fixed inf problem in test_gromacs

atomisticparsers/gromacs/parser.py

@@ -1565,7 +1565,31 @@ def parse_workflow(self):
         #             sec_fe.value_total_energy_differences_magnitude = columns[:, 2:-1]
         #             sec_fe.value_PV_energy_magnitude = columns[:, -1]
 
-    def check_input_parameters_dict_recursive(self, input_dict, key):
+    def standardize_input_parameters_dict_recursive(self, input_dict: dict):
+        """_summary_
+
+        Args:
+            input_dict (dict): _description_
+        """
+        for key, val in input_dict.items():
+            if isinstance(val, dict):
+                self.standardize_input_parameters_dict_recursive(val)
+            elif isinstance(val, str):
+                input_dict[key.replace('_', '-')] = val.lower()
+            elif isinstance(val, float):
+                if abs(val) == np.inf:
+                    input_dict[key] = 'inf' if val > 0 else '-inf'
+
+    def check_input_parameters_dict_recursive(self, input_dict: dict, key: str):
+        """_summary_
+
+        Args:
+            input_dict (dict): _description_
+            key (str): _description_
+
+        Returns:
+            _type_: _description_
+        """
         if key in input_dict:
             return True
         for _, v in input_dict.items():
@@ -1639,10 +1663,12 @@ def write_to_archive(self):
             sec_run.x_gromacs_number_of_tasks = host_info[2]
 
         # parse the input parameters using log file's hierarchical structure as default
-        self.input_parameters = {
-            key.replace('_', '-'): val.lower() if isinstance(val, str) else val
-            for key, val in self.log_parser.get('input_parameters', {}).items()
-        }
+        # self.input_parameters = {
+        #     key.replace('_', '-'): val.lower() if isinstance(val, str) else val
+        #     for key, val in self.log_parser.get('input_parameters', {}).items()
+        # }
+        self.input_parameters = self.log_parser.get('input_parameters', {})
+        self.standardize_input_parameters_dict_recursive(self.input_parameters)
 
         # read the mdp output or input to supplement the log inputs (i.e., only store if not found in log)
         self.mdp_parser.mainfile = self.get_mdp_file()

tests/data/gromacs/free_energy_calculations/alchemical_transformation_single_run/input_parameters.json

@@ -36,7 +36,7 @@
   "rcoulomb-switch": 0,
   "rcoulomb": 1.1,
   "epsilon-r": 15,
-  "epsilon-rf": null,
+  "epsilon-rf": "inf",
   "vdw-type": "cut-off",
   "vdw-modifier": "potential-shift",
   "rvdw-switch": 0,

tests/data/gromacs/input_parameters/input_parameters.json

@@ -36,7 +36,7 @@
   "rcoulomb-switch": 0,
   "rcoulomb": 1.1,
   "epsilon-r": 15,
-  "epsilon-rf": null,
+  "epsilon-rf": "inf",
   "vdw-type": "cut-off",
   "vdw-modifier": "potential-shift",
   "rvdw-switch": 0,

tests/test_gromacsparser.py

@@ -546,9 +546,6 @@ def assert_dict_equal(d1, d2):
         assert d1.keys() == d2.keys(), f'Keys mismatch: {d1.keys()} != {d2.keys()}'
 
         for key in d1:
-            if key == 'epsilon-rf':  # TODO remove this once the inf issue is resolved
-                continue
-
             if isinstance(d1[key], dict) and isinstance(d2[key], dict):
                 assert_dict_equal(d1[key], d2[key])
             else:
@@ -560,6 +557,8 @@ def assert_dict_equal(d1, d2):
                     assert np.isclose(
                         d1[key], d2[key]
                     ).all(), f"Value mismatch for key '{key}': {d1[key]} != {d2[key]}"
+                elif abs(d1[key]) == float('inf'):
+                    assert 'inf' == d2[key] if d1[key] > 0 else '-inf' == d2[key]
                 else:
                     assert d1[key] == approx(
                         d2[key]