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DiffuseStructure/README

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+Structure Format
+
+Essential Parts:
+-   	Metric Tensor: [Å, deg]
+3x3 double precision real matrix as G, header needs to specify the sequence of matrix
+-   	Symmetry of the average structure
+32 Characters that have the space group symbol
+-   	Number of unit cells in a, b, c direction
+3 unsigned integer
+-   	number of atoms (NA) in file
+1 unsigned integer
+-   	List of atom types that are present in the structure, including atomic number, charge and isotope
+         	Four columns:
+o   atom type: 2 characters
+o   Atomic number, unsigned integer number
+o   Charge, signed integer number
+o   Isotope, unsigned integer number
+-   	Atom type and atomic coordinates: this should be a table with 9 columns and NA lines
+o   1st column: Atom id, 1 integer
+o   2nd column: Atom type, 1 integer (identifies the type according to number in list of atom types
+o   3rd – 5th column: x,y,z coordinates in the supercell from 0-1, 3 double precision real, numbers
+o   6th – 9th column: unit cell identifier, coordinates of the atoms unit cell in the supercell and site in the average unit cell, 4 integers
+-   	Flags: Listed as flag name, data type Boolean, brackets as explanation what does
+o   Super structure
+o   Asymmetric unit (only asymmetric unit is stored)
+o   Are periodic boundary conditions sensible
+o   Homogeneity (Is it sensible to collapse the structure in one unit-cell, should be no for structures with drastically different parts, e.g. domains. If this is yes then the average crystallographic cell needs to be stored)
+
+Metadata:
+o   Timestamp
+o   Software: Generated by software including its version version
+
+Optional Parts:
+-   	If possible can we kind of attach a script/macro that created the structure?, e.g. containing Interaction Hamiltonian used in the generation of the structure
+-   	Average structure this should be a table with  12 columns
+o   1st column: Atom type, 1 integer (identifies the type according to number in list of atom types
+o   2nd  – 4th column: x,y,z coordinates
+o   5th column: average occupancy of the atom type in 1st column on this site
+o   6th column: Uiso
+o   7th – 12th column: u_ij
+-   	Molecular identity
+o   2 integers, 1st labelling type of molecule, 2nd labelling number of molecule
+-   	Magnetic spin
+o   3 real numbers, components of spin vectors along crystal axis
+-   	Property flags: List of NA integers TO BE EXTENDED BY DISCUS AND RMC WITH THEIR FLAGS
+o   Surface atom
+o   Domain number