out.xml Parser Changes

masci_tools/io/parsers/fleur/default_parse_tasks.py

@@ -119,6 +119,13 @@
                 'name': 'band'
             }
         },
+        'bz_integration': {
+            'parse_type': 'attrib',
+            'path_spec': {
+                'name': 'mode',
+                'tag_name': 'bzIntegration'
+            }
+        }
     },
     #--------Defintions for general info from outfile (start, endtime, number_iterations)--------
     'general_out_info': {
@@ -138,12 +145,6 @@
                 'name': 'targetComputerArchitectures'
             }
         },
-        'creator_target_structure': {
-            'parse_type': 'text',
-            'path_spec': {
-                'name': 'targetStructureClass'
-            }
-        },
         'output_file_version': {
             'parse_type': 'attrib',
             'path_spec': {
@@ -168,6 +169,13 @@
                 'name': 'ntype'
             }
         },
+        'number_of_kpoints': {
+            'parse_type': 'attrib',
+            'path_spec': {
+                'name': 'count',
+                'contains': 'numericalParameters'
+            }
+        },
         'start_date': {
             'parse_type': 'allAttribs',
             'path_spec': {
@@ -387,7 +395,7 @@
     },
     'distances': {
         '_minimal': True,
-        'charge_density': {
+        'density_convergence': {
             'parse_type': 'attrib',
             'path_spec': {
                 'name': 'distance',
@@ -406,14 +414,14 @@
     'magnetic_distances': {
         '_minimal': True,
         '_modes': [('jspin', 2)],
-        'overall_charge_density': {
+        'overall_density_convergence': {
             'parse_type': 'attrib',
             'path_spec': {
                 'name': 'distance',
                 'tag_name': 'overallChargeDensity'
             }
         },
-        'spin_density': {
+        'spin_density_convergence': {
             'parse_type': 'attrib',
             'path_spec': {
                 'name': 'distance',
@@ -484,6 +492,7 @@
         }
     },
     'bandgap': {
+        '_modes': [('bz_integration', 'hist')],
         'bandgap': {
             'parse_type': 'singleValue',
             'path_spec': {
@@ -514,6 +523,7 @@
         }
     },
     'forces': {
+        '_minimal': True,
         '_modes': [('relax', True)],
         '_conversions': ['convert_forces'],
         'force_units': {

masci_tools/io/parsers/fleur/fleur_outxml_parser.py

@@ -61,7 +61,7 @@ def outxml_parser(outxmlfile, version=None, parser_info_out=None, iteration_to_p
     if parser_info_out is None:
         parser_info_out = {'parser_warnings': [], 'fleur_modes': {}, 'debug_info': {}}
 
-    parser_version = '0.3.0'
+    parser_version = '0.4.0'
     parser_info_out['parser_info'] = f'Masci-Tools Fleur out.xml Parser v{parser_version}'
 
     outfile_broken = False
@@ -309,7 +309,9 @@ def parse_general_information(root, parser, outschema_dict, iteration_to_parse=N
 
     #For certain fleur modes we need to overwrite the tasks
     if fleurmode['dos'] or fleurmode['band']:
-        parser.iteration_tasks = ['iteration_number', 'fermi_energy', 'bandgap']
+        parser.iteration_tasks = ['iteration_number', 'fermi_energy']
+        if fleurmode['bz_integration'] == 'hist':
+            parser.iteration_tasks = ['iteration_number', 'fermi_energy', 'bandgap']
 
     if fleurmode['relax'] and iteration_to_parse == 'last':
         if 'distances' in parser.iteration_tasks:

masci_tools/io/parsers/fleur/fleur_schema/schema_dict.py

@@ -322,17 +322,15 @@ def fromVersion(cls, version, inp_version=None, parser_info_out=None, no_cache=F
             parser_info_out['parser_warnings'].append(
                 f'Creating OutputSchemaDict object for differing versions (out: {version}; inp: {inp_version})')
 
-        version_hash = hash((version, inp_version))
-
-        if version_hash in cls.__schema_dict_cache and not no_cache:
-            return cls.__schema_dict_cache[version_hash]
+        if (version, inp_version) in cls.__schema_dict_cache and not no_cache:
+            return cls.__schema_dict_cache[(version, inp_version)]
 
         inpschema_dict = InputSchemaDict.fromVersion(inp_version, no_cache=no_cache)
-        cls.__schema_dict_cache[version_hash] = cls.fromPath(schema_file_path,
-                                                             inp_path=inpschema_file_path,
-                                                             inpschema_dict=inpschema_dict)
+        cls.__schema_dict_cache[(version, inp_version)] = cls.fromPath(schema_file_path,
+                                                                       inp_path=inpschema_file_path,
+                                                                       inpschema_dict=inpschema_dict)
 
-        return cls.__schema_dict_cache[version_hash]
+        return cls.__schema_dict_cache[(version, inp_version)]
 
     @classmethod
     def fromPath(cls, path, inp_path=None, inpschema_dict=None):

masci_tools/io/parsers/fleur/outxml_conversions.py

@@ -196,7 +196,7 @@ def convert_relax_info(out_dict, parser_info_out=None):
 
     out_dict['relax_atomtype_info'] = []
     for specie in species:
-        out_dict['relax_atomtype_info'].append([specie, species_info[specie]])
+        out_dict['relax_atomtype_info'].append((specie, species_info[specie]))
 
     return out_dict
 
@@ -210,42 +210,39 @@ def convert_forces(out_dict, parser_info_out=None):
     """
     parsed_forces = out_dict.pop('parsed_forces')
 
-    if 'force_largest' not in out_dict:
-        out_dict['force_largest'] = []
+    if 'force_largest_component' not in out_dict:
+        out_dict['force_largest_component'] = []
+        out_dict['force_atoms'] = []
+        out_dict['abspos_atoms'] = []
 
     if isinstance(parsed_forces['atom_type'], int):
         parsed_forces = {key: [val] for key, val in parsed_forces.items()}
 
     largest_force = 0.0
+    forces = []
+    abspos = []
     for index, atomType in enumerate(parsed_forces['atom_type']):
 
-        if f'force_x_type{atomType}' not in out_dict:
-            out_dict[f'force_x_type{atomType}'] = []
-            out_dict[f'force_y_type{atomType}'] = []
-            out_dict[f'force_z_type{atomType}'] = []
-            out_dict[f'abspos_x_type{atomType}'] = []
-            out_dict[f'abspos_y_type{atomType}'] = []
-            out_dict[f'abspos_z_type{atomType}'] = []
-
         force_x = parsed_forces['f_x'][index]
         force_y = parsed_forces['f_y'][index]
         force_z = parsed_forces['f_z'][index]
 
+        x = parsed_forces['x'][index]
+        y = parsed_forces['y'][index]
+        z = parsed_forces['z'][index]
+
+        forces.append((atomType, [force_x, force_y, force_z]))
+        abspos.append((atomType, [x, y, z]))
+
         if abs(force_x) > largest_force:
             largest_force = abs(force_x)
         if abs(force_y) > largest_force:
             largest_force = abs(force_y)
         if abs(force_z) > largest_force:
             largest_force = abs(force_z)
 
-        out_dict[f'force_x_type{atomType}'].append(force_x)
-        out_dict[f'force_y_type{atomType}'].append(force_y)
-        out_dict[f'force_z_type{atomType}'].append(force_z)
-
-        out_dict[f'abspos_x_type{atomType}'].append(parsed_forces['x'][index])
-        out_dict[f'abspos_y_type{atomType}'].append(parsed_forces['y'][index])
-        out_dict[f'abspos_z_type{atomType}'].append(parsed_forces['z'][index])
-
-    out_dict['force_largest'].append(largest_force)
+    out_dict['force_largest_component'].append(largest_force)
+    out_dict['force_atoms'].append(forces)
+    out_dict['abspos_atoms'].append(abspos)
 
     return out_dict

masci_tools/tests/test_fleur_outxml_parser/test_outxml_add_tasks_append.yml

@@ -2,10 +2,9 @@ output_dict:
   bandgap: 2.2729704824
   bandgap_units: eV
   charge_den_xc_den_integral: -41.7653329254
-  charge_density: 0.026112816
   creator_name: fleur 32
   creator_target_architecture: GEN
-  creator_target_structure: null
+  density_convergence: 0.026112816
   density_convergence_units: me/bohr^3
   end_date:
     date: 2020/12/10
@@ -25,6 +24,7 @@ output_dict:
   number_of_atoms: 2
   number_of_iterations: 6
   number_of_iterations_total: 6
+  number_of_kpoints: 2
   number_of_species: 1
   number_of_spin_components: 1
   number_of_symmetries: 48

masci_tools/tests/test_fleur_outxml_parser/test_outxml_add_tasks_overwrite.yml

@@ -1,10 +1,9 @@
 output_dict:
   bandgap: -580.0645652222
   charge_den_xc_den_integral: -41.7653329254
-  charge_density: 0.026112816
   creator_name: fleur 32
   creator_target_architecture: GEN
-  creator_target_structure: null
+  density_convergence: 0.026112816
   density_convergence_units: me/bohr^3
   end_date:
     date: 2020/12/10
@@ -24,6 +23,7 @@ output_dict:
   number_of_atoms: 2
   number_of_iterations: 6
   number_of_iterations_total: 6
+  number_of_kpoints: 2
   number_of_species: 1
   number_of_spin_components: 1
   number_of_symmetries: 48

masci_tools/tests/test_fleur_outxml_parser/test_outxml_additional_tasks_allattribs.yml

@@ -2,7 +2,6 @@ output_dict:
   bandgap: 2.2729704824
   bandgap_units: eV
   charge_den_xc_den_integral: -41.7653329254
-  charge_density: 0.026112816
   core_info:
     core_info_atom_type: 1
     core_info_atomic_number: 14
@@ -12,7 +11,7 @@ output_dict:
     core_info_spin: 1
   creator_name: fleur 32
   creator_target_architecture: GEN
-  creator_target_structure: null
+  density_convergence: 0.026112816
   density_convergence_units: me/bohr^3
   end_date:
     date: 2020/12/10
@@ -32,6 +31,7 @@ output_dict:
   number_of_atoms: 2
   number_of_iterations: 6
   number_of_iterations_total: 6
+  number_of_kpoints: 2
   number_of_species: 1
   number_of_spin_components: 1
   number_of_symmetries: 48

masci_tools/tests/test_fleur_outxml_parser/test_outxml_additional_tasks_simple.yml

@@ -2,11 +2,10 @@ output_dict:
   bandgap: 2.2729704824
   bandgap_units: eV
   charge_den_xc_den_integral: -41.7653329254
-  charge_density: 0.026112816
   core_eig_val_sum: -130.3854013875
   creator_name: fleur 32
   creator_target_architecture: GEN
-  creator_target_structure: null
+  density_convergence: 0.026112816
   density_convergence_units: me/bohr^3
   end_date:
     date: 2020/12/10
@@ -26,6 +25,7 @@ output_dict:
   number_of_atoms: 2
   number_of_iterations: 6
   number_of_iterations_total: 6
+  number_of_kpoints: 2
   number_of_species: 1
   number_of_spin_components: 1
   number_of_symmetries: 48

masci_tools/tests/test_fleur_outxml_parser/test_outxml_alliter.yml

@@ -14,16 +14,15 @@ output_dict:
   - -41.7699610697
   - -41.7648027154
   - -41.7653329254
-  charge_density:
+  creator_name: fleur 32
+  creator_target_architecture: GEN
+  density_convergence:
   - 8.7379598265
   - 8.2515493263
   - 1.0238480245
   - 0.5765372317
   - 0.2277277793
   - 0.026112816
-  creator_name: fleur 32
-  creator_target_architecture: GEN
-  creator_target_structure: null
   density_convergence_units: me/bohr^3
   end_date:
     date: 2020/12/10
@@ -73,6 +72,7 @@ output_dict:
   number_of_atoms: 2
   number_of_iterations: 6
   number_of_iterations_total: 6
+  number_of_kpoints: 2
   number_of_species: 1
   number_of_spin_components: 1
   number_of_symmetries: 48

masci_tools/tests/test_fleur_outxml_parser/test_outxml_broken.yml

@@ -2,12 +2,11 @@ output_dict:
   bandgap: 0.0323610284
   bandgap_units: eV
   charge_den_xc_den_integral: -111.9182938603
-  charge_density:
-  - 9.2786635283
-  - 5.4278279348
   creator_name: fleur 32
   creator_target_architecture: GEN
-  creator_target_structure: null
+  density_convergence:
+  - 9.2786635283
+  - 5.4278279348
   density_convergence_units: me/bohr^3
   end_date:
     date: null
@@ -36,12 +35,13 @@ output_dict:
   number_of_atoms: 2
   number_of_iterations: 4
   number_of_iterations_total: 2
+  number_of_kpoints: 3
   number_of_species: 1
   number_of_spin_components: 2
   number_of_symmetries: 16
   output_file_version: '0.34'
-  overall_charge_density: 10.8914872112
-  spin_density: 10.6059102509
+  overall_density_convergence: 10.8914872112
+  spin_density_convergence: 10.6059102509
   spin_dependent_charge_interstitial:
   - 1.00491
   - 1.0077593
@@ -63,6 +63,7 @@ output_dict:
 warnings:
   fleur_modes:
     band: false
+    bz_integration: hist
     dos: false
     film: false
     jspin: 2
@@ -71,10 +72,9 @@ warnings:
     relax: false
     soc: false
   last_iteration_parsed: 2
-  parser_info: Masci-Tools Fleur out.xml Parser v0.3.0
+  parser_info: Masci-Tools Fleur out.xml Parser v0.4.0
   parser_warnings:
   - The out.xml file is broken I try to repair it.
-  - No text found for tag targetStructureClass
   - No values found for attribute date at tag endDateAndTime
   - No values found for attribute time at tag endDateAndTime
   - Endtime was unparsed, inp.xml prob not complete, do not believe the walltime!