From owner-chemistry@ccl.net Sat Aug 15 00:06:01 2009 From: "Vincent Xianlong Wang xloongw=-=yahoo.com" To: CCL Subject: CCL: Metropolis/Monte-Carlo tutorial Message-Id: <-40003-090814235737-7165-aaDUj9UZEfjEkzLElTdzkQ ~ server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Type: multipart/alternative; boundary="0-825428012-1250308641=:39252" Date: Fri, 14 Aug 2009 20:57:21 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw##yahoo.com] --0-825428012-1250308641=:39252 Content-Type: text/plain; charset=us-ascii Hi Kass, You may take a look the homepage of Jun Liu who is statistician at Harvard. http://www.people.fas.harvard.edu/~junliu/ He did a lot of research using MC methods not in Chemistry but in Bioinformatics. Best regards, Vincent ________________________________ > From: Kaci Tizi_Ouzou kaci.tiziouzou]![gmail.com To: "Wang, Xianlong " Sent: Friday, August 14, 2009 1:04:40 PM Subject: CCL: Metropolis/Monte-Carlo tutorial Hi all, Is there any good sites where I could find tutorials, algorithms for Metropolis/Monte Carlo techniques in chemistry. Thanks all, Cheers Kass --0-825428012-1250308641=:39252 Content-Type: text/html; charset=us-ascii
Hi Kass,

You may take a look the homepage of Jun Liu who is statistician at Harvard.
http://www.people.fas.harvard.edu/~junliu/
He did a lot of research using MC methods not in Chemistry  but in Bioinformatics.

Best regards,
Vincent

From: Kaci Tizi_Ouzou kaci.tiziouzou]![gmail.com <owner-chemistry(a)ccl.net>
To: "Wang, Xianlong " <xloongw(a)yahoo.com>
Sent: Friday, August 14, 2009 1:04:40 PM
Subject: CCL: Metropolis/Monte-Carlo tutorial

Hi all,

Is there any good sites where I could find tutorials, algorithms for Metropolis/Monte Carlo techniques in chemistry.

Thanks all,

Cheers

Kass

--0-825428012-1250308641=:39252-- From owner-chemistry@ccl.net Sat Aug 15 06:35:00 2009 From: "Jose R. Valverde jrvalverde.===.cnb.csic.es" To: CCL Subject: CCL: ZINDO compilation saga continues Message-Id: <-40004-090813120004-19850-wLHUEF672Utx4tU6PwtbpA===server.ccl.net> X-Original-From: "Jose R. Valverde" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Thu, 13 Aug 2009 17:03:26 +0200 Mime-Version: 1.0 Sent to CCL by: "Jose R. Valverde" [jrvalverde=-=cnb.csic.es] That's odd. 'stdio,h' is the most basic C include file, it should be there no matter what, otherwise the GCC compiler is for all purposes practically unusable. I haven't installed GCC on Windows, but it all looks like you have had some problem with the installation. If I where you I would try a reinstall. On Thu, 13 Aug 2009 09:03:20 -0400 "John McKelvey jmmckel(!)gmail.com" wrote: > Folk, > > Kevin Gilbert has gotten a long way in compiling ZINDO with GFortran/GCC om > a MAC(i.e. Linux). I downloaded the Windows version, but GCC complains > about no stdio.h !!!! Most Bazaar!!! Anyone tried Gfort/GCC on Windows and > gotten GCC to work? > > Thanks! > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel~~gmail.com -- EMBnet/CNB Scientific Computing Service Solving all your computer needs for Scientific Research. http://bioportal.cnb.csic.es http://www.es.embnet.org From owner-chemistry@ccl.net Sat Aug 15 07:09:00 2009 From: "neeraj misra neerajmisra*o*hotmail.com" To: CCL Subject: CCL: stucture Message-Id: <-40005-090815065713-10846-7ybO2v8PY+5DtRaY50pQDQ*|*server.ccl.net> X-Original-From: "neeraj misra" Date: Sat, 15 Aug 2009 06:57:10 -0400 Sent to CCL by: "neeraj misra" [neerajmisra.:.hotmail.com] DearAll, I am doing optimization study on about 140 structures of neutral and ionic dimers/trimers of group III elements.Is there any method available by which i can sort out the geometrically correct structure without actually, running the optimization job for each one of them. Your help/suggestion would be invaluable. From owner-chemistry@ccl.net Sat Aug 15 09:16:01 2009 From: "John McKelvey jmmckel:gmail.com" To: CCL Subject: CCL: ZINDO Compilation Saga Winding Down Message-Id: <-40006-090815090448-29872-lWH5YcGkJhbc1LcamlUB4A ~ server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001636988b5c89305104712dcf4b Date: Sat, 15 Aug 2009 09:04:36 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel*o*gmail.com] --001636988b5c89305104712dcf4b Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Folks.. The issue was that source code from four different places crashed in the same spot. Turns out that more recent compilers, such as gfortran found two issues that previous compilers had let slip. Many thanks to all who offered copies of documentation and suggestions for trying various means for compiling, and even volunteering to help compile it. One person took the task to heart as a personal debugging challenge and spent hours helping on the issue and made a critically important observation. Cheers, and thanks again to all.. John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel]-[gmail.com --001636988b5c89305104712dcf4b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Folks..

The issue was that source code from four different places crashed in the same spot.=A0 Turns out that more recent compilers, such as gfortran found two issues that previous compilers had let slip.=A0

Many thanks to all who offered copies of documentation and suggestions for trying various means for compiling, and even volunteering to help compile it.=A0 One person took the task to heart as a personal debugging challenge and spent hours helping= on the issue and made a critically important observation.

Cheers, and thanks again to all..

John

-- <= br>John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-21= 60
jmmckel]-[gmail.com
--001636988b5c89305104712dcf4b-- From owner-chemistry@ccl.net Sat Aug 15 09:56:01 2009 From: "case case-#-biomaps.rutgers.edu" To: CCL Subject: CCL: ZINDO compilation saga continues Message-Id: <-40007-090814085925-23718-+cTVjn++Y9EWoRNvyJjFpw(a)server.ccl.net> X-Original-From: case Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 14 Aug 2009 08:20:15 -0400 Mime-Version: 1.0 Sent to CCL by: case [case : biomaps.rutgers.edu] On Thu, Aug 13, 2009, John McKelvey jmmckel(!)gmail.com wrote: > > Kevin Gilbert has gotten a long way in compiling ZINDO with GFortran/GCC om > a MAC(i.e. Linux). I downloaded the Windows version, but GCC complains > about no stdio.h !!!! This sounds like a problem with your gcc installation, not with the ZINDO code. A compiler than can't find stdio.h won't be able to compile much of anything. The top two google hits for "gcc windows" (MinGW and cygwin) are both excellent choices. Double-check (or re-run) your compiler installation. ...good luck...dave case From owner-chemistry@ccl.net Sat Aug 15 12:04:01 2009 From: "Bachrach, Steven STEVEN.BACHRACH=-=Trinity.edu" To: CCL Subject: CCL: RFP from InChI Trust Message-Id: <-40008-090815115656-12532-eaCd3yCVC/oj2NT8keVtZw:-:server.ccl.net> X-Original-From: "Bachrach, Steven" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sat, 15 Aug 2009 10:24:01 -0500 MIME-Version: 1.0 Sent to CCL by: "Bachrach, Steven" [STEVEN.BACHRACH#,#Trinity.edu] The InChI Trust (http://www.nature.com/press_releases/inchitrust.html) has issued a formal RFP for computer software services. At this time = the InChI Trust Board has NOT yet approved or funded this RFP. Thus anyone or any organization responding and bidding are not assured that this RFP will in fact become an actual contract. The work to be undertaken is as follows: 1. Examine the InChI code and become familiar with it to be able to answer, at least, the following questions: a. Estimate the time/cost to rewrite the code in C++ and = Java. b. Estimate the time/cost to provide a high level documentation of the code in a reasonable fashion so that other = programmers could understand with little effort. This is not a request for = detailed documentation. c. Estimate the effort in time/cost to add various modules (e.g., structure drawing rules, polymers, organometallics, inorganics, Markush, etc.) to the existing code. d. Estimate the time/cost necessary to software which the = Trust can use to "verify" that a set of InChI/InChIKeys are correct. That = is, a testing/validation software program for code that tests that the InChI = code provided by the Trust is producing the intended outputs. Any person or organization who wishes to receive a complete copy of = the contract RFP should send a request for this Word document to: steve^^^inchi-trust.org The contract will be for a fixed price of US $25,000.00 The deadline for receipt of responses to this RFP is September 3, 2009. All responses to this RFP will be evaluated by a technical panel from the IUPAC Division VIII InChI subcommittee, the group responsible for the InChI standard. Steve Heller Project Director InChI Trust From owner-chemistry@ccl.net Sat Aug 15 15:37:00 2009 From: "may abdelghani may01dz:-:yahoo.fr" To: CCL Subject: CCL: Re : CCL: Software for calculation DOS and PDOS Message-Id: <-40009-090815152552-21422-8P6nObCXv/bTxqoOoS+H7g:server.ccl.net> X-Original-From: may abdelghani Content-Type: multipart/alternative; boundary="0-1549805446-1250364337=:66647" Date: Sat, 15 Aug 2009 19:25:37 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz * yahoo.fr] --0-1549805446-1250364337=:66647 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable you have the free Gausssum:http://gausssum.sourceforge.net/ --- En date de=A0: Jeu 13.8.09, Morad M El-Hendawy M80elhendawy],[yahoo.com= a =E9crit=A0: De: Morad M El-Hendawy M80elhendawy],[yahoo.com Objet: CCL: Software for calculation DOS and PDOS =C0: "Abdelghani, May " Date: Jeudi 13 Ao=FBt 2009, 22h13 Sent to CCL by: "Morad M El-Hendawy" [M80elhendawy::yahoo.com] Hi every body, I wonder if anyone tell me about a reputed software for calculating Density= Of State (DOS) and Partial Density Of State (PDOS) My regards Morad El-Hendawy Ireland -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-1549805446-1250364337=:66647 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
you have the free Gausssum:http://gausssum.sour= ceforge.net/

=
--- En date de=A0: Jeu 13.8.09, Morad M El-Hendawy M80elhendawy],[ya= hoo.com <owner-chemistry.:.ccl.net> a =E9crit=A0:

De: Morad M El-Hendawy M80elhendawy],[yahoo.com <owne= r-chemistry.:.ccl.net>
Objet: CCL: Software for calculation DOS and PDOS=C0: "Abdelghani, May " <may01dz.:.yahoo.fr>
Date: Jeudi 13 A= o=FBt 2009, 22h13


Sent to CCL by: "Morad M El-Hend= awy" [M80elhendawy::yahoo.com]
Hi every body,
I wonder if anyone tell= me about a reputed software for calculating Density Of State (DOS) and Par= tial Density Of State (PDOS)
My regards
Morad El-Hendawy
Ireland


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