Various minor repo-wide fixes

Author: alongd

CODE_OF_CONDUCT.md

@@ -1,6 +1,4 @@
-# The Tandem Tool (T3) for automated chemical kinetic model development
-
-# Code of Conduct
+# T3 Code of Conduct
 
 ## Our Pledge
 

t3/main.py

@@ -1152,13 +1152,13 @@ def get_reaction_key(self,
                     try:
                         if label == t3_reaction.get_reaction_smiles_label():
                             return key
-                    except Exception:
+                    except (AttributeError, ValueError):
                         pass
                 elif label_type == 'Chemkin':
                     try:
                         if label == t3_reaction.to_chemkin():
                             return key
-                    except Exception:
+                    except (AttributeError, ValueError):
                         pass
         return None
 

t3/runners/rmg_runner.py

@@ -4,9 +4,11 @@
 """
 
 import datetime
+import logging
 import os
 import shlex
 import shutil
+import subprocess
 import time
 from typing import TYPE_CHECKING, List, Optional, Tuple
 
@@ -171,7 +173,10 @@ def _parse_walltime_to_seconds(walltime: str) -> int:
     parts = walltime.split(':')
     if len(parts) != 4:
         return 0
-    days, hours, minutes, seconds = (int(p) for p in parts)
+    try:
+        days, hours, minutes, seconds = (int(p) for p in parts)
+    except ValueError:
+        return 0
     return days * 86400 + hours * 3600 + minutes * 60 + seconds
 
 
@@ -218,6 +223,9 @@ def run_rmg_incore(rmg_input_file_path: str,
     except subprocess.TimeoutExpired:
         logger.error(f'RMG incore timed out after {timeout_s}s')
         return True
+    if result.returncode != 0:
+        logger.error(f'RMG incore exited with code {result.returncode}')
+        return True
     if 'RMG threw an exception and did not converge.' in stderr_text:
         return True
     return False

t3/schema.py

@@ -477,7 +477,7 @@ class Config:
     @classmethod
     def check_units(cls, value):
         """RMGOptions.units validator"""
-        if value.lower() is not None and value != 'si':
+        if value.lower() != 'si':
             raise ValueError(f'Currently RMG only supports SI units, got "{value}"')
         return value.lower()
 

t3/simulate/cantera_base.py

@@ -8,6 +8,7 @@
 different reactor configuration.
 """
 
+import logging
 import cantera as ct
 import numpy as np
 from abc import abstractmethod
@@ -331,6 +332,9 @@ def simulate(self):
                     non_inert_mask = np.ones(self.num_ct_species, dtype=bool)
                     non_inert_mask[self.inert_index_list] = False
 
+                    if not np.all(np.isfinite(mass_frac_sa)):
+                        logging.getLogger(__name__).warning(
+                            'NaN/inf detected in mass fraction SA matrix — check for numerical issues')
                     kin_correction = mass_frac_sa[non_inert_mask, :self.num_ct_reactions].sum(axis=0)
                     thermo_correction = mass_frac_sa[non_inert_mask, self.num_ct_reactions:].sum(axis=0)
 
@@ -462,9 +466,17 @@ def get_idt_by_T(self):
             time, data_list, reaction_sensitivity_data, thermodynamic_sensitivity_data = condition_data
             T_data = data_list[0]
 
-            dTdt = np.diff(T_data.data) / np.diff(time.data)
-            idt_dict['idt_index'].append(int(np.argmax(dTdt)))
-            idt_dict['idt'].append(time.data[idt_dict['idt_index'][i]])
+            dt = np.diff(time.data)
+            dt = np.where(dt == 0, np.finfo(float).tiny, dt)
+            dTdt = np.diff(T_data.data) / dt
+            valid = np.isfinite(dTdt)
+            if valid.any():
+                masked = np.where(valid, dTdt, -np.inf)
+                idx = int(np.argmax(masked))
+            else:
+                idx = 0
+            idt_dict['idt_index'].append(idx)
+            idt_dict['idt'].append(time.data[min(idx + 1, len(time.data) - 1)])
 
         return idt_dict
 

t3/simulate/cantera_jsr.py

@@ -114,6 +114,8 @@ def reinitialize_simulation(self, T0=None, P0=None, X0=None, V0=None):
         self._jsr_exhaust = ct.Reservoir(self.model)
         self.cantera_reactor = ct.IdealGasReactor(self.model, energy='off', volume=VOLUME)
 
+        if residence_time <= 0:
+            raise ValueError(f'Invalid residence time: {residence_time}')
         self._jsr_mfc = ct.MassFlowController(
             upstream=self._jsr_inlet,
             downstream=self.cantera_reactor,

t3/simulate/cantera_pfr.py

@@ -129,6 +129,7 @@ def _compute_distance(self):
             # Velocity: u = u_0 * mean_MW_0 / mean_MW  (P, T, A all cancel)
             total_residence_time = self.conditions[idx].reaction_time.value_si
             u_0 = LENGTH / total_residence_time
+            mean_MW = np.where(mean_MW > 0, mean_MW, np.finfo(float).tiny)
             u = u_0 * mean_MW[0] / mean_MW
 
             # Axial distance [m] via cumulative integration
@@ -203,6 +204,8 @@ def _simulate_chain(self):
                 sim.advance_to_steady_state()
 
                 # Residence time in this cell
+                if mass_flow_rate <= 0:
+                    raise ValueError(f'Invalid mass flow rate: {mass_flow_rate}')
                 cell_residence_time = reactor.mass / mass_flow_rate
                 cumulative_time += cell_residence_time
 

t3/simulate/cantera_pfr_t_profile.py

@@ -107,6 +107,11 @@
 T_HOT = 900.0          # K, isothermal plateau temperature
 T_OUTLET = 500.0       # K, outlet temperature
 
+if not (0 < RAMP_UP_END < ISO_END < LENGTH):
+    raise ValueError(
+        f'Temperature profile constants must satisfy 0 < RAMP_UP_END ({RAMP_UP_END}) < ISO_END ({ISO_END}) < LENGTH ({LENGTH})'
+    )
+
 
 def temperature_profile(z):
     """
@@ -307,7 +312,11 @@ def simulate(self):
                 # Local velocity at the new (T, rho) and the corresponding
                 # time step to traverse one segment.
                 rho = self.model.density
+                if rho * AREA <= 0:
+                    raise ValueError(f'Invalid density ({rho}) or area ({AREA}) in PFR T-profile cell {n}')
                 u = mass_flow_rate / (rho * AREA)
+                if u <= 0:
+                    raise ValueError(f'Invalid velocity ({u}) in PFR T-profile cell {n}')
                 dt = dz / u
 
                 sim.advance(sim.time + dt)

t3/simulate/rmg_constant_tp.py

@@ -5,6 +5,7 @@
 
 import datetime
 import itertools
+import logging
 import os
 import numpy as np
 from typing import List, Optional, TYPE_CHECKING
@@ -131,6 +132,7 @@ def simulate(self):
 
             if not success:
                 self.logger.error(f"RMG SA subprocess failed.\nDetails: {error_msg}")
+                raise RuntimeError(f"RMG SA subprocess failed: {error_msg}")
             else:
                 self.logger.info("RMG SA subprocess completed successfully.")
         else:
@@ -279,6 +281,12 @@ def get_species_concentration_lists_from_ranged_params(self) -> List[List[dict]]
                 species_lists.append(new_species_list)
 
         for species_list in species_lists:
+            total = sum(s['concentration'] for s in species_list
+                        if isinstance(s['concentration'], (int, float)))
+            if total > 1.0 or total <= 0:
+                logging.getLogger(__name__).warning(
+                    f'Species concentrations sum to {total:.4f}, expected (0, 1]. '
+                    f'Cantera will normalize mole fractions.')
             species_list.sort(key=lambda spc: spc['concentration'][0] if isinstance(spc['concentration'], (tuple, list))
             else spc['concentration'], reverse=True)
         return species_lists

t3/utils/libraries.py

@@ -21,8 +21,8 @@
     from t3.logger import Logger
 
 
-_LOCK_TIMEOUT_S = 3600  # 1 hour wait for lock acquisition
-_LOCK_STALE_S = 3600    # 1 hour before breaking a stale lock
+_LOCK_TIMEOUT_S = 300   # 5 min wait for lock acquisition
+_LOCK_STALE_S = 300     # 5 min before breaking a stale lock
 _LOCK_POLL_S = 10.0     # Poll every 10 seconds