1.basic

Simulate the oxygen−oxygen radial distribution function of bulk waters.

Simulating bulk waters' O-O RDF curves is one of the most classical tasks in the MD community. Thus, I decided to invoke this task as the first SOMD tutorial. In this tutorial we will run a NVT simulation of a bulk water box. After getting the simulation trajectory, we will calculate the O-O RDF curve using the MDTraj package. By finishing this tutorial, you may earn some basic sense about SOMD.

Pre-requirements

The pseudopotential files

Download pseudopotential files of oxygen and hydrogen from here. Then copy the two psf files to the data directory (or you could use the provided pseudopotential files).

Go through the simulation script.

Define the simulated system.

[system]
        structure = "./data/H2O.pdb"

We first create the simulated system. SOMD could read atomic information from two kinds of structure files: the POSCAR and the PDB files. Name of the structure file is defined by the structure option in the [system] table. And here we will use a PDB file called H2O.pdb located at the data directory.

[[group]]
        atom_list = "all"
        initial_temperature = 300.0

After initializing the simulated system, we assign an atom group to the system. Atom group is one of the most important concepts in SOMD, many subroutines in SOMD rely on the specifications of atom groups. In this tutorial, one atom group is required because:

1. We need to assign initial velocities for atom in the system.
2. The thermostats in SOMD need to know the range of the thermostated atoms (you may define more than one atom group in a simulation, if needed).

The group definitions are specifies by the [[group]] array of tables. It is pretty clear that we have assigned all atoms in the system to one group. And the initial velocities of these atoms will be randomly selected according to the Boltzmann distribution under 300 Kelvin.

Set up the potential calculators.

[[potential]]
        type = "SIESTA"
        siesta_options = """
        xc.functional          GGA
        xc.authors             revPBE

        PAO.BasisSize          DZP
        Mesh.Cutoff            300 Ry
        PAO.EnergyShift        10 meV
        PAO.SoftDefault        T

        SCF.Mixer.Variant      Pulay
        SCF.Mixer.History      8
        DM.NumberPulay         8
        DM.Tolerance           1.d-5
        DM.UseSaveDM           T
        DM.History.Depth       5

        SolutionMethod         diagon
        ElectronicTemperature  1 meV
        # If you do not have ELPA installed, comment out this line:
        Diag.Algorithm         ELPA-1stage
        """
        siesta_command = "mpirun -np 90 /path/to/siesta"
        pseudopotential_dir = "./data"
[[potential]]
        type = "DFTD3"
        functional = "revpbe"

Here we first define the parameters of a SIESTA calculation. You should modify the value of siesta_command variable to the actual path of your SIESTA binary. If you compiled SIESTA with MPI support, the mpirun command should also be included in this string, as shown in the example configuration. And since we have save the pseudopotential files in the data directory, the pseudopotential_dir should also be set properly. Then we define a DFTD3 potential to perform the dispersion corrections. Take care of the value the of the functional option (revpbe here). It should be the same as the value of the xc.authors key in the SIESTA parameters (siesta_options).

Set up the integrator.

We choose the BAOAB Langevin integrator to propagate our system, and the integration time step is selected as 0.0005 ps (0.5 fs). The temperature and relaxation time of the thermostat are selected as 300 K and 0.1 ps, correspondingly.

[integrator]
        type = "BAOAB"
        timestep = 0.0005
        temperatures = 300.0
        relaxation_times = 0.1

Set up the trajectory and system data writers.

We will write the simulation trajectory to a HDF5 file (the name of the file will be automatically determined by SOMD, in particular, H2O.trajectory.h5 here), using MDTraj's convention. And we will write the system data (temperatures, pressures, energies, etc.) to a CSV file (the name of the file will be automatically determined by SOMD as well, in particular, H2O.data.csv here). We require SOMD to update the two file after each time step by setting the interval parameters to 1.

[[trajectory]]
        format = "H5"
        interval = 1
[[logger]]
        format = "CSV"
        interval = 1

Set up the simulation protocol.

[run]
        n_steps = 25000

The steps to run is defined in the [run] table. Here we will run the simulation for 25000 timesteps.

Run the simulation.

After the above steps, your working directory should look like this:

.
├── data
│   ├── H2O.pdb
│   ├── O.psf
│   └── H.psf
└── H2O.toml

Now you could run the simulation by:

somd -i H2O.toml

Or you may want to use a job manager like SLURM. You could simply add the above command to your submitting script, let's say, run.sh:

#!/bin/bash
#SBATCH -J somd
#SBATCH -o somd.log
#SBATCH -e somd.err
#SBATCH -N 1
#SBATCH -p cpu
#SBATCH --cpus-per-task=96

somd -i H2O.toml

and submit the job by:

sbatch run.sh

Note: the simulation described here is relatively "expensive". On my 96-core node, this job took about 6 days to finish. You may want to decrease the simulation steps to lower the computational cost.

Analysis the result.

We will use the MDTraj package to compute the O-O RDF curve from the trajectory. Open a python REPL in your working directory and enter the following lines:

>>> import mdtraj
>>> import numpy as np
>>> from matplotlib import pyplot as plt
>>> traj = mdtraj.load('H2O.trajectory.h5')
>>> traj.top = mdtraj.load('./data/H2O.pdb').top
>>> oxygen_pairs = traj.top.select_pairs('name O', 'name O')
>>> rdf = mdtraj.compute_rdf(traj[5000:], oxygen_pairs, (0, 0.6), n_bins=240)
>>> plt.plot(*rdf)
>>> plt.xlabel("O-O distance (nm)")
>>> plt.ylabel("$g_{O-O}$")
>>> plt.show()

The result should look like this:

As can be seen, the resulted RDF curve is similar to the experimental result reported in J. Chem. Phys. 138, 074506 (2013).