From frank@caesar.wustl.edu Sat Nov 5 01:23:51 1994 Received: from caesar.wustl.edu for frank@caesar.wustl.edu by www.ccl.net (8.6.9/930601.1506) id AAA02129; Sat, 5 Nov 1994 00:41:58 -0500 Message-Id: <199411050541.AAA02129@www.ccl.net> Received: by caesar.wustl.edu (16.7/16.2) id AA11561; Fri, 4 Nov 94 23:47:02 -0600 From: Frank Ling Subject: Ising summary To: chemistry@ccl.net, frank@caesar.wustl.edu Date: Fri, 4 Nov 94 23:47:02 CST Mailer: Elm [revision: 66.33] Dear Netters: I asked for general codes that calculate the partition functions for finite Ising networks, and I received the following responses, my sincerest thanks to all. I tested the code Dongchul Lim told me and it runs fine on our Iris station, although it is not exactly what I was looking for. For those who are interested in large networks the code may be useful, and the lattice rule is spin glass, it has to be somewhat modified for lattice gas. To answer the questions raised by some netters, I also apply Ising networks for binding studies, especially site specific properties, that is why I didn't want to use periodic boundary conditions. I suggest Fisher, ME, Physica 106A, 28 (1981) as a general reference for Ising networks. Best regards, Frank ************************************************************************** From frank@caesar.wustl.edu Wed Oct 26 18:30 CDT 1994 Received: by caesar.wustl.edu (16.7/16.2) id AA21388; Wed, 26 Oct 94 18:30:41 -0500 From: Frank Ling Return-Path: Subject: codes for Ising model To: CHEMISTRY@ccl.net Date: Wed, 26 Oct 94 18:30:41 CDT Cc: frank@caesar.wustl.edu Mailer: Elm [revision: 66.33] Status: RO Dear Netters, I am working on the finite 2 dimensional Ising networks, having just calculated the partition function for a 3X3 net by enumerating all 512 configurations, I realized that there must exist general codes that do what I did for the 3X3 network, i.e., enumerating all confi- gurations of one site binding, two, three site cooperative binding, and so on (or one spin up, two spins up, ...). There are genreally speaking 2^N such configurations and for N small workstations are well capable of exhausting all possible configurations and thus obtain the partition function. I will appreciate it very much if someone would kindly privide me with the code or coding information, and I will summerise. Frank From lim@rani.chem.yale.edu Wed Oct 26 20:36 CDT 1994 Received: from rani.chem.yale.edu by caesar.wustl.edu with SMTP (16.7/16.2) id AA21438; Wed, 26 Oct 94 20:36:25 -0500 Return-Path: Received: by rani.chem.yale.edu; Wed, 26 Oct 94 21:31:01 -0400 From: Dongchul Lim Full-Name: Dongchul Lim Message-Id: <9410270131.AA03961@rani.chem.yale.edu> Subject: Re: CCL:codes for Ising model To: frank@caesar.wustl.edu (Frank Ling) Date: Wed, 26 Oct 94 21:31:01 EDT In-Reply-To: <199410262326.TAA19660@www.ccl.net>; from "Frank Ling" at Oct 26, 94 6:30 pm X-Mailer: ELM [version 2.3 PL11] Status: RO Frank Ling writes: > Dear Netters, > > I am working on the finite 2 dimensional Ising networks, having just > calculated the partition function for a 3X3 net by enumerating all > 512 configurations, I realized that there must exist general codes > that do what I did for the 3X3 network, i.e., enumerating all confi- > gurations of one site binding, two, three site cooperative binding, > and so on (or one spin up, two spins up, ...). There are genreally > speaking 2^N such configurations and for N small workstations are well > capable of exhausting all possible configurations and thus obtain the > partition function. I will appreciate it very much if someone would > kindly privide me with the code or coding information, and I will > summerise. > > Frank > I haven't seen a 3D model, but a X-windows program for a simple 2D model is available from freehep.scri.fsu.edu [144.174.128.21] in the directory /freehep/lattice_field_theory/xising. ---------------------------------------------------------------------- XIsing Michael Creutz creutz@wind.phy.bnl.gov March 1994 WHAT IT IS: This is an Xwindow program to illustrate a Monte Carlo simulation of a simple statistical mechanical system. The Ising model demonstrates ferromagnetism, displaying a second order phase transition from a disordered state at high temperature to an ordered state when cool. The program allows dynamical observation of this system under two simple microcanonical Monte Carlo algorithms. The system is a two dimensional array of spins, each of which is represented by a bit in a bit map displayed on the screen. Black and white represent the two possible states of a given spin. The energy of the system is entirely determined by nearest neighbor pairs. If two neighbors are the same, then the energy has one value, and if they differ, it is higher by two units. The source is freely distributable. It is available for anonymous FTP at freehep.scri.fsu.edu [144.174.128.21] in the directory /freehep/lattice_field_theory/xising COMPILING: The program should run on anything supporting Xwindows. If you find an exception, please let me know. To compile, "cc -O xising.c -lm -lX11" should work. If not, possibly the X11 includes are not being found. Then you need to compile with a -I option to where they are and possibly change the -lX11 to help the linker. Remember, as with any Xwindow program, you need to have "xhost" and "DISPLAY" set up properly. WHAT THE SCREEN SHOWS: The Xwindow display shows the spins in the image labeled "spins." This is above another bit map labeled "changes," representing the spins being changed under the current algorithm. The display has a thermometer to indicate the temperature and various buttons for controlling the updating. The inverse temperature, beta, is displayed above the thermometer. The critical value for beta is exactly known to be 0.5*log(1+sqrt(2))=.44068.... The critical temperature is marked on the thermometer. One set of three buttons, labeled "conserve E," "heat," and "cool," are for adjusting the temperature. Normal running is with the energy conserved, but to heat or cool the system press the appropriate button. Another set of buttons controls the boundary conditions. The choices include "periodic," wherein the spin neighbors at an edge are those on the opposite edge, and "antiperiodic," which is similar but with the the wrapped neighbors inverted. The other two boundary choices are constant white or black. The latter two are not permitted when the cluster algorithm, discussed below, is in operation. The algorithm button toggles between two alternatives. The program starts with the "local" case as described in some detail in my paper Phys. Rev. Letters 50, 1411 (1983). A set of "demons" circulates around the lattice trying to flip spins. Each carries a two bit sack of energy ranging from 0 to 16 units in steps of 4. Any energy change associated with a spin flip is compensated by a change in this sack. If the demon's sack cannot accommodate the change, the flip is rejected. The behavior under this algorithm is quite close to that of a conventional Metropolis et al. simulation. The program attains its speed by updating spins one word at a time using multispin coding and bit manipulation. The alternative algorithm operates by constructing a large "cluster" of spins and flipping them in unison. This is based on the approach of R.H. Swendsen and J.-S. Wang, Phys. Rev. Letters 58, 86 (1987), as adapted to a single cluster by U. Wolfe, Phys. Rev. Letters 62, 361 (1989). The particular implementation here is a microcanonical variation I discussed in Phys. Rev. Letters 69, 1002 (1992). The remaining buttons, "quit," and the "pause" "run" toggle are self explanatory. Finally, a mouse click elsewhere in the main window toggles on and off a short "about" message. SOME EXPERIMENTS: After starting the program, press the heat button and observe how the domains get small and the acceptance, as shown in the "changes" display, gets large. Then press the cool button until the temperature, as displayed in the thermometer, is a couple of tic marks below the critical value. Watch the domains grow as the system magnetizes. Note how the acceptance is largest at the domain boundaries. In many cases a single domain will grow to dominate the system. If, however, bands of different phases wrap around the lattice in either a horizontal or vertical direction, then the system can have a hard time deciding which phase will dominate and it can remain metastable for a long time. Switching the boundary conditions to antiperiodic will force the system to have at least one domain wall. Switching between black and white edges allows one to create large included domains which gradually shrink away. Returning the system to near the critical temperature, switch to the cluster algorithm. In this case a few iterations quickly give independent configurations. Heat the system and observe how the typical cluster size becomes quite small. Cooling the system below the critical temperature gives single clusters covering most of the system, which then flashes between dominantly black and dominantly white. To illustrate the power of the cluster algorithm, use the local algorithm to heat the system to a high temperature and then rapidly quench it to somewhat below the critical value. Before the local approach has had time to have the smaller domains dissolve in the dominant one, change to the cluster approach. Note how quickly the cluster sweeps anneal out the included domains. ---------------------------------------------------------------------- From Andrepeter.Heiner@vtt.fi Thu Oct 27 12:12 CDT 1994 Received: from vtt.fi by caesar.wustl.edu with SMTP (16.7/16.2) id AA22031; Thu, 27 Oct 94 12:12:20 -0500 Return-Path: Received: from geeni.bel.vtt.fi (bel.vtt.fi [130.188.30.1]) by vtt.fi (8.6.9/8.6.9) with SMTP id JAA17212 for ; Thu, 27 Oct 1994 09:11:24 +0200 Received: by geeni.bel.vtt.fi (920330.SGI/1.1.geeni) id AA25660; Thu, 27 Oct 94 09:09:38 GMT Date: Thu, 27 Oct 94 09:09:38 GMT From: Andrepeter.Heiner@vtt.fi (Andrepeter Heiner) Message-Id: <9410270909.AA25660@geeni.bel.vtt.fi> To: frank@caesar.wustl.edu Subject: Ising network Cc: heiner@bel.vtt.fi Status: RO Dear Frank, I would very much appreciate when you could send me a summary of replies on your question regarding the ising network. Could I also know what you are using the Ising model for?. I consider using it for binding studies. Thanks in advance, Andrepeter Heiner ----------------------------------------------------------------------------- | A.P. Heiner, Ph.D. | Phone : +358-0-456 5105 | | VTT | Telefax : +358-0-455 2103 | | Biotechnology & Food Research | E-mail : andrepeter.heiner@bel.vtt.fi | | P.O. Box 1503 | | | FIN-02044 VTT Espoo | | | FINLAND | | ----------------------------------------------------------------------------- From given@tiber.nist.gov Thu Oct 27 13:07 CDT 1994 Received: from tiber.nist.gov by caesar.wustl.edu with SMTP (16.7/16.2) id AA22209; Thu, 27 Oct 94 13:07:22 -0500 Return-Path: Received: by tiber.nist.gov (5.64/10.1) id AA05066; Thu, 27 Oct 94 11:31:52 -0400 Date: Thu, 27 Oct 94 11:31:52 -0400 From: given@tiber.nist.gov (James A Given) Message-Id: <9410271531.AA05066@tiber.nist.gov> To: CHEMISTRY@ccl.net, frank@caesar.wustl.edu Subject: Re: CCL:codes for Ising model Status: RO You better connect the spins on each edge to spins on the opposite edge (i.e. use toroidal boundary conditions) or the results probably will be misleading. From marty@ionchannel.med.harvard.edu Thu Oct 27 14:41 CDT 1994 Received: from harvard.harvard.edu by caesar.wustl.edu with SMTP (16.7/16.2) id AA23921; Thu, 27 Oct 94 14:40:50 -0500 Return-Path: Received: by harvard.harvard.edu (5.54/a0.25) (for frank@caesar.wustl.edu) id AA02550; Thu, 27 Oct 94 15:35:52 EDT Received: from ionchannel.med.harvard.edu by heimdall.med.harvard.edu.med.harvard.edu (4.1/SMI-4.1) id AA19155; Thu, 27 Oct 94 19:31:14 GMT Received: from [134.174.159.173] by ionchannel.med.harvard.edu via SMTP (931110.SGI/920502.SGI) for @heimdall.med.harvard.edu:frank@caesar.wustl.edu id AA12656; Thu, 27 Oct 94 15:28:55 -0700 Date: Thu, 27 Oct 94 15:28:55 -0700 Message-Id: <9410272228.AA12656@ionchannel.med.harvard.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: Frank Ling From: marty@ionchannel.med.harvard.edu (Marty Gallagher) Subject: Re: CCL:codes for Ising model Status: RO Hello, I read your post on CCL. Can you recommend any good review articles on Ising networks? Thanks, Marty ========================================================================= Martin J. Gallagher phone: (617) 432-1729 Dept. of Neurobiology fax: (617) 734-7557 Harvard Medical School E-mail: marty@ionchannel.med.harvard.edu 220 Longwood Ave http://ionchannel.med.harvard.edu/~marty Boston, MA 02115 -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran =========================================================================== From mrigank@imtech.ernet.in Sat Nov 5 03:23:52 1994 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.9/930601.1506) id CAA02618; Sat, 5 Nov 1994 02:25:41 -0500 Received: (from root@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id MAA06279 for chemistry@ccl.net; Sat, 5 Nov 1994 12:55:12 +0500 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA06890; Sat, 5 Nov 94 12:45:07+050 Message-Id: <9411050745.AA06890@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Sat, 5 Nov 94 10:27:04 +0530 Date: Sat, 5 Nov 94 10:27:04 +0530 From: Mrigank To: chemistry@ccl.net Subject: Molecular Modelling course ? Hi We are planning to start a course in molecular modelling. I will appreciate to have a look at the syllabus at other places. Can any one taking such course send me the copy of syllbus or pionters to get them? Thanks Mrigank ---- Mrigank \/Phone +91 172 49057 Institute of Microbial Technology /\Email: mrigank@imtech.ernet.in Sector 39A, \/FAX: +91 172 40958, +91 172 28032 Chandigarh 160 014 India. /\ ==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+==+ -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From R29CLOSE@ETSU.EAST-TENN-ST.EDU Sat Nov 5 14:24:00 1994 Received: from phem3 for R29CLOSE@ETSU.EAST-TENN-ST.EDU by www.ccl.net (8.6.9/930601.1506) id NAA06245; Sat, 5 Nov 1994 13:26:45 -0500 Received: from ETSU.EAST-TENN-ST.EDU (MAILER@ETSU) by phem3.acs.ohio-state.edu (PMDF V4.2-13 #5888) id <01HJ4EBU6CJ48YCX0N@phem3.acs.ohio-state.edu>; Sat, 5 Nov 1994 13:26:40 EST Received: from ETSU.EAST-TENN-ST.EDU (NJE origin R29CLOSE@ETSU) by ETSU.EAST-TENN-ST.EDU (LMail V1.2a/1.8a) with BSMTP id 9728; Sat, 5 Nov 1994 13:26:32 -0500 Date: Sat, 05 Nov 1994 13:24:53 -0500 (EST) From: David Close Subject: PDB on CD-ROM To: chemistry@ccl.net Message-id: <01HJ4EBU6CJ68YCX0N@phem3.acs.ohio-state.edu> Organization: East Tennessee State University Content-transfer-encoding: 7BIT Dear Netters: In reference to Jan Radomski's question on where to obtain the PDB files on Cd-ROM. There is a new electronic journal called the Journal of Protein Structure. Libraries take the printed version, but indivi- duals receive an electronic version quarterly on a CD-ROM. Since there is so much unused space in this format, one automatically gets all the updates to the PDB for that quarter. Therefore our lab currently has the entire PDB up to 1993 on CD-ROM and three quarterly updates so far this year. Incidently I agree with the statement about access via FTP to busy sites. It is becoming nearly impossible to use the network. During peak hours during the day one can't even get to step one with GOPHER. Regards, Dave Close. (CLOSED@ETSU.EAST-TENN-ST.EDU)