def load_sample_simulation(mof='single',
setup='run',
tests_dir=tests_dir,
parameters=k_parameters.copy()):
""" Load a sample simulation object from the tests directory """
from thermof import Simulation
if mof == 'single':
trial = os.path.join(tests_dir, 'ideal-mof-trial')
if setup == 'run':
sample_simulation = Simulation(read=os.path.join(trial, 'Run1'),
setup='run',
parameters=parameters)
elif setup == 'trial':
sample_simulation = Simulation(read=trial,
setup='trial',
parameters=parameters)
else:
trial = os.path.join(tests_dir, 'ip-mof-trial')
if setup == 'run':
sample_simulation = Simulation(read=os.path.join(trial, 'Run1'),
setup='run',
parameters=parameters)
elif setup == 'trial':
sample_simulation = Simulation(read=trial,
setup='trial',
parameters=parameters)
return sample_simulation
def test_isotropic_read_run():
"""Test reading a single run and averaging directions"""
k_par = k_parameters.copy()
k_par['isotropic'] = True
run_data = read_run(os.path.join(trial_dir, 'Run2'), k_par=k_par)
flux_file_x = os.path.join(trial_dir, 'Run2', 'J0Jt_tx.dat')
flux_x, time = read_thermal_flux(flux_file_x)
J_x = calculate_k(flux_x, k_par=k_par)
k_x = estimate_k(J_x, time, t0=5, t1=10)
assert np.allclose(run_data['k']['x'], J_x)
assert np.isclose(run_data['k_est']['x'], k_x)
flux_file_y = os.path.join(trial_dir, 'Run2', 'J0Jt_ty.dat')
flux_y, time = read_thermal_flux(flux_file_y)
J_y = calculate_k(flux_y, k_par=k_par)
k_y = estimate_k(J_y, time, t0=5, t1=10)
assert np.allclose(run_data['k']['y'], J_y)
assert np.isclose(run_data['k_est']['y'], k_y)
flux_file_z = os.path.join(trial_dir, 'Run2', 'J0Jt_tz.dat')
flux_z, time = read_thermal_flux(flux_file_z)
J_z = calculate_k(flux_z, k_par=k_par)
k_z = estimate_k(J_z, time, t0=5, t1=10)
assert np.allclose(run_data['k']['z'], J_z)
assert np.isclose(run_data['k_est']['z'], k_z)
J_iso = average_k([J_x, J_y, J_z])
assert np.allclose(run_data['k']['iso'], J_iso)
k_iso = estimate_k(J_iso, time, t0=5, t1=10)
assert np.allclose(run_data['k_est']['iso'], k_iso)
def test_read_run_input_error():
"""Tests whether read_run raises exception for missing flux file correctly"""
run_dir = os.path.join(trial_dir, 'Run1')
k_par = k_parameters.copy()
k_par['prefix'] = 'wrong-name'
with pytest.raises(FluxFileNotFoundError):
read_run(run_dir, k_par=k_par)
def test_thermal_conductivity_estimation():
"""Tests thermal conductivity estimation for given time range"""
flux, time = read_thermal_flux(flux_file)
k_par = k_parameters.copy()
J = calculate_k(flux, k_par=k_par)
k = estimate_k(J, time, t0=5, t1=10)
assert np.isclose(k, 0.8778570946468635)
def test_read_run_read_thermo():
"""Tests whether read_run raises exception for missing flux file correctly"""
run_dir = os.path.join(trial_dir, 'Run1')
k_par = k_parameters.copy()
k_par['read_thermo'] = True
run = read_run(run_dir, k_par=k_par)
assert set(list(run['thermo'].keys())) == set(['NVT', 'NVE1', 'NVE2'])
assert set(list(run['thermo']['NVT'].keys())) == set(
['step', 'temp', 'epair', 'emol', 'etotal', 'press'])
assert len(run['thermo']['NVT']['step']) == 3001
assert run['thermo']['NVT']['step'][0] == 0
assert run['thermo']['NVT']['step'][-1] == 300000
def test_read_run():
"""Test reading a single run with read_run"""
k_par = k_parameters.copy()
run_data = read_run(os.path.join(trial_dir, 'Run1'), k_par=k_par)
with open(k_ref_file, 'r') as kref:
k_ref = yaml.load(kref)
with open(time_ref_file, 'r') as tref:
time_ref = yaml.load(tref)
assert run_data['name'] == 'Run1'
assert np.isclose(run_data['k_est']['x'], 0.8778570946468635)
assert np.allclose(run_data['time'], time_ref)
assert np.allclose(run_data['k']['x'], k_ref)
def test_read_trial_set():
"""Test method for reading a set of trial with multiple runs"""
with open(k_ref_file, 'r') as kref:
k_ref = yaml.load(kref)
with open(time_ref_file, 'r') as tref:
time_ref = yaml.load(tref)
k_par = k_parameters.copy()
k_par['isotropic'] = True
k_par['average'] = True
trial_set = read_trial_set(trial_set_dir, k_par=k_par)
assert np.allclose(trial_set['data']['trial1']['data']['Run1']['k']['x'], k_ref)
assert np.allclose(trial_set['data']['trial2']['data']['Run3']['time'], time_ref)
assert np.isclose(trial_set['data']['trial1']['data']['Run1']['k_est']['iso'], k_est_iso_ref[0])
assert np.isclose(trial_set['data']['trial1']['data']['Run2']['k_est']['iso'], k_est_iso_ref[1])
assert np.isclose(trial_set['data']['trial2']['data']['Run3']['k_est']['iso'], k_est_iso_ref[2])
assert np.isclose(trial_set['data']['trial2']['data']['Run4']['k_est']['iso'], k_est_iso_ref[3])
assert np.isclose(trial_set['data']['trial1']['avg']['k_est']['iso'], (k_est_iso_ref[0] + k_est_iso_ref[1]) / 2)
assert np.isclose(trial_set['data']['trial2']['avg']['k_est']['iso'], (k_est_iso_ref[2] + k_est_iso_ref[3]) / 2)
def test_read_trial():
"""Test method for reading a trial with multiple runs"""
with open(k_ref_file, 'r') as kref:
k_ref = yaml.load(kref)
with open(time_ref_file, 'r') as tref:
time_ref = yaml.load(tref)
k_par = k_parameters.copy()
k_par['isotropic'] = True
k_par['average'] = True
trial = read_trial(trial_dir, k_par=k_par)
assert np.allclose(trial['data']['Run5']['time'], time_ref)
assert np.allclose(trial['data']['Run1']['k']['x'], k_ref)
assert np.isclose(trial['data']['Run1']['k_est']['x'], 0.8778570946468635)
for i, k_ref in enumerate(k_est_iso_ref, start=1):
assert np.isclose(trial['data']['Run%i' % i]['k_est']['iso'], k_ref)
assert np.isclose(trial['avg']['k_est']['iso'], 0.817262775736688)
assert np.isclose(trial['avg']['k_est']['stats']['iso']['std'],
np.std(k_est_iso_ref))
assert np.isclose(trial['avg']['k_est']['stats']['iso']['max'],
max(k_est_iso_ref))
assert np.isclose(trial['avg']['k_est']['stats']['iso']['min'],
min(k_est_iso_ref))
def test_read_run_directory_not_found_error():
"""Tests whether read_run raises exception for missing flux file correctly"""
run_dir = os.path.join(trial_dir, 'Run11')
k_par = k_parameters.copy()
with pytest.raises(RunDirectoryNotFoundError):
read_run(run_dir, k_par=k_par)
"""
Reads thermo data for a list of trials and saves results to a yaml file
"""
import os
import yaml
import numpy as np
from thermof.parameters import k_parameters
from thermof.read import read_run_info, read_thermo, read_log
# --------------------------------------------------------------------------------------------------
main = '' # Directory of trials
results_file = '%s-kest-results.yaml' % os.path.basename(main) # Name of results file
# --------------------------------------------------------------------------------------------------
trial_list = [os.path.join(main, i) for i in os.listdir(main) if os.path.isdir(os.path.join(main, i))]
results = dict(temp=[], press=[], e_pair=[], e_mol=[], tot_eng=[], epsilon=[], sigma=[], trial=[])
k_par = k_parameters.copy()
fix_list = ['NVE1', 'NVE2', 'NVT']
var_list = ['e_pair', 'temp', 'e_mol', 'tot_eng', 'press']
for trial_index, trial in enumerate(trial_list, start=1):
trial_name = os.path.basename(trial)
print('\n%i / %i | %s #################################' % (trial_index, len(trial_list), trial_name), flush=True)
ri = read_run_info(os.path.join(trial, 'Run1'))
results['sigma'].append(ri['sigma'])
results['epsilon'].append(ri['epsilon'])
results['trial'].append(os.path.basename(trial))
if trial_name not in ['S6.00-E0.80', 'S6.00-E1.00']:
for run in os.listdir(trial):
run_dir = os.path.join(trial, run)
def test_get_flux_directions_exception():
"""Tests whether thermal flux files note found exception is raised correctly"""
k_par = k_parameters.copy()
k_par['prefix'] = 'wrong-name'
with pytest.raises(FluxFileNotFoundError):
get_flux_directions(os.path.join(trial_dir, 'Run1'), k_par=k_par)