Species err

environment.yml

@@ -11,7 +11,7 @@ dependencies:
   - cairo
   - cairocffi
   - rmg::cantera >=2.3.0
-  - cclib >=1.6
+  - conda-forge::cclib >=1.6.3
   - rmg::chemprop
   - codecov
   - coolprop
@@ -33,11 +33,12 @@ dependencies:
   - mock
   - rmg::mopac
   - mpmath
+  - rmg::muq2
   - networkx
   - nose
   - rmg::numdifftools
   - numpy >=1.15.4
-  - openbabel
+  - conda-forge::openbabel >= 3
   - paramiko >=2.6.0
   - pandas
   - psutil
@@ -59,4 +60,12 @@ dependencies:
   - scipy
   - sphinx
   - rmg::symmetry
+  - xlrd
   - xlwt
+  - anaconda::sphinx_rtd_theme
+  - anaconda::paramiko >=2.6.0
+  - conda-forge::py3dmol >= 0.8.0
+  - conda-forge::ase >=3.15.0
+  - anaconda::ipython
+  - anaconda::sphinx
+  - conda-forge::qcelemental == 0.20.0

t3/main.py

@@ -55,7 +55,13 @@
 from arc.species import ARCSpecies
 from arc.species.converter import check_xyz_dict
 
-from t3.common import PROJECTS_BASE_PATH, VALID_CHARS, delete_root_rmg_log, get_species_by_label, time_lapse
+from t3.common import (PROJECTS_BASE_PATH,
+                       VALID_CHARS,
+                       delete_root_rmg_log,
+                       get_rmg_species_from_a_species_dict,
+                       get_species_by_label,
+                       time_lapse,
+                       )
 from t3.logger import Logger
 from t3.schema import InputBase
 from t3.simulate.factory import simulate_factory
@@ -304,6 +310,7 @@ def execute(self):
                 # obtain the dictionary containing all SA coefficients for these species
                 self.sa_dict = simulate_adapter.get_sa_coefficients()
 
+
             # determine what needs to be calculated
             additional_calcs_required = self.determine_species_to_calculate()
 
@@ -683,8 +690,12 @@ def determine_species_to_calculate(self) -> bool:
             for input_species in self.rmg['species']:
                 if input_species['observable'] or input_species['SA_observable']:
                     sa_observables_exist = True
-                    if self.species_requires_refinement(species=get_species_by_label(input_species['label'],
-                                                                                     self.rmg_species)):
+                    species = get_species_by_label(input_species['label'], self.rmg_species) or \
+                                get_rmg_species_from_a_species_dict(input_species)
+                    if species is None:
+                        raise ValueError(f'Cannot find species\n{input_species} in the species list,'
+                                         f'and cannot create a species without a proper structure.')
+                    if self.species_requires_refinement(species=species):
                         species_keys.append(self.add_species(
                             species=get_species_by_label(input_species['label'], self.rmg_species),
                             reasons=['SA observable'],
@@ -978,6 +989,8 @@ def species_requires_refinement(self, species: Species) -> bool:
         Returns:
             bool: Whether the species thermochemical properties should be calculated. ``True`` if they should be.
         """
+        if species is None:
+            raise ValueError('Cannot process value None for argument species.')
         thermo_comment = species.thermo.comment.split('Solvation')[0]
         if self.get_species_key(species=species) is None \
                 and ('group additivity' in thermo_comment or '+ radical(' in thermo_comment):

t3/schema.py

@@ -503,7 +503,7 @@ def check_model(cls, value):
     @validator('pdep')
     def check_pdep_only_if_gas_phase(cls, value, values):
         """RMG.pdep validator"""
-        if value is not None and values['reactors'] is not None:
+        if value is not None and 'reactors' in values and values['reactors'] is not None:
             reactor_types = set([reactor.type for reactor in values['reactors']])
             if value is not None and not any(['gas' in reactor for reactor in reactor_types]):
                 raise ValueError(f'A pdep section can only be specified for gas phase reactors, got: {reactor_types}')

t3/simulate/cantera_constantTP.py

@@ -209,6 +209,8 @@ def reinitialize_simulation(self,
         """
         # assign initial conditions
         if V0 is None:
+            T0 = T0[0] if isinstance(T0, np.ndarray) else T0
+            P0 = T0[0] if isinstance(T0, np.ndarray) else P0
             self.model.TPX = T0, P0, X0
         elif P0 is None:
             self.model.TDX = T0, 1 / V0, X0
@@ -394,6 +396,7 @@ def get_sa_coefficients(self):
         Returns:
              sa_dict (dict): a SA dictionary, whose structure is given in the docstring for T3/t3/main.py
         """
+
         sa_dict = {'kinetics': dict(), 'thermo': dict(), 'time': list()}
 
         for condition_data in self.all_data: