Switches to the structure plotting submenu. The structure can be written in a format suitable for plotting by several structure plotting programs such as KUPL, GNUPLOT.
Further help topics are:
Valid commands at this sub level are:
@ ! Executes a macro (see main help) asym ! Lists the content of the asymmetric unit chem ! Lists all type of atoms present in the crystal col ! Defines the sequence in which the xy and z coordinates are written. des ! Deselects atoms or microdomains echo ! Echos a string, just for interactive check (see main help) exit ! Terminates the plot sub level, returns to the main DISCUS level. ext ! Sets the extend of crystal space to be plotted help ! Gives on-line help for 'plot' (see main help) hkl ! Sets reciprocal space direction normal to plot slice outfile ! Name of output file to which the structure is written prog ! Selects the plotting program run ! Starts writing of the structure sel ! Selects which atoms are to be included in the plot set ! Sets type, color and size of atom in plot file show ! Shows settings for the plotting parameters thick ! Sets the half thickness of the plot slice uvw ! Sets direct space direction normal to plot slice system ! Executes operating system command (see main help) type ! Sets type of output - crystal or unit cell projection wait ! Waits for user input (see main help) vec ! Sets a point inside plot slice
Shows the content of the asymmetric unit. The names of those atoms, a number that is used as index for its scattering type, their position and temperature coefficient are listed. The number that is listed, is the number that refers to the scattering curve of that atom. It is contained in the variable m[<index>]. If a cell was read, all atoms are considered to be different, even if they are chemically identical and have the same temperature coefficient. If a whole structure was read, all atoms that are in the unit cell 0 <= xyz < 1, are chemically unique and have a different temperature coefficient are included in the asymmetric unit.
Shows the type of all atoms present in the crystal. For each different atom present, its identifying number, its name and its temperature coefficient are listed. The list contains all the atoms in the asymmetric unit plus any atoms added to the structure. If atoms are removed from the structure, the program does not check whether there are any atoms of this type left. If a particular type of atom is completely removed from the structure, it will remain in the list of different atoms, and will be displayed by 'chem'.
Defines the sequence in which the xy and z coordinates of the atoms are written. If the 'prog' "gnuplot" is used, this will allow the user to view the structure from different direction. For "kupl" this will give projections of the structure along the last direction.
Deselects the atoms.
"all" All atoms are deselected, no atom will be plotted. "mic" The microdomain status is set back to include the host structure and any microdomains. <name> Only the atom specified by <name> is deselected. <number> Only the atom specified by the scattering type <number> is deselected.
More than one atom can be deselected by the command.
Sets the extend of crystal space to be plotted.
"all" The whole crystal is written to the plot file. "x" The extend along the x direction is limited to (including) <xmin> and <xmax>. "y" The extend along the y direction is limited to (including) <ymin> and <ymax>. "z" The extend along the z direction is limited to (including) <zmin> and <zmax>.
If any of the parameters "x","y","z" is used, the extend along the other directions is not changed, even if previously set with the "all" command.
Sets the reciprocal space direction normal to the plot slice. the corresponding direct space direction ==> 'uvw' is calculated automatically. If <hkl> is set to "000", all atoms are plotted, otherwise all atoms are written to the output file, if they are within a slice normal to the <hkl> (and <uvw>) direction. The thickness of the plot slice is defined by the ==> 'thick' command, while the ==> 'vec' command defines a point that represents the center of the slice. Further restrictions on the atoms to be included can be applied by the ==> 'sel' and the ==> 'exte' commands.
Sets the name of the output file to which the structure is written.
Selects the plotting program for which the output is to be formatted.
"gnuplot" The xyz coordinates of all selected atoms are written in the sequence defined by the ==> 'col' command. "kuplot" The xyz coordinates of all selected atoms are written in the sequence defined by the ==> 'col' command. A projection of the structure along the third direction of the 'col' parameter is plotted. The file contains the typ, color and size code set with the ==> 'set' command. Use 'load cr,<file>' to read the file with KUPLOT.
Starts writing of the structure. If no output filename has been provided or no atoms been selected, an error message is given.
Defines which atoms are included in the output. Possible values for the first mandatory parameter are mutually exclusively:
"all" all atoms of the crystal are included. <name> all the atoms called <name> of the crystal are included. This includes symmetrically not equivalent atoms. <number> all atoms of the crystal that are of scattering type <number> are included. "mic" selects the microdomain status. This status defines whether atoms that are inside a microdomain are to be plotted or not. The kind of atoms to be included have to be chosen by an additional 'sel' command. Second parameter: "all" atoms inside any microdomain are selected, all atoms outside all microdomains are not included. "eve" Disregard microdomain status of an atom. Atoms in the host structure and inside any microdomain are plotted alike. <number> Only atoms inside microdomain type <number> are selected. "none" Only atoms outside all microdomains are selected.
The selection made stay valid until explicitely deselected!
This command allows to set the marker type <typ>, its color <col> and size <size> for the given atom. The atom can be given by its name <name> or scattering type number <number>. The resulting file will contains the coordinates of the atom and typ, color and size in a row. This file can be read by KUPLOT using the command
load cr,<file>
The possible values for <typ> are:
0 : no marker 4 : empty square 8 : cross (+) 1 : dot 5 : filled square 9 : vertical line 2 : empty circle 6 : empty triangle 10 : vertical line from 3 : filled circle 7 : cross (x) x-axis
The possible values for the colors <col> are:
1 : red 4 : purple 2 : green 5 : yellow 3 : blue 6 : black
The size of the markers <size> is given relative to the marker size set in the plotprogram KUPLOT, i.e. a value of 1.0 will result in the full marker size whereas 0.5 will reduce the size by 50%.
If you are using 'gnuplot' as program typ (-> 'prog') the settings will be ignored.
Shows the settings for the plotting parameters.
Sets the half thickness of the plot slice in Angstroem. All atoms are written to the output file, if they are within a slice of thickness 2*<value> that contains the direct space point defined by ==> 'vec' and is normal to the direction defined by ==> 'hkl' or 'uvw'. Further restrictions on the atoms to be included can be applied by the ==> 'sel' and the ==> 'exte' commands.
Sets the direct space direction normal to the plot slice. The corresponding reciprocal space direction <hkl> is calculated automatically. If <hkl> is set to "000", all atoms are plotted, otherwise all atoms are written to the output file, if they are within a slice normal to the <uvw> (and <hkl) direction. The thickness of the plot slice is defined by the ==> 'thick' command, while the ==> 'vec' command defines a point that represents the center of the slice. Further restrictions on the atoms to be included can be applied by the ==> 'sel' and the ==> 'exte' commands.
This command switches between to plot modes. The typ "crystal" will write the atom coordinates of the selected (-> 'sele') atoms on a file. The type "projection" will remove the translation and all atoms will be projected in a single unit cell. The second type can be read with KUPLOT using 'load cr,<file>' or 'load de,<file>,<dx>,<dy>'. See the KUPLOT online help for more details on the different file formats.
Sets the vector that represents the center of the plot slice. All atoms are written to the output file, if they are within a slice that is normal to the <hkl> (and <uvw>) direction and contains the direct space vector <v1 ,v2, v3>. The thickness of the plot slice is defined by the ==> 'thick' command, while the ==> 'vec' command defines a point that represents the center of the slice. Further restrictions on the atoms to be included can be applied by the ==> 'sel' and the ==> 'exte' commands.