From owner-chemistry@ccl.net Thu Sep 27 05:06:00 2018 From: "Turbomole Support Team turbomole%cosmologic.de" To: CCL Subject: CCL: Turbomole release notes Message-Id: <-53479-180927043622-6777-jA64+WXLB4eY9uordtNmwg===server.ccl.net> X-Original-From: Turbomole Support Team Content-Language: en-US Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Thu, 27 Sep 2018 10:36:10 +0200 MIME-Version: 1.0 Sent to CCL by: Turbomole Support Team [turbomole__cosmologic.de] Hello, there is a new Turbomole release each year, but it seems that we did not announce that in the CCL for quite a long time. The new 7.3 version contains new features like PNO-CCSD(T), Grimme's latest DFT-D4, periodic DFT with (more or less) arbitrary basis sets, new linear-scaling RI-GW, dRPA and Bethe-Salpeter excitation energies at about the speed of TDDFT, relativistic effects using X2C for spin-orbit coupling terms, modernized NMR module, ... But that is just the latest release, if you want to check all the other things that came in since the last CCL announcement, please just take a look at http://www.cosmologic.de/turbomole/product-info/release-notes.html and/or download the demo version from http://www.cosmologic.de/turbomole/home.html The free graphical user interface, TmoleX, is included in the demo and supports quite a lot of the features of Turbomole. Build molecules, run on local machine or submit to a cluster and visualize and analyze results is (hopefully) easy to use from within TmoleX. Finally, there is a support team which helps whenever problems occur! Just contact us directly, email is given below. Thank you very much for reading this post to its very end, Uwe -- -------------------- Dr. Uwe Huniar TURBOMOLE Support Team COSMOlogic GmbH & Co. KG Leverkusen, Germany e-mail turbomole-#-cosmologic.de From owner-chemistry@ccl.net Thu Sep 27 09:29:01 2018 From: "Phil Hasnip phil.hasnip^-^york.ac.uk" To: CCL Subject: CCL:G: Interaction of QC software components via text files Message-Id: <-53480-180926183907-32401-x/f/xG06zsHhhINLG9EALg:+:server.ccl.net> X-Original-From: Phil Hasnip Content-Type: multipart/alternative; boundary="00000000000074b9e60576cde304" Date: Wed, 26 Sep 2018 23:38:48 +0100 MIME-Version: 1.0 Sent to CCL by: Phil Hasnip [phil.hasnip[-]york.ac.uk] --00000000000074b9e60576cde304 Content-Type: text/plain; charset="UTF-8" Have you tried the optimisation methods in the Atomistic Simulation Environment (ASE)? It's available at: https://wiki.fysik.dtu.dk/ase/ You don't get the performance gains from re-using densities and wavefunctions, but the actual algorithms seem pretty good. I haven't tried the Gaussian calculator ("calculator" is what ASE calls the interface to the simulation code) but generally the calculators are good, and not that difficult to extend. All the best, Phil Hasnip (CASTEP Developer) ------------------------------------------------------------------------------------ Dr Phil Hasnip Email: phil.hasnip^_^york.ac.uk EPSRC RSE Fellow Web: www-users.york.ac.uk/~pjh503 Dept of Physics University of York Tel: +44 (0)1904 322225 York YO10 5DD On Wed, 26 Sep 2018 at 20:06, Grigoriy Zhurko reg_zhurko/achemcraftprog.com wrote: > > Sent to CCL by: Grigoriy Zhurko [reg_zhurko-x-chemcraftprog.com] > I suppose it is well-known that the geometry optimization in Gaussian is > sometimes accompanied with serious problems, and the users have to invent > their own ways of solving them. Besides that, the energy of the final > (optimized) geometry computed with Gaussian is often slightly higher than > the energy of the penultimate (previous) step. This is usually not a big > problem, but this is slightly annoying (unless you use my program > Chemcraft) ). > My question is, whether it is possible to implement a third-party > algorithm of geometry optimization, which implies invoking the Gaussian by > a third-party program. I mean that the third-party program generates a > Gaussian input file (.gjf) with single point and gradient computation, then > Gaussian processes this job and generates the output file, then the program > reads and parses this output file, then it predicts the coordinates of the > next step and runs Gaussian again, etc. until the energy minimum is reached. > If such an approach is possible, I will probably try to implement the > following things: > - geometry optimization and frequencies computation with CCSD(T)/CBS, or > even a composite method like FPD; > - performing several computations with different DFT functionals at same > geometry, and passing their results into a neural network to obtain a very > accurate energy. > So, is this possible to implement such interaction of a third-party > program with Gaussian (preferably the Windows version), or other QC codes? > Grigoriy Zhuko> > > --00000000000074b9e60576cde304 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable
Have you tried the optimisation methods i= n the Atomistic Simulation Environment (ASE)? It's available at:
https://wiki.fysik.= dtu.dk/ase/

You don't get the performance ga= ins from re-using densities and wavefunctions, but the actual algorithms se= em pretty good. I haven't tried the Gaussian calculator ("calculat= or" is what ASE calls the interface to the simulation code) but genera= lly the calculators are good, and not that difficult to extend.=C2=A0
=

All the best,

Phil Hasnip
(CASTEP Developer)

---------------------------= ---------------------------------------------------------
Dr Phil Hasnip= =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Em= ail: phil.hasni= p^_^york.ac.uk
EPSRC RSE Fellow=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2= =A0=C2=A0 Web:=C2=A0 www-users.york.ac.uk/~pjh503
Dept of Physics
Universi= ty of York =C2=A0 =C2=A0 =C2=A0 =C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 Tel: =C2=A0= =C2=A0=C2=A0 +44 (0)1904 322225
York YO10 5DD


On Wed, 26 Sep 2018 at 20:06, Grigoriy Zhurko reg_zhurko/achemcraftprog.com <owner-chemistry^_^ccl.net> wrote:

Sent to CCL by: Grigoriy Zhurko [reg_zhurko-x-chemcraftprog.com= ]
=C2=A0 I suppose it is well-known that the geometry optimization in Gaussia= n is sometimes accompanied with serious problems, and the users have to inv= ent their own ways of solving them. Besides that, the energy of the final (= optimized) geometry computed with Gaussian is often slightly higher than th= e energy of the penultimate (previous) step. This is usually not a big prob= lem, but this is slightly annoying (unless you use my program Chemcraft) ).=
=C2=A0 My question is, whether it is possible to implement a third-party al= gorithm of geometry optimization, which implies invoking the Gaussian by a = third-party program. I mean that the third-party program generates a Gaussi= an input file (.gjf) with single point and gradient computation, then Gauss= ian processes this job and generates the output file, then the program read= s and parses this output file, then it predicts the coordinates of the next= step and runs Gaussian again, etc. until the energy minimum is reached. =C2=A0 If such an approach is possible, I will probably try to implement th= e following things:
=C2=A0- geometry optimization and frequencies computation with CCSD(T)/CBS,= or even a composite method like FPD;
=C2=A0- performing several computations with different DFT functionals at s= ame geometry, and passing their results into a neural network to obtain a v= ery accurate energy.
=C2=A0 So, is this possible to implement such interaction of a third-party = program with Gaussian (preferably the Windows version), or other QC codes?<= br> Grigoriy Zhuko



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--00000000000074b9e60576cde304-- From owner-chemistry@ccl.net Thu Sep 27 10:04:01 2018 From: "Susi Lehtola susi.lehtola=alumni.helsinki.fi" To: CCL Subject: CCL:G: Interaction of QC software components via text files Message-Id: <-53481-180927044653-7174-O7XG1NDYSKCLmqnD4fNlVQ%%server.ccl.net> X-Original-From: Susi Lehtola Content-Language: en-US Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Thu, 27 Sep 2018 11:46:41 +0300 MIME-Version: 1.0 Sent to CCL by: Susi Lehtola [susi.lehtola#,#alumni.helsinki.fi] On 9/26/18 8:34 PM, Grigoriy Zhurko reg_zhurko/achemcraftprog.com wrote: > > Sent to CCL by: Grigoriy Zhurko [reg_zhurko-x-chemcraftprog.com] > I suppose it is well-known that the geometry optimization in Gaussian is sometimes accompanied with serious problems, and the users have to invent their own ways of solving them. Besides that, the energy of the final (optimized) geometry computed with Gaussian is often slightly higher than the energy of the penultimate (previous) step. This is usually not a big problem, but this is slightly annoying (unless you use my program Chemcraft) ). > My question is, whether it is possible to implement a third-party algorithm of geometry optimization, which implies invoking the Gaussian by a third-party program. I mean that the third-party program generates a Gaussian input file (.gjf) with single point and gradient computation, then Gaussian processes this job and generates the output file, then the program reads and parses this output file, then it predicts the coordinates of the next step and runs Gaussian again, etc. until the energy minimum is reached. > If such an approach is possible, I will probably try to implement the following things: > - geometry optimization and frequencies computation with CCSD(T)/CBS, or even a composite method like FPD; > - performing several computations with different DFT functionals at same geometry, and passing their results into a neural network to obtain a very accurate energy. > So, is this possible to implement such interaction of a third-party program with Gaussian (preferably the Windows version), or other QC codes? > Grigoriy Zhuko The freely available open source PySCF program https://github.com/sunqm/pyscf that has recently become extremely popular with theorists due to its elegance and simplicity for developing new methods supports a wide variety of both ab initio as well as dft methods, and employs the pyberny library for geometry optimizations. https://github.com/azag0/pyberny If PySCF does not fulfill your needs, you might find pyberny interesting. pyberny does not have a wrapper to Gaussian, so you would have to implement it yourself, but you can probably look to the existing MOPAC interface in pyberny and the interface in PySCF for inspiration. 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. -- ------------------------------------------------------------------ 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 ------------------------------------------------------------------