LAMMPS trajectories into VNL¶
|Category: VNL as GUI for LAMMPS
Links: LAMMPS website, Notes on LAMMPS
LAMMPS is a classical molecular dynamics code [Pli95] with a very flexible output format for its trajectories. Most of the available output is written as text files. In order to import LAMMPS trajectories into VNL and make full use of the VNL analysis funtionalities, you have to stick to some minimal rules when running LAMMPS simulations, which are explained in this tutorial.
You will learn how to import your LAMMPS simulation trajectories into Virtual NanoLab and make use of the visualization and analysis tools, and how to prepare input files for further simulations based on the imported configurations.
Preparing a LAMMPS script¶
A LAMMPS simulation is typically controlled by an input script, in which all the simulation parameters are listed. The output trajectory is specified by the dump bash command. VNL can currently read trajectory files written in the atom or custom style. The format of the atom style is fixed, so no further specifications have to be made, and the command may simply look like this:
dump d_trajectory all atom 100 trajectory.dat
It will write the coordinates of all atoms every 100 steps to the file
trajectory.dat. The extension of the trajectory file does not
need to be a specific one for VNL, as long as it does not conflict with
other extensions. The atom style does not write velocities, so the resulting
trajectories can not be imported as
MDTrajectory objects (as required
for the Movie Tool or the MDAnalyzer), but only as regular
Trajectory objects. Nevertheless, they can be visualized by the
3D Viewer and drag-and-dropped onto the Builder.
The LAMMPS custom format allows you to specify explicitly which quantities
should be recorded. For compatibility with VNL, at least type, index,
and the coordinates (x, y, z, or xs, ys, zs) have to be present in the
trajectory file. To be imported as an
MDTrajectory object, the trajectory
file also needs to have velocities. This may be accomplished by this command:
dump d_trajectory all custom 100 trajectory.dat id type x y z vx vy vz
MDTrajectory objects you also need to extract the potential energies.
These can be read from the thermodynamic output in the log file that is created
during the simulation. Therefore, the thermodynamic output from LAMMPS must be
written with the same frequency as the trajectory. You can specifiy the frequency
via the keyword thermo. Moreover, you have to make sure that the potential
energies are present in the thermodynamic output, which can be selected under
the thermo_style keyword. A typical example (compatible with one of the above
trajectory dump commands) might look like this:
thermo 100 thermo_style custom step temp pe etotal press
Here, the pe flag specifies that potential energies should be written to the
log file. If all these requirements are fulfilled, the trajectory is read by VNL
MDTrajectory. Alternatively, if only the minimal requirements are
fulfilled, VNL will read it as a regular
Since LAMMPS provides a well defined output format and initial configuration, VNL simply reads at first the log file, in which all these settings are mirrored during a LAMMPS simulation. Based on the statements in this log file, the output files and other possible input files are read. Therefore, you need to make sure that the LAMMPS log file is written properly. You can specify the log file output via the option -log in the LAMMPS command line:
lmp_serial -in in.settings -log log_simulation_1.lammps
You have to select a file name ending with
.lammps, as this extension is
recognized by VNL as a LAMMPS log file. If you are reading your input configuration
from a separate file (typically starting with
data.*) you also need to make
sure that this file is present in your current directory, since VNL reads the
atomic masses from it.
Importing to VNL¶
If you have followed the guidelines in the previous section, the trajectory should
show up on the LabFloor in VNL after the LAMMPS simulation. It will be labelled
according to the name of the log file without extension, i.e. the example simulation
of the previous section will be named
log_simulation_1. If you click the icon,
you will see which plugins are available for this particular trajectory on the
right-hand side panel. For an
MDTrajectory object you can use the Viewer,
the Movie Tool, and the MDAnalyzer. For a regular
Trajectory you can
only use the Viewer.
In the following example, a silicon crystal has been melted by linearly increasing the temperature from 300 to 3000 K over 200 ps at zero pressure. The Stillinger-Weber potential has been used to describe the interactions among the silicon atoms. The resulting LAMMPS trajectory shows up on the LabFloor and can be visualized using the Movie Tool.
LAMMPS simulations are sometimes performed using a system of dimensionless units, enabled by the keyword units lj, together with generic atom types. You can of course import such trajectories into VNL.
However, as there are no physical units associated with the velocities and energies,
the trajectory will be imported as a regular
Trajectory object. The example
below shows the initiation and propagation of a crack in a 2-dimensional system
of generic Lennard-Jones atoms.
Postprocessing LAMMPS trajectories¶
If you have imported a LAMMPS trajectory to the VNL LabFloor, you can of course extract single configurations, and perform further analyses or calculations using VNL and ATK. The following example shows how you can calculate the local structure of a copper polycrystal that has been simulated with LAMMPS. If you want to learn how to generate and simulate polycrystals in VNL-ATK, take a look at the tutorial Simulating a creep experiment of polycrystalline copper.
Open the LAMMPS trajectory with the Movie Tool. Go to the desired snapshot, e.g. the last snapshot, and send this configuration to the Script Generator using the icon in the lower right-hand corner of the Movie Tool widget.
In the Script Generator, add an
block. Open the block by double-clicking it, select a suitable file name, e.g.
Polycrystal_local_structure.nc, uncheck the Print box (the structure is
huge and will otherwise produce a large amount of text output), and click OK to
close the LocalStructure settings.
After the calculation has finished, the local structure file will appear on the LabFloor.
Open it in the Viewer and find the Local Structure plugin in the panel bar of the Viewer. Expand it and you will see a list of local crystal structures. In this example we will highlight the grain boundaries of the polycrystal:
- Select all structure types except FCC, which is the native crystal structure inside the silicon grains.
- Click the Properties plugin to open the scene properties. In the Atoms tab, change the color of the selected atoms, e.g. to white, to distinguish these atoms from grain atoms.
- Additionally, you can click on Ball, to switch off the bonds within the grain boundaries, which increases the transparency of the polycrystal.
- When you close the Properties widget, your changes become active and you will find the grain boundaries clearly visible.
Besides local structure analysis, you can also perform further simulations, e.g. using the ATK-DFT engine for density functional theory calculations on top of the extracted snapshots: Simply add a New Calculator block in the Script Generator. This provides an easy way to interface your classical LAMMPS simulations with quantum mechanical calculations.