Introduction

Plot85 is used to plot and analyze energy-dispersive diffraction data created by the SAM85 or MCA data collection programs. It can be used to determine the channel number, energy, or d-space for any diffraction peak, either by pointing to the peak, or to fit it using GPLS. Reference data can be imported in several file formats, described below: .HKL, .JCPDS, .POW. If the diffraction data is from NaCl, the pressure and differential stress can also be calculated.

Plot85 for Windows is a port and upgrade of Plot85 for VMS. Its upgrades include the ability to directly read APS data, read data created by multiple detectors (up to 4), and includes as subroutines Celrf (a unit cell refinement program) and XPOW (a program written by Bob Downs and Kurt Bartelmehs which calculates powder-pattern data from crystallographic data).

To install and run PLOT85, see INSTALLATION, at the end of this document. The program will run (with somewhat limited features) if you simply click on the PLOT85.EXE file.

When the program starts, it will look for an energy calibration file (DEFAULT.EDF) and a list of hkls for some standards (STANDARD.HKL) in two locations. It will first look in the location specified in the start in selection in the shortcut (see INSTALLATION). If it cannot find the file there, it will look in another, arbitrary directory you may define using an environment variable.

Version History

Version 1.0 - original version, written for VMS running on a VAX or an ALPHA

Version 2.0 - beta version for Windows

Version 3.0 - added support for .JCPDS reference files

Version 3.1 - added Celrf

Version 3.2 -

Version 3.3 - Moved fluorescence reference to be an internal function using the FLUORESCENCE menu, added GPLS and XPOW menus

Version 3.4.0 - Made it possible to increment cell parameters for reference lines input from .HKL, .JCPDS, or .POW files.

Version 3.4.1

Version 3.4.2 - changed look of File menu, and moved import of .MCA files to the Utilities menu.

Version 3.4.3 - Increased the number of lines in a .JCPDS file from 20 to 40, but introduced a bug.

Version 3.4.4 - corrected the bug introduced in 3.4.3

Menus - Many of the functions in the VAX version of Plot85 have been replaced or duplicated in drop-down menus. They are: file, Standards, Xpow, JCPDS, Fluorescence, GPLS, CELRF, and UTILITIES. Reference standards may be displayed using any of the four databases either singly or in combination:  Standards, Xpow, JCPDS, Fluorescence.  To measure Pressure, use the NaCl selection from the Standards menu.  Once your data is displayed, various Operations can be performed on it.  If you are more used to the old, DOS-like format, you can go to the Main Menu, which simulates the VAX program.  However, this has many limitations, and is not recommended.

 

 

 

 

 

 

 

 

The FILE menu consists of several sub-menus, which give navigation panels. The program remembers the last time any navigation panel was used, and uses the same location for the next one. Therefore, any file unique to your experiment should be put in your data directory. The file menu contains the options:

Plot Data - used to plot the data after it has been read in using one of the options below

Plot series of datafiles - not available right now

Read datafile will read data files in the APS format, regardless of their extension. You will not be given the option to save .pks files, although a temp.pks file will always be created and you can manually copy it to the correct .pks file. Files with the .pks extension are ASCII files containing a list of peaks found using one of several methods in the plot. They can be printed for reference, and are used as input for the Celrf cell refinement option.

Read datafile / save current pks file These options will copy the current temp.pks file to a fname.pks file, where fname is the same as the data file, before reading the new data file.

Read HKL file - reads in a new STANDARD.HKL file (see next page)

Read EDF file - reads in a new DEFAULT.EDF file. The DEFAULT.EDF file is a calibration file created either manually or using Autocal.

Import XY file - reads in an X-Y data file, where X is 2q for CuKa ₁ radiation

The program works best if the data are located in a directory that can be written to (i.e. is not read-only). If you use a read-only directory, the program may crash (we are trying to eliminate that bug), but should write the necessary files to the alternate directory defined in the environment (see Installation).

Note: the reading of old, MCA-format data files has been moved to the Utilities menu.

The DEFAULT.EDF file contains four energy calibration parameters, 2q , and a comment, each on separate lines.

The STANDARDS menu lists the materials listed in the current STANDARD.HKL file. The entry "No Standard" removes the current selection from memory, so it isn't plotted. The entry "New Cell" allows you to enter new cell parameters (i.e. to simulate high temperature and/or pressure). The new lines are calculated. Although all six cell parameters are displayed, only the ones required for the current symmetry need be entered; e.g. for cubic, only a needs to be entered. The entry "Set Cell Increment" allows you to change the unit cell parameters a, b, and c using hot keys "I’ and "i". Entering "I" with the graphics window active will increase any or all of a, b, and c by one increment and redraw the plot', "i" will decrease it. Default values are .01 Ångstroms. If you get the message "incorrect data format", you probably used a STANDARD.HKL file without the commas in the second line of one of the standards.

The format of the STANDARD.HKL file is described below:

Each material has four types of entries: an identifying title, the cell parameters, a list of diffraction lines, and a terminating line.

The first line is somewhat arbitrary, but all important information should be included in the first 10 or so characters. It is displayed on the plot.

The second line consists of the six cell parameters, followed by a code for pressure measurement. That code is 1 for NaCl, 4 for MgO, and 0 for anything else. Enough cell parameters must be entered to define the cell. If the angles are left blank, a value of 90° is assumed. All entries must be comma-separated, and have decimals.

The remaining lines consist of h, k, l, d, I, and O, where h, k, and l, are the Miller indices (integer format), d is the d-space in angstroms, I is the intensity (100.0 being the maximum, decimal notation), and O is an orientation parameter for stress calculation. This line of data can also be used for non-diffraction lines (such as gamma or fluorescence lines) by entering the energy in KeV in place of d. If that number is greater than 10, it is assumed to be an energy. See the 4^th entry, Co57. "Dummy" h,k,l s must be entered.

The list is ended with a dummy diffraction line, with 999 as h.

The maximum number of lines is 20; the first ten are identified by the single numeric key 1-0; the next ten are the same keys, shifted: ! through ).

If you get a message stating that the STANDARD.HKL file may be incorrect, the most likely reason is that the individual cell parameters are not in the correct format.

Pressure Measurements using the Decker EOS for NaCl can only be done if NaCl is loaded as the standard in the above menu.

The XPOW menu allows you to create a theoretical powder pattern from a .POW file. This should be used to display your sample data instead of the STANDARD.HKL file. It uses a modification of the XPOW program, written by Bob Downs and Kurt Bartelmehs. For reference, see Downs et al. (1993) American Mineralogist 78, 1104-1107. You will have to get a .POW file. Get the XPOW program from http://www.geo.arizona.edu/xtal/personal.html and download the executable and sample datafiles for XpowWin. The .POW files are the sample data files. To modify them, you will need to know the cell parameters, the space group, and all the positional and occupancy parameters for the structure. Put your selected and/or modified .POW file in your data directory. The XPOW menu has selections:

Read File (this must be done first).

Print - prints on the screen a list of h,k,l, and d for up to 20 strongest lines

New Cell - same as New Cell in the Standards menu

Set Cell Increment – same as Standards menu

Plot lines - adds the new reference lines to the current plot

One acceptable format for the .POW file is shown below:

One .POW file may have more than one entry, but only the first will be used. An entry consists of a title, radiation information (ignored, but must be present), the 6 cell parameters and the space-group, and one line per atom with the chemical symbol and the fractional position of that atom listed.

The JCPDS menu allows you to input a reference file in the APS .JCPDS format. The menu has selections:

Read

Print - prints on the screen the portions of the selected JCPDS file used by this program.

New Cell - same as New Cell in the Standards menu

Set Cell Increment – Same as Standards menu

Plot lines - adds the new reference lines to the current plot

Two formats of the JCPDS file can be used; the current (version 4) format is be shown below:

For version 4 files, each line begins with a keyword.

Several entries are ignored by PLOT85, including all equation of state parameters (Ko, KoP, etc.)

The Fluorescence menu allows you to display the 4 strongest K X-ray fluorescence lines from any element. The menu has selections: The last 5 elements selected will be added to the menu list for easy recall.

List elements

Add element

Plot lines - adds the new reference lines to the current plot

A preselected list of 6 elements

Up to 4 newly added elements

 

 

If you add an element, that element will be added to the bottom of the list. When 4 new elements have been added, the 5^th replaces the first of the newly added element list. Those on the preselected list remain unchanged.

If you want to display another line, select another element and re-plot it. If you press S or s before you replot the fluorescence lines, the old ones will be removed before the new ones are plotted. If you don't, the new ones will be added.

The GPLS menu controls various parameters in the General Program for Least Squares fitting routines.

Options - All enabled.

Options - None enabled. This sets the various GPLS options to:

Do you want the stepping option (y/<n>)?

Give the starting fwhm <0.07>: (in units of 100 channels, i.e. 7 channels)

Do you want individual peak widths (y/<n>)?

Do you want an asymmetry correction (y/<n>)? After answering this, the initial region is plotted, and you are asked to select a smaller region containing only the peaks you want to fit this time.

Select the left edge of the region (X to exit)

Select the right edge of the region (E to expand). After answering this, the region containing only the peaks to be selected is plotted.

Give the number of peaks

Move cursor to peak 1

(Move cursor to peak n is repeated until all peaks are selected. The program then begins the least-squares calculation. After the goodness of fit has been reduced to a small number, you are asked I

Do you wish more Least-Squares cycles (<Y>/N)? If you answer N, the results are plotted and displayed, and you are asked

Add another line (Y/<N>)?

Refit the same region (Y/<N>)? After answering N to the last question, you are returned to question 5 and repeat for the next peak/s.

Peaks fitted - 1 sets the answer to question 7 to 1 when "Options - None enabled" is selected

Peaks fitted - 2

Peaks fitted - 3

Peaks fitted - input during run re-enables question 7 even when "Options - None enabled" is selected

Cycles - 1 sets the answer to question 10 to "N" without asking the question

Cycles - 3 sets the answer to question 10 to "Y" twice, then "N"

Cycles - 5 sets the answer to question 10 to "Y" 4 times, then "N".

Cycles - run time option asks question 10 until you answer "N"

The CELRF menu allows you to run Celrf after you have created a pks file. It has selections:

Setup (this must be done first). You need to know the cell parameters of the starting model.

Refine

Print list file

 

The UTILITIES menu includes

Export to GSAS

Export to Jones

Display Data - text list of data

Color Postscript - changes printer postscript to color (default)

Monochrome Postscript - changes printer postscript to monochrome. Change only takes effect when you read a new file, or re-read the old one.

Toggle main menu on/off. This last item allows you to enable the older, text-based menu system if you wish to use it. It has a reduced menu list. See below for more details.

Enter default title 1 - This allows you to enter text to appear on the top line of the graph. It will remain for all future graphs, unless you either reset it (see below) or restart Plot85. If you have entered something in "Sample title" or "Experiment title", this will be used (although it can be changed). If there is no title 1 in the file, you must enter something here. This new default title is not saved in the file.

Reset default title 1 - deletes the current Title 1 so you can enter a new one.

Enter new title 1 - creates a new Title 1 for the current plot only.

Enter new title 2 - creates a new Title 2 for the current plot only. If nothing was entered in the first "Experiment Comments" field in the MCA program, this must be entered for each graph (since they will all be different). If you have entered something in one or more of the "Experiment Comments" fields, they will be concatenated together (up to 80 characters) and used as Title 2.

The rest of the menus (EDIT, VIEW, STATE, WINDOW, and HELP) are standard Windows menus, and won't be described here.

Once data is plotted the cursor works as follows:

1. The selection commands "..." and "../" will expand the range pointed to by the first two dots . A third dot will expand, and the / will invoke GPLS.

2. If a standard has been selected the number and shifted number keys point to the corresponding standard line.

3. P or p will produce a postscript file of the current graphics screen. Filename is the filename of the data file with the extension ".ps" If you properly set up the printer environment as described below, that file will then be copied to the printer.

4. N or n will read the next data file in the sequence.

5. Q or q will quit and return to the menu.

6. S will redisplay the original data, and s will redisplay the current data selection. Position and XPOW markers will be lost. Standard markers will be retained.

7. Function keys F1 through F4 will select the 2k regions 0-2047, 2048-4095, 4096-6144 and 6145-8196 respectively

8. "I" and "i" will increment or decrement the cell edges of the active reference material (using the Standard, Xpow, or Jcpds menus), recalculate the d-spacing and replot the data. The active reference material is the last one to have the increment values changed or the last one to be plotted with the drop-down menu.

You may have up to 4 sets of reference lines plotted simultaneously (Standard.hkl, Xpow, Jcpds, and Fluorescence). Standard lines are refreshed by refreshing the screen with S or s; the others are refreshed using the plot lines item in their respective drop-down menu.

Some comments regarding PLOT85 when used with 4 detectors. These comments apply to files created by MCA-Genie. MCA-Epics uses a different multi-detector format which we have not yet accommodated in Plot85.

The only format that contains 4-detector information is the default APS format created by Mark’s MCA program. This format has 8k (8192) channels.

There is only one calibration parameter set built into that file; if it is correct at all, it is only correct for the first detector.

When you open an APS format file, select "all files", then one of the "001" extension. Plot85 will read the corresponding HDR file to get the titles. MCA-Epics files already have the header information and do not need a HDR file.

When all 4 detectors are displayed (in one graph), pressing F1, F2, F3, or F4 will select detectors 1-4 respectively. "S" (or F5, hopefully) will re-display the whole spectrum; "s" will re-display the portion you currently have selected. This ("S") must be done before selecting another detector.

Each detector spectrum displays a "reduced" channel number, i.e. a multiple of 2048 is subtracted from each channel number to reduce it to the range 0-2047.

The "standard" which is used may be selected using a drop-down menu; if you use the menu and then enter "s", your spectrum will be re-drawn with the new standard lines.

Main Menu in text mode - this is enabled using the 6^th entry in the Utilities menu, above, and is the old-VAX-style menu. If you use this, some of the new-style drop boxes may not work correctly.

Enter: -1 - To exit

1 - Plot current data

2 - Read new MCA data file

3 - Read new APS data file

4 - Read next data file

5 - Select standard number

6 - Create Jones "Powder pattern" file

7 - Create GSAS "Powder pattern" file

8 - Display data

9 - Enter DOS command

10 - Read default.edf

Options 2 and 3 will bring up a navigation panel. Once a file is selected, its location will

become the new default directory. Subsequent files - *.pks, *.ps etc. - will be located here.

Option 5 will try to reread "standard.hkl" if the standard selected has a volume of 0.0. This will usually occur if there was no standard.hkl in the startup directory.

 

 

1. Create a directory on C: (or wherever else you wish) called PLOT85. To install the program locally, copy the contents of the CD to that directory. To run PLOT85 off the network, for example, map drive X: to the folder where the executable is located. You could also map Z: to your area on a server.

Although the program will run without defining environment variables, it works better if you do. How to set environment variables depends on you operating system, but for most, go to control panel/system/advanced/environment. If given a choice, use the system setting, not the user setting. If you want to check your settings, go to a command (or DOS) prompt, and enter "set", and all the environment settings will be displayed.

Pgplot_font is a variable pointing to the location of the grfont.dat file. Without this file, text will not be shown on the plot.

Plot85_HD is a variable pointing to the default PostScript printer. If it is a network printer, set this equal to the share name (e.g. \\SBMP90\HPLJ4Si_121)

File_path is the location of a writable directory where the program will put files, if it cannot write them to the data directory.

 

Create a shortcut to plot85.exe. You should modify the properties of the shortcut, such as "start in" location or "run" type.

There are four shortcut options you can enter in the Target line, after the name of the .exe file: They are: "printer =", "gpls = ", "cycles = " and "screen =". These are case-sensitive. You may use any or all of the options. The "printer" option overrides the one created as an environment variable. It is especially useful if you want to set a default printer using the environment setting, and temporarily change it. The "gpls" option controls the GPLS menu. Its arguments can be "yes", "no", or "1". "Yes" gives you all GPLS options, "no" gives a minimum of GPLS options, but allows you to select the number of peaks to be fit, and "1" restricts the number of peaks to 1. The default is "no". The "cycles" option will fix the number of gpls cycles to the number entered. "Screen" sets the default screen resolution. "?" gives the following list,

/W9 (Windows95, mode from environment)

/WV (Windows95, 640x480)

/WS (Windows95, 800x600)

/WX (Windows95, 1024x768)

/WZ (Windows95, 1280x1024)

Therefore, if you want to use the printer in room 121, one peak for GPLS, and a 1280x1024 screen, enter

Examples: "printer=\\SBMP90\HPLJ4Si_121" prints to a network printer

"printer=LPT1" prints to a local printer

"gpls=yes" enables all options

"gpls=no" enables a minimum of options (default),

but with an unlimited number of peaks

"gpls=1" same as "no", but restricting the number of peaks to 1

"cycles=1" sets the number of Least Squares cycles in GPLS to 1

"screen=/W9" graphics mode from environment

"screen=/WV" VGA (640 x 480) graphics mode

"screen=/WS" SVGA (800 x 600) graphics mode

"screen=/WX" XGA (1024 x 768) graphics mode

"screen=/WZ" SXGA (1280 x 1024) graphics mode

Note: "gpls" and "cycles" can be overridden in the GPLS drop-down menu.

"Printer" can override the default printer defined in the environment

Autocal is a DOS program that creates a calibration file, called DEFAULT.EDF. It takes a series of known diffraction and fluorescence peaks, and does a cubic fit for energy-to-channel number, along with 2θ, in one step. The input is from a file called STANDARD.EDF, which is described below. Autocal6 is used for one detector, and Autocal7 is used for a 4-element detector array.

Installation

Copy Autocal6 and Autocal7 to the came location as Plot85. If you create a new shortcut, you may want to modify its properties like "start in" location or "run" type. You will need to modify Start in: to be the location of your data EDF files.

Currently, there are two versions of Autocal: Autocal6 is most similar to the version on the VAX. Autocal7 has been modified to handle 4 detectors. They use DIFFERENT FORMATS for the STANDARD.EDF and DEFAULT.EDF files, so don’t mix them.

The STANDARD.EDF file is the input file for Autocal. Versions for 1- and 4-detectors are shown below. The file consists of a list of "diffraction" lines from the data file. For each line, there is the channel number, d or E, and an identifying label. E is the energy of the line, in KeV, and d is the d-spacing, in Ångstroms. The program assumes that if the number is less than 10, it represents d, and if it is greater than 10, it represents energy. The line may be a real diffraction line, an X-ray fluorescence line, or the energy of a gamma ray.

An example of the STANDARD.EDF file for Autocal6 is shown below:

The file for Autocal7 is similar in concept except that the order of the variables has been altered, and there are 4 sets of channel numbers, one for each detector. The channel number for each detector can be the "real" one, or the "reduced" one; the program will convert it. Thus, you can use channel number from either PLOT85 (see below), or from the MCA program. If the channel number is negative, that point will be ignored.

LABEL ENERGY OR D DET1 DET2 DET3 DET4

'Co57 G1', 14.413, 199.85, 199.85, 199.85, 199.85

'Co57 G2', 122.0614, 1729.09, 1729.09, 1729.09, 1729.09

'Co57 G3', 136.4743, 1934.10, 1934.10, 1934.10, 1934.10

'NACL (1-1-1)', 3.258, 473.98, 473.98, 473.98, 473.98

'NaCl (2-0-0)', 2.821, 548.01, 548.01, 548.01, 548.01

'NaCl (2-2-0)', 1.994, 777.86, 777.86, 777.86, 777.86

'NaCl (2-2-2)', 1.628, 954.24, 954.24, 954.24, 954.24

'NaCl (4-2-2)', 1.261, 1235.49, 1235.49, 1235.49, 1235.49

 

For both versions, if the channel number is entered as negative, the program will take its absolute value for analysis, but it won't include it in the fit. That way you can "turn off" a suspect line without having to delete it. For Autocal7, that negative sign could be placed in the "Energy or D column, if you want to ignore the entire line, or in one or more of the DET columns, if you want to turn off the calculation for some detectors, but not all.

When you run the program, the output calibration file, called DEFAULT.EDF will be created. The 1 detector version consists of the four energy calibration parameters, 2θ, and a comment, each on a separate line. The format of the 4-detector version is simply the old one times 4, resulting in 24 lines.

Each detector must be calibrated separately. Each time the program is run, you are asked for which detector you want to calibrate (1, 2, 3, or 4). When the program is run the first time, the DEFAULT.EDF file written will have the same values for all four detectors. When you run it the second time, the old file is read in, the values for the detector you select is modified, and the file is resaved.

Each time you run the program, two files are created: STANDARD.OUT and STANDARD.ERR. These give information about the resulting fit; STANDARD.ERR gives information for all the lines in the DEFAULT.EDF file, even those with negative signs (although these are still not included in the fit). When you run the program the second (or greater) time, these files may be overwritten, so you are given a chance to rename them before you overwrite them. Normally, you will answer "Y" to continue and overwrite these files.