Merge pull request #105 from OpenBioSim/fix_crash_report

Expose missing save_crash_report dynamics option

Author: lohedges

src/somd2/config/_config.py

@@ -152,6 +152,7 @@ def __init__(
         overwrite=False,
         somd1_compatibility=False,
         pert_file=None,
+        save_crash_report=False,
         save_energy_components=False,
         page_size=None,
         timeout="300 s",
@@ -451,6 +452,9 @@ def __init__(
             The path to a SOMD1 perturbation file to apply to the reference system.
             When set, this will automatically set 'somd1_compatibility' to True.
 
+        save_crash_report: bool
+            Whether to save a crash report if the simulation crashes.
+
         save_energy_components: bool
             Whether to save the energy contribution for each force when checkpointing.
             This is useful when debugging crashes.
@@ -544,6 +548,7 @@ def __init__(
         self.use_backup = use_backup
         self.somd1_compatibility = somd1_compatibility
         self.pert_file = pert_file
+        self.save_crash_report = save_crash_report
         self.save_energy_components = save_energy_components
         self.timeout = timeout
         self.num_energy_neighbours = num_energy_neighbours
@@ -1876,6 +1881,16 @@ def pert_file(self, pert_file):
 
         self._pert_file = pert_file
 
+    @property
+    def save_crash_report(self):
+        return self._save_crash_report
+
+    @save_crash_report.setter
+    def save_crash_report(self, save_crash_report):
+        if not isinstance(save_crash_report, bool):
+            raise ValueError("'save_crash_report' must be of type 'bool'")
+        self._save_crash_report = save_crash_report
+
     @property
     def save_energy_components(self):
         return self._save_energy_components

src/somd2/runner/_repex.py

@@ -1144,6 +1144,7 @@ def _run_block(
                 auto_fix_minimise=True,
                 num_energy_neighbours=self._config.num_energy_neighbours,
                 null_energy=self._config.null_energy,
+                save_crash_report=self._config.save_crash_report,
                 # GCMC specific options.
                 excess_chemical_potential=(
                     self._mu_ex if gcmc_sampler is not None else None
@@ -1381,6 +1382,7 @@ def _equilibrate(self, index):
                 frame_frequency=0,
                 save_velocities=False,
                 auto_fix_minimise=True,
+                save_crash_report=self._config.save_crash_report,
             )
 
             # Commit the system.

src/somd2/runner/_runner.py

@@ -519,6 +519,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
                     frame_frequency=0,
                     save_velocities=False,
                     auto_fix_minimise=True,
+                    save_crash_report=self._config.save_crash_report,
                 )
 
                 # Commit the system.
@@ -686,6 +687,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
                                 auto_fix_minimise=True,
                                 num_energy_neighbours=num_energy_neighbours,
                                 null_energy=self._config.null_energy,
+                                save_crash_report=self._config.save_crash_report,
                                 # GCMC specific options.
                                 excess_chemical_potential=(
                                     self._mu_ex if gcmc_sampler is not None else None
@@ -723,6 +725,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
                             auto_fix_minimise=True,
                             num_energy_neighbours=num_energy_neighbours,
                             null_energy=self._config.null_energy,
+                            save_crash_report=self._config.save_crash_report,
                         )
                 except Exception as e:
                     try:
@@ -820,6 +823,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
                         auto_fix_minimise=True,
                         num_energy_neighbours=num_energy_neighbours,
                         null_energy=self._config.null_energy,
+                        save_crash_report=self._config.save_crash_report,
                     )
 
                     # Save the energy contribution for each force.
@@ -895,6 +899,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
                             auto_fix_minimise=True,
                             num_energy_neighbours=num_energy_neighbours,
                             null_energy=self._config.null_energy,
+                            save_crash_report=self._config.save_crash_report,
                         )
 
                         # Perform a GCMC move.
@@ -922,6 +927,7 @@ def generate_lam_vals(lambda_base, increment=0.001):
                         auto_fix_minimise=True,
                         num_energy_neighbours=num_energy_neighbours,
                         null_energy=self._config.null_energy,
+                        save_crash_report=self._config.save_crash_report,
                     )
             except Exception as e:
                 try: