Merge pull request #91 from pyscal/maintain_run

Maintain run

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.4
+current_version = 0.5.5
 commit = True
 tag = False
 

.github/workflows/testing.yml

@@ -28,5 +28,11 @@ jobs:
         pip install -e .
         pip install pytest
         pip install pytest-cov
-        pytest tests/
-        #pytest --cov-report=xml --cov=pyscal tests/    
+        #pytest tests/
+        pytest --cov-report=xml --cov=atomrdf tests/    
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/[email protected]
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: pyscal/atomRDF

CITATION.cff

@@ -20,4 +20,4 @@ url: 'https://atomrdf.pyscal.org'
 license: "MIT"
 repository-code: https://github.com/pyscal/atomRDF
 type: software
-version: 0.5.4
+version: 0.5.5

atomrdf/data/dft_template.yml

@@ -0,0 +1,29 @@
+method: DensityFunctionalTheory
+temperature: 100
+pressure: 0
+dof:
+- AtomicPositions
+- CellVolume
+id: 2314
+xcfunctional: LDA
+workflow_manager:
+  uri: xxxx
+  label: pyiron
+software:
+- uri: xxxx
+  label: lammps
+- uri: xxxx
+  label: pyscal
+outputs:
+- label: TotalEnergy
+  value: 2.301
+  unit: EV
+  associate_to_sample: True
+- label: TotalVolume
+  value: 23.01
+  unit: ANGSTROM3
+  associate_to_sample: True
+inputs:
+- label: AnotherInput
+  value: 0.1
+  unit: None

atomrdf/data/md_template.yml

@@ -0,0 +1,34 @@
+method: MolecularStatics
+temperature: 100
+pressure: 0
+dof:
+- AtomicPositions
+- CellVolume
+ensemble: NPT
+id: 2314
+potential:
+  uri: https://doi.org/xxx
+  type: eam
+  label: string
+workflow_manager:
+  uri: xxxx
+  label: pyiron
+software:
+- uri: xxxx
+  label: lammps
+- uri: xxxx
+  label: pyscal
+outputs:
+- label: TotalEnergy
+  value: 2.301
+  unit: EV
+  associate_to_sample: True
+- label: TotalVolume
+  value: 23.01
+  unit: ANGSTROM3
+  associate_to_sample: True
+inputs:
+- label: AnotherInput
+  value: 0.1
+  unit: None
+

atomrdf/graph.py

@@ -128,6 +128,7 @@ def __init__(self, graph_file=None,
         self._atom_ids = None
         self.store = store
         self._n_triples = 0
+        self._initialize_graph()
 
 
     def add_structure(self, structure):
@@ -180,19 +181,19 @@ def _check_domain_if_uriref(self, triple):
                             break
         return found, dm
 
-    def _check_domain_if_ontoterm(self, triple):
-        found = True
-        domain = triple[0].domain
-        if len(domain) > 0:
-            if 'owl:Thing' not in domain:
-                if triple[1].namespace != triple[0].namespace:
-                    #cross ontology term
-                    self.log(f'ignoring possible cross ontology connection between {triple[1].namespace} and {triple[0].namespace}')
-                    return True, None
-                found = False
-                if triple[1].name in domain:
-                    found = True
-        return found, triple[0].name
+#    def _check_domain_if_ontoterm(self, triple):
+#        found = True
+#        domain = triple[0].domain
+#        if len(domain) > 0:
+#            if 'owl:Thing' not in domain:
+#                if triple[1].namespace != triple[0].namespace:
+#                    #cross ontology term
+#                    self.log(f'ignoring possible cross ontology connection between {triple[1].namespace} and {triple[0].namespace}')
+#                    return True, None
+#                found = False
+#                if triple[1].name in domain:
+#                    found = True
+#        return found, triple[0].name
 
 
     def _check_domain(self, triple):
@@ -204,8 +205,8 @@ def _check_domain(self, triple):
             if type(triple[0]).__name__ == 'URIRef': 
                 found, dm = self._check_domain_if_uriref(triple)
 
-            elif self._is_ontoterm(triple[0]):
-                found, dm = self._check_domain_if_ontoterm(triple)
+            #elif self._is_ontoterm(triple[0]):
+            #    found, dm = self._check_domain_if_ontoterm(triple)
 
             if not found:
                 raise ValueError(f'{dm} not in domain of {triple[1].name}')
@@ -234,20 +235,20 @@ def _check_range_if_uriref(self, triple):
                             break
         return found, rn
 
-    def _check_range_if_ontoterm(self, triple):
-        found = True
-        rang = triple[1].range
-        if len(rang) > 0:
-            if 'owl:Thing' not in rang:
-                if triple[1].namespace != triple[2].namespace:
-                    #cross ontology term
-                    self.log(f'ignoring possible cross ontology connection between {triple[1].namespace} and {triple[2].namespace}')
-                    return True, None
-
-                found = False
-                if triple[2].name in rang:
-                    found = True
-        return found, triple[2].name
+#    def _check_range_if_ontoterm(self, triple):
+#        found = True
+#        rang = triple[1].range
+#        if len(rang) > 0:
+#            if 'owl:Thing' not in rang:
+#                if triple[1].namespace != triple[2].namespace:
+#                    #cross ontology term
+#                    self.log(f'ignoring possible cross ontology connection between {triple[1].namespace} and {triple[2].namespace}')
+#                    return True, None
+#
+#                found = False
+#                if triple[2].name in rang:
+#                    found = True
+#        return found, triple[2].name
 
 
     def _check_range_if_literal(self, triple):
@@ -280,8 +281,8 @@ def _check_range(self, triple):
             if type(triple[2]).__name__ == 'URIRef': 
                 found, dm = self._check_range_if_uriref(triple)
 
-            elif self._is_ontoterm(triple[2]):
-                found, dm = self._check_range_if_ontoterm(triple)
+            #elif self._is_ontoterm(triple[2]):
+            #    found, dm = self._check_range_if_ontoterm(triple)
 
             elif type(triple[2]).__name__ == 'Literal':
                 found, dm = self._check_range_if_literal(triple)
@@ -363,7 +364,7 @@ def _initialize_graph(self):
 
         self.add((CMSO.LatticeVector, RDFS.subClassOf, CMSO.Vector))
         self.add((CMSO.SimulationCellVector, RDFS.subClassOf, CMSO.Vector))
-        self.add((CMSO.PositionVector, RDFS.subClassOf, CMSO.Vector))
+        #self.add((CMSO.PositionVector, RDFS.subClassOf, CMSO.Vector))
         self.add((CMSO.Vector, CMSO.hasUnit, URIRef("http://qudt.org/vocab/unit/ANGSTROM")))
 
 
@@ -376,13 +377,14 @@ def add_calculated_quantity(self, sample, propertyname, value, unit=None):
             self.add((prop, CMSO.hasUnit, URIRef(f'http://qudt.org/vocab/unit/{unit}')))
 
 
-    def inspect_sample(self):
+    def inspect_sample(self, sample):
         natoms = self.value(sample, CMSO.hasNumberOfAtoms).toPython()
         material = list([k[2] for k in self.triples((sample, CMSO.hasMaterial, None))])[0]
         defects = list([k[2] for k in self.triples((material, CMSO.hasDefect, None))])
         composition = list([k[2].toPython() for k in self.triples((material, CMSO.hasElementRatio, None))])
         crystalstructure = self.value(material, CMSO.hasStructure)
-        spacegroupsymbol = self.value(crystalstructure, CMSO.hasSpaceGroupSymbol).toPython()
+        spacegroup = self.value(crystalstructure, CMSO.hasSpaceGroup)
+        spacegroupsymbol = self.value(spacegroup, CMSO.hasSpaceGroupSymbol).toPython()
 
         lattice = self.value(sample, CMSO.hasNumberOfAtoms).toPython()
         defect_types = list([self.value(d, RDF.type).toPython() for d in defects])
@@ -557,7 +559,7 @@ def archive(self, package_name, format='turtle', compress=True):
 
                 #assign corrected path
                 new_relpath = "/".join(['rdf_structure_store', filepath.split('/')[-1]])
-                self.graph.add((URIRef(f'{sample}_{val}'), CMSO.hasPath, Literal(new_relpath, datatype=XSD.string)))
+                self.add((URIRef(f'{sample}_{val}'), CMSO.hasPath, Literal(new_relpath, datatype=XSD.string)))
 
         triple_file = os.path.join(package_name, 'triples')
         self.write(triple_file, format=format)
@@ -731,7 +733,7 @@ def get_system_from_sample(self, sample):
         sys.atoms = at       
         return sys
 
-    def to_file(self, sample, filename=None, format="lammps-dump"):
+    def to_file(self, sample, filename=None, format="poscar"):
         """
         Save a given sample to a file
 

atomrdf/properties.py

@@ -80,19 +80,19 @@ def get_basis_positions(system):
         return system._structure_dict["positions"]
     return None
 
-def get_basis_occupancy(system):
-    if system._structure_dict is None:
-        return None
-
-    if "species" in system._structure_dict.keys():
-        occ_numbers = system._structure_dict['species']
-        tdict = system.atoms._type_dict
-        vals = [val for key, val in tdict.items()]
+#def get_basis_occupancy(system):
+#    if system._structure_dict is None:
+#        return None
+
+#    if "species" in system._structure_dict.keys():
+#        occ_numbers = system._structure_dict['species']
+#        tdict = system.atoms._type_dict
+#        vals = [val for key, val in tdict.items()]
 
-        if vals[0] is not None:
-            occ_numbers = [tdict[x] for x in occ_numbers]
-        return occ_numbers
-    return None
+#        if vals[0] is not None:
+#            occ_numbers = [tdict[x] for x in occ_numbers]
+#        return occ_numbers
+#    return None
 
 def get_lattice_vector(system):
     if system._structure_dict is None:

atomrdf/structure.py

@@ -598,7 +598,7 @@ def add_interstitial_impurities(self, element, void_type='tetrahedral', lattice_
             self.graph.remove((chemical_species, None, None))
             self.graph.remove((self.sample, CMSO.hasSpecies, None))
 
-            composition = self.schema.material.element_ratio()
+            composition = sysn.schema.material.element_ratio()
             valid = False
             for e, r in composition.items():
                 if e in element_indetifiers.keys():

atomrdf/visualize.py

@@ -35,11 +35,7 @@ def get_string_from_URI(x):
     #just a normal url split now
     rawsplit = raw.split("/")
     if len(rawsplit) > 1:
-        return ".".join(rawsplit[-2:]), "URIRef"
-
-    rawsplit = raw.split(':')
-    if len(rawsplit) == 2:
-        return "_".join(rawsplit), "BNode"        
+        return ".".join(rawsplit[-2:]), "URIRef"  
 
     #none of the conditions, worked, which means its a hex string
     return raw, "BNode"

atomrdf/workflow/pyiron.py

@@ -83,13 +83,12 @@ def _identify_method(job):
         ensemble = 'IsothermalisobaricEnsemble'
 
     mdict = {}
-    mdict['md'] = {}
-    mdict['md']['method'] = md_method
-    mdict['md']['temperature'] = temp
-    mdict['md']['pressure'] = press
-    mdict['md']['dof'] = dof
-    mdict['md']['ensemble'] = ensemble
-    mdict['md']['id'] = job.id
+    mdict['method'] = md_method
+    mdict['temperature'] = temp
+    mdict['pressure'] = press
+    mdict['dof'] = dof
+    mdict['ensemble'] = ensemble
+    mdict['id'] = job.id
 
     #now process potential
     inpdict = job.input.to_dict()
@@ -101,47 +100,44 @@ def _identify_method(job):
     if 'url' in potdict[list(potdict.keys())[0]].keys():
         url = potdict[list(potdict.keys())[0]]['url']
 
-    mdict['md']['potential'] = {}
-    mdict['md']['potential']['type'] = ps
-    mdict['md']['potential']['label'] = name
+    mdict['potential'] = {}
+    mdict['potential']['type'] = ps
+    mdict['potential']['label'] = name
     if url is not None:
-        mdict['md']['potential']['uri'] = url
+        mdict['potential']['uri'] = url
     else:
-        mdict['md']['potential']['uri'] = name
+        mdict['potential']['uri'] = name
 
 
-    mdict['md']['workflow_manager'] = {}
-    mdict['md']['workflow_manager']['uri'] = "http://demo.fiz-karlsruhe.de/matwerk/E457491"
-    mdict['md']['workflow_manager']['label'] = "pyiron"
+    mdict['workflow_manager'] = {}
+    mdict['workflow_manager']['uri'] = "http://demo.fiz-karlsruhe.de/matwerk/E457491"
+    mdict['workflow_manager']['label'] = "pyiron"
     #and finally code details
 
 
     software = {'uri':"http://demo.fiz-karlsruhe.de/matwerk/E447986", 
     'label':'LAMMPS'}
-    mdict['md']['software'] = [software]
+    mdict['software'] = [software]
 
     #finally add calculated quantities
     quantdict = extract_calculated_quantities(job)
-    mdict['md']['outputs'] = quantdict
+    mdict['outputs'] = quantdict
     return mdict
 
 
 def extract_calculated_quantities(job):
     aen = np.mean(job.output.energy_tot)
     avol = np.mean(job.output.volume)
-    outdict = {}
-    outdict['TotalEnergy'] = {}
-    outdict['TotalEnergy']['value'] = np.round(aen, decimals=4)
-    outdict['TotalEnergy']['unit'] = 'EV'
-    outdict['TotalEnergy']['associate_to_sample'] = True
-
-
-    outdict['TotalVolume'] = {}
-    outdict['TotalVolume']['value'] = np.round(avol, decimals=4)
-    outdict['TotalVolume']['unit'] = 'ANGSTROM3'
-    outdict['TotalVolume']['associate_to_sample'] = True 
-
-    return outdict
+    outputs = []
+    outputs.append({'label': 'TotalEnergy', 
+        'value': np.round(aen, decimals=4), 
+        'unit': 'EV',
+        'associate_to_sample': True})
+    outputs.append({'label': 'TotalVolume', 
+        'value': np.round(avol, decimals=4), 
+        'unit': 'ANGSTROM3',
+        'associate_to_sample': True})
+    return outputs