4. Input and output files

In this section, we explain the structure of the crystal file in detail.

To seamlessly interact with LAMMPS, both the input and output crystal files of CryDisGen adopt the same structure as data file recognized by the read_data command in LAMMPS. Detailed information on the data file format can be found in the official document of LAMMPS

Since CryDisGen is designed to work with crystal structures, only the data file of atomic type, as illustrated in LAMMPS, needs to be considered. Below is an example of such a data file:

 1LAMMPS description
 2
 3156321 atoms
 41 atom types
 5
 6-61.348560 61.348560 xlo xhi
 7-61.348560 61.348560 ylo yhi
 8-61.455000 61.455000 zlo zhi
 9
10Masses
11
121 63.546000
13
14Atoms
15
161 1 -58.789203 -61.341863 -61.449694
172 1 -61.345336 -61.342109 -61.449910
183 1 -61.345233 -58.785847 -61.449741
194 1 -60.067113 -60.063673 -59.642199
20...

The data files contains a header section and a body section. Typically, the first line is a comment that provides some explainations of the file. The header section specifies the overall informaiton of the crystal structure, such as the number of atoms (line 3), the number of atom types (line 4), and the extent of the atomic region (line 6 ~ 8). The body section begins with keywords like Masses (line 10), Atoms (line 14). The Masses subsection defines the atomic weight of each atom type (line 12), the Atoms subsection consists of lines detailing individual atom information (line 16 ~ end of file). For a data file of the atomic type, the per-atom values have thes meanings and units as follows:

Type of the crystal file:

Atomic items per-line:

atomic

atom-ID atom-type x y z

Description:

  • atom-ID = integer ID of atom

  • atom-type = type of atom (1-Ntype, or type label)

  • x, y, z = coordinates of atom (distance units)