Home

The ISIS OPEN GENIE User Manual

1. SUBROUTINE G2S g2s_get g2s_put EXTERNAL g2s_get g2s_put INTEGER mn lptin lptout PARAMETER mn 33000 REAL 4 Xin mn Yin mn Ein mn Xout mn Yout mn REAL 4 xnew mn yw mn CHARACTER 40 xcaptout ycaptout CHARACTER 10 char LOGICAL LMOD DANGLE 38 1 1 112 150 0 150 0 PI 4 0 ATAN 1 0D0 ws ylabel res ycaptout Bout mn call module_get_int g2s_get lptin lptin call module_get_real_array g2s_get Xin Xin lptin call module_get_real_array g2s_get Yin Yin lptin call module_get_real_array g2s_get Ein Ein lptin call module_get_real g2s_get qmax QMAX call module_get_int g2s_get npt npt call module_get_int g2s_get ic ichar call module_get_real g2s_get rho RHO if lptin eq 0 then call module_error G2S 1 ERROR No input data endif if npt eq 0 then call module_error G2S gt 1 ERROR No of output points zero RETURN endif lptout npt if lptout GT mn then call module_error G2S gt lptout mn endif delq QMAX I1ptout if rho 1lt le 10 then 1 points reduced from 33000 call module_error G2S gt 1 ERROR rho is zero RE URN endif 44 if ichar eq 0 then LMOD false else if ic
2. 0100008 69 Installing on UNIX with Digital UNIX cece ceeceeeeeeeceeeeeeeeeeeeeeeeseeeeeeeeseeeenseees 69 Installing on VMS terpe enri erT Er EEEE rE EEE o EREE 69 iv Part A User Manual What is Open GENIE GENIE is the name of a programs used for the display and analysis of data from the neutron scattering instruments at the S S facility For several years now a stable VAX VMS version of the software GENIE V2 has been in use at SIS Rutherford Appleton Laboratory Oxfordshire UK and at several scientific and commercial establishments world wide Constant improvements in the capabilities of the neutron scattering instruments at ISIS and in the hardware and software available for data analysis has necessitated a re write of GENIE The new GENIE is known as Open GENIE to reflect the intention that the software be used on a wide variety of different computers and operating systems It is aimed at supplying scientists with an inexpensive computer package which provides them with access to their experimental data so that they may analyse the data as required and display the results in a useful format usually in a graphical form Getting Started If you are new to Open GENIE we recommend that you work through The Three Wishes section of the User manual This should give you a clear idea of what facilities Open GENIE provides and how to use them After this working through one or two of the examples programs shoul
3. C the wrapper subroutine for MYFUNC xxx input into array X output into array Y SUBROUTINE DO_MYFUNC PARS_GET PARS_PUT IMPLICIT NONE INTEGER NPT_MAX NPT C We can handle NPT_MAX data points R NPT_MAX 1000 REAL X NPT_MAX Y NPT_MAX EXTERNAL PARS_GET PARS_PUT PARAME T T C print a blue message to the user CALL MODULE_INFORMATION Inside module MYFUNC called C Set NPT to the max size of the array On return NPT will be the number of data points passed NPT NPT_MAX C The input was placed in a workspace field called XVALS in GCL CALL MODULE_GET_REAL ARRAY PARS_GET XVALS X NPT IF NPT GT NPT_MAX THEN CALL MODULE_ERROR myfunc module Too many points RETURN ENDIF CALL MYFUNC X Y NPT C now return the result Y in a workspace field called YVALS CALL MODULE_PUT_REAL ARRAY PARS_PUT YVALS Y NPT RETURN END 41 3 Make the Module Library You need to compile the file containing the function and its associated wrapper using the Module Compile command this will produce a so file to load into Open GENIE gt gt Module Compile myfunc for Symbols do_myfunc This command first runs a FORTRAN compiler on the code then it produces a shared library from the object code If
4. Current default extension RAW Current default input AXPLIBSDISK OPENGENIE GENIE EXAMPLES DATA HRP08639 RAW Current default output gt gt To read a spectrum or multiple spectra from a raw data file the assign and spectrum commands can be used An alternative to this is to use the Get command The Get command is able to read data from either a raw data file or another of the supported data formats see Appendix B However this assumes that the data items in a file are either named explicitly or numbered For example the data read from a raw data file could be a spectrum or a user name The most useful parameters which can be taken from a raw data file are TITL the run title USER the user information NAME the instrument name NDET the number of detectors TTHE the two theta table Nsp1 the total number of spectra NTC1 the number of time channels LEN2 L2 for each detector and each individual spectra file are specified by an associated integer i e specifying 5 would get the fifth spectra from within a file For example print the user name then read in all the spectra in the file finally read every third spectrum from a file gt gt printn get USER usr local genie examples data hrp08639 raw WIFD RMI gt gt d2 get 1 get NSP1 gt gt spin_up get 1 50 3 Note if a file has been set using the Set File Input command then if
5. Handling Functions in the Reference Manual The basic operations on arrays are those of the corresponding data type plus e Arrayli j k This indexing allows individual array elements to be accessed using integer indices Note all indices start at one For example gt gt printn my_array 12 34 5 3 2 32 Array 11 12 13 14 This slicing of an array produces a smaller array with limits of 11 to 12 13 to 14 If variables are used as limits extra brackets must be included For example gt gt a my_array 2 4 4 100 gt gt b another_array i k e amp Appends the RHS array to the end of the LHS array for this operation both arrays must be of the same variable type Note the unary trig and transcendental functions are applied individually to each element of the array The binary operations are applied to the elements of the two arrays if the arrays differ in dimensionality the corresponding elements are selected using storage order The result of the operation is to create a new array of identical structure to the array on the left hand side of the operator If the LHS array is longer the extra elements are set to the undefined value nil in the result array while if the LHS array is shorter the result array is truncated to the length of the LHS array The comparisons test whether the elements and or length differ The basic operations on workspaces are those of the corresponding data type plus
6. Table of contents PART A USER MANUA D icsccssecscaccosssiacssasesstascatantesasscunsesassenstecescesscatecdeeueeteccsedsseaess WHATIS OPEN GENIE Voren iiia R AR E E N ona a e S 1 GETTING STARTED piion les tas aides a e a easy de A A AREN 1 STARTING UP OPEN GENIE fo a a a A AA AOA EA AAE a A AES 2 Remote operation of Open GENIE At ISTS ccccccccsccccecssececeessececeessaceceessneeesnssseeeens 2 Wad Dele States EEE eet cantata tate a tage hectares toes cot 2 b Viaa terminal emulator emenn aces sive see deve sees sees sagen vg son oben dette av seve nspas steve ob AEE 2 A FEW USEFUL FACTS ABOUT OPEN GENIE i sscicistessseuiisseescdsescsesiensbncaaseeiceassadonasvacts 3 COMTI S ori tac Seas a E n A E E a E A a EE OA 3 Data typ Sorri a EE EE E R A a a east 4 OPEV ALON Sass acts e a a a a a a a ea 6 Filenames aes enee S i atta elas 8 System commands from inside Open GENIE cccceccsceceessecesesnsecececsseeeeesseseeeenees 9 GETTING HELP svavinisacisnerssnuabasa i e a A a AA A R Na 11 A SIMPLE EXAMPLE oc 2 aha iai rii ii i i a a 12 THEPIRST WISH ACCESS TO DATA nnno snoaninneninanin tinu eana 16 Accessing raw data Spectra sscca accu sistas oes eacapcse ipsa eadeecial ns Meola eieate caste 16 Accessin ASCH FCN ninanais 18 THE SECOND WISH TO DISPLAY DATA sssseseseesesesssseseseesesesssseseseenesesssseseseenesesssses 20 Opening a graphics device seisein eieiei soeren r ioe uoe aeS Ee rore EE ESTEE Eoi EEEE kE Se CSEE 20 Displ
7. The basic mathematical functions are e trigonometric functions with the angle in radians Arccos Arcsin Arctan Cos Sin Tan For example print result in degrees gt gt y Arccos 0 5 180 Spi take the arccos of all elements in an array gt gt a Dimensions 10 create a 10 element array 30 SS fila 0 5 Set all elements to 0 5 gt gt y Arccos a e transcendental functions Exp Ln Log For example antilog a data array which is in logs to base 10 gt gt data Exp w y 1n 10 0 e other functions Abs L Sqrt For example Calculate the square root of Pi gt gt printn Sgrt SPL 1 77245310234149 Abs calculates the absolute value of a number or of the numbers in an array All negative numbers will be returned as positive numbers of the same magnitude 31 Workspace operations Workspace operations and transformations form the he allow analysis of the data taking into account its underl art of Open GENIE These ying form For example the Units command can be used to convert the units of a time of flight TOF spectrum This is only possible if some assumptions are made about the fields which are present in the workspaces containing the experimental data For the units command to work a workspace also requires fields giv ing parameters such as the primary flight path and incident angle a TOF spectrum
8. error 2341 4700 1027 1312 Array 2 sum 5482585 0 1054968 0 Array 2 The result of the integrate command is returned as a workspace with two fields the sum field contains either a single value or an array of integrals and the ERROR field contains the propagated error of the result Peak Provides interactive peak fitting of a workspace allowing selection of the bounds of the peak and the form of fit to use The available fits for use are 1 Gaussian a Gaussian peak sitting with a straight line background 2 Gaussian convoluted with an exponential a Gaussian convoluted with a sharp edged exponential sitting on a straight line background 3 Lorentzian a Lorentzian peak sitting on a straight line background 4 Lorentzian convoluted with exponential a Lorentzian convoluted with a sharp edged exponential sitting on a straight line background 5 Voigt a Voigt convoluted with a sharp edged exponential sitting on a straight line background th 6 Polynomial fits ann degree polynomial 36 7 Voigt convoluted with an exponential a Voigt convoluted with an exponential Once fitted the peak parameters of the fit are displayed and made available as a result so that they can be used later For example Fit peaks from a genie intermediate fil gt gt fit peak get 3 mydata in3 gt gt printn fit Note See the Peakfit and Peakgen in the Op
9. gt gt Asciifile Readfree Handle X Y E Swhitespace 30 gt gt wkl Asciifile data handle gt gt The second method enables several different items of data to be accumulated into a workspace before it is returned For example gt gt Asciifile Readfree Handle X1 Y1 E1 SWHITESPACE 4 gt gt Asciifile Readfree Handle X2 Y2 E2 SWHITESPACE 4 gt gt wkl Asciifile data Handle gt gt printn wkl Workspace x1 1 0 1 1 1 2 1 3 Array 4 yl 2 1 2 1 2 2 2 0 Array 4 18 el 0 0 0 1 0 2 0 0 Array 4 x2 1 4 1 5 1 61 7 Array 4 y2 2 0 2 0 2 0 2 0 Array 4 e2 0 1 0 1 0 2 0 0 Array 4 Note you can also use the Put Ascii command to output data to an Asciifile Other commands concerned with the input and output of data can be found in the Open GENIE reference manual 19 The Second Wish To Display Data Opening a graphics device Examples of the use of many of these commands may be found in the gcl procedures in the usr local genie examples directory on ISIS UNIX systems or AXPLIBSDISK OPENGENIE GENIE EXAMPLES on ISIS VMS Before you can plot any data you need to select a device on which to display the data gt gt Device open device type width height The default device is an X window XW Other supported devices include TEK4010 Tek 4010 compatible PS postscript CPS co
10. t work then it may be the result of picking the wrong FORTRAN compiler To change this you can edit the file config cache and then re run the configure command 63 Appendices Appendix A Features of the command line Pressing lt TAB gt on a partially completed command will complete the command if it is unambiguous otherwise pressing lt 7AB gt a second time will list possible options Pressing lt TAB gt also works for partially completed file directory paths Pressing lt Ctrl gt H on a partially complete command will give a one line summary of all commands matching that pattern Pressing lt Ctrl gt K will start a command keyword help search type in a one word query and all commands whose description matches this will be printed Pressing lt Ctrl gt R will start an incremental reverse search of previously typed commands Pressing lt Ctrl gt L will clear the screen and redraw the current line at the top Additional features Pressing lt Ctrl gt _ will undo a last edit change you made to the command line Pressing lt Ctrl gt X lt Ctrl gt U will also undo the last edit change Pressing lt Ctrl gt U will discard the rest of the line starting from the current cursor position Pressing lt Ctrl gt A will move the cursor to the beginning of line Pressing lt Ctrl gt E will move to end of the current line 64 Appendix B Supported Data File Formats Open GENIE supports access to the file formats
11. then held constant The data the fit and the residuals are then plotted e prisma diffuse gcl phon gcl examples of publication graphics by Mark Harris Loads ASCII data from a file creating a graph and plotting observed and theoretical data as markers and lines respectively e report report gcl this procedure demonstrates the ability to read data using an external FORTRAN program and the use of CONTOUR and CELL_ARRAY commands in making a colour contour plot on data taken on MARI e simple_graphics boxes gcl this procedure draws boxes on the plot window with corners chosen by the operator 52 dopamine gcl this procedure reads in a PRO file It then plots two ranges of observed data as points with the calculated data plotted as a line The difference between the calculated and data plot below The data file OPT17 PRO was obtained from a Rietveld fit of a structural model of deuterated dopamine hydrobromide to HRPD data funcplot gcl this plots a function of your own specification by writing a module on the fly and then using this module to generate the data points test_mutitplot gcl a procedure which produces a multi plot from a spectra and then Examples of multiplots constructs a multiplot from a 2 D array textcirc gcl draws the string A simple text string in a circle e slides slides gcl this procedure is a slide demonstration of Open GENIE s main features e two_d_graphics con
12. Workspace_divide w1 w2 Workspace_raised_to wl w2 Workspace_subtract wl w2 Workspace_modulo wl w2 Workspace_multiply wl w2 The characteristics i e final length dimensionality of arrays of the left hand workspace define those of the resultant workspace 33 e Comparison Operations Workspace_equal wl w2 Workspace_not_equal wl w2 The definition of the default routines are stored in the file workspace_user gcl which is included in the library directory of the Open GENIE distribution 34 Data Analysis Functions Arguably the most important purpose of Open GENIE is as a tool for scientific data analysis Not just for preliminary data analysis but as a framework which provides or from which can be called all the tools necessary to perform a complete analysis of the data Currently a large amount of data analysis is performed with a set of disparate FORTRAN programs which have to support their own routines to access data to drive a user interface and to work with a variety of different graphics packages What is critical and is very much at the heart of the philosophy of Open GENIE is that the scientist must have control over is how the data is processed A scientist may trust the Open GENIE peak fitting routines alternatively and probably more the case at the moment the scientists will want to continue to use their own analysis code in a C or FORTRAN subroutine for most things Open GENIE can be
13. corrected The corrected spectrum can now be displayed on a graph using the display command and the binning number altered to 10 gt gt alter binning 10 13 gt gt display corrected Opening graphics device XW Displayed using bin grouping of 10 To plot the two original spectra on the same plot but using different colours to show them clearly gt gt alter plotcolour blue gt gt plot background Plotted using bin grouping of 10 gt gt alter plotcolour red gt gt plot w Plotted using bin grouping of 10 gt gt The plot produced is shown below inatrument HAFO User WIFOL FRI Run number 0834 Run siyi te debe 19048 ST lt S Specht 7 Pkt date 12 Sepe D7 1Oe2052 C0 5K 20 120ms Im iS Heutran counts a J E 2x10 4x10 Bx10 axit 10 Time of Flight cs This brief example should have given you a good idea what an Open GENIE session looks like and a mental framework into which the more detailed information in the next three sections will fit The data file plotted here is typically available in the usr local genie examples data directory on UNIX or AXPLIBSDISK OPENGENIE GENIE EXAMPLES DATA and by changing the file locations in the example above you can reproduce this plot Note when help is typed 14 from within Open GENIE you will be told where Open GENIE is installed and from that you can deduce the position of the examples directory 15 The Firs
14. For example for a 2 D TOF Spectrum needs Ylabel Units for Y values Workspace Field Description Variable type X 1 D array of X values RealArray Y 2 D 2 D array of Y values RealArray E 2 D 2 D array of errors for Y field RealArray L1 primary flight path m Real L2 1 D secondary flight path m Real array Twotheta 1 D scattering angle degrees Real array Delta hold off in microseconds Real Emode energy mode Integer O inelastic 1 incident 2 transmitted Efixed fixed energy if applicable Real Xlabel Units for X values String String 32 Ut 1 D User parameters this array RealArray may be of any length and caters for information not already named in a field For more on the necessary fields required for operations then see the Open GENIE reference manual Template routines are called whenever an intrinsic operation involving workspaces is specified In most cases the errors are propagated through the calculation The template routines on workspaces are e Unary operations Trigonometric and transcendental functions For example w2 1n w1 is equivalent to w2 workspace_1n w1 and Workspace_arccos w is equivalent to acos w Other unary functions Workspace_sqrt sqrt w Workspace_abs Iwl and Workspace_negated w e Binary Operations Workspace_add wl w2 Workspace_append joins one end of one histogram to another w1 amp w2
15. Limits Alter Status Reports the values of all settings Alter Binning Sets bin grouping for plotting If the bin grouping value is set to a value greater than one the display command groups the data by averaging the values of n bin groups It is possible to apply the same operation to a standard workspace permanently using the Groupbins command Alter Device Changes the interactive device Alter Font Sets the text font for all the text used in the display Alter Hardcopy Changes the default hardcopy device when a Hardcopy command is issued Alter Linecolour Changes the axes and box colour Alter Linetype Changes the line style for line plots Alter Linewidth Changes the overall line thickness 23 Alter Markers Alter Markersize Alter Plot Alter Plotcolour Alter Size Alter Textheight Alter Textcolour For example Sets the marker plot symbol Changes the size of markers Changes the plot size Changes the data plot colour X window display size by a scale factor Text height as the percentage height of the display Label and title colour Change the axis colour to blue gt gt Alter linecolour SBLUE For a list of supported graphics devices supported colours supported fonts supported linestyles and supported markers see appendix D The Toggle command can be used to amend plots acting like an on off switch for various settings All the toggle comma
16. e lt workspace gt lt field name gt This field accessing allows its value to be read or set A field is automatically created in a workspace when a value is assigned to it The comparisons when operated on workspaces assume that the workspace is an Open GENIE spectrum but these operations can be modified by the user see the Open GENIE reference manual File names Open GENIE takes file names in either the VMS style or UNIX style depending on the system being used For VMS USERSDISK FAA GENIE TEST DAT or on UNIX usr users cmm genie test dat System commands from inside Open GENIE The cd command changes the default working directory while in Open GENIE For example Change to th xamples directory on UNIX gt gt cd usr local genie examples gt gt dir Note the directory path is as specified on the native operating system e g VMS or UNIX The dir command lists the files in the current directory or the directory specified on the host operating system For example List th xamples directory on VMS gt gt dir examples The pwd prints the current working directory For example Change to th xamples directory gt gt cd usr local genie examples gt gt pwd usr local genie examples The Os command prints the operating system Open GENIE is currently running For example Print the current operating system gt gt printn Os OSF The s
17. gz tar xvf genie 1 1 alpha dec osf3 2 tar cd genie 1 1 alpha dec osf3 2 To install GENIE in the default system location with data files in usr local genie executable files in usr local bin and library links in usr local lib type configure make install You will need to do the make install from the superuser or root account If you wish to see what make install will do without actually performing the install type make n install Note the above install can only be executed by the superuser and does a system wide installation If you do not have access to the superuser account you may 57 change the configure command to give different default installation directories for yourself for example configure prefix SHOME will change the default installation directories putting any binary files into your personal account s S HOME bin directory the rest of genie into a SHOME genie directory and library symbolic links in SHOME ib Note to run Open GENIE automatically your bin directory will need to be in your PATH Once Open GENIE is installed it can be invoked by running the genie script in the bin directory If the bin directory is specified in your shell PATH environment variable you should be able to just type genie If you are using a C shell then before the command will work properly you need to type rehash b VMS Installation Below are the steps needed to get Open G
18. histograms lines or markers respectively While the Multiplot qualifier expands a region of a multiplot For example Zoom in on the current plot and re display with error bars gt gt zoom errors Plotting data from an ASCII file In this example the data used is prs_001 obs which can be found in the directory of genie examples prisma To construct a plot if you have read in a non Open 25 GENIE type file e g an ASCII X Y E file into w x w y w e then after opening a new graphics device using gt gt Device Open a window must be created with the win_ commands In this case a Scaled or AutoScaled window is created by gt gt Win_Scaled 0 1 0 9 0 1 0 9 0 975 7 475 0 02 0 17 The first four numbers define the device co ordinates the position of the plotting box on the page and the last four numbers are the global co ordinates the X and Y range of the plot The points of the graphical device range from 0 0 and 1 0 By using the Win_Autoscale command and quoting the x and y arrays in the parameter list the range of the plot are chosen automatically for example gt gt Win_Autoscaled 0 1 0 9 0 1 0 9 w x w y w e SRed where w is the workspace containing the data and the red parameter will paint the chosen window red instead of the default black Now we can create the graph gt gt Graph Draw w x w y green axes can be drawn by gt gt axes draw colour Sgreen By default the axes are linear and the
19. listed below e ISIS Raw File Read only e GENIE II Intermediate file Read only e Open GENIE Intermediate File Read and Write Machine independent e Open GENIE ASCII File Read and Write e HDF Files Write only These files can all be read directly with the Get and Put commands by specifying numbered or named data elements Open GENIE supports access to any format of ASCII file via the Asciifile command 65 Appendix C Supported Graphics Devices Below is a list of graphics devices currently supported by Open GENIE these rely upon the PGPLOT package and it may well be possible to use other pgplot drivers with Open GENIE In the distributed version of Open GENIE we have only checked out the functioning of the devices below on all platforms To see other devices which may be available on a particular version of Open GENIE type gt gt Device Open Help Device Name Description String Tcl Tk driver TK or tk X Windows devices XWINDOW or xw Postscript portrait PS or ps Colour Postscript portrait CPS or cps Postscript landscape PS or ps Colour Postscript VCPS or veps landscape 66 Appendix D Supported Graphics Attributes Fonts Open GENIE uses the PGPLOT fonts when drawing fonts onto the open graphics device currently the supported fonts available are SNORMAL SROMAN SITALIC
20. no file is stipulated it defaults to this file To save Open GENIE variables to an intermediate binary file the Put command is used These variables may optionally be tagged with a label which can be used for later reading or comments may also be added For example Copy a whole multidimensional spectrum from a raw file into a single item in an intermediate fil gt gt Set File Input usr local genie examples data irs12839 raw gt gt Set File Output example in3 gt gt Put get 1 20 label bigspec comment demo 17 which can then be read with gt gt get bigspec Accessing ASCII files To read in data from an ASCII file for example from the file prs_001 obs which can be found in the PRISMA directory of the Open GENIE example area Read in three data arrays of 30 points in columns separated by a whitespace and assign to arrays in fields X Y and E in the new workspace gt gt handle Asciifile Open usr local genie examples prisma prs_0 O1 obs gt gt wk1l Asciifile Readfree Handle X Y E Swhitespace 30 gt gt printn wkl Workspace x 0 925 0 975 1 02499999999999 1 07499999999999 1 125 Array 30 y 0 22526098 0 11728537 0 126243569999999 0 144312439999999 0 15559034 Array 30 e 0 009967181499999 0 0043424088 0 004095190999999 0 003976735 0 0038093579 Array 30 gt gt or alternatively
21. of a returned workspace containing various data types with named variables The wrapper subroutine must obey the following rules e It must be a SUBROUTINE taking just two parameters called PARS_GET and PARS_PUT These parameters should be declared EXTERNAL and not be accessed in anyway except via module_ commands e It must allocate the variables needed by the user s SUBROUTINE and transfer data to from them using module_get_ and module_put_ calls e As input output devices are re assigned by Open Genie READ 5 commands should be avoided and screen output should be handled via the module_print 40 and module_information commands Inside the module Open GENIE variables are accessed by workspace field names For example in the program below the array X is loaded from the field labelled XVALS where it has been placed by a GCL procedure There is no restriction on how you label a variable but often you will use the variable name itself All module_get_ routines must specify Pars_Get as the first parameter and similarly all module_put routines specify Pars_Put these variables are in fact just references to the input output parameter workspaces of the Module Execute command For a full list of module_ functions see the FORTRAN module interface in the Open GENIE reference manual For our example myfunc the wrapper would be
22. picture on the current device type gt gt Redraw 0 Display a cursor on the graphics screen to allow annotation This is done using the cursor command An obvious use is for tagging peaks with the data value in the X or Y direction at the point selected by the cursor For example Display a cursor near th xpected position of a peak in world co ordinates gt gt Cursor Horizontal 10000 0 50 0 28 If vertical is used instead then the text is drawn vertically a cursor is displayed and waits for a pressed key if X displays X co ordinate Y displays Y co ordinate P displays both co ordinates T to add text and E exit See also the Get Cursor command in the Open GENIE reference manual To save a hardcopy of the graphics into a file The Hardcopy command allows a copy to be made of either the currently displayed window or an earlier picture to a postscript file For example Save a copy of the last but one picture as colour postscript found with Redraw Info gt gt Hardcopy filename test cps picture my_pict The default name of the file into which the hardcopy is placed is GENIE PS The filename extension is one of the supported hardcopy graphics devices For full details of supported devices on each machine type see the appendix The default picture selected is 0 the last picture created Normally just typing Hardcopy is sufficient to make a hardcopy of the current scree
23. the compilation fails for any reason you will see various error messages on the screen and the creation of the shared library will be aborted On a successful run you will see a message similar to the following Module now compiled load with Module Load myfunc so The Symbols parameter must be set to a comma separated list of wrapper subroutines that you wish to call from Open GENIE via Module Execute 4 Load the module into Open GENIE To load the module use Module Load command with the name of the so file created by the Module Compile You can also supply a comment that will be displayed when you later type Module List gt gt Module List myfunc so My function module You only need to reload a module if you change the source code and have executed another Module Compile command 5 Package function arguments into a workspace You now need to create a workspace to hold the parameters for the Subroutine you wish to call in the module The fields in the workspace must have the same names as those you specified in the second argument of your module_get calls above In our case we only have one variable and we called it XVALS so assuming X is the array we wish to send gt gt X Dimensions 10 create a new array gt gt Fill X 1 0 1 0 Fill array with numbers 1 0 to 10 0 42 gt gt Pars Fields create an empty workspace for module arguments gt gt P
24. the display surface on the currently open device gt gt Device Clear While gt gt Device Close deactivates the currently open graphics device Performing a multiplot of 2 D spectra on the same x axis This is done using the Mult iplot command and it is useful for comparing groups of spectra from different detectors A pseudo Y axis is produced where successive plots are placed with an artificial Y offset value ygap Currently multiplot only plots as a histogram If used to plot a spectra from a raw file then the data source for the multiplot can be specified using the Set File command For example Do multiplots from a file gt gt multiplot 1 20 file mydata raw ygap 10 0 gt gt multiplot 1 300 3 plot every third spectrum Optional parameters note the types are Linecolour Colour Linetype LineStyle Linewidth Real Textcolour Colour1 Textheight Real 22 Overplotting an existing graph This is done using the Plot command which does not have the ability to create axes or scale the data For example Plot a vanadium spectrum on top of the data as a comparison gt gt Display s 5 xmin 20000 0 gt gt Plot Line get vanadiuml normal in3 Qualifiers Histogram Line Markers Errors Altering the graphics parameters in the Display Plot and Multiplot commands Modifying characteristics of the plot is achieved using the commands Alter Toggle Or
25. this will usually find the appropriate data files and set up the appropriate data directory link It is best that these programs are load and run from the appropriate directory For example using the the file dopamine gcl in the directory usr local genie examples simple_graphics Firstly change to this directory and then load the program using gt gt Load dopamine gcl and run these programs using the name of the file in this case gt gt dopamine Before running most of the programs you will have to execute adevice open command e Analysis focus_example gcl this example puts the necessary defaults into a workspace that is required for focusing data from an IRIS raw data file For large data files a link is made in the program directory to an external data area to avoid keeping large files in the source tree however the access remains the same 50 integrate_example gcl integrates a single spectra and a set of single spectra rebin_example gcl rebins the data to the same range but different number of time channels then integrates the spectra The procedure then rebins to a given X range to a set of given X values and to linear steps in a given range and then integrated The data is then rebinned using logarithmic steps and integrated e Contour contour_test gcl draws a filled colour contour plot and then overplots two sets of contour lines e IRIS add gcl procedure to analyse I
26. used to provide the user interface graphics and file access This mechanism is described fully in the next section of this manual on modules and these allow the code to be run as if it was a compiled part of Open GENIE Routines which have been found to be useful in several different areas of analysis are hard coded in C C or FORTRAN for efficiency The current routines available are Focus Focus a range of time of flight spectra from detectors at different scattering angles with given parameters This command although written specifically for focusing multiple banks of detectors consecutively can be used for single scanning detectors data To focus the spectra in d spacing with the D switch or in momentum transfer with the Q switch the time of flight parameters are required which can be specified from a file the default are the values from the raw file Note the default is the p switch where spectra are summed in d space For example Focus a time of flight spectrum in D spacing get the TOF parameters from the raw data file 35 gt gt w focus 1 17 irs12838 raw Focus default file every third period gt gt assign 3045 gt gt refl focus 3 90 3 _ mydet Integrate Integrate a D or 2 D spectra For example print the integrals of two spectra gt gt printn integrate 1 2 38000 78000 tfx00345 raw INTEGRATE Integrating between 38000 and 7800 Workspace
27. within double quotes e g my_quote to avoid any conflict with variable names When the character is used in a string it introduces control sequences for example w puts in a newline For more see the section on storage in the Open GENIE reference manual Data types may be either constants or variables Constants are prefixed by a s and can only have a value assigned to them once usually when they are first created All available constants can be viewed by typing gt gt Show Const System constants are prefixed by _ and can be viewed with gt gt show const sys Variables are created by assigning a value to an unused variable name A variable oe 393 name may consist of alphanumeric characters the character or numbers but must start with a letter Examples are gt gt A 2 0 B 6 To see all the defined variables type gt gt Show Var oe 99 All variables are preceded by an underscore are reserved for internal use by Open GENIE and these may change or be removed at any time and therefore you should avoid using any variable starting with _ The command gt gt Show Var Sys will show all system variables Arrays are structures that contain more than one variable There are three array types one for each of the basic variable types An array is created by first generating an empty array of the appropriate size and dimensionality using the Dimensions function and then by assigni
28. x and y axes are labelled horizontally and vertically respectively To display x y labels on the graphics device gt gt labels draw X Axis Y Axis To draw text on the graphics device gt gt text draw 0 0 1 0 some text colour Syellow size 3 0 angle 45 0 font Sscript the position is specified in world co ordinates To display a title on the graphics device gt gt title draw A Title 26 Comparing this data with the data from the file prs_001_Imf cor after loading the ASCII data file into the w1 x wl y and wl e plot the data with markers as blue crosses gt gt markers draw wl x wl y Blue S Cross 2 To include Y error bars gt gt errors draw Vertical w x w y w e SBlue 2 and to draw a green graticule on the window gt gt graticule draw colour green Note for a complete list of qualifiers associated with these commands see the Open GENIE reference manual To ensure the above picture and its associated objects can be referred to later after a new picture has been created then initially a picture should be created gt gt picturel Picture and then the following commands used gt gt scaledl Win_Scaled 0 1 0 9 0 1 0 9 0 975 7 475 0 02 0 17 gt gt graphl GRAPH DRAW w x w y gt gt axesl axes draw colour Sgreen gt gt labelsl labels draw X Axis Y Axis gt gt textl text draw 0 0 1 0 some text colour Syellow size 3 0 angle 45 font Sscript gt gt
29. ENIE running on a Dec alpha AXP machine running VMS6 2 or later All VMS alpha kits are supplied as compressed zip files made by the public domain zip program To decompress you will need to have unzip installed If unzip is not installed by default on your system then to set up the command type the following line Sunzip disk directory unzip_axp exe where disk directory is the location of the unzip_axp exe file this is available from the Open GENIE web pages Uncompress the Open GENIE kit using the command below you will need approximately 40000 blocks of disk space to successfully uncompress and install Open GENIE 58 Sunzip genie 1_0 alpha dec vms6_2 zip This creates a directory called disk directory OPENGENIE_1_1 To run Open GENIE you will need to set up the definition Sopengenie disk directory opengenie_1_1 genie_setup either your own LOGIN COM or the system wide SYLOGIN COM This enables Open GENIE to be run using the command opengenie For installing Open GENIE on a system which is shared between several users you may want to install the shared library and executable files as known shareable images This is done by adding the lines SINSTALL ADD disk directory OPENGENIE_1_1 GENIE genie so OPEN HEADER SHARED RESIDENT SINSTALL ADD disk directory OPENGENIE_1_1 GENIE G
30. LLATION eieren E a T saat aeeaane 57 SOURCE CODE INSTALLATION necie oseiro aieea ea eee E EEA A EE a 60 Operating system specific NnoteS ssessssseeensseeeesseseessssessssesssseresssereessesesssssreses gt 62 TATU En cae bes EEE EEE EEE E EE E E EEE 62 LIRIK E EE SEEE E E EATE EE E E E EE EE te 63 NMS e Mah a a a at Maia a Maca ett 63 APPENDIX Arshat n Megs ste dre ines ca cecut T tat de duce n e deg ioe desa ieee ieee 64 ili Features of the Command Me dccauwanindasu neha da wide 64 Additional featuies 2 3 sei eee da sedis eed ee eee A Sede erk i Ree 64 ACPPENDIX B ve ssidesceszoctuncesinaverulet uizes E 65 Supported Data File FOTIMMGS sccssie Meats wise siass aaltaasaveadts sbeaaisiawasstegs aa iandauandee dt eabas 65 APPEND CG ease eee Ge BE ee ee BGO Cie re Gina 66 Supported Graphics Devices is sntvcicaveccndesvdtworaavsciaiaiorns teousoceduaranensianeouatinorcorbedaes 66 APPENDIX Doeiii etss ae tate esie aeonit at aae aleoj ea aaa 67 Supported Graphics Attributes esssssessssseeessseseosseseosssseesssseressseseesseseessssessssee 67 Fonts E EE ee a eee es eee i oe eee eed 67 Markers sccsia coiieeccisneon heihind A ai E ohne eee Res 67 TEIMESCV IES Fassett tna ie Nectar E EES coettees Gabon Shed E ETE Bedi Shih od aes 67 COIGUES os vec eA hte othe eile SE nes oe eh i de A LE st ce cae 68 JANINDA EEEE E sa ae cay cece eee ea calcd ated tases eee cates Gees 69 Commands required for installing Open GENIE from a CD ROM
31. MAIN OPEN HEADER SHARED RESIDENT to the SYSTARTUP_VMS COM file in SYS STARTUP c WindowsNT amp WINDOWS 95 installation Windows NT and Windows 95 are currently not supported but will be made available in subsequent releases 59 Source Code Installation Unless you are fully prepared to compile a fairly complex software system written in C C we recommend that you check for a binary installation of Open GENIE and install that instead Source code installation is normally more complicated than the Binary installation but it is useful if a you need to install Open GENIE on a machine operating system combination for which we have not yet provided a binary installation b you wish to develop or modify the Open GENIE code in some way It is also very likely that you will need to have some familiarity with the C C and FORTRAN compilers on your system Generally we would recommend that you install GNU g and use either g77 or the native FORTRAN compiler for building Open GENIE Before embarking on a source code build it may well be worth mailing us at genie isise rl ac uk to check that we are not planning to do a similar build or that someone else has not already done one The source code is distributed in a compressed tar file which you will need to unwind in a suitable development area The PGPLOT and Splash libraries are distributed as separate distributions which will need to b
32. RIS diffraction data Developed by P Marshall e Data This directory holds the data used for some of the procedures in the examples section e exl dssdemo gcl this demonstrates the use of different plot styles with error bars and line plots of linear and logarithmic scales contains various examples of programs concerned with the input and output of data from genie ascii_file gcl demonstrates the use of Open GENIE routines to read write ASCII data using the ASCIIFILE command ascii_io gcl demonstrates the use of Open GENIE routines to output and input data in a fixed easy reading ASCII file format using the Get and Put command intermediate_file gcl gives an example of the use of the Open GENIE routines to manipulate intermediate files 51 raw_file gcl example of the use of Open GENIE routines to read and manipulate spectra from ISIS raw files e modules This directory gives examples of wrapping routines c_example gcl and fortran_example gcl for the calling of a module from within Open GENIE written in gcl and examples of a such modules for C and FORTRAN c_example c and fortran_example f e newget In this section examples are given of C C and FORTRAN files which can be used like the get function of Open GENIE e peak pktest gcl a procedure which generates data from a quadratic equation and then fits a cubic equation to the data with the linear part of the function inputted by the user and
33. SCRIPT Note For accessing special scientific Greek characters within these fonts the documented PGPLOT escape sequences may be used in the Open GENIE text string being plotted For example Time of Flight gms where gm produces a Greek u character For further details see the PGPLOT documentation available at ftp astro caltech edu pub pgplot Markers Markers types available for plotting SPOINT SPLUS SSTAR SCIRCLE SCROSS SBOX Linestyles Linestyles available for plotting SFULL SDASH SDOT_DASH SDOT 67 Colours Pre defined colours available for the graphics by default For using further colours in the graphics see the Open Genie reference manual SBLACK SWHIT ti pa D Gl UO SPURPLE SCRIMSON SDARK_GRAY SLIGHT_GRAY 68 Appendix E Commands required for installing Open GENIE from a CD ROM Please note that these commands vary depending on the version of the operating system you are using Installing on UNIX with Digital UNIX Initially find the CD gt file dev rrz c and look for an RRD device e g RRD42 on dev rrz4c then mount the CD gt mount t cdfs o ro rrip dev rz4c mnt then get the kit gt cp mnt osf genie 1 1 31F Note you will need to have the CDFS kernel option enabled Installing on VMS Type in for example Smount DKA400 GENIE11 Scopy sys scratch log 69
34. The ISIS OPEN GENIE User Manual F A Akeroyd R L Ashworth S D Johnston J M Martin C M Moreton Smith D S Sivia version l l Forward This manual should enable you to become familiar with Open GENIE quickly and easily It therefore complements the Open GENIE Reference Manual which should be used to understand the full meaning of Open GENIE commands The reference manual is accessible on the ISIS web server at http www isis rl ac uk GENIEReferenceManual and the user manual is planned to be accessible by January 98 at http www isis rl ac uk GENIEUserManual The Open GENIE User Manual is separated into two parts e Part A The User Manual An introduction to the use of Open GENIE e Part B The nstallation Guide General information on how to install and run Open GENIE Assuming that you are new to Open GENIE and have just downloaded a copy you will need to consult the Installation Guide to get Open GENIE installed on your machine After this we recommend you experiment with some of the example files to get an idea of the capabilities of Open GENIE For further information comments additions of routines that you feel should be included please contact us at genie isise rl ac uk To be kept up to date with new releases send a message to genie announce request isise rl ac uk with no subject and the body of the message containing the two lines this will add you to the mailing list SUBSCRIBE QUIT
35. ars Xvals X add X to workspace as field Xvals 6 Execute the module and get the result This is achieved by gt gt MY_RESULT Module Execute my_func Pars where my_func is the name of the FORTRAN wrapper routine you wrote and Pars is the packaged arguments workspace created above The values specified in module_put calls will appear in the returned workspace MY_RESULT in the above case MY_RESULT will contain one entry called YVALS so we can type gt gt Printn MY_RESULT YVALS and see squared X values A Real Life Sample Module The following module was created by Spencer Howells at ISIS the code is available in the ex2 subdirectory of the examples area as g2s gcl and g2s for First the GCL procedure that calls the module Procedures for G2S PROCEDURE g2s PARAMETERS wg workspace RESULT ws LOCAL g2s res ws wg g2s fields g2s lptin wg ntc g2s Xin wg x g2s Yin wg y g2s Ein wg e g2s qmax inquire g2s gt qmax g2s npt inguire g2s gt number of points g2s ic inquire g2s gt window function code g2s rho inguire g2s gt number density module load g2s so res module execute g2s g2s ws ntc res lptout ws x res xXout ws y res Yout ws e res Hout 43 ws Xlabel res xcaptout ENDPROCEDURE Now the FORTRAN program that performs the actual calculation
36. ay cmodule_get_real_array pars_get name amp val_array amp len do some manipulations and return new values cmodule_put_real_array pars_put name val_array len free val_array release storage If a pointer is not NULL the routine will assume it points to valid storage of size len on return Jen will be set to the number of elements of the array actually set or 0 on an error A C module must contain the following header files include lt genie_cmodule h gt include lt genie_cmodule_ver h gt to set up the correct definitions and typedefs The MODULE COMPILE C Open GENIE command will insert the correct path for picking up these header files but they are contained in the GENIE_DIR library directory if you wish to peruse them The C module function must be declared like void my_cmodule GenieWorkspace pars_get GenieWorkspace pars_put if cmodule_version_ok CMODULE_MAJOR_VERSION CMODULE_MINOR_VERSION cmodule_print Library version mismatch in MY_C_MODULE CMODULE_PRINT_ERROR return all OK proceed Variables are obtained and set by calling the following functions with either pars_get or pars_put and the variable name taken from Genie_Dir library genie_cmodule h 47 Get REAL parameter NAME from GENIE as VAL void cmodule_get_real GenieWorkspace pars_get co
37. aying a graphical plot of spectra from a workspace eeessseeesseresssrrersreersrrerrrreseereseees 20 Performing a multiplot of 2 D spectra on the same X aXis ssssessesesesssessesresseessrsseresseeseeseee 22 Overplotting an existing Qraph a cece ese cesecseecceeecseecseesaecseecaeecsecseecaeecaecaaecaaeeaeesaeeaeeeas 23 Altering the graphics parameters in the Display Plot and Multiplot commands 23 Magnify a portion of the plot chosen interactively eee cecesecseecseeesecsseceeseceaecaeecaeenaeaee 25 Plotting data from an ASCII file oo eee eeececsceeeeeeeceeeeseeeeceseeeaeseaeesessaeseeeeseeeaeseaeeeeseneeeas 25 ii Making alterations oc enren aoai iaa a a a a a E E E a Si 27 Display a cursor on the graphics screen to allow annotation eeesseesseeeseeseeresesrerrsresesreesees 28 To save a hardcopy of the graphics into a file eee ces ceeceeceeceseceseesecaecaeeseesseeaeenees 29 Procedures iou nan E E E E A EE E E AEE 29 THE FINAL WISH TO MANIPULATE DATA s ssssssssssssseseseesesessseseseenesennsseseseenesesseses 30 Mathematical functions s ssoseesnsseeesseeeessssesssseseessereosseseessssresssseeeessereesseseesssseees 30 Wo rkspa ce operatl onssa a a aaa aa aa a aiai siaaa 32 Da ta Analysis FUNC NS minien a aa Ea 35 The Open GENIE Module Interface cess cesonthasa te tosh ial thle hoe acanegshentac Ua vlbead daes 39 Whats a MOUS oreca e Sehack phe belb end vdecen A E E a E E E T 39 Whe
38. c1 next time This is achieved using the save gt gt Save my_saved_session The session can be re started by the command Wwa genie my_saved_session The are needed because the first argument can be used to load up a gc file on start up instead of SHOME genieinit gcl Thus you are able to define commands for different start ups for example VMS marigenie opengenie sys login mariinit gcl UNIX C shell alias marigenie genie SHOME mariinit gcl 55 Part B Installation Guide Installing Open GENIE Open GENIE is available as a binary distribution for the common machine types and in a source code distribution for anything else If the binary distribution is available for your machine and operating system this is the easiest way to install Open GENIE The binary distribution kits are marked with the name of the machine the operating system and the manufacturer of the machine range if known For example alpha dec osf3 2 means that the version of Open GENIE in the binary distribution was made for a machine with an alpha AXP processor in a machine manufactured by Digital Equipment Corporation and running Version 3 2 of the OSF operating system which is now called Digital UNIX In general all these should match with your system for a binary kit to work If you are running a version of UNIX but are unsure of these details you can download the file config guess directly fr
39. d provide sufficient knowledge to enable you to work with Open Genie For the more experienced GENIE user a brief read of the User manual is recommended to determine the differences between older versions of GENIE and the new revised Open GENIE Starting up Open Genie Remote operation of Open GENIE at ISIS a Via Telnet Firstly telnet into one of the main VMS server machines ptath horus or thoth using gt telnet ptath nd rl ac uk If you want to use the graphics you will need to set the X display back to your local machine Sset display create tran tcpip node your own machines ip address and start Open GENIE by typing Sopengenie b Via a terminal emulator If you start remote sessions on a UNIX workstation via a terminal emulator such as eXceed or eXcursion you can start Open GENIE directly by telling rexec to run the rgenie command Note the full pathname may be required for example gt usr local bin rgenie The rgenie command can take several parameters for further details type gt man rgenie A typical use may be to start Open GENIE with your own genieinit gcl file for example gt rgenie myinit gcl An alternative is to use the terminal emulator to set up an xterm or a decterm on one of the UNIX or VMS workstations from which Open GENIE can then be run A few useful facts about Open GENIE Commands Commands in GENIE are entered via the command line The command li
40. e unpacked in PGLOT and Splash subdirectories respectively We have to do this because Open GENIE is being distributed under the GNU licence and the other packages though freely available are not Following this the trees must be patched to update them with modifications and files added for Open GENIE The commands needed will be similar to the ones shown below cat genie 1 l tar gz gunzip tar xf cd genie 1 1 cat pgplot5 1 1 tar gz gunzip tar xf cd splash cat splashl 7 tar Z gunzip tar xf 60 The pgplot tree should now be in the pgplof subdirectory and splash in the splash subdirectory The patches can be applied with the commands cd genie 1 1 pgplot patch p2 s lt pgplot 5 1 1 patch cd splash patch p2 s lt splash 1 7 patch These patches should apply fully without asking questions if you get a question such as File to patch check that pgplot and splash were extracted correctly so that the paths genie 1 1 pgplot makemake and genie 1 1 splash Makefile in both point to valid files Ideally the code will now build automatically if you type cd genie 1 1 configure make all this builds the development version of Open GENIE which can be run by typing parser from within the src directory To go the whole way and build an install kit for your system you will need to do a make kit to build a compressed tar file for a binary installation This can then be i
41. en GENIE reference manual for more control and detail Rebin The rebin command performs an interpolation from one histogram into another histogram with the same integrated count but with modified X boundaries Some numerical precision is lost during a re binning operation and there is usually a degree of peak broadening so multiple re binning is to be avoided The Lin and Log qualifiers allow a Linear or Logarithmic rebinning between the specified boundaries to be performed For linear rebinning the boundaries are specified in steps for logarithmic bin widths these are calculated such that for any given binning range Xn 1 Xn Step Xn For example given the command gt gt w rebin log w 10 0 0 1 15 0 Here the step is 0 1 and the range of the rebinning is between 10 and 15 The bin boundaries generated will be 10 11 12 1 13 31 14 641 15 A workspace can also be rebinned according to another workspace For example Read a spectrum and re bin the same as an already loaded vanadium workspace gt gt w s 1 gt gt w rebin w vanadium x Units 37 This command converts the units of time of flight spectra Using the switches they can be converted respectively to C or Channel to Channel numbers one way D To D Spacing A Pa E To Energy meV LAM To Wavelength A Q To Momentum Transfer D SQ To Momentum Transfer A T To Time of Flight us LA1 To p
42. ensionsal array to GENIE the array val has ndims dimensions and these are stored sequentially in the array dims_array fort_int cmodule_put_nd_real_array GenieWorkspace pars_put const char name const fort_real val const fort_int dims_array fort_int ndims return MAJOR and MINOR version of genie module interface fort_int cmodule_get_version fort_int major fort_int minor Check versions MAJOR and MINOR are compatable with the current genie module interface return 1 if all OK O0 if an error fort_int cmodule_version_ok fort_int major fort_int minor An example of a program to illustrate calling a module from C can be found in the directory GENIEDIR examples modules c_example c While an example of a GCL procedure to call the C module can be found at G ENI EDIR examples modules c_example gcl 49 Example Open GENIE programs The basic commands of Open GENIE plus multiline commands for example IF ELSE ENDIF statements can be combined into gc procedures Below is a list of examples these are arranged so that the programs can be easily run by Open GENIE test routines or by someone trying to get an idea of what Open GENIE can do Most programs have their own directory with the data required taken from files stored in this area If program fails to link change into the example directory and type gt make links
43. erations The normal operations on integers and real numbers are e x y If x is an integer then the result will be an integer no matter whether y is fractional or not e and the remainder or modulo function For the quotient and remainder operations on integers the convention is to truncate towards zero e lt gt lt gt The comparisons of less than and greater than equal to gt 2 less than or equal to greater than or equal to and not equal to respectively e Sin x Cos x Tan x Arcsin x Arccos x Arctan x The trigonometric functions where x is quoted in radians The constant P1 is available for conversion to degrees Log x Ln x Exp x the Transcendental functions Note the results of the trig and transcendental operations on integers are given as real numbers and when an expression contains integers and real numbers the result is given as real after implicitly converting any integer values to corresponding real values The normal operations on strings are e or concatenates two strings For example gt gt A Hello there amp I e lt gt lt gt For strings of the same length the comparisons act as a test based on the collating order of the text in the strings For strings of different lengths comparisons are between the string lengths e Substring Locate Length for more information see String
44. har eq 1 then LMOD true else LMOD false endif endif if LMOD then A PI xin lptin do nn 1 1lptin yw nn SIN xin nn A xin nn A end do else do nn 1 1lptin yw nn 1 0 end do endif C FORM VECTOR OF EQUALLY SPACED R S AT WHICH THE FOURIER TRANSFORM C IS TO BE COMPUTED RMAX IN ANGSTROMS AND THE NUMBER OF R POINTS Cc Fl DO NR 1 1lptout xout NR delq NR end do C THE NUMBER OF POINTS IN THE RANGE OF DATA TO BE TRANSFORMED xd xin 2 xin 1 2 half x channel do n 1 lptin C xnew n xin n xd offset mid channel xnew n xin n yw n yw n yin n 1 xnew n end do C COMPUTE FOURIER TRANSFORM OF THE DATA Cc delr xin lptin xin 1 lptin 1 AFACT delr 2 0 PI DO 35 NR 1 1ptout FS 0 0 RP xout NR DO N 2 1ptin SINUS1 SIN xnew N 1 RP SINUS SIN xnew N RP 45 FS FS SINUS yw N 1 SINUS1 yw N 1 2 0 end do yout NR FS AFACT 35 CONTINU Gl pir PI PI 2 RHO do n 1 1lptout yout n yout n pir xout n 1 end do xcaptout Q Angstrom 1 ycaptout Structure Factor S of Q call module_put_int g2s_put lptout LPTOUT call module_put_real_array g2s_put Xout Xout lptout call module_put_real_array g2s_put Yout Yout npt call module_put_real_array g2s_put Eout Eout npt call module_put_st
45. ilename extension raw On UNIX the commands for setting defaults are similar and use the appropriate syntax for UNIX file names except no Set Disk command is needed However on all operating systems it is essential to put string arguments in double quotes gt gt set instrument hrp Default instrument hrp gt gt set directory usr local genie examples data Default directory usr local genie examples data n gt gt set extension raw Default filename extension raw Any raw set of data can then be collected using the Assign command followed by the run number gt gt assign 8639 Default input usr local genie examples data hrp08639 raw An alternative is to use the Set File Input command which explicitly sets the file to be used For example gt gt Set File Input usr local genie examples data hrp08639 raw Default input usr local genie examples data hrp08639 raw Now that the source for the data has been selected individual spectra can be extracted from the data set using the spect rum function which can be normally abbreviated to oe 29 gt gt w s 7 Reading spectrum 7 usr local genie examples data hrp08639 raw gt gt noise s 1 Reading spectrum 1 usr local genie examples data hrp08639 raw gt gt corrected w nois Here the seventh spectrum is read into the workspace w The first spectrum in the file is subtracted from the spectrum in w and the result is put into the workspace
46. lour postscript and HPGL HPGL driver for 7475A For full details of the supported devices on each machine see the supported graphics devices in appendix B The size of the page in inches is defined by the width and height parameters the default value is taken to be 8 inches Alternatively you can open a device with a name gt gt devicel Device Open type width height This is useful as Open GENIE supports multiple open devices a given window can then be selected using the Select command For example gt gt Select Devicel Displaying a graphical plot of spectra from a workspace After the data has been read into a workspace from a RAW file or intermediate GENIE file the data can then be plotted using the display command The plot will be automatically scaled and titled with other relevant information from the workspace For example Display a spectrum but change the title first gt gt wm s 10 gt gt wm title This is my Nobel plot gt gt display wm 0 100 35 70 20 Alternatively you can plot it directly using gt gt display s 10 which displays the 10 spectra of the default input file or alternatively use the Get play p p command gt gt Display get 10 hrp00273 raw The parameters after the workspace wm are respectively xmin xmax ymin ymax All the parameters except for the workspace are optional and where omitted a default value will apply Specifying a keyword for each
47. m a file or directly from the data acquisition electronics Wish 2 Display their data on the screen and make a hardcopy on a printer Wish 3 Manipulate their data for example to focus or normalise it These are described separately in the following sections but first this A Simple Example Below is a description of a simple Open GENIE session to access time of flight data taken on the High Resolution Powder Diffraction HRPD instrument which gives you some idea of the usage of Open GENIE commands Sopengenie Open GENIE V1 0 BUILD 23 Linked Thu Jan 2 15 26 39 GMT 1997 library version 1 0 Running on alpha VMS 6 2 built with DEC C V5 3 gt gt for UNIX systems use gt genie Now that Open GENIE is running most people will wish to set up some defaults to allow easy access to files in the data area of the instrument they are using If you always use one instrument these defaults can be set up in a command file to be run automatically when Open GENIE starts Normally Open GENIE looks for the file genieinit gcl in your home directory so the defaults can be placed in that file gt gt set disk axplib disk Default disk axplib disk gt gt set instrument hrp Default instrument hrp 12 gt gt set directory OPENGENIE GENIE EXAMPLES DATA Default directory OPENGENIE GENIE EXAMPLES DATA n gt gt set extension raw Default f
48. mand to perform the plot as a line rather than a histogram and w1 is the parameter When the Open GENIE procedure is implemented in an expression in the functional style qualifiers are specified by placing a colon separated list after the function name and before the parentheses containing the parameter list For example in the case of the Asciifile command to open a file gt gt file Asciifile open mydata dat functional style gt gt Asciifile Close mydata dat keyword command style Note comments can be included by using the symbol before the comment everything following this is ignored Data types In Open GENIE you can create new data easily and these can be independent from each other or grouped together into arrays or workspaces The data can be either an integer number a real number or a character string Integers are used mainly for counting or specifying quantities for example array indices Real numbers are always stored as floating point double precision values They can be specified as a number with a decimal point or in scientific notation Examples are 233 0 0 5 01 33 1 6e 19 Note the type of Open GENIE data can change with the way it is assigned for example gt R 1 0 R is a real value of 1 0 gt R 2 R is now an integer Strings may be of variable length and combined and assigned just like the other types of Open GENIE variables Literal strings are always specified
49. n Procedures A whole series of graphics commands can be strung together and stored as a procedure See for example the various directories of usr local genie examples The procedures are then loaded using the command gt gt Load File gcl and executed using the command gt gt File 29 The Final Wish To Manipulate Data This section can be separated into three distinct areas e mathematical functions e workspace operations e data analysis functions Mathematical functions As well as providing intrinsic arithmetic operations for different data types Open GENIE provides several basic functions for performing mathematical operations These are coded generically so that the same function can be applied to any data type which is capable of undergoing the operation For example the sin function may be used on a single number an array or a workspace Normally the result of the operation is of the same data type as the value operated upon Where the operand contains several values e g an array each value is operated on individually For example we can create an array of real numbers and square root them gt gt my_numbers Dimensions 10 20 First create a 10 x 20 array gt gt fill my_numbers 1 0 1 0 Fill the array with some data gt gt printn my_numbers 1 0 2 0 3 0 4 0 5 0 Array 10 20 gt gt printn sqrt my_numbers print the square roots 1 0 1 414213 1 732050 2 0 2 236067 Array 10 20
50. n would I want to use MOdUIES eee eeeeeseeceeececsseceeceecaeceseeecsaececeecaeceeeeecaeeeteeeesaeeeees 39 How do Twite a module sitesi cs cive eenen E E te dace EE E E E E E EAE EROS 39 1 Write FORTRAN Subroutines to do your tasks 000 0 ee ee eescesecssecseeceecneeeeeeeeeeeeeeerenseeeaees 40 2 Write a FORTRAN wrapper subroutine to interface between Open GENIE and your Calculation Subroutine 5 22 asic cece enie caee each take ae Ee E AEAEE EE TEE ETENEE A OE 40 3 Make the Module a brary icc scsccccscsesses sees sesedsveshunsas gobsseseevess sada snsdveestoo dees SE PRES eSEE EE aooi 42 4 Load the module into Open GENIE 0 cccesccessssessseeneeeeeeseeeeeeseeeseeesecnsecsecsaecsaecsaeseeenaeenes 42 5 Package function arguments into a WOrKSPace e ee eect eee cece cree eneeeeeeeeceeseeeenseeseesaeenaes 42 6 Execute the module and get the result cece eeeeeeeceeeeesecesecaecsaecsaecaeesseseaeseneeeees 43 A Real Life Sample Module 00 0 eee ceecesecssecseecseeeeeeeeeeeeeeseeeeeesecesecaecsaecsaecsaecaeeeaeseneeeeeees 43 The C Module Interfac n seinri A a coteeves sence vet Gaal eee R EER EE 46 Example Open GENIE programs eicoctasiiatadccdcassasdadedslesssdeg hanes usdssasscebsangeeessee boners 50 FURTHER DEVELOPMENTS AND ADVANCED PROGRAMMING c cscceseessesesseeseseeees 54 THEEND OF PART Feistis i uean i ai aran i e i fae 55 I STALLINGOREN GENIE oprade teats be ccass Seasons Douaadudieaacanevasa 56 BINAR Y INSTA
51. nds switch the setting to its opposite value unless off or On is specified Toggl Togg e Status e Logx Togg e Logy Toggl Toggl Toggl Toggl e Clear e Graticule e Header e RX Reports the values of all toggle settings X axis log linear Y axis log linear Screen clearing between plots Toggle graticule off on Header plotted on Display command X axis rounding off on 24 Toggle RY Y axis rounding off on Toggle Info Informational message printing on off On Toggles item on Off Toggles item off For example Switch off informational messages and display a data plot with no banner heading gt gt Toggle info gt gt Toggle header gt gt Display s 22 The limits of the graph can be changed using the Limits command For example Set the limits before doing a display gt gt Limits X xmin 10 0E4 xmax 50 0E4 gt gt Display Redisplays previous plot with new limits The command Limits Default clears this Note the actual setting of the limits will still be dependent on whether rounding is switched on for the X axis Magnify a portion of the plot chosen interactively This is done using the Zoom command which redraws a plot scaling to a box which is selected by the cursor the lower left hand corner and the upper r h corner of the box The qualifiers Errors Histogram Line Markers will redraw the plot using error bars
52. ne is based on the GNU readline library and you will find that you can recall and edit previous commands by using the arrow cursor keys Commands are saved between sessions in a genie_history file in your home directory and this can be searched for previous commands For features of the command line see the appendix A Commands in Open GENIE consist of either assignments or keyword commands oe 39 Assignments are made using the sign for example lt destination location gt lt expression gt The dest ination location is a variable or an element of a compound variable such as an array or workspace and the expression can be e a literal value e g 5 6 or hello e a variable or part of a variable e g Two_theta or w1 npts e function expression e g Sin Pi e unary or binary expression e g or 1 2 Any Open GENIE procedure can be implemented by a keyword command and if the procedure returns a value it can also be invoked in an expression where the value is assigned to a variable A keyword command starts with a keyword followed by a list of qualifiers and parameters The keyword specifies the basic command while the qualifiers modify the action of the command and the parameters supply the values which the command operates on For example a keyword command is gt gt display Line wl This command plots the workspace w1 as a line By itself the display command plots a histogram the 1ine qualifier modifies the com
53. ng values to its elements For example Create a RealArray gt gt two_d_data Dimensions 100 200 created in 2 dimensions gt gt two_d_data 1 1 5 0 type is set here to real gt gt Printn two_d_data O60 a See Array 100 200 gt Arrays may be manipulated as a whole or alternatively individual elements may be accessed and modified separately Note all elements which have not had a value assigned to them are marked as _ You can specify a value for undefined elements using the FIx command Workspaces are compound variables where individual elements of the variable maybe of different types contrast with arrays which are all of one type Examples of similar structures in other languages are a record in Pascal or a struct in C The following example shows the construction of a simple workspace interactively create a brand new workspace gt gt mywork fields creates an empty workspace gt gt Printn mywork look at it now Workspace gt gt Now put some fields in it gt gt mywork description My test workspace gt gt mywork some_value 3 14159 gt gt mywork anarray dimensions 2 3 gt gt mywork anarray 1 1 25 gt gt Printn mywork now look again Workspace some_value 3 14159 anarray 25 ___ Array 2 3 description My test workspace gt gt Note structure may be used instead of fields Op
54. nst char name fort_real val Gl E7 void cmodule_put_real GenieWorkspace pars_put const char Return REAL variable VAL to GENIE as NAM name fort_real val T K void cmodule_put_double GenieWorkspace pars_put const char Return DOUBLE variable VAL to GENIE as NAME name fort_double val Get STRING parameter NAME from GENIE as VAL This routine ALWAYS allocates space for val with malloc and you will need to free at a later stage void cmodule_get_string GenieWorkspace pars_get const char name char val T Bey void cmodule_put_string GenieWorkspace pars_put const char Return STRING variable VAL to GENIE as NAME name const char val Return STRING array VAL of LEN elements to GENIE as NAME void cmodule_put_string_array GenieWorkspace pars_put const char name const char val fort_int len Get INTEGER parameter NAME from GENIE as VAL void cmodule_get_int GenieWorkspace pars_get const char name fort_int val Return INTEGER variable VAL to GENIE as NAME void cmodule_put_int GenieWorkspace pars_put const char name fort_int val Get REAL array parameter NAME from GENIE as VAL On Input The routine will malloc space for the array if val NULL otherwi
55. nstalled to a users directory or system wide as described in the section on Binary Installation Note that to build a kit you will also need a copy of GNU autoconf installed see ftp ftp nd rl ac uk pub packages gnu If you are struggling email genie isise rl ac uk and we will endeavour to help When you do contact us for advice please provide us with examples of the errors that occur in the mail message Remember that we probably can only guess at what might be wrong as we are unlikely to have the same system that you have to test things on Please check out the operating system specific notes below they could save you a lot of time 61 Operating system specific notes At the moment our primary development platform is Digital UNIX OSF 1 on alpha AXP and this is generally the one which works best for building without a hitch Linux works fine but may need a bit of fiddling if you run a different distribution to us IRIX for version 5 3 works but is likely not to work immediately for later versions For VMS only attempt this if you are strong willed and familiar with VMS POSIX and have it installed on VMS 6 2 or later VMS building on VAX is not recommended although we have done it We provide notes to help you with building on specific operating systems these notes can also be found in the README lt os gt files of the source code distribution Linux This is not an exhaustive list but should help 1 One version
56. of g on the Linux we build on 1 2 13 does not find its own include files by default Before building define the include path with export CPLUS_INCLUDE_PATH usr include g include 2 It may also be necessary to edit src Makefile and remove the flag extend_source from the F77 rule 3 After the first build attempt Scd library Smake i Note g77 return status of 4 stops a correct build 4 cd sre and touch lexcommands c To ensure that flex doesn t overwrite this with unworking code 5 go into pgplot and edit the makefile to remove f2c from the begining of the LIBS line Re make to build the pgxwin_server properly 62 6 Now try make all again it should run through this time IRIX First run configure currently this picks up f2c if it is installed which is probably not what is wanted Now edit config cache and change the line f2c_c_cos ac_cv_lib_f2c_c_cos yes to read f2c_c_cos ac_cv_lib_f2c_c_cos no and re run configure VMS These are the instructions for compiling under VMS POSIX tested on Open VMS AXP 6 2 with POSIX 2 0 Before entering VMS POSIX DEFINE JOB POSIX INCLUDE SYS SCRATCH After entering POSIX sh vms_posix setup will building the kit using a fairly large number of rather VMS POSIX specific routines and produce a similar file to the UNIX versions In general it is possible that if the configure doesn
57. om the ISIS website at http www isis rl ac uk GenieUsermanual config guess website and run it on your system with the command gt sh config guess This script will attempt to guess which version of UNIX you are running and return a string similar to the one above If it matches one of the GENIE binary distributions this will be the appropriate version to use for your machine Installation instructions for VMS and UNIX machines are different so there are different sections describing how to install each one If your machine does not have a binary version of the kit available you may be able to build one from the source code to do this you will need to read the section on Source code installation Note for example instructions to mount the CD ROM see appendix E 56 Binary Installation Choose the binary installation instructions below which match the type of hardware on which you are installing Open GENIE a UNIX Installation All UNIX kits are supplied as compressed tar files made by the tar program on the appropriate machine To decompress these files you will need to have gunzip installed NB gunzip is available from the web site as a tar file if you do not have this for building on your system To install Open GENIE follow the instructions given here for a Digital Alpha machine but substituting the appropriate names and version numbers for your distribution kit of Open GENIE gunzip genie 1 1 alpha dec osf3 2 tar
58. parameter allows you to define each individual limit For example if the X limits should be defaulted but the Y limits defined then you could use gt gt Display wm ymin 35 ymax 70 The parameters may also be expressions using functions of variables for example gt gt Display wl noise 0 xmax 100 0 ymin Min wl y ymax Max wl y Anonymous placeholders may also be used to indicate a default value in Open GENIE the character _ is used The above example could then be written as gt gt Display wl _ _ 35 70 gt gt Other optional parameters that may be specified are Linecolour the colour for drawing the axes and surrounding boxes Linewidth the line width used for drawing line plots Textcolour the colour used for drawing text Other qualifiers HISTOGRAM displays as a histogram assuming that the binned data has one more X value than Y value 21 LINE displays a spectrum as if it is a numerically calculated function i e with the same number of X values as Y values and join the points with straight lines Note if histogram data is displayed with the Line qualifier the data will be transformed to take the bin centre positions as the X values for the data points this is done with the centre_bins function MARKERS displays a plot with markers symbols For a list of marker types see appendix D ERRORS display as error bars taken from the workspace error array In order to clear
59. ram to provide for example the input to the program or to display the output How do I write a module A module consists of subroutines only there is NO main program These subroutines can be divided into two types those that perform the actual calculations and those that pass data to from Open GENIE and the calculation routines the latter called wrappers as they provide a jacket for the original calculation routines 39 1 Write FORTRAN Subroutines to do your tasks The subroutines can take any parameters you desire Our example will be based on the subroutine myfunc for in the examples directory C The function just square the X array SUBROUTINE MYFUNC X Y NPT IMPLICIT NONE T R NTEGER NPT I EAL X NPT Y NPT DO I 1 NPT Y I X I X T ENDDO RETURN END 2 Write a FORTRAN wrapper subroutine to interface between Open GENIE and your calculation subroutine Open GENIE variables are passed to and from the module using a temporary workspace Data is placed into the input workspace with chosen field names and then accessed in FORTRAN by using this field name and an access routine appropriate for the data type being sent For example the frame count could be stored in the variable NRAW and accessed using the module_get_int function in FORTRAN Returning data is similar the various module_put FORTRAN subroutines allow the construction
60. rimary flight path wavelength w To energy transfer E1 E2 meV wN To energy transfer E1 E2 cm TAU To reciprocal time of flight us m For example Read in a spectrum whilst converting to Wavelength gt gt w units Lam s 1 The t o f parameters must be set correctly in the input workspace or set using the Set Par command in order to perform the conversion and if the keyword syntax is used i e Units C w the workspace will be converted destructively 38 The Open GENIE Module Interface This section will answer the following questions e What is a module e When would I want to use modules e How do I write a module e How do I load and run a module e Where can I find out about other pre compiled modules What is a module A module is a compiled FORTRAN program that can be loaded into and become part of a running Open GENIE process Subroutines in the module provided they follow a given set of rules can be called to manipulate arbitrary Open GENIE variables A module is usually implemented as a shared library or dynamic linked library When would I want to use modules Modules are used when e A numerically intensive task must be performed for which GCL would be too slow and for which there is no in built Open GENIE command e You already have a working FORTRAN program for the task and do not wish to rewrite the application in GCL e You wish to use Open GENIE as an add on to another prog
61. ring g2s_put ycaptout ycaptout call module_put_string g2s_put xcaptout xcaptout call module_information G2S gt output is in point mode RETURN END The C Module Interface The C module interface is used in almost exactly the same way as the FORTRAN interface and provides similar routines in fact most have the same name but with a prefix of cmodule_ rather than module_ Invoking from the GCL command line is similar except that an extra qualifier of c must be specified for COMPILE and EXECUTE operations it could also be specified on a load for consistency but is not strictly necessary For example gt gt MODULE COMPILE C myprog c gt gt MODULE LOAD myprog so gt gt VALS MODULE EXECUTE C myfunc PARS The major difference between the two is in the arguments the C module routines can allocate memory for returned array structures using malloc unlike in FORTRAN77 where a pre allocated array must always be passed To indicate that you wish a routine to allocate the memory for you set the array pointer to NULL before passing the address of it to the routine For example 46 GenieWorkspace pars_get pars_put passed from GENIE const char name twotheta parameter to get fort_real val_array NULL tell routine to malloc memory fort_int len then get array the arr
62. se it will assume val points to an array of size len On Output On error len will be set to 0 Otherwise len will be set to the number of elements read into val void cmodule_get_real_array GenieWorkspace pars_get const char name fort_real val fort_int len 48 Comments as for cmodule_get_real_array void cmodule_get_double_array GenieWorkspace pars_get const char name fort_double val fort_int len Return a REAL array VAL of length LEN to GENIE as NAME void cmodule_put_real_array GenieWorkspace pars_put const char name const fort_real val fort_int len Return a DOUBLE array VAL of length LEN to GENIE as NAME void cmodule_put_double_array GenieWorkspace pars_put const char name const fort_double val fort_int len Return an INTEGER array VAL of length LEN to GENIE as NAME void cmodule_put_int_array GenieWorkspace pars_put const char name const fort_int val fort_int len Print a message s to an output stream governed by option void cmodule_print const char s fort_int option possible values for option in cmodule_print are define CMODULE_PRINT_NORMAL 0 Like GCL PRINTN define CMODULE_PRINT_INFORMATION 1 Like GCL PRINTIN define CMODULE_PRINT_ERROR 2 Like GCL PRINTEN Return a multi dim
63. t Wish Access to Data At ISIS and all other neutron scattering centres data is collected in runs These are typically periods of time in which the sample is kept in constant conditions The data for a run is stored in a raw data file and at ISIS the naming convention is lt instrumentxxxx raw gt where the run number is xxxx The raw file itself contains one or more time of flight spectra and other associated parameters needed for the analysis of the data This section describes the commands necessary to access data from Open GENIE The description that follows is based on the data formats found at ISIS However Open GENIE can be modified to read other formats used at other facilities This section details all the commands used to access data from Open GENIE Accessing raw data spectra One of the major strengths of Open GENIE is the flexibility available in accessing data The first way of accessing data is based on the old GENIE V2 where several internal variables control the a current input file b current output file c current disk d current directory e current instrument f current file extension The status of these variables is changed by using the set command detailed on page 12 The show defaults command gives the input output defaults for example gt gt show defaults Current default disk AXPLIBSDISK Current default directory OPENGENIE GENIE EXAMPLES DATA Current default instrument HRP 16
64. titlel title draw A Title gt gt markersl markers draw wl x wl y SBlue Cross 2 gt gt errorsl errors draw Vertical w x w y w e SBlue 2 gt gt graticulel graticule draw colour Sgreen Now to view this plot open a new device gt gt devicel device open gt gt Redraw picturel Making alterations If you wish now to change part of the graphs for example the text in picturel 27 Want the font to be italic gt gt title alter font Sitalic object titlel or you want to change the graticule gt gt graticule alter colour Sred object graticulel In order to remove the changes caused by the draw qualifier the Undraw command can be used For example if you wanted to undraw markers1 then type gt gt Undraw markersl Note if the Undraw command is followed by a negative integer N then it is the previous N Draw that is undone In other words Undraw 1 undoes the previous Draw command the default whereas Undraw 3 undoes the command two before the last one For a whole set of pictures and opened devices made for example picture1 picture2 picture3 picture4 etc and devicel device2 device3 device4 etc then to redraw picture4 on device5 and picture 6 on device2 then type gt gt Redraw picture4 deviced gt gt Redraw picture6 device2 In order to redraw a previous plot then type gt gt Redraw 1 After a number of device open commands have been executed then to redraw the current
65. tour_test gcl displays a contour plot of a set of neutron inelastic spectra taken on IRIS glad gcl draws a colour intensity map of S Q data taken on MARI which also allows you to see slices of the intensity variation with constant energy and momentum 53 Further Developments and Advanced programming A Tk Tcl Interface is currently under development at ISIS and the idea is to provide a rudimentary interface and also a set of useful utilities e g a tcl display command that will as well as drawing a plot allow you to interactively change e g line colour by clicking on a line However the above should allow anybody who wishes the ability to knock up a GUI for a GCL command procedure they write Open GENIE is a much more detailed and powerful system than is obvious from the rest of this manual There are many things which can be done using Open GENIE for example write procedures in an object oriented command syntax extend the data class system to advanced data types code procedures directly in smalltalk or extend Open GENIE by writing in C 54 The End of Part I At the end of a session all variables created during it are lost when gt gt Exit GENIE exiting is typed However all the variables from one Open GENIE session can be saved into a binary image file This is useful when a number of gcl procedures have been loaded and will mean you don t have to type Load procedure g
66. ystem command allows you to execute a single command or a command session of the native operating system from within Open GENIE For example find some user details on VMS gt gt system SEARCH journal txt flux IRS14142ZAB NJR Flux tests 18 FEB 1997 12 00 01 163 2 IRS14143ZAB NJR Flux tests 18 FEB 1997 13 43 40 6 1 gt gt If no command is given as a parameter the System command starts a sub shell process which is terminated by an exit on UNIX or a Logout on VMS systems Note 9 that on VMS some normal logical name definitions may be missing in the sub process 10 Getting help Online Help in Open GENIE is available in a number of ways e to see a list of all Open GENIE commands press lt Ctrl gt H on a blank command line if it pressed after a letter a list of all commands that start with that letter will be printed e pressing lt fab gt twice will list all commands that match with what has already been typed so far Therefore pressing lt tab gt twice on an empty command line lists all the commands e if the command name is not known use lt Ctrl gt K to perform a keyword search of the command descriptions e if the command name is known run it with the HELP qualifier to get a description and list of parameters For example gt gt display help 11 The Three Wishes Most people using Open GENIE will wish to do one of three things Wish 1 Access their data either fro

The ISIS OPEN GENIE User Manual

Contents

Download Pdf Manuals

Related Search

Related Contents