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                  A GENTLE INTRODUCTION TO USING  D D P L O T
                         Roman Groger ([email protected])
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FILE FORMATS

Following is a list of file formats that are readable by ddplot. If you want to
use this code for plotting, you are supposed to prepare your data in one of the
supported formats. The only format that ddplot uses for saving is the internal
.dd format that whose complexity will evolve in future releases to accommodate
all possible information required for effective plotting of the dislocation
displacement maps. 


[ .xyz format ]

This is the most trivial format that does not contain any information about the
orientation of the block, periodicity and like. It is entirely up to the user of
ddplot to remember these parameters.

ninit
title_init
el1  x(1)  y(1)  z(1)
el2  x(2)  y(2)  z(2)
 :    :     :     :                   # coordinates of atoms in the initial
 :    :     :     :                   # configuration (ideal lattice)
eln  x(n)  y(n)  z(n)
nrel
title_rel
el1  x(1)  y(1)  z(1)
el2  x(2)  y(2)  z(2)
 :    :     :     :                   # coordinates of atoms in the relaxed
 :    :     :     :                   # configuration (relaxed structure)
eln  x(n)  y(n)  z(n)
BVECT value                           # Burgers vector of screw dislocation (if any)


[ .plt format ]

This is an old format used in one of our simulation codes. Note, that the number
of atoms in the relaxed configuration should be identical to that in the perfect
lattice. The relaxed configuration is usually obtained by stressing a perfect
crystal, where the initial positions of atoms correspond to the perfect lattice.

nrel                              # number of atoms in the relaxed configuration
z(1)         
z(2)
 :                                # z-positions of atoms in the relaxed 
 :                                # configuration
z(nrel)
x(1)      y(1)    zlayer(1)
x(2)      y(2)    zlayer(2)
 :         :         :            # (x,y) positions of atoms in the 
 :         :         :            # relaxed configuration
x(nrel)  y(nrel)  zlayer(nrel)
ninit                             # number of atoms in the perfect lattice
z(1)         
z(2)
 :                                # z-positions of atoms in the perfect lattice
 :
z(nrel)
x(1)        y(1)
x(2)        y(2)
 :           :                    # (x,y) positions of atoms in the perfect
 :           :                    # lattice
x(ninit)  y(ninit)
0                                 # unused, don't ask me why
xperiod
yperiod                           # periodicity in the x, y, z directions
zperiod
CORE { xpos; ypos }               # (x,y) position of the screw dislocation

If the block does not contain any screw dislocation, simply omit the last line.


[ .bl format]

This is another format from the same simulation code that we are using. The
format is a bit complicated and is not supposed to be used any more. It is left
in ddplot only for the sake of quick visualization of the results of our
simulations.

LEN
  xlen  ylen  zlen               # x, y and z size of the block

LATPAR
  latpar                         # lattice parameter

ND
  nd                             # number of active atoms

D
  x(1)   y(1)   z(1)   elem(1)
  x(2)   y(2)   z(2)   elem(2)   # coordinates of active atoms in the
   :      :      :        :      # relaxed configuration and the name
   :      :      :        :      # of the element, e.g. Mo
  x(nd)  y(nd)  z(nd)  elem(nd) 

NINERT
  ninert                         # number of inert atoms

DINERT
  x(1)       y(1)       z(1)       elem(1)
  x(2)       y(2)       z(2)       elem(2)      # coordinates of inert atoms in the
   :          :          :           :          # relaxed configuration and the name
   :          :          :           :          # of the element, e.g. Mo
  x(ninert)  y(ninert)  z(ninert)  elem(ninert) 

UNRLD
  x(1)       y(1)       z(1)       elem(1)
  x(2)       y(2)       z(2)       elem(2)      # coordinates of atoms in the
   :          :          :            :         # perfect lattice and the name
   :          :          :            :         # of the element, e.g. Mo
  x(nunrld)  y(nunrld)  z(nunrld)  elem(nunrld) # nurld=nd+ninert

In our simulations, the block is usually divided into two parts. Outer part of
the (x,y) plane contains inert atoms into which we apply anisotropic
displacements corresponding to a given stress field. The inner part then
contains active atoms whose position is obtained by minimization. In the relaxed
configuration, the force on each atom is essentially zero.


[ .dd format]

This is the internal ddplot's format that contain all possible information about
the block, including the orientation of the block, positions of dislocations,
periodicity, etc. Each block starts with a header that is written below in
capital letters. Comments begin with '#' and are ignored by ddplot. Number of
spaces between each number in a row and between lines is arbitrary.

CSYS                             # orientation of the block given by three 
  x1  x2  x3                     # vectors defined in the cube coordinate system
  y1  y2  y3                     # [100], [010], [001]
  z1  z2  z3

PERIOD
  xperiod  yperiod  zperiod      # periodicity along x, y and z

DISLO_CENTER
  xpos  ypos                     # (x,y) position of the screw dislocation

NUM_UNREL
  ninit                          # number of atoms in the perfect lattice
  
COOR_UNREL
  x(1)      y(1)      z(1)      elem(1)
  x(2)      y(2)      z(2)      elem(2)        # coordinates of atoms in the
   :         :         :           :           # perfect lattice and the index
   :         :         :           :           # of the element of this atom
  x(ninit)  y(ninit)  z(ninit)  elem(ninit)    # (count from 0)

NUM_REL
  nrel                           # number of atoms in the relaxed configuration

COOR_REL
  x(1)     y(1)     z(1)     
  x(2)     y(2)     z(2)         # coordinates of atoms in the relaxed
   :        :        :           # configuration
   :        :        :       
  x(nrel)  y(nrel)  z(nrel)  

The mandatory fields are NUM_UNREL, COOR_UNREL, NUM_REL, COOR_REL and PERIOD.