From owner-chemistry@ccl.net Mon Jul 27 10:37:01 2009 From: "cesar alejandro adrianzen hernani harryspeedy_06#%#hotmail.com" To: CCL Subject: CCL: LAMMPS Message-Id: <-39854-090726232909-25352-zwkDwrlmTdzbO2VyndkGsA|,|server.ccl.net> X-Original-From: "cesar alejandro adrianzen hernani" Date: Sun, 26 Jul 2009 23:29:06 -0400 Sent to CCL by: "cesar alejandro adrianzen hernani" [harryspeedy_06/a\hotmail.com] Dear colleagues, I'm a chemical engeniering student, and I'm working with LAMMPS, now I'm installing the program using cygwin.. the create the linux environment, in my country no body knows about lammps, so if someone knows about it, books I can read.. or anything.. I would appreciate it. From owner-chemistry@ccl.net Mon Jul 27 11:12:02 2009 From: "Alexander Hofmann alexander.hofmann[a]eu.umicore.com" To: CCL Subject: CCL: compilation of parallel VASP on SGI Altix ICE architecture Message-Id: <-39855-090727034443-18800-9pM+WR8BOeLJOLKh6eneBw-#-server.ccl.net> X-Original-From: "Alexander Hofmann" Date: Mon, 27 Jul 2009 03:44:39 -0400 Sent to CCL by: "Alexander Hofmann" [alexander.hofmann#eu.umicore.com] Susan, you may wish to check the VASP-forum for these kind of questions: http://cms.mpi.univie.ac.at/vasp-forum/ There are lively discussions around every VASP related topic you may never dream of. Cheers Alex > -----Ursprngliche Nachricht----- > Von: owner-chemistry+alexander.hofmann==eu.umicore.com~!~ccl.net > [mailto:owner-chemistry+alexander.hofmann==eu.umicore.com~!~ccl.net] Im > Auftrag von Susan R Atlas susie[*]sapphire.phys.unm.edu > Gesendet: Samstag, 25. Juli 2009 02:16 > An: Hofmann, Alexander > Betreff: CCL: compilation of parallel VASP on SGI Altix ICE > architecture > > > Sent to CCL by: "Susan R Atlas" [susie|*|sapphire.phys.unm.edu] Hi, > > A member of my group is trying to build (parallel) VASP on an SGI > Altix ICE cluster, and is running into serious problems with the BLACS > and ScaLAPACK underlying components. We are using the Intel 11.0 > compiler on Xeon 5300 series CPUs, SLES Linux OS. The interconnect is > Infiniband and MPI is MVAPICH 1.0 from OSU. > > The BLACS configuration utilities either lead to error messages or > failures on the self-tests; if we push through the ScaLAPACK build > with one of these BLACS, the ScaLAPACK self-tests generate numerous segfaults. > > Does anyone have experience with compiling VASP (and in particular > the underlying BLACS and ScaLAPACK) on this SGI > architecture/environment? Any advice and/or scripts would be greatly appreciated. > > Thanks, > > Susan > > > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the ~!~ sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > From owner-chemistry@ccl.net Mon Jul 27 13:14:01 2009 From: "Yang, Zheng yang.zheng79{=}gmail.com" To: CCL Subject: CCL:G: Transition state optimization with Gaussian 03 and frozen atoms Message-Id: <-39856-090727121354-7304-aMOuE/hDbfYqLlMe5JkzbA|server.ccl.net> X-Original-From: "Yang, Zheng" Content-Type: multipart/alternative; boundary=0003255750f6b4ea4b046fb23ce4 Date: Mon, 27 Jul 2009 11:13:40 -0500 MIME-Version: 1.0 Sent to CCL by: "Yang, Zheng" [yang.zheng79*|*gmail.com] --0003255750f6b4ea4b046fb23ce4 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Yes, you can freeze the geometry by adding 'constants' to the end of the input file. For example: # HF/6-31G(d) Opt Test Partial optimization for water 0 1 O H1 O R H2 O R H1 A Variables: R 1.0 Constants: A 105.4 2009/7/24 Ben Janesko bjanesko * rice.edu > > Sent to CCL by: Ben Janesko [bjanesko_+_rice.edu] > Hello. I would like to optimize the transition state of a reaction on a > metal cluster. I want to freeze the cluster geometry. Is this possible > with Gaussian 03? It doesn't appear to work with the QST2 and QST3 > methods. > > Ben Janesko> > > --0003255750f6b4ea4b046fb23ce4 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Yes, you can freeze the geometry by adding 'constants' to the end o= f the input file. For example:

# HF/6-31G(d) Opt Test
Partial opt= imization for water
0 1
O
H1 O R
H2 O R H1 A
Variables:
R 1.0
Constants:
A 105.4

2009/7/24 = Ben Janesko bjanesko * rice.edu <owner-chemistry+*+ccl= .net>

Sent to CCL by: Ben Janesko [bjanesko_+_rice.edu]
Hello. I would like to optimize the transition state of a reaction on a
metal cluster. I want to freeze the cluster geometry. Is this possible
with Gaussian 03? It doesn't appear to work with the QST2 and QST3
methods.

=A0Ben Janesko



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--0003255750f6b4ea4b046fb23ce4-- From owner-chemistry@ccl.net Mon Jul 27 13:49:00 2009 From: "Ron Salesky rsalesky%a%unm.edu" To: CCL Subject: CCL: Tinker dynamic limits? Message-Id: <-39857-090727132949-20701-RqaXVAH7qzpJaWbBFc/Wrg%x%server.ccl.net> X-Original-From: "Ron Salesky" Date: Mon, 27 Jul 2009 13:29:45 -0400 Sent to CCL by: "Ron Salesky" [rsalesky : unm.edu] Hi, I'm attempting to use Tinker's dynamic function on a 4432 atom system from the command line and it never seems to complete. I have even asked it to do a very small number of dynamics steps, e.g. 2, w/ a time step of 1 fs and time between dumps of .001 ps and receive no data back. Trying smaller number of atoms in the system results in the same situation... if it is small enough to do 'regular' MD, dynamic completes. Once it becomes large enough to do stochastics, it announces it is using the modified Beeman algorithm and never completes. Indeed, I added some feedback lines in Beeman and find it doesn't get past the 'call gradient' command within Beeman. Does anyone have experience w/ dynamic and its limitations/expected run times? Thanks, Ron From owner-chemistry@ccl.net Mon Jul 27 20:42:01 2009 From: "Gennady L. Gutsev gennady.gutsev-,-famu.edu" To: CCL Subject: CCL:G: IR or optical spectra plotting software for Mac 10.5.7 Message-Id: <-39858-090727193333-11951-v8h6GpsYiuSSHwf9IwvNZQ##server.ccl.net> X-Original-From: "Gennady L. Gutsev" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01CA0EF2.34DD9A02" Date: Mon, 27 Jul 2009 15:41:16 -0400 MIME-Version: 1.0 Sent to CCL by: "Gennady L. Gutsev" [gennady.gutsev..famu.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01CA0EF2.34DD9A02 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, Could you please advise me (free or non-expensive) software for Mac (Leopard) for transformation of bar spectra into=20 Gaussian/Lorentzian broadened spectra and plotting them=20 desirably one on the top another in the same figure. Thanks, Gennady =20 ------_=_NextPart_001_01CA0EF2.34DD9A02 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable IR or optical spectra plotting software for Mac 10.5.7

Dear all,

Could you please advise me (free or non-expensive) software
for Mac (Leopard) for transformation of bar spectra into
Gaussian/Lorentzian broadened spectra and plotting them
desirably one on the top another in the same figure.
Thanks,
Gennady 

------_=_NextPart_001_01CA0EF2.34DD9A02-- From owner-chemistry@ccl.net Mon Jul 27 22:18:00 2009 From: "Ron Salesky rsalesky%unm.edu" To: CCL Subject: CCL: Tinker dynamic function strange data Message-Id: <-39859-090727190015-10123-fVfUhFkupBPKBJcErUR73g]_[server.ccl.net> X-Original-From: "Ron Salesky" Date: Mon, 27 Jul 2009 19:00:11 -0400 Sent to CCL by: "Ron Salesky" [rsalesky:_:unm.edu] Is anyone on this list familiar with Tinker's dynamic function? Please note that this should supersede an earlier request posted on this board as it describes more accurately and in greater detail the issue at hand. I get very strange results as follows: 1. Without using a periodic box, the Cartesian coordinates 'dump' file contains either ****** for some coordinates and outlandish coordinate values for other coordinates, e.g. 46000.0 angstroms where the largest value in the input coordinates file was 20 angstroms. The input file contains ~4600 atoms OR 2. If a periodic box is defined in the key file, it simply never runs... several text output lines were placed in the fortran source to attempt a trace and it gets "lost" upon entering the gradient subroutine. This happens both for the largish 4600 atom file and for a 158 atom file. The prm file in both cases is amber99. Thank you for any assistance, Ron Salesky