from scm.plams.core.basejob import SingleJob
from scm.plams.core.results import Results
from scm.plams.core.settings import Settings
from scm.plams.core.functions import requires_optional_package
from scm.plams.mol.molecule import Molecule
from scm.plams.tools.units import Units
from pathlib import Path
import numpy as np
import h5py
import shutil
import os
__all__ = ["SerenityJob", "SerenityResults", "SerenitySettings"]
class SerenitySettings(Settings):
"""A Subclass of the Settings class to set the iteration order through keys."""
def __iter__(self):
"""Iteration through keys follows insertion order instead of lexicographical order."""
return iter(self.keys())
[docs]class SerenityResults(Results):
"""A Subclass of the Results class to access the results given in the Serenity output. Can be extended as required."""
def _get_energy_type(self, search="Total Energy", index=-1, unit="a.u."):
s = self.grep_output(search)
s = [item for item in s if not "..." in item]
s = s[index]
def convert_with_fallback(item):
try:
return float(item.split()[-1])
except ValueError:
try:
return float(item.split()[-2])
except ValueError:
raise ValueError("Can not convert type to float.")
if not isinstance(index, slice):
return Units.convert(convert_with_fallback(s), "a.u.", unit)
else:
return [Units.convert(convert_with_fallback(x), "a.u.", unit) for x in s]
[docs] def get_energy(self, index=-1, unit="a.u."):
"""Returns 'Total Energy (DFT)/(HF):' from the output file. Set ``index`` to choose the n-th occurence of the total energy in the output. Defaults to the last occurence."""
return self._get_energy_type("Total Energy", index=index, unit=unit)
[docs] def get_ccsd_energy_correction(self, index=-1, unit="a.u."):
"""Returns the 'CCSD Energy Correction' from the output file. Set ``index`` to choose the n-th occurrence of the CCSD energy correction in the output. Defaults to the last occurrence."""
return self._get_energy_type("CCSD Energy Correction", index=index, unit=unit)
def get_triples_energy_correction(self, index=-1, unit="a.u."):
return self._get_energy_type("Triples Energy Correction", index=index, unit=unit)
def get_local_ccsd_energy(self, index=-1, unit="a.u."):
return self._get_energy_type("Total Local-CCSD Energy", index=index, unit=unit)
[docs]class SerenityJob(SingleJob):
"""A Subclass of the SingleJob class representing a computational job with Serenity."""
_result_type = SerenityResults
def _get_ready(self):
"""If molecule is defined, xyz files are generated accordingly. If there is data to transfer between ADF and Serenity, file formats are converted."""
super()._get_ready()
if isinstance(self.molecule, dict):
for name, mol in self.molecule.items():
mol.write(os.path.join(self.path, f"{name}.xyz"))
elif isinstance(self.molecule, Molecule):
self.molecule.write(os.path.join(self.path, "mol.xyz"))
base_path = Path(self.path).parent
ams_job_dirs = [
d for d in base_path.iterdir() if d.is_dir() and any(f.startswith("SerenityAMS") for f in os.listdir(d))
]
if ams_job_dirs:
self._translate_AMSJob_to_Serenity(ams_job_dirs[0]) # Processes the first matching directory
return
@requires_optional_package("h5py")
def _translate_AMSJob_to_Serenity(self, AMSJob_folder):
def convert_to_HDF5(binary_file, hdf5_file, dataset_name, shape=None):
hdf5_file_path = Path(self.path) / hdf5_file
data = np.fromfile(str(binary_file), dtype=np.float64)
if shape:
data = data.reshape(shape)
with h5py.File(str(hdf5_file_path), "w") as h5file:
h5file.create_dataset(dataset_name, data=data, dtype="float64")
n_basis_func_file_source = AMSJob_folder / "SerenityAMS.nBasisFunc.txt"
n_basis_func_file_dest = Path(self.path) / "SerenityAMS.nBasisFunc.txt"
shutil.copy(n_basis_func_file_source, n_basis_func_file_dest)
with open(n_basis_func_file_dest, "r") as file:
dim_size = int(file.readline().strip())
convert_to_HDF5(
AMSJob_folder / "SerenityAMS.ERIs.bin",
"SerenityAMS.ERIs.h5",
"ERIs",
(dim_size, dim_size, dim_size, dim_size),
)
convert_to_HDF5(AMSJob_folder / "SerenityAMS.orbEnergies.bin", "SerenityAMS.orbEnergies.h5", "orbitalEnergies")
[docs] def get_runscript(self):
"""Returned runscript: ``serenity myinput.in |tee ser_myinput.out`` or ``serenity myinput.in``"""
input_file = self._filename("inp")
# output_file = self._filename("out")
# return 'serenity {} |tee ser_{}'.format(input_file, output_file)
return "serenity {}".format(input_file)
