dos + tests

parser/parser-elk/elk_parser_dos.py

-import xml.sax
-import logging
-
-class DosHandler(xml.sax.handler.ContentHandler):
-    def __init__(self, backend):
-        self.backend = backend
-        self.dosSectionGIndex = -1
-        self.inDos = False
-
-    def endDocument(self):
-        pass
-
-    def startElement(self, name, attrs):
-        if name == "dos":
-            self.dosSectionGIndex = self.backend.openSection("x_exciting_section_dos")
-            self.inDos = True
-        elif name == "point" and self.inDos:
-            self.backend.addValue("x_exciting_dos_value",float(attrs.getValue('dos')))
-            self.backend.addValue("x_exciting_dos_energy",float(attrs.getValue('e')))
-        # attrDict={}
-        # for name in attrs.getNames():
-        #     attrDict[name] = attrs.getValue(name)
-        # logging.error("start element %s attr %s", name, attrDict)
-
-    def endElement(self, name):
-        if name == 'dos':
-            self.inDos = False
-            self.backend.closeSection("x_exciting_section_dos",self.dosSectionGIndex)
-            self.dosSectionGIndex = -1
-        # logging.error("end element %s", name)
-
-    def startElementNS(self, name, qname, attrs):
-        attrDict={}
-        for name in attrs.getNames():
-            attrDict[name] = attrs.getValue(name)
-        logging.error("start element %s ns %s attr %s", name, qname, attrDict)
-
-    def endElementNS(self, name, qname):
-        logging.error("end element %s ns %s", name, qname)
-
-    def characters(self, content):
-        pass
-
-def parseDos(inF, backend):
-    handler = DosHandler(backend)
-    logging.error("will parse")
-    xml.sax.parse(inF, handler)
-    logging.error("did parse")

parser/parser-elk/parser_elk.py

@@ -4,7 +4,8 @@ import numpy as np
 from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel
 from nomadcore.simple_parser import SimpleMatcher as SM
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
-import os, sys, json, elk_parser_dos
+from nomadcore.unit_conversion import unit_conversion
+import os, sys, json, logging
 
 class ElkContext(object):
     """context for elk parser"""
@@ -44,8 +45,23 @@ class ElkContext(object):
       dirPath = os.path.dirname(self.parser.fIn.name)
       dosFile = os.path.join(dirPath, "TDOS.OUT")
       if os.path.exists(dosFile):
+        dosGIndex=backend.openSection("section_dos")
         with open(dosFile) as f:
-          elk_parser_dos.parseDos(f, backend)
+            dosE=[]
+            dosV=[]
+            fromH = unit_conversion.convert_unit_function("hartree", "J")
+            while True:
+                line = f.readline()
+                if not line: break
+                nrs = list(map(float,line.split()))
+                if len(nrs) == 2:
+                    dosV.append(nrs[1])
+                    dosE.append(fromH(nrs[0]))
+                elif len(nrs) != 0:
+                    raise Exception("Found more than two values in dos file %s" % dosFile)
+            backend.addArrayValues("dos_values", np.asarray(dosV))
+            backend.addArrayValues("dos_energies", np.asarray(dosE))
+        backend.closeSection("section_dos", dosGIndex)
 
     def onClose_section_system(self, backend, gIndex, section):
       backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))

src/test/scala/eu/nomad_lab/parsers/ElkParserSpec.scala

@@ -4,11 +4,17 @@ import org.specs2.mutable.Specification
 
 object ElkTests extends Specification {
   "ElkParserTest" >> {
-    "test with json-events" >> {
-      ParserRun.parse(ElkParser, "parsers/elk/test/examples/ok/ok.scf", "json-events") must_== ParseResult.ParseSuccess
+    "test with json-events GaAs" >> {
+      ParserRun.parse(ElkParser, "parsers/elk/test/examples/GaAs/INFO.OUT", "json-events") must_== ParseResult.ParseSuccess
     }
-    "test with json" >> {
-      ParserRun.parse(ElkParser, "parsers/elk/test/examples/ok/ok.scf", "json") must_== ParseResult.ParseSuccess
+    "test with json GaAs" >> {
+      ParserRun.parse(ElkParser, "parsers/elk/test/examples/GaAs/INFO.OUT", "json") must_== ParseResult.ParseSuccess
+    }
+    "test with json-events Al" >> {
+      ParserRun.parse(ElkParser, "parsers/elk/test/examples/Al/INFO.OUT", "json-events") must_== ParseResult.ParseSuccess
+    }
+    "test with json Al" >> {
+      ParserRun.parse(ElkParser, "parsers/elk/test/examples/Al/INFO.OUT", "json") must_== ParseResult.ParseSuccess
     }
   }
 }

test/examples/Al/DTOTENERGY.OUT

+  0.1198769544E-02
+  0.2799643479E-02
+  0.1175652643E-01
+  0.2392171444E-01
+  0.3584530053E-01
+  0.4335915746E-01
+  0.4394082265E-01
+  0.3804421405E-01
+  0.2847828394E-01
+  0.1859043836E-01
+  0.1066293543E-01
+  0.5410512229E-02
+  0.2441357323E-02
+  0.9817180543E-03
+  0.3518649715E-03
+  0.1126689946E-03
+  0.3257301847E-04

test/examples/Al/EFERMI.OUT

+  0.2674453034    

test/examples/Al/EIGVAL.OUT

+    10 : nkpt
+     9 : nstsv
+
+     1  0.1250000000      0.1250000000      0.1250000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122364679       2.000000000    
+     2  -2.122259438       2.000000000    
+     3  -2.122259438       2.000000000    
+     4 -0.1286748619       2.000000000    
+     5  0.5745589210       0.000000000    
+     6  0.7051658566       0.000000000    
+     7  0.7051658566       0.000000000    
+     8  0.8151136384       0.000000000    
+     9  0.8605767411       0.000000000    
+
+
+     2  0.3750000000      0.1250000000      0.1250000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122741574       2.000000000    
+     2  -2.122411847       2.000000000    
+     3  -2.122334851       2.000000000    
+     4 -0.4678368645E-01   2.000000000    
+     5  0.3448210862       0.000000000    
+     6  0.5063335941       0.000000000    
+     7  0.6997894076       0.000000000    
+     8  0.7856802707       0.000000000    
+     9  0.8006252452       0.000000000    
+
+
+     3  0.6250000000      0.1250000000      0.1250000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122993479       2.000000000    
+     2  -2.122438302       2.000000000    
+     3  -2.122380402       2.000000000    
+     4  0.7353923216E-01   2.000000000    
+     5  0.1525458423       2.000000000    
+     6  0.5441924906       0.000000000    
+     7  0.5896331272       0.000000000    
+     8  0.6650293833       0.000000000    
+     9  0.8356862943       0.000000000    
+
+
+     4  0.8750000000      0.1250000000      0.1250000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122581428       2.000000000    
+     2  -2.122336125       2.000000000    
+     3  -2.122330979       2.000000000    
+     4 -0.8756585904E-01   2.000000000    
+     5  0.4593570587       0.000000000    
+     6  0.5896431645       0.000000000    
+     7  0.6561578100       0.000000000    
+     8  0.6997691538       0.000000000    
+     9  0.7958323137       0.000000000    
+
+
+     5  0.3750000000      0.3750000000      0.1250000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122790135       2.000000000    
+     2  -2.122463957       2.000000000    
+     3  -2.122434744       2.000000000    
+     4 -0.6380235792E-02   2.000000000    
+     5  0.3817063939       0.000000000    
+     6  0.4690786282       0.000000000    
+     7  0.5148235813       0.000000000    
+     8  0.5802200862       0.000000000    
+     9  0.7261290494       0.000000000    
+
+
+     6  0.6250000000      0.3750000000      0.1250000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122869897       2.000000000    
+     2  -2.122682147       2.000000000    
+     3  -2.122510464       2.000000000    
+     4  0.1507310056       2.000000000    
+     5  0.2285441300       2.000000000    
+     6  0.3154891470      0.2728059484E-20
+     7  0.3936611581       0.000000000    
+     8  0.7117965260       0.000000000    
+     9  0.8710552053       0.000000000    
+
+
+     7  0.8750000000      0.3750000000      0.1250000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122864752       2.000000000    
+     2  -2.122537526       2.000000000    
+     3  -2.122409389       2.000000000    
+     4  0.3373996622E-01   2.000000000    
+     5  0.2674457264      0.9997884984    
+     6  0.4306935410       0.000000000    
+     7  0.5070639965       0.000000000    
+     8  0.7471363675       0.000000000    
+     9  0.8351001601       0.000000000    
+
+
+     8  0.6250000000      0.6250000000      0.1250000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122963098       2.000000000    
+     2  -2.122576667       2.000000000    
+     3  -2.122517646       2.000000000    
+     4  0.1117263429       2.000000000    
+     5  0.2759063707      0.4230028254E-03
+     6  0.3436488571       0.000000000    
+     7  0.4781416554       0.000000000    
+     8  0.5396484561       0.000000000    
+     9  0.6904329374       0.000000000    
+
+
+     9  0.3750000000      0.3750000000      0.3750000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122916936       2.000000000    
+     2  -2.122351729       2.000000000    
+     3  -2.122351729       2.000000000    
+     4 -0.6328542043E-02   2.000000000    
+     5  0.2305217279       2.000000000    
+     6  0.6637824424       0.000000000    
+     7  0.6637824424       0.000000000    
+     8  0.7556756622       0.000000000    
+     9  0.7556756622       0.000000000    
+
+
+    10  0.6250000000      0.3750000000      0.3750000000     : k-point, vkl
+ (state, eigenvalue and occupancy below)
+     1  -2.122892972       2.000000000    
+     2  -2.122646630       2.000000000    
+     3  -2.122429945       2.000000000    
+     4  0.1129446001       2.000000000    
+     5  0.1900341612       2.000000000    
+     6  0.3547527304       0.000000000    
+     7  0.5520317928       0.000000000    
+     8  0.6304422575       0.000000000    
+     9  0.9658781777       0.000000000    
+

test/examples/Al/EQATOMS.OUT

+
+Species :    1 (Al)
+ atom    1 is equivalent to atom(s)
+   1

test/examples/Al/EVALCORE.OUT

+
+Species :    1 (Al), atom :    1
+ n =  1, l =  0, k =  1 :   -54.83607356    
+ n =  2, l =  0, k =  1 :   -3.511752279    

test/examples/Al/FERMIDOS.OUT

+   93.79381046    
+   93.79313701    
+   93.79231979    
+   93.79151253    
+   93.79083328    
+   93.79033045    
+   93.78999830    
+   93.78980281    
+   93.78970213    
+   93.78965849    
+   93.78964396    
+   93.78964136    
+   93.78964213    
+   93.78964311    
+   93.78964363    
+   93.78964384    
+   93.78964390    
+   93.78964393    
+   93.78964393    

test/examples/Al/GAP.OUT

+    0.367907732220E-01
+    0.368044960624E-01
+    0.368228800917E-01
+    0.368434558093E-01
+    0.368638235136E-01
+    0.368819830650E-01
+    0.368966956680E-01
+    0.369075704624E-01
+    0.369149057106E-01
+    0.369194078453E-01
+    0.369219071736E-01
+    0.369231504502E-01
+    0.369236975143E-01
+    0.369239069369E-01
+    0.369239752487E-01
+    0.369239937401E-01
+    0.369239977553E-01
+    0.369239984296E-01
+    0.369239985193E-01

test/examples/Al/GEOMETRY.OUT

+
+scale
+ 1.0
+
+scale1
+ 1.0
+
+scale2
+ 1.0
+
+scale3
+ 1.0
+
+avec
+   3.826700000       3.826700000       0.000000000    
+   3.826700000       0.000000000       3.826700000    
+   0.000000000       3.826700000       3.826700000    
+
+atoms
+   1                                    : nspecies
+'Al.in'                                 : spfname
+   1                                    : natoms; atpos, bfcmt below
+    0.00000000    0.00000000    0.00000000    0.00000000  0.00000000  0.00000000

test/examples/Al/IADIST.OUT

+
+Distance between is =    1 (Al), ia =    1 and
+ is =    1 (Al), ia =    1 :    0.000000000    

test/examples/GaAs/EFERMI.OUT

+  0.1929746200