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_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')
assert 2 == df['num_particles_of_type0'][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_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')
assert 2 == df['num_particles_of_type0'][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_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')
assert 1 == df['num_particles_of_type0'][0]
assert 1 == df['num_particles_of_type1'][0]
assert np.abs(-0.0006260058345921262 + -23.35505043002061 - df['F3C'][0]) < 12

# Usage: ./fst < file.txt
FEASST version 0.25.6
MonteCarlo
Configuration particle_type0 /home/user/feasst/plugin/models/test/data/f3c_o.fstprt xyz_file two.xyz
Potential Asc 1 Model F3C
ThermoParams beta 1000000
Metropolis
#Info 0 [plugin/models/src/f3c.cpp:67] en_lj -0.0415671
#Info 0 [plugin/models/src/f3c.cpp:68] en_q 46.7101
#Info 0 [plugin/models/src/f3c.cpp:67] en_lj -0.0415671
#Info 0 [plugin/models/src/f3c.cpp:68] en_q 46.7101
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:744] No Trials to attempt.
# Usage: ./fst < file.txt
FEASST version 0.25.6
MonteCarlo
Configuration particle_type0 /home/user/feasst/plugin/models/test/data/f3c_h.fstprt xyz_file two.xyz
Potential Asc 1 Model F3C
ThermoParams beta 1000000
Metropolis
#Info 0 [plugin/models/src/f3c.cpp:67] en_lj -6.37718e-07
#Info 0 [plugin/models/src/f3c.cpp:68] en_q 11.6775
#Info 0 [plugin/models/src/f3c.cpp:67] en_lj -6.37718e-07
#Info 0 [plugin/models/src/f3c.cpp:68] en_q 11.6775
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:744] No Trials to attempt.
# Usage: ./fst < file.txt
FEASST version 0.25.6
MonteCarlo
Configuration add_particles_of_type0 1 add_particles_of_type1 1 particle_type0 /home/user/feasst/plugin/models/test/data/f3c_o.fstprt particle_type1 /home/user/feasst/plugin/models/test/data/f3c_h.fstprt xyz_file two.xyz
Potential Asc 1 Model F3C
ThermoParams beta 1000000
Metropolis
#Info 0 [plugin/models/src/f3c.cpp:67] en_lj -0.000626006
#Info 0 [plugin/models/src/f3c.cpp:68] en_q -23.3551
#Info 0 [plugin/models/src/f3c.cpp:67] en_lj -0.000626006
#Info 0 [plugin/models/src/f3c.cpp:68] en_q -23.3551
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:744] No Trials to attempt.

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