From owner-chemistry@ccl.net Fri May 27 07:02:00 2011 From: "Arne Dieckmann adieckma^^^googlemail.com" To: CCL Subject: CCL: MD simulations with CPMD Message-Id: <-44771-110527065934-12659-XswqJo+J/F4+mtafuIxkGQ++server.ccl.net> X-Original-From: "Arne Dieckmann" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: 27 May 2011 12:59:23 +0200 MIME-Version: 1.0 Sent to CCL by: "Arne Dieckmann" [adieckma!^!googlemail.com] Now where exactly is the problem? Did you read the manual? ----------------------- Arne Dieckmann Organic Chemistry I Ruhr-University Bochum email: adieckma]![googlemail.com http://www.ruhr-uni-bochum.de/oc1/mitarbeiter/Arne-Dieckmann.html On Friday, May 27, 2011 at 12:39 AM, jacques denis jacquedenis]|[live.com wrote: > Thanks for you reply > it's an orthorombic cell formed by Al, Si, Mg, O and H > I need to make optimization and Energie minimization > > Thanks a lot > > > > From: owner-chemistry[A]ccl.net (http://ccl.net) > > To: jacquedenis[A]live.com (http://live.com) > > Subject: CCL: MD simulations with CPMD > > Date: Thu, 26 May 2011 19:47:54 +0200 > > > > > > Sent to CCL by: "Arne Dieckmann" [adieckma*_*googlemail.com (http://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://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 (http://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> > r> > > > E-mail to administrators: CHEMISTRY-REQUEST[A]ccl.net (http://ccl.net) or use> > > > r From owner-chemistry@ccl.net Fri May 27 08:26:00 2011 From: "Bhaskarjyoti Borah bhaskargreen%%gmail.com" To: CCL Subject: CCL: way to convert .cif file to a complete lattice Message-Id: <-44772-110527054957-12288-o0CEAy2tFhwOp781szC+gw()server.ccl.net> X-Original-From: "Bhaskarjyoti Borah" Date: Fri, 27 May 2011 05:49:55 -0400 Sent to CCL by: "Bhaskarjyoti Borah" [bhaskargreen**gmail.com] Dear all, I am having a situation here. I have a .cif file of a zeolite framework obtained from zeolite database. Now I want to obtain the super lattice( say one unit cell of the zeolite lattice in real coordinates) of the zeolite. Does anybody know any program which can do this for me? Or if anybody has some script to do this, could you kindly share the same with me. Any suggestions will be highly appreciated. Thanks in advance. kind regards Bhaskar From owner-chemistry@ccl.net Fri May 27 10:16:01 2011 From: "Sathya Perumal sathya/./theochem.kth.se" To: CCL Subject: CCL: way to convert .cif file to a complete lattice Message-Id: <-44773-110527095221-13680-Tj4H7LK1zMY+9YjPO30VWA^server.ccl.net> X-Original-From: Sathya Perumal Content-Type: multipart/alternative; boundary=bcaec5315085684f3e04a4423c63 Date: Fri, 27 May 2011 19:21:15 +0530 MIME-Version: 1.0 Sent to CCL by: Sathya Perumal [sathya ~ theochem.kth.se] --bcaec5315085684f3e04a4423c63 Content-Type: text/plain; charset=ISO-8859-1 Dear Bhaskar, Try openbabel, It's an opensource and can convert bunch of different file formats. openbabel.org regards Sathya On 27 May 2011 15:19, Bhaskarjyoti Borah bhaskargreen%%gmail.com < owner-chemistry-$-ccl.net> wrote: > > Sent to CCL by: "Bhaskarjyoti Borah" [bhaskargreen**gmail.com] > Dear all, > > I am having a situation here. I have a .cif file of a zeolite framework > obtained from zeolite database. Now I want to obtain the super lattice( say > one unit cell of the zeolite lattice in real coordinates) of the zeolite. > Does anybody know any program which can do this for me? Or if anybody has > some script to do this, could you kindly share the same with me. Any > suggestions will be highly appreciated. Thanks in advance. > > kind regards > Bhaskar> > > --bcaec5315085684f3e04a4423c63 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Bhaskar,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0 Try openbabel, It's an opensource and can convert bunch of differen= t file formats.

=A0=A0 openbabel.or= g


regards
Sathya

On 27 May 2011 15:19, Bhaskarjyoti Borah bhaskargreen%%gmail.com <owner-chemistry-$-ccl.net> wrote:

Sent to CCL by: "Bhaskarjyoti =A0Borah" [bhaskargreen**gmail.com]
Dear all,

I am having a situation here. I have a .cif file of a zeolite framework obt= ained from zeolite database. Now I want to obtain the super lattice( say on= e unit cell of the zeolite lattice in real coordinates) of the zeolite. Doe= s anybody know any program which can do this for me? Or if anybody has some= script to do this, could you kindly share the same with me. Any suggestion= s will be highly appreciated. Thanks in advance.

kind regards
Bhaskar



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--bcaec5315085684f3e04a4423c63-- From owner-chemistry@ccl.net Fri May 27 12:49:01 2011 From: "Jerome Kieffer Jerome.Kieffer---terre-adelie.org" To: CCL Subject: CCL: way to convert .cif file to a complete lattice Message-Id: <-44774-110527094854-12859-YpTkGrkpK+OLp4Fhu0z+dw/./server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Fri, 27 May 2011 15:47:50 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [Jerome.Kieffer---terre-adelie.org] On Fri, 27 May 2011 05:49:55 -0400 "Bhaskarjyoti Borah bhaskargreen%%gmail.com" wrote: > > Sent to CCL by: "Bhaskarjyoti Borah" [bhaskargreen**gmail.com] > Dear all, > > I am having a situation here. I have a .cif file of a zeolite framework obtained from zeolite database. Now I want to obtain the super lattice( say one unit cell of the zeolite lattice in real coordinates) of the zeolite. Does anybody know any program which can do this for me? Or if anybody has some script to do this, could you kindly share the same with me. Any suggestions will be highly appreciated. Thanks in advance. > Use Mercury (from the CCDC) which has this nice "bug" of saving all atoms displayed: -open the cif -display full cell -save as xyz -- Jerome Kieffer PS: I reported this as a bug and I got the answer this is a feature :) From owner-chemistry@ccl.net Fri May 27 13:24:00 2011 From: "Gary Battle battle*o*ccdc.cam.ac.uk" To: CCL Subject: CCL: way to convert .cif file to a complete lattice Message-Id: <-44775-110527104549-23583-SYDJ03d/5BHVm8EDcoDvKA.:.server.ccl.net> X-Original-From: Gary Battle Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 27 May 2011 15:45:32 +0100 MIME-Version: 1.0 Sent to CCL by: Gary Battle [battle%ccdc.cam.ac.uk] Dear Bhaskar, The crystal structure visualiser Mercury provides the ability to display any number of unit cells in any direction from a .cif file, then save out the super lattice. Mercury is provided as a free download on the CCDC website: http://www.ccdc.cam.ac.uk/products/mercury/ For instructions on how to build up assemblies of unit cells, see: http://www.ccdc.cam.ac.uk/support/documentation/mercury/2_4_5/mercury.3.94.html#224322 Regards, Gary. -----Original Message----- > From: owner-chemistry+battle==ccdc.cam.ac.uk,+,ccl.net [mailto:owner-chemistry+battle==ccdc.cam.ac.uk,+,ccl.net] On Behalf Of Bhaskarjyoti Borah bhaskargreen%%gmail.com Sent: 27 May 2011 10:50 To: Gary Battle Subject: CCL: way to convert .cif file to a complete lattice Sent to CCL by: "Bhaskarjyoti Borah" [bhaskargreen**gmail.com] Dear all, I am having a situation here. I have a .cif file of a zeolite framework obtained from zeolite database. Now I want to obtain the super lattice( say one unit cell of the zeolite lattice in real coordinates) of the zeolite. Does anybody know any program which can do this for me? Or if anybody has some script to do this, could you kindly share the same with me. Any suggestions will be highly appreciated. Thanks in advance. kind regards Bhaskarhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtLEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmaster,+,ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ. From owner-chemistry@ccl.net Fri May 27 14:00:01 2011 From: "Harry Stern hstern16\a/mac.com" To: CCL Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN? Message-Id: <-44776-110527103652-18564-jK9nuHx6SGKeQtV5XCCCag() server.ccl.net> X-Original-From: Harry Stern Content-type: multipart/alternative; boundary="Boundary_(ID_lFkNHzHV4xi4GfdsmiX47A)" Date: Fri, 27 May 2011 10:35:25 -0400 MIME-version: 1.0 Sent to CCL by: Harry Stern [hstern16__mac.com] --Boundary_(ID_lFkNHzHV4xi4GfdsmiX47A) Content-type: text/plain; CHARSET=US-ASCII; format=flowed; delsp=yes Content-transfer-encoding: 7BIT hi all, I've written some code that might be useful for C++ users, including a perl script for generating a simple parser from C++ header files, and vector/matrix classes and wrapper for some LAPACK routines (I used the approach of linking to the Fortran library) http://chem.rochester.edu/~hstern/group/downloads.html Harry On May 26, 2011, at 10:42 PM, Tschijnmo Tschau tschijnmotschau^^^gmail.com wrote: > > 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 KniziaConferences >> : >> http://server.ccl.net/chemistry/announcements/conferences/> > >> >> > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > - - - - Harry A. Stern Assistant Professor, Department of Chemistry University of Rochester RC Box 270216 Rochester, NY 14627-0216 (585) 275-8804 --Boundary_(ID_lFkNHzHV4xi4GfdsmiX47A) Content-type: text/html; CHARSET=US-ASCII Content-transfer-encoding: quoted-printable
hi all, I've written some = code that might be useful for C++ users, including a perl script = for generating a simple parser from C++ header files, and = vector/matrix classes and wrapper for some LAPACK routines (I used = the approach of linking to the Fortran = library)


= Harry

On May 26, 2011, at 10:42 PM, = Tschijnmo Tschau tschijnmotschau^^^gmail.com wrote:


Sent to CCL by: Tschijnmo Tschau = [tschijnmotschau=3D=3D=3Dgmail.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 = <owner-chemistry###ccl.net> 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.utex= as.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://ww= w.ccl.net/chemistry/sub_unsub.shtmlConferences:
http:/= /server.ccl.net/chemistry/announcements/conferences/>   =  >





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


- - - -

Harry A. Stern

Assistant Professor, Department of Chemistry

University of = Rochester

RC Box = 270216

Rochester, NY 14627-0216

(585) 275-8804

=

= --Boundary_(ID_lFkNHzHV4xi4GfdsmiX47A)-- From owner-chemistry@ccl.net Fri May 27 14:35:00 2011 From: "Mehdi Esrafili m_esrafili]_[yahoo.com" To: CCL Subject: CCL: way to convert .cif file to a complete lattice Message-Id: <-44777-110527120244-27962-U+SVJjY7jCqa4B1UKx5tBw##server.ccl.net> X-Original-From: Mehdi Esrafili Content-Type: multipart/alternative; boundary="0-1422245439-1306512136=:82285" Date: Fri, 27 May 2011 09:02:16 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Mehdi Esrafili [m_esrafili[#]yahoo.com] --0-1422245439-1306512136=:82285 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Bhaskar;=0AYou can=A0use Mercury (http://www.ccdc.cam.ac.uk/products/m= ercury/).=0AWith Best Regards=0AMehdi=0A=A0=0A=A0=0A-----------------------= ---------------------------------------------------------------------------= ----------------------------=A0=A0=0A=0A`The man who makes no mistakes does= not usually make anything.'=0A=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Edward John Phelp= s (1822-1900)=0A-----------------------------------------------------------= -------------------------------------------------------------------=0A =0AM= ehdi D. Esrafili=0AAssistant Professor of Physical Chemistry=A0=0ACurrent a= ddress:=A0Department of Chemistry, =0AFaculty of Basic Sciences,University = of=0AMargheh, Iran. =0AE-mail 1:m_esrafili..yahoo.com=0AE-mail 2: esrafili..m= aragheh.ac.ir=0A-----------------------------------------------------------= -------------------------------------------------------------------=0A =0A= =0A=0A=0A=0A________________________________=0AFrom: Sathya Perumal sathya/= ./theochem.kth.se =0ATo: "Esrafili, Mehdi D -id#3z= a-" =0ASent: Fri, May 27, 2011 6:21:15 PM=0ASubject: = CCL: way to convert .cif file to a complete lattice=0A=0ADear Bhaskar,=0A= =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Try openbabel,= It's an opensource and can convert bunch of =0Adifferent file formats.=0A= =0A=A0=A0 openbabel.org=0A=0A=0Aregards=0ASathya=0A=0A=0AOn 27 May 2011 15:= 19, Bhaskarjyoti Borah =0Abhaskargreen%%gmail.com wrote:=0A=0A=0A>Sent to CCL by: "Bhaskarjyoti =A0Borah" [bhaskargreen**gm= ail.com]=0A>Dear all,=0A>=0A>I am having a situation here. I have a .cif fi= le of a zeolite framework obtained =0A>from zeolite database. Now I want to= obtain the super lattice( say one unit cell =0A>of the zeolite lattice in = real coordinates) of the zeolite. Does anybody know =0A>any program which c= an do this for me? Or if anybody has some script to do this, =0A>could you = kindly share the same with me. Any suggestions will be highly =0A>appreciat= ed. Thanks in advance.=0A>=0A>kind regards=0A>Bhaskar=0A>=0A>=0A>=0A>-=3D T= his is automatically added to each message by the mailing script =3D-=0A>= =0A>E-mail to subscribers: CHEMISTRY|-|ccl.netor use:=0A>=A0 =A0 =A0http://= www.ccl.net/cgi-bin/ccl/send_ccl_message=0A>=0A>E-mail to administrators: C= HEMISTRY-REQUEST|-|ccl.netor use=0A>=A0 =A0 =A0http://www.ccl.net/cgi-bin/c= cl/send_ccl_message=0A>=0A>Subscribe/Unsubscribe:=0A>=A0 =A0 =A0http://www.= ccl.net/chemistry/sub_unsub.shtml=0A>=0A>Before posting, check wait time at= : http://www.ccl.net=0A>=0A>Job: http://www.ccl.net/jobs=0A>Conferences: ht= tp://server.ccl.net/chemistry/announcements/conferences/=0A>=0A>Search Mess= ages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A>=0A>=A0 =A0 =A0==0A>=0A>RTFI: http://www.ccl.net/chemistry/a= boutccl/instructions/=0A>=0A>=0A>=0A --0-1422245439-1306512136=:82285 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
=0A=0A
With Best Regards=0A
Mehdi
=  
=0A
 
=0A
-------------------------------------------------------------= ----------------------------------------------------------------- &nbs= p;
=0A
`The man who makes no mistakes does not usually make anything.'=0A
 &n= bsp;            = ;            &n= bsp;       Edward John Phelps (1822-1900)
=0A
---= ---------------------------------------------------------------------------= ------------------------------------------------
Mehdi D. Esrafili
=0A
Assi= stant Professor of Physical Chemistry 
Current address: Department of Chemistry,
=0A
Faculty of Basic Sciences,University o= f
=0A
E-mail 1: m_esrafili..yahoo.com
E-mail 2: = esrafili..maragheh.ac.ir
=0A
--------------------------------------------= ---------------------------------------------------------------------------= -------
=0A

=0A

=0A
=0A
=0AFrom: Sathya Perumal sathya/./theochem.kth.se &= lt;owner-chemistry..ccl.net>
To:<= /SPAN> "Esrafili, Mehdi D " <m_esrafili..yahoo.com>
= Sent: Fri, May 27, 2011 6:21:1= 5 PM
Subject: CCL: way t= o convert .cif file to a complete lattice

Dear Bhaskar,
 &nb= sp;            =        Try openbabel, It's an opensource and = can convert bunch of different file formats.

   openbabel.org


regards
Sathy= a

=0A
On 27 May 2011 15:19, Bhaskarjyoti Borah bhaskargre= en%%gmail.com <owner-chemistry|-|ccl.net> wrote:
=0A

Sent= to CCL by: "Bhaskarjyoti  Borah" [bhaskargreen**gmail.com]
Dear all,

I am having a situation he= re. I have a .cif file of a zeolite framework obtained from zeolite databas= e. Now I want to obtain the super lattice( say one unit cell of the zeolite= lattice in real coordinates) of the zeolite. Does anybody know any program= which can do this for me? Or if anybody has some script to do this, could = you kindly share the same with me. Any suggestions will be highly appreciat= ed. Thanks in advance.

kind regards
Bhaskar



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=
--0-1422245439-1306512136=:82285-- From owner-chemistry@ccl.net Fri May 27 15:10:00 2011 From: "Close, David M. CLOSED[*]mail.etsu.edu" To: CCL Subject: CCL: way to convert .cif file to a complete lattice Message-Id: <-44778-110527104113-20732-hh3gn/LHy+CWPgOMlQZSHw(0)server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 27 May 2011 14:40:29 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED|a|mail.etsu.edu] Bhaskar: Yes I wrote a program to do this, and sent it to CCL. It should still be in their archive of programs. Look under DrawCrys. There is a listing of the program, and a compiled version. Do you have a way of compiling and running a FORTRAN program? If not, I can run this job for you. The idea is that all this information is available in crystallographic programs developed at Oak Ridge. They have names like ORFEE and ORTEP. Anyway, one can take the fractional coordinates from an x-ray paper and the symmetry information and generate the unit cell. My program can add unit cells to unit cells if needed to generate all of the neighboring molecules. Regards, Dave Close -----Original Message----- > From: owner-chemistry+closed==etsu.edu[A]ccl.net [mailto:owner-chemistry+closed==etsu.edu[A]ccl.net] On Behalf Of Bhaskarjyoti Borah bhaskargreen%%gmail.com Sent: Friday, May 27, 2011 5:50 AM To: Close, David M. Subject: CCL: way to convert .cif file to a complete lattice Sent to CCL by: "Bhaskarjyoti Borah" [bhaskargreen**gmail.com] Dear all, I am having a situation here. I have a .cif file of a zeolite framework obtained from zeolite database. Now I want to obtain the super lattice( say one unit cell of the zeolite lattice in real coordinates) of the zeolite. Does anybody know any program which can do this for me? Or if anybody has some script to do this, could you kindly share the same with me. Any suggestions will be highly appreciated. Thanks in advance. kind regards Bhaskarhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt