MAPVIEW

MAPVIEW is used to visualise the electron-density maps written by FOURIER_MAP, the Fourier calculation program of the WinGX package. Drawings are either vector (i.e. line) drawings or bitmap plots. It is effectively an updated version of CONTOUR, with many more features and styles of plots.

MapFiles may now be read dynamically into the program. MapFiles are direct-access binary files with the file structure outlined in Section 7.3.6. The MapFiles written by FOURIER_MAP contain electron densities, but in principle other properties, e.g. Laplacian, electrostatic potential etc may also be visualised using MAPVIEW if this file structure is adhered to.
All screen illustrations may be saved as PostScript files (either monochrome or colour), or as Windows BMP files, or copied to the clipboard (from where they may be inserted into word processor or graphics programs). The vector illustrations may also be directly printed to a local printer.
Illustrations are scaled according to the axial lengths and non-orthogonal axes are handled automatically.
Display colours (foreground, background, text colour etc) are user-selectable.
Six different plot-styles are available. Five of these styles may be used with any MapFile, but the 3D-IsoSurface option requires a Mapfile containing more than one plane. The available plot-styles are
1. 2D-Contour. This option draws a contour plot of a single map-section. No interpolation is used. The foreground colour is used for both negative and positive contours, negative contours being drawn with dashed lines and positive contours with solid lines.
2. 2D-PixelMap. This option draws a single map-section with each discrete grid-point shown as a colour-coded rectangular pixel. Since the number of pixels corresponds to the actual digital resolution of the MapFile, this is a scientifically accurate representation of the data. The colour-scheme is fixed, with blue representing the lowest density levels and yellow the highest levels.
3. 2D-BitMap. This option draws a single map-section as a bitmapped image. The electron- density is interpolated between grid-points and colour-coded according to the currently selected colour-table. There are five available colour-tables, GRAY-SCALE, HEAT, RAINBOW, BGYRW and SERPENT, the default being BGYRW. The image is calculated on a pixel-by-pixel basis, so the drawing time is longer than for options 1 and 2.
4. 3D-Relief. This option draws a single map-section as a relief-plot with the Z-axis representing the magnitude of the density at that point. Each grid-point is connected to neighbouring points to give the familiar “net-like” appearance.
5. 3D-Surface. This option is similar to 4, except that the height-field surface is rendered. This bitmapped surface may be rendered in a single colour, or a colour-table may be used to emphasise the height. This option gives a more photo-realistic view of the surface than option 4, but as the image is calculated on a pixel-by-pixel basis, it takes considerably longer to draw.
6. 3D-IsoSurface. This option is only available if the Mapfile contains more than one plane. A bitmapped iso-surface at the selected level is drawn either as a single colour or as a colour-coded height-field. It is possible to select either negative or positive levels for the iso-surface.

7.3.2 General information

For all the 2D-options, when the mouse cursor lies over the map image, a continuous display of the current cursor position (map x- and y-coordinates) and function density at that point is given. In this mode the cursor changes from the normal arrow-cursor to a cross-hair cursor. Maps containing more than one section may be advanced or retraced using the Frame or Frame buttons and a particular section may be selected with the Select Section button. If the map contains more than one section, it may be quickly visualised with the StartMovie button which moves continuously, section by section up and down the map until any key is hit or the mouse-cursor is moved over the canvas. The StartMovie option is only available for the vector-illustrations (styles 1,2 and 5), since the other styles are too time-consuming to draw. Parameters relating to the currently loaded map and currently selected section is given in a panel to the side of the graphics window. A number of options may be set using the dialog window shown below.

7.3.2.1 Contours

No interpolation is used to generate the contours, so if smoother sections are required, the map must be recalculated using a finer grid. Contours are drawn at equal intervals between the maximum and minimum densities, so that the contour interval is given by : contour interval = (max-r - min-r)/(NCONT+1) The contour interval may be explicitly set using the Options[Set Contours] menu item. If the required number of contour levels is less than 25, then this number of contours is used. If the required number of contour levels is greater than 25, then the number of contour levels used is unchanged from the current value, but the map maximum is reduced to give the required contour interval.

7.3.2.2 Maximum/minumum density
The maximum density is by default the highest point in the MapFile, the minimum density the lowest point. Different values may be selected for either parameter. This has the effect of truncating the density at these level(s), a feature which is useful in examining weak features in the presence of intense peaks.

7.3.2.3 Atoms, bonds and atom labels
Atoms, bonds and atom-labels may be overlaid in the 2D-options only. The bond-distance calculation is unsophisticated - a bond will be drawn between every pair of atoms whose distance fulfils the criterion.
Min. bond distance > distance > Max. bond distance

7.3.2.4 Colour-tables
The colours for the colour-tables are taken from PGXTAL and are stored internally. It is possible to modify these colours in two ways. The colour-intensity may be reduced from the normal level of 1.0 (which gives the pure colour-map) since these pure colours are quite garish and difficult to look at. The default colour intensity of 0.75 gives a more reasonable colour scheme. The contrast may also be changed from the default value. A value smaller than 1.0 emphasises the lower intensities, while a value larger than 1.0 emphasises the higher intensities. The user needs to experiment to find the optimum settings.

7.3.2.5 Axial scaling
If the angle between the two projected axes (given as ANGLE in the display) differs from 90o or the axial lengths are unequal, then axial scaling is automatically chosen if options 1 or 3 are selected (axial scaling cannot be used for option 2). This action may be deselected using the Options[Use axial scaling] menu item.

7.3.3 Menu Options
7.3.3.1 Open Mapfile...
Reads in a new MapFile, which will be called either MapFile or name.MAP. On startup, MAPVIEW will load the file MapFile if it finds it in the current working directory. Axial scaling is set automatically if non-equal or non-orthogonal axes are read from the MapFile.

7.3.3.2 Save as PostScript
The current image will be saved as a colour or monochrome PostScript file. It is named automatically as MAPVxxx.PS where xxx = 001-999. Previously written PostScript files will not be overwritten.

7.3.3.3 Save as BMP
The current image will be saved as a Window BMP file. It is named automatically as MAPVxxx.BMP where xxx = 001-999. Previously written BMP files will not be overwritten. The size will depend on the graphical resolution and colour-depth of your monitor.

7.3.3.4 Copy To Clipboard
The current image is copied to the clip-board, form where it may be inserted as a graphical object into other programs.

7.3.3.5 Print...
The current image is sent to the local printer. The current colour scheme will be used (except that the background is always printed as white).

7.3.3.6 Select Colours/Load Default Colours
The display colours may be individually selected. The foreground colours is used for the contours. The colour tables are unaffected by this option. Load Default Colours returns all individually selected colours to their default values.

7.3.7 Options
This opens the above-shown dialog box which allows the user to set a number of parameters.

7.3.4 Program limitations

The maximum number of grid points allowed in the x- and y-directions (NX and NY) is 200. There is no general restriction on the number of planes (NPLANES), except for the 3D-Iso-Surface option where the whole map needs to be read into memory. This option sets a limit of 100 grid-points in ALL directions.
The continuous electron-density read-out only functions for the 2D-options. If PostScript hardcopy is selected, this function is temporarily switched off until a new image is drawn (simply reselect the appropriate menu item).
The maximum number of contour levels is 25

7.3.5 Known bugs

If using the 2D-BitMap option, selecting the HEAT colour-table sometimes causes a blank screen to appear. Re-selection of the menu item 2D-BitMap cures this. This only occurs occasionally with some maps and the cause remains obscure.

7.3.6 MapFile structure
For reasons of efficiency, the WinGX MapFile is a binary direct-access file. Each record is one word (4 bytes) in length. The file starts with a header of 19 records containing the information shown in Table 1 of the document Ch7_3.doc (in documents directory of WinGX). This is followed by NX*NY*NPLANES records which give the function values F(I,J,K) in the FORTRAN format :
( ( ( F(I,J,K), J=1,NY), I=1,NX), K=1,NPLANES)
The file ends with the atom co-ordinates starting with record number XX = (20 + NX*NY*NPLANES ) which gives the number of atoms NAT, followed by NAT*5 records for these NAT atoms.

7.3.7 Graphics acknowledgement
The graphics in this program use the PGPLOT library (version 5.2.0) of Tim Pearson (http://astro.caltech.edu/~tjp/pgplot/index.html) and a heavily modified version of the PGXTAL library of Devinder Sivia . (http://www.isis.rl.ac.uk/dataanalysis/dsplot/).