def test_minimal_example():
"""Tests that the minimal example is functional (ARC is not being called)"""
delete_minimal_example_dirs()
functional_minimal_directory = os.path.join(DATA_BASE_PATH, 'functional_minimal_example')
input_file = os.path.join(functional_minimal_directory, 'input.yml')
input_dict = read_yaml_file(path=input_file)
verbose = 20
input_dict['verbose'] = verbose
input_dict['project_directory'] = functional_minimal_directory
# check that RMG and ARC are available
check_dependencies()
# run the minimal example
t3_object = T3(**input_dict)
t3_object.execute()
# check that the minimal example ran to completion by checking for existence of some files and directories
assert os.path.isfile(os.path.join(functional_minimal_directory, 't3.log'))
assert os.path.isdir(os.path.join(functional_minimal_directory, 'iteration_1'))
assert os.path.isfile(os.path.join(functional_minimal_directory, 'iteration_1',
'RMG', 'chemkin', 'species_dictionary.txt'))
assert os.path.isdir(os.path.join(functional_minimal_directory, 'iteration_2'))
assert os.path.isfile(os.path.join(functional_minimal_directory, 'iteration_2',
'RMG', 'chemkin', 'species_dictionary.txt'))
delete_minimal_example_dirs()
def test_no_t3_no_qm():
"""Test proper execution of T3 without specifying neither of the t3 nor qm args"""
rmg_args = {'database': {'thermo_libraries': ['primaryThermoLibrary', 'BurkeH2O2'],
'kinetics_libraries': ['BurkeH2O2inN2']},
'species': [{'label': 'H2',
'smiles': '[H][H]',
'concentration': 0.67},
{'label': 'O2',
'smiles': '[O][O]',
'concentration': 0.33}],
'reactors': [{'type': 'gas batch constant T P',
'T': 1000,
'P': 1,
'termination_conversion': {'H2': 0.1},
'termination_time': [1, 'ms']}],
'model': {'core_tolerance': 0.01}}
t3_object = T3(project='T3_functional_test_1',
rmg=rmg_args,
clean_dir=True,
)
t3_object.execute()
with open(os.path.join(t3_object.project_directory, 't3.log'), 'r') as f:
lines = f.readlines()
for line in ['# The Tandem Tool (T3) #\n',
'Starting project T3_functional_test_1\n',
'T3 iteration 1:\n',
]:
assert line in lines
assert not any('T3 iteration 0:\n' in line for line in lines)
assert any('T3 execution terminated' in line for line in lines)
shutil.rmtree(t3_object.project_directory, ignore_errors=True)
def main() -> None:
"""
The main T3 executable function.
"""
args = parse_command_line_arguments()
input_file = args.file
project_directory = os.path.abspath(os.path.dirname(args.file))
input_dict = read_yaml_file(path=input_file)
if 'project' not in list(input_dict.keys()):
raise ValueError('A project name must be provided.')
verbose = 20
if args.debug:
verbose = 10
elif args.quiet:
verbose = 30
input_dict['verbose'] = input_dict['verbose'] if 'verbose' in input_dict else verbose
if 'project_directory' not in input_dict or not input_dict['project_directory']:
input_dict['project_directory'] = project_directory
# check that RMG and ARC are available
check_dependencies()
t3_object = T3(**input_dict)
t3_object.execute()
def test_minimal_example():
"""Tests that the minimal example is functional (ARC is not being called)"""
input_file = os.path.join(functional_minimal_directory, 'input.yml')
input_dict = read_yaml_file(path=input_file)
verbose = 20
input_dict['verbose'] = verbose
input_dict['project_directory'] = functional_minimal_directory
# check that RMG and ARC are available
check_dependencies()
# run the minimal example
t3_object = T3(**input_dict)
t3_object.execute()
# check that the minimal example ran to completion by checking for existence of some files and directories
assert os.path.isfile(os.path.join(functional_minimal_directory, 't3.log'))
assert os.path.isdir(
os.path.join(functional_minimal_directory, 'iteration_0'))
assert os.path.isfile(
os.path.join(functional_minimal_directory, 'iteration_0', 'RMG',
'chemkin', 'species_dictionary.txt'))
assert os.path.isdir(
os.path.join(functional_minimal_directory, 'iteration_1'))
assert os.path.isfile(
os.path.join(functional_minimal_directory, 'iteration_1', 'RMG',
'chemkin', 'species_dictionary.txt'))
# remove directories created by this functional test
log_file = os.path.join(functional_minimal_directory, 't3.log')
if os.path.isfile(log_file):
os.remove(log_file)
iteration_directories = [
os.path.join(functional_minimal_directory, f'iteration_{i}')
for i in range(2)
]
for iteration_dir in iteration_directories:
if os.path.isdir(iteration_dir):
shutil.rmtree(iteration_dir)
def execute(self):
"""
Execute APIOxy by calling T3 with the respective arguments.
Todo:
Make self.apioxy['run_in_parallel'] functional
"""
self.write_apioxy_input_file()
for i, api_dict in enumerate(self.apioxy['api_structures']):
rmg = self.rmg.copy()
api_dict_copy = api_dict.copy()
if self.apioxy['model_level'] != 0:
# Rename the API so RMG won't H_abstract from the API (but only if level != 0)
api_dict_copy['label'] = 'API'
if 'seed_all_rads' not in api_dict_copy:
api_dict_copy['seed_all_rads'] = ['radical', 'peroxyl']
self.set_species_constraints(api_dict_copy)
rmg['species'].append(api_dict_copy)
if len(self.apioxy['api_structures']) > 1:
project = f"{i + 1}_{api_dict['label']}"
project_directory = os.path.join(
self.project_directory, f"{i + 1}_{api_dict['label']}")
else:
project = self.project
project_directory = self.project_directory
t3_object = T3(
project=project,
rmg=self.rmg,
t3=self.t3,
qm=self.qm,
project_directory=project_directory,
verbose=self.verbose,
clean_dir=False,
)
t3_object.execute()
self.logger.log_footer()
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
カオス的な振る舞いのビークル実験用コード
"""
import sys, os
sys.path.append(os.pardir) # 親ディレクトリのファイルをインポートするための設定
import numpy as np
from t3 import T3
from alifebook_lib.simulators import VehicleSimulator
simulator = VehicleSimulator(obstacle_num=0)
t3 = T3(omega0=0.9, omega1=0.3, epsilon=0.1)
t3.set_parameters(omega0=np.random.rand())
t3.set_parameters(omega1=np.random.rand())
while simulator:
sensor_data = simulator.get_sensor_data()
x, y = t3.next()
left_wheel_speed = 50 * x
right_wheel_speed = 50 * y
action = [left_wheel_speed, right_wheel_speed]
simulator.update(action)
import numpy as np
from matplotlib import pyplot as plt
from matplotlib import animation
from t3 import T3
"""
t3.pyの出力をプロットします.
実行するにはmatplotlibが必要です.
インストール方法
$ pip install matplotlib
"""
fig = plt.figure()
ax = plt.axes(xlim=(0, 1), ylim=(0, 1))
ax.set_xlim(0, 1)
ax.set_ylim(0, 1)
t3 = T3()
def update(frame):
ax.clear()
d = np.array([t3.next() for i in range(1000)])
ax.scatter(d[:, 0], d[:, 1], s=1)
ax.set_xlim(0, 1)
ax.set_ylim(0, 1)
return
anim = animation.FuncAnimation(fig, update, interval=20, blit=False)
plt.show(anim)
piece = t3.board[pos]
if piece == ' ':
w.setPropertyValue("text", str(pos))
else:
w.setPropertyValue("text", str(piece).upper())
def showInfo(text):
w = display.runtimeChildren().getChildByName("info")
w.setPropertyValue("text", str(text))
t3 = display.getUserData("T3")
if t3 is None:
# Initialize new board
t3 = T3()
display.setUserData("T3", t3)
showBoard(t3)
else:
# User entered a move
pos = int(PVUtil.getString(pvs[0]))
if not (0 <= pos < 9):
showInfo("Field must be 0 .. 8")
elif t3.board[pos] != ' ':
showInfo("Field %d already occupied!" % pos)
else:
# Perform user's move
t3.board[pos] = 'x'
showBoard(t3)
# Compute computer's move
def on_init(self):
self.add_child_module('avoid', AvoidModule())
self.t3 = T3(omega0=0.9, omega1=0.3, epsilon=0.1)
self.t3.set_parameters(omega0=np.random.rand())
self.t3.set_parameters(omega1=np.random.rand())