From chemistry-request@server.ccl.net Thu Feb 24 07:37:57 2000 Received: from terra.ifi.unicamp.br (terra.ifi.unicamp.br [143.106.6.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA22870 for ; Thu, 24 Feb 2000 07:19:01 -0500 Received: from ifi.unicamp.br (lua [143.106.6.13]) by terra.ifi.unicamp.br (8.9.3/8.9.3) with ESMTP id JAA29996 for ; Thu, 24 Feb 2000 09:09:36 -0200 (BDB) Received: (from daemon@localhost) by ifi.unicamp.br (8.9.3/8.9.3) id JAA13750 for ; Thu, 24 Feb 2000 09:09:34 -0200 (BDB) Received: from sala18.ifi.unicamp.br(143.106.72.138), claiming to be "pasteur" via SMTP by lua.ifi.unicamp.br, id smtpdAAAa003Mj; Thu Feb 24 08:09:27 2000 From: "Scheila" To: Subject: X-RAY - SUMMARIZED ANSWERS Date: Thu, 24 Feb 2000 09:02:03 -0300 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 I would like to thanks all the contributions of the CClers. I'm going to summarize the answers received. Scheila ___________________________________________________ QUESTION I need a help to convert some x-ray data disposed in a paper. This paper shows the data group, the a, b and c parameters and the atomic coordinates in the format: x y z C1 7866(3) 3480(6) -1818(4) C2 7641(2) 4107(6) -2989(4) C3 7896(2) 5715(6) -3240(4) : : OMEI 9490(2) 7341(7) 3845(4) CMEI 9845(5) 5894(15) 3795(10) W1/2* 9230 923 2984 W2/2* 8963 2070 3358 *occupancy factor f=0.5 ______________________________________________________ ANSWERS 1- There is a good converter named BABEL or BABELWIN (for windows). You can convert to many file formats. I don't know which format you are using but what you need to know is name of the program you used to get the result you have given in your mail. You can find the program at the following site ftp://laue.chem.ncsu.edu/pub/X-ray/babel/ I hope this will help you. Dr Ivan Basic Rudjer Boskovic Institute Bijenicka 54 HR-10001 Zagreb CROATIA 2- a very good and free program is BABEL. You can find a download site at http://www.eyesopen.com/download/babelwin.zip or at ftp://www.ccl.net/pub/chemistry/software/UNIX/babel/ (also win and mac and unix) It handles over 50 different formats. Find other related chemistry software in my chemistry software list (>300 in categories) at http://www.claessen.net/chemistry/soft_en.html Regards, Rolf Claessen 3- It doesn't appear to be in any particular format, so it's up to you to put it into some machine readable format, like PDB Cambridge FDAT format has a rather complicated header, and I don't recommend it as a starting point, unless you have access to the CCDB programs and data. Since it's crystal data, the coords are probably fractional, and have an implied decimal point in front, e.g. 7866 is really 0.7866 (fractional coords are mostly less than 1.0). Rick Venable [rvenable@deimos.cber.nih.gov] 4- Following is a C program that will convert crystal structure coordinates to cartesians. It expects the first line to have the a, b, c axis lengths, and and the alpha, beta, and gamma angles. Subsequent lines are an atom label and fractional coordinates. I'll include a sample input and output file for comparison. -------- acamox.abc -- input file -------- 6.0690 7.5820 7.3640 84.970 79.660 114.160 C1 .21800 .25770 .10540 C2 .32530 .16210 -.03000 C3 .39920 .15780 .34360 C4 .14350 .33540 .41450 H10 .01900 .45500 -.14400 H21 .29300 .18400 -.14600 H22 .26100 .01600 .01900 H23 .50500 .20800 -.04900 H31 .56300 .26100 .32500 H32 .34600 .11400 .46200 H33 .38300 .04700 .29100 H41 0 .33200 .41000 H42 .12700 .28800 .53900 H43 .23600 .47000 .38700 N1 .22880 .22820 .28880 N2 .10890 .36370 .06280 O1 .08840 .36910 -.12780 -------- acamox.xyz -- output file -------- Unit cell volume = 299.2115 C1 0.662659 1.919812 0.751155 C2 1.431563 1.082369 -0.213801 C3 2.387214 1.538509 2.448738 C4 0.377954 2.859331 2.954022 H10 -1.486982 2.960348 -1.026246 H21 1.014250 1.083006 -1.040500 H22 1.559471 0.135396 0.135408 H23 2.354612 1.375188 -0.349209 H31 3.036481 2.228242 2.316181 H32 2.356760 1.389492 3.292541 H33 2.563208 0.703601 2.073873 H41 -0.488344 2.829957 2.921952 H42 0.589466 2.693343 3.841297 H43 0.485297 3.754710 2.758037 N1 1.062159 1.954256 2.058194 N2 -0.384716 2.597701 0.447557 O1 -0.777815 2.387172 -0.910794 -------- abc2xyz.c -------- #include #include #include #include #define MAXLINLEN 81 #define MAXLABLEN 8 char line [MAXLINLEN+1]; char lab [MAXLABLEN+1]; /* * prototype for utility routine */ char *fgetln (char *s, int n, FILE *str); /* * convert crystal structure fractional coordinates to cartesian */ int main (int argc, char *argv []) { double a, b, c; double alpha, beta, gamma; double z, x [2], y [3]; double yy; char *tok, *sep = "\t ,"; double degrad = M_PI / 180.0; double vol; /* * first line of input is unit cell dimensions and angles in degrees */ fgetln (line, MAXLINLEN, stdin); sscanf (line, "%lf %lf %lf %lf %lf %lf", &a, &b, &c, &alpha, &beta, &gamma); alpha *= degrad; beta *= degrad; gamma *= degrad; /* * put 'a' along the z axis */ z = a; /* * put 'b' in the zx plane */ x [0] = b * sin (gamma); x [1] = b * cos (gamma); /* * = |c| |a| cos (beta) * = |c| |b| cos (alpha) * from this 'c' can be determined */ yy = (cos (alpha) - cos (gamma) * cos (beta)) / (sin (gamma) * sin (beta)); y [0] = c * sin (beta) * yy; y [1] = c * sin (beta) * sqrt (1.0 - yy * yy); y [2] = c * cos (beta); /* * volume = (a X b) . c * with the conventions above, (a X b) is along the y axis */ vol = z * x [0] * y [1]; printf ("Unit cell volume = %8.4lf\n", vol); /* * the rest of the file is lines of atom label and fractional coordinates */ while (fgetln (line, MAXLINLEN, stdin)) { fprintf (stderr, "%s\n", line); (void) strncpy (lab, strtok (line, sep), MAXLABLEN); tok = strtok (0, sep); a = atof (tok); tok = strtok (0, sep); b = atof (tok); tok = strtok (0, sep); c = atof (tok); a = a * z + b * x [1] + c * y [2]; b = b * x [0] + c * y [0]; c = c * y [1]; printf ("%-8s %11.6lf %11.6lf %11.6lf\n", lab, a, b, c); } return 0; } /* * fgetln * like fgets but always reads a full line * newline character is never returned in s */ char *fgetln (char *s, int n, FILE *str) { int ch, nc; nc = 0; ch = getc (str); while ((ch != EOF) && (ch != '\n') && (nc < n-1)) { s [nc++] = (char) ch; ch = getc (str); } s [nc] = 0; /* * if EOF and no characters read, return null */ if ((ch == EOF) && (nc == 0)) s = 0; /* * if a newline hasn't been read, keep reading */ while ((ch != EOF) && (ch != '\n')) { ch = getc (str); } return s; } -------- Dave Heisterberg 5- I dont know if this helps. it depends on what software you have at your disposal. I've solved the same problem by writing a small spreadsheet program to convert from crystalographic coordinates to x,y,z's. Unfortunatly the one I built was specific to the molecule I was working on but it should be pretty trivial, its just a matrix multiplication. The I used Gaussian's newzmat to convert this file to pdf which spartan could then read. I dont know if this helps Larry Cuffe 6- A FORTRAN PROGRAM C program convert C This program is able to convert fractional X-Ray coordinates C to cartesian orthonormal coordinates C Eduardo Lemos de Sa REAL*8 AA, BB, CC, FACTOR, ALPHA, BETHA, GAMMA REAL*8 XX, YY, ZZ, XXCART, YYCART, ZZCART REAL*8 PI INTEGER NCOUNT CHARACTER TITLE*80, ATOM*5 C C FACTOR IS THE NUMBER THAT SHOULD MULTIPLIED THE FRACTIONAL COORDINATE READ(5,10) TITLE 10 FORMAT(A80) READ(5,*) AA, BB, CC, FACTOR 20 FORMAT(4(D14.7)) READ(5,*) ALPHA, BETHA, GAMMA 30 FORMAT(3(F10.3)) READ(5,*) NCOUNT 40 FORMAT(I4) C SETS THE PI (3.141592..) VALUE PI=4*ATAN(1.0D0) C C CONVERT THE ANGLE (DEG - > RADIAN) ALPHA=ALPHA*PI/180.0D0 BETHA=BETHA*PI/180.0D0 GAMMA=GAMMA*PI/180.0D0 WRITE(6,40) NCOUNT WRITE(6,10) TITLE C 150 FORMAT(A2, 3F10.5) C BEGINS THE READ DATA INPUT (TITLE) DO 100 J=1,NCOUNT READ(5,150) ATOM, XX, YY, ZZ XX=XX*AA*FACTOR YY=YY*BB*FACTOR ZZ=ZZ*CC*FACTOR XXCART=XX+YY*COS(GAMMA)+ZZ*COS(BETHA) YYCART=YY*SIN(GAMMA)-ZZ*SIN(BETHA)*COS(ALPHA) ZZCART=ZZ*SIN(BETHA)*SIN(ALPHA) WRITE(6,150) ATOM, XXCART, YYCART, ZZCART 100 CONTINUE STOP END INPUT MODEL Dados provenientes do raios-X de Giovana - dimero Ti 10.8611 10.5932 15.3648 1.000D-4 90.000 102.826 90.000 4 ti 1139.0 967.0 346.0 cl 3057.0 546.0 1406.0 o 388.0 -794.0 596.0 o 304.0 1635.0 1170.0 OUTPUT MODEL 4 Dados provenientes do raios-X de Giovana - dimero Ti ti 1.11906 1.02436 .51836 cl 2.84067 .57839 2.10639 o .21812 -.84110 .89289 o -.06889 1.73199 1.75283 EDUARDO LEMOS DE SÁ From chemistry-request@server.ccl.net Thu Feb 24 11:01:51 2000 Received: from mailout03.sul.t-online.de (mailout03.sul.t-online.de [194.25.134.81]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA24120 for ; Thu, 24 Feb 2000 11:01:50 -0500 Received: from fwd03.sul.t-online.de by mailout03.sul.t-online.de with smtp id 12Nzes-0004Mb-03; Thu, 24 Feb 2000 15:54:26 +0100 Received: from gmx.de (320058217573-0001@[62.155.158.119]) by fwd03.sul.t-online.de with esmtp id 12Nzee-2DOx9MC; Thu, 24 Feb 2000 15:54:12 +0100 Sender: essmann@t-online.de Message-ID: <38B5543E.2EDAD48C@gmx.de> Date: Thu, 24 Feb 2000 16:54:38 +0100 From: 320058217573-0001@t-online.de (Ulrich Essmann) Reply-To: Ulrich.Essmann@gmx.de X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.10 i586) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Molecular Modelling example Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Sender: 320058217573-0001@t-dialin.net Dear CCL'ers, I have to give a presentation on 'Practical Molecular Modelling' on a college level. I would like to present an example which can be performed as a lab exam on a PC. To show that molecular modelling can produce new insights, the result of this exercise should not be completely trivial. Is this too much to ask for ? Any suggestions or pointers are welcome. Thanks in advance, Ulrich Essmann e-mail: Ulrich.Essmann@gmx.de From chemistry-request@server.ccl.net Thu Feb 24 10:38:11 2000 Received: from ns.mnc.md (root@ns.mnc.md [212.0.192.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA23958 for ; Thu, 24 Feb 2000 10:38:03 -0500 Received: from ppp-237.mnc.md (ppp-237.mnc.md [212.0.193.237]) by ns.mnc.md (8.8.7/8.8.7) with ESMTP id QAA11429; Thu, 24 Feb 2000 16:29:28 +0200 Date: Thu, 24 Feb 2000 16:31:21 +0200 From: Mike Peleah X-Mailer: The Bat! (v1.39) Reply-To: Mike Peleah X-Priority: 3 (Normal) Message-ID: <19688.000224@mnc.md> To: gamess-users@Glue.umd.edu Subject: Ferrocene in GAMESS problem Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit +======================---------------- --- -- - - - - . | Dear gamess-users, : . I tried to calculate ferrocene [Fe(C5H5)2] in PC GAMESS (v.5.4.b1732) using TZV basis for Fe and STO-6 basis for C and H, but received warning on partial linear dependence in atomic basis. The same result I obtained using MIDI basis for all atoms. Could somebody tell me where I am wrong? Here is part output: --------------------------- 8< --------------------------- 8< --------------------------- ****************************************************** * GAMESS VERSION = 6 MAY 1998 * ********Intel x86 (WIN32, OS/2, DOS32) VERSION******** * PC GAMESS version 5.4, build number 1732 * * Compiled on Wednesday, 01-12-1999, 15:10:55 * ****************************************************** Pentium / Win32 PC GAMESS version running under Windows 9x Running on Intel CPU: Family 5, Model 4, Stepping 3 CPU Features : MMX Data cache sizes : L1 16 KB, L2 0 KB [......skip......] INPUT CARD>! INPUT CARD>! INPUT CARD> $CONTRL SCFTYP=RHF INPUT CARD> RUNTYP=ENERGY INPUT CARD> COORD=UNIQUE INPUT CARD> EXETYP=RUN INPUT CARD> $END INPUT CARD> $GUESS GUESS=HUCKEL $END INPUT CARD> $DATA INPUT CARD>.Ferrocene..........[D5h]...... INPUT CARD>DNH 5 INPUT CARD> INPUT CARD>FE 26.0 0.0000000000 0.0000000000 0.0000000000 INPUT CARD> TZV INPUT CARD> INPUT CARD>C 6.0 1.2147000000 0.0000000000 1.6600000000 INPUT CARD> STO 6 INPUT CARD> INPUT CARD>H 1.0 2.3317000000 0.0000000000 1.6600000000 INPUT CARD> STO 6 INPUT CARD> INPUT CARD> $END [......skip......] * * * WARNING * * * ------------------------------------------------------------------------------ THE OVERLAP MATRIX HAS 1 EIGENVALUES BELOW 1.0E-05. THE SMALLEST OF THESE IS 7.42817E-06. THIS INDICATES A PARTIAL LINEAR DEPENDENCE IN YOUR ATOMIC BASIS. TO OBTAIN SCF CONVERGENCE MAY REQUIRE MORE ACCURATE INTEGRAL EVALUATION (INTTYP=HONDO, ICUT=11, ITOL=30 IN $CONTRL), MORE ACCURATE DIRECT SCF FOCK MATRIX FORMATION (FDIFF=.FALSE. IN $SCF), OR CHANGING CONVERGERS (DIIS=.T. SOSCF=.F. IN $SCF). EIGENVALUES BELOW 1.0D-07 PROBABLY WON'T CONVERGE. EIGENVALUES BETWEEN 1.0D-07 AND 1.0D-06 MAY REQUIRE LOOSENING OF -NCONV- DENSITY CONVERGENCE IN $SCF. THE OVERALL DEGREES OF AOS LINEAR INDEPENEDENCE ARE: 0.9157 - C 11 S, SHELL 40, AO 98 [......skip......] 0.1055E-04 - FE 1 S, SHELL 9, AO 9 YOU MAY CONSIDER DROPPING ONE OR MORE AOS, STARTING FROM THE END OF THIS LIST. [......skip......] --------------------------- 8< --------------------------- 8< --------------------------- Best regards, Mike mailto:mike@mnc.md . : | . - - - - -- --- ----------------======================+ From chemistry-request@server.ccl.net Thu Feb 24 10:59:25 2000 Received: from zeus.ruca.ua.ac.be (root@zeus.ruca.ua.ac.be [143.129.201.210]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA24078 for ; Thu, 24 Feb 2000 10:59:24 -0500 Received: from secnat1 (secnat1.ruca.ua.ac.be [143.129.150.72]) by zeus.ruca.ua.ac.be (8.8.6 (PHNE_14041)/8.8.6) with SMTP id PAA07793 for ; Thu, 24 Feb 2000 15:51:59 +0100 (MET) Message-ID: <013d01bf7ed7$461ae7a0$4896818f@ruca.ua.ac.be> From: "density" To: Subject: International Conference "Density functional theory ...", Antwerpen, June 18-20, 2000 Date: Thu, 24 Feb 2000 15:56:00 +0100 Dear Madam, Dear Sir, May I ask you to circulate the following second announcement of the International Conference on "Density functional theory and its applications to materials", to be held at the University of Antwerp from June 8 till 10, 2000, to the members of your mailing list. Thanks in advance, Best regards, Vic Vic Van Doren Department of Physics University of Antwerp Groenenborgerlaan 171 B-2020 Antwerpen, Belgium Tel. +32/3/2180317 Fax +32/3/2180318 e-mail: vandoren@ruca.ua.ac.be Second Announcement of the International Conference on Density Functional Theory and its Applications to Materials University of Antwerp, Belgium June 8 till 10, 2000 A WEBSITE FOR THE CONFERENCE HAS NOW BEEN OPENED AT: http://www.ruca.ua.ac.be/dft2000 Contributions Applications are invited for the above International Conference. Any density functional studies relevant to materials science may be proposed, whether on three-dimensional materials (e.g. emiconductors and metallic alloys), or on low-dimensional systems (e.g. polymers or 2D electron gases in heterojunctions). Calculations on medium- or large-sized clusters will also be considered, if they clearly throw light on the understanding of bulk or surface properties of materials. The following scientists havealready accepted the invitation to lecture: N.W. Ashcroft (Cornell University, Ithaca, U.S.A.) G.B. Bachelet (University of Rome, Italy) A. Baldereschi (Swiss Federal Institute of Technology, Lausanne, Switzerland) R. Car (Princeton University, U.S.A.) T.C. Collins (Oklahoma State University, Stillwater, U.S.A.) J.T. Devreese (University of Antwerp, Belgium) R.W. Godby (University of York, U.K.) E.K.U. Gross (University of Wurzburg, Germany) O. Gunnarsson (Max-Planck Institute, Stuttgart, Germany) J. Krieger (Brooklyn College of CUNY, U.S.A.) J. Ladik (University of Erlangen, Germany) M. Levy (Tulane University, U.S.A.) S. Louie (University of California, Berkeley, U.S.A.) N.H. March (University of Oxford, U.K. - presently at: University of Antwerp, Belgium) J.L. Martins (INESC, Lisbon, Portugal) J. Mintmire (Naval Research Laboratories, Washington, U.S.A.) M. Payne (University of Cambridge, U.K.) F. Peeters (University of Antwerp, Belgium) J.P. Perdew (Tulane University, New Orleans, U.S.A.) G. Straub (Los Alamos National Laboratory, U.S.A.) D. Wallace (Los Alamos National Laboratory, U.S.A.) Persons whose applications are accepted will be encouraged to offer one hour poster presentations during the meeting. All participants (maximum 150), except students, are required to pay a registration fee of 250 EURO/$ (10000 BEF), which gives entitlement to conference documentation and proceedings, coffee and lunch, transportation to lecture hall and social events. The student fee is 125 EURO/$ (5000 BEF). A limited number of grants will be available. For further information please contact: V.E. Van Doren, Department of Physics, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium, tel. +32/3/2180317, fax +32/3/2180318, e-mail: density@ruca.ua.ac.be From chemistry-request@server.ccl.net Thu Feb 24 12:25:14 2000 Received: from davisson.uni2.net (davisson.uni2.net [129.142.7.104]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA24794 for ; Thu, 24 Feb 2000 12:25:13 -0500 Received: from srv130.novo.dk (srv130.novo.dk [152.73.7.2]) by davisson.uni2.net (8.9.3/8.9.1) with SMTP id RAA27156 for ; Thu, 24 Feb 2000 17:17:49 +0100 Received: (qmail 8876 invoked from network); 24 Feb 2000 15:16:55 -0000 Received: from srv2.novo.dk (130.227.199.2) by 10.254.6.1 with SMTP; 24 Feb 2000 15:16:55 -0000 Received: (qmail 5324 invoked from network); 24 Feb 2000 12:13:42 -0000 Received: from it6923.research.novo.dk (HELO bisse.novo.dk) (152.73.27.11) by srv2.novo.dk with SMTP; 24 Feb 2000 12:13:42 -0000 Received: (from lnl@localhost) by bisse.novo.dk (980427.SGI.8.8.8/950213.SGI.AUTOCF) id NAA67627; Thu, 24 Feb 2000 13:13:42 +0100 (MET) Date: Thu, 24 Feb 2000 13:13:42 +0100 (MET) From: lnl@novo.dk (Leif Norskov) Message-Id: <200002241213.NAA67627@bisse.novo.dk> To: yz0@hotmail.com Subject: Re: CCL:Three dimensional FFT Cc: CHEMISTRY@ccl.net On Sun, 20 Feb 2000 02:18:53 EST "Y Z" asked: > Are there any way to calculate a (256,256,256) order > DOUBLE COMPLEX FFT in FORTRAN77? I tried to do the > following subrouitine but cannot pass the compiling. Sorry if this comes a bit late, but couldn't you simply raise the system limit: % f77 -c -o /tmp/fft /tmp/fft.f "/tmp/fft.f": Warning: Stack frame size (268436320) larger than system limit (67108864) % limit stacksize 270M % f77 -c -o /tmp/fft /tmp/fft.f % (this is from tcsh under IRIX 6.5.6f on an SGI Origin200) /Leif Norskov Novo Nordisk A/S Copenhagen Denmark LNL@novo.dk From chemistry-request@server.ccl.net Thu Feb 24 11:50:14 2000 Received: from milin3.leeds.ac.uk (milin3.leeds.ac.uk [129.11.138.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA24569 for ; Thu, 24 Feb 2000 11:50:12 -0500 Received: (from stuartg@localhost) by milin3.leeds.ac.uk (8.9.3/8.8.7) id PAA18204; Thu, 24 Feb 2000 15:45:46 GMT Date: Thu, 24 Feb 2000 15:45:46 +0000 From: Stuart Green To: chemistry@ccl.net, help@gaussian.com Subject: G98, Linda and node scratch Message-ID: <20000224154546.E11716@milin3.leeds.ac.uk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.4us We are attempting to run a MP2 calculation with Gaussian98 with Linda on our 10-processor Linux cluster. When the job is run on a single processor we prevent the scratch files from exceeding the 2GB file limit with the %rwf option. The job runs but is slow and we want to use our parallel capability. On specifying %nprocl=10 (with the same %rwf option) the jobs starts okay does its parallel stuff reaches l905 then dies because a scratch file local to one of the nodes now exceeds 2GB. Is there anyway of controlling the file size of these local scratch files? Thanks, Stuart -- Stuart M. Green S.M.Green@chem.leeds.ac.uk School of Chemistry University of Leeds Tel +44 113 233 6596 Leeds, LS2 9JT, England Fax +44 113 233 6565