def main(pdb_path, splitAt, work_dir):
monomers = create_monomers(pdb_path, splitAt, work_dir)
settings = Settings()
settings.basis = "DZP"
# settings.functional = "CAMY-B3LYP"
settings.specific.adf.basis.core = "None"
settings.specific.adf.symmetry = "Nosym"
settings.specific.adf.xc.hybrid = "CAMY-B3LYP"
settings.specific.adf.xc.xcfun = ""
fde_settings = Settings()
# fde_settings.functional = "camy-b3lyp"
fde_settings.specific.adf.xc.hybrid = "CAMY-B3LYP"
fde_settings.specific.adf.xc.xcfun = ""
fde_settings.basis = "DZP"
fde_settings.specific.adf.symmetry = "Nosym"
fde_settings.specific.adf.fde.PW91k = ""
fde_settings.specific.adf.fde.fullgrid = ""
fde_settings.specific.adf.allow = "Partialsuperfrags"
fde_settings.specific.adf.fde.GGAPOTXFD = "Becke"
fde_settings.specific.adf.fde.GGAPOTCFD = "LYP"
# Read input from molfiles
jobs = chain(*list(
map(lambda xs: create_jobs(settings, fde_settings, *xs),
enumerate(monomers))))
run(gather(*jobs), n_processes=2)
def test_opt_orca():
"""
Test Orca input generation and run functions.
"""
h2o = Molecule('test/test_files/h2o.xyz', 'xyz', charge=0, multiplicity=1)
h2o_geometry = dftb(templates.geometry, h2o)
s = Settings()
# generic keyword "basis" must be present in the generic dictionary
s.basis = "sto_dzp"
# "specific" allows the user to apply specific keywords for a
# package that are not in a generic dictionary
# s.specific.adf.basis.core = "large"
r = templates.singlepoint.overlay(s)
h2o_singlepoint = orca(r, h2o_geometry.molecule)
dipole = h2o_singlepoint.dipole
final_result = run(dipole, n_processes=1)
expected_dipole = [0.82409, 0.1933, -0.08316]
diff = sqrt(sum((x - y)**2 for x, y in zip(final_result, expected_dipole)))
print("Expected dipole computed with Orca 3.0.3 is:", expected_dipole)
print("Actual dipole is:", final_result)
assert diff < 1e-2
def cp2k_input(range_orbitals,
cell_parameters,
cell_angles,
added_mos,
basis="DZVP-MOLOPT-SR-GTH",
potential="GTH-PBE"):
"""
# create ``Settings`` for the Cp2K Jobs.
"""
# Main Cp2k Jobs
cp2k_args = Settings()
cp2k_args.basis = fun_format(basis)
cp2k_args.potential = fun_format(potential)
cp2k_args.cell_parameters = cell_parameters
cp2k_args.cell_angles = cell_angles
main_dft = cp2k_args.specific.cp2k.force_eval.dft
main_dft.scf.added_mos = added_mos
main_dft.scf.max_scf = 40
main_dft.scf.eps_scf = 5e-4
main_dft['print']['mo']['mo_index_range'] = '"{} {}"'.format(
*range_orbitals)
cp2k_args.specific.cp2k.force_eval.subsys.cell.periodic = fun_format(
'None')
# Setting to calculate the wave function used as guess
cp2k_OT = Settings()
cp2k_OT.basis = fun_format(basis)
cp2k_OT.potential = fun_format(potential)
cp2k_OT.cell_parameters = cell_parameters
cp2k_OT.cell_angles = cell_angles
ot_dft = cp2k_OT.specific.cp2k.force_eval.dft
ot_dft.scf.scf_guess = fun_format('atomic')
ot_dft.scf.ot.minimizer = fun_format('DIIS')
ot_dft.scf.ot.n_diis = 7
ot_dft.scf.ot.preconditioner = fun_format('FULL_SINGLE_INVERSE')
ot_dft.scf.added_mos = 0
ot_dft.scf.eps_scf = 1e-06
ot_dft.scf.scf_guess = fun_format('restart')
cp2k_OT.specific.cp2k.force_eval.subsys.cell.periodic = fun_format('None')
return cp2k_args, cp2k_OT
def main():
# Current Work Directory
cwd = os.getcwd()
# ========== Fill in the following variables
# Varaible to define the Path ehere the Cp2K jobs will be computed
scratch = "/path/to/scratch"
project_name = 'My_awesome_project' # name use to create folders
# Path to the basis set used by Cp2k
basisCP2K = "/Path/to/CP2K/BASIS_MOLOPT"
potCP2K = "/Path/to/CP2K/GTH_POTENTIALS"
path_to_trajectory = 'Path/to/trajectory/in/XYZ'
# Number of MO used to compute the coupling
nHOMO = None
couplings_range = None
# Basis
basis = "DZVP-MOLOPT-SR-GTH"
# Algorithm to compute the NAC
algorithm = 'levine'
# Integation step used for the dynamics (femtoseconds)
dt = 1
# ============== End of User definitions ===================================
cp2k_args = Settings()
cp2k_args.basis = basis
# Results folder
results_dir = join(cwd, 'total_results')
if not os.path.exists(results_dir):
os.mkdir(results_dir)
# Merge all the HDF5 files
file_hdf5 = merge_hdf5(scratch, project_name, cwd, results_dir)
# compute missing couplings
script_name = "merge_data.py"
write_python_script(scratch, 'total_results', path_to_trajectory,
project_name, basisCP2K, potCP2K, cp2k_args,
Settings(), 0, script_name, file_hdf5, nHOMO,
couplings_range, algorithm, dt)
# Script using SLURM
write_slurm_script(scratch, results_dir, script_name)
def test_linear_ts():
"""
compute a first approximation to the TS.
"""
# Read the Molecule from file
cnc = Molecule('test/test_files/C-N-C.mol', 'mol')
# User define Settings
settings = Settings()
settings.functional = "pbe"
settings.basis = "SZ"
settings.specific.dftb.dftb.scc
constraint1 = Distance(0, 4)
constraint2 = Distance(2, 3)
# scan input
pes = PES(cnc,
constraints=[constraint1, constraint2],
offset=[2.3, 2.3],
get_current_values=False,
nsteps=2,
stepsize=[0.1, 0.1])
# returns a set of results object containing the output of
# each point in the scan
lt = pes.scan([dftb, adf], settings)
# Gets the object presenting the molecule
# with the maximum energy calculated from the scan
apprTS = select_max(lt, "energy")
# Run the TS optimization, using the default TS template
ts = run(apprTS)
expected_energy = -3.219708290363864
assert abs(ts.energy - expected_energy) < 0.02
def bond_distance(r1, r2):
return sqrt(sum((x - y)**2 for x, y in zip(r1, r2)))
# ========== =============
plams.init()
# Read the Molecule from file
cnc = Molecule('C-N-C.mol', 'mol')
# User define Settings
settings = Settings()
settings.functional = "pbe"
settings.basis = "TZ2P"
settings.specific.dftb.dftb.scc
constraint1 = "dist 1 5"
constraint2 = "dist 3 4"
# scan input
scan = {
'constraint': [constraint1, constraint2],
'surface': {
'nsteps': 6,
'start': [2.3, 2.3],
'stepsize': [0.1, 0.1]
}
}
# ----------------------------------------------------------------
plams.init()
# Read the Molecule from file
m_h2o_1 = Molecule('FDE-H2O-1.xyz')
m_h2o_2 = Molecule('FDE-H2O-2.xyz')
m_mol = Molecule('FDE-mol.xyz')
m_tot = m_mol + m_h2o_1 + m_h2o_2
print(m_tot)
settings = Settings()
settings.basis = 'SZ'
settings.specific.adf.nosymfit = ''
# Prepare first water molecule
r_h2o_1 = adf(templates.singlepoint.overlay(settings), m_h2o_1, job_name="h2o_1")
# Prepare second water molecule
r_h2o_2 = adf(templates.singlepoint.overlay(settings), m_h2o_2, job_name="h2o_2")
frozen_frags = [Fragment(r_h2o_1, [m_h2o_1]),
Fragment(r_h2o_2, [m_h2o_2])]
fde_res = run(fragmentsjob(settings, m_mol, *frozen_frags))
print(fde_res.dipole)
def fun_ethylene(scratch_path):
"""
Test Ethylene singlw
"""
project_name = 'ethylene'
# create Settings for the Cp2K Jobs
s = Settings()
s.basis = "DZVP-MOLOPT-SR-GTH"
s.potential = "GTH-PBE"
s.cell_parameters = [12.74] * 3
dft = s.specific.cp2k.force_eval.dft
dft.scf.added_mos = 20
dft.scf.eps_scf = 1e-4
dft['print']['ao_matrices']['overlap'] = ''
dft['print']['ao_matrices']['filename'] = join(scratch_path, 'overlap.out')
# Copy the basis and potential to a tmp file
shutil.copy('test/test_files/BASIS_MOLOPT', scratch_path)
shutil.copy('test/test_files/GTH_POTENTIALS', scratch_path)
# Cp2k configuration files
basiscp2k = join(scratch_path, 'BASIS_MOLOPT')
potcp2k = join(scratch_path, 'GTH_POTENTIALS')
cp2k_config = {"basis": basiscp2k, "potential": potcp2k}
# HDF5 path
path_hdf5 = join(scratch_path, 'ethylene.hdf5')
# all_geometries type :: [String]
path_xyz = 'test/test_files/ethylene.xyz'
geometries = split_file_geometries(path_xyz)
# Input/Output Files
file_xyz = join(scratch_path, 'coordinates.xyz')
file_inp = join(scratch_path, 'ethylene.inp')
file_out = join(scratch_path, 'ethylene.out')
file_MO = join(scratch_path, 'mo_coeffs.out')
files = JobFiles(file_xyz, file_inp, file_out, file_MO)
schedule_job = schedule(prepare_job_cp2k)
promise = schedule_job(geometries[0],
files,
s,
scratch_path,
project_name=project_name,
hdf5_file=path_hdf5,
wfn_restart_job=None,
store_in_hdf5=True,
nHOMOS=25,
nLUMOS=25,
package_config=cp2k_config)
cp2k_result = run(promise)
path_properties = cp2k_result.orbitals
with h5py.File(path_hdf5) as f5:
assert (all(p in f5 for p in path_properties))