Lennard Jones potential test

In this example, an instantaneous configuration is compared against published values for the potential energy.

First, the potential energy between two particles is compared to the analytical value. Next, the energy of an entire configuration is compared against the NIST SRSW reference calculations.

import math
import sys
import subprocess
import unittest
import pandas as pd

# Run a feasst simulation with the given parameters
def run_fst(params):
    with open("launch0.txt", "w") as myfile: myfile.write("""
MonteCarlo
Configuration {config_params}
Potential Model LennardJones
Potential VisitModel LongRangeCorrections
ThermoParams beta 1000000
Metropolis
Log output_file lj.csv max_precision true clear_file true
Run num_trials 1
""".format(**params))
    syscode = subprocess.call("../../../build/bin/fst < launch0.txt > launch0.log", shell=True, executable='/bin/bash')
    if syscode > 0: sys.exit(1)

class TestMonteCarloLJRef(unittest.TestCase):
    def test_two_particle(self):
        """Test the LJ potential against analytical calculation of two particles"""
        params = {"displacement": 1.2345}
        with open("two.xyz", "w") as myfile: myfile.write(
"""2
-1 8 8 8
0 0 0 0
1 0 0 {displacement}""".format(**params))
        run_fst({"config_params": "particle_type0 /feasst/particle/lj.fstprt xyz_file two.xyz"})
        df = pd.read_csv('lj.csv')
        self.assertEqual(2, df['num_particles_of_type0'][0])

        # compute the expected analytical LJ and LRC energies
        enlj = 4*(params["displacement"]**(-12) - params["displacement"]**(-6))
        rcut = 3 #mc.system().configuration().model_params().select("cutoff").value(0)
        enlrc = (8./3.)*math.pi*2**2/ 8**3*((1./3.)*rcut**(-9) - rcut**(-3))

        # Compare the analytical results with the FEASST computed energies.
        self.assertAlmostEqual(enlj, df['LennardJones'][0], 12)
        self.assertAlmostEqual(enlrc, df['LongRangeCorrections'][0], 12)
        self.assertAlmostEqual(enlj + enlrc, df['energy'][0], 12)

    def test_srsw_ref_config(self):
        """Test the LJ potential against a configuration of 30 particles.
        In particular, the 4th configuration of the LJ SRSW reference:
        https://www.nist.gov/mml/csd/chemical-informatics-research-group/lennard-jones-fluid-reference-calculations
        """
        run_fst({"config_params": "cubic_side_length 8 particle_type0 /feasst/particle/lj.fstprt \
                  xyz_file /feasst/plugin/configuration/test/data/lj_sample_config_periodic4.xyz"})
        df = pd.read_csv('lj.csv')
        self.assertEqual(df['num_particles_of_type0'][0], 30)
        enlj = -16.790321304625856
        enlrc = -0.5451660014945704
        self.assertAlmostEqual(enlj, df['LennardJones'][0], 12)
        self.assertAlmostEqual(enlrc, df['LongRangeCorrections'][0], 12)
        self.assertAlmostEqual(enlj + enlrc, df['energy'][0], 12)

    def test_srsw_ref_config_triclinic(self):
        """Test the LJ potential against a configuration of 300 particles in a trinclinic cell.
        In particular, the 3th configuration of the triclinic LJ SRSW reference:
        https://www.nist.gov/mml/csd/chemical-informatics-group/lennard-jones-fluid-reference-calculations-non-cuboid-cell
        """
        run_fst({"config_params": "side_length0 10.0 side_length1 9.84807753012208 side_length2 9.64974312607518 \
            xy 1.7364817766693041 xz 2.5881904510252074 yz 0.42863479791864567 \
            particle_type0 /feasst/particle/lj.fstprt \
            xyz_file /feasst/plugin/configuration/test/data/lj_triclinic_sample_config_periodic3.xyz"})
        df = pd.read_csv('lj.csv')
        self.assertEqual(df['num_particles_of_type0'][0], 300)
        enlj = -505.78567945268367
        enlrc = -29.37186430697248
        self.assertAlmostEqual(enlj, df['LennardJones'][0], 12)
        self.assertAlmostEqual(enlrc, df['LongRangeCorrections'][0], 12)
        self.assertAlmostEqual(enlj + enlrc, df['energy'][0], 12)

unittest.main(argv=[''], verbosity=2, exit=False)

test_srsw_ref_config (__main__.TestMonteCarloLJRef.test_srsw_ref_config)
Test the LJ potential against a configuration of 30 particles. ... ok
test_srsw_ref_config_triclinic (__main__.TestMonteCarloLJRef.test_srsw_ref_config_triclinic)
Test the LJ potential against a configuration of 300 particles in a trinclinic cell. ... ok
test_two_particle (__main__.TestMonteCarloLJRef.test_two_particle)
Test the LJ potential against analytical calculation of two particles ... ok

----------------------------------------------------------------------
Ran 3 tests in 0.028s

OK

<unittest.main.TestProgram at 0x7f5036b8c4a0>

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