atomsk --gather <listfile> <outputfile> [<formats>] [options]
In this mode, Atomsk will read several files, and write them to a single output file that will contain all the configurations (or snapshots).
The names of the input files must be provided in the <listfile>, a text file with the same format as list files used in mode file list. Such a list file can easily be produced e.g. with "ls >mylist.lst".
The output formats supported in this mode are:
Concerning animated XSF format, on one hand if forces on atoms exist in the first file of the <listfile> then forces will be written for all snapshots in the final animated XSF file. If forces are missing when reading other files from the <listfile>, then the forces will be set to zero for these snapshots. On the other hand, if forces do not appear in the first file of the <listfile>, then no force will be written at all for any snapshot in the animated XSF file.
When writing to normal XYZ format, auxiliary properties are ignored and only atom positions are written. When writing to extended XYZ format, all auxiliary properties are conserved and written in the final file.
If several formats are specified, then the multi-snapshot output files will be produced in all these formats.
If you use this mode with one or several options, then these options will be applied to each snapshot before they are written to the outputfile.
For the opposite operation (split a file containing several snapshots into several files), see the mode --unfold.
atomsk --gather mylist.lst animation.xsf
This will read files which names are specified in mylist.lst, and output all snapshots to the animated XSF file animation.xsf.
atomsk --gather mylist.lst snapshots.xyz exyz xsf
This will read files which names are specified in mylist.lst, and output all snapshots to snapshots.xyz (in extended XYZ format), and to the animated XSF file snapshots.xsf.