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inverse


inverse

branches to the inverse Fourier transform level of DISCUS The inverse Fourier transform is calculated from two input files. The two files must contain the intensity, real or imaginary part amplitude or phase in one of the following combinations:

file a          file b
-------------------------
intensity       phase
amplitude       phase
real            imaginary

The user must specify the Fourier plane that had been calculated and the real space plane to be calculated.

Further help topics are:

commands

Valid commands at this level are:

@       ! execute a macro file (see main help level)
=       ! assigns the value to a variable (see main help level)
abs     ! defines the coordinate of the abszissa
echo    ! echo a string (see main help level)
eval    ! Evaluates an expression (see main help level)
exit    ! terminates Fourier level
file    ! defines the input file name(s)
form    ! defines the input file format
help    ! help to fourier commands (see main help level)
layer   ! defines the layer in reciprocal space to be calculated
ll      ! defines the lower left corner in reciprocal space
lr      ! defines the lower right corner in reciprocal space
na      ! defines the number of points along the abszissa
no      ! defines the number of points along the ordinate
ord     ! defines the coordinate of the ordinate
rhoabs  ! defines the coordinate of the real space abszissa
rholayer! defines the layer in real space to be calculated
rholl   ! defines the lower left corner in real space
rholr   ! defines the lower right corner in real space
rhona   ! defines the number of points along the real space abszissa
rhono   ! defines the number of points along the real space ordinate
rhoord  ! defines the coordinate of the real space ordinate
rhoul   ! defines the upper left corner in real space
run     ! starts the calculation
scale   ! defines an overall scale factor
set     ! sets various parameters
show    ! shows the current settings for the inverse Fourier transform
system  ! Executes operating system command (see main help)
ul      ! defines the upper left corner in reciprocal space
wait    ! Waits for user input (see main help level)

abs

abs <switch>

Defines which the component of the vector parallel to the abszissa is written to the output file.

file

file {"a"|"b"},<filename>

Defines the filenames needed for the inverse Fourier.

The inverse Fourier transform is calculated from two input files. The two files must contain the intensity, real or imaginary part amplitude or phase in one of the following combinations:

file a          file b
-------------------------
intensity
amplitude
real            imaginary

If the input format is 'shelxl' then one input file is sufficient. DISCUS assumes the input file to be a SHELXL List type 5 containing <h> <k> <l> <Fobs> <Fcalc> <phase angle in degree> The file is read as free format.

format

form {"gnu" | "stan" | "shelxl"}

Defines the input format that will be used. Valid parameters are: "gnu" Sets the type of the output file to gnuplot. The intensities are written in blocks of intensities along the abscissa, with an empty line separating each block. Each line of each block contains: index along abscissa, index along ordinate, intensity, third index. "stan" Sets the output to standard file format, which is used by KUPL. The output file contains two initial lines and then a block for each data line separated by an empty line. The first line contains the number of data points along the abszissa and the ordinate, the second line the minimum and maximum value of the indices in reciprocal space along the abscissa and ordinate respectively. "shelxl" Sets the input file format to SHELXL. DISCUS assumes the input file to be a SHLEXL List type 5 containing <h> <k> l> <Fobs> <Fcalc> <phase angle in degree> The file is read as free format. All reflections are expanded by the appropriate symmetry operations, including proper phase transformation.

layer

layer <e11,e12,e13, e21,e22,e23, e31,e32,e33, inc1,inc2>

sets the lower left, lower right and upper left corner of the Fourier plane to be calculated and sets the number of data points along the horizontal and the vertical

ll

ll <e11> , <e12> , <e13>

Sets the lower left corner of the Fourier plane to be calculated.

lr

lr <e21> , <e22> , <e23>

Sets the lower right corner of the Fourier plane to be calculated.

na

na <inc1>

Sets the number of data points that will be calculated along the abszissa.

no

no <inc2>

Sets the number of data points that will be calculated along the ordinate.

ord

ord <switch>

Defines which the component of the vector parallel to the ordinate is written to the output file.

rhoabs

rhoabs <switch>

Defines which the component of the vector parallel to the real space abszissa is written to the output file.

rholayer

rholayer <e11,e12,e13, e21,e22,e23, e31,e32,e33, inc1,inc2>

sets the lower left, lower right and upper left corner of the real space plane to be calculated and sets the number of data points along the horizontal and the vertical

rholl

rholl <e11> , <e12> , <e13>

Sets the lower left corner of the real space plane to be calculated.

rholr

rholr <e21> , <e22> , <e23>

Sets the lower right corner of the ral space plane to be calculated.

rhona

rhona <inc1>

Sets the number of data points that will be calculated along the real space abszissa.

rhono

rhono <inc2>

Sets the number of data points that will be calculated along the real space ordinate.

rhoord

rhoord <switch>

Defines which the component of the vector parallel to the real space ordinate is written to the output file.

rhoul

rhoul <e31> , <e32> , <e33>

Sets the upper left corner of the real space plane to be calculated.

run

run

Starts the inverse Fourier calculation.

scale

scale <scale-factor>

Defines an overall scale factor. Together with the automatic scaling by 1/vol(unit cell), this scale factor serves to put the electron density on an absolute scale of electrons per cubic Angstroem. The scale factor should effectively multiply the observed F(000) such that it is equal to F(000) calculated for one unit cell of the average structure.

Every time you enter "inverse" the scale factor is calculated to be number of atoms in crystal / number of atoms in one unit cell. If you use experimental data, you MUST specify the scalefactor everytime you enter the "inverse" submenu.

set

set "accu",{"init"|"add"}

Set defines various parameters. "accu" Sets the mode for the accumulation of inverse Fourier transforms. "init" The electron density array is initialised, i.e. set to zero. "add" The next inverse Fourier transform is added to the previous value. This way several inverse Fourier transforms will contribute to a single layer in direct space, which is necessary to create a inverse Fourier section rather than a Projection onto the layer. See the manual for further details.

show

show

shows the current settings for the Fourier transform file

type

type {"a"|"b"},
{"intensity"|"amplitude"|"real"|"imaginary"|"phase"|"fobs"|"fcalc"}

Defines the content of file "a" or "b".

The inverse Fourier transform is calculated from two input files. The two files must contain the intensity, real or imaginary part amplitude or phase in one of the following combinations:

file a          file b
-------------------------
intensity       phase
amplitude       phase
real            imaginary

If the input format is "shelxl", DISCUS reads just one file. You can calculate the inverse Fourier from Fobs or Fcalc data by choosing the appropriate file type from one of the following choices:

file a          file b
-------------------------
amplitude
fobs
fcalc

ul

ul <e31> , <e32> , <e33>

Sets the upper left corner of the Fourier plane to be calculated.


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