LAMMPS trajectories into VNL

Category: VNL as GUI for LAMMPS

Links: LAMMPS website, Notes on LAMMPS

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With VNL you can import, visualize, and analyze output data generated by
a variety of other simulation codes like VASP, Quantum ESPRESSO,
and many more. It is also possible to import classical MD trajectories
generated by LAMMPS, and use for example the Movie Tool, the 3D Viewer,
or the MD Analyzer to take a closer look at your simulations.
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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.

Tip

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

For 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 as an MDTrajectory. Alternatively, if only the minimal requirements are fulfilled, VNL will read it as a regular Trajectory object.

Running LAMMPS

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

Attention

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.

snap1

Note

Dimensionless units

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.

../../_images/snap2.gif

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 script_generator_icon using the sendto_icon icon in the lower right-hand corner of the Movie Tool widget.

In the Script Generator, add an analysis_icon Analysis ‣ LocalStructure 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.

Run the calculation using the Job Manager job_manager_icon.

snap3

After the calculation has finished, the local structure file will appear on the LabFloor.

labfloor_localstructure_icon LocalStructure

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.

snap4

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 calculator_icon New Calculator block in the Script Generator. This provides an easy way to interface your classical LAMMPS simulations with quantum mechanical calculations.

References

[Pli95]Steve Plimpton. Fast parallel algorithms for short-range molecular dynamics. Journal of Computational Physics, 117(1):1 – 19, 1995. doi:10.1006/jcph.1995.1039.