# 2.1. Data conversion

One needs to provide the following information to train a model: the atom type, the simulation box, the atom coordinate, the atom force, system energy and virial. A snapshot of a system that contains these information is called a frame. We use the following convention of units:

Property

Unit

Time

ps

Length

Å

Energy

eV

Force

eV/Å

Virial

eV

Pressure

Bar

The frames of the system are stored in two formats. A raw file is a plain text file with each information item written in one file and one frame written on one line. The default files that provide box, coordinate, force, energy and virial are box.raw, coord.raw, force.raw, energy.raw and virial.raw, respectively. We recommend you use these file names. Here is an example of force.raw:

$cat force.raw -0.724 2.039 -0.951 0.841 -0.464 0.363 6.737 1.554 -5.587 -2.803 0.062 2.222 -1.968 -0.163 1.020 -0.225 -0.789 0.343  This force.raw contains 3 frames with each frame having the forces of 2 atoms, thus it has 3 lines and 6 columns. Each line provides all the 3 force components of 2 atoms in 1 frame. The first three numbers are the 3 force components of the first atom, while the second three numbers are the 3 force components of the second atom. The coordinate file coord.raw is organized similarly. In box.raw, the 9 components of the box vectors should be provided on each line. In virial.raw, the 9 components of the virial tensor should be provided on each line in the order XX XY XZ YX YY YZ ZX ZY ZZ. The number of lines of all raw files should be identical. We assume that the atom types do not change in all frames. It is provided by type.raw, which has one line with the types of atoms written one by one. The atom types should be integers. For example the type.raw of a system that has 2 atoms with 0 and 1: $ cat type.raw
0 1


Sometimes one needs to map the integer types to atom name. The mapping can be given by the file type_map.raw. For example

$cat type_map.raw O H  The type 0 is named by "O" and the type 1 is named by "H". The second format is the data sets of numpy binary data that are directly used by the training program. User can use the script $deepmd_source_dir/data/raw/raw_to_set.sh to convert the prepared raw files to data sets. For example, if we have a raw file that contains 6000 frames,

$ls box.raw coord.raw energy.raw force.raw type.raw virial.raw$ $deepmd_source_dir/data/raw/raw_to_set.sh 2000 nframe is 6000 nline per set is 2000 will make 3 sets making set 0 ... making set 1 ... making set 2 ...$ ls
box.raw  coord.raw  energy.raw  force.raw  set.000  set.001  set.002  type.raw  virial.raw


It generates three sets set.000, set.001 and set.002, with each set contains 2000 frames. One do not need to take care of the binary data files in each of the set.* directories. The path containing set.* and type.raw is called a system.

If one needs to train a non-periodic system, an empty nopbc file should be put under the system directory. box.raw is not necessary is a non-periodic system.