Document for the package COSY/SYNDAT/MODFUN ********************************************** * * * USER'S MANUAL FOR * * COSY, SYNDAT, MODFUN and SIMKIN * * v4.

0 * * * ********************************************** (Last edit of this version 20.9.1989 Released on 23.9.1989 ) address Marc Eberhard Biocenter of the University Department of Biophysical Chemistry Klingelbergstrasse 70 CH-4056 Basel, SWITZERLAND

tel 061 / 25 38 80 fax 061 / 25 67 60 ean EBERHARD@URZ.UNIBAS.CH CONTENTS: 1.OVERVIEW 1-1.How to read this document. 1-2.The programs of the package. 1-3.Disclaimer 2.A DOS PRIMER 2-1.What is a file? 2-2.What is DOS? 2-3.What is a directory? 2-4.Where am I? The PROMPT command. 2-5.How to start a program. 2-6.The PATH command. 2-7.The AUTOEXEC.BAT file 3.INSTALLATION 3-1.Hardware requirements. 3-2.Software requirements. 3-3.What is on the distribution disk? 3-4.Installation on your computer. 3-5.System configuration. 3-6.The utility CINST. 3-7.The utility MINIEDIT. 3-6.First run. 1.OVERVIEW: 1-1.How to read this document. -If you are new to computers or to DOS, you may have trouble understanding certain terms used in this manual. Chapter 2 provides a brief overview of the most important DOS concepts and functions. If you want to have more information please refer to the DOS manual of your computer. -Read chapter 3 to assure that the programs run on your system.

-Read chapter 4, 5, 6 and 8 to learn to use the four programs. These Chapters explain most of the features of the four programs. Examples are provided. -Chapter 7 explanes how to introduce new model functions. -Chapter 9 contains reference materials. 1-2.The programs of the package. COSY is a program for analysis of kinetic and equilibrium data. Data may be given manually via keyboard. COSY provides an editor that allows to conveniently handle data. Alternatively data may be aquired from text files. COSY allows to process data in many ways (linear transformation, scaling, integration, differentiation etc) and provides an universal nonlinear least-squares fit procedure to fit data to various model functions. Additionally some special algorithms are provided (Direct linear plot, initial velocity estimation). COSY allows to graphically represent data on the screen, a plotter or a matrix printer. SYNDAT is used to generate data according to fixed parameters. Experimental error are simulated by an algorithm, which scatters the calculated data according to a standard deviation. The synthetic data generated in this way may be analyzed by least-squares fit. MODFUN evaluates the model functions and their derivatives with respect to the fit parameters for a given argument. MODFUN may be used to estimate parameters and to check wether the model functions are correctly evaluated. All four programs of the package provide an DOS-shell, that is they allow you to switch to the operating system during program operation. The program continues subsequently at the same point you left. All four programs allow redirection of output to devices or files. Several utilities are also provided: MINIEDIT a small editor. CCODE a tool to define or modify parameters of model function. CONF gives estimates on errors of parameters (From Monte-Carlo analysis by SYNDAT). CINST may be used to define colors of COSY, MODFUN, SYNDAT, CCODE, and MINIEDIT. 1-3.Disclaimer While every effort has been made to appropriately debug the programs no guarantee can be given that data are processed in the correct way in each case nor that programs behave as described under all circumstances. Some of the bugs are documented throughout the manual. All the programs are equipped with a runtime error library, that is they report on the causes of runtime errors (see section 9-11). User-made hazards are intercepted wherever possible. 2.A DOS PRIMER If you are new to computers or to DOS, you may have trouble understanding certain terms used in this manual. This section provides a brief overview of the most important DOS concepts and functions: -What is a file? -What is DOS? -What is a directory? -Where am I? The PROMPT command.

-How to start a program. -The PATH command. -The AUTOEXEC.BAT file. This information is by no means a complete explanation of the DOS operating system. If you need more details, please refer to the MS-DOS or PC-DOS user's manual of your computer system. 2-1.What is a file? In the computer world nearly every information is laid down in files. Files can be of very different size, contain different information. A file is a collection of information stored on a disk under a filename. The document you are reading now is the content of a file, a so-called text file. Other files contain numbers (these files are called binary files) or both text and numbers. A third category of files are program files. These files contain a code, which can be read an executed by your computer system. Each file has a name of the formate FILENAME.EXT where FILENAME refers to a string of up to 8 characters, and EXT to a string of up to 3 characters. Program files always have the filename extension EXE or COM. This extension uniquely identifies a file as a program file. Filenames are subjected to some restrictions: Do not use following characters within filenames: .[]?\/="+*:;-<> Do not use following filenames: AUX,CLOCK$,COM,CON,KYBD$,LPT,LPT1,LPT2,LPT3,LST,NUL,PRN,SCRN$ (All these filenames are used by DOS.) Do not use following filename extensions: .EXE, .BAT, .BAK, .COM, .OVL, .$$$ (All these extensions are used by DOS.) Note: the file manager (see section 4-10) of the programs of this package eliminates forbidden characters from filenames given by the user. 2-2.What is DOS? DOS is shorthand for Disk Operating System. MS-DOS is Microsoft's version of DOS, while PC-DOS is IBM's version. DOS is the housekeeper of your computer system. DOS operates in the background, taking care of many tasks you would not want to think about, for instance, the flow of characters between your keyboard and the computer, between computer and printer and between your disks and the computer's memory (RAM). Other transactions are initiated by entering commands on the DOS command line, immediately after the DOS prompt. The DOS prompt you see on the screen probably looks like one of the following: A> B> C> The capital letter refers to the active disk (the one DOS and you are using right now). For instance, if the prompt is A>, it means you are working with the files on drive A, and the commands you give DOS will refer to that drive. When you want to switch to another disk, all you do is type the letter of the disk followed by a colon and press <Enter>. To switch to drive B for example, type B:<Enter> Since DOS does not care about uppercase or lowercase letters, you also

can type b:<Enter> There are few commands you will often use with DOS, such as DIR DEL or ERASE COPY to get a list of files on the logged disk to erase a file to copy files from one disk to another

-The DIR command. If you want to get a list of the names of the files present on your disk, type DIR<Enter> DOS displays a list of all the files present on your disk. If the list is long and scrolls through the screen, hold down the <Control> key and hit <S>. The display will stop and allow you to read the list. To resume scolling, again press <Control><S>. To interrupt the output hit <Control><C>. In order to get a page-by-page output, type DIR /P <Enter> after the DOS prompt. You can specify filenames or parts of filenames to get a selection of particular files. For instance type DIR *.DAT<Enter> after the DOS prompt to get a list of all files with the filename extension DAT. Type DIR EXAM???.*<Enter> to get a list of all files having filenames 7 characters long and beginning with EXAM. You will notice that the * represents a string of variable length and ? represents a single character. -The DEL command To erase a file EXAMPLE.DAT from your disk, type DEL EXAMPLE.DAT<Enter> immediately after the DOS prompt. If you want to erase all files with the filename EXAMPLE, irrespective of the filename extension, then type DEL EXAMPLE.*<Enter> after the DOS prompt. If you want to erase all files with filenames that are 7 characters long and begin with EXAM, then type DEL EXAM???.*<Enter> after the DOS prompt. As you see, the star represents a string of characters (variable in length) while the question mark represents one single character. Consequently, if you want to erase all files of a disk, type DEL *.*<Enter>

after the DOS prompt. DOS asks you now wether you are sure to erase all the files. Enter Y<Enter> for yes, N<Enter> for no. -The COPY command. To copy a file EXAMPLE.DAT from your logged disk to disk C, for example, type COPY EXAMPLE.DAT C: after the DOS prompt. To copy the content of a file EXAMPLE.DAT present on your logged disk to a file ANYTHING.CAL on disk B, type COPY EXAMPLE.DAT B:\ANYTHING.CAL after the DOS prompt. If a file ANYTHING.CAL is already present on disk B, then DOS will overwrite this file. If no file ANYTHING.CAL is present on disk B, then DOS will create a new file with that name and put in the content of EXAMPLE.DAT. 2-3.What is a directory? A directory is a convenient way to organize your floppy or hard disk files. Directories allow you to subdivide your disk into sections. For instance you might want to put all the files having something to do with experimental data into a box labeled EXPDATA. To create such a box type MKDIR EXPDATA<Enter> after the C> prompt (or any other DOS prompt ). DOS has now created a directory EXPDATA into which you can put all the files containing experimental data, using the COPY command, as explained above: COPY xxxxx.yyy C:\EXPDATA<Enter> xxxxx.yyy represents any file you may want to have in the EXPDATA directory. To switch to the EXPDATA directory, type CD EXPDATA<Enter> To switch back to the disk type CD..<Enter> To remove the directory EXPDATA from the disk, switch to the EXPDATA directory as explained above and erase all files (Please confirm that you are in the EXPDATA directory using the command DIR, in order to avoid unwanted loss of files! ). To erase all files type DEL *.*<Enter> then switch back to the disk and enter RMDIR EXPDATA<Enter> to remove the directory EXPDATA. If you are someone who really likes organization, you can subdivide your directories into subdirectories. You can create as many directories and subdirectories as you like - just do not forget where you put your files! Subdirecties are created and handled in the same way as directories. For example, when you are in the EXPDIR directory, type

MKDIR UNIT.DIR<Enter> DOS creates now a new directory within the directory EXPDIR. To move into the newly created directory, type CD UNIT.DIR<Enter> To move from a subdirectory (like UNIT) into its parent directory (in the present case EXPDIR), type CD..<Enter> and DOS will move you back to the EXPDIR directory. To move to the root directory, the lowest directory in the hierarchy, type CD\<Enter> 2-4.Where am I? The PROMPT command. You have probably noticed when you switch between directories that you still see the C> prompt (or any other DOS prompt). There is no evidence of the directory or subdirectory you are currently in. Since this can be confusing, DOS gives you an easy way to find out. Type PROMPT=$P $G<Enter> and from now on (until you turn off your computer or reboot), the prompt will show you where you are. If you are still in the EXPDATA directory then your DOS prompt will look like C:\EXPDATA > If you are within the UNIT.DIR directory then your DOS prompt will look like C:\EXPDATA\UNIT.DIR > If your computer is used by other people or installed by a service manager then PROMPT is probably automatically performed (see section 2-7). 2-5.How to start a program. On one of your distribution disks, you will find the program CINST.EXE. Please copy CINST.EXE to another disk or to hard disk and keep the distribution disk save. This is because if something is wrong with your disks or if you loose the disk, the program has gone. To start CINST from drive C for example type CINST<Enter> after the C:\ > prompt. Of course, CINST.EXE has to be present on disk C. As you see, programs are started by typing the filename, without the filename extension, followed by <Enter>. Remember that all the program files have the filename extension .EXE or .COM. Now DOS gives the control of input and output to the program. All the following commands are given to the program and DOS handles only the housekeeping processes, in the background. As soon as you leave the program, the DOS prompt reappears on the screen.

2-6 The PATH command. The PATH command tells your computer where to look for commands it does not recognize. DOS only recognizes programs in the current (logged) directory, unless there is a path to other directories. Suppose you are in the C:\EXPDATA directory, but CINST.EXE is on the C disk. If you type CINST<Enter> after the C:\EXPDATA > prompt, in order to start CINST, then DOS will give you the message Bad command or file name. because it cannot find the file CINST.EXE in the EXPDATA directory. In this case, in order to run CINST, you can either type C:\CINST<Enter> or you can force DOS to find files outside the current directory, by typing PATH=C:\;C:\EXPDATA;C:\EXPDATA\UNIT From now on (until you turn off your computer or reboot), DOS will find any program present in one of the specified directories (C EXPDATA and UNIT ). Do not forget to separate the different directory specifications by semicolons. If you want to find out the PATH installed previously then type PATH<Enter> after the DOS prompt. 2-7.The AUTOEXEC.BAT file To avoid typing the PROMPT command discussed in section 2-4 and the PATH command mentioned in section 2-6. every time you turn on the computer, you can set up an AUTOEXEC.BAT file. The AUTOEXEC.BAT file makes the computer to do things when it is started up. If you have an AUTOEXEC.BAT file on your main directory, your computer will do everything in that file when you turn on or boot the computer. To create an AUTOEXEC.BAT file you may use MINIEDIT present on one of the distribution disks and type CD\<Enter> to get to the root directory and type MINIEDIT AUTOEXEC.BAT<Enter> after the DOS prompt, in order to create an AUTOEXEC.BAT file or edit an existing AUTOEXEC.BAT. Now enter the PROMPT and PATH command you want to execute whenever the computer is started up: PROMPT=$P $G PATH=C:;C:\EXPDATA CD EXPDATA The last command switches to the EXPDATA directory. To save the AUTOEXEC.BAT

file, select 'F1-Save' from the menu by typing <F1>. Move with the cursor to the first entry "AUTOEXEC.BAT" of the list using the arrow keys and hit <Enter>. Alternatively you may use DOS to setup an AUTOEXEC.BAT file. Type CD\<Enter> to get to the main directory. Type COPY CON AUTOEXEC.BAT<Enter> to tell DOS that you want to write text from the keyboard (CON for console) into AUTOEXEC.BAT. Then type PROMPT=$P $G<Enter> PATH=C:\EXPDATA<Enter> CD EXPDATA<Enter> Now hold down the <Control> key, hit <Z> and press <Enter>. This tells DOS to terminate the input from the keyboard and to save your commands into the AUTOEXEC.BAT file. Of course you also can introduce COPY and other DOS commands into the AUTOEXEC.BAT file. To see the content of AUTOEXEC.BAT type TYPE AUTOEXEC.BAT<Enter> after the DOS prompt. DOS writes now the content of AUTOEXEC.BAT onto the screen. To test your new AUTOEXEC.BAT file, reboot your computer by holding down the <Control> and <Alt> keys and pressing <Del> or typing AUTOEXEC<Enter> after the DOS prompt. After a while the C:\EXPDATA prompt should appear. This chapter has presented only a quick look at DOS and some of its functions. Once you are familiar with the information given here, you may want to study your DOS manual and discover all the other things you can do with your computer's operating system. There are many DOS functions not mentioned here that can simplify and enhance your computer use. This quick introduction into DOS should be sufficent to work with the program package described in this manual, because most of the operations are done within the programs and not with DOS. 3.INSTALLATION 3-1.Hardware requirements. Each of the programs COSY,MODFUN,SYNDAT and SIMKIN runs on a PC, PC-XT/AT or compatible with 512 Kbyte RAM, two 360 Kbyte floppy drive or one 1.2 Mbyte floppy drive or a hard disk, and graphics (Hercules, CGA, MCGA, EGA, VGA, 3270PC and IBM8514 are supported by the programs). The use of a hard disk is highly recommended. Some parts of the programs are very slow when run on a 4.77 MHz 8088 system without numeric coprocessor (graphics and fit procedures are especially time consuming on minimal systems). So far the programs have been successfully tested on the following systems: Twix 88-XT with 640 Kbyte memory, two floppy drives, no coprocessor, 20 Mbyte hard disk, Hercules graphics. Twix 88-XT with 640 Kbyte memory, two floppy drives, a 8087 coprocessor,

20 Mbyte hard disk, Hercules graphics. Twix 286-AT with 640 Kbyte memory, one floppy drive, no coprocessor, 20 Mbyte hard disk, VGA graphics. HP vectra ES10 with 640 kByte memory, one floppy drive, no coprocessor, 20 Mbyte hard disk, HP-VGA graphics. Twix 386-AT with 1 Mbyte memory, one floppy drive, no coprocessor, 60 Mbyte hard disk, VGA graphics. Tandon 486-AT 25 with 1 Mbyte memory, two floppy drives, 110 Mbyte hard disk, VGA-16 graphics. 3-2.Software requirements. MS-DOS or PC-DOS version 2.00 or later is required. All other software is present on the distribution disk. Read Chapter 2 or consult your DOS manual if you are not familiar with DOS. If you want to modify the model functions or create new ones, Turbo Pascal v5.0 or later is required. Turbo Pascal 5.0 is available for about $ 200 from many PC software dealers. See section 9-12 for a list of headquarters of Borland Inc, the manufacturer of Turbo Pascal. 3-3.What is on the distribution disk? Version 4.0 of COSY/MODFUN/SYNDAT is distributed on 6 360 kByte formatted 5 1/4 inch disks: Volume in drive B is C1-TPU Directory of B:\ INOUT COSYDEC COSYFILE COSYMODU DRIVERS ALGOMODU COSYEDIT DATAMODU HPLOT TPU 16512 9-21-90 TPU 41552 9-21-90 TPU 29920 9-21-90 TPU 63616 9-21-90 TPU 37488 9-21-90 TPU 59664 9-21-90 TPU 31280 9-21-90 TPU 44944 9-21-90 TPU 29488 9-21-90 9 File(s) 3072 bytes 2:58p 3:46p 3:46p 3:46p 2:58p 3:46p 3:47p 3:47p 2:59p free

Volume in drive B is C2-FUNC Directory of B:\ HCOPY PLOTMODU MEDIT FUNC COMPILE MINIEDIT CINST TPU 5040 9-21-90 3:49p TPU 62560 9-21-90 3:47p TPU 46784 9-21-90 4:01p TPU 79968 9-21-90 2:58p BAT 59 9-21-90 9:42a EXE 89200 9-21-90 4:11p EXE 72960 9-21-90 10:50p 7 File(s) 1024 bytes free

Volume in drive B is C3-UTIL Directory of B:\ MODFUN CCODE CONF EXE 180784 9-21-90 EXE 104720 9-21-90 EXE 65824 9-21-90 3 File(s) 9216 bytes 4:08p 4:08p 4:09p free

Volume in drive B is C4-COSY Directory of B:\ COSY COSY COSY COSY CS FREERAM FUNC EXE 305776 9-21-90 5:07p PAS 18022 9-21-90 5:04p INS 1871 9-21-90 10:33p ITF 155 9-21-90 6:34p BAT 16 9-21-90 4:49p EXE 2976 9-07-90 5:06p PAS 28787 9-20-90 9:01p 7 File(s) 1024 bytes free

Volume in drive B is C5-SYNDAT Directory of B:\ SYNDAT SYNDAT MODFUN SYNDAT COSY EXE 307984 9-23-90 10:59a PAS 35852 9-21-90 11:18p PAS 5048 9-21-90 4:08p INS 107 9-09-90 9:42p DFP 5172 9-14-90 3:19p 5 File(s) 5120 bytes free

Volume in drive B is C6-DOC Directory of B:\ CC CC1 CC2 CC3 CC4 CC5 COSY SYNDAT DOC 4996 9-21-90 10:19a DOC 40039 9-21-90 10:19a DOC 63005 9-21-90 10:19a DOC 37893 9-21-90 4:42p DOC 44000 9-21-90 10:20a DOC 39895 9-21-90 10:20a OVR 61344 9-21-90 5:07p OVR 64560 9-21-90 4:05p 8 File(s) 3072 bytes free

Six types of files are present on the distribution disks: -Programs (*.EXE, *.OVR). -Turbo Pascal unit files (*.TPU). -Turbo Pascal source code files (*.PAS). -Configuration files. -Command files. -Documentation (*.DOC). Programs: COSY.EXE, COSY.OVR MODFUN.EXE SYNDAT.EXE, SYNDAT.OVR Each of these programs checks the hardware for the presence of a numerical coprocessor and uses it if present. The programs of the package detect automatically the graphics system you use (except the IBM8514 adapter; see section 3-5). MINIEDIT a text editor. CCODE a tool to define or modify parameters of model function. CONF gives estimates on errors of parameters (From Monte-Carlo analysis by SYNDAT).

CINST defines the colors used by COSY, MODFUN and SYNDAT. The program MINIEDIT present on one of the distribution disks can be used to conveniently read text files and print text files in a useful formate, with perforation skip, page numbers and the file name at the top of each page. If you want to use the perforation skip property, assure that your printer uses the correct form feed (12 inch. Usually this is set by DIP switches) Turbo Pascal unit files: INOUT.TPU COSYDEC.TPU COSYFILE.TPU COSYMODU.TPU DRIVERS.TPU ALGOMODU.TPU COSYEDIT.TPU DATAMODU.TPU HPLOT.TPU HCOPY.TPU PLOTMODU.TPU MEDIT.TPU FUNC.TPU These files are required for the setup of COSY, MODFUN and SYNDAT with different sets of model functions. Turbo Pascal source code files: FUNC.PAS COSY.PAS SYNDAT.PAS MODFUN.PAS These files are required for the implementation of new model functions. Configuration files: COSY.INS Basic installations of COSY, MODFUN, SYNDAT, CCODE, CONF, MINIEDIT and CINST. SYNDAT.INS Special configuration of SYNDAT. COSY.DFP Parameter definitions for COSY, MODFUN, SYNDAT and CCODE. Command files: COSY.PAR Contains the last status of COSY, MODFUN and SYNDAT. COSY.ITF Example file used by the interface section of COSY (see section 5-7). CS.BAT MS-DOS batch file for the use of COSY's interface section. COMPILE.BAT may be used for compilation of COSY and SYNDAT. A note to data files. COSY, MODFUN and SYNDAT use data files of two different formats: ASCII format and binary format. ASCII files are text files which may be read and manipulated using MINIEDIT or any text processing program, while binary files can be read only by COSY, MODFUN and SYNDAT. On the other hand, binary data files occupy about three times less disk space. See section 5-10 for details. 3-4.Installation on your computer. Make copies from each of the distribution disks, using the MS-DOS command COPY or DISKCOPY. Read chapter 2 or refer your the DOS manual if you are not familiar with MS-DOS or PC-DOS. Keep the original disks

save and work with the copies exclusively. -If you have a hard disk then just copy everything present on the distribution disks into a directory onto the hard disk. You may copy the programs into different directories, but then assure that COSY.DFP is present in those directories. All the files together require about 2.1 Mbyte disk space. -If you do not have a hard disk, then you need at least two floppy drives (360 Kbyte format) to run COSY and SYNDAT. Copy COSY.EXE COSY.DFP COSY.INS COSY.IFT CS.BAT onto one disk (COSY program disk) and COSY.OVR SYNDAT.OVR onto another (accessory disk). Insert the first disk into drive A and the second into drive B (or vice versa). Specify A: and B: in the PATH command, by typing PATH=A:;B:; after the DOS prompt. Then start COSY from the disk containing COSY.DFP. You may use the remaining space of the disk containing COSY.OVR for data. In the same way, you may create a SYNDAT program disk containing SYNDAT.EXE SYNDAT.INS and use it in conjunction with the accessory disk to run SYNDAT. Each of the other programs can be operated from one disk. Note: Starting COSY with the above procedure takes more than one minute on a 8088-PC operated at 4.77 MHz. In addition, switching to graphics or the data manager (see section 4-12 and 5-4, respectively) causes a delay because these part of the program are overlaid from COSY.OVR. -If you have a 1.2 Mbyte drive and no hard disk then copy COSY.EXE COSY.OVR COSY.DFP COSY.INS COSY.IFT CS.BAT SYNDAT.EXE SYNDAT.OVR SYNDAT.INS onto a 1.2 Mbyte disk and start COSY and SYNDAT from that drive. You may also use separate disk for COSY and SYNDAT. COSY, MODFUN and SYNDAT are detect automatically and use each of the following graphics systems: AT&T 400 line CGA

EGA VGA Hercules 3270-PC An IBM 8514 graphics system is recognized as VGA. If you want to accept COSY, MODFUN and SIMKIN to use IBM 8514 then replace "detect" in the file COSY.INS by "IBM8514" (not by "IBM 8514"!). You may use MINIEDIT to do that. See section 3-5 for more details about the COSY.INS file. The AT&T adapter is also not automatically detected. Replace "detect" in COSY.INS by "ATT400". -To see whether the programs run on your computer system proceed as described in section 3-8. COSY, SYNDAT and CINST use graphics. 3-5.The system configuration (COSY.INS). COSY, MODFUN, SYNDAT, MINIEDIT and CINST use the configuration file COSY.INS. The setup described in this chapter is not required for program operation: You can run and work with all the programs with the configuration file present on the distribution disk or without the configuration file. If COSY, MODFUN, SYNDAT, MINIEDIT or CINST do not find the file COSY.INS on the current directory, then they create one with default settings. To change COSY.INS according to your demands, use a text program or MINIEDIT: Type MINIEDIT COSY.INS after the DOS prompt. If COSY.INS is on the present directory then it will show up, otherwise you get a blank screen. You may also load a file by selecting 'F2-Load' from the menu of MINIEDIT. The configuration file COSY.INS present on the distribution disk contains the following: General installations: Path: "C:\*.*" Parameter definitions: "COSY.DFP" Log file: "COSY.PAR" Username: Number size: 10 ; Decimal places: 7 ; Graphics driver: autodetect ; Graphics resolution: 2 ; Printer installations: Printer output: "PRN" Line feed: #13 #10 ; Form feed: #12 ; Spacing for text: #27 #50 ; Spacing for graphics: #27 #51 #24 ; Graphics mode: #27 #42 #0 ; Graphics Y-factor: 1 ; {default mask for file handling} {optional} {determines the numeric format} {higher numbers: lower resolution} {output port for printer} {use decimal numbers (ASCII codes)} {1/6 inch spacing for text} {1/9 inch spacing for graphics} {bit map mode 0} {determines width of hardcopy}

Plotter installations: Communication port: 0 ; {serial port 0} Communication parameters: 2400, 0, 2, 7 ; (baud rate, parity, stop bits, word length ; [166] ) Plotter controls: >#27.J#27.M50;#00;#10;#13: {initial HPGL commands} >#27.I81;#00;#17: >#27.N10;#00;#00:

delay : 3000,500,5000,1000,0,0,0,0 ; Colors: Normal text: lightgray Normal background: black Reverse text: black Reverse background: lightgray Information (text): blue Title (text): yellow Prompt (text): green Echo (text): magenta Menu (text): cyan Menu hotkeys (text): lightcyan Warnings (text): red Comments (text): lightgray Normal graphics: Information (graphics): Menu (graphics): Menu hotkeys (graphics): Axes (graphics): Residuals (graphics): Horizontal cursors (graphics): Vertical cursors (graphics): Background (graphics): Curve 1 : Curve 2 : Curve 3 : Curve 4 : Curve 5 : Curve 6 : Curve 7 : Curve 8 : Curve 9 : Curve 10 :

{delays during plot}

lightgray blue cyan lightcyan lightgray white white white black blue cyan magenta lightgray lightblue lightcyan lightmagenta white blue cyan

Comments: -If you change the name of the parameter file (COSY.DFP by default) then assure that there is a parameter file with that name on the current directory. See chapter 7-1 to learn how to setup a new parameter file. -If you fill in the username, it will show up in COSY and SYNDAT. In addition, you may fill in the username into the comment with one keystroke. Place the username in quote marks ("). -The graphics resolution is just the length of the lines which are used to make a screen plot. The smallest length is 1. A small number increases the resolution but requires more time to draw the plot. -The printer installations are made for dot matrix printers (8,9 or 24 needles). Currently the programs do not support hardcopies on other devices (laser printers, ink jet printers). Refer to the manual of your printer if the hardcopy function ('3-Graphics/F6-Hardcp' in COSY or SYNDAT) does not produce an acceptable output. Note that some of the old matrix printers do not support bit map graphics. Hardcopies will be enlarged by the factor "Graphics Y-factor" in Y-direction (perpendicular to the paper feed direction of your matrix printer ). Possible printer outputs: "PRN","LST1" printer 1 "LST2" printer 2 "LST3" printer 3 "CON" console "COM1" serial port 1

"COM2" serial port 2 "NUL" ignores output none current standard output (usually the screen) You can also specify a normal DOS filename as printer output. In this case, however, the file is overwritten each time you start COSY, SYNDAT, MODFUN, MINIEDIT or CCODE. Note: place the output name in quote (") marks. -Following plotter installations are valid: -Communication port meaning 0 RS232 port 1 RS232 port 2 text file, 10 RS232 port 11 RS232 port 12 text file, Note: provide one integer number in this comments are ignored. -Communication parameters (default) 1st parameter (2400) 0, for HP-GL plotters. 1, for HP-GL plotters. for HP-GL plotters. 0, for HP-7221A and compatibles. 1, for HP-7221A and compatibles. for HP-7221A and compatibles. line. Any further numbers or

meaning baud rate: 110,150,300,600,1200 1200,2400,4800,9600 are accepted. 2nd parameter (0) parity: 0 = none 1 = odd 2 = even 3rd parameter (2) number of stop bits: 1 or 2. 4th parameter (7) word length in bits: 7 or 8. These parameters should be set to those of the plotter. (Refer to the interfacing and operation manual of your plotter). Note: Insert an empty line or a line without numeric values to leave previous settings unchanged. In this way you may configure the RS232 port by other programs (MSKERMIT for instance ). In any other case provide 4 integer numbers, separated by any delimiter, in this line. If you specify less than 4 numbers, then the remaining numbers will be set to zero. Abort device control instructions Set output mode turnaround delay, 0..9999 ms output trigger character echo terminate character output #27.I81;#00;#17: Set hadshake mode 2 Xoff threshold level enquiry character Xon trigger character #27.N10;#00: Set extended output and handshake mode 10 <DEC> intercharacter delay, 0..9999 ms #00 <ASC> Xoff trigger character Formates <STR> = string, <DEC> = decimal string, <ASC> = ASCI character. Delimiter = ; Terminator = : The # operator converts the following number to its ASCII character equivalent. The above four commands belong to the device-control instructions of HP-GL, the Hewlett-Packard graphics language. meaning #27.J <STR> #27.M <STR> 50 <DEC> #00 <ASC> #10 <ASC> #13 <ASC> #27.I <STR> 81 <DEC> #00 <ASC> #17 <ASC> #27.N <STR>

-Handshake default #27.J #27.M50;#00;#10;#13:

Note: the Handshake default is a series of HP-GL instructions which are performed in the beginning of a plot. You can specify one or more HP-GL instructions per line. Begin the instruction with a > character, followed immediately by the instruction. Before the > you may insert any comments. After the > use exclusively HP-GL instructions. Specify special ASCI characters (ESC, ENQ, CR for instance) as # followed by its numerical equivalent. Provide two lines in any case (insert empty lines if reqired). The #27.N command is ignored by HP-7221A. Note: the Handshake default makes use of a command #27.P1: (Set handshake mode, valid instructions are #27.P0: for none, #27.P1: for Xon-Xoff, #27.P2: for ENQ/ACK, #27.P3: for hardwire ) that is ignored by the HP-7221 plotter. COSY and SYNDAT may be forced to make delays during plotting a graph. This is useful if your interface protocol does not work properly, for instance if the computer does not recieve the interrupt requests sent by the plotter. The default delay protocol has been successfully used with HP-7221 and HP-7470 plotters. -Which plotter can you use? In principle all those that understand HP-GL, such as the following: HP-7440 HP-7470 HP-7475 HP-7550 HP-7580 HP-7585 HP-7586 HP-9872 (?) Additionally you can use the HP-7221. Refer to the manual of your plotter or just try if you are not sure or if your plotter is not in above list. -Colors: 16 different colors are supported by COSY, MODFUN and SYNDAT: black blue green cyan red magenta brown lightgray darkgray lightblue lightgreen lightcyan lightred lightmagenta yellow white You may use the utility CINST (section 3-6) to change the colors, or change the color in the COSY.INS file. CINST takes automatically care about the correct nomenclature and change COSY.INS accordingly. Use CINST if you are not sure how the colors look on your monitor. 3-6.The utility CINST. To start CINST type CINST after the DOS prompt and terminate with <Enter>. On the left side, a

vertical color panel will show up, on the right side various labels. Move up and down the cursor with the arrow keys, until the label on the right side has the desired color. Then switch the cursor control to the other side by pressing the space bar. Move up and down the cursor with the arrow keys to activate the desired item. Note: If you select the black square in the color panel, then the item on the right side will disappear because the background color is also black. If you have finished, hit <Enter> to validate the settings, or <Esc> to leave without changes.If you hit <Enter>, the the graphics panels will show up. Set the colors in the same way as before. The changes made with CINST will be saved in COSY.INS. Note: Your computer may crash upon executing CINST if you specify a spurious graphics driver in COSY.INS. In this case delete COSY.INS from the current directory and start CINST once more. Note that the AT&T400 adapter is not automatically detected (see section 3-5). 3-7.The utility MINIEDIT. To start MINIEDIT type MINIEDIT or MINIEDIT and a filename of a text file after the DOS prompt. If you omit the filename, then MINIEDIT will start with a blank screen, otherwise the content of the file will be loaded and shown on the screen. Following operations may be performed with MINIEDIT: -Save the current text: 'F1-Save' selected from the menu (hit <F1>) will show up the pick list where the 16 most recent files will be logged, and two options, namely the file manager and the possibility to enter a file name. The file manager (default) displays on the left half of the screen a list of all the files present on the current directory, on the right side a short description of various commands (See section 4-9). Further commands: <Control><Home> moves the cursor to the top of the list. <Control><End> moves the cursor to the bottom of the list. <Control><PgUp> and <Control><PgDn> moves the cursor by five entries. <Control><S> to toggle between two modes of sorting the list: the first mode (default) sorts the list alphabetically according to the filename, the second mode according to the extender. If you hit <Backspace> or <Control><C> then you have to edit the current filename or path, respectively. The old string will show up with a text cursor in the middle of the string. Hit <Esc> to remove the old string and give a new one. Hit <Control><F> to restore the original string. Hit <Enter> to validate your choice. If you hit <Control><D>, the program will display "Enter drive" and a list of all drives present in your computer. Enter one of these drive letters and hit <Enter>. If you select an existing file, the file manager will ask you whether you want to overwrite it. -Load a text: 'F2-Load' selected from the menu will show the pick list and the two options, as described under "Save". The file manager allows you to select a file from the list of your directory (see section 4-10). -'F3-Incl' allows you to include the content of a text file between the line containing the cursor and the line before. -'F4-Prnt' prints the text, with a head line containing the file name and the page number. If there are numbers like 1-1 present in the text, as it is the case in the present one, MINIEDIT will log these numbers in the head line. Inclusion of @@@- will force MINIEDIT to make a new page. Printing may be interrupted with <Esc>. -'F5-Stol' deletes the line containing the cursor and appends it to the buffer. The size of the buffer (number of lines present in the buffer) is given on the top right corner.

Bug: MINIEDIT sometimes crashes with an "Invalid pointer operation" error when this option is carried out. -'F6-Delb' erases the buffer. -'F7-Insb' inserts the complete content of the buffer between the line containing the cursor and the line before. -<Alt><H> shows information about further keystroke commands. -<Alt><I> displays the avaliable memory. MINIEDIT works like any text processing program. If you reach the right edge of the screen, then MINIEDIT will insert a new line and place the cursor at the beginning of the new line. If you insert characters in the middle of a line and the line becomes too long to be displayed, then MINIEDIT moves the protruding word to a new line. If MINIEDIT beeps if it is not able to perform an operation (e.g. if there is no memory left). 3-8.First run. -A quick check whether the programs run on your computer: copy MODFUN.EXE from one of the distribution disks to your working directory (if you did not yet copy the programs before) and type MODFUN<Enter> after the DOS prompt. The screen should show the main menu of MODFUN: ---------------------------------------------------------------------------I MODFUN - a utility for testing model functions of COSY I I I I 1-Save I I 2-Load I I 3-Select model function I I 4-Edit parameter I I 5-Define parameter I I 6-Calculate function I I 7-Switch records I I 8-Show parameter I I 9-Comments I I 10-Quit I I I I version 4.00 (5.9.1990) Model EC-400-00 Author: Marc Eberhard I I Hit <Enter> for OK, <Esc> for Cancel... I ---------------------------------------------------------------------------If you the message Program too big to fit in memory then try to remove memory resident utilities (RAMdisks, Sidekick). MODFUN requires about 240 Kbyte free memory. The message "Parameter definition file not found" means that the definition file (defined in the second line of "General installations" in COSY.INS: see section 3-5) is missing. Copy the file COSY.DFP (the default definition file, present on one of the distribution disks) into the current directory in this case. If you have the main menu of MODFUN on the screen, press <Esc> to exit. MODFUN asks you Do you really want to leave MODFUN? Please confirm... (Y/N) Press <Y> to leave. Try the programs SYNDAT and COSY in the same way. Each

of them should present first a menu similar to that of MODFUN. If you get the message "graphic error: ..." you may have defined the wrong graphics driver in COSY.INS (cf section 3-5). The programs usually crash with undefined run-time errors or without error message if you force them to use wrong graphics drivers (cf section 3-5). It's the safest way to define the graphics as "detect" in order to let the programs to detect the graphics system you are using.