1.37 transform

tran

Switches to the unit cell transformation submenu of DISCUS. At this sublevel you can define the relationship between an old and a new unit cell and perform the transformation of the atoms in the crystal. An interactive transformation allows to calculate the result for any single real and reciprocal space vector in both directions: old ==> new and new ==> old.

You can specify the relation ship between the two unit cells in any of four possible options: define the new base vectors a,b,c in terms of the old base define the old base vectors a,b,c in terms of the new base define the new coordinates x,y,z in terms of the old coordinates define the old coordinates x,y,z in terms of the new coordinates define the new base vectors a*,b*,c* in terms of the old reciprocal base define the old base vectors a*,b*,c* in terms of the new reciprocal base

Independent of the choice above, you can define an optional shift of the origin by: defining the coordinates of the new origin in terms of the old base defining the coordinates of the old origin in terms of the new base

If all atoms in the crystal are transformed to the new base vectors, then the unit cell dimensions and the metric tensors are transformed as well. The space group is set to "P1" to prevent erroneous symmetry operations once the present crystal is saved to file and read again.

1.37.1 commands

Valid commands at this level are

@       ! Execute a macro file (see main help)
=       ! assigns the value to a variable (see main help)
anew    ! sets the new base vector "a" in terms of the old base
aold    ! sets the old base vector "a" in terms of the new base
asnew   ! sets the new reciprocal base vector "a" in terms of the old base
asold   ! sets the old reciprocal base vector "a" in terms of the new base
asym    ! Shows asymmetric unit
bnew    ! sets the new base vector "b" in terms of the old base
bold    ! sets the old base vector "b" in terms of the new base
bsnew   ! sets the new reciprocal base vector "b" in terms of the old base
bsold   ! sets the old reciprocal base vector "b" in terms of the new base
c2new   ! Calculates the transformation to "new" for a single vector
c2old   ! Calculates the transformation to "old" for a single vector
chem    ! Shows the atoms present in the crystal
cnew    ! sets the new base vector "c" in terms of the old base
cold    ! sets the old base vector "c" in terms of the new base
csnew   ! sets the new reciprocal base vector "c" in terms of the old base
csold   ! sets the old reciprocal base vector "c" in terms of the new base
continue! Coninue a stopped macro (see main help level)
des     ! deselects atoms
echo    ! echo a string (see main help)
eval    ! Evaluates an expression for interactive check (see main help)
exit    ! terminates 'tran'
help    ! gives on line help for unit cell transformations (see main help)
incl    ! sets the range of atoms to be included in the transformation
onew    ! sets the new origin in terms of the old base
oold    ! sets the old origin in terms of the new base
run     ! starts the transformation for the selected atoms
sel     ! selects atoms to be included in the transformation
show    ! shows the current parameters
stop    ! Stops execution of a macro (see main help level)
system  ! Executes operating system command (see main help)
wait    ! Waits for user input (see main help)
xnew    ! sets the new coordinate "x" in terms of the old x,y,z
xold    ! sets the old coordinate "x" in terms of the new x,y,z
ynew    ! sets the new coordinate "y" in terms of the old x,y,z
yold    ! sets the old coordinate "y" in terms of the new x,y,z
znew    ! sets the new coordinate "z" in terms of the old x,y,z
zold    ! sets the old coordinate "z" in terms of the new x,y,z

1.37.2 anew

anew a,b,c

Defines the new base vector "a" in terms of multiples <a>, <b>, <c> of the old base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'anew','bnew' and 'cnew'.

1.37.3 aold

aold a,b,c

Defines the old base vector "a" in terms of multiples <a>, <b>, <c> of the new base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'aold','bold' and 'cold'.

1.37.4 asnew

asnew a,b,c

Defines the new reciprocal base vector "a" in terms of multiples <a>, <b>, <c> of the old reciprocal base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'asnew','bsnew' and 'csnew'.

1.37.5 asold

asold a,b,c

Defines the old reciprocal base vector "a" in terms of multiples <a>, <b>, <c> of the new reciprocal base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'asold','bsold' and 'csold'.

1.37.6 asym

asym

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.

1.37.7 bnew

bnew a,b,c

Defines the new base vector "b" in terms of multiples <a>, <b>, <c> of the old base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'anew','bnew' and 'cnew'.

1.37.8 bold

bold a,b,c

Defines the old base vector "b" in terms of multiples <a>, <b>, <c> of the new base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'aold','bold' and 'cold'.

1.37.9 bsnew

bsnew a,b,c

Defines the new reciprocal base vector "b" in terms of multiples <a>, <b>, <c> of the old reciprocal base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'asnew','bsnew' and 'csnew'.

1.37.10 bsold

bsold a,b,c

Defines the old reciprocal base vector "b" in terms of multiples <a>, <b>, <c> of the new reciprocal base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'asold','bsold' and 'csold'.

1.37.11 c2new

c2new x,y,z [, ["d" | "r" $\}$ ]

Calculates the transformation from the old coordinate system to the new system for a single vector <x>,<y>,<z>. Default is a direct space vector, the fourth optional parameter allows you to define <x>,<y>,<z> as a reciprocal space vector. The result of the transformation is displayed on the screen and stored in the first three elements of the result array "res[i]".

1.37.12 c2old

c2old x,y,z [, ["d" | "r" $\}$ ]

Calculates the transformation from the new coordinate system to the old system for a single vector <x>,<y>,<z>. Default is a direct space vector, the fourth optional parameter allows you to define <x>,<y>,<z> as a reciprocal space vector. The result of the transformation is displayed on the screen and stored in the first three elements of the result array "res[i]".

1.37.13 csnew

csnew a,b,c

Defines the new reciprocal base vector "c" in terms of multiples <a>, <b>, <c> of the old reciprocal base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'asnew','bsnew' and 'csnew'.

1.37.14 csold

csold a,b,c

Defines the old reciprocal base vector "c" in terms of multiples <a>, <b>, <c> of the new reciprocal base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'asold','bsold' and 'csold'.

1.37.15 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.

1.37.16 cnew

cnew a,b,c

Defines the new base vector "c" in terms of multiples <a>, <b>, <c> of the old base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'anew','bnew' and 'cnew'.

1.37.17 cold

cold a,b,c

Defines the old base vector "c" in terms of multiples <a>, <b>, <c> of the new base vectors. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'aold','bold' and 'cold'.

1.37.18 des

des $\{$ "all" |<name>|<number>$\}$ [ , $\{$<name>|<number>$\}$ ...]

des "mic"

Deselects choices made by ==> 'sel' . Possible values for the parameter are mutually exclusively:

"all"     all atoms of the crystal are deselected.
"mic"     The selection of atoms that are inside a microdomain is canceled.
<name>    all the atoms called <name> of the crystal are deselected.
          This includes symmetrically not equivalent atoms.
<number>  all atoms of the crystal that are of scattering type <number>
          are deselected.

More than one atom may be deselected at once.

1.37.19 incl

incl $\{$<start>,<end>| "all" $\}$

The unit cell transformation includes all atoms numbered <start> to <end> inclusively. All other atoms are ignored. If, instead of explicit numbers, the parameter "all" is given, the unit cell transformation will include all atoms of the crystal. This holds even, if at a later time you include further atoms in the crystal. Thus, you can define a setup for the unit cell transformations early in a lengthy macro, then modify the crystal and just run the unit cell transformation later on. In addition you can define the atoms that are affected by the unit cell transformation operation with the ==>'sele' and 'dese' commands.

1.37.20 onew

onew a,b,c

Defines the position of the new origin in terms of multiples <a>,<b>,<c> of the old base vectors. The default at program startup is 0.0, 0.0, 0.0

1.37.21 oold

oold a,b,c

Defines the position of the old origin in terms of multiples <a>,<b>,<c> of the new base vectors. The default at program startup is 0.0, 0.0, 0.0

1.37.22 run

run

Starts the transformation operation.

1.37.23 sel

sel $\{$ "all" |<name>|<number>$\}$ [ , $\{$<name>|<number>$\}$ ...]

sel "mic",$\{$ "all" | "eve" | "non" |<number>$\}$

This command executes two different functions. It serves to select those atoms that will be modified by the unit cell transformation and secondly it can set the microdomain status.

First function:

Defines which atoms are included in unit cell transformations. Possible values for the first mandatory parameter are mutually exclusively:

"all"     all atoms of the crystal are included.

This includes the "voids" in the structure, which are stored as scattering curve number zero.

<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.

More than one atom may be selected at once.

Second function:

Defines how atoms inside any microdomains are to be treated. The second parameter serves to distinguish different possible values of the status.

"mic"     selects whether atoms that are inside a microdomain are to be
          modified by the unit cell transformation operation or not.
          The kind of atoms to be included are 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 included
                   alike.
          "none"   Only atoms outside all microdomains are selected.
          <number> Only atoms inside microdomain type <number> are selected.

The selection made stay valid until explicitly deselected!

1.37.24 show

show

Shows the current parameters of the transformation operation.

1.37.25 xnew

xnew a,b,c

Defines the transformation through the relationship between the new "x" coordinate of an atom in terms of multiples <x>, <y>, <z> of the old coordinates of the atom. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'xnew','ynew' and 'znew'.

1.37.26 xold

xold a,b,c

Defines the transformation through the relationship between the old "x" coordinate of an atom in terms of multiples <x>, <y>, <z> of the new coordinates of the atom. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'xold','yold' and 'zold'.

1.37.27 ynew

ynew a,b,c

Defines the transformation through the relationship between the new "y" coordinate of an atom in terms of multiples <x>, <y>, <z> of the old coordinates of the atom. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'xnew','ynew' and 'znew'.

1.37.28 yold

yold a,b,c

Defines the transformation through the relationship between the old "y" coordinate of an atom in terms of multiples <x>, <y>, <z> of the new coordinates of the atom. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'xold','yold' and 'zold'.

1.37.29 znew

znew a,b,c

Defines the transformation through the relationship between the new "z" coordinate of an atom in terms of multiples <x>, <y>, <z> of the old coordinates of the atom. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'xnew','ynew' and 'znew'.

1.37.30 zold

zold a,b,c

Defines the transformation through the relationship between the old "z" coordinate of an atom in terms of multiples <x>, <y>, <z> of the new coordinates of the atom. If you choose this definition of the unit cell transformation, you MUST define all three ==> 'xold','yold' and 'zold'.