Switches to the microdomain calculation level of discus.
Further help topics are:
Valid commands at this level are:
@ ! Executes a macro (see main help level) = ! assigns the value to a variable (see main help level) ang ! Sets the current units to Angstroem asym ! Displays the content of the asymmetric unit base ! Defines the superlattice boun ! Sets the current boundary type ccol ! Reads a single column of the correlation matrix chem ! Displays the different atoms that are present in the crystal cele ! Reads a single element of the correlation matrix cont ! Sets the current content type for the microdomains crea ! Creates the list of microdomains crow ! Reads a single row of the correlation matrix dens ! Sets the density of randomly distributed microdomains dist ! Sets the distribution type of the microdomains dlu ! Sets the current units to direct lattice units echo ! Echos a string (see main help level) eval ! Evaluates an expression for interactive check exit ! Terminates the microdomain sublevel help ! Gives on line help for micro (see main help level) grid ! Sets the fitting of microdomain origins to the host lattice ini ! Initializes the microdomain menu ins ! Inserts the currently defined microdomain parameters into the list log ! Turns log of microdomain positions on/off mrow ! Read a single row of the orientation matrix orie ! Sets the default value for the orientation matrix number place ! Places a single microdomain into the crystal radi ! Sets the current radius and its sigma for the microdomains remo ! Removes all or a single microdomain type from the list rbase ! Defines the superlattice in reciprocal space run ! Starts the calculation of the microdomain distribution sep ! Defines minimum interatomic distance for "fuzzy" microdomains shift ! Constant shift of all microdomain origins. show ! Shows the current settings for micro sigm ! Defines the FWHM for Gaussian distributions six ! Defines the FWHM for Gaussian distributions along the ! x axis of the superlattice siy ! Defines the FWHM for Gaussian distributions along the ! y axis of the superlattice siz ! Defines the FWHM for Gaussian distributions along the ! z axis of the superlattice system ! Executes operating system command (see main help) wait ! Waits for user input (see main help level)
Sets the current unit to Angstroem. All radii read from now on will be understood as given in Angstrom.
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.
Defines the base vectors of the superlattice on which the microdomains are located. The indices are to be given as multiples of the base vectors of the host crystal. <b1*> gives the a axis of the superlattice, <b2*> the b and <b3*> the c axis.
Sets the boundary type of the next microdomain type. The three options are mutually exclusive.
"block": The microdomains are limited by {100} (as if cubic). The radii of the faces are determined by the size of the structure file read. "face,<h>,<k>,<l>": The microdomain is limited by (several) faces with indices <h>,<k>,<l>. The distance of this face from the origin of the microdomain is taken from the current radius. The set of faces must form a closed shape in real space. "fuzzy" The microdomain is defined only through the atoms that are read from the input file. Only those host atoms, whose distance to any microdomain atom is less than the separation defined by the command: sep fuzzy,<dist> are replaced by the microdomain. "sphere": The microdomain is limited by a sphere with radius as defined by the ==> 'radius' command.
Read a single column <nr> of the correlation matrix. Following the index <nr>, as many parameters as there are microdomain types must follow. The sum of any column need not be equal to one. The number of array elements requested by 'ccol' is equal to the number of new microdomain types introduced since the last ==>'crea' command.
Reads the value <value> that is stored in element <i>,<j> of the correlation matrix.
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 content of a microdomain type. The parameters are mutually exclusive.
"cell",<file> : Under development "free" : The structure of the microdomain can freely be modified by the user. For each atom the number of the closest microdomain is stored in the variable ==> "md_next[<i>]". If this is negative, the atom is inside the microdomain, else outside. The distance to the nearest surface is stored in md_dist[<i>]. Again, if this is negative or zero the atom is inside the microdomain. "structure",<file> : The structure read from file <file> is used to fill the microdomain.
Creates the list of microdomain origins. No changes are done to the actual structure, this is performed by the command ==> 'run'. The list of origins may be edited by the user.
Read a single row <nr> of the correlation matrix. Following the index <nr>, as many parameters as there are microdomain types must follow. The sum of any row need not be equal to one, as long as the sum of all rows is identical. The number of array elements requested by 'ccol' is equal to the number of new microdomain types introduced since the last ==>'crea' command.
Defines the density of microdomains in microdomains per unit cell. This is used in case of a random distribution of microdomains.
Defines the type of distribution to be used.
"lattice" : The origins of all microdomains are located on the nodes of a perfect lattice defined by the base. "para": The microdomains are distributed on a paracrystalline lattice. The average separation of two microdomain origins is defined by the base vectors. The length and direction of each individual separation is Gaussian distributed with the mean value given by ==> 'base' and the sigma given by ==> 'si..'. "random" : The origins are randomly distributed with a density of ==> 'dens' microdomains per unit cell.
Sets the current unit to direct lattice units. All radii read from now on will be understood as given in multiples of the lattice constant a of the host lattice.
Defines the fitting of the microdomain origins to the nodes of the host lattice.
"host" : The microdomain origins are forced to be integer multiples of the host lattice, including any centering positions. "free" : The microdomain origins may assume any value, in effect creating an incoherrent intergrowth of the two structures.
Initializes the microdomain distribution. The number of microdomain types, microdomain origins is set to zero. The actual crystal is not modified by this command, nor are any previous modifications undone.
Inserts a microdomain type with the current parameters into the list of microdomain types.
Determines whether the list of microdomain origins is written to files "fort.97", "fort.98" and "fort.99". This command serves mainly for testing. Files "fort.97" and "fort.99" contains the list of microdomain origins in a form identical to the structure files of DISCUS. Each site is denoted by a point scatterer "E1- ". This file can be read and its Fourier transform be calculated. File "fort.98" contains just a list of x,y,z positions to be displayed by a suitable graphics program. "fort.98" and "fort.99" contain the list of all microdomains created by the ==>'crea' command, while "fort.97" contains only those microdomains that are at least partially inside the crystal.
Read a single row <nr> of the orientation matrix. Following the index <nr>, the four elements of the orientation matrix are read. As soon as the first three rows of the orientation matrix have been read, the matrix is stored.
Sets the default for the orientation matrix number. All following microdomains inserted until the next "orie" command will have the orientation specified by the orientation matrix <nr>.
With this command an individual microdomain can be placed into the crystal. The microdomain of type <type> is placed at coordinates <x>,<y>,<z> and the structure of the crystal modified according to the microdomain type <type>. The type must be a previously defined microdomain type. The current distribution type has no effect on the position of the microdomain. The fitting to the host grid is determined by the current value set by ==> 'grid'.
Sets the current radius for microdomains. In case of boundary type "sphere", this is the actual radius, in case of boundary type "face" it is the distance from the origin of the microdomain to the boundary face. The radius <value> is interpreted according to the current unit ==> 'dlu' and 'ang'. If the optional value <sig> is given, the radii of the individual microdomains are distributed according to a gaussian distribution with sigma <sig>.
Removes all microdomain types or a specified microdomain type from the list of microdomain types. Only those microdomain types can be removed that have been defined by ==> 'inse' but whose origins have not yet been distributed throughout the crystal with the ==> 'crea' command.
Defines the reciprocal base vectors of the superlattice on which the microdomains are located. The indices are to be given as multiples of the reciprocal base vectors of the host crystal. <b1*> gives the a* axis of the superlattice, <b2*> the b* and <b3*> the c* axis.
Starts the calculation of the modification of the structure. The original atoms of the host that are inside a microdomain are removed. If the content type of the microdomain is "free", the atoms are marked but not removed. The structure read from the content file is used to fill the available space. If this command is not used, no modifications of the structure take effect.
Defines the maximum separation between host atoms and microdomain atoms that are inside a "fuzzy" microdomain. All host atoms are removed, if their distance to any microdomain atom is less or equal to <distance>.
The vector xyz is added to all microdomain origins, except for a random distribution. Thus two distributions with the same lattice can be generated that are shifted with respect to each other by the vector xyz.
Shows the current settings for micro. If no parameter is given, all information is shown, else only the information for the specific parameter is shown:
"def" : Shows the current default values for the next microdomain type. "dist" : Shows the parameters describing the microdomain distribution. "type" : Shows the microdomain type inserted so far. "corr" : Shows the correlationmatrix. "orie" : Shows the orientation matrices that have been defined.
Defines the SIGMA's of the Gaussian distribution. <sii> are the SIGMA's along the base vectors, the <sij> give the SIGMA of the Gaussian distribution in direction of base vector j at the end of base vector i.
Defines the SIGMA's of the Gaussian distribution along the base vector x. <sii> are the SIGMA's along the base vectors, the <sij> give the SIGMA of the Gaussian distribution in direction of base vector j at the end of base vector i.
Defines the SIGMA's of the Gaussian distribution along the base vector y. <sii> are the SIGMA's along the base vectors, the <sij> give the SIGMA of the Gaussian distribution in direction of base vector j at the end of base vector i.
Defines the FWHM's of the Gaussian distribution along the base vector z. <sii> are the FWHM's along the base vectors, the <sij> give the FWHM of the Gaussian distribution in direction of base vector j at the end of base vector i.