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Commit ede0f512 authored by Mohamed, Fawzi Roberto (fawzi)'s avatar Mohamed, Fawzi Roberto (fawzi)
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parser/parser-vasp/vaspparser/parser_vasprun.py
+ 36
− 33
View file @ ede0f512
...@@ -258,6 +258,7 @@ class VasprunContext(object): ...@@ -258,6 +258,7 @@ class VasprunContext(object):
self.eFermi = None self.eFermi = None
self.cell = None self.cell = None
self.angstrom_cell = None self.angstrom_cell = None
self.waveCut = None
sectionMap = { sectionMap = {
"modeling": ["section_run", "section_method"], "modeling": ["section_run", "section_method"],
...@@ -304,7 +305,7 @@ class VasprunContext(object): ...@@ -304,7 +305,7 @@ class VasprunContext(object):
if (el.tag != "i"): if (el.tag != "i"):
backend.pwarn("unexpected tag %s %s %r in incar" % (el.tag, el.attrib, el.text)) backend.pwarn("unexpected tag %s %s %r in incar" % (el.tag, el.attrib, el.text))
else: else:
name = el.attrib.get("name", None) name = el.attrib.get("name", None).lower()
meta = metaEnv['x_vasp_incar_' + name] meta = metaEnv['x_vasp_incar_' + name]
valType = el.attrib.get("type") valType = el.attrib.get("type")
if not meta: if not meta:
...@@ -330,7 +331,7 @@ class VasprunContext(object): ...@@ -330,7 +331,7 @@ class VasprunContext(object):
backend.addValue(meta["name"], [converter(x) for x in vals]) backend.addValue(meta["name"], [converter(x) for x in vals])
else: else:
backend.addValue(meta["name"], converter(el.text)) backend.addValue(meta["name"], converter(el.text))
if name == 'GGA': if name == 'gga':
fMap = { fMap = {
'91': ['GGA_X_PW91', 'GGA_C_PW91'], '91': ['GGA_X_PW91', 'GGA_C_PW91'],
'PE': ['GGA_X_PBE', 'GGA_C_PBE'], 'PE': ['GGA_X_PBE', 'GGA_C_PBE'],
...@@ -342,17 +343,17 @@ class VasprunContext(object): ...@@ -342,17 +343,17 @@ class VasprunContext(object):
backend.pwarn("Unknown XC functional %s" % el.text.strip()) backend.pwarn("Unknown XC functional %s" % el.text.strip())
else: else:
for f in functs: for f in functs:
backend.openNonOverlappingSection("section_XC_functionals") backend.openNonOverlappingSection("section_xc_functionals")
backend.addValue("XC_functional_name", f) backend.addValue("xc_functional_name", f)
backend.closeNonOverlappingSection("section_XC_functionals") backend.closeNonOverlappingSection("section_xc_functionals")
elif name == "ISPIN": elif name == "ispin":
self.ispin = int(el.text.strip()) self.ispin = int(el.text.strip())
elif name == "LDAU": elif name == "ldau":
if re.match(".?[Tt](?:[rR][uU][eE])?.?|[yY](?:[eE][sS])?|1", el.text.strip()): if re.match(".?[Tt](?:[rR][uU][eE])?.?|[yY](?:[eE][sS])?|1", el.text.strip()):
dft_plus_u = True dft_plus_u = True
elif name == "IBRION": elif name == "ibrion":
ibrion = int(el.text.strip()) ibrion = int(el.text.strip())
elif name == "NSW": elif name == "nsw":
nsw = int(el.text.strip()) nsw = int(el.text.strip())
if ibrion is None: if ibrion is None:
ibrion = -1 if nsw == 0 or nsw == 1 else 0 ibrion = -1 if nsw == 0 or nsw == 1 else 0
...@@ -437,8 +438,8 @@ class VasprunContext(object): ...@@ -437,8 +438,8 @@ class VasprunContext(object):
if pathStr != "modeling/calculation/eigenvalues": if pathStr != "modeling/calculation/eigenvalues":
return True return True
backend = parser.backend backend = parser.backend
eigenvalues = None eigenvalues = []
occupation = None occupation = []
for el in element: for el in element:
if el.tag == "array": if el.tag == "array":
for arrEl in el: for arrEl in el:
...@@ -456,27 +457,26 @@ class VasprunContext(object): ...@@ -456,27 +457,26 @@ class VasprunContext(object):
if kEl.tag == "set": if kEl.tag == "set":
ik += 1 ik += 1
bands = np.asarray(getVector(kEl, field = "r")) bands = np.asarray(getVector(kEl, field = "r"))
if eigenvalues is None: if len(eigenvalues) <= isp:
eigenvalues = np.zeros((self.ispin, self.kpoints.shape[0], bands.shape[0]), dtype = float) eigenvalues.append(np.zeros((self.kpoints.shape[0], bands.shape[0]), dtype = float))
occupation = np.zeros((self.ispin, self.kpoints.shape[0], bands.shape[0]), dtype = float) occupation.append(np.zeros((self.kpoints.shape[0], bands.shape[0]), dtype = float))
eigenvalues[isp, ik] = bands[:,0] eigenvalues[isp][ik] = bands[:,0]
occupation[isp, ik] = bands[:,1] occupation[isp][ik] = bands[:,1]
else: else:
backend.pwarn("unexpected tag %s in k array of the eigenvalues" % kEl.tag) backend.pwarn("unexpected tag %s in k array of the eigenvalues" % kEl.tag)
else: else:
backend.pwarn("unexpected tag %s in spin array of the eigenvalues" % spinEl.tag) backend.pwarn("unexpected tag %s in spin array of the eigenvalues" % spinEl.tag)
else: else:
backend.pwarn("unexpected tag %s in array of the eigenvalues" % arrEl.tag) backend.pwarn("unexpected tag %s in array of the eigenvalues" % arrEl.tag)
if eigenvalues is not None: if eigenvalues:
ev = eV2JV(np.array(eigenvalues))
ev = eV2JV(eigenvalues)
vbTopE = [] vbTopE = []
ebMinE = [] ebMinE = []
for ispin in range(occupation.shape[0]): for ispin in range(len(occupation)):
vbTopE.append(float('-inf')) vbTopE.append(float('-inf'))
ebMinE.append(float('inf')) ebMinE.append(float('inf'))
for ik in range(occupation.shape[1]): for ik in range(occupation[ispin].shape[0]):
ebIndex = bisect.bisect_right(-occupation[ispin, ik, :], -0.5) - 1 ebIndex = bisect.bisect_right(-occupation[ispin][ik, :], -0.5) - 1
vbTopIndex = ebIndex -1 vbTopIndex = ebIndex -1
if vbTopIndex >= 0: if vbTopIndex >= 0:
vbTopK = ev[ispin, ik, vbTopIndex] vbTopK = ev[ispin, ik, vbTopIndex]
...@@ -495,8 +495,9 @@ class VasprunContext(object): ...@@ -495,8 +495,9 @@ class VasprunContext(object):
backend.openNonOverlappingSection("section_k_band") backend.openNonOverlappingSection("section_k_band")
nsegments = self.kpoints.shape[0] // divisions nsegments = self.kpoints.shape[0] // divisions
kpt = np.reshape(self.kpoints, (nsegments, divisions, 3)) kpt = np.reshape(self.kpoints, (nsegments, divisions, 3))
energies = np.reshape(ev, (self.ispin, nsegments, divisions , bands.shape[0])) ispin = len(eigenvalues)
occ = np.reshape(occupation, (self.ispin, nsegments, divisions, bands.shape[0])) energies = np.reshape(ev, (ispin, nsegments, divisions , bands.shape[0]))
occ = np.reshape(np.array(occupation), (ispin, nsegments, divisions, bands.shape[0]))
for isegment in range(nsegments): for isegment in range(nsegments):
backend.openNonOverlappingSection("section_k_band_segment") backend.openNonOverlappingSection("section_k_band_segment")
backend.addArrayValues("band_energies", energies[:, isegment, :, :]) backend.addArrayValues("band_energies", energies[:, isegment, :, :])
...@@ -527,7 +528,7 @@ class VasprunContext(object): ...@@ -527,7 +528,7 @@ class VasprunContext(object):
else: else:
backend.openNonOverlappingSection("section_eigenvalues") backend.openNonOverlappingSection("section_eigenvalues")
backend.addArrayValues("eigenvalues_values", ev) backend.addArrayValues("eigenvalues_values", ev)
backend.addArrayValues("eigenvalues_occupation", occupation) backend.addArrayValues("eigenvalues_occupation", np.array(occupation))
backend.closeNonOverlappingSection("section_eigenvalues") backend.closeNonOverlappingSection("section_eigenvalues")
else: else:
backend.pwarn("unexpected tag %s in the eigenvalues" % el.tag) backend.pwarn("unexpected tag %s in the eigenvalues" % el.tag)
...@@ -538,7 +539,7 @@ class VasprunContext(object): ...@@ -538,7 +539,7 @@ class VasprunContext(object):
def onStart_calculation(self, parser, event, element, pathStr): def onStart_calculation(self, parser, event, element, pathStr):
gIndexes = parser.tagSections[pathStr] gIndexes = parser.tagSections[pathStr]
self.singleConfCalcs.append(gIndexes["section_single_configuration_calculation"]) self.singleConfCalcs.append(gIndexes["section_single_configuration_calculation"])
if self.waveCut: if self.waveCut is not None:
backend.openNonOverlappingSection("section_basis_set") backend.openNonOverlappingSection("section_basis_set")
backend.addValue("mapping_section_basis_set_cell_dependent", self.waveCut) backend.addValue("mapping_section_basis_set_cell_dependent", self.waveCut)
backend.closeNonOverlappingSection("section_basis_set") backend.closeNonOverlappingSection("section_basis_set")
...@@ -555,8 +556,8 @@ class VasprunContext(object): ...@@ -555,8 +556,8 @@ class VasprunContext(object):
backend.addValue("sampling_method", sampling_method) backend.addValue("sampling_method", sampling_method)
backend.closeSection("section_sampling_method", samplingGIndex) backend.closeSection("section_sampling_method", samplingGIndex)
frameSequenceGIndex = backend.openSection("section_frame_sequence") frameSequenceGIndex = backend.openSection("section_frame_sequence")
backend.addValue("frame_sequence_to_sampling_ref", samplingGIndex) backend.addValue("frame_sequence_to_sampling_method_ref", samplingGIndex)
backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs)) backend.addArrayValues("frame_sequence_to_frames_ref", np.asarray(self.singleConfCalcs))
backend.closeSection("section_frame_sequence", frameSequenceGIndex) backend.closeSection("section_frame_sequence", frameSequenceGIndex)
def onEnd_calculation(self, parser, event, element, pathStr): def onEnd_calculation(self, parser, event, element, pathStr):
...@@ -566,7 +567,7 @@ class VasprunContext(object): ...@@ -566,7 +567,7 @@ class VasprunContext(object):
backend = parser.backend backend = parser.backend
backend.addValue("single_configuration_calculation_to_system_ref", self.lastSystemDescription) backend.addValue("single_configuration_calculation_to_system_ref", self.lastSystemDescription)
gIndexes = parser.tagSections["/modeling"] gIndexes = parser.tagSections["/modeling"]
backend.addValue("single_configuration_to_calculation_method_ref", gIndexes["section_method"]) backend.addValue("single_configuration_calculation_to_method_ref", gIndexes["section_method"])
for el in element: for el in element:
if el.tag == "energy": if el.tag == "energy":
for enEl in el: for enEl in el:
...@@ -580,14 +581,16 @@ class VasprunContext(object): ...@@ -580,14 +581,16 @@ class VasprunContext(object):
backend.addValue("energy_total", value) backend.addValue("energy_total", value)
elif name == "e_0_energy": elif name == "e_0_energy":
value = eConv(float(enEl.text.strip())) value = eConv(float(enEl.text.strip()))
backend.addValue("energy_total_T0", value) backend.addValue("energy_total_t0", value)
else: else:
backend.pwarn("Unexpected i tag with name %s in energy section" % name) backend.pwarn("Unexpected i tag with name %s in energy section" % name)
elif enEl.tag == "varray": elif enEl.tag == "varray":
name = enEl.attrib.get("name", None) name = enEl.attrib.get("name", None)
if name == "forces": if name == "forces":
f = getVector(enEl, lambda x: fConv(float(x))) f = getVector(enEl, lambda x: fConv(float(x)))
fId = backend.openSection('section_atom_forces')
backend.addValue("atom_forces", f) backend.addValue("atom_forces", f)
backend.closeSection('section_atom_forces', fId)
elif name == 'stress': elif name == 'stress':
f = getVector(enEl, lambda x: pConv(float(x))) f = getVector(enEl, lambda x: pConv(float(x)))
backend.addValue("stress_tensor", f) backend.addValue("stress_tensor", f)
...@@ -743,9 +746,9 @@ class VasprunContext(object): ...@@ -743,9 +746,9 @@ class VasprunContext(object):
backend.pwarn("Unknown XC functional %s" % el.text.strip()) backend.pwarn("Unknown XC functional %s" % el.text.strip())
else: else:
for f in functs: for f in functs:
backend.openNonOverlappingSection("section_XC_functionals") backend.openNonOverlappingSection("section_xc_functionals")
backend.addValue("XC_functional_name", f) backend.addValue("xc_functional_name", f)
backend.closeNonOverlappingSection("section_XC_functionals") backend.closeNonOverlappingSection("section_xc_functionals")
elif name == "ISPIN": elif name == "ISPIN":
self.ispin = int(el.text.strip()) self.ispin = int(el.text.strip())
......
src/main/scala/eu/nomad_lab/parsers/VaspParser.scala
+ 2
− 2
View file @ ede0f512
...@@ -46,7 +46,7 @@ object VaspParser extends SimpleExternalParserGenerator( ...@@ -46,7 +46,7 @@ object VaspParser extends SimpleExternalParserGenerator(
"parser-vasp/vaspparser/setup_paths.py", "parser-vasp/vaspparser/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json", "nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json", "nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json", "nomad_meta_info/meta.nomadmetainfo.json",
"nomad_meta_info/vasp.nomadmetainfo.json" "nomad_meta_info/vasp.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(), ) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map( dirMap = Map(
...@@ -89,7 +89,7 @@ object VaspRunParser extends SimpleExternalParserGenerator( ...@@ -89,7 +89,7 @@ object VaspRunParser extends SimpleExternalParserGenerator(
"parser-vasp/vaspparser/vaspmainparser.py", "parser-vasp/vaspparser/vaspmainparser.py",
"nomad_meta_info/public.nomadmetainfo.json", "nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json", "nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json", "nomad_meta_info/meta.nomadmetainfo.json",
"nomad_meta_info/vasp.nomadmetainfo.json" "nomad_meta_info/vasp.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(), ) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map( dirMap = Map(
......
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