def workflow_derivative_couplings(workflow_settings: Dict):
"""
Compute the derivative couplings from an MD trajectory.
:param workflow_settings: Arguments to compute the oscillators see:
`data/schemas/derivative_couplings.json
:returns: None
"""
# Arguments to compute the orbitals and configure the workflow. see:
# `data/schemas/general_settings.json
config = workflow_settings['general_settings']
# Dictionary containing the general configuration
config.update(initialize(**config))
# compute the molecular orbitals
mo_paths_hdf5 = calculate_mos(**config)
# Overlap matrix at two different times
promised_overlaps = calculate_overlap(
config['project_name'], config['path_hdf5'], config['dictCGFs'],
config['geometries'], mo_paths_hdf5,
config['hdf5_trans_mtx'], config['enumerate_from'],
workflow_settings['overlaps_deph'], nHOMO=workflow_settings['nHOMO'],
couplings_range=workflow_settings['couplings_range'])
# Create a function that returns a proxime array of couplings
schedule_couplings = schedule(lazy_couplings)
# Calculate Non-Adiabatic Coupling
promised_crossing_and_couplings = schedule_couplings(
promised_overlaps, config['path_hdf5'], config['project_name'],
config['enumerate_from'], workflow_settings['nHOMO'],
workflow_settings['dt'], workflow_settings['tracking'],
workflow_settings['write_overlaps'],
algorithm=workflow_settings['algorithm'])
# Write the results in PYXAID format
work_dir = config['work_dir']
path_hamiltonians = join(work_dir, 'hamiltonians')
if not os.path.exists(path_hamiltonians):
os.makedirs(path_hamiltonians)
# Inplace scheduling of write_hamiltonians function.
# Equivalent to add @schedule on top of the function
schedule_write_ham = schedule(write_hamiltonians)
# Number of matrix computed
nPoints = len(config['geometries']) - 2
# Write Hamilotians in PYXAID format
promise_files = schedule_write_ham(
config['path_hdf5'], mo_paths_hdf5, promised_crossing_and_couplings,
nPoints, path_dir_results=path_hamiltonians,
enumerate_from=config['enumerate_from'], nHOMO=workflow_settings['nHOMO'],
couplings_range=workflow_settings['couplings_range'])
run(promise_files, folder=work_dir)
remove_folders(config['folders'])
def workflow_stddft(config: dict) -> None:
"""
Compute the excited states using simplified TDDFT
:param workflow_settings: Arguments to compute the oscillators see:
`data/schemas/absorption_spectrum.json
:returns: None
"""
# Dictionary containing the general configuration
config.update(initialize(config))
# Single Point calculations settings using CP2K
mo_paths_hdf5, energy_paths_hdf5 = unpack(calculate_mos(config), 2)
# Read structures
molecules_au = [
change_mol_units(parse_string_xyz(gs))
for i, gs in enumerate(config.geometries) if (i % config.stride) == 0
]
# Noodles promised call
scheduleTDDFT = schedule(compute_excited_states_tddft)
results = gather(*[
scheduleTDDFT(config, mo_paths_hdf5[i],
DictConfig({
'i': i * config.stride,
'mol': mol
})) for i, mol in enumerate(molecules_au)
])
return run(gather(results, energy_paths_hdf5), folder=config['workdir'])
def workflow_stddft(config: dict) -> None:
"""
Compute the excited states using simplified TDDFT
:param workflow_settings: Arguments to compute the oscillators see:
`data/schemas/absorption_spectrum.json
:returns: None
"""
# Dictionary containing the general configuration
config.update(initialize(config))
# Single Point calculations settings using CP2K
mo_paths_hdf5, energy_paths_hdf5 = unpack(calculate_mos(config), 2)
# Read structures
molecules_au = [change_mol_units(parse_string_xyz(gs))
for i, gs in enumerate(config.geometries)
if (i % config.stride) == 0]
# Noodles promised call
scheduleTDDFT = schedule(compute_excited_states_tddft)
results = gather(
*[scheduleTDDFT(config, mo_paths_hdf5[i], DictConfig(
{'i': i * config.stride, 'mol': mol}))
for i, mol in enumerate(molecules_au)])
return run(gather(results, energy_paths_hdf5), folder=config['workdir'])
def workflow_derivative_couplings(config: dict) -> list:
"""
Compute the derivative couplings from an MD trajectory.
:param workflow_settings: Arguments to compute the oscillators see:
`nac/workflows/schemas.py
:returns: None
"""
# Dictionary containing the general configuration
config.update(initialize(config))
logger.info("starting couplings calculation!")
# compute the molecular orbitals
mo_paths_hdf5, energy_paths_hdf5 = unpack(calculate_mos(config), 2)
# mo_paths_hdf5 = run(calculate_mos(config), folder=config.workdir)
# Overlap matrix at two different times
promised_overlaps = calculate_overlap(config, mo_paths_hdf5)
# Calculate Non-Adiabatic Coupling
promised_crossing_and_couplings = lazy_couplings(config, promised_overlaps)
# Write the results in PYXAID format
config.path_hamiltonians = create_path_hamiltonians(config.workdir)
# Inplace scheduling of write_hamiltonians function.
# Equivalent to add @schedule on top of the function
schedule_write_ham = schedule(write_hamiltonians)
# Number of matrix computed
config["nPoints"] = len(config.geometries) - 2
# Write Hamilotians in PYXAID format
promise_files = schedule_write_ham(
config, promised_crossing_and_couplings, mo_paths_hdf5)
results = run(
gather(promise_files, energy_paths_hdf5), folder=config.workdir, always_cache=False)
remove_folders(config.folders)
return results
def workflow_oscillator_strength(workflow_settings: Dict):
"""
Compute the oscillator strength.
:param workflow_settings: Arguments to compute the oscillators see:
`data/schemas/absorption_spectrum.json
:returns: None
"""
# Arguments to compute the orbitals and configure the workflow. see:
# `data/schemas/general_settings.json
config = workflow_settings['general_settings']
# Dictionary containing the general configuration
config.update(initialize(**config))
# Point calculations Using CP2K
mo_paths_hdf5 = calculate_mos(**config)
# geometries in atomic units
molecules_au = [change_mol_units(parse_string_xyz(gs))
for gs in config['geometries']]
# Construct initial and final states ranges
transition_args = [workflow_settings[key] for key in
['initial_states', 'final_states', 'nHOMO']]
initial_states, final_states = build_transitions(*transition_args)
# Make a promise object the function the compute the Oscillator Strenghts
scheduleOscillator = schedule(calc_oscillator_strenghts)
oscillators = gather(
*[scheduleOscillator(
i, mol, mo_paths_hdf5, initial_states, final_states,
config) for i, mol in enumerate(molecules_au)
if i % workflow_settings['calculate_oscillator_every'] == 0])
energies, promised_cross_section = create_promised_cross_section(
oscillators, workflow_settings['broadening'], workflow_settings['energy_range'],
workflow_settings['convolution'], workflow_settings['calculate_oscillator_every'])
cross_section, data = run(
gather(promised_cross_section, oscillators), folder=config['work_dir'])
return store_data(data, energies, cross_section)
def workflow_derivative_couplings(config: dict) -> list:
"""
Compute the derivative couplings from an MD trajectory.
:param workflow_settings: Arguments to compute the oscillators see:
`nac/workflows/schemas.py
:returns: None
"""
# Dictionary containing the general configuration
config.update(initialize(config))
logger.info("starting!")
# compute the molecular orbitals
mo_paths_hdf5, energy_paths_hdf5 = unpack(calculate_mos(config), 2)
# mo_paths_hdf5 = run(calculate_mos(config), folder=config.workdir)
# Overlap matrix at two different times
promised_overlaps = calculate_overlap(config, mo_paths_hdf5)
# Calculate Non-Adiabatic Coupling
promised_crossing_and_couplings = lazy_couplings(config, promised_overlaps)
# Write the results in PYXAID format
config.path_hamiltonians = create_path_hamiltonians(config.workdir)
# Inplace scheduling of write_hamiltonians function.
# Equivalent to add @schedule on top of the function
schedule_write_ham = schedule(write_hamiltonians)
# Number of matrix computed
config["nPoints"] = len(config.geometries) - 2
# Write Hamilotians in PYXAID format
promise_files = schedule_write_ham(
config, promised_crossing_and_couplings, mo_paths_hdf5)
results = run(gather(promise_files, energy_paths_hdf5), folder=config.workdir)
remove_folders(config.folders)
return results
def workflow_single_points(config: dict) -> list:
"""
Single point calculations for a given trajectory
:param workflow_settings: Arguments to run the single points calculations see:
`nac/workflows/schemas.py
"""
# Dictionary containing the general configuration
config.update(initialize(config))
logger.info("starting!")
# compute the molecular orbitals
# Unpack
mo_paths_hdf5 = calculate_mos(config)
# Pack
results = run(mo_paths_hdf5, folder=config.workdir)
return results
def workflow_single_points(config: dict) -> list:
"""
Single point calculations for a given trajectory
:param workflow_settings: Arguments to run the single points calculations see:
`nac/workflows/schemas.py
"""
# Dictionary containing the general configuration
config.update(initialize(config))
logger.info("starting!")
# compute the molecular orbitals
# Unpack
mo_paths_hdf5 = calculate_mos(config)
# Pack
results = run(mo_paths_hdf5, folder=config.workdir)
return results
def calculate_ETR(
package_name: str, project_name: str, package_args: Dict,
path_time_coeffs: str=None, geometries: List=None,
initial_conditions: List=None, path_hdf5: str=None,
basis_name: str=None,
enumerate_from: int=0, package_config: Dict=None,
calc_new_wf_guess_on_points: str=None, guess_args: Dict=None,
work_dir: str=None, traj_folders: List=None,
dictCGFs: Dict=None, orbitals_range: Tuple=None,
pyxaid_HOMO: int=None, pyxaid_Nmin: int=None, pyxaid_Nmax: int=None,
fragment_indices: None=List, dt: float=1, **kwargs):
"""
Use a md trajectory to calculate the Electron transfer rate.
:param package_name: Name of the package to run the QM simulations.
:param project_name: Folder name where the computations
are going to be stored.
:param package_args: Specific settings for the package.
:param path_hdf5: Path to the HDF5 file that contains the
numerical results.
:param geometries: List of string cotaining the molecular geometries.
:paramter dictCGFS: Dictionary from Atomic Label to basis set
:type dictCGFS: Dict String [CGF],
CGF = ([Primitives], AngularMomentum),
Primitive = (Coefficient, Exponent)
:param calc_new_wf_guess_on_points: number of Computations that used a
previous calculation as guess for the
wave function.
:param nHOMO: index of the H**O orbital.
:param couplings_range: Range of MO use to compute the nonadiabatic
:param pyxaid_range: range of HOMOs and LUMOs used by pyxaid.
:param enumerate_from: Number from where to start enumerating the folders
create for each point in the MD.
:param traj_folders: List of paths to where the CP2K MOs are printed.
:param package_config: Parameters required by the Package.
:param fragment_indices: indices of atoms belonging to a fragment.
:param dt: integration time used in the molecular dynamics.
:returns: None
"""
# Start logging event
file_log = '{}.log'.format(project_name)
logging.basicConfig(filename=file_log, level=logging.DEBUG,
format='%(levelname)s:%(message)s %(asctime)s\n',
datefmt='%m/%d/%Y %I:%M:%S %p')
# prepare Cp2k Job point calculations Using CP2K
mo_paths_hdf5 = calculate_mos(
package_name, geometries, project_name, path_hdf5, traj_folders,
package_args, guess_args, calc_new_wf_guess_on_points,
enumerate_from, package_config=package_config)
# geometries in atomic units
molecules_au = [change_mol_units(parse_string_xyz(gs))
for gs in geometries]
# Time-dependent coefficients
time_depend_coeffs = read_time_dependent_coeffs(path_time_coeffs)
msg = "Reading time_dependent coefficients from: {}".format(path_time_coeffs)
logger.info(msg)
# compute_overlaps_ET
scheduled_overlaps = schedule(compute_overlaps_ET)
fragment_overlaps = scheduled_overlaps(
project_name, molecules_au, basis_name, path_hdf5, dictCGFs,
mo_paths_hdf5, fragment_indices, enumerate_from, package_name)
# Delta time in a.u.
dt_au = dt * femtosec2au
# Indices relation between the PYXAID active space and the orbitals
# stored in the HDF5
map_index_pyxaid_hdf5 = create_map_index_pyxaid(
orbitals_range, pyxaid_HOMO, pyxaid_Nmin, pyxaid_Nmax)
# Number of ETR points calculated with the MD trajectory
n_points = len(geometries) - 2
# Read the swap between Molecular orbitals obtained from a previous
# Coupling calculation
swaps = read_swaps(path_hdf5, project_name)
# Electron transfer rate for each frame of the Molecular dynamics
scheduled_photoexcitation = schedule(compute_photoexcitation)
etrs = scheduled_photoexcitation(
path_hdf5, time_depend_coeffs, fragment_overlaps,
map_index_pyxaid_hdf5, swaps, n_points, dt_au)
# Execute the workflow
electronTransferRates, path_overlaps = run(
gather(etrs, fragment_overlaps), folder=work_dir)
for i, mtx in enumerate(electronTransferRates):
write_ETR(mtx, dt, i)
write_overlap_densities(path_hdf5, path_overlaps, dt)
def workflow_electron_transfer(workflow_settings: Dict):
"""
Use a MD trajectory to calculate the Electron transfer rate.
:param workflow_settings: Arguments to compute the oscillators see:
`data/schemas/electron_transfer.json
:returns: None
"""
# Arguments to compute the orbitals and configure the workflow. see:
# `data/schemas/general_settings.json
config = workflow_settings['general_settings']
# Dictionary containing the general configuration
config.update(initialize(**config))
# Point calculations Using CP2K
mo_paths_hdf5 = calculate_mos(**config)
# geometries in atomic units
molecules_au = [
change_mol_units(parse_string_xyz(gs)) for gs in config['geometries']
]
# Time-dependent coefficients
path_time_coeffs = workflow_settings['path_time_coeffs']
time_depend_coeffs = read_time_dependent_coeffs(path_time_coeffs)
msg = "Reading time_dependent coefficients from: {}".format(
path_time_coeffs)
logger.info(msg)
# compute_overlaps_ET
scheduled_overlaps = schedule(compute_overlaps_ET)
fragment_overlaps = scheduled_overlaps(
config['project_name'], molecules_au, config['basis_name'],
config['path_hdf5'], config['dictCGFs'], mo_paths_hdf5,
workflow_settings['fragment_indices'], config['enumerate_from'],
config['package_name'])
# Delta time in a.u.
dt = workflow_settings['dt']
dt_au = dt * femtosec2au
# Indices relation between the PYXAID active space and the orbitals
# stored in the HDF5
args_map_index = [
workflow_settings[key] for key in
['orbitals_range', 'pyxaid_HOMO', 'pyxaid_Nmin', 'pyxaid_Nmax']
]
map_index_pyxaid_hdf5 = create_map_index_pyxaid(*args_map_index)
# Number of points in the pyxaid trajectory:
# shape: (initial_conditions, n_points, n_states)
n_points = len(config['geometries']) - 2
# Read the swap between Molecular orbitals obtained from a previous
# Coupling calculation
swaps = read_swaps(['path_hdf5'], ['project_name'])
# Electron transfer rate for each frame of the Molecular dynamics
scheduled_photoexcitation = schedule(compute_photoexcitation)
etrs = scheduled_photoexcitation(config['path_hdf5'], time_depend_coeffs,
fragment_overlaps, map_index_pyxaid_hdf5,
swaps, n_points, ['pyxaid_iconds'], dt_au)
# Execute the workflow
electronTransferRates, path_overlaps = run(gather(etrs, fragment_overlaps),
folder=config['work_dir'])
for i, mtx in enumerate(electronTransferRates):
write_ETR(mtx, dt, i)
write_overlap_densities(config['path_hdf5'], path_overlaps, swaps, dt)
def generate_pyxaid_hamiltonians(package_name: str,
project_name: str,
package_args: Dict,
guess_args: Dict = None,
geometries: List = None,
dictCGFs: Dict = None,
calc_new_wf_guess_on_points: str = None,
path_hdf5: str = None,
enumerate_from: int = 0,
package_config: Dict = None,
dt: float = 1,
traj_folders: List = None,
work_dir: str = None,
basisname: str = None,
hdf5_trans_mtx: str = None,
nHOMO: int = None,
couplings_range: Tuple = None,
algorithm='levine',
ignore_warnings=False,
tracking=True) -> None:
"""
Use a md trajectory to generate the hamiltonian components to run PYXAID
nonadiabatic molecular dynamics.
:param package_name: Name of the package to run the QM simulations.
:param project_name: Folder name where the computations
are going to be stored.
:param package_args: Specific Settings for the package that will compute
the MOs.
:param geometries: List of string cotaining the molecular geometries
numerical results.
:paramter dictCGFS: Dictionary from Atomic Label to basis set
:param calc_new_wf_guess_on_points: Calculate a guess wave function either
in the first point or on each point of the trajectory.
:param path_hdf5: path to the HDF5 file were the data is going to be stored.
:param enumerate_from: Number from where to start enumerating the folders
create for each point in the MD.
:param hdf5_trans_mtx: Path into the HDF5 file where the transformation
matrix (from Cartesian to sphericals) is stored.
:param dt: Time used in the dynamics (femtoseconds)
:param package_config: Parameters required by the Package.
:type package_config: Dict
:param nHOMO: index of the H**O orbital.
:param couplings_range: Range of MO use to compute the nonadiabatic
coupling matrix.
:returns: None
"""
# Start logging event
file_log = '{}.log'.format(project_name)
logging.basicConfig(filename=file_log,
level=logging.DEBUG,
format='%(levelname)s:%(message)s %(asctime)s\n',
datefmt='%m/%d/%Y %I:%M:%S %p')
# Log initial config information
log_config(work_dir, path_hdf5, algorithm)
# prepare Cp2k Jobs
# Point calculations Using CP2K
mo_paths_hdf5 = calculate_mos(package_name,
geometries,
project_name,
path_hdf5,
traj_folders,
package_args,
guess_args,
calc_new_wf_guess_on_points,
enumerate_from,
package_config=package_config,
ignore_warnings=ignore_warnings)
# Overlap matrix at two different times
promised_overlaps = calculate_overlap(project_name,
path_hdf5,
dictCGFs,
geometries,
mo_paths_hdf5,
hdf5_trans_mtx,
enumerate_from,
nHOMO=nHOMO,
couplings_range=couplings_range)
# Calculate Non-Adiabatic Coupling
schedule_couplings = schedule(lazy_couplings)
promised_crossing_and_couplings = schedule_couplings(promised_overlaps,
path_hdf5,
project_name,
enumerate_from,
nHOMO,
dt,
tracking,
algorithm=algorithm)
# Write the results in PYXAID format
path_hamiltonians = join(work_dir, 'hamiltonians')
if not os.path.exists(path_hamiltonians):
os.makedirs(path_hamiltonians)
# Inplace scheduling of write_hamiltonians function.
# Equivalent to add @schedule on top of the function
schedule_write_ham = schedule(write_hamiltonians)
# Number of matrix computed
nPoints = len(geometries) - 2
# Write Hamilotians in PYXAID format
promise_files = schedule_write_ham(path_hdf5,
mo_paths_hdf5,
promised_crossing_and_couplings,
nPoints,
path_dir_results=path_hamiltonians,
enumerate_from=enumerate_from,
nHOMO=nHOMO,
couplings_range=couplings_range)
run(promise_files, folder=work_dir)
remove_folders(traj_folders)
def workflow_oscillator_strength(
package_name: str,
project_name: str,
package_args: Dict,
guess_args: Dict = None,
geometries: List = None,
dictCGFs: Dict = None,
enumerate_from: int = 0,
calc_new_wf_guess_on_points: str = None,
path_hdf5: str = None,
package_config: Dict = None,
work_dir: str = None,
initial_states: Any = None,
final_states: Any = None,
traj_folders: List = None,
hdf5_trans_mtx: str = None,
nHOMO: int = None,
couplings_range: Tuple = None,
calculate_oscillator_every: int = 50,
convolution: str = 'gaussian',
broadening: float = 0.1, # eV
energy_range: Tuple = None, # eV
geometry_units='angstrom',
**kwargs):
"""
Compute the oscillator strength
:param package_name: Name of the package to run the QM simulations.
:param project_name: Folder name where the computations
are going to be stored.
:param geometry:string containing the molecular geometry.
:param package_args: Specific settings for the package
:param guess_args: Specific settings for guess calculate with `package`.
:type package_args: dict
:param initial_states: List of the initial Electronic states.
:type initial_states: [Int]
:param final_states: List containing the sets of possible electronic
states.
:type final_states: [[Int]]
:param calc_new_wf_guess_on_points: Points where the guess wave functions
are calculated.
:param package_config: Parameters required by the Package.
:param convolution: gaussian | lorentzian
:param calculate_oscillator_every: step to compute the oscillator strengths
:returns: None
"""
# Start logging event
file_log = '{}.log'.format(project_name)
logging.basicConfig(filename=file_log,
level=logging.DEBUG,
format='%(levelname)s:%(message)s %(asctime)s\n',
datefmt='%m/%d/%Y %I:%M:%S %p')
# Point calculations Using CP2K
mo_paths_hdf5 = calculate_mos(package_name,
geometries,
project_name,
path_hdf5,
traj_folders,
package_args,
guess_args,
calc_new_wf_guess_on_points,
enumerate_from,
package_config=package_config)
# geometries in atomic units
molecules_au = [
change_mol_units(parse_string_xyz(gs)) for gs in geometries
]
# Construct initial and final states ranges
initial_states, final_states = build_transitions(initial_states,
final_states, nHOMO)
# Schedule the function the compute the Oscillator Strenghts
scheduleOscillator = schedule(calcOscillatorStrenghts)
oscillators = gather(*[
scheduleOscillator(i,
project_name,
mo_paths_hdf5,
dictCGFs,
mol,
path_hdf5,
hdf5_trans_mtx=hdf5_trans_mtx,
initial_states=initial_states,
final_states=final_states)
for i, mol in enumerate(molecules_au)
if i % calculate_oscillator_every == 0
])
energies, promised_cross_section = create_promised_cross_section(
oscillators, broadening, energy_range, convolution,
calculate_oscillator_every)
cross_section, data = run(gather(promised_cross_section, oscillators),
folder=work_dir)
# Transform the energy to nm^-1
energies_nm = energies * 1240
# Save cross section
np.savetxt(
'cross_section_cm.txt',
np.stack((energies, energies_nm, cross_section, cross_section * 1e16),
axis=1),
header=
'Energy[eV] Energy[nm^-1] photoabsorption_cross_section[cm^2] photoabsorption_cross_section[^2]'
)
# molar extinction coefficients (e in M-1 cm-1)
nA = physical_constants['Avogadro constant'][0]
cte = np.log(10) * 1e3 / nA
extinction_coefficients = cross_section / cte
np.savetxt(
'molar_extinction_coefficients.txt',
np.stack((energies, energies_nm, extinction_coefficients), axis=1),
header='Energy[eV] Energy[nm^-1] Extinction_coefficients[M^-1 cm^-1]')
print("Data: ", data)
print("Calculation Done")
# Write data in human readable format
write_information(data)
return data