fixed z bug

src/scgenerator/cli/cli.py

@@ -43,7 +43,7 @@ def create_parser():
         default=None,
     )
     run_parser.add_argument(
-        "--output-name", "--o", help="path to the final output folder", default=None
+        "--output-name", "-o", help="path to the final output folder", default=None
     )
     run_parser.set_defaults(func=run_sim)
 
@@ -65,7 +65,7 @@ def create_parser():
         "path", help="path to the final simulation folder containing 'initial_config.toml'"
     )
     merge_parser.add_argument(
-        "--output-name", "--o", help="path to the final output folder", default=None
+        "--output-name", "-o", help="path to the final output folder", default=None
     )
     merge_parser.set_defaults(func=merge)
 

src/scgenerator/initialize.py

@@ -139,14 +139,14 @@ class RecoveryParamSequence(ParamSequence):
     def __iter__(self) -> Iterator[Tuple[List[Tuple[str, Any]], dict]]:
         for variable_list, full_config in required_simulations(self.config):
 
-            sub_folder = os.path.join(
+            data_dir = os.path.join(
                 io.get_data_folder(self.id), utils.format_variable_list(variable_list)
             )
 
-            if not io.propagation_initiated(sub_folder):
+            if not io.propagation_initiated(data_dir):
                 yield variable_list, compute_init_parameters(full_config)
-            elif io.num_left_to_propagate(sub_folder, self.config["simulation"]["z_num"]) != 0:
-                yield variable_list, recover_params(full_config, variable_list, self.id)
+            elif io.num_left_to_propagate(data_dir, self.config["simulation"]["z_num"]) != 0:
+                yield variable_list, recover_params(full_config, data_dir)
             else:
                 continue
 
@@ -515,15 +515,20 @@ def _ensure_consistency(config):
     return config
 
 
-def recover_params(params: dict, variable_only: List[Tuple[str, Any]], task_id: int):
-    params = compute_init_parameters(params)
-    vary_str = utils.format_variable_list(variable_only)
-    path = os.path.join(io.get_data_folder(task_id), vary_str)
-    num, last_spectrum = io.load_last_spectrum(path)
+def recover_params(config: Dict[str, Any], data_folder: os.PathLike) -> Dict[str, Any]:
+    path = Path(data_folder)
+    params = compute_init_parameters(config)
+    try:
+        prev_params = io.load_toml(path / "params.toml")
+    except FileNotFoundError:
+        prev_params = {}
+    for k, v in prev_params.items():
+        params.setdefault(k, v)
+    num, last_spectrum = io.load_last_spectrum(str(path))
     params["spec_0"] = last_spectrum
     params["field_0"] = np.fft.ifft(last_spectrum)
     params["recovery_last_stored"] = num
-    params["cons_qty"] = np.load(os.path.join(path, "cons_qty.npy"))
+    params["cons_qty"] = np.load(os.path.join(data_folder, "cons_qty.npy"))
     return params
 
 

src/scgenerator/io.py

@@ -361,6 +361,7 @@ def find_last_spectrum_file(path: str):
 
 
 def load_last_spectrum(path: str) -> Tuple[int, np.ndarray]:
+    """return the last spectrum stored in path as well as its id"""
     num = find_last_spectrum_file(path)
     return num, np.load(os.path.join(path, f"spectrum_{num}.npy"))
 
@@ -421,10 +422,10 @@ def update_appended_params(param_path, new_path, z):
     params = load_toml(param_path)
     if "simulation" in params:
         params["simulation"]["z_num"] = z_num
-        params["simulation"]["z_targets"] = z_num
+        params["simulation"]["z_targets"] = z
     else:
         params["z_num"] = z_num
-        params["z_targets"] = z_num
+        params["z_targets"] = z
     save_toml(new_path, params)
 
 

src/scgenerator/physics/simulate.py

@@ -124,13 +124,13 @@ class RK4IP:
 
     def _setup_sim_parameters(self):
         # making sure to keep only the z that we want
+        self.z_stored = list(self.z_targets.copy()[0 : self.starting_num + 1])
         self.z_targets = list(self.z_targets.copy()[self.starting_num :])
         self.z_targets.sort()
         self.store_num = len(self.z_targets)
 
         # Initial setup of simulation parameters
         self.d_w = self.w_c[1] - self.w_c[0]  # resolution of the frequency grid
-        self.z_stored = list(self.z_targets.copy()[0 : self.starting_num + 1])
         self.z = self.z_targets.pop(0)
 
         # Setup initial values for every physical quantity that we want to track
@@ -497,7 +497,7 @@ class SequencialSimulations(Simulations, priority=0):
 
     def new_sim(self, variable_list: List[tuple], params: Dict[str, Any]):
         v_list_str = utils.format_variable_list(variable_list)
-        self.logger.info(f"launching simulation with {v_list_str}")
+        self.logger.info(f"{self.param_seq.name} : launching simulation with {v_list_str}")
         SequentialRK4IP(
             params, self.overall_pbar, save_data=True, job_identifier=v_list_str, task_id=self.id
         ).run()
@@ -678,7 +678,9 @@ class RaySimulations(Simulations, priority=2):
         self.actors[new_job.task_id()] = new_actor
         self.jobs.append(new_job)
 
-        self.logger.info(f"launching simulation with {v_list_str}, job : {self.jobs[-1].hex()}")
+        self.logger.info(
+            f"{self.param_seq.name} : launching simulation with {v_list_str}, job : {self.jobs[-1].hex()}"
+        )
 
     def finish(self):
         while len(self.jobs) > 0: