From owner-chemistry@ccl.net Wed Mar 6 05:32:39 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id EAA15176; Wed, 6 Mar 1996 04:48:30 -0500 (EST) Received: from gate.sinica.edu.tw for ccchuang@gate.sinica.edu.tw by bedrock.ccl.net (8.7.1/950822.1) id EAA00379; Wed, 6 Mar 1996 04:48:27 -0500 (EST) Received: by gate.sinica.edu.tw (5.x/SMI-SVR4) id AA13871; Wed, 6 Mar 1996 17:49:07 +0800 Date: Wed, 6 Mar 1996 17:49:06 +0800 (CST) From: Chyh-chong Chuang To: chemistry@ccl.net Cc: str-nmr@net.bio.net, molmodel@net.bio.net, bio-soft@net.bio.net Subject: FFTRC sub-rountine Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear netters: When I compiled a fortran code, I met a message 'Unresolved:fftrc_'. After checking the source code, I found there is a funtion call exist: 'call FFTRC(tmfct,nptm,fqfct1,iwk,xxx)'. Does any one know where I can get this subroutine, it is sure that our mechine does not have this routine. Thanks all ccchuang ============================================ Chyh-Chong Chuang Institude of Biological Chemistry, Academia Sinica,Taipei, Taiwan -------------------------------------------- Phone: 886-2-7858981 ext 7091 Fax: 886-2-7883473 E-Mail: ccchuang@gate.sinica.edu.tw ============================================ From states@ibc.WUStL.EDU Wed Mar 6 09:32:41 1996 Received: from medicine.wustl.edu for states@ibc.WUStL.EDU by www.ccl.net (8.7.1/950822.1) id IAA18491; Wed, 6 Mar 1996 08:51:12 -0500 (EST) From: Received: from ibc.WUStL.EDU (bison [128.252.122.174]) by medicine.wustl.edu (8.7/8.7) with SMTP id HAA00657; Wed, 6 Mar 1996 07:47:57 -0600 (CST) Received: from 0.0.0.0 (bcl) by ibc.WUStL.EDU (5.x/SMI-SVR4) id AA08656; Wed, 6 Mar 1996 07:50:42 -0600 Date: Wed, 6 Mar 1996 07:50:41 -0600 Message-Id: <9603061350.AA08656@ibc.WUStL.EDU> Subject: Re: CCL:Conservation of Difficulty To: , chemistry@www.ccl.net X-Mailer: AIR Mail 3.X (SPRY, Inc.) Equivalence of computational complexity is well known. If you could solve the traveling salesman problem, you could solve many other difficult computing problems. By gross extrapolation, not only have alot of smart people been trying to find simple analytical solutions to the solutions to the many body Schroedinger equation without success, many more people in other fields have been working on problems that are computationally equivalent, also without success. If there is a simple solution, finding it certainly is not easy! That most of the problems we have solved tend to have simple solutions (Occam's razor), does not imply that all problems have simple solutions. Maybe we just are not smart enough to solve the problems with really complicated solutions. The conclusion from computer science is that there seem to be whole classes of problems that are just plain hard. David From hebant@ext.jussieu.fr Wed Mar 6 11:32:51 1996 Received: from shiva.jussieu.fr for hebant@ext.jussieu.fr by www.ccl.net (8.7.1/950822.1) id LAA20811; Wed, 6 Mar 1996 11:16:28 -0500 (EST) Received: from idf.ext.jussieu.fr (idf.ext.jussieu.fr [134.157.81.129]) by shiva.jussieu.fr (8.7.3/jtpda-5.2) with ESMTP id RAA09870 for ; Wed, 6 Mar 1996 17:16:10 +0100 (MET) Received: from [134.157.11.16] by idf.ext.jussieu.fr (8.6.10/jtpda-4.0) with SMTP; Wed, 6 Mar 1996 17:16:02 +0100 X-Sender: hebant@idf.ext.jussieu.fr Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Wed, 6 Mar 1996 17:15:00 +0100 To: CHEMISTRY@www.ccl.net From: hebant@ext.jussieu.fr (Pascal HEBANT) Subject: Compiling DeMon Hi all, Is it possible to compile DeMon with a maximum number of orbitals higher than 600? And if it is, where do I have to make the changes in the source? Regards Pascal ***************************************************************************** Pascal HEBANT Laboratoire d'Electrochimie et de Chimie Analytique Ecole Nationale Superieure de Chimie de Paris 11 rue Pierre et Marie Curie 75005 Paris FRANCE tel: 33 (1) 44 27 66 94 fax: 33 (1) 44 27 67 50 http://alcyone.enscp.jussieu.fr/Pages/LECA/Electrochimie.html ***************************************************************************** From hinsenk@ERE.UMontreal.CA Wed Mar 6 11:44:52 1996 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.7.1/950822.1) id LAA20712; Wed, 6 Mar 1996 11:00:42 -0500 (EST) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id KAA05127 (8.6.11/IDA-1.6); Wed, 6 Mar 1996 10:59:25 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id KAA26471; Wed, 6 Mar 1996 10:59:24 -0500 Received: by cyclone.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id KAA28585; Wed, 6 Mar 1996 10:56:39 -0500 Date: Wed, 6 Mar 1996 10:56:39 -0500 Message-Id: <199603061556.KAA28585@cyclone.ERE.UMontreal.CA> To: young@argus.cem.msu.edu CC: chemistry@www.ccl.net In-reply-to: <199603060204.VAA29033@slater.cem.msu.edu> (young@argus.cem.msu.edu) Subject: Re: CCL:Conservation of Difficulty From: hinsenk@ERE.UMontreal.CA (Konrad HINSEN) > right. I firmly believe that the Schrodinger equation will one day > be as easily dealt with as trignometric functions on a calculator. Which means by numerical approximation ;-) Seriously, I wonder what your confidence is based on. Of course it may be possible to find further analytic solutions, but I don't see why this should necessarily be true. Much less do I see how you can make such a claim for *all* applications of the Schroedinger equation. Of course all this depends on what you call a "solution". In the case of trigonometry, all we have is a set of analytic relations between various functions that often occur together. With the exception of a few special cases, there is no "analytic" answer to a trigonometric problem, in the sense that the result cannot be expressed in simpler functions (i.e. sums, products, and powers). A comparative level of "solution" of the Schroedinger equation would be a safe numerical procedure that can find the solution to any problem to a specified accuracy. This procedure could then be put into the theoretical chemist's equivalent of a pocket calculator. If that's what you mean by solution, I agree that it will probably one day be available. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Mar 6 13:32:49 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id MAA22156; Wed, 6 Mar 1996 12:34:43 -0500 (EST) Received: from ENH.NIST.GOV for gilson@indigo14.carb.nist.gov by bedrock.ccl.net (8.7.1/950822.1) id MAA06087; Wed, 6 Mar 1996 12:34:40 -0500 (EST) Received: from indigo14.carb.nist.gov by ENH.NIST.GOV (PMDF V5.0-5 #10952) id <01I20OCH7IG000KNRY@ENH.NIST.GOV> for chemistry@ccl.net; Wed, 06 Mar 1996 12:32:15 -0400 (EDT) Received: by indigo14.carb.nist.gov (931110.SGI/930416.SGI) for @enh.nist.gov:chemistry@ccl.net id AA12830; Wed, 06 Mar 1996 12:32:02 -0500 Date: Wed, 06 Mar 1996 12:32:02 -0500 From: gilson@indigo14.carb.nist.gov (Michael K. Gilson) Subject: Conservation of Difficulty To: chemistry@ccl.net Message-id: <9603061732.AA12830@indigo14.carb.nist.gov> Content-transfer-encoding: 7BIT The discussion raises the following possibly naive question: Are there mathematical problems that can be solved analytically, whose numerical solutions look like hard, NP-complete problems? Mike From owner-chemistry@ccl.net Wed Mar 6 13:41:42 1996 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.7.1/950822.1) id MAA22258; Wed, 6 Mar 1996 12:59:17 -0500 (EST) Received: from uni-paderborn.de for GF@chemie.uni-paderborn.de by bedrock.ccl.net (8.7.1/950822.1) id MAA06409; Wed, 6 Mar 1996 12:59:14 -0500 (EST) Received: from physik.uni-paderborn.de (physik.uni-paderborn.de [131.234.242.11]) by uni-paderborn.de (8.7.5/8.7.3) with SMTP id SAA03414 for ; Wed, 6 Mar 1996 18:59:05 +0100 (MET) Received: From FB6/WORKQ1 by physik.uni-paderborn.de via Charon-4.0A-VROOM with IPX id 100.960306185734.480; 06 Mar 96 18:59:16 +0100 Message-ID: From: "Gregor Fels" Organization: Universitaet-GH Paderborn FB13 To: chemistry@ccl.net Date: Wed, 6 Mar 1996 18:57:27 GST Subject: parallel computing Priority: normal X-mailer: Pegasus Mail for Windows (v2.0-WB3) Could somebody please point me to literature on using parallel computing for semiempirical and/or ab initio calculation. Thanks in advance, Gregor Dr. Gregor Fels Universitaet-GH-Paderborn FB 13-Org. Chemie Warburgerstr. 100 D-33098 Paderborn, Germany Tel. 0049-5251-602181/Fax -603245 EMail GF@chemie.uni-paderborn.de From hinsenk@ERE.UMontreal.CA Wed Mar 6 14:32:44 1996 Received: from harfang.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.7.1/950822.1) id OAA23481; Wed, 6 Mar 1996 14:20:53 -0500 (EST) Received: from eole.ERE.UMontreal.CA (eole.ERE.UMontreal.CA [132.204.10.20]) by harfang.CC.UMontreal.CA with ESMTP id OAA14282 (8.6.11/IDA-1.6); Wed, 6 Mar 1996 14:19:29 -0500 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id OAA29523; Wed, 6 Mar 1996 14:19:28 -0500 Received: by cyclone.ERE.UMontreal.CA (951211.SGI.8.6.12.PATCH1042/5.17) id OAA09155; Wed, 6 Mar 1996 14:19:27 -0500 Date: Wed, 6 Mar 1996 14:19:27 -0500 Message-Id: <199603061919.OAA09155@cyclone.ERE.UMontreal.CA> To: chemistry@www.ccl.net, python-list@cwi.nl Subject: More Python code for computational chemistry From: hinsenk@ERE.UMontreal.CA (Konrad HINSEN) I have made some major additions to the Python code for computational chemistry that I published earlier on the CCL archive. The most interesting addition is probably the code that automatically calculates gradients and force constants for an arbitrary potential energy function (these are analytic derivatives, not finite-difference calculations). There are also some minor improvements in the PDB code; it can now handle compressed files and understands filenames containing "~" to refer to a home directory (the last two features are for Unix only). The code can be found via the URLs ftp://www.ccl.net:/pub/chemistry/software/SOURCES/PYTHON/HINSEN gopher://www.ccl.net:73/11/software/SOURCES/PYTHON/HINSEN Here is a short description of the modules: PDB.py (requires TextFile.py, Vector.py and umath.py) High-level I/O with PDB files. Allows you to deal with PDB files as if they were lists of residues and atoms. Example: for residue in PDBConfiguration('protein.pdb'): for atom in residue: print atom.name, atom.position TextFile.py Unified access to compressed and uncompressed files, plus access to text files as a sequence of lines. ONLY FOR UNIX SYSTEMS! Derivatives.py (requires Vector.py and umath.py) Automatic derivatives. Calculates analytical derivatives numerically, given only the original function, to any order and for any number of variables. Example: x = DerivVar(1.1,0) y = DerivVar(0.44, 1) f = exp(x**2+y**2) print f prints: (4.06982499598, [8.95361499116, 3.58144599646]) FirstDerivatives.py (requires Vector.py and umath.py) Automatic first-order derivatives. This module is a subset of Derivatives.py and compatible as far as possible. The restriction to first-order derivatives makes it faster. Potential.py (requires Derivatives.py, FirstDerivatives.py, Vector.py and umath.py) Automatic gradient and force constant calculation for potential functions (or any function). Example: def harmonic(k, r1, r2): dr = r1-r2 return k*dr*dr harmonic_g = PotentialWithGradientsAndForceConstants(harmonic) energy, gradients, force_constants = \ harmonic_g(100., Vector(0,3,1), Vector(1,2,0)) print energy print gradients print force_constants prints: 300.0 [Vector(-200.0,200.0,200.0), Vector(200.0,-200.0,-200.0)] [[200.0, 0.0, 0.0, -200.0, 0.0, 0.0], [0.0, 200.0, 0.0, 0.0, -200.0, 0.0], [0.0, 0.0, 200.0, 0.0, 0.0, -200.0], [-200.0, 0.0, 0.0, 200.0, 0.0, 0.0], [0.0, -200.0, 0.0, 0.0, 200.0, 0.0], [0.0, 0.0, -200.0, 0.0, 0.0, 200.0]] Vector.py (requires umath.py) 3d-vectors, used by the three other modules. umath.py Simplified substitute for the module "umath" from the numerics package. Use only if you don't have the numerics package. This module is used by all the other modules in this directory. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. Centre-Ville | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) -------------------------------------------------------------------------------