Fix/parsing lattice file (#18)

*  make references to original file instead of parsing them

* update code with respect to parsing of structures

* update unit tests

* debug energy landscape refinement

* debug adp

* update syntactic settings

* update wrapper tools for binding site calculation

* update defaults in syntactic settings

* make neighbour cut off optional in PES exploration

* update wrong variable

* update bad indent

* debug initializing mesoscale model

* mute neighbour cut off mapping for now

* update default value for neighbor cut off

* update wrong variable for process parallelization

* update retrieval of mechanisms

* update mode of temporary files

* add function to replace site types

* debug: print molar fractions and gas species

* uncomment unneeded code lines

* comment further lines for debug

* debug:comment unneeded lines for cluster expansion

* debug: comment unneeded lines

* debug:update list indexing

* move pz job out of get_rate-function

* debug: print lattice ids

* debug: print lattice ids

* debug:add seek mechanism while writing to temp file

* debug: update wrong variable

* debug: add example which imports the graph at mesoscopic level

* mute molar fraction for O2 in ADP

* remove printing, change CO2 to CO

* add needed comma to result output var

* add needed comma in tuple

* move from list to tuple

* debug: print resulting data from scan job

* debug:print settings

* update wrapping function for snapshots, uncomment pressure division

* remove float conversion in generic setting for zacros

* also remove float conversion from other generic settings

* move float conversion to other function and add asterisk

* remove print statements, successfully run adp

* update examples

* correct indentation

* add plot and update example

* update engine paths

* update function for mapping results

* update path variables

* update path keyword

* update path variable

examples/CO+Pt111_models.py

@@ -36,14 +36,14 @@
         "n_gas_species": 1,                                                                                                       
         "gas_specs_names": ["CO"],
         "gas_molar_fracs": [0.1],
-        "snapshots": ["on time", 3.5],
+        "snapshots": ["on logtime", 1e-8, 3.5],
         "species_numbers": ["on time", 3.5],
         "process_statistics": ["on time", 3.5],
         "max_time": 0.00001,
     },
     "adp": {
-        "min": 0.2,
-        "max": 0.8,
+        "min": 0.001,
+        "max": 0.999,
         "num": 5
     }
 }

examples/plot.py

@@ -0,0 +1,16 @@
+import numpy as np
+import adaptiveDesignProcedure as adp
+import matplotlib.pyplot as plt
+
+path = "plams_workdir/adp.results/"
+
+x_CO_model = np.linspace(0.001,0.999,201)
+TOF_CO2_model, = adp.predict( x_CO_model.reshape(-1,1), path ).T
+
+ax = plt.axes()
+ax.set_xlabel('Molar Fraction CO', fontsize=14)
+ax.set_ylabel("TOF (mol/s/site)", fontsize=14)
+ax.plot(x_CO_model, TOF_CO2_model, color='red', linestyle='-', lw=2, zorder=0)
+plt.tight_layout()
+plt.savefig("apd.png")
+

osp/tools/mapping_functions.py

@@ -1577,7 +1577,7 @@ def map_energies(root_cuds_object: Cuds) -> list:
     return electronic_energy_values
 
 
-def map_results(engine, root_cuds_object: Cuds) -> str:
+def map_results(engine, root_cuds_object: Cuds, path:str=None) -> str:
     """
     Add main results to the Cuds (Wrapper) object.
 
@@ -1760,7 +1760,7 @@ def map_results(engine, root_cuds_object: Cuds) -> str:
         search_calculation = search.find_cuds_objects_by_oclass(
                                    emmo.MesoscopicCalculation, root_cuds_object,
                                    rel=cuba.relationship)
-        tarball = map_tarball(engine, search_calculation[0])
+        tarball = map_tarball(engine, search_calculation[0], path=path)
 
     else:
         raise_error(file=os.path.basename(__file__), function=map_results.__name__,
@@ -1901,9 +1901,10 @@ def map_tarball(engine, root_cuds_object, path=None) -> str:
 
     :return str: file system path to tarball
    """
+    path = path or engine.path
 
     tar = tempfile.NamedTemporaryFile().name
-    shutil.make_archive(tar, "tar", engine.path)
+    shutil.make_archive(tar, "tar", path)
     tar_file = f"{tar}.tar"
 
     print(f"Job output dumped to {tar_file}")

osp/wrappers/simzacros/simzacros_session.py

@@ -112,26 +112,26 @@ def get_rate( conditions ):
             uuid = get_upload(adpML.forestFileForCFD)
             pkl = emmo.PKLFile(uid=UUID(uuid))
             self.adp_cuds.add(pkl, rel=emmo.hasOutput)
+            self._tarball = map_results(pz_job, root_cuds_object, path=self.workdir)
 
         else:
             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(pz_job, root_cuds_object)
-
-        # Attributes to easily access (syntactic) info from results.
-        self.get_reaction_network = results.get_reaction_network()
-        self.provided_quantities_names = results.provided_quantities_names()
-        self.provided_quantities = results.provided_quantities()
-        self.number_of_lattice_sites = results.number_of_lattice_sites()
-        self.gas_species_names = results.gas_species_names()
-        self.surface_species_names = results.surface_species_names()
-        self.site_type_names = results.site_type_names()
-        self.number_of_snapshots = results.number_of_snapshots()
-        self.number_of_process_statistics = results.number_of_process_statistics()
-        self.elementary_steps_names = results.elementary_steps_names()
-
+            # Attributes to easily access (syntactic) info from results.
+            self.get_reaction_network = results.get_reaction_network()
+            self.provided_quantities_names = results.provided_quantities_names()
+            self.provided_quantities = results.provided_quantities()
+            self.number_of_lattice_sites = results.number_of_lattice_sites()
+            self.gas_species_names = results.gas_species_names()
+            self.surface_species_names = results.surface_species_names()
+            self.site_type_names = results.site_type_names()
+            self.number_of_snapshots = results.number_of_snapshots()
+            self.number_of_process_statistics = results.number_of_process_statistics()
+            self.elementary_steps_names = results.elementary_steps_names()
+
+            self._tarball = map_results(pz_job, root_cuds_object)
     # OVERRIDE
     def _load_from_backend(self, uids, expired=None):
         """Load the cuds object from the simulation engine."""