From owner-chemistry@ccl.net Thu May 26 05:06:00 2011 From: "James Womack james.c.womack,,gmail.com" To: CCL Subject: CCL: shell script books Message-Id: <-44755-110526050007-10639-2S2NfeZBnB4bywAoHJMPQQ-*-server.ccl.net> X-Original-From: James Womack Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="UTF-8" Date: Thu, 26 May 2011 09:59:47 +0100 Mime-Version: 1.0 Sent to CCL by: James Womack [james.c.womack*o*gmail.com] I have found "UNIX in a nutshell" to be a good reference book for shell scripting. Here's a link to the publisher's description: http://oreilly.com/catalog/9781565924277 -- James C. Womack PhD research student School of Chemistry University of Bristol BRISTOL BS8 1TS Email: james.c.womack:-:bristol.ac.uk -- On Wed, 2011-05-25 at 18:59 +0200, Valentín Alba Aparicio valentin.alba-$-pas.uned.es wrote: > Sent to CCL by: =?ISO-8859-1?Q?Valent=EDn_Alba_Aparicio?= > [valentin.alba-#-pas.uned.es] > The term "shell scripting" involve multiple languages and tools: bash, > cshell, awk, sed, perl... > > There are plenty of information available on the web, even on different > languages. > > I suggest you to start up visiting the following URL: > http://tldp.org/ > where you can find free books, guides, tutorials and howtos. > > Hope it helps! > Val > > El 25/05/11 13:21, hirdesh kumar hirdeshs8**gmail.com escribió: > > Hi All, > > I am beginner to programming field, interested in learning the shell > > scripting. Please suggest me some good books. > > > > Thanks > > Hirdesh > > > > --> > From owner-chemistry@ccl.net Thu May 26 07:03:00 2011 From: "Thomas Mitterfellner thomas.mitterfellner__tugraz.at" To: CCL Subject: CCL: Spectral Deconvolution Software Message-Id: <-44756-110526053317-18528-As/FOBGnOJQ9jqxGeD/meg~~server.ccl.net> X-Original-From: Thomas Mitterfellner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 26 May 2011 11:33:05 +0200 MIME-Version: 1.0 Sent to CCL by: Thomas Mitterfellner [thomas.mitterfellner##tugraz.at] Hello! fityk is quite good at that. I used it for fitting overlapping peaks to UV curves. http://fityk.nieto.pl/ Kind regards, Thomas From owner-chemistry@ccl.net Thu May 26 08:07:00 2011 From: "Pradeep Kumar Gurunathan geepradeep]_[gmail.com" To: CCL Subject: CCL:G: CASSCF - Transition Dipole Moments Message-Id: <-44757-110526005915-18444-G2a39anfKjDUeqjnOtizCQ!=!server.ccl.net> X-Original-From: "Pradeep Kumar Gurunathan" Date: Thu, 26 May 2011 00:59:13 -0400 Sent to CCL by: "Pradeep Kumar Gurunathan" [geepradeep ~ gmail.com] Dear Sir, I am using CASSCF calculations for computing the properties in excited states. I would like to know how to extract the information regarding transition dipole moments for these molecules. For example, I would like to compute the transition dipole moment (or oscillator strength) from ground to the first excited state. How do I proceed? Kindly suggest. Regards, Pradeep Kumar Gurunathan. Version: Gaussian03 Architecture: Linux/Ubuntu-x86 Pradeep Kumar Gurunathan, Summer Intern Fellow, University of Hyderabad, Hyderabad - 500046. INDIA. From owner-chemistry@ccl.net Thu May 26 08:42:01 2011 From: "Tschijnmo Tschau tschijnmotschau : gmail.com" To: CCL Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN? Message-Id: <-44758-110526063724-10578-iuhTQn2FpfQCL0g+OMqxjw,+,server.ccl.net> X-Original-From: Tschijnmo Tschau Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 26 May 2011 18:37:16 +0800 MIME-Version: 1.0 Sent to CCL by: Tschijnmo Tschau [tschijnmotschau:-:gmail.com] Please excuse me for being a newcomer wanting to ask some basic questions. I am new to C++ and found that indeed it has a lot of convenient language features and a rich pool of libraries. But it seems that for numerical problems in computational chemistry, in C++ there do not seem to be some quite established and stable libraries like BLAS, LAPACK, etc, which can be highly optimized, yet. In spite of the fact that storing everything in one-dimensional arrays according to the column major rule and calling external Fortran subroutines directly is able to work and seems to have been used in ORCA, it still seems to be a somewhat awkward way to do that. Maybe the usage of some reliable C++ libraries can appear as a better solution. But the seemingly reliable TNT library by NIST seems to have offered a rather narrow spectrum of functionality, there is even no function to obtain the pointer to the memory location where actual data lies, which might be very important for interoperation with existing Fortran code. Eigen seems to have such a function, but I a little wonder if it is stable and reliable enough to be used in serious big projects, and it is not possible to utilize external optimized BLAS libraries, at least currently, and the API might will undergo major modification still. The boost library seems to have several parts for numerics, but the uBLAS library seems to be quite inefficient, while the promising GLAS library seems to be still under development, which seems to have been stagnant for quite a long time. So is the Flens library, which also seems to be out of maintenance. And the library with the MPQC project also seems to be out of maintenance years long along with the MPQC project. So, could anyone help me with the problem, which numerical library should I use if I really want to do something seriously in C++? Thank you so much. Also there is another problem with non-numerics. The boost library is indeed very rice and profound. But when I had a try with the spirit parsing library, which seems to be quite convenient, a coupled of lines of code induced cryptic error information screen after screen. Could anyone suggest some reading materials for people new to template generic programming and the BOOST library, so that a less painful learning curve can be possible? I think that maybe answers to the two questions can be of great help to other new-comers as well, hence asked here. I am really grateful to any suggestion. Thank you! On Sun, May 8, 2011 at 7:17 AM, uekstrom..gmail.com uekstrom..gmail.com wrote: > > Sent to CCL by: "uekstrom/a\gmail.com" [uekstrom/a\gmail.com] >>> If you know what you are doing it's possible to write efficient C++ >>> code as well. On the other hand there are many things which are almost >>> impossible to program in Fortran, >> >> Which ones are impossible ??? >> Almost impossible means possible. Once adequates routines are done, >> anything becomes easy (bit access, string handling functions, etc.). > > Of course since both Fortran and C(++) are Turing complete anything is > possible (except in F77 where pointers are not standardized). > > Here are some almost impossible things: Destructors were not available > prior to Fortran 2003, which made it difficult to deal with resources > with something like resource-acquisition-is-initialization. Is garbage > collection at all possible? I still don't know to make my own memory > allocator in Fortran 2003, which there might be very good reasons to > do in large programs that use almost all system memory. Is it > possible? Can I do templates in Fortran? > > Saying that "anything becomes easy" in Fortran is simply ridiculous > when you compare to C++ with Boost which is an incredibly rich and > well designed library.  If anything it's an afternoon of work in C++ > to wrap BLAS with an interface that lets you use 1-based indexing and > allows you to do slices. This has the advantage over plain Fortran > that you are guaranteed a certain performance of the matrix > multiplication routines. > >>> so you may save a lot of time programming in C++. >> >> Not true for many numerical algorithms programming. >> The indices starting from 0 in C/C++ are a nightmare for matrix >> calculus and other applications. > > This is probably true, although once you start dealing with abstract > types such as sparse matrices the differences disappears. If you are > allowed to make your own library of functions in Fortran I will use my > BLAS wrapper for C+++, which can easily use 1-based indexing if you so > desire. It has the advantage that you know exactly which BLAS you get > :-) > >>> Also, since the Fortran market is >>> so small the C++ compilers are much less buggy, >> >> Is there data to support that ? >> I would be delighted to know about bugs for actual fortran compilers. > > Unfortunately I am not making this up, for every few releases of Ifort > there is typically something that goes wrong, specially with -O3 and > inter-procedural optimizations turned on. Some of this is clear > mis-compilation or internal compiler error, some of it is hard to > diagnose for large old programs that may contain bugs. This is my > experience with Dalton, Dirac and once commercial program. > > [..] > >> My opinion is that working the algorithms (complexity, precision) is >> by far much more important rather than having an optimizer producing >> the best results. > > Indeed. But the OP was asking about why some new quantum chemistry > programs are written in C++. I think the answer is that when you write > a large program with many modules then things which are awkward in > Fortran become more and more of a problem. Numerics is not everything, > although Fortran makes you believe that this is the case. > > Sincerely, > Ulf>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu May 26 09:18:01 2011 From: "Andras Borosy andras.borosy|*|givaudan.com" To: CCL Subject: CCL: shell script books Message-Id: <-44759-110526031622-18678-a+zYzsxYFqFaonewi6+Hmg ~~ server.ccl.net> X-Original-From: Andras Borosy Content-Type: multipart/alternative; boundary="=_alternative 0027ECAAC125789C_=" Date: Thu, 26 May 2011 09:16:12 +0200 MIME-Version: 1.0 Sent to CCL by: Andras Borosy [andras.borosy*givaudan.com] This is a multipart message in MIME format. --=_alternative 0027ECAAC125789C_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Many thanks, it looks really good! Best wishes, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "Vincent Leroux vincent.leroux^=5F^loria.fr" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com[]ccl.net 25.05.2011 15:40 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: shell script books Sent to CCL by: Vincent Leroux [vincent.leroux*loria.fr] Hi, This one is really excellent, I highly recommend it: Classic Shell Scripting Arnold Robbins, Nelson H.F. Beebe O'Reilly Regards VL Le 25/05/11 13:21, hirdesh kumar hirdeshs8**gmail.com a =E9crit : > Hi All, > I am beginner to programming field, interested in learning the shell > scripting. Please suggest me some good books. > > Thanks > Hirdesh > > -- > -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessagehttp://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage Subscribe/Unsubscribe:=20 http://www.ccl.net/chemistry/sub=5Funsub.shtmlJob: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--=_alternative 0027ECAAC125789C_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Many thanks, it looks really good!

Best wishes,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com



"Vincent Leroux = vincent.leroux^=5F^loria.fr" <owner-chemistry[]ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com[]ccl.net

25.05.2011 15:40
Please respond to
"CCL Subscribers" <chemistry[]ccl.net>
To
"Borosy, Andras " <andras.borosy[]givaudan.com>
cc
Subject
CCL: shell script books





Sent to CCL by: Vincent Leroux [vincent.leroux*loria.fr]
Hi,

This one is really excellent, I highly recommend it:

Classic Shell Scripting
Arnold Robbins, Nelson H.F. Beebe
O'Reilly

Regards
VL



Le 25/05/11 13:21, hirdesh kumar hirdeshs8**gmail.com a =E9crit :
> Hi All,
> I am beginner to programming field, interested in learning the shell > scripting. Please suggest me some good books.
>
> Thanks
> Hirdesh
>
> --
>



-=3D This is automatically added to each message by the mailing script =3D-=      http://www.ccl.net/cgi-bin/ccl/send=5Fccl=5Fmessage
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--=_alternative 0027ECAAC125789C_=-- From owner-chemistry@ccl.net Thu May 26 09:53:00 2011 From: "=?ISO-8859-1?Q?Valent=EDn_Alba_Aparicio?= valentin.alba{}pas.uned.es" To: CCL Subject: CCL:G: Spectral Deconvolution Software Message-Id: <-44760-110526030605-24651-Qda366XXAoDy4vYlBWwkIA]-[server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Valent=EDn_Alba_Aparicio?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 26 May 2011 09:06:02 +0200 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Valent=EDn_Alba_Aparicio?= [valentin.alba_._pas.uned.es] You have the following free tools: Fityk: http://www.unipress.waw.pl/fityk/ JSpecView: http://jspecview.sourceforge.net/ CrystalSleuth: http://rruff.info/about/about_download.php Spekwin32: http://www.effemm2.de/spekwin/index_en.html ShowSP: http://www.epa.gov/ttn/emc/ftir/showspc.html Or these commercial ones: Origin by http://www.originlab.com GRAMS/32 AI by Galactic Industries Corporation I extremely suggest you the first one: Fityk, it's superb! Hope it helps! Val El 25/05/11 22:15, Joe Golab joseph.golab]=[ineos.com escribió: > Sent to CCL by: "Joe Golab" [joseph.golab*|*ineos.com] > I am looking for a program (share/ freeware would be ideal) that can do non-linear curve fitting to X-Y data. > > Specifically, I want to deconvolute a curve (like UV-Vis absorbance data) into component Gaussian curves. > > If there is an application that has been developed for MathCad, I could use that; reliable applications on the web would be okay as well. > > I am not looking for a (costly) spectroscopy software suite, just the curve fitting part. > > Suggestions are appreciated. > > Thanks. > > Joe Golab > Senior Research Associate > INEOS Technologies, Nitriles R&D > Email: Joseph.Golab_at_ineos.com> > > From owner-chemistry@ccl.net Thu May 26 10:27:00 2011 From: "Eustis Soren soren.eustis[-]env.ethz.ch" To: CCL Subject: CCL: Spectral Deconvolution Software Message-Id: <-44761-110526081249-30240-Tjr/qfxC1E3e0wIUzAt2Sg++server.ccl.net> X-Original-From: "Eustis Soren" Content-ID: <7C5FE286650413488FC163C79AAC7E85++intern.ethz.ch> Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 26 May 2011 12:12:40 +0000 MIME-Version: 1.0 Sent to CCL by: "Eustis Soren" [soren.eustis*|*env.ethz.ch] Greetings, I second Thomas' vote for Fityk. There are new versions out that are available for a fee, but there are still beta versions available for free. The program works on all systems, and it is quite robust. I have used is for fitting all sorts of different types of data, and it is quite easy to add functions to the already large function library. Marcin, the developer, is quite responsive and knowledgeable as well. Best, Soren Soren N. Eustis, Ph.D. ETH ­ Zürich Environmental Organic Chemistry Group Institute for Biogeochemistry and Pollutant Dynamics Universitatstrasse 16 CHN F33 8092 ZürichSWITZERLAND +41 44 632 93 48 (office) +41 44 632 14 38 (fax) soren[]env.ethz.ch On 5/26/11 11:33 , "Thomas Mitterfellner thomas.mitterfellner__tugraz.at" wrote: > >Sent to CCL by: Thomas Mitterfellner [thomas.mitterfellner##tugraz.at] >Hello! > >fityk is quite good at that. I used it for fitting overlapping peaks to >UV curves. > >http://fityk.nieto.pl/ > >Kind regards, > >Thomas> > From owner-chemistry@ccl.net Thu May 26 11:37:00 2011 From: "Gerald Knizia knizia-*-theochem.uni-stuttgart.de" To: CCL Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN? Message-Id: <-44762-110526110356-12046-sd3I4UxXtGTQDBdiwicT9w*_*server.ccl.net> X-Original-From: Gerald Knizia Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 26 May 2011 11:03:48 -0400 MIME-Version: 1.0 Sent to CCL by: Gerald Knizia [knizia{:}theochem.uni-stuttgart.de] Tschijnmo Tschau tschijnmotschau : gmail.com wrote: > Sent to CCL by: Tschijnmo Tschau [tschijnmotschau:-:gmail.com] > Please excuse me for being a newcomer wanting to ask some basic > questions. I am new to C++ and found that indeed it has a lot of > convenient language features and a rich pool of libraries. But it > seems that for numerical problems in computational chemistry, in C++ > there do not seem to be some quite established and stable libraries > like BLAS, LAPACK, etc, which can be highly optimized, yet. This is indeed the case. My rather elaborate search for a reliable linear algebra library also turned up with no results. Everything out there has massive defect. You're basically bound to wrappers for BLAS and LAPACK. Don't try anything else, you'll only waste time. libflame (http://z.cs.utexas.edu/wiki/flame.wiki/FrontPage ) may at some future point in time become competitive with LAPACK, but that's still a long way. > Also there is another problem with non-numerics. The boost library is > indeed very rice and profound. But when I had a try with the spirit > parsing library, which seems to be quite convenient, a coupled of > lines of code induced cryptic error information screen after screen. > boost::spirit is also a waste of time. It can only generate trivial parsers, and getting *anything* to actually work requires more time than simply writing the parsers by hand (and I mean *anything*, not necessarily the thing you really want). I tried it two times, and I've given up. Maybe the best proof that spirit is pointless comes with boost itself: Try compiling boost::wave (a C-preprocessor written with spirit). A few years ago this still generated 2 GB (!!!) of object files and required >1h compilation time *for a C preprocessor*. In short: If you want parsers, writing them by hand is usually the fastest and easiest method. Go for LR-parsers if possible, these are very powerful and easiest to hand-write. > Could anyone suggest some reading materials for people new to template > generic programming and the BOOST library, so that a less painful > learning curve can be possible? These things are discussed in many advanced C++ textbooks. However, note that while template meta-programming may sound exciting at first, in most cases you will get better and simpler-to-maintain code in a quicker time when avoiding it. C++ is really not a functional programming language, and while you CAN program it like that, there rarely is a good reason to do it. Look into boost::spirit or boost::lambda and try to understand their error messages if you want to know why. -- Gerald Knizia From owner-chemistry@ccl.net Thu May 26 12:12:00 2011 From: "quartarolo-#-unical.it" To: CCL Subject: CCL:G: Spectral Deconvolution Software Message-Id: <-44763-110526074137-6574-fHCrGHo0rsawQxH2erEMuQ[a]server.ccl.net> X-Original-From: quartarolo:-:unical.it Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 26 May 2011 13:41:08 +0200 MIME-Version: 1.0 Sent to CCL by: quartarolo||unical.it Hi, Look at: http://www.sg-chem.net/swizard/. It's a free Windows software and reads different quantum chemistry software outputs (including free format). Or at www.chemissian.com/. You can download a trial version. best regards Quartarolo Domenico Department of Chemistry Università della Calabria, Rende (Italy) > I am looking for a program (share/ freeware would be ideal) that can > do non-linear curve fitting to X-Y data. > > Specifically, I want to deconvolute a curve (like UV-Vis absorbance > data) into component Gaussian curves. > > If there is an application that has been developed for MathCad, I > could use that; reliable applications on the web would be okay as > well. > > I am not looking for a (costly) spectroscopy software suite, just > the curve fitting part. > > Suggestions are appreciated. > > Thanks. > > Joe Golab > Senior Research Associate > INEOS Technologies, Nitriles R&D > Email: Joseph.Golab_at_ineos.com> > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. **** Riservatezza / Confidentiality **** In ottemperanza al D.Lgs. n. 196 del 30/6/2003 in materia di protezione dei dati personali, le informazioni contenute in questo messaggio sono strettamente riservate ed esclusivamente indirizzate al destinatario indicato (oppure alla persona responsabile di rimetterlo al destinatario). Vogliate tener presente che qualsiasi uso, riproduzione o divulgazione di questo messaggio e' vietato. Nel caso in cui aveste ricevuto questo messaggio per errore, vogliate cortesemente avvertire il mittente e distruggere il presente messaggio. From owner-chemistry@ccl.net Thu May 26 12:47:00 2011 From: "jacques denis jacquedenis**live.com" To: CCL Subject: CCL: MD simulations with CPMD Message-Id: <-44764-110526093707-8712-6pHpHtpOYFe8DRe/sX48wA/./server.ccl.net> X-Original-From: "jacques denis" Date: Thu, 26 May 2011 09:37:05 -0400 Sent to CCL by: "jacques denis" [jacquedenis|a|live.com] Dear all, I am new in the MD simulations and I am looking to run MD jobs with the CPMD program, any help to start will be appreciate Thanks From owner-chemistry@ccl.net Thu May 26 13:22:00 2011 From: "Vladimir Banovic omnivoyager+/-hotmail.com" To: CCL Subject: CCL: ONIOM link atom charge Message-Id: <-44765-110526103346-16105-UGDCcJVilowrepIFmAWPkQ . server.ccl.net> X-Original-From: "Vladimir Banovic" Date: Thu, 26 May 2011 10:33:45 -0400 Sent to CCL by: "Vladimir Banovic" [omnivoyager++hotmail.com] Does anybody know how to set the (MM) link atom charges in an ONIOM (QM/MM) calculation? Should they: a) mimic the the MM atom host charges in the real system? b) mimic the charge of the link atom in the QM model system? (since the link atom in the MM calculation of the model system is a correction to the QM link atom energy) or C) a different approach? Many thanks! Vladimir Banovic From owner-chemistry@ccl.net Thu May 26 13:56:00 2011 From: "James Justin Robinson jameschums*_*yahoo.com" To: CCL Subject: CCL: Program languages in Qunatum Chemistry (C++, Fortran) Message-Id: <-44766-110526114203-23539-B4jnB1a3r92AZNFFflyiRw]^[server.ccl.net> X-Original-From: "James Justin Robinson" Date: Thu, 26 May 2011 11:42:00 -0400 Sent to CCL by: "James Justin Robinson" [jameschums::yahoo.com] Dear Tschijnmo, There are other libraries such as Libint and LibXC, when I HAVE to do something with C, I use the GSL libraries. Python is another language interested people may want to explore. I have also gained a better numerical understanding by using MatLab and Octave. Many codes are written using C and Fortran together. There a many considerations that should be taken into account when coding scientific programs, Fortran has been around for 50 years and with good reason. Students I suspect may need to arm themselves with C and Fortran; fortran for numerical calculation and C for when they cannot get a chemistry job and decide to move into IT. I was unaware of the TNT library from NIST - thank you for that. Regards James J Robinson, UK. From owner-chemistry@ccl.net Thu May 26 14:31:01 2011 From: "Jim Kress ccl_nospam=kressworks.com" To: CCL Subject: CCL:G: Spectral Deconvolution Software Message-Id: <-44767-110526120321-430-ZMWjUcuCXa3k/S3ADrfR/g=server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 26 May 2011 12:02:57 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam|a|kressworks.com] Another alternative that has not been mentioned is ORCA. While ORCA is a general purpose Quantum Chemistry program, its abilities to analyze, fit and interpret UV, Vis, IR, and Raman spectra are quite remarkable. In fact, it was originally designed to be a tools for the analysis and understanding of spectral properties of molecular systems. It will allow you to perform the task you have mentioned while, at the same time, give you a much deeper insight into the physics that is actually occurring. Frank Neese (the primary author) has always been quite helpful in the use and application of ORCA. FWIW, I'd recommend you give it a look and possibly try it out. http://www.thch.uni-bonn.de/tc/orca/ Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com]^[ccl.net [mailto:owner- > chemistry+ccl_nospam==kressworks.com]^[ccl.net] On Behalf Of Joe Golab > joseph.golab]=[ineos.com > Sent: Wednesday, May 25, 2011 4:15 PM > To: Kress, Jim > Subject: CCL:G: Spectral Deconvolution Software > > > Sent to CCL by: "Joe Golab" [joseph.golab*|*ineos.com] > I am looking for a program (share/ freeware would be ideal) that can do > non-linear curve fitting to X-Y data. > > Specifically, I want to deconvolute a curve (like UV-Vis absorbance > data) into component Gaussian curves. > > If there is an application that has been developed for MathCad, I could > use that; reliable applications on the web would be okay as well. > > I am not looking for a (costly) spectroscopy software suite, just the > curve fitting part. > > Suggestions are appreciated. > > Thanks. > > Joe Golab > Senior Research Associate > INEOS Technologies, Nitriles R&D > Email: Joseph.Golab_at_ineos.com> To recover the email address of the author of the message, please > change> From owner-chemistry@ccl.net Thu May 26 15:06:01 2011 From: "Arne Dieckmann adieckma^-^googlemail.com" To: CCL Subject: CCL: MD simulations with CPMD Message-Id: <-44768-110526134808-23205-GIGYuCzkC9DeCGTO9S4Nrw _ server.ccl.net> X-Original-From: "Arne Dieckmann" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: 26 May 2011 19:47:54 +0200 MIME-Version: 1.0 Sent to CCL by: "Arne Dieckmann" [adieckma*_*googlemail.com] I would help if you were more specific about what kind of system you would like to simulate. A good place to start might the CPMD manual as well as the CPMD mailing list. If you are new to ab initio MD you should perform some extensive reading first as many things can go wrong in a simulation. Arne ----------------------- Arne Dieckmann Organic Chemistry I Ruhr-University Bochum email: adieckma||googlemail.com http://www.ruhr-uni-bochum.de/oc1/mitarbeiter/Arne-Dieckmann.html On Thursday, May 26, 2011 at 3:37 PM, jacques denis jacquedenis**live.com wrote: > > Sent to CCL by: "jacques denis" [jacquedenis|a|live.com (http://live.com)] > Dear all, > > I am new in the MD simulations and I am looking to run MD jobs with the CPMD program, any help to start will be appreciate > > Thanks> > E-mail to subscribers: CHEMISTRY||ccl.net (mailto:CHEMISTRY||ccl.net) or use:> > E-mail to administrators: CHEMISTRY-REQUEST||ccl.net (mailto:CHEMISTRY-REQUEST||ccl.net) or use From owner-chemistry@ccl.net Thu May 26 19:35:01 2011 From: "jacques denis jacquedenis]|[live.com" To: CCL Subject: CCL: MD simulations with CPMD Message-Id: <-44769-110526183912-19447-TKJUA1UeCFFtb7agft0p7g.:.server.ccl.net> X-Original-From: jacques denis Content-Type: multipart/alternative; boundary="_b501bf39-aaf3-4fe9-b201-2f082865d360_" Date: Thu, 26 May 2011 22:39:00 +0000 MIME-Version: 1.0 Sent to CCL by: jacques denis [jacquedenis|live.com] --_b501bf39-aaf3-4fe9-b201-2f082865d360_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Thanks for you reply it's an orthorombic cell formed by Al=2C Si=2C Mg=2C O and H I need to make optimization and Energie minimization Thanks a lot > From: owner-chemistry++ccl.net > To: jacquedenis++live.com > Subject: CCL: MD simulations with CPMD > Date: Thu=2C 26 May 2011 19:47:54 +0200 >=20 >=20 > Sent to CCL by: "Arne Dieckmann" [adieckma*_*googlemail.com] > I would help if you were more specific about what kind of system you woul= d like to simulate. A good place to start might the CPMD manual as well as = the CPMD mailing list. If you are new to ab initio MD you should perform so= me extensive reading first as many things can go wrong in a simulation.=20 >=20 > Arne >=20 >=20 > ----------------------- > Arne Dieckmann >=20 > Organic Chemistry I > Ruhr-University Bochum=20 >=20 > email: adieckma-.-googlemail.com > http://www.ruhr-uni-bochum.de/oc1/mitarbeiter/Arne-Dieckmann.html >=20 > On Thursday=2C May 26=2C 2011 at 3:37 PM=2C jacques denis jacquedenis**li= ve.com wrote: >=20 > >=20 > > Sent to CCL by: "jacques denis" [jacquedenis|a|live.com (http://live.co= m)] > > Dear all=2C=20 > >=20 > > I am new in the MD simulations and I am looking to run MD jobs with the= CPMD program=2C any help to start will be appreciate > >=20 > > Thanks>=20 > > E-mail to subscribers: CHEMISTRY-.-ccl.net (mailto:CHEMISTRY-.-ccl.net)= or use:>=20 > > E-mail to administrators: CHEMISTRY-REQUEST-.-ccl.net (mailto:CHEMISTRY= -REQUEST-.-ccl.net) or use >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message=2C please chang= e>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20 > Before posting=2C check wait time at: http://www.ccl.net >=20 > Job: http://www.ccl.net/jobs=20>=20>=20 > If your mail bounces from CCL with 5.7.1 error=2C check:>=20>=20 >=20 = --_b501bf39-aaf3-4fe9-b201-2f082865d360_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Thanks for you reply
it's an orthorombic cell formed by Al=2C Si=2C Mg= =2C O and H
I need to make optimization and Energie minimization

= Thanks a lot


>=3B From: owner-chemistry++ccl.net
>=3B To: = jacquedenis++live.com
>=3B Subject: CCL: MD simulations with CPMD
&g= t=3B Date: Thu=2C 26 May 2011 19:47:54 +0200
>=3B
>=3B
>= =3B Sent to CCL by: "Arne Dieckmann" [adieckma*_*googlemail.com]
>=3B = I would help if you were more specific about what kind of system you would = like to simulate. A good place to start might the CPMD manual as well as th= e CPMD mailing list. If you are new to ab initio MD you should perform some= extensive reading first as many things can go wrong in a simulation.
&= gt=3B
>=3B Arne
>=3B
>=3B
>=3B ---------------------= --
>=3B Arne Dieckmann
>=3B
>=3B Organic Chemistry I
>= =3B Ruhr-University Bochum
>=3B
>=3B email: adieckma-.-googlema= il.com
>=3B http://www.ruhr-uni-bochum.de/oc1/mitarbeiter/Arne-Dieckma= nn.html
>=3B
>=3B On Thursday=2C May 26=2C 2011 at 3:37 PM=2C ja= cques denis jacquedenis**live.com wrote:
>=3B
>=3B >=3B
&g= t=3B >=3B Sent to CCL by: "jacques denis" [jacquedenis|a|live.com (http:/= /live.com)]
>=3B >=3B Dear all=2C
>=3B >=3B
>=3B >= =3B I am new in the MD simulations and I am looking to run MD jobs with the= CPMD program=2C any help to start will be appreciate
>=3B >=3B
= >=3B >=3B Thanks>=3B
>=3B >=3B E-mail to subscribers: CHEMIST= RY-.-ccl.net (mailto:CHEMISTRY-.-ccl.net) or use:>=3B
>=3B >=3B E= -mail to administrators: CHEMISTRY-REQUEST-.-ccl.net (mailto:CHEMISTRY-REQU= EST-.-ccl.net) or use
>=3B
>=3B
>=3B -=3D This is automati= cally added to each message by the mailing script =3D-
>=3B To recover= the email address of the author of the message=2C please change
>=3B =
>= =3B
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>= =3B
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>=3B Conferences: http= ://server.ccl.net/chemistry/announcements/conferences/
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= --_b501bf39-aaf3-4fe9-b201-2f082865d360_-- From owner-chemistry@ccl.net Thu May 26 23:54:01 2011 From: "Tschijnmo Tschau tschijnmotschau^^^gmail.com" To: CCL Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN? Message-Id: <-44770-110526224245-5279-DhvkCYMZPYuc+pChcLNVDw]|[server.ccl.net> X-Original-From: Tschijnmo Tschau Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 27 May 2011 10:42:31 +0800 MIME-Version: 1.0 Sent to CCL by: Tschijnmo Tschau [tschijnmotschau===gmail.com] Thanks so much for all the comments, they are really helpful and explained a lot of problems. But for the advocated wrappers for BLAS and LAPACK in C++, I am still a little curious about the details about what kind of wrappers should it be. Thank you! Maybe there seems to be many ways to wrap BLAS and LAPACK in C++, should we include the CBLAS and CLAPACK headers under extern "C" and call the CBLAS and CLAPACK library, or should we write some wrappers to the Fortran library by writing header files for the Fortran subroutines with techniques such as underscore appending? Or should we write wrapper functions in Fortran using the Fortran-C interoperation feature, which calls the internal Fortran subroutines? This might seem more portable. I am really a little curious about these, thank you so much for your help! And thank you really for the comments on the spirit library, which might be able to spare new-comers a lot of learning time. Thank you! And thanks a lot for the indications of the libint and libxc libraries, which are really good examples of serious production computational chemistry code in C or C++, thank you! On Thu, May 26, 2011 at 11:03 PM, Gerald Knizia knizia-*-theochem.uni-stuttgart.de wrote: > > Sent to CCL by: Gerald Knizia [knizia{:}theochem.uni-stuttgart.de] > Tschijnmo Tschau tschijnmotschau : gmail.com wrote: >> >> Sent to CCL by: Tschijnmo Tschau [tschijnmotschau:-:gmail.com] >> Please excuse me for being a newcomer wanting to ask some basic >> questions. I am new to C++ and found that indeed it has a lot of >> convenient language features and a rich pool of libraries. But it >> seems that for numerical problems in computational chemistry, in C++ >> there do not seem to be some quite established and stable libraries >> like BLAS, LAPACK, etc, which can be highly optimized, yet. > > This is indeed the case. My rather elaborate search for a reliable linear > algebra library also turned up with no results. Everything out there has > massive defect. You're basically bound to wrappers for BLAS and LAPACK. > Don't try anything else, you'll only waste time. libflame > (http://z.cs.utexas.edu/wiki/flame.wiki/FrontPage ) may at some future point > in time become competitive with LAPACK, but that's still a long way. > >> Also there is another problem with non-numerics. The boost library is >> indeed very rice and profound. But when I had a try with the spirit >> parsing library, which seems to be quite convenient, a coupled of >> lines of code induced cryptic error information screen after screen. >> > > boost::spirit is also a waste of time. It can only generate trivial parsers, > and getting *anything* to actually work requires more time than simply > writing the parsers by hand (and I mean *anything*, not necessarily the > thing you really want). I tried it two times, and I've given up. Maybe the > best proof that spirit is pointless comes with boost itself: Try compiling > boost::wave (a C-preprocessor written with spirit). A few years ago this > still generated 2 GB (!!!) of object files and required >1h compilation time > *for a C preprocessor*. > > In short: If you want parsers, writing them by hand is usually the fastest > and easiest method. Go for LR-parsers if possible, these are very powerful > and easiest to hand-write. > >> Could anyone suggest some reading materials for people new to template >> generic programming and the BOOST library, so that a less painful >> learning curve can be possible? > > These things are discussed in many advanced C++ textbooks. However, note > that while template meta-programming may sound exciting at first, in most > cases you will get better and simpler-to-maintain code in a quicker time > when avoiding it. C++ is really not a functional programming language, and > while you CAN program it like that, there rarely is a good reason to do it. > Look into boost::spirit or boost::lambda and try to understand their error > messages if you want to know why. > -- > Gerald Knizia>    >         http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/>    > > >