def run_simulation(request):
_voronoi = request.param["voronoi"]
_hop_range_value = request.param["hop_range"]
_transiting = request.param["transiting"]
_koopmans = request.param["koopmans"]
if _hop_range_value != 10.0:
_hop_range = True
else:
_hop_range = False
_modifiers = {"True": [], "False": []}
for _key in request.param.keys():
_boolean = eval("".join(["_", _key]))
_modifiers[repr(_boolean)].append(_key)
# ---==============================================---
# ---======== Directory and File Structure ========---
# ---==============================================---
input_morph_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_morph_dir = os.path.join(TEST_ROOT, "output_OC")
output_orca_dir = None
input_device_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_device_dir = os.path.join(TEST_ROOT, "output_OC")
# ---==============================================---
# ---========== Input Morphology Details ==========---
# ---==============================================---
morphology = "donor_polymer.xml"
input_sigma = 3.0
device_morphology = None
device_components = {}
overwrite_current_data = True
random_seed_override = 929292929
# ---==============================================---
# ---============= Execution Modules ==============---
# ---==============================================---
execute_fine_graining = False # Requires: None
execute_molecular_dynamics = False # Requires: fine_graining
execute_obtain_chromophores = (
True) # Requires: Atomistic morphology, or molecular_dynamics
execute_ZINDO = False # Requires: obtain_chromophores
execute_calculate_transfer_integrals = False # Requires: execute_ZINDO
execute_calculate_mobility = False # Requires: calculate_transfer_integrals
execute_device_simulation = (
False
) # Requires: calculate_transfer_integrals for all device_components
# ---==============================================---
# ---============ Chromophore Parameters ==========---
# ---==============================================---
molecule_terminating_connections = {"C1": [[2, 1]], "C10": [[2, 1]]}
AA_rigid_body_species = {}
CG_site_species = {"A": "donor", "B": "none", "C": "none"}
use_voronoi_neighbours = _voronoi
maximum_hole_hop_distance = _hop_range
maximum_electron_hop_distance = _hop_range
permit_hops_through_opposing_chromophores = _transiting
remove_orca_inputs = False
remove_orca_outputs = True
chromophore_length = 3
# ---==============================================---
# ---=== Chromophore Energy Scaling Parameters ====---
# ---==============================================---
chromophore_species = {
"donor": {
"literature_MO": -5.0,
"target_DOS_std": 0.1,
"reorganisation_energy": 0.3064,
"species": "donor",
"VRH_delocalisation": 2e-10,
}
}
use_koopmans_approximation = _koopmans
koopmans_hopping_prefactor = 1E-3
# ---==============================================---
# ---================= Begin run ==================---
# ---==============================================---
parameter_file = os.path.realpath(__file__)
proc_IDs = hf.get_CPU_cores()
parameter_names = [
i for i in dir() if (not i.startswith("_")) and (
not i.startswith("@")) and (not i.startswith("Test")) and (
not i.startswith("test")) and (i not in [
"run_MorphCT",
"helper_functions",
"hf",
"os",
"shutil",
"TestCommand",
"TEST_ROOT",
"setup_module",
"teardown_module",
"testing_tools",
"sys",
"pytest",
"request",
])
]
parameters = {}
for name in parameter_names:
parameters[name] = locals()[name]
# ---==============================================---
# ---=============== Setup Prereqs ================---
# ---==============================================---
try:
shutil.rmtree(output_morph_dir)
except OSError:
pass
os.makedirs(
os.path.join(output_morph_dir,
os.path.splitext(morphology)[0], "code"))
shutil.copy(
os.path.join(
TEST_ROOT,
"assets",
os.path.splitext(morphology)[0],
"OC",
morphology.replace(".xml", "_post_run_HOOMD.pickle"),
),
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"code",
morphology.replace(".xml", ".pickle"),
),
)
run_MorphCT.simulation(
**parameters) # Execute MorphCT using these simulation parameters
# The output dictionary from this fixing
fix_dict = {}
# Load the output pickle
output_pickle_data = hf.load_pickle(
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"code",
morphology.replace(".xml", ".pickle"),
))
fix_dict["output_AA_morphology_dict"] = output_pickle_data[0]
fix_dict["output_CG_morphology_dict"] = output_pickle_data[1]
fix_dict["output_CG_to_AAID_master"] = output_pickle_data[2]
fix_dict["output_parameter_dict"] = output_pickle_data[3]
fix_dict["output_chromophore_list"] = output_pickle_data[4]
# Load the correct expected pickle
pickle_name = os.path.join(
input_morph_dir, "OC",
morphology.replace(".xml", "_post_obtain_chromophores"))
pickle_name_modified = "_".join([pickle_name] + sorted(_modifiers["True"]))
expected_pickle_data = hf.load_pickle("".join(
[pickle_name_modified, ".pickle"]))
fix_dict["expected_AA_morphology_dict"] = expected_pickle_data[0]
fix_dict["expected_CG_morphology_dict"] = expected_pickle_data[1]
fix_dict["expected_CG_to_AAID_master"] = expected_pickle_data[2]
fix_dict["expected_parameter_dict"] = expected_pickle_data[3]
fix_dict["expected_chromophore_list"] = expected_pickle_data[4]
return fix_dict
def run_simulation(request):
_voltage = request.param["voltage"]
_no_dark = request.param["no_dark"]
_no_coulomb = request.param["no_coulomb"]
_stdout_log = request.param["stdout_log"]
# ---==============================================---
# ---======== Directory and File Structure ========---
# ---==============================================---
input_morph_dir = os.path.join(TEST_ROOT, "output_DBL", "morph_inputs")
output_morph_dir = os.path.join(TEST_ROOT, "output_DBL", "morph_outputs")
output_orca_dir = None
input_device_dir = os.path.join(TEST_ROOT, "output_DBL", "device_inputs")
output_device_dir = os.path.join(TEST_ROOT, "output_DBL", "device_outputs")
# ---==============================================---
# ---========== Input Morphology Details ==========---
# ---==============================================---
morphology = None
input_sigma = 1.0
device_morphology = "bilayer"
device_components = {
0: "donor_crystal",
1: "acceptor_crystal",
2: "mixed_crystal_bilayer",
}
overwrite_current_data = True
random_seed_override = 929292929
# ---==============================================---
# ---============= Execution Modules ==============---
# ---==============================================---
execute_fine_graining = False # Requires: None
execute_molecular_dynamics = False # Requires: fine_graining
execute_obtain_chromophores = (
False) # Requires: Atomistic morphology, or molecular_dynamics
execute_ZINDO = False # Requires: obtain_chromophores
execute_calculate_transfer_integrals = False # Requires: execute_ZINDO
execute_calculate_mobility = False # Requires: calculate_transfer_integrals
execute_device_simulation = (
True
) # Requires: calculate_transfer_integrals for all device_components
# ---==============================================---
# ---=== General Kinetic Monte Carlo Parameters ===---
# ---==============================================---
# ---=== Universal KMC Parameters ===---
system_temperature = 290
use_simple_energetic_penalty = False
record_carrier_history = True
use_VRH = True
# ---=== Device Specific KMC Parameters ===---
# Material parameters
absorption_coefficient = 1.3E4
relative_permittivity = 3
donor_HOMO = -5.3
acceptor_LUMO = -3.9
cathode_work_function = -4.2
anode_work_function = -5.0
recombination_rate = 1E9
coulomb_capture_radius = 1E-9
wrap_device_xy = False
exciton_lifetime = 0.5E-9
forster_radius = 4.3E-9
hopping_prefactor = 1E-4
MA_prefactor = 1E11
MA_localisation_radius = 1E-9
# External parameters
incident_flux = 100
incident_wavelength = 500E-9
# Simulation
voltage_sweep = _voltage
morphology_cell_size = 1E-8
minimum_number_of_photoinjections = 10
fastest_event_allowed = 1E-18
slowest_event_allowed = 1E-8
disable_dark_injection = _no_dark
disable_coulombic = _no_coulomb
output_log_to_stdout = _stdout_log
# ---==============================================---
# ---================= Begin run ==================---
# ---==============================================---
parameter_file = os.path.realpath(__file__)
# Force serial running
proc_IDs = [0]
parameter_names = [
i for i in dir() if (not i.startswith("_")) and (
not i.startswith("@")) and (not i.startswith("Test")) and (
not i.startswith("test")) and (i not in [
"run_MorphCT",
"helper_functions",
"hf",
"os",
"shutil",
"TestCommand",
"TEST_ROOT",
"setup_module",
"teardown_module",
"testing_tools",
"sys",
"pytest",
"pickle",
"request",
])
]
parameters = {}
for name in parameter_names:
parameters[name] = locals()[name]
# ---==============================================---
# ---=============== Setup Prereqs ================---
# ---==============================================---
try:
shutil.rmtree(os.path.join(TEST_ROOT, "output_DBL"))
except OSError:
pass
shutil.copytree(
os.path.join(TEST_ROOT, "assets", "device_bilayer"),
os.path.join(TEST_ROOT, "output_DBL"),
)
run_MorphCT.simulation(
**parameters) # Execute MorphCT using these simulation parameters
return voltage_sweep
"""
Boolean that can be used to toggle Coulombic interactions between carriers in the device at the same time
"""
disable_coulombic = True
"""
Divert log output to the terminal rather than the KMC_log files (useful for testing or when running only one voltage
on a single core)
"""
output_log_to_stdout = True
# ---==============================================---
# ---================= Begin run ==================---
# ---==============================================---
if __name__ == "__main__":
from morphct import run_MorphCT
from morphct.code import helper_functions as hf
parameter_file = __os.path.realpath(__file__)
proc_IDs = hf.get_CPU_cores()
parameter_names = [
i for i in dir()
if (not i.startswith("__")) and (not i.startswith("@")) and (
i not in ["run_MorphCT", "helper_functions", "hf"])
]
parameters = {}
for name in parameter_names:
parameters[name] = locals()[name]
run_MorphCT.simulation(
**parameters) # Execute MorphCT using these simulation parameters
def run_simulation():
# ---==============================================---
# ---======== Directory and File Structure ========---
# ---==============================================---
input_morph_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_morph_dir = os.path.join(TEST_ROOT, "output_FG")
output_orca_dir = None
input_device_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_device_dir = os.path.join(TEST_ROOT, "output_FG")
# ---==============================================---
# ---========== Input Morphology Details ==========---
# ---==============================================---
morphology = "donor_polymer.xml"
input_sigma = 3.0
device_morphology = None
device_components = {}
overwrite_current_data = True
random_seed_override = 929292929
# ---==============================================---
# ---============= Execution Modules ==============---
# ---==============================================---
execute_fine_graining = True # Requires: None
execute_molecular_dynamics = False # Requires: fine_graining
execute_obtain_chromophores = (
False) # Requires: Atomistic morphology, or molecular_dynamics
execute_ZINDO = False # Requires: obtain_chromophores
execute_calculate_transfer_integrals = False # Requires: execute_ZINDO
execute_calculate_mobility = False # Requires: calculate_transfer_integrals
execute_device_simulation = (
False
) # Requires: calculate_transfer_integrals for all device_components
# ---==============================================---
# ---========== Fine Graining Parameters ==========---
# ---==============================================---
CG_to_template_dirs = {
"A": os.path.join(TEST_ROOT, "assets", "donor_polymer"),
"B": os.path.join(TEST_ROOT, "assets", "donor_polymer"),
"C": os.path.join(TEST_ROOT, "assets", "donor_polymer"),
}
CG_to_template_files = {
"A": "P3HT_template.xml",
"B": "P3HT_template.xml",
"C": "P3HT_template.xml",
}
CG_to_template_force_fields = {
"A": "test_FF.xml",
"B": "test_FF.xml",
"C": "test_FF.xml",
}
CG_to_template_AAIDs = {
"A": [0, 1, 2, 3, 4, 24],
"B": [5, 6, 7, 18, 19, 20, 21, 22, 23],
"C": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17],
}
CG_to_template_bonds = {"bondB": ["C2-C3", 2, 5], "bondC": ["C5-C6", 7, 8]}
rigid_body_sites = {"A": [0, 1, 2, 3, 4]}
additional_constraints = [
["C1-C10", 3, 25],
["C1-C10-C9", 3, 25, 26],
["C1-C10-S1", 3, 25, 29],
["S1-C1-C10", 4, 3, 25],
["C2-C1-C10", 2, 3, 25],
["C1-C10-C9-C2", 3, 25, 26, 27],
["C1-C10-S1-C1", 3, 25, 29, 28],
["S1-C1-C10-S1", 4, 3, 25, 29],
["C2-C1-C10-S1", 2, 3, 25, 29],
]
molecule_terminating_connections = {"C1": [[2, 1]], "C10": [[2, 1]]}
# ---==============================================---
# ---================= Begin run ==================---
# ---==============================================---
parameter_file = os.path.realpath(__file__)
proc_IDs = hf.get_CPU_cores()
parameter_names = [
i for i in dir() if (not i.startswith("__")) and (
not i.startswith("@")) and (not i.startswith("Test")) and (
not i.startswith("test")) and (i not in [
"run_MorphCT",
"helper_functions",
"hf",
"os",
"shutil",
"TestCommand",
"TEST_ROOT",
"setup_module",
"teardown_module",
"testing_tools",
"sys",
"pytest",
])
]
parameters = {}
for name in parameter_names:
parameters[name] = locals()[name]
run_MorphCT.simulation(
**parameters) # Execute MorphCT using these simulation parameters
# The output dictionary from this fixing
fix_dict = {}
# Load the output pickle
output_pickle_data = hf.load_pickle(
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"code",
morphology.replace(".xml", ".pickle"),
))
fix_dict["output_AA_morphology_dict"] = output_pickle_data[0]
fix_dict["output_CG_morphology_dict"] = output_pickle_data[1]
fix_dict["output_CG_to_AAID_master"] = output_pickle_data[2]
fix_dict["output_parameter_dict"] = output_pickle_data[3]
fix_dict["output_chromophore_list"] = output_pickle_data[4]
# Load the expected pickle
expected_pickle_data = hf.load_pickle(
os.path.join(
input_morph_dir,
"FG",
morphology.replace(".xml", "_post_fine_graining.pickle"),
))
fix_dict["expected_AA_morphology_dict"] = expected_pickle_data[0]
fix_dict["expected_CG_morphology_dict"] = expected_pickle_data[1]
fix_dict["expected_CG_to_AAID_master"] = expected_pickle_data[2]
fix_dict["expected_parameter_dict"] = expected_pickle_data[3]
fix_dict["expected_chromophore_list"] = expected_pickle_data[4]
return fix_dict
def run_simulation():
# ---==============================================---
# ---======== Directory and File Structure ========---
# ---==============================================---
input_morph_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_morph_dir = os.path.join(TEST_ROOT, "output_TI")
output_orca_dir = None
input_device_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_device_dir = os.path.join(TEST_ROOT, "output_TI")
# ---==============================================---
# ---========== Input Morphology Details ==========---
# ---==============================================---
morphology = "donor_polymer.xml"
input_sigma = 3.0
device_morphology = None
device_components = {}
overwrite_current_data = True
random_seed_override = 929292929
# ---==============================================---
# ---============= Execution Modules ==============---
# ---==============================================---
execute_fine_graining = False # Requires: None
execute_molecular_dynamics = False # Requires: fine_graining
execute_obtain_chromophores = (
False) # Requires: Atomistic morphology, or molecular_dynamics
execute_ZINDO = False # Requires: obtain_chromophores
execute_calculate_transfer_integrals = True # Requires: execute_ZINDO
execute_calculate_mobility = False # Requires: calculate_transfer_integrals
execute_device_simulation = (
False
) # Requires: calculate_transfer_integrals for all device_components
remove_orca_inputs = False
remove_orca_outputs = False
# ---==============================================---
# ---================= Begin run ==================---
# ---==============================================---
parameter_file = os.path.realpath(__file__)
proc_IDs = hf.get_CPU_cores()
parameter_names = [
i for i in dir() if (not i.startswith("__")) and (
not i.startswith("@")) and (not i.startswith("Test")) and (
not i.startswith("test")) and (i not in [
"run_MorphCT",
"helper_functions",
"hf",
"os",
"shutil",
"TestCommand",
"TEST_ROOT",
"setup_module",
"teardown_module",
"testing_tools",
"sys",
"pytest",
])
]
parameters = {}
for name in parameter_names:
parameters[name] = locals()[name]
# ---==============================================---
# ---=============== Setup Prereqs ================---
# ---==============================================---
try:
shutil.rmtree(output_morph_dir)
except OSError:
pass
os.makedirs(
os.path.join(output_morph_dir,
os.path.splitext(morphology)[0], "code"))
shutil.copy(
os.path.join(
TEST_ROOT,
"assets",
os.path.splitext(morphology)[0],
"TI",
morphology.replace(".xml", "_post_execute_ZINDO.pickle"),
),
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"code",
morphology.replace(".xml", ".pickle"),
),
)
shutil.copytree(
os.path.join(TEST_ROOT, "assets",
os.path.splitext(morphology)[0], "TI", "input_orca"),
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"chromophores",
"input_orca",
),
)
shutil.copytree(
os.path.join(TEST_ROOT, "assets",
os.path.splitext(morphology)[0], "TI", "output_orca"),
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"chromophores",
"output_orca",
),
)
run_MorphCT.simulation(
**parameters) # Execute MorphCT using these simulation parameters
# The output dictionary from this fixing
fix_dict = {}
# Load the output pickle
output_pickle_data = hf.load_pickle(
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"code",
morphology.replace(".xml", ".pickle"),
))
fix_dict["output_AA_morphology_dict"] = output_pickle_data[0]
fix_dict["output_CG_morphology_dict"] = output_pickle_data[1]
fix_dict["output_CG_to_AAID_master"] = output_pickle_data[2]
fix_dict["output_parameter_dict"] = output_pickle_data[3]
fix_dict["output_chromophore_list"] = output_pickle_data[4]
# Load the expected pickle
expected_pickle_data = hf.load_pickle(
os.path.join(
input_morph_dir,
"TI",
morphology.replace(".xml",
"_post_calculate_transfer_integrals.pickle"),
))
fix_dict["expected_AA_morphology_dict"] = expected_pickle_data[0]
fix_dict["expected_CG_morphology_dict"] = expected_pickle_data[1]
fix_dict["expected_CG_to_AAID_master"] = expected_pickle_data[2]
fix_dict["expected_parameter_dict"] = expected_pickle_data[3]
fix_dict["expected_chromophore_list"] = expected_pickle_data[4]
return fix_dict
def run_simulation():
# ---==============================================---
# ---======== Directory and File Structure ========---
# ---==============================================---
input_morph_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_morph_dir = os.path.join(TEST_ROOT, "output_MKMC")
output_orca_dir = None
input_device_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_device_dir = os.path.join(TEST_ROOT, "output_MKMC")
# ---==============================================---
# ---========== Input Morphology Details ==========---
# ---==============================================---
morphology = "donor_polymer.xml"
input_sigma = 3.0
device_morphology = None
device_components = {}
overwrite_current_data = True
random_seed_override = 929292929
# ---==============================================---
# ---============= Execution Modules ==============---
# ---==============================================---
execute_fine_graining = False # Requires: None
execute_molecular_dynamics = False # Requires: fine_graining
execute_obtain_chromophores = (
False) # Requires: Atomistic morphology, or molecular_dynamics
execute_ZINDO = False # Requires: obtain_chromophores
execute_calculate_transfer_integrals = False # Requires: execute_ZINDO
execute_calculate_mobility = True # Requires: calculate_transfer_integrals
execute_device_simulation = (
False
) # Requires: calculate_transfer_integrals for all device_components
# ---==============================================---
# ---=== General Kinetic Monte Carlo Parameters ===---
# ---==============================================---
# ---=== Universal KMC Parameters ===---
system_temperature = 290
use_simple_energetic_penalty = False
record_carrier_history = True
use_VRH = True
# ---=== Mobility Specific KMC Parameters ===---
number_of_holes_per_simulation_time = 10
number_of_electrons_per_simulation_time = 0
hop_limit = 0
simulation_times = [1.00e-13, 1.00e-12, 1.00e-11]
combine_KMC_results = True
use_average_hop_rates = False
average_intra_hop_rate = 8.07E14
average_inter_hop_rate = 3.92E14
# ---==============================================---
# ---================= Begin run ==================---
# ---==============================================---
parameter_file = os.path.realpath(__file__)
# Force serial running
proc_IDs = [0]
parameter_names = [
i for i in dir() if (not i.startswith("__")) and (
not i.startswith("@")) and (not i.startswith("Test")) and (
not i.startswith("test")) and (i not in [
"run_MorphCT",
"helper_functions",
"hf",
"os",
"shutil",
"TestCommand",
"TEST_ROOT",
"setup_module",
"teardown_module",
"testing_tools",
"sys",
"pytest",
"pickle",
])
]
parameters = {}
for name in parameter_names:
parameters[name] = locals()[name]
# ---==============================================---
# ---=============== Setup Prereqs ================---
# ---==============================================---
try:
shutil.rmtree(output_morph_dir)
except OSError:
pass
os.makedirs(
os.path.join(output_morph_dir,
os.path.splitext(morphology)[0], "code"))
shutil.copy(
os.path.join(
TEST_ROOT,
"assets",
os.path.splitext(morphology)[0],
"MKMC",
morphology.replace(".xml",
"_post_calculate_transfer_integrals.pickle"),
),
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"code",
morphology.replace(".xml", ".pickle"),
),
)
run_MorphCT.simulation(
**parameters) # Execute MorphCT using these simulation parameters
# The output dictionary from this fixing
fix_dict = {}
# Load the output pickle
output_pickle_data = hf.load_pickle(
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"code",
morphology.replace(".xml", ".pickle"),
))
fix_dict["output_AA_morphology_dict"] = output_pickle_data[0]
fix_dict["output_CG_morphology_dict"] = output_pickle_data[1]
fix_dict["output_CG_to_AAID_master"] = output_pickle_data[2]
fix_dict["output_parameter_dict"] = output_pickle_data[3]
fix_dict["output_chromophore_list"] = output_pickle_data[4]
# Load the expected pickle
expected_pickle_data = hf.load_pickle(
os.path.join(
input_morph_dir,
"MKMC",
morphology.replace(".xml", "_post_calculate_mobility.pickle"),
))
fix_dict["expected_AA_morphology_dict"] = expected_pickle_data[0]
fix_dict["expected_CG_morphology_dict"] = expected_pickle_data[1]
fix_dict["expected_CG_to_AAID_master"] = expected_pickle_data[2]
fix_dict["expected_parameter_dict"] = expected_pickle_data[3]
fix_dict["expected_chromophore_list"] = expected_pickle_data[4]
return fix_dict
def run_simulation():
# ---==============================================---
# ---======== Directory and File Structure ========---
# ---==============================================---
input_morph_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_morph_dir = os.path.join(TEST_ROOT, "output_RH")
output_orca_dir = None
input_device_dir = os.path.join(TEST_ROOT, "assets", "donor_polymer")
output_device_dir = os.path.join(TEST_ROOT, "output_RH")
# ---==============================================---
# ---========== Input Morphology Details ==========---
# ---==============================================---
morphology = "donor_polymer.xml"
input_sigma = 3.0
device_morphology = None
device_components = {}
overwrite_current_data = True
random_seed_override = 929292929
# ---==============================================---
# ---============= Execution Modules ==============---
# ---==============================================---
execute_fine_graining = False # Requires: None
execute_molecular_dynamics = True # Requires: fine_graining
execute_obtain_chromophores = (
False) # Requires: Atomistic morphology, or molecular_dynamics
execute_ZINDO = False # Requires: obtain_chromophores
execute_calculate_transfer_integrals = False # Requires: execute_ZINDO
execute_calculate_mobility = False # Requires: calculate_transfer_integrals
execute_device_simulation = (
False
) # Requires: calculate_transfer_integrals for all device_components
# ---==============================================---
# ---=========== Forcefield Parameters ============---
# ---==============================================---
CG_to_template_dirs = {
"A": os.path.join(TEST_ROOT, "assets", "donor_polymer"),
"B": os.path.join(TEST_ROOT, "assets", "donor_polymer"),
"C": os.path.join(TEST_ROOT, "assets", "donor_polymer"),
}
CG_to_template_force_fields = {
"A": "test_FF.xml",
"B": "test_FF.xml",
"C": "test_FF.xml",
}
pair_r_cut = 10.0
pair_dpd_gamma_val = 0.0
# ---==============================================---
# ---===== Molecular Dynamics Phase Parameters ====---
# ---==============================================---
number_of_phases = 4
temperatures = [1.0]
taus = [1.0]
pair_types = ["none", "dpd", "lj", "lj", "lj", "lj", "lj", "lj"]
bond_types = ["harmonic"]
angle_types = ["harmonic"]
dihedral_types = ["opls"]
integration_targets = ["all"]
timesteps = [1E-3, 1E-3, 1E-7, 1E-4]
durations = [1E5, 5E4, 1E4, 5E4]
termination_conditions = ["ke_min", "max_t", "max_t", "max_t"]
group_anchorings = ["all", "all", "all", "none"]
dcd_file_write = True
dcd_file_dumpsteps = [0]
# ---==============================================---
# ---================= Begin run ==================---
# ---==============================================---
parameter_file = os.path.realpath(__file__)
proc_IDs = hf.get_CPU_cores()
parameter_names = [
i for i in dir() if (not i.startswith("__")) and (
not i.startswith("@")) and (not i.startswith("Test")) and (
not i.startswith("test")) and (i not in [
"run_MorphCT",
"helper_functions",
"hf",
"os",
"shutil",
"TestCommand",
"TEST_ROOT",
"setup_module",
"teardown_module",
"testing_tools",
"sys",
"pytest",
])
]
parameters = {}
for name in parameter_names:
parameters[name] = locals()[name]
# ---==============================================---
# ---=============== Setup Prereqs ================---
# ---==============================================---
try:
shutil.rmtree(output_morph_dir)
except OSError:
pass
os.makedirs(
os.path.join(output_morph_dir,
os.path.splitext(morphology)[0], "code"))
shutil.copy(
os.path.join(
TEST_ROOT,
"assets",
os.path.splitext(morphology)[0],
"RH",
morphology.replace(".xml", "_post_fine_graining.pickle"),
),
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"code",
morphology.replace(".xml", ".pickle"),
),
)
run_MorphCT.simulation(
**parameters) # Execute MorphCT using these simulation parameters
# The output dictionary from this fixing
fix_dict = {}
# Load the output pickle
output_pickle_data = hf.load_pickle(
os.path.join(
output_morph_dir,
os.path.splitext(morphology)[0],
"code",
morphology.replace(".xml", ".pickle"),
))
fix_dict["output_AA_morphology_dict"] = output_pickle_data[0]
fix_dict["output_CG_morphology_dict"] = output_pickle_data[1]
fix_dict["output_CG_to_AAID_master"] = output_pickle_data[2]
fix_dict["output_parameter_dict"] = output_pickle_data[3]
fix_dict["output_chromophore_list"] = output_pickle_data[4]
# Load the expected pickle
expected_pickle_data = hf.load_pickle(
os.path.join(input_morph_dir, "RH",
morphology.replace(".xml", "_post_run_HOOMD.pickle")))
fix_dict["expected_AA_morphology_dict"] = expected_pickle_data[0]
fix_dict["expected_CG_morphology_dict"] = expected_pickle_data[1]
fix_dict["expected_CG_to_AAID_master"] = expected_pickle_data[2]
fix_dict["expected_parameter_dict"] = expected_pickle_data[3]
fix_dict["expected_chromophore_list"] = expected_pickle_data[4]
return fix_dict