From owner-chemistry@ccl.net Tue Oct 2 12:35:01 2018 From: "Robert Molt r.molt.chemical.physics|-|gmail.com" 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 Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary=Apple-Mail-EB545649-5470-4C34-91C9-B410318038C1 Date: Tue, 2 Oct 2018 11:51:26 -0400 Mime-Version: 1.0 (1.0) Sent to CCL by: Robert Molt [r.molt.chemical.physics__gmail.com] --Apple-Mail-EB545649-5470-4C34-91C9-B410318038C1 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable 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= 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 --Apple-Mail-EB545649-5470-4C34-91C9-B410318038C1 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable What nonsense about a code being free impli= es ANYTHING about socialism?

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.

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

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.


On Oct 2= , 2018, at 4:35 AM, 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 ef= ficient. ORCA's optimizer can be used
as an external optimizer and can be used for the described s= cenario.
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 ac= ademic
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 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.

The likewise freely available open source Psi4 prog= ram also has a
varie= ty of ab initio and DFT methods implemented, and also supports a
=
variety of CBS extrapolations f= or energies and geometry optimizations
out of the box.

<= span>As far as I understand, the Psi program is state-funded too?
=
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>

What you de= scribe can be achieved by using the Atomic Simulation
Environment (ASE). The peer-reviewed articl= e for ASE can be found
here and main webpage found here. ASE is a Python-based code meant<= br>
to manipulate, run, and anal= yse quantum-chemical calculations. ASE
has a built-in set of optimization routines (described her= e), and
the quantum-c= hemical program of your choice can be used just to
calculate the energies and forces required for= ASE to update the
at= omic positions. You then do not have to rely on the optimizers
built into Gaussian, and it operat= es using the exact same workflow
you proposed. ASE does support Gaussian as a calculator (as list= ed
here), but it is c= urrently lacking documentation and would probably
require some modifications to suit all your nee= ds.

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?
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).

One m= ore 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 chem= istry code is written by
professionals and it will be very challenging to "beat" built in<= br>
optimizers. Sometimes, slow o= ptimization is rather a consequence of
chemical system at hand (too shallow PES minimum, noisy
energy/gradients, etc).=

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).

Could you be a bit more specific about DFT functi= onals and neural networks?

&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.
 Grigoriy Zhurko

<= /span>

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