<br>
<br>
<br>
&gt; But please, be aware that any serious quantum chemistry code is writte=
n by<br>
&gt; professionals and it will be very challenging to &quot;beat&quot; buil=
t in<br>
&gt; optimizers. Sometimes, slow optimization is rather a consequence of<br=
>
&gt; chemical system at hand (too shallow PES minimum, noisy<br>
&gt; energy/gradients, etc).<br>
<br>
I have some experience of implementing a non-gradient optimization (e.g. Ch=
emcraft performs it for setting a point group). Besides that, I suppose it =
can be a good approach to perform an optimization and frequencies computati=
on in curvilinear coordinates specified manually by the user (using a GUI).=
<br>
<br>
&gt; Could you be a bit more specific about DFT functionals and neural netw=
orks?<br>
<br>
=C2=A0 Currently, this is just an idea; neural networks are powerful paradi=
gms for some tasks, and implementing by me a NN for processing multiple sin=
gle point DFT computations to obtain a single point energy is in principle =
possible.<br>
=C2=A0 Grigoriy Zhurko<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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--000000000000a420530577406539--


From owner-chemistry@ccl.net Tue Oct  2 12:35:01 2018
From: "Robert Molt r.molt.chemical.physics|-|gmail.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: Interaction of QC software components via text files
Message-Id: <-53486-181002115135-23031-SvKToa1BbSGTxsA/R4cw1g**server.ccl.net>
X-Original-From: Robert Molt <r.molt.chemical.physics{=}gmail.com>
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Date: Tue, 2 Oct 2018 11:51:26 -0400
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Sent to CCL by: Robert Molt [r.molt.chemical.physics__gmail.com]

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What nonsense about a code being free implies ANYTHING about socialism?

ACES is a free code, as are many others, and outcompetes all codes in CCSD(T=
) for massive parallelization 100s to 1000s of processors). There is no gove=
rnment funding for ACES. It=E2=80=99s written by CC people who have a need f=
or its usage in work themselves and do not wish to charge others for it.

Moreover, by your logic, your email thoughts are sent freely, so you must be=
 being paid by a government to do it! You=E2=80=99re a secret socialist agen=
t...=F0=9F=98=A0

Denigrating comments to free software like ORCA, GAMESS, ACES, CFOUR are not=
 appreciated. We=E2=80=99re scientists; a lot of us do it because we love it=
 and we do a better job because we love it.

Dr. Robert Molt Jr.
r.molt.chemical.physics(-)gmail.com


> On Oct 2, 2018, at 4:35 AM, Grigoriy Zhurko reg_zhurko_._chemcraftprog.com=
 <owner-chemistry(-)ccl.net> wrote:
>=20
>=20
> Sent to CCL by: Grigoriy Zhurko [reg_zhurko#%#chemcraftprog.com]
>> the ORCA optimizer is robust and efficient. ORCA's optimizer can be used
>> as an external optimizer and can be used for the described scenario.
>> Besides that, ORCA by itself provides plenty of density functionals and
>> efficient Post-HF methods. Using ORCA's optimizer as external optimizer
>> is well documented in the manual. ORCA is free of charge for academic
>> use (https://orcaforum.cec.mpg.de/).
>=20
> ORCA seems to be an interesting choice (as far as I know, it provides 90% o=
f features provided by Gaussian). I am thinking of switching from Gaussian t=
o Orca in my research work, and in this case implementing the external use o=
f ORCA will be easy for me. However, the main problem for me is that ORCA is=
 a freeware code (state-funded). I greatly dislike socialism in any form, an=
d I think that state-funded codes can provide good quality only if they comp=
ete with the commercial codes like Gaussian (and steal their algorithms). If=
 the commercial codes disappear, the computation chemistry will go into stag=
nation.
>=20
>> The likewise freely available open source Psi4 program also has a=20
>> variety of ab initio and DFT methods implemented, and also supports a=20
>> variety of CBS extrapolations for energies and geometry optimizations=20
>> out of the box.
>=20
> As far as I understand, the Psi program is state-funded too?
>=20
> I=E2=80=99ve heard that the ADF program offers the external interaction. B=
ut ADF uses Slater functions instead of Gaussian ones; sorry for my profanit=
y, but I can=E2=80=99t understand why such approach has not been rejected ye=
t by the chemical community.
>=20
>=20
>=20
>> What you describe can be achieved by using the Atomic Simulation
>> Environment (ASE). The peer-reviewed article for ASE can be found
>> here and main webpage found here. ASE is a Python-based code meant
>> to manipulate, run, and analyse quantum-chemical calculations. ASE
>> has a built-in set of optimization routines (described here), and
>> the quantum-chemical program of your choice can be used just to
>> calculate the energies and forces required for ASE to update the
>> atomic positions. You then do not have to rely on the optimizers
>> built into Gaussian, and it operates using the exact same workflow
>> you proposed. ASE does support Gaussian as a calculator (as listed
>> here), but it is currently lacking documentation and would probably
>> require some modifications to suit all your needs.
>=20
> So, if using Gaussian as an external calculator is in principle possible, I=
=E2=80=99d like to clarify some more points. I=E2=80=99ve heard that Gaussia=
n authors even prohibit such manipulations, do they not?
> The Gaussian package contains two exe files: e.g., g09w.exe (a GUI) and g0=
9.exe. The first one evidently can be run to handle a gjf file only manually=
 (not by another program). Maybe running the g09.exe file by my program woul=
d be a good choice, but as far as I remember, in previous version of Gaussia=
n (G98) the g98w.exe and g98.exe files sometimes produced different outputs f=
rom the same gjf input (sorry for not sufficiently reliable information, I t=
ried to reproduce this error with g09.exe but found difficult to run it).
>=20
> One more question is, how high (low) is the speed of Windows QC codes if t=
hey are run from Linux via Wine.
>=20
>=20
>> But please, be aware that any serious quantum chemistry code is written b=
y
>> professionals and it will be very challenging to "beat" built in
>> optimizers. Sometimes, slow optimization is rather a consequence of
>> chemical system at hand (too shallow PES minimum, noisy
>> energy/gradients, etc).
>=20
> I have some experience of implementing a non-gradient optimization (e.g. C=
hemcraft performs it for setting a point group). Besides that, I suppose it c=
an be a good approach to perform an optimization and frequencies computation=
 in curvilinear coordinates specified manually by the user (using a GUI).
>=20
>> Could you be a bit more specific about DFT functionals and neural network=
s?
>=20
>  Currently, this is just an idea; neural networks are powerful paradigms f=
or some tasks, and implementing by me a NN for processing multiple single po=
int DFT computations to obtain a single point energy is in principle possibl=
e.
>  Grigoriy Zhurko
>=20
>=20
>=20
> -=3D This is automatically added to each message by the mailing script =3D=
->=20>=20>=20
> Subscribe/Unsubscribe:=20>=20>=20
> Job: http://www.ccl.net/jobs=20>=20>=20>=20>=20
>=20

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<html><head><meta http-equiv=3D"content-type" content=3D"text/html; charset=3D=
utf-8"></head><body dir=3D"auto">What nonsense about a code being free impli=
es ANYTHING about socialism?<div><br></div><div>ACES is a free code, as are m=
any others, and outcompetes all codes in CCSD(T) for massive parallelization=
 100s to 1000s of processors). There is no government funding for ACES. It=E2=
=80=99s written by CC people who have a need for its usage in work themselve=
s and do not wish to charge others for it.</div><div><br></div><div>Moreover=
, by your logic, your email thoughts are sent freely, so you must be being p=
aid by a government to do it! You=E2=80=99re a secret socialist agent...=F0=9F=
=98=A0<br><br>Denigrating comments to free software like ORCA, GAMESS, ACES,=
 CFOUR are not appreciated. We=E2=80=99re scientists; a lot of us do it beca=
use we love it and we do a better job because we love it.<br><br><div id=3D"=
AppleMailSignature" dir=3D"ltr"><div><span style=3D"background-color: rgba(2=
55, 255, 255, 0); ">Dr. Robert Molt Jr.</span></div><div><span class=3D"Appl=
e-style-span" style=3D"border-collapse: separate; border-spacing: 0px; "><a h=
ref=3D"mailto:r.molt.chemical.physics(-)gmail.com">r.molt.chemical.physics(-)gma=
il.com</a><br></span></div><div><br></div></div><div dir=3D"ltr"><br>On Oct 2=
, 2018, at 4:35 AM, Grigoriy Zhurko reg_zhurko_._<a href=3D"http://chemcraft=
prog.com">chemcraftprog.com</a> &lt;<a href=3D"mailto:owner-chemistry(-)ccl.ne=
t">owner-chemistry(-)ccl.net</a>&gt; wrote:<br><br></div><blockquote type=3D"c=
ite"><div dir=3D"ltr"><span></span><br><span>Sent to CCL by: Grigoriy Zhurko=
 [reg_zhurko#%#<a href=3D"http://chemcraftprog.com">chemcraftprog.com</a>]</=
span><br><blockquote type=3D"cite"><span>the ORCA optimizer is robust and ef=
ficient. ORCA's optimizer can be used</span><br></blockquote><blockquote typ=
e=3D"cite"><span>as an external optimizer and can be used for the described s=
cenario.</span><br></blockquote><blockquote type=3D"cite"><span>Besides that=
, ORCA by itself provides plenty of density functionals and</span><br></bloc=
kquote><blockquote type=3D"cite"><span>efficient Post-HF methods. Using ORCA=
's optimizer as external optimizer</span><br></blockquote><blockquote type=3D=
"cite"><span>is well documented in the manual. ORCA is free of charge for ac=
ademic</span><br></blockquote><blockquote type=3D"cite"><span>use (<a href=3D=
"https://orcaforum.cec.mpg.de/">https://orcaforum.cec.mpg.de/</a>).</span><b=
r></blockquote><span></span><br><span>ORCA seems to be an interesting choice=
 (as far as I know, it provides 90% of features provided by Gaussian). I am t=
hinking of switching from Gaussian to Orca in my research work, and in this c=
ase implementing the external use of ORCA will be easy for me. However, the m=
ain problem for me is that ORCA is a freeware code (state-funded). I greatly=
 dislike socialism in any form, and I think that state-funded codes can prov=
ide good quality only if they compete with the commercial codes like Gaussia=
n (and steal their algorithms). If the commercial codes disappear, the compu=
tation chemistry will go into stagnation.</span><br><span></span><br><blockq=
uote type=3D"cite"><span>The likewise freely available open source Psi4 prog=
ram also has a </span><br></blockquote><blockquote type=3D"cite"><span>varie=
ty of ab initio and DFT methods implemented, and also supports a </span><br>=
</blockquote><blockquote type=3D"cite"><span>variety of CBS extrapolations f=
or energies and geometry optimizations </span><br></blockquote><blockquote t=
ype=3D"cite"><span>out of the box.</span><br></blockquote><span></span><br><=
span>As far as I understand, the Psi program is state-funded too?</span><br>=
<span></span><br><span>I=E2=80=99ve heard that the ADF program offers the ex=
ternal interaction. But ADF uses Slater functions instead of Gaussian ones; s=
orry for my profanity, but I can=E2=80=99t understand why such approach has n=
ot been rejected yet by the chemical community.</span><br><span></span><br><=
span></span><br><span></span><br><blockquote type=3D"cite"><span>What you de=
scribe can be achieved by using the Atomic Simulation</span><br></blockquote=
><blockquote type=3D"cite"><span>Environment (ASE). The peer-reviewed articl=
e for ASE can be found</span><br></blockquote><blockquote type=3D"cite"><spa=
n>here and main webpage found here. ASE is a Python-based code meant</span><=
br></blockquote><blockquote type=3D"cite"><span>to manipulate, run, and anal=
yse quantum-chemical calculations. ASE</span><br></blockquote><blockquote ty=
pe=3D"cite"><span>has a built-in set of optimization routines (described her=
e), and</span><br></blockquote><blockquote type=3D"cite"><span>the quantum-c=
hemical program of your choice can be used just to</span><br></blockquote><b=
lockquote type=3D"cite"><span>calculate the energies and forces required for=
 ASE to update the</span><br></blockquote><blockquote type=3D"cite"><span>at=
omic positions. You then do not have to rely on the optimizers</span><br></b=
lockquote><blockquote type=3D"cite"><span>built into Gaussian, and it operat=
es using the exact same workflow</span><br></blockquote><blockquote type=3D"=
cite"><span>you proposed. ASE does support Gaussian as a calculator (as list=
ed</span><br></blockquote><blockquote type=3D"cite"><span>here), but it is c=
urrently lacking documentation and would probably</span><br></blockquote><bl=
ockquote type=3D"cite"><span>require some modifications to suit all your nee=
ds.</span><br></blockquote><span></span><br><span>So, if using Gaussian as a=
n external calculator is in principle possible, I=E2=80=99d like to clarify s=
ome more points. I=E2=80=99ve heard that Gaussian authors even prohibit such=
 manipulations, do they not?</span><br><span>The Gaussian package contains t=
wo exe files: e.g., g09w.exe (a GUI) and g09.exe. The first one evidently ca=
n be run to handle a gjf file only manually (not by another program). Maybe r=
unning the g09.exe file by my program would be a good choice, but as far as I=
 remember, in previous version of Gaussian (G98) the g98w.exe and g98.exe fi=
les sometimes produced different outputs from the same gjf input (sorry for n=
ot sufficiently reliable information, I tried to reproduce this error with g=
09.exe but found difficult to run it).</span><br><span></span><br><span>One m=
ore question is, how high (low) is the speed of Windows QC codes if they are=
 run from Linux via Wine.</span><br><span></span><br><span></span><br><block=
quote type=3D"cite"><span>But please, be aware that any serious quantum chem=
istry code is written by</span><br></blockquote><blockquote type=3D"cite"><s=
pan>professionals and it will be very challenging to "beat" built in</span><=
br></blockquote><blockquote type=3D"cite"><span>optimizers. Sometimes, slow o=
ptimization is rather a consequence of</span><br></blockquote><blockquote ty=
pe=3D"cite"><span>chemical system at hand (too shallow PES minimum, noisy</s=
pan><br></blockquote><blockquote type=3D"cite"><span>energy/gradients, etc).=
</span><br></blockquote><span></span><br><span>I have some experience of imp=
lementing a non-gradient optimization (e.g. Chemcraft performs it for settin=
g a point group). Besides that, I suppose it can be a good approach to perfo=
rm an optimization and frequencies computation in curvilinear coordinates sp=
ecified manually by the user (using a GUI).</span><br><span></span><br><bloc=
kquote type=3D"cite"><span>Could you be a bit more specific about DFT functi=
onals and neural networks?</span><br></blockquote><span></span><br><span> &n=
bsp;Currently, this is just an idea; neural networks are powerful paradigms f=
or some tasks, and implementing by me a NN for processing multiple single po=
int DFT computations to obtain a single point energy is in principle possibl=
e.</span><br><span> &nbsp;Grigoriy Zhurko</span><br><span></span><br><span><=
/span><br><span></span><br><span>-=3D This is automatically added to each me=
ssage by the mailing script =3D-</span><br><span>To recover the email addres=
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ckquote></div></body></html>=

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From owner-chemistry@ccl.net Tue Oct  2 13:11:00 2018
From: "Susi Lehtola susi.lehtola##alumni.helsinki.fi" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL:G: Interaction of QC software components via text files
Message-Id: <-53487-181002121255-4026-np682dmazBtaH+HZ5HzWuw : server.ccl.net>
X-Original-From: Susi Lehtola <susi.lehtola:+:alumni.helsinki.fi>
Content-Language: en-US
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Date: Tue, 2 Oct 2018 19:12:44 +0300
MIME-Version: 1.0


Sent to CCL by: Susi Lehtola [susi.lehtola * alumni.helsinki.fi]
On 10/2/18 11:35 AM, Grigoriy Zhurko reg_zhurko_._chemcraftprog.com wrote:
> Sent to CCL by: Grigoriy Zhurko [reg_zhurko#%#chemcraftprog.com]
>> the ORCA optimizer is robust and efficient. ORCA's optimizer can be
>> used as an external optimizer and can be used for the described
>> scenario. Besides that, ORCA by itself provides plenty of density
>> functionals and efficient Post-HF methods. Using ORCA's optimizer
>> as external optimizer is well documented in the manual. ORCA is
>> free of charge for academic use (https://orcaforum.cec.mpg.de/).
> 
> ORCA seems to be an interesting choice (as far as I know, it provides
> 90% of features provided by Gaussian). I am thinking of switching
> from Gaussian to Orca in my research work, and in this case
> implementing the external use of ORCA will be easy for me. However,
> the main problem for me is that ORCA is a freeware code
> (state-funded). I greatly dislike socialism in any form, and I think
> that state-funded codes can provide good quality only if they compete
> with the commercial codes like Gaussian (and steal their algorithms).
> If the commercial codes disappear, the computation chemistry will go
> into stagnation.

Okay, that's a bit of a funny stance for several reasons.

First, ORCA is only free as in free beer, not free as in free speech. 
(Free software satisfies both criteria.) Furthermore, it's only free for 
academic users, not for anybody. Calling ORCA state-funded freeware is 
just not true: industry users have to pay $$$.

Second, by selling licenses to software you also end up having to ship 
the software and support its userbase, which may take a significant 
amount of resources. Generally open source programs don't have as much 
user support. However, the beauty of open source is that you *don't* 
have to ship and support binaries yourself, since thanks to the 
permissive licensing, linux distributions can ship your program for you. 
For instance, Fedora has packages of e.g. OpenMolcas and Psi4, and you 
can get them on your laptop or server with a simple
# yum install OpenMolcas psi4

Third, basically *all* quantum chemistry (QC) programs have been 
developed as a result of public funding. Furthermore, many established 
commercial codes actually *rely* on government funding for developing 
new features. It's not like you can make big bucks selling QC codes. If 
your criterion is receiving any state funding at all, I'm afraid you 
won't be able to use *any code at all*.

Fourth, it's not typically the *program* that gets government funding, 
but rather the *scientist* for a specific funding proposal unrelated to 
program development. For instance, ORCA comes from Frank Neese's group, 
who is a member of the International Academy of Quantum Molecular 
Science (http://www.iaqms.org/members/neese.php).

Fifth, the program you mention as example ["and steal their algorithms"] 
is pretty funny given that very little new functionality has been added 
in the last decade; most of which has been "stolen" from other codes, 
i.e. the methods have been originally implemented in other codes but the 
algorithms have been published in scientific articles.

Sixth, open source software is generally easier to develop, since you 
don't have to implement all the functionalities yourself. For instance, 
I started writing ERKALE (https://github.com/susilehtola/erkale) as a 
graduate student only because I knew I wouldn't have to handle any of 
the messy stuff myself, i.e. the two-electron integrals and evaluation 
of exchange-correlation functionals, which were already implemented in 
Ed Valeev's LIBINT and Miguel Marques' LIBXC, respectively. [I probably 
wouldn't write a completely new code today given that great open source 
software, e.g. PySCF and Psi4, already exist.] LIBINT is also used in 
Psi4, and LIBXC both in Psi4 and PySCF. There's no reason to keep 
reinventing the wheel, and open source makes this generally very easy.

Seventh, open source software may also be included as part of commercial 
programs. E.g. PySCF, LIBXC, LIBINT, and PSI4 carry licenses that allow 
for inclusion as part of a closed source program. For instance ORCA is 
already using LIBINT, and the last I heard LIBXC was also making its way 
into it. Again, no reason to keep reinventing the wheel.

> I’ve heard that the ADF program offers the external interaction. But
> ADF uses Slater functions instead of Gaussian ones; sorry for my
> profanity, but I can’t understand why such approach has not been
> rejected yet by the chemical community.

[ADF originated in Baerend's group in Amsterdam and Ziegler's group in 
Calgary; both receivers of state funding.]

>> Could you be a bit more specific about DFT functionals and neural
>> networks?
> 
> Currently, this is just an idea; neural networks are powerful
> paradigms for some tasks, and implementing by me a NN for processing
> multiple single point DFT computations to obtain a single point
> energy is in principle possible. Grigoriy Zhurko

This is not really a new point. Neural Networks have been used for a 
long time to model DFT computations; e.g. Jörg Behler is one of the 
pioneers. For more recent developments see, for instance, the work done 
in the Parkhill group at Notre Dame with the TensorMol model chemistry
   https://github.com/jparkhill/TensorMol
(which is also open source). The newest paper
   http://dx.doi.org/10.1039/C7SC04934J
   https://arxiv.org/abs/1711.06385
demonstrated DFT accuracy results but at orders of magnitude smaller 
cost. According to the project homepage, you can do an energy and force 
evaluation of a cube of 24,000 atoms in less than 100 seconds on a 2015 
Macbook Pro.
-- 
------------------------------------------------------------------
Mr. Susi Lehtola, PhD             Junior Fellow, Adjunct Professor
susi.lehtola=-=alumni.helsinki.fi   University of Helsinki
http://www.helsinki.fi/~jzlehtol  Finland
------------------------------------------------------------------
Susi Lehtola, dosentti, FT        tutkijatohtori
susi.lehtola=-=alumni.helsinki.fi   Helsingin yliopisto
http://www.helsinki.fi/~jzlehtol
------------------------------------------------------------------


From owner-chemistry@ccl.net Tue Oct  2 13:46:00 2018
From: "Soaring Bear soaringbear]^[yahoo.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: NN rigor?
Message-Id: <-53488-181002122855-13614-tbS7X+q/weVnPs6lFdytJg#,#server.ccl.net>
X-Original-From: "Soaring  Bear" <soaringbear!=!yahoo.com>
Date: Tue, 2 Oct 2018 12:28:54 -0400


Sent to CCL by: "Soaring  Bear" [soaringbear:+:yahoo.com]
to NN experts, I wonder if this seems rigorous to you?

deep neural network (DNN) model that had only 2000 hidden units.
After forward propagation, the feature dimensionality was
reduced approximately 200 times. By the conclusion of
training, the DNN model derived a decision boundary
to classify positive and negative samples with the desired
accuracy, and the model was able to predict reliable DTIs.


ref: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156897/


From owner-chemistry@ccl.net Tue Oct  2 14:20:00 2018
From: "Jeya Vimalan jeyavimalan2k-*-gmail.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: Relative Stability of species.
Message-Id: <-53489-181002135747-17936-9tyThiEmiQEQQTQ9Ea+M3Q : server.ccl.net>
X-Original-From: Jeya Vimalan <jeyavimalan2k()gmail.com>
Content-Type: multipart/alternative; boundary="0000000000006dcc6a057742a80a"
Date: Tue, 2 Oct 2018 10:57:23 -0700
MIME-Version: 1.0


Sent to CCL by: Jeya Vimalan [jeyavimalan2k(-)gmail.com]
--0000000000006dcc6a057742a80a
Content-Type: text/plain; charset="UTF-8"

Dear all,

I have the following question that i need your help to get
it cleared.

I have three molecular species that differs in the composition.
Say for example, TiCl3, TiCl2, and TiCl4.

> From the vibrational frequencies, i can understand if they
are stable in the PES (potential energy surface). But
are there any way that i can determine the relative stability
of these three species.

There is a tutorial in G09, that describes the thermochemistry
to determine the free energy of molecules, but i see that certain
parameters are taken from literature and it is not available
for the complete set of periodic table.

Can any one point me some tutorials/work outs that have been made
earlier for a novice user.

Thanks in advance.
Vimal.

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<div dir=3D"ltr"><div dir=3D"ltr"><div>Dear all,<br></div><div><br></div><d=
iv>I have the following question that i need your help to get</div><div>it =
cleared.</div><div><br></div><div>I have three molecular species that diffe=
rs in the composition.=C2=A0</div><div>Say for example, TiCl3, TiCl2, and T=
iCl4.=C2=A0</div><div><br></div><div>From the vibrational frequencies, i ca=
n understand if they=C2=A0</div><div>are stable in the PES (potential energ=
y surface). But</div><div>are there any way that i can determine the relati=
ve stability</div><div>of these three species.=C2=A0</div><div><br></div><d=
iv>There is a tutorial in G09, that describes the thermochemistry</div><div=
>to determine the free energy of molecules, but i see that certain</div><di=
v>parameters are taken from literature and it is not available</div><div>fo=
r the complete set of periodic table.=C2=A0</div><div><br></div><div>Can an=
y one point me some tutorials/work outs that have been made</div><div>earli=
er for a novice user.=C2=A0</div><div><br></div><div>Thanks in advance.</di=
v><div>Vimal.</div><div><br></div></div></div>

--0000000000006dcc6a057742a80a--


From owner-chemistry@ccl.net Tue Oct  2 14:56:01 2018
From: "Chris Swain swain{:}mac.com" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: Mojave
Message-Id: <-53490-181002142915-12431-eu1NsLLR5OVtozQ9HU8dmg\a/server.ccl.net>
X-Original-From: Chris Swain <swain###mac.com>
Content-type: multipart/alternative;
 boundary="Apple-Mail=_691E1ECB-1185-4D06-AF17-CBA73A58DC36"
Date: Tue, 02 Oct 2018 19:29:07 +0100
MIME-version: 1.0 (Mac OS X Mail 11.5 \(3445.9.1\))


Sent to CCL by: Chris Swain [swain~~mac.com]

--Apple-Mail=_691E1ECB-1185-4D06-AF17-CBA73A58DC36
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain;
	charset=utf-8

Hi,

I=E2=80=99ve created a page to summarise the status of scientific apps =
under Mac OSX 10.14 Mojave.

=
https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a206df3d-2359=
.php =
<https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a206df3d-235=
9.php?utm_source=3Dfeedburner&utm_medium=3Dtwitter&utm_campaign=3DFeed:+ma=
cinchemblog+(MacinChemBlog)#unique-entry-id-2359>

Feel free to contact me with any additional information.

Kind Regards,

Chris


Dr Chris Swain BA MA (Cantab) PhD CChem FRSC
Macs in Chemistry
swain%a%mac.com
https://www.macinchem.org


--Apple-Mail=_691E1ECB-1185-4D06-AF17-CBA73A58DC36
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
	charset=utf-8

<html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space;" class=3D"">Hi,<div class=3D""><br =
class=3D""></div><div class=3D"">I=E2=80=99ve created a page to =
summarise the status of scientific apps under Mac OSX 10.14 =
Mojave.</div><div class=3D""><br class=3D""></div><div class=3D""><a =
href=3D"https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a206d=
f3d-2359.php?utm_source=3Dfeedburner&amp;utm_medium=3Dtwitter&amp;utm_camp=
aign=3DFeed:+macinchemblog+(MacinChemBlog)#unique-entry-id-2359" =
class=3D"">https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a2=
06df3d-2359.php</a></div><div class=3D""><br class=3D""></div><div =
class=3D"">Feel free to contact me with any additional =
information.</div><div class=3D""><br class=3D""></div><div =
class=3D"">Kind Regards,</div><div class=3D""><br class=3D""></div><div =
class=3D"">Chris</div><br class=3D""><br class=3D""><div class=3D""><div =
style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; line-break: =
after-white-space;" class=3D""><div style=3D"word-wrap: break-word; =
-webkit-nbsp-mode: space; line-break: after-white-space;" class=3D""><div =
style=3D"orphans: 2; widows: 2;" class=3D"">Dr Chris Swain BA MA =
(Cantab) PhD&nbsp;CChem FRSC<br class=3D"">Macs in Chemistry<br =
class=3D""><a href=3D"mailto:swain%a%mac.com" =
class=3D"">swain%a%mac.com</a><br =
class=3D"">https://www.macinchem.org</div><div class=3D""><br =
class=3D""></div></div></div></div></body></html>=

--Apple-Mail=_691E1ECB-1185-4D06-AF17-CBA73A58DC36--


From owner-chemistry@ccl.net Tue Oct  2 16:43:00 2018
From: "Peter Kraus peter.kraus,geeksonbikes.net" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL:G: Relative Stability of species.
Message-Id: <-53491-181002164138-11305-ZEtApOORuJwEnBkHTw+nog|-|server.ccl.net>
X-Original-From: Peter Kraus <peter.kraus/./geeksonbikes.net>
Content-Type: multipart/alternative; boundary="00000000000052b0f0057744f250"
Date: Tue, 2 Oct 2018 22:41:19 +0200
MIME-Version: 1.0


Sent to CCL by: Peter Kraus [peter.kraus],[geeksonbikes.net]
--00000000000052b0f0057744f250
Content-Type: text/plain; charset="UTF-8"

Dear Vimal,

it looks as if you're conflating two issues: first is whether a point on
your potential energy hypersurface (i.e. your geometry) is at a minimum in
energy - this, at least for small covalent (single reference) compounds
should be true as long as your geometry optimisation converges (the "four
YES's" in Gaussian). It is good to check it's a minimum by doing a
frequency calculation after the optimization step. If there are no
imaginary frequencies, you're good to go.

As for "stability", the question is - at what temperature? You could
compare the absolute energies of your three compounds directly, as long as
they have the same elemental composition. If not, you have to calculate the
heat of formation by difference from the correct number of infinitely
separated atoms. However, even at 0 K, you will have zero-point effects,
which you can estimate by the vibrational frequencies. They might be large
enough to shift the balance of stability around. Then there are the more
important thermal effects, where the "tutorial" you mentioned comes in -
the Gibbs energy is a function of both enthalpy and entropy, and entropy is
related to partition functions, which can be calculated from the
vibrational frequencies and rotational constants. If you need help with
that, you can always contact the folks at Gaussian Inc. directly, after all
you're paying them a lot of money to use their software. I've found them
very helpful.

Best regards,

Peter

On Tue, 2 Oct 2018 at 21:41, Jeya Vimalan jeyavimalan2k-*-gmail.com <
owner-chemistry^ccl.net> wrote:

> Dear all,
>
> I have the following question that i need your help to get
> it cleared.
>
> I have three molecular species that differs in the composition.
> Say for example, TiCl3, TiCl2, and TiCl4.
>
> From the vibrational frequencies, i can understand if they
> are stable in the PES (potential energy surface). But
> are there any way that i can determine the relative stability
> of these three species.
>
> There is a tutorial in G09, that describes the thermochemistry
> to determine the free energy of molecules, but i see that certain
> parameters are taken from literature and it is not available
> for the complete set of periodic table.
>
> Can any one point me some tutorials/work outs that have been made
> earlier for a novice user.
>
> Thanks in advance.
> Vimal.
>
>

-- 
Sent from your iPhone. No, really.

--00000000000052b0f0057744f250
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><div dir=3D"ltr"><div>Dear Vimal,</div><div><br></div><div=
>it looks as if you&#39;re conflating two issues: first is whether a point =
on your potential energy hypersurface (i.e. your geometry) is at a minimum =
in energy - this, at least for small covalent (single reference) compounds =
should be true as long as your geometry optimisation converges (the &quot;f=
our YES&#39;s&quot; in Gaussian). It is good to check it&#39;s a minimum by=
 doing a frequency calculation after the optimization step. If there are no=
 imaginary frequencies, you&#39;re good to go.</div><div><br></div><div>As =
for &quot;stability&quot;, the question is - at what temperature? You could=
 compare the absolute energies of your three compounds directly, as long as=
 they have the same elemental composition. If not, you have to calculate th=
e heat of formation by difference from the correct number of infinitely sep=
arated atoms. However, even at 0 K, you will have zero-point effects, which=
 you can estimate by the vibrational frequencies. They might be large enoug=
h to shift the balance of stability around. Then there are the more importa=
nt thermal effects, where the &quot;tutorial&quot; you mentioned comes in -=
 the Gibbs energy is a function of both enthalpy and entropy, and entropy i=
s related to partition functions, which can be calculated from the vibratio=
nal frequencies and rotational constants. If you need help with that, you c=
an always contact the folks at Gaussian Inc. directly, after all you&#39;re=
 paying them a lot of money to use their software. I&#39;ve found them very=
 helpful.<br></div><div><br></div><div>Best regards,<br></div><div><br></di=
v><div>Peter</div></div></div><br><div class=3D"gmail_quote"><div dir=3D"lt=
r">On Tue, 2 Oct 2018 at 21:41, Jeya Vimalan jeyavimalan2k-*-<a href=3D"htt=
p://gmail.com" target=3D"_blank">gmail.com</a> &lt;<a href=3D"mailto:owner-=
chemistry^ccl.net" target=3D"_blank">owner-chemistry^ccl.net</a>&gt; wrote:=
<br></div><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;bord=
er-left:1px #ccc solid;padding-left:1ex"><div dir=3D"ltr"><div dir=3D"ltr">=
<div>Dear all,<br></div><div><br></div><div>I have the following question t=
hat i need your help to get</div><div>it cleared.</div><div><br></div><div>=
I have three molecular species that differs in the composition.=C2=A0</div>=
<div>Say for example, TiCl3, TiCl2, and TiCl4.=C2=A0</div><div><br></div><d=
iv>From the vibrational frequencies, i can understand if they=C2=A0</div><d=
iv>are stable in the PES (potential energy surface). But</div><div>are ther=
e any way that i can determine the relative stability</div><div>of these th=
ree species.=C2=A0</div><div><br></div><div>There is a tutorial in G09, tha=
t describes the thermochemistry</div><div>to determine the free energy of m=
olecules, but i see that certain</div><div>parameters are taken from litera=
ture and it is not available</div><div>for the complete set of periodic tab=
le.=C2=A0</div><div><br></div><div>Can any one point me some tutorials/work=
 outs that have been made</div><div>earlier for a novice user.=C2=A0</div><=
div><br></div><div>Thanks in advance.</div><div>Vimal.</div><div><br></div>=
</div></div>
</blockquote></div><br clear=3D"all"><br>-- <br><div dir=3D"ltr" class=3D"m=
_8015550280786952515m_-7612148070089669404m_5493799166817601566gmail_signat=
ure" data-smartmail=3D"gmail_signature"><div dir=3D"ltr">Sent from your iPh=
one. No, really.<br></div></div>

--00000000000052b0f0057744f250--


From owner-chemistry@ccl.net Tue Oct  2 18:25:01 2018
From: "Matthias Heger heger##ualberta.ca" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: Interaction of QC software components via text files
Message-Id: <-53492-181002151511-23112-bTXbk1GmsQF8sskol5MgtA]_[server.ccl.net>
X-Original-From: Matthias Heger <heger(!)ualberta.ca>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=utf-8; format=flowed
Date: Tue, 2 Oct 2018 13:15:01 -0600
MIME-Version: 1.0


Sent to CCL by: Matthias Heger [heger(a)ualberta.ca]


> I am thinking of switching from Gaussian to Orca in my research work, and in this case implementing the external use of ORCA will be easy for me. However, the main problem for me is that ORCA is a freeware code (state-funded). I greatly dislike socialism in any form, and I think that state-funded codes can provide good quality only if they compete with the commercial codes like Gaussian (and steal their algorithms).


"Socialism is when the government does stuff. The more stuff it does, the socialister it is."

-- Karl Marx, probably


From owner-chemistry@ccl.net Tue Oct  2 19:00:01 2018
From: "Pezhman Zarabadi-Poor pzarabadip * gmail.com" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: Mojave
Message-Id: <-53493-181002170510-23182-wUBjmEtOKA1rA80pk+MxPA[*]server.ccl.net>
X-Original-From: Pezhman Zarabadi-Poor <pzarabadip/a\gmail.com>
Content-Type: multipart/alternative; boundary="0000000000008aaa1f0577454650"
Date: Tue, 2 Oct 2018 23:04:52 +0200
MIME-Version: 1.0


Sent to CCL by: Pezhman Zarabadi-Poor [pzarabadip^^^gmail.com]
--0000000000008aaa1f0577454650
Content-Type: text/plain; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

Dear Chris,

I would add iRASPA (www.iraspa.org) to the list as well.

My best regards,
Pezhman

On Tue, Oct 2, 2018 at 10:45 PM Chris Swain swain{:}mac.com <
owner-chemistry=-=ccl.net> wrote:

> Hi,
>
> I=E2=80=99ve created a page to summarise the status of scientific apps un=
der Mac
> OSX 10.14 Mojave.
>
>
> https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a206df3d-235=
9.php
> <https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a206df3d-23=
59.php?utm_source=3Dfeedburner&utm_medium=3Dtwitter&utm_campaign=3DFeed:+ma=
cinchemblog+(MacinChemBlog)#unique-entry-id-2359>
>
> Feel free to contact me with any additional information.
>
> Kind Regards,
>
> Chris
>
>
> Dr Chris Swain BA MA (Cantab) PhD CChem FRSC
> Macs in Chemistry
> swain^^mac.com
> https://www.macinchem.org
>
>

--=20

*Pezhman Zarabadi-Poor, PhD* Marie Sk=C5=82odowska-Curie / SoMoPro Postdoct=
oral
Fellow

CEITEC =E2=80=93 Central European Institute of Technology

Masaryk University

Kamenice 5 =E2=80=93 Bld. A4 =E2=80=93 Office 2.26

62500 Brno =E2=80=93 Czech Republic


Google Scholar Profile
<https://scholar.google.com/citations?user=3DrAe2VNwAAAAJ&hl=3Den>

--0000000000008aaa1f0577454650
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><div dir=3D"ltr">Dear Chris,=C2=A0<div><br></div><div>I wo=
uld add iRASPA (<a href=3D"http://www.iraspa.org">www.iraspa.org</a>) to th=
e list as well.=C2=A0</div><div><br></div><div>My best regards,</div><div>P=
ezhman=C2=A0</div></div></div><br><div class=3D"gmail_quote"><div dir=3D"lt=
r">On Tue, Oct 2, 2018 at 10:45 PM Chris Swain swain{:}<a href=3D"http://ma=
c.com">mac.com</a> &lt;<a href=3D"mailto:owner-chemistry=-=ccl.net">owner-che=
mistry=-=ccl.net</a>&gt; wrote:<br></div><blockquote class=3D"gmail_quote" st=
yle=3D"margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div =
style=3D"word-wrap:break-word">Hi,<div><br></div><div>I=E2=80=99ve created =
a page to summarise the status of scientific apps under Mac OSX 10.14 Mojav=
e.</div><div><br></div><div><a href=3D"https://www.macinchem.org/blog/files=
/be86eb06d79280048fbaa855a206df3d-2359.php?utm_source=3Dfeedburner&amp;utm_=
medium=3Dtwitter&amp;utm_campaign=3DFeed:+macinchemblog+(MacinChemBlog)#uni=
que-entry-id-2359" target=3D"_blank">https://www.macinchem.org/blog/files/b=
e86eb06d79280048fbaa855a206df3d-2359.php</a></div><div><br></div><div>Feel =
free to contact me with any additional information.</div><div><br></div><di=
v>Kind Regards,</div><div><br></div><div>Chris</div><br><br><div><div style=
=3D"word-wrap:break-word;line-break:after-white-space"><div style=3D"word-w=
rap:break-word;line-break:after-white-space"><div>Dr Chris Swain BA MA (Can=
tab) PhD=C2=A0CChem FRSC<br>Macs in Chemistry<br><a href=3D"mailto:swain%5E=
%5Emac.com" target=3D"_blank">swain^^mac.com</a><br><a href=3D"https://www.=
macinchem.org" target=3D"_blank">https://www.macinchem.org</a></div><div><b=
r></div></div></div></div></div></blockquote></div><br clear=3D"all"><div><=
br></div>-- <br><div dir=3D"ltr" class=3D"gmail_signature" data-smartmail=
=3D"gmail_signature"><div dir=3D"ltr"><div><div dir=3D"ltr"><div><div dir=
=3D"ltr"><p>


=09
=09
=09
=09


</p>


=09
=09
=09
=09


<h3><font color=3D"#000000"><font style=3D"font-size:11pt" size=3D"2"><span=
 style=3D"text-decoration:none"><b>Pezhman
Zarabadi-Poor, PhD</b></span></font></font></h3>
<h3 style=3D"line-height:100%"><font style=3D"font-size:10pt" size=3D"2"><f=
ont color=3D"#000000"><span style=3D"text-decoration:none"><span style=3D"f=
ont-weight:normal">Marie
Sk=C5=82odowska-Curie / </span></span></font><font color=3D"#000000"><span =
style=3D"text-decoration:none"><span style=3D"font-weight:normal">SoMoPro
Postdoctoral Fellow</span></span></font></font></h3>
<p style=3D"line-height:100%"><font style=3D"font-size:10pt" size=3D"2"><fo=
nt color=3D"#000000"><span style=3D"text-decoration:none"><span style=3D"fo=
nt-weight:normal">CEITEC
=E2=80=93 Central European Institute of Technology </span></span></font></f=
ont>
</p>
<p style=3D"line-height:100%"><font style=3D"font-size:10pt" size=3D"2"><fo=
nt color=3D"#000000"><span style=3D"text-decoration:none"><span style=3D"fo=
nt-weight:normal">Masaryk
University</span></span></font></font></p>
<p style=3D"line-height:100%"><font style=3D"font-size:10pt" size=3D"2"><fo=
nt color=3D"#000000"><span style=3D"text-decoration:none"><span style=3D"fo=
nt-weight:normal">Kamenice 5 =E2=80=93 Bld. A4 =E2=80=93 Office 2.26</span>=
</span></font></font></p>
<p style=3D"line-height:100%"><font style=3D"font-size:10pt" size=3D"2"><fo=
nt color=3D"#000000"><span style=3D"text-decoration:none"><span style=3D"fo=
nt-weight:normal">62500
Brno =E2=80=93 Czech Republic </span></span></font></font>
</p>
<p style=3D"margin-bottom:0in;line-height:100%"><br>

</p><a href=3D"https://scholar.google.com/citations?user=3DrAe2VNwAAAAJ&amp=
;hl=3Den" target=3D"_blank">Google Scholar Profile</a> </div></div></div></=
div></div></div>

--0000000000008aaa1f0577454650--


From owner-chemistry@ccl.net Tue Oct  2 21:13:00 2018
From: "Guzman, Francisco fg58 ~ njit.edu" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: Mojave
Message-Id: <-53494-181002203850-20392-3hQ1sqbLGWEkS64JajNzDQ-,-server.ccl.net>
X-Original-From: "Guzman, Francisco" <fg58.-,-.njit.edu>
Content-Type: multipart/alternative; boundary="000000000000a8cca50577484251"
Date: Tue, 2 Oct 2018 20:38:31 -0400
MIME-Version: 1.0


Sent to CCL by: "Guzman, Francisco" [fg58,njit.edu]
--000000000000a8cca50577484251
Content-Type: text/plain; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

Chris,

Thank you for posting such an informative link. I'm close to going to the
darkside (apple) from RHEL/Debian as support is seemingly better, and this
info might just do it.  Although I do still love GNOME...


On Tue, Oct 2, 2018 at 4:54 PM Chris Swain swain{:}mac.com <
owner-chemistry#ccl.net> wrote:

> Hi,
>
> I=E2=80=99ve created a page to summarise the status of scientific apps un=
der Mac
> OSX 10.14 Mojave.
>
>
> https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a206df3d-235=
9.php
> <https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a206df3d-23=
59.php?utm_source=3Dfeedburner&utm_medium=3Dtwitter&utm_campaign=3DFeed:+ma=
cinchemblog+(MacinChemBlog)#unique-entry-id-2359>
>
> Feel free to contact me with any additional information.
>
> Kind Regards,
>
> Chris
>
>
> Dr Chris Swain BA MA (Cantab) PhD CChem FRSC
> Macs in Chemistry
> swain^^mac.com
> https://www.macinchem.org
>
>

--=20
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

--000000000000a8cca50577484251
Content-Type: text/html; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable

<div dir=3D"ltr"><div>Chris,</div><div><br></div><div>Thank you for posting=
 such an informative link. I&#39;m close to going to the darkside (apple) f=
rom RHEL/Debian as support is seemingly better, and this info might just do=
 it.=C2=A0 Although I do still love GNOME...<br></div><div><br></div></div>=
<br><div class=3D"gmail_quote"><div dir=3D"ltr">On Tue, Oct 2, 2018 at 4:54=
 PM Chris Swain swain{:}<a href=3D"http://mac.com">mac.com</a> &lt;<a href=
=3D"mailto:owner-chemistry#ccl.net">owner-chemistry#ccl.net</a>&gt; wrote:<=
br></div><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;borde=
r-left:1px #ccc solid;padding-left:1ex"><div style=3D"word-wrap:break-word"=
>Hi,<div><br></div><div>I=E2=80=99ve created a page to summarise the status=
 of scientific apps under Mac OSX 10.14 Mojave.</div><div><br></div><div><a=
 href=3D"https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a206d=
f3d-2359.php?utm_source=3Dfeedburner&amp;utm_medium=3Dtwitter&amp;utm_campa=
ign=3DFeed:+macinchemblog+(MacinChemBlog)#unique-entry-id-2359" target=3D"_=
blank">https://www.macinchem.org/blog/files/be86eb06d79280048fbaa855a206df3=
d-2359.php</a></div><div><br></div><div>Feel free to contact me with any ad=
ditional information.</div><div><br></div><div>Kind Regards,</div><div><br>=
</div><div>Chris</div><br><br><div><div style=3D"word-wrap:break-word;line-=
break:after-white-space"><div style=3D"word-wrap:break-word;line-break:afte=
r-white-space"><div>Dr Chris Swain BA MA (Cantab) PhD=C2=A0CChem FRSC<br>Ma=
cs in Chemistry<br><a href=3D"mailto:swain%5E%5Emac.com" target=3D"_blank">=
swain^^mac.com</a><br><a href=3D"https://www.macinchem.org" target=3D"_blan=
k">https://www.macinchem.org</a></div><div><br></div></div></div></div></di=
v></blockquote></div><br clear=3D"all"><br>-- <br><div dir=3D"ltr" class=3D=
"gmail_signature" data-smartmail=3D"gmail_signature"><div dir=3D"ltr"><div>=
<div dir=3D"ltr"><div><div dir=3D"ltr"><span style=3D"color:rgb(34,34,34);f=
ont-family:arial;font-size:small;font-style:normal;font-variant:normal;font=
-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;te=
xt-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;backg=
round-color:rgb(255,255,255);display:inline!important;float:none">Francisco=
 Guzman</span><br style=3D"color:rgb(34,34,34);font-family:arial;font-size:=
small;font-style:normal;font-variant:normal;font-weight:normal;letter-spaci=
ng:normal;line-height:normal;text-align:start;text-indent:0px;text-transfor=
m:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255=
)"><span style=3D"color:rgb(34,34,34);font-family:arial;font-size:small;fon=
t-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal=
;line-height:normal;text-align:start;text-indent:0px;text-transform:none;wh=
ite-space:normal;word-spacing:0px;background-color:rgb(255,255,255);display=
:inline!important;float:none">PhD Candidate</span><div style=3D"color:rgb(3=
4,34,34);font-family:arial;font-size:small;font-style:normal;font-variant:n=
ormal;font-weight:normal;letter-spacing:normal;line-height:normal;text-alig=
n:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing=
:0px;background-color:rgb(255,255,255)"><span style=3D"background-color:rgb=
(255,255,255)"><font color=3D"#000000"></font></span>Otto H. York Departmen=
t of Chemical, Biological and Pharmaceutical Engineering<br>New Jersey Inst=
itute of Technology</div><div style=3D"color:rgb(34,34,34);font-family:aria=
l;font-size:small;font-style:normal;font-variant:normal;font-weight:normal;=
letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;t=
ext-transform:none;white-space:normal;word-spacing:0px;background-color:rgb=
(255,255,255)">Email:=C2=A0<font color=3D"#0000ff"><a href=3D"mailto:fg58#n=
jit.edu" style=3D"color:rgb(17,85,204)" target=3D"_blank">fg58#njit.edu</a>=
,<span>=C2=A0</span><a href=3D"mailto:guzman.research#gmail.com" style=3D"c=
olor:rgb(17,85,204)" target=3D"_blank">guzman.research#gmail.com</a></font>=
</div></div></div></div></div></div></div>

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