diff --git a/parser/parser-vasp/parser_vasprun.py b/parser/parser-vasp/parser_vasprun.py
index 8d19e9863b5b7aea315420cc985497d2fcef6302..6b9a6da3866fa1dd3705d45e47d6cf5aff11b716 100644
--- a/parser/parser-vasp/parser_vasprun.py
+++ b/parser/parser-vasp/parser_vasprun.py
@@ -73,8 +73,10 @@ class VasprunContext(object):
self.kpoints = None
self.weights = None
self.ispin = None
+ self.ibrion = None
self.lastSystemDescription = None
self.labels = None
+ self.singleConfCalcs = []
sectionMap = {
"modeling": ["section_run", "section_method"],
@@ -85,7 +87,7 @@ class VasprunContext(object):
def startedParsing(self, parser):
self.parser = parser
- def onEnd_generator(self, parser, event, element):
+ def onEnd_generator(self, parser, event, element, pathStr):
backend = parser.backend
program_name = g(element, "i/[@name='program']")
if program_name:
@@ -95,6 +97,7 @@ class VasprunContext(object):
g(element, "i/[@name='platform']", ""))
if not version.isspace():
backend.addValue("program_version", version)
+ backend.addValue("program_basis_set_type", "plane waves")
date = g(element, "i/[@name='date']")
pdate = None
time = g(element, "i/[@name='time']")
@@ -108,10 +111,12 @@ class VasprunContext(object):
if i.tag != "i" or not i.attrib.get("name") in set(["program", "version", "subversion", "platform", "program_version", "date", "time"]):
backend.pwarn("unexpected tag %s %s %r in generator" % (i.tag, i.attrib, i.text))
- def onEnd_incar(self, parser, event, element):
+ def onEnd_incar(self, parser, event, element, pathStr):
backend = parser.backend
metaEnv = parser.backend.metaInfoEnv()
dft_plus_u = False
+ ibrion = None
+ nsw = 0
for el in element:
if (el.tag != "i"):
backend.pwarn("unexpected tag %s %s %r in incar" % (el.tag, el.attrib, el.text))
@@ -162,13 +167,20 @@ class VasprunContext(object):
elif name == "LDAU":
if re.match(".?[Tt](?:[rR][uU][eE])?.?|[yY](?:[eE][sS])?|1", el.text.strip()):
dft_plus_u = True
+ elif name == "IBRION":
+ ibrion = int(el.text.strip())
+ elif name == "NSW":
+ nsw = int(el.text.strip())
+ if ibrion is None:
+ ibrion = -1 if nsw == 0 or nsw == 1 else 0
+ self.ibrion = ibrion
if dft_plus_u:
backend.addValue("electronic_structure_method", "DFT+U")
else:
backend.addValue("electronic_structure_method", "DFT")
- def onEnd_kpoints(self, parser, event, element):
+ def onEnd_kpoints(self, parser, event, element, pathStr):
backend = parser.backend
self.bands = None
self.kpoints = None
@@ -199,9 +211,9 @@ class VasprunContext(object):
backend.pwarn("Unknown tag %s in kpoints" % el.tag)
- def onEnd_structure(self, parser, event, element):
+ def onEnd_structure(self, parser, event, element, pathStr):
backend = parser.backend
- gIndexes = parser.tagSections["/".join([x.tag for x in parser.path[:]]) + "/" + element.tag]
+ gIndexes = parser.tagSections[pathStr]
self.lastSystemDescription = gIndexes["section_system"]
for el in element:
if (el.tag == "crystal"):
@@ -236,7 +248,7 @@ class VasprunContext(object):
backend.addArrayValues("atom_labels", self.labels)
- def onEnd_eigenvalues(self, parser, event, element):
+ def onEnd_eigenvalues(self, parser, event, element, pathStr):
backend = parser.backend
eConv = convert_unit_function("eV", "J")
eigenvalues = None
@@ -294,10 +306,30 @@ class VasprunContext(object):
else:
backend.pwarn("unexpected tag %s in the eigenvalues" % el.tag)
- def onEnd_scstep(self, parser, event, element):
+ def onEnd_scstep(self, parser, event, element, pathStr):
pass
- def onEnd_calculation(self, parser, event, element):
+ def onStart_calculation(self, parser, event, element, pathStr):
+ gIndexes = parser.tagSections[pathStr]
+ self.singleConfCalcs.append(gIndexes["section_single_configuration_calculation"])
+
+ def onEnd_modeling(self, parser, event, element, pathStr):
+ backend = parser.backend
+ if self.ibrion is None or self.ibrion == -1:
+ return
+ samplingGIndex = backend.openSection("section_sampling_method")
+ if self.ibrion == 0:
+ sampling_method = "molecular_dynamics"
+ else:
+ sampling_method = "geometry_optimization"
+ backend.addValue("sampling_method", sampling_method)
+ backend.closeSection("section_sampling_method", samplingGIndex)
+ frameSequenceGIndex = backend.openSection("section_frame_sequence")
+ backend.addValue("frame_sequence_to_sampling_ref", samplingGIndex)
+ backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs))
+ backend.closeSection("section_frame_sequence", frameSequenceGIndex)
+
+ def onEnd_calculation(self, parser, event, element, pathStr):
eConv = convert_unit_function("eV", "J")
fConv = convert_unit_function("eV/angstrom", "N")
pConv = convert_unit_function("eV/angstrom^3", "Pa")
@@ -330,7 +362,7 @@ class VasprunContext(object):
f = getVector(enEl, lambda x: pConv(float(x)))
backend.addValue("stress_tensor", f)
- def onEnd_atominfo(self, parser, event, element):
+ def onEnd_atominfo(self, parser, event, element, pathStr):
nAtoms = None
nAtomTypes = None
atomTypes = []
@@ -396,6 +428,7 @@ class VasprunContext(object):
else:
backend.pwarn("unexpected tag %s in atominfo" % el.tag)
self.labels = np.asarray(labels)
+
def incarOutTag(self, el):
backend = parser.backend
metaEnv = parser.backend.metaInfoEnv()
@@ -463,7 +496,7 @@ class VasprunContext(object):
else:
backend.pwarn("unexpected tag %s %s in parameters at depth %d" % (separators.tag, separators.attrib, depth))
- def onEnd_parameters(self, parser, event, element):
+ def onEnd_parameters(self, parser, event, element, pathStr):
backend = parser.backend
self.separatorScan(element)
@@ -515,25 +548,28 @@ class XmlParser(object):
try:
for event, el in xml.etree.ElementTree.iterparse(self.fIn, events=["start","end"], parser = xmlParser):
if event == 'start':
+ pathStr = "/".join([x.tag for x in self.path]) + "/" + el.tag
sectionsToOpen = self.sectionMap.get(el.tag, None)
if sectionsToOpen:
- pathStr = "/".join([x.tag for x in self.path]) + "/" + el.tag
gIndexes = {}
for sect in sectionsToOpen:
gIndexes[sect] = backend.openSection(sect)
self.tagSections[pathStr] = gIndexes
callback = self.callbacks.get("onStart_" + el.tag, None)
if callback:
- callback(self, event, el)
+ callback(self, event, el, pathStr)
self.path.append(el)
elif event == 'end':
lastEl = self.path.pop()
if lastEl != el:
raise Exception("mismatched path at end, got %s expected %s" % (lastEl, el))
tag = el.tag
+ pathStr = "/".join([x.tag for x in self.path]) + "/" + tag
callback = self.callbacks.get("onEnd_" + tag, None)
if callback:
- if not callback(self, event, el):
+ if not callback(self, event, el, pathStr):
+ # if callback does not return True then assume that the current element has been processed
+ # and can be removed
el.clear()
if self.path:
self.path[-1].remove(el)
@@ -543,7 +579,6 @@ class XmlParser(object):
self.path[-1].remove(el)
sectionsToClose = self.sectionMap.get(tag, None)
if sectionsToClose:
- pathStr = "/".join([x.tag for x in self.path]) + "/" + tag
gIndexes = self.tagSections[pathStr]
del self.tagSections[pathStr]
for sect in reversed(sectionsToClose):