=A0* Visualization of every step in a geometry optimization= , with the ability to save any of those structures as XYZ or PDB files,

=A0* A simple, yet powerful, XYZ editor with tools that allow translat= ions and rotations to align bonds to specific axes,

=A0* Animatio= n of the normal modes of a frequency calculation, and

=A0* A plot= of electronic transitions and a easy-to-read list of the corresponding orb= ital excitations from TDDFT/CIS calculations.

I encourage you to visit http://qmforge.sourceforge.net to see screenshots that dem= onstrate the various capabilities. On that page, you will also find links t= o download pre-packaged Windows and Mac OS X binaries, as well as links to = the source code.

Sincerely,

Adam Tenderholt

--089e01160174922e3504f091d238-- From owner-chemistry@ccl.net Wed Jan 22 13:04:01 2014 From: "Raghu R raghu.rama.chem ~ gmail.com" To: CCL Subject: CCL: negative values in Mulliken spin distribution Message-Id: <-49592-140122130328-31427-nj9deOSQbf/UJc/7TjOj2A:_:server.ccl.net> X-Original-From: Raghu R Content-Type: multipart/alternative; boundary=001a11c2f482c04a1704f092f080 Date: Wed, 22 Jan 2014 19:03:21 +0100 MIME-Version: 1.0 Sent to CCL by: Raghu R [raghu.rama.chem- -gmail.com] --001a11c2f482c04a1704f092f080 Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Hello, There seems to be an explanation to negative spin densities in radicals, e.g., see this book chapter digital.csic.es/bitstream/10261/76135/1/Spin%20Density.pdf On p. 170, the author says, "The negative spin density at the carbon atom is due to a polarisation effect produced by the SOMO orbital on some of the doubly occupied orbitals. ...." On Wed, Jan 22, 2014 at 12:20 PM, Martin Rahm martin.rahm- -gmail.com < owner-chemistry|,|ccl.net> wrote: > Hi, > > To my knowledge negative atomic orbital occupations in Mulliken populatio= n > analysis can sometimes occur due to MPAs direct partitioning of CMOs into > non-orthogonalized atomic orbitals. Hoffman et al. have rationalized this > effect for Huckel and limited basis set SCF calculations, as being a > natural consequence of the wave function normalization in certain cases (= J. > chem. Phys. 68, 5498 and J. Am. Chem. Soc. 100, 3686 ). > > Best, > Martin > > > On Wed, Jan 22, 2014 at 9:57 AM, Raghu R raghu.rama.chem[]gmail.com < > owner-chemistry.:.ccl.net> wrote: > >> Hello, >> >> Negative spin density is encountered in approximate theories like H=FCc= kel >> MO theory. For a system with one unpaired electron, the sum of >> spin-densities on all atomic sites add up to 1, but the sum of >> their absolute values >> is > 1, implying that some sites have negative densities of this odd >> electron. >> >> See for example, >> "Free radicals with large negative spin densities", >> M. S. Davis , K. Morokuma , R. W. Kreilick, >> J. Am. Chem. Soc., 1972, 94 (16), pp 5588=965592 >> >> ps. I do not think that negative density has anything to do with >> Mulliken's population, in particular. >> >> Best, >> Raghu >> >> >> >> On Wed, Jan 22, 2014 at 7:36 AM, Haya Kornweitz hayak]|[ariel.ac.il < >> owner-chemistry%a%ccl.net > wrote: >> >>> >>> Sent to CCL by: "Haya Kornweitz" [hayak=3D=3D=3Dariel.ac.il] >>> Can someone explain, or give a reference, the meaning of negative value= s >>> in >>> Mulliken spin distribution? thanks a lot. >>> >>> >>> >>> -=3D This is automatically added to each message by the mailing script = =3D- >>> E-mail to subscribers: CHEMISTRY%a%ccl.net or >>> use:>>> >>> E-mail to administrators: CHEMISTRY-REQUEST%a%ccl.netor use>>> >>> >>> >> > --001a11c2f482c04a1704f092f080 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable

Hello,

There seems to be an explanation to negative spin densities in radicals, e.= g., see this book chapter

digital.csic.es/bitstream/10261/76135/1/Spin= %20Density.pdf

On p. 170, the author says, "The negative spin density at the carbon= =20 atom is due to a polarisation effect produced by the SOMO orbital on=20 some of the doubly occupied orbitals. ...."

On Wed, Jan 22, 2014 at 12:20 P= M, Martin Rahm martin.rahm- -gmail.com <owner-chemistry|,|ccl.net> wrote:

Hi,=A0

To my knowledge negative atomic orbital occupatio= ns in Mulliken population analysis can sometimes occur due to MPAs direct p= artitioning of CMOs into non-orthogonalized atomic orbitals. Hoffman et al.= have rationalized this effect for Huckel and limited basis set SCF calcula= tions, as being a natural consequence of the wave function normalization in= certain cases (J. chem. Phys. 68, 5498 and J. Am. Chem. Soc. 100, 3686 ).= =A0

Best,=A0
Martin=A0

On Wed, Jan 22, 2014 at 9:57= AM, Raghu R raghu.rama.chem[]gmail.com <owner-chemistry.:.ccl.net> wrote:
Hello,

Negative spin density=A0 is encountered in approximate theories like H=FCck= el MO theory. For a system with one unpaired electron, the sum of spin-dens= ities on all atomic sites add up to 1, but the sum of

their absolute values
is > 1, = implying that some sites have negative densities of this odd electron.

See for example,

"Free radicals with large negative spin densities", M. S. Davis , K. Morokuma , R. W. Kreilick,
J. Am. Chem. Soc., 1972, 9= 4 (16), pp 5588=965592

ps. I do not think that negative density has anything to do with Mulliken&#= 39;s population, in particular.

Best,
Raghu

On Wed, Jan 22, 2014 at 7:36 AM, Haya Kornweitz h= ayak]|[ariel.ac.il <owner-chemistry%a%ccl.net> wrote:

Sent to CCL by: "Haya =A0Kornweitz" [hayak=3D=3D=3Dariel.ac.il]
Can someone explain, or give a reference, the meaning of negative values in=
Mulliken spin distribution? thanks a lot.

-=3D This is automatically added to each message by the mailing script =3D-=
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--001a11c2f482c04a1704f092f080-- From owner-chemistry@ccl.net Wed Jan 22 16:35:00 2014 From: "Salter-Duke, Brian James - brian.james.duke(-)gmail.com" To: CCL Subject: CCL:G: Announcement: QMForge 2.3.1 Message-Id: <-49593-140122143925-1894-lEFU/izy0QoJeCj0x+DUcA^server.ccl.net> X-Original-From: "Salter-Duke, Brian James -" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Thu, 23 Jan 2014 06:39:08 +1100 MIME-Version: 1.0 Sent to CCL by: "Salter-Duke, Brian James -" [brian.james.duke^^gmail.com] This looks like a usefull program. However, is there any prospect of a Linux version for those of us who only use Linux? Brian Duke. On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A!gmail.com wrote: > I am pleased to announce the release of QMForge 2.3.1, which is a > cross-platform, open-source program for interpreting and analyzing the > results of QM calculations. > > QMForge 2.3.1 builds upon the previous versions with the addition of the > following features: > > * Plots of Convergence and Energy in the Geometry Optimization tab, > * Plots of IR and/or Raman spectra in the Frequency Tab, > * Ability to save the normal modes of a Frequency calculation as animated > GIFs, > * Gross Population Analysis to compare Mulliken and Lowdin populations and > spin densities for each atom and orbital > > Other notable features include: > > * The support of several QM output formats including Gaussian, ADF, GAMESS > (and its various derivatives), Jaguar, and ORCA, > * Population analyses such as Mulliken, Lowdin, C-squared, and Overlap on > user-defined sets ("fragments") of basis functions, > * Fragment Analysis to interpret the contributions of fragment MOs to > molecular MOs, > * Charge Decomposition Analysis, > * Mayer's bond orders, > * Visualization of every step in a geometry optimization, with the ability > to save any of those structures as XYZ or PDB files, > * A simple, yet powerful, XYZ editor with tools that allow translations > and rotations to align bonds to specific axes, > * Animation of the normal modes of a frequency calculation, and > * A plot of electronic transitions and a easy-to-read list of the > corresponding orbital excitations from TDDFT/CIS calculations. > > I encourage you to visit http://qmforge.sourceforge.net to see screenshots > that demonstrate the various capabilities. On that page, you will also find > links to download pre-packaged Windows and Mac OS X binaries, as well as > links to the source code. > > Sincerely, > > Adam Tenderholt -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke(0)monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia From owner-chemistry@ccl.net Wed Jan 22 17:19:00 2014 From: "Adam Tenderholt atenderholt(_)gmail.com" To: CCL Subject: CCL:G: Announcement: QMForge 2.3.1 Message-Id: <-49594-140122171257-10868-sBABjMp9IrWLjmg8drpSDw]-[server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=bcaec51b1cfffc19a704f0966c2a Date: Wed, 22 Jan 2014 14:12:30 -0800 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt\a/gmail.com] --bcaec51b1cfffc19a704f0966c2a Content-Type: text/plain; charset=ISO-8859-1 This is the first request I've had for a Linux version, so I haven't given much thought to it. If others also have interest, please email me directly. Make sure to mention which distro you are using. Thanks, Adam On Wed, Jan 22, 2014 at 11:39 AM, Salter-Duke, Brian James brian.james.duke(-)gmail.com wrote: > > Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke^^ > gmail.com] > This looks like a usefull program. However, is there any prospect of a > Linux version for those of us who only use Linux? > > Brian Duke. > > On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A! > gmail.com wrote: > > I am pleased to announce the release of QMForge 2.3.1, which is a > > cross-platform, open-source program for interpreting and analyzing the > > results of QM calculations. > > > > QMForge 2.3.1 builds upon the previous versions with the addition of the > > following features: > > > > * Plots of Convergence and Energy in the Geometry Optimization tab, > > * Plots of IR and/or Raman spectra in the Frequency Tab, > > * Ability to save the normal modes of a Frequency calculation as animated > > GIFs, > > * Gross Population Analysis to compare Mulliken and Lowdin populations > and > > spin densities for each atom and orbital > > > > Other notable features include: > > > > * The support of several QM output formats including Gaussian, ADF, > GAMESS > > (and its various derivatives), Jaguar, and ORCA, > > * Population analyses such as Mulliken, Lowdin, C-squared, and Overlap > on > > user-defined sets ("fragments") of basis functions, > > * Fragment Analysis to interpret the contributions of fragment MOs to > > molecular MOs, > > * Charge Decomposition Analysis, > > * Mayer's bond orders, > > * Visualization of every step in a geometry optimization, with the > ability > > to save any of those structures as XYZ or PDB files, > > * A simple, yet powerful, XYZ editor with tools that allow translations > > and rotations to align bonds to specific axes, > > * Animation of the normal modes of a frequency calculation, and > > * A plot of electronic transitions and a easy-to-read list of the > > corresponding orbital excitations from TDDFT/CIS calculations. > > > > I encourage you to visit http://qmforge.sourceforge.net to see > screenshots > > that demonstrate the various capabilities. On that page, you will also > find > > links to download pre-packaged Windows and Mac OS X binaries, as well as > > links to the source code. > > > > Sincerely, > > > > Adam Tenderholt > > -- > Brian Salter-Duke (Brian Duke) Brian.Salter-Duke---monash.edu > Adjunct Associate Professor > Monash Institute of Pharmaceutical Sciences > Monash University Parkville Campus, VIC 3052, Australia> > > --bcaec51b1cfffc19a704f0966c2a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

This is the first request I've had for a Linux version= , so I haven't given much thought to it. If others also have interest, = please email me directly. Make sure to mention which distro you are using.= =A0

Thanks,

Adam

On Wed, J= an 22, 2014 at 11:39 AM, Salter-Duke, Brian James brian.james.duke= (-)gmail.com <owner-chemistry+/-ccl.n= et> wrote:

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.= duke^^gmail.com]
This looks like a usefull program. However, is there any prospect of a
Linux version for those of us who only use Linux?

Brian Duke.

On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A!gmail.com wrote:
> I am pleased to announce the release of QMForge 2.3.1, which is a
> cross-platform, open-source program for interpreting and analyzing the=
> results of QM calculations.
>
> QMForge 2.3.1 builds upon the previous versions with the addition of t= he
> following features:
>
> * Plots of Convergence and Energy in the Geometry Optimization tab, > * Plots of IR and/or Raman spectra in the Frequency Tab,
> * Ability to save the normal modes of a Frequency calculation as anima= ted
> GIFs,
> * Gross Population Analysis to compare Mulliken and Lowdin populations= and
> spin densities for each atom and orbital
>
> Other notable features include:
>
> =A0* The support of several QM output formats including Gaussian, ADF,= GAMESS
> (and its various derivatives), Jaguar, and ORCA,
> =A0* Population analyses such as Mulliken, Lowdin, C-squared, and Over= lap on
> user-defined sets ("fragments") of basis functions,
> =A0* Fragment Analysis to interpret the contributions of fragment MOs = to
> molecular MOs,
> =A0* Charge Decomposition Analysis,
> =A0* Mayer's bond orders,
> =A0* Visualization of every step in a geometry optimization, with the = ability
> to save any of those structures as XYZ or PDB files,
> =A0* A simple, yet powerful, XYZ editor with tools that allow translat= ions
> and rotations to align bonds to specific axes,
> =A0* Animation of the normal modes of a frequency calculation, and
> =A0* A plot of electronic transitions and a easy-to-read list of the > corresponding orbital excitations from TDDFT/CIS calculations.
>
> I encourage you to visit http://qmforge.sourceforge.net to see screenshots
> that demonstrate the various capabilities. On that page, you will also= find
> links to download pre-packaged Windows and Mac OS X binaries, as well = as
> links to the source code.
>
> Sincerely,
>
> Adam Tenderholt

--
=A0 =A0Brian Salter-Duke (Brian Duke) =A0 Brian.Salter-Duke---monash.edu
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Adjunct Associate Professor
=A0 =A0 =A0 =A0 =A0 =A0 Monash Institute of Pharmaceutical Sciences
=A0 =A0 =A0 Monash University Parkville Campus, VIC 3052, Australia

-=3D This is automatically added to each message by the mailing script =3D-=
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--bcaec51b1cfffc19a704f0966c2a-- From owner-chemistry@ccl.net Wed Jan 22 18:09:00 2014 From: "Bennion, Brian Bennion1],[llnl.gov" To: CCL Subject: CCL:G: Announcement: QMForge 2.3.1 Message-Id: <-49595-140122180812-18680-itSRKv7pqo9GdqlhdUFvjQ],[server.ccl.net> X-Original-From: "Bennion, Brian" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_2FD898B2B3ACB44289F398FACE042B4A3A15C0F8PRDEXMBX02thela_" Date: Wed, 22 Jan 2014 23:08:04 +0000 MIME-Version: 1.0 Sent to CCL by: "Bennion, Brian" [Bennion1_-_llnl.gov] --_000_2FD898B2B3ACB44289F398FACE042B4A3A15C0F8PRDEXMBX02thela_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I for one would like access to a linux version of the source code as well. = I imagine that there would be more users in the linux realm than the mac a= nd windows combined. Brian Bennion > From: owner-chemistry+bennion1=3D=3Dllnl.gov{}ccl.net [mailto:owner-chemistr= y+bennion1=3D=3Dllnl.gov{}ccl.net] On Behalf Of Adam Tenderholt atenderholt(= _)gmail.com Sent: Wednesday, January 22, 2014 2:13 PM To: Bennion, Brian Subject: CCL:G: Announcement: QMForge 2.3.1 This is the first request I've had for a Linux version, so I haven't given = much thought to it. If others also have interest, please email me directly.= Make sure to mention which distro you are using. Thanks, Adam On Wed, Jan 22, 2014 at 11:39 AM, Salter-Duke, Brian James brian.james.duke= (-)gmail.com

> wrote: Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke^^gmail.com] This looks like a usefull program. However, is there any prospect of a Linux version for those of us who only use Linux? Brian Duke. On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A!gma= il.com wrote: > I am pleased to announce the release of QMForge 2.3.1, which is a > cross-platform, open-source program for interpreting and analyzing the > results of QM calculations. > > QMForge 2.3.1 builds upon the previous versions with the addition of the > following features: > > * Plots of Convergence and Energy in the Geometry Optimization tab, > * Plots of IR and/or Raman spectra in the Frequency Tab, > * Ability to save the normal modes of a Frequency calculation as animated > GIFs, > * Gross Population Analysis to compare Mulliken and Lowdin populations an= d > spin densities for each atom and orbital > > Other notable features include: > > * The support of several QM output formats including Gaussian, ADF, GAME= SS > (and its various derivatives), Jaguar, and ORCA, > * Population analyses such as Mulliken, Lowdin, C-squared, and Overlap o= n > user-defined sets ("fragments") of basis functions, > * Fragment Analysis to interpret the contributions of fragment MOs to > molecular MOs, > * Charge Decomposition Analysis, > * Mayer's bond orders, > * Visualization of every step in a geometry optimization, with the abili= ty > to save any of those structures as XYZ or PDB files, > * A simple, yet powerful, XYZ editor with tools that allow translations > and rotations to align bonds to specific axes, > * Animation of the normal modes of a frequency calculation, and > * A plot of electronic transitions and a easy-to-read list of the > corresponding orbital excitations from TDDFT/CIS calculations. > > I encourage you to visit http://qmforge.sourceforge.net to see screenshot= s > that demonstrate the various capabilities. On that page, you will also fi= nd > links to download pre-packaged Windows and Mac OS X binaries, as well as > links to the source code. > > Sincerely, > > Adam Tenderholt -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke---monash.edu Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences Monash University Parkville Campus, VIC 3052, Australia -=3D This is automatically added to each message by the mailing script =3D-=
or u= se:E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml

I for one would like acce= ss to a linux version of the source code as well. I imagine that ther= e would be more users in the linux realm than the mac and windows combined.

Brian Bennion<= /span>

<= /p>

From: owner-ch= emistry+bennion1=3D=3Dllnl.gov{}ccl.net [mailto:owner-chemistry+benn= ion1=3D=3Dllnl.gov{}ccl.net] On Behalf Of Adam Tenderholt atenderholt(_)gmail.com
Sent: Wednesday, January 22, 2014 2:13 PM
To: Bennion, Brian
Subject: CCL:G: Announcement: QMForge 2.3.1

This is the first request I've had for a Linux versi= on, so I haven't given much thought to it. If others also have interest, pl= ease email me directly. Make sure to mention which distro you are using.&nb= sp;

Thanks,

Adam

On Wed, Jan 22, 2014 at 11:39 AM, Salter-Duke, Brian= James brian.james.duke(-)gmail.com <owner-chemistr= y!A!ccl.net> wrote:

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke^^gmail.com]
This looks like a usefull program. However, is there any prospect of a
Linux version for those of us who only use Linux?

Brian Duke.

On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A!gmail.com wrote:
> I am pleased to announce the release of QMForge 2.3.1, which is a
> cross-platform, open-source program for interpreting and analyzing the=
> results of QM calculations.
>
> QMForge 2.3.1 builds upon the previous versions with the addition of t= he
> following features:
>
> * Plots of Convergence and Energy in the Geometry Optimization tab, > * Plots of IR and/or Raman spectra in the Frequency Tab,
> * Ability to save the normal modes of a Frequency calculation as anima= ted
> GIFs,
> * Gross Population Analysis to compare Mulliken and Lowdin populations= and
> spin densities for each atom and orbital
>
> Other notable features include:
>
> * The support of several QM output formats including Gaussian, A= DF, GAMESS
> (and its various derivatives), Jaguar, and ORCA,
> * Population analyses such as Mulliken, Lowdin, C-squared, and O= verlap on
> user-defined sets ("fragments") of basis functions,
> * Fragment Analysis to interpret the contributions of fragment M= Os to
> molecular MOs,
> * Charge Decomposition Analysis,
> * Mayer's bond orders,
> * Visualization of every step in a geometry optimization, with t= he ability
> to save any of those structures as XYZ or PDB files,
> * A simple, yet powerful, XYZ editor with tools that allow trans= lations
> and rotations to align bonds to specific axes,
> * Animation of the normal modes of a frequency calculation, and<= br> > * A plot of electronic transitions and a easy-to-read list of th= e
> corresponding orbital excitations from TDDFT/CIS calculations.
>
> I encourage you to visit http://qmforge.sourceforge.net to see screenshots
> that demonstrate the various capabilities. On that page, you will also= find
> links to download pre-packaged Windows and Mac OS X binaries, as well = as
> links to the source code.
>
> Sincerely,
>
> Adam Tenderholt

--
Brian Salter-Duke (Brian Duke) Brian.Salter-Duke---monash.edu
Adjun= ct Associate Professor
Monash Institute of Pharmaceutica= l Sciences
Monash University Parkville Campus, VIC 3052, Australi= a

-=3D This is automatically added to each message by the mailing script =3D-= <br

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--_000_2FD898B2B3ACB44289F398FACE042B4A3A15C0F8PRDEXMBX02thela_-- From owner-chemistry@ccl.net Wed Jan 22 20:35:00 2014 From: "Billy McCann thebillywayne]|[gmail.com" To: CCL Subject: CCL:G: Announcement: QMForge 2.3.1 Message-Id: <-49596-140122203323-24716-4omVjlut3nu/uskr6evWtA..server.ccl.net> X-Original-From: Billy McCann Content-Type: multipart/alternative; boundary=001a11c2fa92b9aee404f0993923 Date: Wed, 22 Jan 2014 20:32:59 -0500 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne*gmail.com] --001a11c2fa92b9aee404f0993923 Content-Type: text/plain; charset=UTF-8 For linux users, the source can be obtained via git clone git://git.code.sf.net/p/qmforge/git-code qmforge-git-code Installs cleanly with *Python 2.7 *cclib (git version, requires swig to build) *pyqt4 *numpy *cclib *pyqwt (requires qmake to build. it looks for /usr/bin/qmake. On Arch Linux, it's in /usr/lib/qt4/bin/qmake. symlink it) *PyOpenGL built against it *Qt4 I installed pyqt4, numpy, pyopengl using pip to fetch from PyPI. The cclib in PyPI wasn't playing nicely. Pull it from github. I compiled pyqwrt after downloading it from their website (requires qmake). I'm pretty sure you can find Qt4 in your distro's repositories. In any case, you should already be using KDE. :) Qmake 2.01a GCC 4.8.2 20131219 (prerelease) Linux 3.12.8 x86_64 bit architecture Kind regards, Billy Wayne McCann, Ph.D. Google+ PGP Key irc://irc.freenode.net:bwayne "A rich man will always desire what his wealth cannot acquire." ~ Faust (Goethe) [00(01|10)11] On Wed, Jan 22, 2014 at 6:08 PM, Bennion, Brian Bennion1],[llnl.gov < owner-chemistry~!~ccl.net> wrote: > I for one would like access to a linux version of the source code as well. > I imagine that there would be more users in the linux realm than the mac > and windows combined. > Brian Bennion > > > From: owner-chemistry+bennion1==llnl.gov]_[ccl.net [mailto: > owner-chemistry+bennion1==llnl.gov]_[ccl.net] On Behalf Of Adam > Tenderholt atenderholt(_)gmail.com > Sent: Wednesday, January 22, 2014 2:13 PM > To: Bennion, Brian > Subject: CCL:G: Announcement: QMForge 2.3.1 > > This is the first request I've had for a Linux version, so I haven't given > much thought to it. If others also have interest, please email me directly. > Make sure to mention which distro you are using. > > Thanks, > > Adam > > > On Wed, Jan 22, 2014 at 11:39 AM, Salter-Duke, Brian James > brian.james.duke(-)gmail.com

> wrote: > > Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke^^gmail.com< > http://gmail.com>] > This looks like a usefull program. However, is there any prospect of a > Linux version for those of us who only use Linux? > > Brian Duke. > > On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A! > gmail.com wrote: > > I am pleased to announce the release of QMForge 2.3.1, which is a > > cross-platform, open-source program for interpreting and analyzing the > > results of QM calculations. > > > > QMForge 2.3.1 builds upon the previous versions with the addition of the > > following features: > > > > * Plots of Convergence and Energy in the Geometry Optimization tab, > > * Plots of IR and/or Raman spectra in the Frequency Tab, > > * Ability to save the normal modes of a Frequency calculation as animated > > GIFs, > > * Gross Population Analysis to compare Mulliken and Lowdin populations > and > > spin densities for each atom and orbital > > > > Other notable features include: > > > > * The support of several QM output formats including Gaussian, ADF, > GAMESS > > (and its various derivatives), Jaguar, and ORCA, > > * Population analyses such as Mulliken, Lowdin, C-squared, and Overlap > on > > user-defined sets ("fragments") of basis functions, > > * Fragment Analysis to interpret the contributions of fragment MOs to > > molecular MOs, > > * Charge Decomposition Analysis, > > * Mayer's bond orders, > > * Visualization of every step in a geometry optimization, with the > ability > > to save any of those structures as XYZ or PDB files, > > * A simple, yet powerful, XYZ editor with tools that allow translations > > and rotations to align bonds to specific axes, > > * Animation of the normal modes of a frequency calculation, and > > * A plot of electronic transitions and a easy-to-read list of the > > corresponding orbital excitations from TDDFT/CIS calculations. > > > > I encourage you to visit http://qmforge.sourceforge.net to see > screenshots > > that demonstrate the various capabilities. On that page, you will also > find > > links to download pre-packaged Windows and Mac OS X binaries, as well as > > links to the source code. > > > > Sincerely, > > > > Adam Tenderholt > -- > Brian Salter-Duke (Brian Duke) Brian.Salter-Duke---monash.edu< > http://Brian.Salter-Duke---monash.edu> > Adjunct Associate Professor > Monash Institute of Pharmaceutical Sciences > Monash University Parkville Campus, VIC 3052, Australia
> > E-mail to subscribers: CHEMISTRY!A!ccl.net or > use:E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net CHEMISTRY-REQUEST!A!ccl.net> or usehttp:// > www.ccl.net/chemistry/sub_unsub.shtml > Content-Type: text/html; charset"us-ascii" > Content-Transfer-Encoding: quoted-printable > > xmlns:o="urn:schemas-microsoft-com:office:office" > xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m=" > http://schemas.microsoft.com/office/2004/12/omml" xmlns=" > http://www.w3.org/TR/REC-html40"> > > > > > > >

style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I > for one would like access to a linux version of the source code as > well. I imagine that there would be more users in the linux realm > than the mac and windows > combined.

style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Brian > Bennion

style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">

style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From: style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> > owner-chemistry+bennion1==llnl.gov]_[ccl.net [mailto:owner-chemistry& > #43;bennion1==llnl.gov]_[ccl.net] > On Behalf Of Adam Tenderholt atenderholt(_)gmail.com
> Sent: Wednesday, January 22, 2014 2:13 PM
> To: Bennion, Brian
> Subject: CCL:G: Announcement: QMForge 2.3.1

This is the first request I've had for a Linux > version, so I haven't given much thought to it. If others also have > interest, please email me directly. Make sure to mention which distro you > are using.

Thanks,

Adam

On Wed, Jan 22, 2014 at 11:39 AM, Salter-Duke, Brian > James brian.james.duke(-)gmail.com < href="mailto:owner-chemistry!A!ccl.net" target="_blank">owner-chemistry!A! > ccl.net> wrote:

> Sent to CCL by: "Salter-Duke, Brian James " > [brian.james.duke^^gmail.com > ]
> This looks like a usefull program. However, is there any prospect of a
> Linux version for those of us who only use Linux?
>
> Brian Duke.

> On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A! href="http://gmail.com" target="_blank">gmail.com wrote:
> > I am pleased to announce the release of QMForge 2.3.1, which is a
> > cross-platform, open-source program for interpreting and analyzing > the
> > results of QM calculations.
> >
> > QMForge 2.3.1 builds upon the previous versions with the addition of > the
> > following features:
> >
> > * Plots of Convergence and Energy in the Geometry Optimization > tab,
> > * Plots of IR and/or Raman spectra in the Frequency Tab,
> > * Ability to save the normal modes of a Frequency calculation as > animated
> > GIFs,
> > * Gross Population Analysis to compare Mulliken and Lowdin > populations and
> > spin densities for each atom and orbital
> >
> > Other notable features include:
> >
> > * The support of several QM output formats including Gaussian, > ADF, GAMESS
> > (and its various derivatives), Jaguar, and ORCA,
> > * Population analyses such as Mulliken, Lowdin, C-squared, and > Overlap on
> > user-defined sets ("fragments") of basis functions,
> > * Fragment Analysis to interpret the contributions of fragment > MOs to
> > molecular MOs,
> > * Charge Decomposition Analysis,
> > * Mayer's bond orders,
> > * Visualization of every step in a geometry optimization, with > the ability
> > to save any of those structures as XYZ or PDB files,
> > * A simple, yet powerful, XYZ editor with tools that allow > translations
> > and rotations to align bonds to specific axes,
> > * Animation of the normal modes of a frequency calculation, > and
> > * A plot of electronic transitions and a easy-to-read list of > the
> > corresponding orbital excitations from TDDFT/CIS calculations.
> >
> > I encourage you to visit target="_blank"> > http://qmforge.sourceforge.net to see screenshots
> > that demonstrate the various capabilities. On that page, you will > also find
> > links to download pre-packaged Windows and Mac OS X binaries, as well > as
> > links to the source code.
> >
> > Sincerely,
> >
> > Adam Tenderholt

--
> Brian Salter-Duke (Brian Duke) > Brian.Salter-Duke---monash.edu
> > Adjunct Associate Professor
> Monash Institute of > Pharmaceutical Sciences
> Monash University Parkville Campus, VIC 3052, > Australia
>
>
>
> -= This is automatically added to each message by the mailing script > =- 
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>
>

> > > --001a11c2fa92b9aee404f0993923 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

For linux users, the source can be obtained via

git clon= e git://git.code.sf.n= et/p/qmforge/git-code qmforge-git-code

Installs cleanly with
*Python 2.7
=C2=A0=C2=A0 *cclib (git ver= sion, requires swig to build)
=C2=A0=C2=A0 *pyqt4
=C2=A0=C2=A0 *numpy=
=C2=A0=C2=A0 *cclib
=C2=A0=C2=A0 *pyqwt (requires qmake to build. it= looks for /usr/bin/qmake. On Arch Linux, it's in /usr/lib/qt4/bin/qmak= e. symlink it)
=C2=A0=C2=A0 *PyOpenGL built against it
*Qt4

I installed pyqt4, = numpy, pyopengl using pip to fetch from PyPI. The cclib in PyPI wasn't = playing nicely. Pull it from github.=C2=A0 I compiled pyqwrt after download= ing it from their website (requires qmake).

I'm pretty sure you can find Qt4 in your distro's repositories= .=C2=A0 In any case, you should already be using KDE. :)

Qmake 2.01a

GCC 4.8.2 20131219 (prerelease)

Linux 3.12.8

<= div class=3D"gmail_default" style=3D"font-family:verdana,sans-serif"> x86_64 bit architecture

Kind regards,

Billy Wayne McCann, Ph.D.
Google+

PGP Key

irc://irc.freenode.net:= bwayne

"A rich man will always desire what his wealth ca= nnot acquire." ~ Faust (Goethe)

[00(01|10)11]

<= /div>

On Wed, Jan 22, 2014 at 6:08 PM, Bennion= , Brian Bennion1],[llnl.gov <owner-c= hemistry~!~ccl.net> wrote:

I for one would like access to a linux versi= on of the source code as well. =C2=A0I imagine that there would be more use= rs in the linux realm than the mac and windows combined.
Brian Bennion

> From: owner-chemistry+bennion1=3D=3Dllnl.gov]_[ccl= .net [mailto:owner-chemis= try+bennion1=3D=3Dllnl.go= v]_[ccl.net] On Behalf= Of Adam Tenderholt atenderholt(_)gmail.com
Sent: Wednesday, January 22, 2014 2:13 PM
To: Bennion, Brian
Subject: CCL:G: Announcement: QMForge 2.3.1

This is the first request I've had for a Linux version, so I haven'= t given much thought to it. If others also have interest, please email me d= irectly. Make sure to mention which distro you are using.

Thanks,

Adam

On Wed, Jan 22, 2014 at 11:39 AM, Salter-Duke, Brian James brian.jame= s.duke(-)gmail.com<http://gmail.com> <o= wner-chemistry!A!ccl.net&l= t;mailto:owner-chemistry!A!ccl.net>> wrote:

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke^^gmail.com<http://gmail.com>]

This looks like a usefull program. However, is there any = prospect of a
Linux version for those of us who only use Linux?

Brian Duke.

On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam= Tenderholt atenderholt!A!gm= ail.com<http://gmail.= com> wrote:
> I am pleased to announce the release of QMForge 2.3.1, which is a
> cross-platform, open-source program for interpreting and analyzing the=
> results of QM calculations.
>
> QMForge 2.3.1 builds upon the previous versions with the addition of t= he
> following features:
>
> * Plots of Convergence and Energy in the Geometry Optimization tab, > * Plots of IR and/or Raman spectra in the Frequency Tab,
> * Ability to save the normal modes of a Frequency calculation as anima= ted
> GIFs,
> * Gross Population Analysis to compare Mulliken and Lowdin populations= and
> spin densities for each atom and orbital
>
> Other notable features include:
>
> =C2=A0* The support of several QM output formats including Gaussian, A= DF, GAMESS
> (and its various derivatives), Jaguar, and ORCA,
> =C2=A0* Population analyses such as Mulliken, Lowdin, C-squared, and O= verlap on
> user-defined sets ("fragments") of basis functions,
> =C2=A0* Fragment Analysis to interpret the contributions of fragment M= Os to
> molecular MOs,
> =C2=A0* Charge Decomposition Analysis,
> =C2=A0* Mayer's bond orders,
> =C2=A0* Visualization of every step in a geometry optimization, with t= he ability
> to save any of those structures as XYZ or PDB files,
> =C2=A0* A simple, yet powerful, XYZ editor with tools that allow trans= lations
> and rotations to align bonds to specific axes,
> =C2=A0* Animation of the normal modes of a frequency calculation, and<= br> > =C2=A0* A plot of electronic transitions and a easy-to-read list of th= e
> corresponding orbital excitations from TDDFT/CIS calculations.
>
> I encourage you to visit http://qmforge.sourceforge.net to see screenshots
> that demonstrate the various capabilities. On that page, you will also= find
> links to download pre-packaged Windows and Mac OS X binaries, as well = as
> links to the source code.
>
> Sincerely,
>
> Adam Tenderholt
--

=C2=A0 =C2=A0Brian Salter-Duke (Brian Duke) =C2=A0 Brian.Salter-Duke--= -monash.edu<http://Brian.Salter-Duke---monash.edu>

=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 =C2=A0 Adjunct Associate Professor
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 Monash Institute of Pharmaceutica= l Sciences
=C2=A0 =C2=A0 =C2=A0 Monash University Parkville Campus, VIC 3052, Australi= a

-=3D This is automatically added to each message by the mailing scrip= t =3D- or use:E-mail to = administrators: CHEMISTRY-REQUEST!A!ccl.net<mailto:CHEMISTRY-= REQUEST!A!ccl.net> = or usehttp://www.ccl.net/chemistry/sub_unsub.shtml<br--_000_2FD898B2= B3ACB44289F398FACE042B4A3A15C0F8PRDEXMBX02thela_
Content-Type: text/html; charset"us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:v=3D"urn:schemas-microsoft-com:vml" xmlns:o=3D&quo= t;urn:schemas-microsoft-com:office:office" xmlns:w=3D"urn:schemas= -microsoft-com:office:word" xmlns:m=3D"http://schemas.microso= ft.com/office/2004/12/omml" xmlns=3D"http://www.w3.org/TR/REC-html40&q= uot;>
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<body lang=3D"EN-US" link=3D"blue" vlink=3D"pur= ple">
<div class=3D"WordSection1">
I for one would like access to a linux version of th= e source code as well.  I imagine that there would be more users i= n the linux realm than the mac and windows
=C2=A0combined.<o:p></o:p>
Brian Bennion<o:p></o:p><= ;/p>
<o:p> </o:p></p= >
From: owner-chemistry+bennion1=3D=3Dllnl.gov]_[ccl.net [mailto:owner-ch= emistry+bennion1=3D=3Dllnl.gov]_[ccl.net]
On Behalf Of Adam Tenderholt atenderholt(_)gmail.com 
Sent: Wednesday, January 22, 2014 2:13 PM 
To: Bennion, Brian 
Subject: CCL:G: Announcement: QMForge 2.3.1<o:p>&l= t;/o:p>
<o:p> </o:p><= ;/p>
<div>
This is the first request I've h= ad for a Linux version, so I haven't given much thought to it. If other= s also have interest, please email me directly. Make sure to mention which = distro you are using. <o:p></o:p>
<div>
<o:p> </o:p><= ;/p>
</div>
<div>
Thanks,<o:p></o:p></p= >
</div>
<div>
<o:p> </o:p><= ;/p>
</div>
<div>
Adam<o:p></o:p>= ;
</div>
<div>
<o:p> </o:p><= ;/p>
</div>
</div>
<div>
<o:p> </o:p>
<div>
On Wed, Jan 22, 2014 at 11:39 AM, Sa= lter-Duke, Brian James brian.james.duke(-)<a href=3D"http://gmail.com">gmail.com</a> <<a hr= ef=3D"mailto:owner-chemistry!A!= ccl.net" target=3D&qu= ot;_blank">owner-chemistry!A!ccl.net</a>> wrote:<o:p></o:p>= ;
 
Sent to CCL by: "Salter-Duke, Brian James " [brian.james.= duke^^<a href=3D"htt= p://gmail.com" target=3D"_blank">gmail.com</a>] 
This looks like a usefull program. However, is there any prospect of a<b= r>
Linux version for those of us who only use Linux? 
 
Brian Duke.<o:p></o:p>
<div>
<div>
 
On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A!<= ;a href=3D"http://gmail= .com" target=3D"_blank">gmail.com</a> wrote: 
> I am pleased to announce the release of QMForge 2.3.1, which is a&= lt;br>
> cross-platform, open-source program for interpreting and analyzing= the 
> results of QM calculations. 
> 
> QMForge 2.3.1 builds upon the previous versions with the addition = of the 
> following features: 
> 
> * Plots of Convergence and Energy in the Geometry Optimization tab= , 
> * Plots of IR and/or Raman spectra in the Frequency Tab, =
> * Ability to save the normal modes of a Frequency calculation as a= nimated 
> GIFs, 
> * Gross Population Analysis to compare Mulliken and Lowdin populat= ions and 
> spin densities for each atom and orbital 
> 
> Other notable features include: 
> 
>  * The support of several QM output formats including Gau= ssian, ADF, GAMESS 
> (and its various derivatives), Jaguar, and ORCA, 
>  * Population analyses such as Mulliken, Lowdin, C-square= d, and Overlap on 
> user-defined sets ("fragments") of basis functio= ns, 
>  * Fragment Analysis to interpret the contributions of fr= agment MOs to 
> molecular MOs, 
>  * Charge Decomposition Analysis, 
>  * Mayer's bond orders, 
>  * Visualization of every step in a geometry optimization= , with the ability 
> to save any of those structures as XYZ or PDB files, 
>  * A simple, yet powerful, XYZ editor with tools that all= ow translations 
> and rotations to align bonds to specific axes, 
>  * Animation of the normal modes of a frequency calculati= on, and 
>  * A plot of electronic transitions and a easy-to-read li= st of the 
> corresponding orbital excitations from TDDFT/CIS calculations.<= br>
> 
> I encourage you to visit <a href=3D"http://qmforge.sourceforge.net&q= uot; target=3D"_blank">
http://qmforge= .sourceforge.net</a> to see screenshots 
> that demonstrate the various capabilities. On that page, you will = also find 
> links to download pre-packaged Windows and Mac OS X binaries, as w= ell as 
> links to the source code. 
> 
> Sincerely, 
> 
> Adam Tenderholt<o:p></o:p>
</div>
</div>
-- 
   Brian Salter-Duke (Brian Duke)   <a href= =3D"http://Brian.Salter-Duke---monash.edu" target=3D"_blank&quo= t;>
Brian.S= alter-Duke---monash.edu</a> 
            &nbsp= ;       Adjunct Associate Professor             Monash In= stitute of Pharmaceutical Sciences 
      Monash University Parkville Campus, VIC 30= 52, Australia 
 
 
 
-=3D This is automatically added to each message by the mailing script =3D-= <br 
 
 
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--001a11c2fa92b9aee404f0993923-- From owner-chemistry@ccl.net Wed Jan 22 22:26:00 2014 From: "Adam Tenderholt atenderholt**gmail.com" To: CCL Subject: CCL:G: Announcement: QMForge 2.3.1 Message-Id: <-49597-140122222350-15901-jnXYRpyx88igNz9tEkJccQ[*]server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: multipart/alternative; boundary=089e01160174bc556504f09ac449 Date: Wed, 22 Jan 2014 19:23:23 -0800 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt*|*gmail.com] --089e01160174bc556504f09ac449 Content-Type: text/plain; charset=ISO-8859-1 I'll just add a few other pointers: * OpenBabel and its Python bindings are required for saving structures (XYZ, PDB, etc.); this was probably the first bullet after Python 2.7 * PIL is required for saving animated GIFs * If you want version v2.3.1, make sure you checkout the 2.3 branch. I haven't tagged the newest version yet. Adam On Wed, Jan 22, 2014 at 5:32 PM, Billy McCann thebillywayne]|[gmail.com < owner-chemistry^ccl.net> wrote: > For linux users, the source can be obtained via > > git clone git://git.code.sf.net/p/qmforge/git-code qmforge-git-code > > Installs cleanly with > *Python 2.7 > *cclib (git version, requires swig to build) > *pyqt4 > *numpy > *cclib > *pyqwt (requires qmake to build. it looks for /usr/bin/qmake. On Arch > Linux, it's in /usr/lib/qt4/bin/qmake. symlink it) > *PyOpenGL built against it > *Qt4 > > I installed pyqt4, numpy, pyopengl using pip to fetch from PyPI. The cclib > in PyPI wasn't playing nicely. Pull it from github. I compiled pyqwrt > after downloading it from their website (requires qmake). > > I'm pretty sure you can find Qt4 in your distro's repositories. In any > case, you should already be using KDE. :) > > Qmake 2.01a > GCC 4.8.2 20131219 (prerelease) > Linux 3.12.8 > x86_64 bit architecture > > > Kind regards, > > > Billy Wayne McCann, Ph.D. > Google+ > PGP Key > irc://irc.freenode.net:bwayne > > "A rich man will always desire what his wealth cannot acquire." ~ Faust > (Goethe) > > [00(01|10)11] > > > > On Wed, Jan 22, 2014 at 6:08 PM, Bennion, Brian Bennion1],[llnl.gov < > owner-chemistry[#]ccl.net> wrote: > >> I for one would like access to a linux version of the source code as >> well. I imagine that there would be more users in the linux realm than the >> mac and windows combined. >> Brian Bennion >> >> > From: owner-chemistry+bennion1==llnl.gov]_[ccl.net [mailto: >> owner-chemistry+bennion1==llnl.gov]_[ccl.net] On Behalf Of Adam >> Tenderholt atenderholt(_)gmail.com >> Sent: Wednesday, January 22, 2014 2:13 PM >> To: Bennion, Brian >> Subject: CCL:G: Announcement: QMForge 2.3.1 >> >> This is the first request I've had for a Linux version, so I haven't >> given much thought to it. If others also have interest, please email me >> directly. Make sure to mention which distro you are using. >> >> Thanks, >> >> Adam >> >> >> On Wed, Jan 22, 2014 at 11:39 AM, Salter-Duke, Brian James >> brian.james.duke(-)gmail.com

> > wrote: >> >> Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke^^gmail.com< >> http://gmail.com>] >> This looks like a usefull program. However, is there any prospect of a >> Linux version for those of us who only use Linux? >> >> Brian Duke. >> >> On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A! >> gmail.com wrote: >> > I am pleased to announce the release of QMForge 2.3.1, which is a >> > cross-platform, open-source program for interpreting and analyzing the >> > results of QM calculations. >> > >> > QMForge 2.3.1 builds upon the previous versions with the addition of the >> > following features: >> > >> > * Plots of Convergence and Energy in the Geometry Optimization tab, >> > * Plots of IR and/or Raman spectra in the Frequency Tab, >> > * Ability to save the normal modes of a Frequency calculation as >> animated >> > GIFs, >> > * Gross Population Analysis to compare Mulliken and Lowdin populations >> and >> > spin densities for each atom and orbital >> > >> > Other notable features include: >> > >> > * The support of several QM output formats including Gaussian, ADF, >> GAMESS >> > (and its various derivatives), Jaguar, and ORCA, >> > * Population analyses such as Mulliken, Lowdin, C-squared, and Overlap >> on >> > user-defined sets ("fragments") of basis functions, >> > * Fragment Analysis to interpret the contributions of fragment MOs to >> > molecular MOs, >> > * Charge Decomposition Analysis, >> > * Mayer's bond orders, >> > * Visualization of every step in a geometry optimization, with the >> ability >> > to save any of those structures as XYZ or PDB files, >> > * A simple, yet powerful, XYZ editor with tools that allow translations >> > and rotations to align bonds to specific axes, >> > * Animation of the normal modes of a frequency calculation, and >> > * A plot of electronic transitions and a easy-to-read list of the >> > corresponding orbital excitations from TDDFT/CIS calculations. >> > >> > I encourage you to visit http://qmforge.sourceforge.net to see >> screenshots >> > that demonstrate the various capabilities. On that page, you will also >> find >> > links to download pre-packaged Windows and Mac OS X binaries, as well as >> > links to the source code. >> > >> > Sincerely, >> > >> > Adam Tenderholt >> -- >> Brian Salter-Duke (Brian Duke) Brian.Salter-Duke---monash.edu< >> http://Brian.Salter-Duke---monash.edu> >> Adjunct Associate Professor >> Monash Institute of Pharmaceutical Sciences >> Monash University Parkville Campus, VIC 3052, Australia
> >> >> E-mail to subscribers: CHEMISTRY!A!ccl.net >> or use:E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net> CHEMISTRY-REQUEST!A!ccl.net> or usehttp:// >> www.ccl.net/chemistry/sub_unsub.shtml >> > Content-Type: text/html; charset"us-ascii" >> Content-Transfer-Encoding: quoted-printable >> >> > xmlns:o="urn:schemas-microsoft-com:office:office" >> xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m=" >> http://schemas.microsoft.com/office/2004/12/omml" xmlns=" >> http://www.w3.org/TR/REC-html40"> >> >> >> >> >> >> >>

> style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I >> for one would like access to a linux version of the source code as >> well. I imagine that there would be more users in the linux realm >> than the mac and windows >> combined.

> style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Brian >> Bennion

> style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">

> style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:> style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> >> owner-chemistry+bennion1==llnl.gov]_[ccl.net [mailto:owner-chemistry& >> #43;bennion1==llnl.gov]_[ccl.net] >> On Behalf Of Adam Tenderholt atenderholt(_)gmail.com
>> Sent: Wednesday, January 22, 2014 2:13 PM
>> To: Bennion, Brian
>> Subject: CCL:G: Announcement: QMForge 2.3.1

This is the first request I've had for a Linux >> version, so I haven't given much thought to it. If others also have >> interest, please email me directly. Make sure to mention which distro you >> are using.

Thanks,

Adam

On Wed, Jan 22, 2014 at 11:39 AM, Salter-Duke, Brian >> James brian.james.duke(-)gmail.com <> href="mailto:owner-chemistry!A!ccl.net" >> target="_blank">owner-chemistry!A!ccl.net> wrote:

>> Sent to CCL by: "Salter-Duke, Brian James " >> [brian.james.duke^^gmail.com >> ]
>> This looks like a usefull program. However, is there any prospect of a
>> Linux version for those of us who only use Linux?
>>
>> Brian Duke.

>> On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt >> atenderholt!A!gmail.com >> wrote:
>> > I am pleased to announce the release of QMForge 2.3.1, which is a
>> > cross-platform, open-source program for interpreting and analyzing >> the
>> > results of QM calculations.
>> >
>> > QMForge 2.3.1 builds upon the previous versions with the addition of >> the
>> > following features:
>> >
>> > * Plots of Convergence and Energy in the Geometry Optimization >> tab,
>> > * Plots of IR and/or Raman spectra in the Frequency Tab,
>> > * Ability to save the normal modes of a Frequency calculation as >> animated
>> > GIFs,
>> > * Gross Population Analysis to compare Mulliken and Lowdin >> populations and
>> > spin densities for each atom and orbital
>> >
>> > Other notable features include:
>> >
>> > * The support of several QM output formats including Gaussian, >> ADF, GAMESS
>> > (and its various derivatives), Jaguar, and ORCA,
>> > * Population analyses such as Mulliken, Lowdin, C-squared, and >> Overlap on
>> > user-defined sets ("fragments") of basis functions,
>> > * Fragment Analysis to interpret the contributions of fragment >> MOs to
>> > molecular MOs,
>> > * Charge Decomposition Analysis,
>> > * Mayer's bond orders,
>> > * Visualization of every step in a geometry optimization, with >> the ability
>> > to save any of those structures as XYZ or PDB files,
>> > * A simple, yet powerful, XYZ editor with tools that allow >> translations
>> > and rotations to align bonds to specific axes,
>> > * Animation of the normal modes of a frequency calculation, >> and
>> > * A plot of electronic transitions and a easy-to-read list of >> the
>> > corresponding orbital excitations from TDDFT/CIS calculations.
>> >
>> > I encourage you to visit > target="_blank"> >> http://qmforge.sourceforge.net to see screenshots
>> > that demonstrate the various capabilities. On that page, you will >> also find
>> > links to download pre-packaged Windows and Mac OS X binaries, as >> well as
>> > links to the source code.
>> >
>> > Sincerely,
>> >
>> > Adam Tenderholt

--
>> Brian Salter-Duke (Brian Duke) >> Brian.Salter-Duke---monash.edu
>> >> Adjunct Associate Professor
>> Monash Institute of >> Pharmaceutical Sciences
>> Monash University Parkville Campus, VIC 3052, >> Australia
>>
>>
>>
>> -= This is automatically added to each message by the mailing script >> =- >
>>
>> E-mail to subscribers: CHEMISTRY!A! >> ccl.net or use:
>>
>>
>> E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net or use
>>
>>
>> Subscribe/Unsubscribe:
>>
>>
>> Before posting, check wait time at: > target="_blank"> >> http://www.ccl.net
>>
>> Job: >> http://www.ccl.net/jobs
>> Conferences: > target="_blank"> >> http://server.ccl.net/chemistry/announcements/conferences/
>>
>> Search Messages: >> http://www.ccl.net/chemistry/searchccl/index.shtml
>> > > target="_blank">http://www.ccl.net/spammers.txt
>>
>> RTFI: > target="_blank"> >> http://www.ccl.net/chemistry/aboutccl/instructions/
>>
>>

>> >> >> > > --089e01160174bc556504f09ac449 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

I'll just add a few other pointers:

* OpenBabel and its Python bindings are required for saving structures (XY= Z, PDB, etc.); this was probably the first bullet after Python 2.7

* PIL is required for saving animated GIFs

* If you want version = v2.3.1, make sure you checkout the 2.3 branch. I haven't tagged the new= est version yet.

Adam

On Wed,= Jan 22, 2014 at 5:32 PM, Billy McCann thebillywayne]|[gmail.com <owner-chemistry^ccl.net> wrote= :

For linux users, the source can = be obtained via

git clone git://git.code.sf.net/p/qmforge/git-code qmforge-git-code
Installs cleanly with
*Python 2.7
=A0=A0 *cclib (git version, = requires swig to build)
=A0=A0 *pyqt4
=A0=A0 *numpy
=A0=A0 *cclib<= br>=A0=A0 *pyqwt (requires qmake to build. it looks for /usr/bin/qmake. On = Arch Linux, it's in /usr/lib/qt4/bin/qmake. symlink it)
=A0=A0 *PyOpenGL built against it
*Qt4

I installed pyqt4, numpy,= pyopengl using pip to fetch from PyPI. The cclib in PyPI wasn't playin= g nicely. Pull it from github.=A0 I compiled pyqwrt after downloading it fr= om their website (requires qmake).

I'm pretty sure you can find Qt4 in your distro's repositories= .=A0 In any case, you should already be using KDE. :)

Qmake 2.01a
GCC 4.8.2 20131219 (prerelease)
Linux 3.12.8
<= div class=3D"gmail_default" style=3D"font-family:verdana,sans-serif"> x86_64 bit architecture

Kind regards,

Billy Wayne McCann, Ph.D.
Google+

PGP Key

irc://irc.freenode.net:= bwayne

"A rich man will always desire what his wealth ca= nnot acquire." ~ Faust (Goethe)

[00(01|10)11]

<= /div>

On Wed, Jan 22, 2014 at 6:08 PM, Bennion= , Brian Bennion1],[llnl.gov <owner-chemistry[#]ccl.net> wrote:

I for one would like access to a linux versi= on of the source code as well. =A0I imagine that there would be more users = in the linux realm than the mac and windows combined.
Brian Bennion

> From: owner-chemistry+bennion1=3D=3Dllnl.gov]_[ccl= .net [mailto:owner-chemistry+bennion1=3D=3Dllnl.gov]_[ccl= .net] On Behalf Of Adam Tenderholt atenderholt(_)gmail.com
Sent: Wednesday, January 22, 2014 2:13 PM
To: Bennion, Brian
Subject: CCL:G: Announcement: QMForge 2.3.1

This is the first request I've had for a Linux version, so I haven'= t given much thought to it. If others also have interest, please email me d= irectly. Make sure to mention which distro you are using.

Thanks,

Adam

On Wed, Jan 22, 2014 at 11:39 AM, Salter-Duke, Brian James brian.jame= s.duke(-)gmail.com<http://gmail.com> <o= wner-chemistry!A!ccl.net&l= t;mailto:owner-chemist= ry!A!ccl.net>> w= rote:

Sent to CCL by: "Salter-Duke, Brian James " [brian.james.duke^^gmail.com<http://gmail.com>]

This looks like a usefull program. However, is there any prospect of a=
Linux version for those of us who only use Linux?

Brian Duke.

On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt a= tenderholt!A!gmail.com&l= t;http://gmail.com> w= rote:
> I am pleased to announce the release of QMForge 2.3.1, which is a
> cross-platform, open-source program for interpreting and analyzing the=
> results of QM calculations.
>
> QMForge 2.3.1 builds upon the previous versions with the addition of t= he
> following features:
>
> * Plots of Convergence and Energy in the Geometry Optimization tab, > * Plots of IR and/or Raman spectra in the Frequency Tab,
> * Ability to save the normal modes of a Frequency calculation as anima= ted
> GIFs,
> * Gross Population Analysis to compare Mulliken and Lowdin populations= and
> spin densities for each atom and orbital
>
> Other notable features include:
>
> =A0* The support of several QM output formats including Gaussian, ADF,= GAMESS
> (and its various derivatives), Jaguar, and ORCA,
> =A0* Population analyses such as Mulliken, Lowdin, C-squared, and Over= lap on
> user-defined sets ("fragments") of basis functions,
> =A0* Fragment Analysis to interpret the contributions of fragment MOs = to
> molecular MOs,
> =A0* Charge Decomposition Analysis,
> =A0* Mayer's bond orders,
> =A0* Visualization of every step in a geometry optimization, with the = ability
> to save any of those structures as XYZ or PDB files,
> =A0* A simple, yet powerful, XYZ editor with tools that allow translat= ions
> and rotations to align bonds to specific axes,
> =A0* Animation of the normal modes of a frequency calculation, and
> =A0* A plot of electronic transitions and a easy-to-read list of the > corresponding orbital excitations from TDDFT/CIS calculations.
>
> I encourage you to visit http://qmforge.sourceforge.net to see screenshots
> that demonstrate the various capabilities. On that page, you will also= find
> links to download pre-packaged Windows and Mac OS X binaries, as well = as
> links to the source code.
>
> Sincerely,
>
> Adam Tenderholt
--

=A0 =A0Brian Salter-Duke (Brian Duke) =A0 Brian.Salter-Duke---monash.e= du<http://Brian.Salter-Duke---monash.edu>

=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Adjunct Associate Professor =A0 =A0 =A0 =A0 =A0 =A0 Monash Institute of Pharmaceutical Sciences
=A0 =A0 =A0 Monash University Parkville Campus, VIC 3052, Australia

-=3D This is automatically added to each message by the mailing scrip= t =3D- = or use:E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net<mailto:CHEMISTRY-REQUEST!A!ccl.net> or usehttp://www.ccl.net/chemistry/sub_= unsub.shtml<br--_000_2FD898B2B3ACB44289F398FACE042B4A3A15C0F8PRDEXMB= X02thela_
Content-Type: text/html; charset"us-ascii"
Content-Transfer-Encoding: quoted-printable

<html xmlns:v=3D"urn:schemas-microsoft-com:vml" xmlns:o=3D&quo= t;urn:schemas-microsoft-com:office:office" xmlns:w=3D"urn:schemas= -microsoft-com:office:word" xmlns:m=3D"http://schemas.microso= ft.com/office/2004/12/omml" xmlns=3D"http://www.w3.org/TR/REC-html40&q= uot;>
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<meta http-equiv=3D"Content-Type" content=3D"text/html; c= harset=3Dus-ascii">
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</head>
<body lang=3D"EN-US" link=3D"blue" vlink=3D"pur= ple">
<div class=3D"WordSection1">
I for one would like access to a linux version of th= e source code as well.  I imagine that there would be more users i= n the linux realm than the mac and windows
=A0combined.<o:p></o:p>
Brian Bennion<o:p></o:p><= ;/p>
<o:p> </o:p></p= >
From: owner-chemistry+bennion1=3D=3Dllnl.gov]_[ccl.net [mailto:owner-chemistry+bennion1=3D=3Dllnl.gov]_[ccl.net]
On Behalf Of Adam Tenderholt atenderholt(_)gmail.com 
Sent: Wednesday, January 22, 2014 2:13 PM 
To: Bennion, Brian 
Subject: CCL:G: Announcement: QMForge 2.3.1<o:p>&l= t;/o:p>
<o:p> </o:p><= ;/p>
<div>
This is the first request I've h= ad for a Linux version, so I haven't given much thought to it. If other= s also have interest, please email me directly. Make sure to mention which = distro you are using. <o:p></o:p>
<div>
<o:p> </o:p><= ;/p>
</div>
<div>
Thanks,<o:p></o:p></p= >
</div>
<div>
<o:p> </o:p><= ;/p>
</div>
<div>
Adam<o:p></o:p>= ;
</div>
<div>
<o:p> </o:p><= ;/p>
</div>
</div>
<div>
<o:p> </o:p>
<div>
On Wed, Jan 22, 2014 at 11:39 AM, Sa= lter-Duke, Brian James brian.james.duke(-)<a href=3D"http://gmail.com">gmail.com</a> <<a hr= ef=3D"mailto:owne= r-chemistry!A!ccl.net&= quot; target=3D"_blank">owner-chemistry!A!ccl.net</a>> wrote:<o:p><= ;/o:p>
 
Sent to CCL by: "Salter-Duke, Brian James " [brian.james.= duke^^<a href=3D"htt= p://gmail.com" target=3D"_blank">gmail.com</a>] 
This looks like a usefull program. However, is there any prospect of a<b= r>
Linux version for those of us who only use Linux? 
 
Brian Duke.<o:p></o:p>
<div>
<div>
 
On Wed, Jan 22, 2014 at 08:43:00AM -0800, Adam Tenderholt atenderholt!A!<= ;a href=3D"http://gmail= .com" target=3D"_blank">gmail.com</a> wrote: 
> I am pleased to announce the release of QMForge 2.3.1, which is a&= lt;br>
> cross-platform, open-source program for interpreting and analyzing= the 
> results of QM calculations. 
> 
> QMForge 2.3.1 builds upon the previous versions with the addition = of the 
> following features: 
> 
> * Plots of Convergence and Energy in the Geometry Optimization tab= , 
> * Plots of IR and/or Raman spectra in the Frequency Tab, =
> * Ability to save the normal modes of a Frequency calculation as a= nimated 
> GIFs, 
> * Gross Population Analysis to compare Mulliken and Lowdin populat= ions and 
> spin densities for each atom and orbital 
> 
> Other notable features include: 
> 
>  * The support of several QM output formats including Gau= ssian, ADF, GAMESS 
> (and its various derivatives), Jaguar, and ORCA, 
>  * Population analyses such as Mulliken, Lowdin, C-square= d, and Overlap on 
> user-defined sets ("fragments") of basis functio= ns, 
>  * Fragment Analysis to interpret the contributions of fr= agment MOs to 
> molecular MOs, 
>  * Charge Decomposition Analysis, 
>  * Mayer's bond orders, 
>  * Visualization of every step in a geometry optimization= , with the ability 
> to save any of those structures as XYZ or PDB files, 
>  * A simple, yet powerful, XYZ editor with tools that all= ow translations 
> and rotations to align bonds to specific axes, 
>  * Animation of the normal modes of a frequency calculati= on, and 
>  * A plot of electronic transitions and a easy-to-read li= st of the 
> corresponding orbital excitations from TDDFT/CIS calculations.<= br>
> 
> I encourage you to visit <a href=3D"http://qmforge.sourceforge.net&q= uot; target=3D"_blank">
http://qmforge= .sourceforge.net</a> to see screenshots 
> that demonstrate the various capabilities. On that page, you will = also find 
> links to download pre-packaged Windows and Mac OS X binaries, as w= ell as 
> links to the source code. 
> 
> Sincerely, 
> 
> Adam Tenderholt<o:p></o:p>
</div>
</div>
-- 
   Brian Salter-Duke (Brian Duke)   <a href= =3D"http://Brian.Salter-Duke---monash.edu" target=3D"_blank&quo= t;>
Brian.S= alter-Duke---monash.edu</a> 
            &nbsp= ;       Adjunct Associate Professor             Monash In= stitute of Pharmaceutical Sciences 
      Monash University Parkville Campus, VIC 30= 52, Australia 
 
 
 
-=3D This is automatically added to each message by the mailing script =3D-= <br 
 
 
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Call for Papers <= /h1>

European User Group Meeting (UGM) May 20^<=
small>th-21^st

Call for Papers <= /h1>

European User Group Meeting (UGM) May 20<= small>th-21st

European User Group Meeting (UGM) May 20^<=
small>th-21^st