Defining symmetry
Symmetry can be defined in "symmetry"
blocks at the top level of the JSON configuration file in lists of "sym_tr3ds"
.
Multiple symmetries can be defined and used simultaneously.
Using a symmetry axis information
{
"symmetry": {
"sym_tr3ds": [
{
"name": "2fold",
"axis": "vector of the symmetry axis",
"center": "symmetry point (through which the above symmetry axis is passing through)",
"type": "cyclic symmetry type like C2, C3, C8 and so on"
}
]
}
}
For example:
{
"symmetry": {
"sym_tr3ds": [
{
"name": "2fold",
"axis": [0, 0, -1],
"center": [246.39112398, 246.41114644, 248.600000],
"type": "C2"
}
]
}
}
How to get this transformation information? Follow Calculating symmetry instruction how to do it based on an EM map.
Using transformation matrix
{
"symmetry": {
"sym_tr3ds": [
{
"name": "a unique custom name",
"rot": "list of 9 values for rotation, 3 for each row of the symmetry matrix",
"trans": "list of 3 values for translation"
}
]
}
}
For example:
{
"symmetry": {
"sym_tr3ds": [
{
"name": "2-fold",
"rot": [0.70712087, 0.70709269, 0.00003928, -0.70709269, 0.70712087, 0.00000394, 0.00003057, -0.00002499, 1.00000000],
"trans": [-411.56570152, 993.5285317, 0.09136987]
}
]
}
}
How to get this transformation matrices? Follow Calculating symmetry instruction how to do it based on an EM map.