********** * Jana98 * ********** Crystallographic Computing System for Ordinary and Modulated Structures JANA98 is free software accessible by anonymous ftp from the server ftp.fzu.cz, directory pub/cryst/jana98 or from ftp.unige.ch, directory pub/soft/crystal/jana/jana98. The following files are available: README.TXT this downloading and installation notes jana98.tar.Z the UNIX version compressed by compress jana98.tar.gz the UNIX version compressed by gzip jana98Pack.exe the UNIX self-extracting archive janainst.exe the PC self-extracting archive manual the directory containing manual files Jana can also be downloaded via the Jana98 WWW page: http://www-xray.fzu.cz/jana/jana.html or ftp://ftp.unige.ch/pub/soft/crystal/jana/hpageJ98/jana.html. There are also links to anonymous ftp sites. Sometimes, however, it is necessary to start command line ftp: ****************************** * An example of ftp commands * ****************************** ftp ftp.fzu.cz Connects to ftp.fzu.cz cd pub/cryst/jana98 Changes remote directory to jana98 binary Sets binary transfer get jana98.tar.Z Copies the compressed archive (for UNIX workstation in this example) quit Exits ftp The program has been tested on several computer platforms (Sun, DEC, HP, IBM and Silicon UNIX workstations and PC with MSDOS or Windows95/98 DOS emulation). It is distributed in the form of the source files for UNIX workstations and as executables for PC. ************************************************* * Installing of the JANA98 on UNIX Workstations * ************************************************* The package is distributed as source files. You need FORTRAN and C compiler and X11 graphics library to install the software. *** Installing Jana98 from self-extracting archive jana98Pack.exe: If you work under csh or tcsh start the installation by command source jana98Pack.exe If you work with other shell you need to start csh as the installation script is written in C-shell. It can be done by several ways: 1. csh source jana98Pack.exe exit 2. csh -c "source jana98Pack.exe" 3. csh -t source jana98Pack.exe The installation procedure first extracts the gzipped archive from jana98Pack and then it does the same work as described in the step by step instructions below. *** Installing Jana98 from gzipped archive jana98.tar.gz: *** Step by step instructions: gunzip jana98.tar Replaces compressed file jana98.tar.gz with the uncompressed jana98.tar. Jana98.tar.Z should be uncompressed by "uncompress" tar xf jana98.tar Extracts all files from the archive jana98.tar to the directory jana98. The files of the same name will be overwritten without any warning. The tar creates the following directory structure: jana98 -> source -> fg -> data -> test The directory jana98 contains Makefile - the description file for the compilation tool make. The directory source and fg contains source files. The directory data contains the cif directory and data for program icons. The testing examples are in the directory test. cd jana98 Changes directory to jana98. edit Makefile You need edit the Makefile before the compilation. Find editable section corresponding to your computer and remove "#" from the first column. Make Executes the list of commands from the Makefile. Builds the libraries and compiles all programs of the package. make clean_up removes object files, libraries and temporary files which are not necessary for using of jana98. The source files in directory source and source/fg can also be deleted except the *.fnt files, which are outline fonts necessary for the run of JANA98. cd test Changes directory to the testing examples ../jana98 testa Runs the testing example 1 ../jana98 testb ../jana98 testc ../jana98 testm *** The environmental variable JANADIR: The executable jana98 can be moved elsewhere under the condition that the directory beta98 with all its contents remains in the original location. It is also possible to move directory beta98. Jana98 then needs the environmental variable JANADIR containing the pathname of beta98. *************************** * Installing UNIX patches * *************************** *** Installing Jana98 from self-extracting archive patches98Pack.exe: Use the same commands like in the previous chapter for jana98Pack.exe. The self-extracted archive should be located in the same directory like the di- rectory jana98. *** Installing Jana98 from gzipped archive patches98.tar.gz: Use the same commands like in the previous chapter for jana98.tar.gz. The only difference is that the archive is extracted to directory patches98 instead of jana98. If you prefer the name "jana98" you should rename the directory BEFORE compilation. **************************************** * Installing of JANA98 on the MSDOS PC * **************************************** The package is distributed as executables built by Lahey FORTRAN compiler. 16 MB of operating memory is minimal, 32 MB sufficient and 64MB optimal for running JANA98. The basic setting concerning display and colours are written in the initialisation file jana98.ini, which can be changed by user in JANA98 Tools-Preferences. For some graphics cards, however, the program couldn't work properly with mouse pointer and needs another configuration. Please contact the authors in such cases. *** Step by step instructions: 1. Make the new directory for JANA98 ("janadir"). The recommended name is c:\jana98 2. Copy the installation file janainst.exe into "janadir" 3. Run janainst.exe in the "janadir" 4. Add the following line into your autoexec.bat : SET JANADIR="janadir" 5. Add "janadir" into the path command in your autoexec.bat. 6. Restart PC 7. Change directory to "janadir"\test 8. Run testing examples: jana98 testa jana98 testb jana98 testc jana98 testm In the case that "janadir" was already made and/or autoexec.bat was already changed skip the relevant points. ***************************** * The Adjustable Parameters * ***************************** In JANA98 there are limits for number of atoms, molecules etc. The user can control some of them by changing the corresponding parameter statement in the source code and recompiling the program. The following table lists the adjustable parameters of JANA98. All the parameters are defined in the file params.cmn. Name initial purpose value ------------------------------------------------------------------------ MXA 200 maximal number of atoms MXM 5 maximal number of molecules MXP 5 maximal number of the positions of single molecule MXW 16 maximal number of modulation waves MXREF 50000 maximal number of the reflections for the refinement MXE 500 maximal number of equations in the m50 MXEP 10 maximal number of the parameters in single equation MXPARRF 1000 maximal number of the refined parameters *************************************** * Printing and Updating JANA98 Manual * *************************************** **** This information will not be true for manual of JANA98, ver. May 99. **** Current version of manual is from November 1997. **** We recommend to wait for new version. It will be announced in **** the JANA98 WWW page, hopefully before summer 1998 The manual is available in ftp.fzu.cz, directory pub/cryst/jana98/manual or in ftp.unige.ch, directory /pub/soft/crystal/jana/jana98/manual as MSWord 97 document and also as PostScript and PCL print files. The PostScript files are written in Adobe 3.0 format. The PCL files are configured for HP LaserJet III printer. The name of each print file consists of the abbreviated name of the chapter and of the prefix, which sorts the files alphabetically to the same order as they appear in the manual. The printer command for one-sided printing of the whole manual from PostScript print files can look like "copy *.ps lpt1" for MSDOS or "lpr *.ps " for UNIX. The Word document uses fonts Times New Roman, Courier New, Arial and Arial Narrow, which are expected to be available for each installation. The "head" and the "tables" sections, however, contain also special Czech fonts and should be printed from the print files. The Word document is huge and can be scarcely used on computer with memory less than 32M. The Postscript output is useful if the manual will be read online by ghostview or similar viewer. The PCL output is better for printing as it is fast and the result is better than from the Postscript files. The best online browser of JANA98 manual is MSWord97 or Word97 viewer used for Word97 document as it can take advantage of the hypertext features of the manual. The recent changes of the manual are announced in the JANA98 WWW page. The information is available which print files were affected. As the page numbering of main chapters is independent it is not necessary to print the whole manual after each change. *** Notes for double sided printing: 1. Print all odd pages (all filenames starting with letter "o") The Unix print command will look like "lpr *.o" The alphabetical order of the files corresponds to proper order of the chapters in the document 2. Print even pages (all filenames starting with letter "e") to the second side of the odd pages. The first page of the o* files corresponds to the first one of the e* files. 3. Some printers (for instance HP 4ML) can take electric charge when working with already printed papers. It can be avoided by opening the rear door for paper output.