F3C potential test

In this example, the potential energy between two sites is compared to the analytical value.

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

def run_fst(params):
    """ Run a feasst simulation with the given parameters """
    with open("launch0.txt", "w") as myfile: myfile.write("""
MonteCarlo
Configuration {config_params}
Potential Model F3C Asc 1
ThermoParams beta 1000000
Metropolis
Log output_file {log}.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)

def write_xyz(params):
    """ Write an xyz file"""
    with open("two.xyz", "w") as myfile: myfile.write(
"""2
-1 20 20 20
0 0 0 0
1 0 0 {displacement}""".format(**params))

class TestMonteCarloF3COxygenRef(unittest.TestCase):
    def test_two_oxygen_sites(self):
        """Test the F3C potential against analytical calculation of two oyxgen sites"""
        params = {"displacement": 5, "log": "f3c_o",
                  "config_params": "particle_type0 /feasst/plugin/models/test/data/f3c_o.fstprt xyz_file two.xyz"}
        write_xyz(params)
        run_fst(params)
        df = pd.read_csv(params['log']+'.csv')
        self.assertEqual(2, df['num_particles_of_type0'][0])
        self.assertAlmostEqual(-0.041567117565916176 + 46.71010086004122, df['F3C'][0], 12)

    def test_two_hydrogen_sites(self):
        """Test the LJ potential against analytical calculation of two hydrogen sites"""
        params = {"displacement": 5, "log": "f3c_h",
                  "config_params": "particle_type0 /feasst/plugin/models/test/data/f3c_h.fstprt xyz_file two.xyz"}
        write_xyz(params)
        run_fst(params)
        df = pd.read_csv(params['log']+'.csv')
        self.assertEqual(2, df['num_particles_of_type0'][0])
        self.assertAlmostEqual(-6.377176514562533e-07 + 11.677525215010306, df['F3C'][0], 12)

    def test_oxygen_hydrogen_sites(self):
        """Test the LJ potential against analytical calculation of an oxygen and hydrogen site"""
        params = {"displacement": 5, "log": "f3c_h",
                  "config_params": "particle_type0 /feasst/plugin/models/test/data/f3c_o.fstprt particle_type1 /feasst/plugin/models/test/data/f3c_h.fstprt add_particles_of_type0 1 add_particles_of_type1 1 xyz_file two.xyz"}
        write_xyz(params)
        run_fst(params)
        df = pd.read_csv(params['log']+'.csv')
        self.assertEqual(1, df['num_particles_of_type0'][0])
        self.assertEqual(1, df['num_particles_of_type1'][0])
        self.assertAlmostEqual(-0.0006260058345921262 + -23.35505043002061, df['F3C'][0], 12)

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

test_oxygen_hydrogen_sites (__main__.TestMonteCarloF3COxygenRef.test_oxygen_hydrogen_sites)
Test the LJ potential against analytical calculation of an oxygen and hydrogen site ... ok
test_two_hydrogen_sites (__main__.TestMonteCarloF3COxygenRef.test_two_hydrogen_sites)
Test the LJ potential against analytical calculation of two hydrogen sites ... ok
test_two_oxygen_sites (__main__.TestMonteCarloF3COxygenRef.test_two_oxygen_sites)
Test the F3C potential against analytical calculation of two oyxgen sites ... ok

----------------------------------------------------------------------
Ran 3 tests in 0.030s

OK

<unittest.main.TestProgram at 0x7f6b0f959310>

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