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chem


chem

Enters the 'chem' sublevel. Here all kind of statistics about the model crystal can be obtained like relative amount of elements, distribution of bond-lengths, ...

Further information is available for commands

commands

Valid commands at this sub level are:

@       ! Executes a macro (see main help level)
=       ! Algebra (see main help level)
aver    ! Calculates average structure and occupancies
blen    ! Calculates distribution of bond lengths
chem    ! Shows atomtypes within the model crystal
echo    ! Echos a string (see main help level)
elem    ! Show rel. abundances of elements in crystal
eval    ! Evaluate an expression (see main help level)
exit    ! Terminates the chem sublevel.
freq    ! Calculates neighbour frequencies/probabilities
help    ! Gives on-line help for 'chem' (see main help level)
set     ! Change settings of 'chem' parameters
show    ! Show current parameters
system  ! Executes operating system command (see main help)
trans   ! Transforms between atomindex and unitcell/site
wait    ! Waits for user input (see main help level)

aver

aver

This command allows to calculate the average structure of the current model crystal. The average position, the standard deviation and the occupancy of every site within the unit cell is given. The average positions and sigmas are stored in the variable array 'res'.

Warning: This command works only correct, if the structure is given
         in the order created by the 'read cell' command. Appended
         atoms are simply ignored ! However, using the PURGE command
         is not recommended when using this commands !!!!

blen

blen { "all" | <name> | <number> },
{ "all" | <name> | <number> }, [<filename>]

This command calculates the bond length distribution between the selected atoms (by <name>, <number> or "all"). The histogram is saved to the file <filename>. The number of points of the histogram is given by 'set bin,<ip>'. The calculation mode can be switched between "quick" and "exact". The mode "exact" calculates the bondlength for EVERY Atompair within the crystal whereas the mode "quick" only looks at neighbouring unit cells. BUT in the "quick" mode errors can occur due to using the "purge" command or appending atoms to the structure. Allowed bondlength range, calculation mode and sigmas for a neighbour matching criteria are given with the 'set' command.

chem

chem

Displays the type of atoms present in the crystal. For each type of atom, its scattering curve number, its name and its temperature factor are listed. Warning, even, if all atoms of a particular type have been deleted, its scattering type will remain in the list. This list could therefore include more types of atoms than are actually present in the crystal.

elem

elem [ { "on" | "off" } ]

Displays information about elements in the model crystal like relative abundances of the elements. 'void' stands for a vacancy. The results (range 0..1 rather than %) are stored in the variable res[<i>], with <i> the number of the atomtyp. The optional parameter "on" or "off" controls if screen output is produced.

freq

freq { <name> | <number> }, { <name> | <number> }, <u>,<v>,<w>

This command allows to calculate the probability (frequency) for the given pairs of atoms in the specified direction <u>,<v>,<w>. The correlation coefficient is also calculated.

correlation > 0 : preferred neighbours of the same type
correlation = 0 : random distribution
correlation < 0 : preferred neighbours of different type

The setting done by "set fsig,<value>" determines how exact the distance given by uvw has to be matched. As for the command 'blen', the user can select between the "quick" and the "exact" calculation mode (see help for command 'set').

The resulting frequencies are stored in the variables res[<i>] in the following order:

res[1] = probability for atom 1 - atom 1 pair
res[2] = probability for atom 1 - atom 2 pair (or 2,1)
res[3] = probability for atom 2 - atom 2 pair
res[4] = correlation coefficient

The variable res[0] contains as usual the number of variables returned by the command (here 4).

set

set <subcommand>,...

This command sets various parameters within the 'chem' section of the DISCUS program. Valid <subcommands> are:

commands

"blen"    : sets range for bond length calculations
"bin"     : sets number of points for bond length histogram
"check"   : controls neighbour determination for 'freq'
"cryst"   : setting crystal dimensions (if wrong determined by read stru)
"fsig"    : sets allowed "distance-sigma" for frequency calculation
"mode"    : sets calculation mode ("quick"/"exact")
"outfile" : redirects screen output to a file
"wsig"    : sets allowed "angle-sigma" for frequency calculation

blen

set "blen",<min>,<max>

This command sets the range <min> to <max> of the bond-length to be calculated and binned to the histogram.

bin

set "bin",<number>

This command sets the number of points for the histograms created by 'chem'.

check

set "check",{"on" | "off"} [,{"on" | "off"}]

This command controls if only the neighouring distance ("off") given by the direction with the 'freq' command should be used for neighbour determination or the given direction as well ("on"). The second parameter specifies if symmetrically equivalent directions to the given direction should be used ("on") or not ("off"). The tolerance for the neighbouring direction check is set by "set wsig,<value>". The direction check causes the calculation to take significantly longer.

Examples:

  set check,off,off    : all neighbours in the given distance
                         intervall will be counted.
  set check,on,off     : only neighbours in the given distance
                         intervall AND direction will be counted.
  set check,on,on      : neighbours in the given distance inter-
                         vall AND given direction or symmetrically
                         equivalent directions will be counted.

cryst

set "cryst",<nx>,<ny>,<nz>,<natoms>

A bug in the current version of DISCUS sometimes causes wrong crystal- dimensions. This command allows to rewrite the values for the crystal- dimension <nx>,<ny>,<nz> and number of atoms in a unit cell <natoms>.

fsig

set "fsig",<sigma>

The bondlength along a certain direction is only accepted within +-<<sigma>/2) around the given distance. If there are big relaxations within the crystal it is a good idea to set <sigma> to a reasonable big value.

mode

set "mode",{"quick"|"exact"}

This command switches the calculation mode between "quick" and "exact". In the "quick" mode only the neighbouring unit cells around a certain atom are taken into account. If the command 'purge' is performed or a structure is read where the atoms are not listed in the DISCUS order this mode might fail, because the calculation of the index of an atom in a neighouring unit cell can be wrong. In this case the "exact" mode should be used which taken ALL other atoms into account.

outfile

set "outfile",{"on"|"off"},[<filename>]

This command allows to redirect the screen output of the results of the commands in the 'chem' section to the file <filename>. If no filename is given, the default "chem.log" is used.

wsig

set "wsig",<sigma>

The bondlength along a certain direction is only accepted within +-<<sigma>/2) of angle difference between the actual bondlength and the given direction. If there are big relaxations within the crystal it is a good idea to set <sigma> to a reasonable big value.

trans

trans <atomindex> or
trans <x>,<y>,<z>,<site>

This command allows to transform between a given index of the storage array <atomindex> and the corresponding unitcell <x>,<y>,<z> and site <site>. The parameter not given is calculated ...


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