diff --git a/parser/parser-vasp/parser_vasprun.py b/parser/parser-vasp/parser_vasprun.py
index f91869b98b9fafcba2ae2f04826f67fdaf2df223..48fe2a8c855db88d086fdb4e78ebc0b9beac297d 100644
--- a/parser/parser-vasp/parser_vasprun.py
+++ b/parser/parser-vasp/parser_vasprun.py
@@ -13,6 +13,9 @@ import numpy as np
import setup_paths
from nomadcore.unit_conversion.unit_conversion import convert_unit_function
+eV2J = convert_unit_function("eV","J")
+eV2JV = np.vectorize(eV2J)
+
def secondsFromEpoch(date):
epoch = datetime(1970,1,1)
ts=date-epoch
@@ -250,7 +253,6 @@ class VasprunContext(object):
def onEnd_eigenvalues(self, parser, event, element, pathStr):
backend = parser.backend
- eConv = convert_unit_function("eV", "J")
eigenvalues = None
occupation = None
for el in element:
@@ -282,7 +284,7 @@ class VasprunContext(object):
else:
backend.pwarn("unexpected tag %s in array of the eigenvalues" % arrEl.tag)
if eigenvalues is not None:
- ev = [eConv(x) for x in eigenvalues]
+ ev = eV2JV(eigenvalues)
if self.bands:
divisions = int(self.bands['divisions'])
backend.openNonOverlappingSection("section_k_band")
@@ -301,7 +303,8 @@ class VasprunContext(object):
backend.closeNonOverlappingSection("section_k_band")
else:
backend.openNonOverlappingSection("section_eigenvalues")
- backend.addArrayValues("eigenvalues_values", np.asarray(ev))
+ backend.addArrayValues("eigenvalues_values", ev)
+ backend.addArrayValues("eigenvalues_occupation", occupation)
backend.closeNonOverlappingSection("section_eigenvalues")
else:
backend.pwarn("unexpected tag %s in the eigenvalues" % el.tag)
@@ -330,7 +333,7 @@ class VasprunContext(object):
backend.closeSection("section_frame_sequence", frameSequenceGIndex)
def onEnd_calculation(self, parser, event, element, pathStr):
- eConv = convert_unit_function("eV", "J")
+ eConv = eV2J
fConv = convert_unit_function("eV/angstrom", "N")
pConv = convert_unit_function("eV/angstrom^3", "Pa")
backend = parser.backend
@@ -480,7 +483,7 @@ class VasprunContext(object):
elif name == "ISPIN":
self.ispin = int(el.text.strip())
- def separatorScan(self, element, depth = 0):
+ def separatorScan(self, element, backend, depth = 0):
for separators in element:
if separators.tag == "separator":
separatorName = separators.attrib.get("name")
@@ -488,7 +491,7 @@ class VasprunContext(object):
if el.tag == "i":
self.incarOutTag(el)
elif el.tag == "separator":
- self.separatorScan(el, depth + 1)
+ self.separatorScan(el, backend, depth + 1)
else:
backend.pwarn("unexpected tag %s %s in parameters separator %s at depth %d" % (el.tag, el.attrib, separatorName, depth))
elif separators.tag == "i":
@@ -497,8 +500,97 @@ class VasprunContext(object):
backend.pwarn("unexpected tag %s %s in parameters at depth %d" % (separators.tag, separators.attrib, depth))
def onEnd_parameters(self, parser, event, element, pathStr):
+ self.separatorScan(element, parser.backend)
+
+ def onEnd_dos(self, parser, event, element, pathStr):
+ "density of states"
backend = parser.backend
- self.separatorScan(element)
+ backend.openNonOverlappingSection("section_dos")
+ for el in element:
+ if el.tag == "i":
+ if el.attrib.get("name") == "efermi":
+ backend.addValue("dos_fermi_energy",eV2J(float(el.text.strip())))
+ else:
+ backend.pwarn("unexpected tag %s %s in dos" % (el.tag, el.attrib))
+ elif el.tag == "total":
+ for el1 in el:
+ if el1.tag == "array":
+ for el2 in el1:
+ if el2.tag == "dimension" or el2.tag == "field":
+ pass
+ elif el2.tag == "set":
+ dosL = []
+ for spinComponent in el2:
+ if spinComponent.tag == "set":
+ dosL.append(getVector(spinComponent, field = "r"))
+ else:
+ backend.pwarn("unexpected tag %s %s in dos total array set" % (spinComponent.tag, spinComponent.attrib))
+ dosA = np.asarray(dosL)
+ if len(dosA.shape) != 3:
+ raise Exception("unexpected shape %s (%s) for total dos (ragged arrays?)" % (dosA.shape), dosA.dtype)
+ dosE = eV2JV(dosA[:,:,0])
+ dosI = dosA[:,:,2]
+ dosV = dosA[:,:,1]
+ backend.addArrayValues("dos_energies", dosE)
+ backend.addArrayValues("dos_values", dosV)
+ backend.addArrayValues("dos_integrated_values", dosI)
+ else:
+ backend.pwarn("unexpected tag %s %s in dos total array" % (el2.tag, el2.attrib))
+ else:
+ backend.pwarn("unexpected tag %s %s in dos total" % (el2.tag, el2.attrib))
+ elif el.tag == "partial":
+ for el1 in el:
+ if el1.tag == "array":
+ lm=[]
+ for el2 in el1:
+ if el2.tag == "dimension":
+ pass
+ elif el2.tag == "field":
+ if el2.text.strip() == "energy":
+ pass
+ else:
+ strLm = {
+ "s": [0,0],
+ "px":[1,0],
+ "py":[1,1],
+ "pz":[1,2],
+ "dx2":[1,0],
+ "dxy":[1,1],
+ "dxz":[1,2],
+ "dy2":[1,3],
+ "dyz":[1,4],
+ "dz2":[1,5]
+ }
+ lm.append(strLm[el2.text.strip()])
+ elif el2.tag == "set":
+ dosL = []
+ for atom in el2:
+ if atom.tag == "set":
+ atomL = []
+ dosL.append(atomL)
+ for spinComponent in atom:
+ if spinComponent.tag == "set":
+ atomL.append(getVector(spinComponent, field = "r"))
+ else:
+ backend.pwarn("unexpected tag %s %s in dos partial array set set" % (spinComponent.tag, spinComponent.attrib))
+ else:
+ backend.pwarn("unexpected tag %s %s in dos partial array set" % (spinComponent.tag, spinComponent.attrib))
+ dosLM = np.asarray(dosL)
+ assert len(dosLM.shape) == 4, "invalid shape dimension in projected dos (ragged arrays?)"
+ backend.addArrayValues("dos_values_lm", dosLM[:,:,:,1:])
+ else:
+ backend.pwarn("unexpected tag %s %s in dos total array" % (el2.tag, el2.attrib))
+ backend.addArrayValues("dos_lm", np.asarray(lm))
+ backend.addValue("dos_m_kind", "polynomial")
+ else:
+ backend.pwarn("unexpected tag %s %s in dos total" % (el2.tag, el2.attrib))
+ else:
+ backend.pwarn("unexpected tag %s %s in dos" % (el2.tag, el2.attrib))
+ backend.closeNonOverlappingSection("section_dos")
+
+ def onEnd_projected(self, parser, event, element, pathStr):
+ "projected eigenvalues"
+ return None
class XmlParser(object):
@staticmethod