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Merge pull request #1223 from pyiron/spx_other_parsers
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SPHInX: Separate other output parsers
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@samwaseda
samwaseda authored Nov 29, 2023
2 parents 4d36d6b + 7fc647f commit a66edac
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Showing 2 changed files with 218 additions and 99 deletions.
156 changes: 60 additions & 96 deletions pyiron_atomistics/sphinx/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,15 @@
)
from pyiron_atomistics.sphinx.structure import read_atoms
from pyiron_atomistics.sphinx.potential import SphinxJTHPotentialFile
from pyiron_atomistics.sphinx.output_parser import SphinxLogParser, splitter
from pyiron_atomistics.sphinx.output_parser import (
SphinxLogParser,
collect_energy_dat,
collect_residue_dat,
collect_spins_dat,
collect_relaxed_hist,
collect_energy_struct,
collect_eps_dat,
)
from pyiron_atomistics.sphinx.potential import (
find_potential_file as find_potential_file_jth,
)
Expand Down Expand Up @@ -2133,7 +2141,7 @@ def __init__(self, job):
self.generic.create_group("dft")
self.old_version = False

def collect_spins_dat(self, file_name="spins.dat", cwd=None):
def collect_spins_dat(self, file_name="spins.dat", cwd="."):
"""
Args:
Expand All @@ -2143,14 +2151,16 @@ def collect_spins_dat(self, file_name="spins.dat", cwd=None):
Returns:
"""
if not os.path.isfile(posixpath.join(cwd, file_name)):
return None
spins = np.loadtxt(posixpath.join(cwd, file_name))
self.generic.dft.atom_scf_spins = splitter(
np.array([ss[self._job.id_spx_to_pyi] for ss in spins[:, 1:]]), spins[:, 0]
)
try:
results = collect_spins_dat(
file_name=file_name, cwd=cwd, index_permutation=self._job.id_spx_to_pyi
)
except FileNotFoundError:
return
for k, v in results.items():
self.generic.dft[k] = v

def collect_energy_dat(self, file_name="energy.dat", cwd=None):
def collect_energy_dat(self, file_name="energy.dat", cwd="."):
"""
Args:
Expand All @@ -2160,26 +2170,14 @@ def collect_energy_dat(self, file_name="energy.dat", cwd=None):
Returns:
"""
if not os.path.isfile(posixpath.join(cwd, file_name)):
return None
energies = np.loadtxt(posixpath.join(cwd, file_name))
self.generic.dft.scf_computation_time = splitter(energies[:, 1], energies[:, 0])
self.generic.dft.scf_energy_int = splitter(
energies[:, 2] * HARTREE_TO_EV, energies[:, 0]
)

def en_split(e, counter=energies[:, 0]):
return splitter(e * HARTREE_TO_EV, counter)

if len(energies[0]) == 7:
self.generic.dft.scf_energy_free = en_split(energies[:, 3])
self.generic.dft.scf_energy_zero = en_split(energies[:, 4])
self.generic.dft.scf_energy_band = en_split(energies[:, 5])
self.generic.dft.scf_electronic_entropy = en_split(energies[:, 6])
else:
self.generic.dft.scf_energy_band = en_split(energies[:, 3])
try:
results = collect_energy_dat(file_name=file_name, cwd=cwd)
except FileNotFoundError:
return
for k, v in results.items():
self.generic.dft[k] = v

def collect_residue_dat(self, file_name="residue.dat", cwd=None):
def collect_residue_dat(self, file_name="residue.dat", cwd="."):
"""
Args:
Expand All @@ -2189,17 +2187,14 @@ def collect_residue_dat(self, file_name="residue.dat", cwd=None):
Returns:
"""
if not os.path.isfile(posixpath.join(cwd, file_name)):
return None
residue = np.loadtxt(posixpath.join(cwd, file_name))
if len(residue) == 0:
return None
if len(residue[0]) == 2:
self.generic.dft.scf_residue = splitter(residue[:, 1], residue[:, 0])
else:
self.generic.dft.scf_residue = splitter(residue[:, 1:], residue[:, 0])
try:
results = collect_residue_dat(file_name=file_name, cwd=cwd)
except FileNotFoundError:
return
for k, v in results.items():
self.generic.dft[k] = v

def collect_eps_dat(self, file_name="eps.dat", cwd=None):
def collect_eps_dat(self, file_name=None, cwd="."):
"""
Args:
Expand All @@ -2209,17 +2204,15 @@ def collect_eps_dat(self, file_name="eps.dat", cwd=None):
Returns:
"""
if isinstance(file_name, str):
file_name = [file_name]
values = []
for f in file_name:
file_tmp = posixpath.join(cwd, f)
if not os.path.isfile(file_tmp):
return
values.append(np.loadtxt(file_tmp)[..., 1:])
values = np.stack(values, axis=0)
if "bands_eigen_values" not in self.generic.dft.list_nodes():
self.generic.dft.bands_eigen_values = values.reshape((-1,) + values.shape)
try:
results = collect_eps_dat(
file_name=file_name, cwd=cwd, spins=self._job._spin_enabled
)
for k, v in results.items():
if k not in self.generic.dft:
self.generic.dft[k] = v
except FileNotFoundError:
return

def collect_energy_struct(self, file_name="energy-structOpt.dat", cwd=None):
"""
Expand All @@ -2231,11 +2224,12 @@ def collect_energy_struct(self, file_name="energy-structOpt.dat", cwd=None):
Returns:
"""
file_name = posixpath.join(cwd, file_name)
if os.path.isfile(file_name):
self.generic.dft.energy_free = (
np.loadtxt(file_name).reshape(-1, 2)[:, 1] * HARTREE_TO_EV
)
try:
results = collect_energy_struct(file_name=file_name, cwd=cwd)
except FileNotFoundError:
return
for k, v in results.items():
self.generic.dft[k] = v

def collect_sphinx_log(self, file_name="sphinx.log", cwd="."):
"""
Expand Down Expand Up @@ -2271,7 +2265,7 @@ def collect_sphinx_log(self, file_name="sphinx.log", cwd="."):
self.generic.dft.scf_energy_int = self._spx_log_parser.get_energy_int()
if "scf_energy_free" not in self.generic.dft.list_nodes():
self.generic.dft.scf_energy_free = self._spx_log_parser.get_energy_free()
if "forces" in self.generic.list_nodes():
if "forces" not in self.generic.list_nodes():
self.generic.forces = self._spx_log_parser.get_forces(
index_permutation=self._job.id_spx_to_pyi
)
Expand All @@ -2292,41 +2286,14 @@ def collect_relaxed_hist(self, file_name="relaxHist.sx", cwd=None):
Returns:
"""
file_name = posixpath.join(cwd, file_name)
if not os.path.isfile(file_name):
return None
with open(file_name, "r") as f:
file_content = "".join(f.readlines())
natoms = len(self._job.id_spx_to_pyi)

def get_value(term, file_content=file_content, natoms=natoms):
value = (
np.array(
[
re.split("\[|\]", line)[1].split(",")
for line in re.findall(term, file_content, re.MULTILINE)
]
)
.astype(float)
.reshape(-1, natoms, 3)
)
return np.array([ff[self._job.id_spx_to_pyi] for ff in value])

self.generic.positions = get_value("coords.*$") * BOHR_TO_ANGSTROM
self.generic.forces = (
get_value("force.*$") * HARTREE_OVER_BOHR_TO_EV_OVER_ANGSTROM
)
self.generic.cells = (
np.array(
[
json.loads(line)
for line in re.findall(
"cell =(.*?);", file_content.replace("\n", ""), re.MULTILINE
)
]
try:
results = collect_relaxed_hist(
file_name=file_name, cwd=cwd, index_permutation=self._job.id_spx_to_pyi
)
* BOHR_TO_ANGSTROM
)
except FileNotFoundError:
return
for k, v in results.items():
self.generic[k] = v

def collect_charge_density(self, file_name, cwd):
if (
Expand Down Expand Up @@ -2364,23 +2331,20 @@ def _get_electronic_structure_object(self):
es.generate_from_matrices()
return es

def collect(self, directory=os.getcwd()):
def collect(self, directory=None):
"""
The collect function, collects all the output from a SPHInX simulation.
Args:
directory (str): the directory to collect the output from.
"""
if directory is None:
directory = self._job.working_directory
self.collect_energy_struct(file_name="energy-structOpt.dat", cwd=directory)
self.collect_sphinx_log(file_name="sphinx.log", cwd=directory)
self.collect_energy_dat(file_name="energy.dat", cwd=directory)
self.collect_residue_dat(file_name="residue.dat", cwd=directory)
if self._job._spin_enabled:
self.collect_eps_dat(file_name="eps.dat", cwd=directory)
else:
self.collect_eps_dat(
file_name=[f"eps.{i}.dat" for i in [0, 1]], cwd=directory
)
self.collect_eps_dat(file_name=None, cwd=directory)
self.collect_spins_dat(file_name="spins.dat", cwd=directory)
self.collect_relaxed_hist(file_name="relaxHist.sx", cwd=directory)
self.collect_electrostatic_potential(file_name="vElStat-eV.sxb", cwd=directory)
Expand Down
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