From 31e56cb7b84f9a375d58c96057a2a94f9af1a27c Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Mon, 3 Aug 2020 14:16:34 +0200
Subject: [PATCH] Make workflow information searchable.
---
vaspparser/parser_vasprun.py | 99 +++++++++++++++++++-----------------
1 file changed, 51 insertions(+), 48 deletions(-)
diff --git a/vaspparser/parser_vasprun.py b/vaspparser/parser_vasprun.py
index 178a438..9b281b1 100644
--- a/vaspparser/parser_vasprun.py
+++ b/vaspparser/parser_vasprun.py
@@ -35,7 +35,7 @@ from nomad.datamodel.metainfo.public import section_run as msection_run
from nomad.datamodel.metainfo.public import section_method as msection_method
from nomad.datamodel.metainfo.public import section_sampling_method as msection_sampling_method
from nomad.datamodel.metainfo.public import section_frame_sequence as msection_frame_sequence
-from nomad.datamodel.metainfo.public import section_workflow as msection_workflow
+from nomad.datamodel.metainfo.public import Workflow
from nomad.datamodel.metainfo.public import section_single_configuration_calculation as msection_single_configuration_calculation
from nomad.datamodel.metainfo.public import section_basis_set as msection_basis_set
from nomad.datamodel.metainfo.public import section_XC_functionals as msection_XC_functionals
@@ -176,10 +176,10 @@ class VasprunContext(object):
self._parser = name
def on_end_generator(self, element, path_str):
- root_section = self.parser.root_section
+ run = self.parser.run
program_name = g(element, "i/[@name='program']")
if program_name.strip().upper() == 'VASP':
- root_section.program_name = 'VASP'
+ run.program_name = 'VASP'
else:
raise Exception('unexpected program name: %s' % program_name)
@@ -189,9 +189,9 @@ class VasprunContext(object):
g(element, "i/[@name='platform']", ""))
if not version.isspace():
- root_section.program_version = version
+ run.program_version = version
- root_section.program_basis_set_type = "plane waves"
+ run.program_basis_set_type = "plane waves"
date = g(element, "i/[@name='date']")
pdate = None
time = g(element, "i/[@name='time']")
@@ -202,7 +202,7 @@ class VasprunContext(object):
pdate = datetime.combine(pdate.date(), datetime.strptime(
time.strip(), "%H:%M:%S").timetz())
if pdate:
- root_section.program_compilation_datetime = seconds_from_epoch(pdate)
+ run.program_compilation_datetime = seconds_from_epoch(pdate)
for i in element:
if i.tag != "i" or not i.attrib.get("name") in set(
[
@@ -211,9 +211,9 @@ class VasprunContext(object):
pass
def on_end_incar(self, element, path_str):
- root_section = self.parser.root_section
+ run = self.parser.run
m_env = self.parser.metainfo_env
- section_method = root_section.m_create(msection_method)
+ section_method = run.m_create(msection_method)
dft_plus_u = False
ibrion = None
nsw = 0
@@ -299,7 +299,7 @@ class VasprunContext(object):
section_method.electronic_structure_method = 'DFT+U' if dft_plus_u else 'DFT'
def on_end_kpoints(self, element, path_str):
- root_section = self.parser.root_section
+ run = self.parser.run
self.bands = None
self.kpoints = None
self.weights = None
@@ -307,7 +307,7 @@ class VasprunContext(object):
if el.tag == "generation":
param = el.attrib.get("param", None) # eg. listgenerated, Monkhorst-Pack, Gamma
if param:
- root_section.section_method[-1].x_vasp_k_points_generation_method = param
+ run.section_method[-1].x_vasp_k_points_generation_method = param
if param == "listgenerated":
# This implies a path on k-space, potentially a bandstructure calculation
# Save k-path info into a dictionary
@@ -326,13 +326,13 @@ class VasprunContext(object):
name = el.attrib.get("name", None)
if name == "kpointlist":
self.kpoints = np.asarray(get_vector(el))
- root_section.section_method[-1].k_mesh_points = self.kpoints
+ run.section_method[-1].k_mesh_points = self.kpoints
elif name == "weights":
self.weights = np.asarray(get_vector(el))
- root_section.section_method[-1].k_mesh_weights = self.weights.flatten()
+ run.section_method[-1].k_mesh_weights = self.weights.flatten()
elif name == "tetrahedronlist":
self.tetrahedrons = np.asarray(get_vector(el), dtype=np.int)
- root_section.section_method[-1].x_vasp_tetrahedrons_list = self.tetrahedrons
+ run.section_method[-1].x_vasp_tetrahedrons_list = self.tetrahedrons
else:
self.logger.warn("Unknown array %s in kpoints" % name)
elif el.tag == "i":
@@ -344,13 +344,13 @@ class VasprunContext(object):
vol_cubic_angs = float(el.text.strip())
vol_cubic_meters = ang2m(ang2m(ang2m(vol_cubic_angs)))
- root_section.section_method[-1].x_vasp_tetrahedron_volume = vol_cubic_meters
+ run.section_method[-1].x_vasp_tetrahedron_volume = vol_cubic_meters
else:
self.logger.pwarn("Unknown tag %s in kpoints" % el.tag)
def on_end_structure(self, element, path_str):
- root_section = self.parser.root_section
- section_system = root_section.m_create(msection_system)
+ run = self.parser.run
+ section_system = run.m_create(msection_system)
self.cell = None
for el in element:
if (el.tag == "crystal"):
@@ -399,7 +399,7 @@ class VasprunContext(object):
def on_end_eigenvalues(self, element, path_str):
if path_str != "modeling/calculation/eigenvalues":
return True
- root_section = self.parser.root_section
+ run = self.parser.run
eigenvalues = None
occupation = None
for el in element:
@@ -458,11 +458,11 @@ class VasprunContext(object):
ebMinE[ispin] = ebMinK
self.vbTopE = vbTopE
self.ebMinE = ebMinE
- root_section.section_single_configuration_calculation[-1].energy_reference_highest_occupied = np.array(vbTopE)
- root_section.section_single_configuration_calculation[-1].energy_reference_lowest_unoccupied = np.array(ebMinE)
+ run.section_single_configuration_calculation[-1].energy_reference_highest_occupied = np.array(vbTopE)
+ run.section_single_configuration_calculation[-1].energy_reference_lowest_unoccupied = np.array(ebMinE)
if self.bands:
divisions = int(self.bands['divisions'])
- section_k_band = root_section.section_single_configuration_calculation[-1].m_create(msection_k_band)
+ section_k_band = run.section_single_configuration_calculation[-1].m_create(msection_k_band)
nsegments = self.kpoints.shape[0] // divisions
kpt = np.reshape(
self.kpoints, (nsegments, divisions, 3))
@@ -479,7 +479,7 @@ class VasprunContext(object):
section_k_band_segment.band_segm_start_end = np.asarray(
[kpt[isegment, 0], kpt[isegment, divisions - 1]])
- section_k_band_normalized = root_section.section_single_configuration_calculation[-1].m_create(msection_k_band_normalized)
+ section_k_band_normalized = run.section_single_configuration_calculation[-1].m_create(msection_k_band_normalized)
for isegment in range(nsegments):
section_k_band_segment_normalized = section_k_band_normalized.m_create(msection_k_band_segment_normalized)
section_k_band_segment_normalized.band_energies_normalized = energies[:, isegment, :, :] - max(self.vbTopE)
@@ -489,36 +489,36 @@ class VasprunContext(object):
[kpt[isegment, 0], kpt[isegment, divisions - 1]])
else:
- section_eigenvalues = root_section.section_single_configuration_calculation[-1].m_create(msection_eigenvalues)
+ section_eigenvalues = run.section_single_configuration_calculation[-1].m_create(msection_eigenvalues)
section_eigenvalues.eigenvalues_values = ev
section_eigenvalues.eigenvalues_occupation = occupation
else:
self.logger.warn("unexpected tag %s in the eigenvalues" % el.tag)
def on_start_calculation(self, element, path_str):
- root_section = self.parser.root_section
- sscc = root_section.m_create(msection_single_configuration_calculation)
+ run = self.parser.run
+ sscc = run.m_create(msection_single_configuration_calculation)
if self.waveCut:
section_basis_set = sscc.m_create(msection_basis_set)
section_basis_set.mapping_section_basis_set_cell_dependent = self.waveCut
def on_end_modeling(self, element, path_str):
- root_section = self.parser.root_section
- root_section.section_method[-1].x_vasp_unknown_incars = self.unknown_incars
+ run = self.parser.run
+ run.section_method[-1].x_vasp_unknown_incars = self.unknown_incars
if self.ibrion is None or self.ibrion == -1:
return
- section_sampling_method = root_section.m_create(msection_sampling_method)
+ section_sampling_method = run.m_create(msection_sampling_method)
if self.ibrion == 0:
sampling_method = "molecular_dynamics"
else:
sampling_method = "geometry_optimization"
section_sampling_method.sampling_method = sampling_method
- section_frame_sequence = root_section.m_create(msection_frame_sequence)
+ section_frame_sequence = run.m_create(msection_frame_sequence)
section_frame_sequence.frame_sequence_to_sampling_ref = section_sampling_method
- section_frame_sequence.frame_sequence_local_frames_ref = root_section.section_single_configuration_calculation[-1]
- section_workflow = root_section.m_create(msection_workflow)
+ section_frame_sequence.frame_sequence_local_frames_ref = run.section_single_configuration_calculation[-1]
+ section_workflow = self.parser.archive.m_create(Workflow)
section_workflow.workflow_type = sampling_method
- section_workflow.workflow_final_calculation_ref = root_section.section_single_configuration_calculation[-1]
+ section_workflow.workflow_final_calculation_ref = run.section_single_configuration_calculation[-1]
if len(self._energies) > 1:
delta_energy = abs(self._energies[-1] - self._energies[-2])
section_workflow.relaxation_energy_tolerance = delta_energy
@@ -527,10 +527,10 @@ class VasprunContext(object):
e_conv = eV2J
f_conv = convert_unit_function("eV/angstrom", "N")
p_conv = convert_unit_function("eV/angstrom^3", "Pa")
- root_section = self.parser.root_section
- sscc = root_section.section_single_configuration_calculation[-1]
- sscc.single_configuration_calculation_to_system_ref = root_section.section_system[-1]
- sscc.single_configuration_to_calculation_method_ref = root_section.section_method[-1]
+ run = self.parser.run
+ sscc = run.section_single_configuration_calculation[-1]
+ sscc.single_configuration_calculation_to_system_ref = run.section_system[-1]
+ sscc.single_configuration_to_calculation_method_ref = run.section_method[-1]
for el in element:
if el.tag == "energy":
for en_el in el:
@@ -556,7 +556,7 @@ class VasprunContext(object):
sscc.stress_tensor = f
def on_end_atominfo(self, element, path_str):
- root_section = self.parser.root_section
+ run = self.parser.run
atom_types = []
labels = []
labels2 = None
@@ -625,7 +625,7 @@ class VasprunContext(object):
n_el = {}
kind_labels = []
for atom_desc in atom_types_desc:
- section_method_atom_kind = root_section.section_method[-1].m_create(msection_method_atom_kind)
+ section_method_atom_kind = run.section_method[-1].m_create(msection_method_atom_kind)
if 'element' in atom_desc:
elName = atom_desc['element'].strip()
try:
@@ -647,7 +647,7 @@ class VasprunContext(object):
section_method_atom_kind.method_atom_kind_explicit_electrons = atom_desc["valence"]
if "pseudopotential" in atom_desc:
section_method_atom_kind.method_atom_kind_pseudopotential_name = atom_desc["pseudopotential"]
- root_section.section_method[-1].x_vasp_atom_kind_refs = root_section.section_method[-1].section_method_atom_kind
+ run.section_method[-1].x_vasp_atom_kind_refs = run.section_method[-1].section_method_atom_kind
labels2 = [kind_labels[i - 1] for i in atom_types]
else:
self.logger.warn(
@@ -674,7 +674,7 @@ class VasprunContext(object):
self.logger.warn("unexpected tag %s %s %r in incar" % (el.tag, el.attrib, el.text))
else:
- root_section = self.parser.root_section
+ run = self.parser.run
name = el.attrib.get("name", None)
val_type = el.attrib.get("type")
try:
@@ -729,12 +729,12 @@ class VasprunContext(object):
(metainfo_type, meta))
elif shape:
vals = re.split(r"\s+", el.text.strip())
- setattr(root_section.section_method[-1], meta["name"], [converter(x) for x in vals])
+ setattr(run.section_method[-1], meta["name"], [converter(x) for x in vals])
else:
# If-block to handle incars without value
if not el.text:
el.text = ''
- setattr(root_section.section_method[-1], meta["name"], converter(el.text))
+ setattr(run.section_method[-1], meta["name"], converter(el.text))
except Exception:
self.logger.warn("Exception trying to handle incarOut %s: %s" % (
@@ -762,7 +762,7 @@ class VasprunContext(object):
self.logger.warn("Unknown XC functional %s" % el.text.strip())
else:
for f in functs:
- section_XC_functionals = root_section.section_method[-1].m_create(msection_XC_functionals)
+ section_XC_functionals = run.section_method[-1].m_create(msection_XC_functionals)
section_XC_functionals.XC_functional_name = f
elif name == "ISPIN":
self.ispin = int(el.text.strip())
@@ -784,15 +784,15 @@ class VasprunContext(object):
def on_end_parameters(self, element, path_str):
self._separator_scan(element)
- root_section = self.parser.root_section
+ run = self.parser.run
try:
self.prec
try:
self.enmax
- self.waveCut = root_section.m_create(msection_basis_set_cell_dependent)
+ self.waveCut = run.m_create(msection_basis_set_cell_dependent)
self.waveCut.basis_set_planewave_cutoff = eV2J(self.enmax * self.prec)
- section_method_basis_set = root_section.section_method[-1].m_create(msection_method_basis_set)
+ section_method_basis_set = run.section_method[-1].m_create(msection_method_basis_set)
section_method_basis_set.mapping_section_method_basis_set_cell_associated = self.waveCut
except AttributeError:
import traceback
@@ -805,8 +805,8 @@ class VasprunContext(object):
def on_end_dos(self, element, path_str):
"density of states"
- root_section = self.parser.root_section
- section_dos = root_section.section_single_configuration_calculation[-1].m_create(msection_dos)
+ run = self.parser.run
+ section_dos = run.section_single_configuration_calculation[-1].m_create(msection_dos)
for el in element:
if el.tag == "i":
if el.attrib.get("name") == "efermi":
@@ -953,6 +953,8 @@ class XmlParser(object):
self.path = []
self.tagSections = {}
self.metainfo_env = metainfo_env
+ self.run = None
+ self.archive = None
def parse(self, main_file_uri, f_in, archive):
if self.path:
@@ -960,7 +962,8 @@ class XmlParser(object):
"Parse of %s called with non empty path, parse already in progress?" % main_file_uri)
self.main_file_uri = main_file_uri
self.f_in = f_in
- self.root_section = archive.m_create(msection_run)
+ self.archive = archive
+ self.run = archive.m_create(msection_run)
self.super_context.parser = self
# there are invalid characters like esc in the files, we do not want to crash on them
xml_parser = MyXMLParser()
--
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