From owner-chemistry@ccl.net Wed Feb 1 04:36:00 2012 From: "Saman Mandegar mandegar_saman---yahoo.com" To: CCL Subject: CCL:G: script to extract intermediate strcutures in Gaussian Message-Id: <-46217-120201043437-10033-6DgPiJw2oDSm8wRJn7WNiQ{=}server.ccl.net> X-Original-From: "Saman Mandegar" Date: Wed, 1 Feb 2012 04:34:36 -0500 Sent to CCL by: "Saman Mandegar" [mandegar_saman_-_yahoo.com] Dear Users, I am looking for a script to extract the intermediate structures in an optimization output of Gaussian to do further analysis. I would thank if anybody has already have written that and could share it with me. Thanks in advance. Kind wishes, Saman From owner-chemistry@ccl.net Wed Feb 1 05:11:01 2012 From: "Ramon Crehuet rcsqtc|-|iqac.csic.es" To: CCL Subject: CCL:G: script to extract intermediate strcutures in Gaussian Message-Id: <-46218-120201050527-29121-/zmOHwQPTyeaRAKpxtYi7A#%#server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 01 Feb 2012 11:02:37 +0100 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc##iqac.csic.es] Dear Saman, Take a look at cclib. Its very useful and flexible. http://sourceforge.net/apps/mediawiki/cclib/index.php?title=Main_Page Best regards, RAmon On 01/02/12 10:34, Saman Mandegar mandegar_saman---yahoo.com wrote: > Sent to CCL by: "Saman Mandegar" [mandegar_saman_-_yahoo.com] > Dear Users, > > I am looking for a script to extract the intermediate structures in an optimization output of Gaussian to do further analysis. I would thank if anybody has already have written that and could share it with me. > Thanks in advance. > Kind wishes, > > Saman> > > From owner-chemistry@ccl.net Wed Feb 1 06:37:00 2012 From: "Toomas Tamm tt-ccl2]![yki.ttu.ee" To: CCL Subject: CCL:G: How to calculate Enthalpy value from Gaussian out put files Message-Id: <-46219-120201041352-24385-WE2mu+tJVM9GNR4648WXaA*o*server.ccl.net> X-Original-From: Toomas Tamm Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 01 Feb 2012 11:13:37 +0200 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl2/./yki.ttu.ee] On Tue, 2012-01-31 at 16:33 +0100, Jean Jules FIFEN julesfifen---gmail.com wrote: > Yes, It is the right answer. However, you might add the Zero-point > correction to make it more sense accounting the Heisenberg principle. > Thus, for the corrected enthalpy, you would have: -1454.648584 + > 0.005319 = -1454.643265. According to http://www.gaussian.com/g_whitepap/thermo/thermo.pdf, page 9, zero-point energy is already included in all the quantities printed by Gaussian in this section. Thus your suggestion would lead to double counting of the zero-point energy. -- Toomas Tamm e-mail: tt-ccl2 (at) kky . ttu . ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From owner-chemistry@ccl.net Wed Feb 1 08:28:00 2012 From: "Christoph Schuster secondlawfreak,gmail.com" To: CCL Subject: CCL: imaginary part of second hyperpolarizability g09 Message-Id: <-46220-120201070425-16949-kY2mO5AT8omaRztMfb208Q,+,server.ccl.net> X-Original-From: "Christoph Schuster" Date: Wed, 1 Feb 2012 07:04:23 -0500 Sent to CCL by: "Christoph Schuster" [secondlawfreak###gmail.com] Dear CCLers, I want to calculate the tow-photon-cross-section of a molecule using G09. For this purpose I need to calculate the imaginary part of second hyperpolarizability. I've used "td=sos" and "polar" in the link section and also the wavelength at the end of my input file. In the output file I find the line; SCF Beta(W,W;-2W) for W =... My first question: Is this the right section of the output file? and the second: How do I proceed from there to get the imaginary part of second hyperpolarizability (literature)? thank in advance Christoph From owner-chemistry@ccl.net Wed Feb 1 09:45:01 2012 From: "Jean Jules FIFEN julesfifen++gmail.com" To: CCL Subject: CCL:G: How to calculate Enthalpy value from Gaussian out put files Message-Id: <-46221-120201094138-29279-M95F/OB8WrmoBhIMhf+GmA\a/server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=20cf30051430045ae104b7e81326 Date: Wed, 1 Feb 2012 15:41:25 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen##gmail.com] --20cf30051430045ae104b7e81326 Content-Type: text/plain; charset=ISO-8859-1 Dear Toomas, I think you do a mistake, saying so. I suggest the carefully reading of the suggest file (thermo.pdf). I do not think that enthalpy printed out by gaussian, already encompasses ZPE. To convince your self, take the electronic energy printed out, add the thermal correction for enthalpy. What is the answer? Problably Sum of electronic and thermal enthalpy, which stand for Ee+Erot+Etrans+Evib+PV. Furthermore, I did a program which computes the thermochemistry of a system (without including ZPE) from its optimized geometry and, I found the same results printed by gaussian output in enthalpy and free energy. Have a look. On 1 February 2012 10:13, Toomas Tamm tt-ccl2]![yki.ttu.ee < owner-chemistry(0)ccl.net> wrote: > > Sent to CCL by: Toomas Tamm [tt-ccl2/./yki.ttu.ee] > On Tue, 2012-01-31 at 16:33 +0100, Jean Jules FIFEN > julesfifen---gmail.com wrote: > > Yes, It is the right answer. However, you might add the Zero-point > > correction to make it more sense accounting the Heisenberg principle. > > Thus, for the corrected enthalpy, you would have: -1454.648584 + > > 0.005319 = -1454.643265. > > According to http://www.gaussian.com/g_whitepap/thermo/thermo.pdf, page > 9, zero-point energy is already included in all the quantities printed > by Gaussian in this section. Thus your suggestion would lead to double > counting of the zero-point energy. > > -- > Toomas Tamm e-mail: tt-ccl2 (at) kky . ttu > . ee > Chair of Inorganic Chemistry voice: INT+372-620-2810 > Tallinn University of Technology fax: INT+372-620-2828 > Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/> > > -- Jules. --20cf30051430045ae104b7e81326 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Toomas,
I think you do a mistake, saying so.
I = suggest the carefully reading of the suggest file (thermo.pdf).=A0 I do not= think that enthalpy printed out by gaussian, already encompasses ZPE. To c= onvince your self, take the electronic energy printed out, add the thermal = correction for enthalpy. What is the answer? Problably Sum of electronic an= d thermal enthalpy, which stand for=A0 Ee+Erot+Etrans+Evib+PV. Furthermore,= I did a program which computes the thermochemistry of a system (without in= cluding ZPE) from its optimized geometry and, I found the same results prin= ted by gaussian output in enthalpy and free energy.
Have a look.=A0

On 1 February 2012 10:13= , Toomas Tamm tt-ccl2]![yki.ttu.ee <owner-chemistry(0)= ccl.net> wrote:

Sent to CCL by: Toomas Tamm [tt-ccl2/./yki.ttu.ee]
On Tue, 2012-01-31 at 16:33 +0100, Jean Jules FIFEN
julesfifen---gm= ail.com wrote:
> Yes, It is the right answer. However, you might add the Zero-point
> correction to make it more sense accounting the Heisenberg principle.<= br> > Thus, for the corrected enthalpy, you would have: -1454.648584 +
> 0.005319 =3D -1454.643265.

According to http://www.gaussian.com/g_whitepap/thermo/thermo.pdf, page
9, zero-point energy is already included in all the quantities printed
by Gaussian in this section. Thus your suggestion would lead to double
counting of the zero-point energy.

--
Toomas Tamm =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0= e-mail: tt-ccl2 (at) kky . ttu . ee
Chair of Inorganic Chemistry =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0voice: =A0INT+372-620-2810
Tallinn University of Technology =A0 =A0 =A0 =A0 =A0 =A0fax: =A0 =A0INT+372-620-2828
Ehitajate tee 5, EE-19086 Tallinn, Estonia =A0http://www.kk.ttu.ee/toomas/



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--
Jules.
=
--20cf30051430045ae104b7e81326-- From owner-chemistry@ccl.net Wed Feb 1 16:22:00 2012 From: "Eustis Soren soren.eustis!=!env.ethz.ch" To: CCL Subject: CCL: Best Source for Purchasing High Performance Workstation or Rack Systems? Message-Id: <-46222-120201125539-4272-8QBsuoun1f+8DqQ5yyEsMw() server.ccl.net> X-Original-From: "Eustis Soren" Content-ID: <583953F6C290A74A85F3B19CD5745A86() intern.ethz.ch> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Wed, 1 Feb 2012 17:55:31 +0000 MIME-Version: 1.0 Sent to CCL by: "Eustis Soren" [soren.eustis]-[env.ethz.ch] I am about to establish an experimental/theoretical research lab in the US. I am very interested to hear which vendors the CCL community prefers when it comes to purchasing rack or workstation systems for quantum chemistry work. I have worked with JNCS and Electronics Nexus in the past with some satisfaction. Thank you in advance for your responses. Soren Soren N. Eustis, Ph.D. ETH – Zürich Environmental Chemistry Group Inst. for Biogeochem. and Pollutant Dynamics Universitätstrasse 16 CHN F33 8092 Zürich SWITZERLAND +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren{:}env.ethz.ch From owner-chemistry@ccl.net Wed Feb 1 16:57:00 2012 From: "Senthil kumar Krishnasamy supersenthil73*_*rediffmail.com" To: CCL Subject: CCL:G: Energy of hydrogen atom by PM3 method Message-Id: <-46223-120130120425-21006-dNE3NGwe0JO6veqr1QVh3A---server.ccl.net> X-Original-From: "Senthil kumar Krishnasamy" Date: Mon, 30 Jan 2012 12:04:23 -0500 Sent to CCL by: "Senthil kumar Krishnasamy" [supersenthil73{}rediffmail.com] Dear all Pl clarify my doubt I used the following input to find the energy of hydrogen atom by PM3 method # PM3 Hydrogen atom PM3 spe calculation 0,2 1 0.000000000 0.000000000 0.000000000 I didn't get the completed output for a long time with the status of performing semiempirical calculations and the output section appeared as below %chk=C:\Hydrogen atom PM3 Opt -------- # PM3 sp -------- 1/30=1,38=1/1; 2/17=6,18=5,40=1/2; 3/5=2,11=9,12=1,16=1,25=1,30=1/1; 4/5=3,11=1,20=7,24=3,35=1/1,2; 6/7=2,8=2,9=2,10=2/1; 99/5=1,9=1/99; --------------------------------- Hydrogen atom PM3 spe calculation --------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 2 1 0. 0. 0. Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 1 0 0.000000 0.000000 0.000000 --------------------------------------------------------------------- Stoichiometry H(2) Framework group OH[O(H)] Deg. of freedom 0 Full point group OH Largest Abelian subgroup D2H NOp 8 Largest concise Abelian subgroup C1 NOp 1 Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 1 0 0.000000 0.000000 0.000000 --------------------------------------------------------------------- Standard basis: VSTO-3G (5D, 7F) There are 1 symmetry adapted basis functions of AG symmetry. There are 0 symmetry adapted basis functions of B1G symmetry. There are 0 symmetry adapted basis functions of B2G symmetry. There are 0 symmetry adapted basis functions of B3G symmetry. There are 0 symmetry adapted basis functions of AU symmetry. There are 0 symmetry adapted basis functions of B1U symmetry. There are 0 symmetry adapted basis functions of B2U symmetry. There are 0 symmetry adapted basis functions of B3U symmetry. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 1 basis functions, 3 primitive gaussians, 1 cartesian basis functions 1 alpha electrons 0 beta electrons nuclear repulsion energy 0.0000000000 Hartrees. NAtoms= 1 NActive= 1 NUniq= 1 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F Simple Huckel Guess. Initial guess orbital symmetries: Alpha Orbitals: Occupied (A1G) Beta Orbitals: Virtual (A1G) The electronic state of the initial guess is 2-A1G. of initial guess= 0.7500 I get the completed output within a few seconds when the same calculation performed in DFT method Thanks in advance By K. Senthil kumar Faculty of Physics Hindusthan college of engg & tech Coimbatore-32 Tamilnadu India From owner-chemistry@ccl.net Wed Feb 1 20:08:00 2012 From: "Wibe Albert de Jong bert.dejong^-^pnnl.gov" To: CCL Subject: CCL:G: Announcing release of NWChem 6.1 open-source software Message-Id: <-46224-120201173740-18909-q7bE1r+KtjrN1hYXltcRvg.@.server.ccl.net> X-Original-From: "Wibe Albert de Jong" Date: Wed, 1 Feb 2012 17:37:38 -0500 Sent to CCL by: "Wibe Albert de Jong" [bert.dejong*pnnl.gov] Dear CCL-ers, NWChem 6.1 has been released and can be downloaded from http://www.nwchem-sw.org/index.php/Download . An overview of the changes in this new version is listed below. With kind regards, NWChem developers. NWChem 6.1 is released with the latest Global Arrays Toolkit (GA-5.1) providing tuned and additional platform support. New functionality ----------------- High accuracy New Activespace non-iterative methods New improved Equation-of-Motion solvers for excited states Restart capabilities added Improved iterative performance Gaussian basis DFT & TDDFT New density functionals (LC-wPBE,LC-wPBEh,BHLYP) Analytical Hessians for open-shell systems Core states with TDDFT TDDFT with scalar ZORA Finite nucleus ZORA calculations Proper restart for Davidson procedure in TDDFT Spin-density initialization DFT in general Quadratic-convergence DFT DFT-D3 implementation Extension of SMEAR directive controlling Sz Plane-wave DFT and dynamics Unit cell geometry optimization Meta-dynamics plane wave module WHAM method plane wave module Hybrid DFT Exchange HSE plane wave New DFT functionals (need a list here) Spin-density initialization DFT in general Auto-restart CPMD Automatic generation of g(r) CPMD Born-Oppenheimer MD Parallel I/O for large processor counts k-point parallelization String method PAW/PSPW/Band integration Full PSPW Pseudopotential set Properties (Para)magnetic NMR with scalar ZORA (experimental) Electric field gradients with scalar ZORA (Z4) Optical rotation Raman spectra Range separated functionals with NMR properties Plane-wave EFG (experimental) ESP for spherical basis sets Molecular Dynamics Multiple ensemble MD Input Support for all space groups CAR reader PDB reader XYZ reader Other New implementation CCCA All basis sets from the Basis Set Exchange (http://bse.pnl.gov) Dihedral constraints for optimizations Various new QM/MM features Embedding charges via bq_charges file (format: Bq x y z charge) Expanded python scripting functionality Documentation Extensive How To Install and Compile Expanded Users Documentation with examples Expanded Developers Documentation Complex simulation tutorials Bug fixes COSMO Rsolve now consistent with standard implementations ROHF Gradients Rys-roots hondo integrals for properties for high angular momenta Origin independence of NMR calculations with COSMO and Bq charges DFT + D (dispersion) fixes with ECPs SR and SO-ZORA calculations can now be performed with fragment guesses Reduced memory footprint with Bq gradient Proper handling of ECP core in initial guess Performance improvement CPHF Avoiding zero length arrays for 1 electron calculations Constrained DFT the code tests for valid atoms Fixed xc_active parameter in the runtime database Reduced the output from the Mulliken analysis in the property module Use of ga_initialize_ltd to address memory management problems BSSE code now always uses sensible masses Fixed logic of ATOM directive in prepare module Fixed basis set input trying to close an undefined file unit number Fixed an uninitialized variable problem in the VS98 correlation functional Fixed a problem with not creating a GA if no electrons exist in a spin-channel movecs_print_anal Fixed density functionals handling small and even slightly negative densities Fixed a file name dimension to avoid truncation Proper handling of combinations of AO and fitting basis sets (such a mixing Cartesian and Spherical Harmonics) Removed Fortran STOP statements from the integral code Added an extra check on Z-matrix lines to trap instances where the same atom is referred to twice Fixed the memory usage of the direct MP2