From chemistry-request@ccl.net Wed Jan 22 00:58:16 1992 Date: Wed, 22 Jan 1992 07:40:26 +0200 From: Leif Laaksonen To: STOUCH@dino.bms.com, chemistry@ccl.net Status: R It should be possible to reach Anders Wallqvist through the switch board at Chemical Center Lund, phone -46-107000 --------------------------------------------------------- laaksone@convex.csc.fi Centre for Scientific Computing P.O. Box 40 SF-02101 Espoo FINLAND Phone: +358 0 4572378 Telefax: + 358 0 4572302 "In every job to be done there is an element of fun" Mary Poppins --------------------------------------------------------- From chemistry-request@ccl.net Wed Jan 22 08:23:46 1992 Date: Wed, 22 Jan 1992 07:55 EST From: "dwj@lilly.com (Doug Johnson, MC7R7)" Subject: Restarting AMSOL 1.0 To: chemistry@ccl.net Status: R Hello, I have been using AMSOL 1.0 recently and have run into a problem when my job times out and I try to restart the calculation. I was wondering if anybody might know what's happening. Here's the situation: We are running the program on a Cray-2 under UNICOS 6.1; I have had a couple jobs time out and I get .den, .out, .res files written to my directory (among others). According the the .out file, all I have to do is insert the "RESTART" keyword to start the job back up again. However, something goes awry because after reading the .res file (I know this is happening because the new .out file reflects the total time spent so far) the calculation quickly bombs because of a floating point exception and I get the traceback errors. I looked through the AMSOL documentation and noted that the program has been developed for UNICOS 5.X and we are running 6.1. Does anyone know if this could be the problem? Or does anyone know the email address of Christopher Cramer at US Army Chemical Research, Development, and Engineering (Aberdeen Proving Ground) -----or---- Donald Truhlar at Dept of Chemistry, University of Minnesota (or are you guys also reading this list?? Thanks a lot. Doug Johnson, Lilly Research Labs, "dwj@lilly.com" From: JOHNSON DOUGLAS W (MCVAX0::RX23376) To: VMS MAIL ADDRESSEE (IN::"chemistry@ccl.net") cc: JOHNSON DOUGLAS W (MCVAX0::RX23376) From chemistry-request@ccl.net Wed Jan 22 08:58:03 1992 Date: Wed, 22 Jan 92 08:41:53 -0500 From: jle@world.std.com (Joe M Leonard) To: chemistry@ccl.net Subject: QM/MM compute server Status: R Has anybody developed a compute server running molecular mechanics codes or QM codes such as MOPAC/AMPAC? This would be something that is active all of the time, available for communication via a socket. This permits other codes to use the package without requiring reloading from disk (and the associated startup times). If you have or know of such work, is it accessable? If not, do you think it's a good idea? Thanx, Joe Leonard jle@world.std.com From chemistry-request@ccl.net Wed Jan 22 12:03:24 1992 Date: Wed, 22 Jan 92 11:12:47 EST From: "Abbas Farazdel, Ph.D." To: chemistry@ccl.net Subject: TMP Cations Status: R Hello Netters: I was wondering if anybody has any info about the structure of different isomers of trimethylpentyl cation C8H17+. Any help would be appreciated. Abbas Farazdel, Ph.D. Technical Computing Specialist IBM Corporation From chemistry-request@ccl.net Wed Jan 22 12:11:50 1992 Date: Wed, 22 Jan 92 11:16:47 EST From: "Dr./CPT Christopher J. Cramer" To: chemistry@ccl.net Subject: Restarting of AMSOL 1.0 (AMPAC 2.1 ?) Status: R THIS MESSAGE RESPONDS TO: ---------------------------------------------------------- Hello, I have been using AMSOL 1.0 recently and have run into a problem when my job times out and I try to restart the calculation. I was wondering if anybody might know what's happening. Here's the situation: We are running the program on a Cray-2 under UNICOS 6.1; I have had a couple jobs time out and I get .den, .out, .res files written to my directory (among others). According the the .out file, all I have to do is insert the "RESTART" keyword to start the job back up again. However, something goes awry because after reading the .res file (I know this is happening because the new .out file reflects the total time spent so far) the calculation quickly bombs because of a floating point exception and I get the traceback errors. I looked through the AMSOL documentation and noted that the program has been developed for UNICOS 5.X and we are running 6.1. Does anyone know if this could be the problem? From: JOHNSON DOUGLAS W (MCVAX0::RX23376) To: VMS MAIL ADDRESSEE (IN::"chemistry@ccl.net") cc: JOHNSON DOUGLAS W (MCVAX0::RX23376) ---------------------------------------------------------- 1) OK, simple stuff first. AMSOL 1.0 works fine on the Cray-II running under UNICOS 6.1 or 5.x. On the X-MP, there may be problems with the 6.x operating system (we promise to address this in future releases) -- 5.x works fine. 2) In addressing this bug (which actually appears to have nothing to do with the new AMSOL portions of the code, although I can't rule out having accidentally damaged the particular subroutine in the AMPAC 2.1 original) I did also note that in the script files 'amsoli' and 'amsolb', which execute AMSOL in the interactive and batch modes respectively, the assign statement for the restart file refers to 'fort.09'. However, the Cray actually assigns this unit as 'fort.9' (no '0'). To prevent two jobs from potentially colliding on this file, the script files should be changed to read 'fort.9' (i.e. delete the '0'), thus generating a file called $input'.res', which should ostensibly be unique. 3) Now, to fix the restart bug, modify subroutine FLEPO in source code file ampac.unmod.f as follows: JNRST=JNRST+1 IF(RESTRT) THEN CC1-92 RESTRT=.FALSE. CC1-92 GOTO 70 CC1-92 ENDIF CC1-92 IF (LNSTOP.NE.1 .AND. COS.GT.RST .AND. JNRST.LT.NRST) GOTO 160 where line 'JNRST= . . .' is the original line 277 of the subroutine and the line 'IF (LNSTOP . . .' is the original line 278 of the subroutine. Since this really relates only to AMPAC coding, I can not guarantee this fix, but it seems to work in the cases I've tested. Without this patch, the vector HESINV is never changed from the starting zero vector and a division by zero occurs in the loop indexed to CONTINUE statement 180. Perhaps an AMPAC guru with more detailed insights into subroutine FLEPO would be gracious enough to provide the net with a better explanation (and patch, if required) if I'm far off base. Alas, now source code file ampac.unmod.f is no longer really 'unmod' -- sorry for inconvenience. Chris Cramer From chemistry-request@ccl.net Wed Jan 22 12:45:12 1992 Date: Wed, 22 Jan 92 12:05:20 EST From: alper@zohar.bms.com Subject: looking for rob rosenberg... To: chemistry@ccl.net Status: R rob rosenberg, are you out there? howard alper and eric bruskin would like to contact you! e-mail to alper@zohar.bms.com does anyone else know where RR might be? From chemistry-request@ccl.net Wed Jan 22 15:07:00 1992 Date: Wed, 22 Jan 92 13:35:09 EST From: "Abbas Farazdel, Ph.D." Subject: Structure of TMP Cation To: chemistry@ccl.net Status: R Does anybody have any info about the structure of different isomers of trimethylpentyl cation (C8H18+)? Any help would be appreciated. Abbas Farazdel, Ph.D. Technical Computing Specialist IBM Corporation From chemistry-request@ccl.net Wed Jan 22 16:47:05 1992 Date: Wed, 22 Jan 92 13:14:01 CST From: george@archimedes.cray.com (George Fitzgerald) To: chemistry@ccl.net Subject: postdoctoral position available Status: R Cray Research has an immediate opening for a post-doctoral position in the area of compuational density functional theory. Cray currently markets a DFT program called Dgauss as part of its UniChem computational chemistry package. The responsibilities for this position include the formulation, design, implementation, and optimization of new functionality for the Dgauss program. Additional responsibilities include the application of DFT to problems of relevance to the chemical industry, as well as oral and written reports of all these activities. Candidates should have a Ph.D. in chemisty or physics, experience in developing DFT methods, and good communication skills. Cray is anxious to fill this position as quickly as possible. The deadline for applications is February 15, 1992. Applicants should send a resume and letters of recommendation to George Fitzgerald Cray Research 655E Lone Oak Dr. Eagan, MN 55121 From chemistry-request@ccl.net Wed Jan 22 16:55:40 1992 From: haedener@iacrs1.unibe.ch (Konrad Haedener) Subject: Programming STO Overlaps To: CHEMISTRY@ccl.net Date: Wed, 22 Jan 92 22:17:29 NFT Organization: University of Berne, Switzerland Status: R I'm currently trying to track down the origin (publication) of the algorithm used in some semiempirical packages (MOPAC, ICON8) for the computation of the STO overlap component independent of the angles between the two atoms (subroutine SS in MOPAC, subroutine LOVLAP in ICON8). This algorithm characteristically uses binomial coefficients and a compound of DO loops of nesting level 7, as in MOPAC: DO 50 J=0,LBM1,2 IB=NB+J-LB ID=LB-J-M SUM1=0.D0 IAB=IA+IB DO 40 K1=0,IA DO 40 K2=0,IB DO 40 K3=0,IC DO 40 K4=0,ID DO 40 K5=0,M IAF=IAB-K1-K2+K3+K4+2*K5 DO 40 K6=0,M IBF=K1+K2+K3+K4+2*K6 JX=(-1)**(M+K2+K4+K5+K6) SUM1=SUM1+BI(ID,K4)* 1BI(M,K5)*BI(IC,K3)*BI(IB,K2)*BI(IA,K1)* 2BI(M,K6)*JX*AF(IAF)*BF(IBF) 40 CONTINUE SUM=SUM+SUM1*AFF(LA,M,I)*AFF(LB,M,J) 50 CONTINUE SS=SUM*R**(NA+NB+1)*UA**NA*UB**NB/(2.D0**(M+1))* 1SQRT(UA*UB/(FA(NA+NA)*FA(NB+NB))*((LA+LA+1)*(LB+LB+1))) I found myself ordering J.Chem.Phys. papers of of the Roothaan-Ruedenberg epoch (we don't have these JCP issues in our library) only to find -- so far -- that the compact formalism used here has probably appeared later on. Precise pointers to the key publication of this method would be of great help. Thanks. -- Konrad Haedener Phone: +41 31 65 42 25 Institute for Physical Chemistry FAX: +41 31 65 44 99 University of Berne Switzerland haedener@iac.unibe.ch From chemistry-request@ccl.net Wed Jan 22 18:08:39 1992 Date: Wed, 22 Jan 92 17:34:40 EST From: "Dr./CPT Christopher J. Cramer" To: chemistry@ccl.net Subject: Message proliferation Status: R Netters, Hey, please don't send me hate mail! I only sent that AMSOL patch message once -- I can't explain why it seems to have been broadcast three times. Perhaps Pasteur got spontaneous generation wrong after all . . . Chris Cramer