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Structure definition

The first step is to run the program preparation.py, followed by the name of a file containing the structure :

python preparation.py <structure_file_name>
( see section 6 to see how to invoke OpenPhonon at ESRF or with the pre-compiled version). The structure file specifies the atoms and their position in the cell. This is accomplished by setting the variables AtomNames, CellVectors, PositionsList at the beginning of the input file ( note that the input file is simply executed as a Python script, so one has to use Python sintax).

We show here an example input file for preparation.py referring to a literature case [4]. It can be found in the distribution archive ( binary or source) in the directory test_OP:

AtomNames=['Cu',   'O',  'Nd' ]
cellvectors=Numeric.array( 
         [ 
           [3.95  , 0.0     ,  0.0],
           [0.0   , 3.95    ,  0.0], 
           [0.0   , 0.0     ,  12.06556] 
         ] )
PositionsList=[
          Numeric.array(  
              [ [0.0,       0.0,       0.0  ],
                [0.5,       0.5,       0.5  ]
              ]    
          ),
          Numeric.array(
              [ [0.5,       0.0,       0.0  ],
                [0.0,       0.5,       0.0  ],
                [0.5,       0.0,       0.25 ],
                [0.0,       0.5,       0.25 ],
                [1.0,       0.5,       0.5  ],
                [0.5,       1.0,       0.5  ],
                [1.0,       0.5,       0.75],
                [0.5,       1.0,       0.75],            
              ]
           ),
           Numeric.array(
              [ [0.0,       0.0,       0.352],
                [0.5,       0.5,       0.148],
                [0.5,       0.5,       0.852],
                [1.0,       1.0,       0.648]        
              ]
           )
]
SeekedTetragon=[('Cu',0),('O',1),('Nd',0),('Nd',2)]

CellsCoo=[(0,0,0),(0,0,0),(0,0,0),(0,0,0)]   # optional
dr_shell=0.05                                # optional
num_nei=3                                    # optional
The SeekedTetragon array must specify a non degenerate 3-D solid that is rotated and translated in all possible ways to look for symmetries and equivalent atoms.

CellsCoo defines the cell in which the vertices are. This variable is optional and is set by default to all vertices in the same cell.

dr_shell defines the width of a shell. Two-body bonds are catalogued according to their length and the type of atoms that they concern. This variable is set by default to 0.1.

Finally num_nei, which is set by default to 2, is the number of neighbours.

The distribution archive contains an example file ( preparationinput ).

This file being set, the script preparation.py can be run (python preparation.py structure-file-name). The script does a rough evaluation of the symmetries and of inequivalent bonds and creates two files. Both files need to be stored somewhere for subsequent use by the program that calculates dispersions. One of these file, cella contains all the needed structural informations, while the other,parinput is a template file that can be edited with the parameters of the interatomic potentials as explained in the next subsection.


next up previous contents
Next: Definition of Potentials and Up: Files structure and use Previous: Files structure and use   Contents
Alessandro Mirone 2003-11-17