LAMMPS internally keeps track of the evolution of atomistic systems. Such a system is described as a simulation box containing an ensemble of particles interacting with one another according to set of rules, and each with their own position, velocities etc.
In this section, you will learn how to create a very simple simulation box using LAMMPS built-in tools.
In an empty directory, open a text file and copy the following text inside:
lattice sc 1.
region box block 0 5 0 5 0 5
create_box 1 box
create_atoms 1 box
mass 1 1
write_data data.lmp
write_dump all atom dump.lammpstrj
Let's save the file with the name in.lmp. Now in the command-line you can run the following command to execute LAMMPS with this input:
lmp -i in.lmpYou should see a bunch of lines appear in your screen. The first one should start with LAMMPS followed by a parentheses with the specification of the version of the code you are using. The last line should read something like Total wall time: 00:00:00. If you've never executed LAMMPS before, congratulation! This is maybe your first successful (very simple) simulation!
You will also notice that two files appeared in the directory: data.lmp and dump.lammpstrj. Let's start by opening the first one.
The first file of the two is usually referred to as a data file. Its format is rather strict and you can see that there are general information at the top of the file and several sections starting with a capitalized word, a blank line and some numbers. Let's slowly go through all of this.
The first part of the file is called the header. The first line of the file is always a comment that LAMMPS does not read but which can contain information on the way the file was generated. Here we see the LAMMPS version and some more information like timestep and units. The following lines contain the number of atoms (125), the number of atom types (1) and three lines containing xlo xhi like indications. This header is simple, but generally, headers can contain much more information. The first two lines are explicit, you define a system with 125 atoms all of which have the same characteristics. The last three lines define the volume in which these atoms are contained. It is a box with edge coordinates starting at 0 and ending at 5 in every direction (x, y and z).
From here starts the body of the file. The order of the sections is not important but all of them must come in the format:
Section name # Capitalized, correctly spelled
# blank line
Section input # Number of line and format depend on the section.
The first section you should see is the Masses section. In LAMMPS, masses are assigned to atom types so you only have one line here. All types have their own masses but several types can have the same mass. Types are LAMMPS way to refer to properties of particles that are the same for all particles of the same type. They are also used to determine how particles interact with one another. Types are not always binded to chemical species and you will see in further tutorials how it can be convenient to define different types for similar atoms.
The Atoms section contains 125 lines, one per atom. The number on each line are ordered and are for each particle: * The particle ID which LAMMPS uses to refer to that particle internally * The type of the particle * The x, y and z coordinates in absolute distance value * The xflag, yflag and zflag values, which you can put aside for now
Below you can also see the Velocities section which also contains 125 lines. Each lines gives the particle ID followed by the instantaneous velocities of the particles along the x, y and z axis in that order. The particle ID refers to the same ID as in the Atoms section.
The format and meaning of the number in the Atoms and Velocities sections will depend on the atom_style the code is told to use. In most recents versions of LAMMPS, writing a data file with write_data will append a comment next to the Atoms section name (here # atomic). This helps human readers to know the meaning of the different number. Some formats can include more information like a molecule tag, particles' charges, particles' spins or orientation etc. For the velocities, some atom_style can require keeping track of angular momentum, angular velocities etc. You'll find a detailed description of each format in the read_data section of the manual.
As a first takeaway, remember that data files contain detailed information on a simulation system at a given time. They are more convenient for input and output. Several simulation softwares allow you to export files as LAMMPS data files and take them as input. But data format are not straightforward to use for analyses: they are heavy and may contain useless information. This is what the dump file format is for.
Following the previous sections, open the dump.lammpstrj file that should have appeared in your directory. This is a dump file containing a single snapshot You should see something like this:
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
125
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 5.0000000000000000e+00
0.0000000000000000e+00 5.0000000000000000e+00
0.0000000000000000e+00 5.0000000000000000e+00
ITEM: ATOMS id type xs ys zs
1 1 0 0 0
2 1 0.2 0 0
3 1 0.4 0 0
4 1 0.6 0 0
5 1 0.8 0 0
...
The format is more simple compared to the data file. Each section is labeled with a header directly followed by the data we wanted to dump. Here we used the basic atom dump_style so we only have atoms' id, types and scaled coordinates (that is coordinates divided by box length in each dimension).
You can compare the dump file with the data file, and see that they basically contain the same information, with few exceptions, namely the total number of types, masses and the velocities. Getting only the scaled coordinates of the atoms is not alway ideal, but fortunately we can get much more.
In your in.lmp file, replace the write_dump line with the following:
write_dump all custom dump.lammpstrj id type x y z vx vy vz
Save the file, and run the code as previously:
lmp -i in.lmpNow the dump.lammpstrj file should have changed to the following:
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
125
ITEM: BOX BOUNDS pp pp pp
0.0000000000000000e+00 5.0000000000000000e+00
0.0000000000000000e+00 5.0000000000000000e+00
0.0000000000000000e+00 5.0000000000000000e+00
ITEM: ATOMS id type x y z vx vy vz
1 1 0 0 0 0 0 0
2 1 1 0 0 0 0 0
3 1 2 0 0 0 0 0
4 1 3 0 0 0 0 0
5 1 4 0 0 0 0 0
...
The custom format allows you to write every properties of each atoms to the file. There are a series of keywords that you can use depending on the atom_style and values that you can also calculate through the use of LAMMPS computes and variables. More on that in later tutorials.
For now on we haven't done much with our atoms. Let's see how to run an actual simulation.