atomsk --copy-properties <file1> <file2> [options] [<outputfile>] [formats]
This mode copies auxiliary properties from <file1> into <file2>.
This mode copies all auxiliary properties of <file2> (if any), and then copies the properties from <file1>. If a property has the same name in both systems, then values from <file2> are overwritten by values from <file1>. Otherwise, a new column is created to store the data.
The two files must contain the same number of atoms for the properties to be copied for all atoms. Otherwise, if <file1> and <file2> contain different numbers of atoms N1 and N2, then properties are copied only for the smallest number of atoms. If N1 > N2, then some properties from <file1> can not be copied and are lost. If N1 < N2, then atoms with an index greater than N1 will have a value equal to zero for copied properties.
The final system contains the atom positions and auxiliary properties of <file2>, and additionaly the auxiliary properties copied from <file1>.
If you use this mode with one or several options they will be applied to the <file2> before the properties are copied.
If a selection was defined (with the option -select), then auxiliary properties are copied only for the selected atoms. Other (unselected) atoms will keep the previous values of the properties that were defined in <file2>, or be assigned a zero value for properties that did not exist in <file2>.
atomsk --copy-properties system1.cfg system2.cfg result.cfg
This will read the files system1.cfg and system2.cfg, and copy auxiliary properties. The output file result.cfg will contain the atom positions and auxiliary properties of system2.cfg, and also the auxiliary properties of system1.cfg. If the same property exist in both systems, only values from system1.cfg will appear in final file.