debug retrieval of results from zacrosjob

examples/XYZ/lattice_input.dat

@@ -0,0 +1,37 @@
+lattice periodic_cell
+
+cell_vectors       # in row format (Angstroms)
+   2.774687009376012   0.000000000000000
+   0.000000000000000   2.774687009376012
+
+repeat_cell       6   6
+
+n_site_types      2
+site_type_names   brg hol
+
+n_cell_sites      3
+site_types        brg brg hol
+
+site_coordinates   # fractional coordinates (x,y) in row format
+
+   0.500000000000000   0.000000000000000
+   0.000000000000000   0.500000000000000
+   0.500000000000000   0.500000000000000
+
+neighboring_structure # site-neighsite cell
+
+   1-2  self
+   1-3  self
+   2-3  self
+
+   2-1  north
+   3-1  north
+
+   1-2  east
+   3-2  east
+
+   1-2  southeast   
+
+end_neighboring_structure
+
+end_lattice

examples/Ziff-Gulari-Barshad-model-variants.json

@@ -19,7 +19,7 @@
         "wall_time": 100 
     },
 
-  "lattice_input": {"xyz_file": "../tests/test_files/lattice_input.dat"},
+  "lattice_input": {"xyz_file": "XYZ/lattice_input.dat"},
 
   "energetics_input": [
     { "name": "CO_Point_brg",

examples/Ziff-Gulari-Barshad-model.json

@@ -19,7 +19,7 @@
         "wall_time": 3600 
     },
 
-  "lattice_input": {"xyz_file": "./Zacros_inputs/lattice_input.dat"},
+  "lattice_input": {"xyz_file": "./XYZ/lattice_input.dat"},
 
   "energetics_input": [
     { "name": "CO_Point",

examples/zacros_model_example.py

@@ -1,21 +1,16 @@
 """Example of py/Zacros model"""
 
 import os
-import json
 from osp.models.zacros.co_pyzacros import COpyZacrosModel
 from osp.wrappers.simzacros.simzacros_session import SimzacrosSession
-from osp.core.namespaces import emmo, cuba
+from osp.core.namespaces import cuba
 from osp.core.utils import import_cuds
-from osp.core.utils import pretty_print
 
-#path = os.path.join(os.path.dirname(__file__), "Ziff-Gulari-Barshad-model.json")
-path = os.path.join(os.path.dirname(__file__), "Ziff-Gulari-Barshad-model-variants.json")
-
-with open(path, mode="r+") as file:
-    content = json.loads(file.read())
 
 # alternatively with the standard file. Needs connection to minio!
-#content = COpyZacrosModel.Config.schema_extra["example"]
+content = COpyZacrosModel.Config.schema_extra["example"]
+directory = os.path.dirname(__file__)
+content["lattice_input"]["xyz_file"] = os.path.join(directory, "XYZ", "lattice_input.dat")
 model = COpyZacrosModel(**content)
 
 

osp/tools/mapping_functions.py

@@ -1664,7 +1664,7 @@ def map_results(engine, root_cuds_object: Cuds) -> str:
 
             tarball = map_tarball(engine, last_calculation[0])
 
-    elif isinstance(engine, pz.ZacrosResults):
+    elif isinstance(engine, pz.ZacrosJob):
         search_calculation = search.find_cuds_objects_by_oclass(
                                    emmo.MesoscopicCalculation, root_cuds_object,
                                    rel=cuba.relationship)
@@ -1810,10 +1810,8 @@ def map_tarball(engine, root_cuds_object, path=None) -> str:
     :return str: file system path to tarball
    """
 
-    path = "plams_workdir/"
-
     tar = tempfile.NamedTemporaryFile().name
-    shutil.make_archive(tar, "tar", path)
+    shutil.make_archive(tar, "tar", engine.path)
     tar_file = f"{tar}.tar"
 
     print(f"Job output dumped to {tar_file}")

osp/wrappers/simzacros/simzacros_session.py

@@ -5,12 +5,9 @@
 from osp.tools.io_functions import raise_error
 from osp.tools.mapping_functions import map_function, map_results
 from osp.core.utils import simple_search as search
-from arcp import is_arcp_uri, parse_arcp
 from osp.models.utils.general import get_download
 import scm.pyzacros as pz
 import os
-from urllib.parse import parse_qs
-from pathlib import Path
 # from osp.core.utils import pretty_print
 
 
@@ -41,7 +38,7 @@ def _run(self, root_cuds_object: Cuds):
         pz_job = pz.ZacrosJob(settings=pz_settings, lattice=pz_lattice,
                               mechanism=pz_mechanism, cluster_expansion=pz_cluster_expansion)
         results = pz_job.run()
-        self._tarball = map_results(results, root_cuds_object)
+        self._tarball = map_results(pz_job, root_cuds_object)
 
         # Attributes to easily access (syntactic) info from results.
         self.get_reaction_network = results.get_reaction_network()
@@ -118,7 +115,7 @@ def _apply_added(self, root_obj, buffer):
             lattice = search_lattice.pop()
             if "file://" in str(lattice.iri):
                 split = str(lattice.iri).split("file://")
-                self.lattice = Path(split[-1]).resolve()
+                self.lattice = split[-1]
             else:
                 self.lattice = get_download(str(lattice.uid), as_file=True)
         else: