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 numpy as np
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", 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))

"""Test the F3C potential against analytical calculation of two oyxgen sites"""
params = {"displacement": 5, "log": "f3c_o",
          "config_params": "particle_type=f3c:/feasst/plugin/models/test/data/f3c_o.txt xyz_file=two.xyz"}
write_xyz(params)
run_fst(params)
df = pd.read_csv(params['log']+'.csv')
assert 2 == df['num_particles_f3c'][0]
assert np.abs(-0.041567117565916176 + 46.71010086004122 - df['F3C'][0]) < 12

"""Test the LJ potential against analytical calculation of two hydrogen sites"""
params = {"displacement": 5, "log": "f3c_h",
          "config_params": "particle_type=f3c:/feasst/plugin/models/test/data/f3c_h.txt xyz_file=two.xyz"}
write_xyz(params)
run_fst(params)
df = pd.read_csv(params['log']+'.csv')
assert 2 == df['num_particles_f3c'][0]
assert np.abs(-6.377176514562533e-07 + 11.677525215010306 - df['F3C'][0]) < 12

"""Test the LJ potential against analytical calculation of an oxygen and hydrogen site"""
params = {"displacement": 5, "log": "f3c_h",
          "config_params": "particle_type=f3c_o:/feasst/plugin/models/test/data/f3c_o.txt,f3c_h:/feasst/plugin/models/test/data/f3c_h.txt 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')
assert 1 == df['num_particles_f3c_o'][0]
assert 1 == df['num_particles_f3c_h'][0]
assert np.abs(-0.0006260058345921262 + -23.35505043002061 - df['F3C'][0]) < 12

# Usage: /home/user/feasst/build/bin/fst < file.txt
FEASST version 0.25.13
MonteCarlo
Configuration particle_type=f3c:/feasst/plugin/models/test/data/f3c_o.txt xyz_file=two.xyz
Potential Asc=1 Model=F3C
ThermoParams beta=1000000
Metropolis
Log clear_file=true max_precision=true output_file=f3c_o.csv
Run num_trials=1
#Warn 0 [plugin/monte_carlo/src/monte_carlo.cpp:786] No Trials to attempt.
# Usage: /home/user/feasst/build/bin/fst < file.txt
FEASST version 0.25.13
MonteCarlo
Configuration particle_type=f3c:/feasst/plugin/models/test/data/f3c_h.txt xyz_file=two.xyz
Potential Asc=1 Model=F3C
ThermoParams beta=1000000
Metropolis
Log clear_file=true max_precision=true output_file=f3c_h.csv
Run num_trials=1
#Warn 0 [plugin/monte_carlo/src/monte_carlo.cpp:786] No Trials to attempt.
# Usage: /home/user/feasst/build/bin/fst < file.txt
FEASST version 0.25.13
MonteCarlo
Configuration add_particles_of_type0=1 add_particles_of_type1=1 particle_type=f3c_o:/feasst/plugin/models/test/data/f3c_o.txt,f3c_h:/feasst/plugin/models/test/data/f3c_h.txt xyz_file=two.xyz
# Renamed Site name:0->1 for particle_type:1 in:/home/user/feasst/plugin/models/test/data/f3c_h.txt
# Renamed Site type:0->1 for particle_type:1 in:/home/user/feasst/plugin/models/test/data/f3c_h.txt
Potential Asc=1 Model=F3C
ThermoParams beta=1000000
Metropolis
Log clear_file=true max_precision=true output_file=f3c_h.csv
Run num_trials=1
#Warn 0 [plugin/monte_carlo/src/monte_carlo.cpp:786] No Trials to attempt.

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