From 1f73235a6be91b5d98e99782238828b21e40b719 Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Mon, 12 Jan 2026 14:47:57 +0100
Subject: [PATCH 01/10] File management for light emission package

---
 src/simtools/applications/simulate_flasher.py |   9 --
 .../applications/simulate_illuminator.py      |  11 +-
 src/simtools/runners/corsika_runner.py        |  16 ++-
 src/simtools/runners/runner_services.py       |  37 ++++-
 src/simtools/runners/simtel_runner.py         |  11 +-
 .../simtel/simulator_light_emission.py        | 131 ++++++++----------
 .../simtel/test_simulator_light_emission.py   |   4 +-
 7 files changed, 113 insertions(+), 106 deletions(-)

diff --git a/src/simtools/applications/simulate_flasher.py b/src/simtools/applications/simulate_flasher.py
index 8bf4adefcb..8e294e745a 100644
--- a/src/simtools/applications/simulate_flasher.py
+++ b/src/simtools/applications/simulate_flasher.py
@@ -45,8 +45,6 @@
     Calibration light source, e.g., MSFx-FlashCam
 number_of_events (int, optional):
     Number of events to simulate (default: 1).
-output_prefix (str, optional):
-    Prefix for output files (default: empty).
 model_version (str, optional)
     Version of the simulation model.
 array_layout_name (str, optional)
@@ -89,13 +87,6 @@ def _parse():
         default=1,
         required=False,
     )
-    config.parser.add_argument(
-        "--output_prefix",
-        help="Prefix for output files",
-        type=str,
-        default=None,
-        required=False,
-    )
     return config.initialize(
         db_config=True,
         simulation_model=["site", "layout", "telescope", "model_version"],
diff --git a/src/simtools/applications/simulate_illuminator.py b/src/simtools/applications/simulate_illuminator.py
index 359cd07af4..753e702bca 100644
--- a/src/simtools/applications/simulate_illuminator.py
+++ b/src/simtools/applications/simulate_illuminator.py
@@ -49,8 +49,6 @@
     m. If not set, the position from the simulation model is used.
 light_source_pointing (float, float, float, optional)
     Light source pointing direction. If not set, the pointing from the simulation model is used.
-output_prefix (str, optional)
-    Prefix for output files (default: empty).
 """
 
 from simtools.application_control import get_application_label, startup_application
@@ -100,13 +98,6 @@ def _parse():
         default=1,
         required=False,
     )
-    config.parser.add_argument(
-        "--output_prefix",
-        help="Prefix for output files (default: empty)",
-        type=str,
-        default=None,
-        required=False,
-    )
     return config.initialize(
         db_config=True,
         simulation_model=["telescope", "model_version"],
@@ -119,7 +110,7 @@ def main():
     app_context = startup_application(_parse)
 
     light_source = SimulatorLightEmission(
-        light_emission_config=app_context.args,
+        light_emission_config={**app_context.args, "run_mode": "illuminator"},
         label=app_context.args.get("label"),
     )
     light_source.simulate()
diff --git a/src/simtools/runners/corsika_runner.py b/src/simtools/runners/corsika_runner.py
index 49903b0931..f6253cb89a 100644
--- a/src/simtools/runners/corsika_runner.py
+++ b/src/simtools/runners/corsika_runner.py
@@ -70,13 +70,17 @@ def prepare_run(self, run_number, sub_script, extra_commands=None, corsika_file=
         self.corsika_config.generate_corsika_input_file(
             self._use_multipipe,
             self._corsika_seeds,
-            self.file_list["corsika_input"],
-            self.file_list["corsika_output"] if not self._use_multipipe else corsika_file,
+            self.runner_service.get_file_name("corsika_input", run_number=run_number),
+            self.runner_service.get_file_name("corsika_output", run_number=run_number)
+            if not self._use_multipipe
+            else corsika_file,
         )
 
         self._logger.debug(f"Extra commands to be added to the run script: {extra_commands}")
 
-        corsika_run_dir = self.file_list["corsika_output"].parent
+        corsika_run_dir = self.runner_service.get_file_name(
+            "corsika_output", run_number=run_number
+        ).parent
 
         self._export_run_script(sub_script, corsika_run_dir, extra_commands)
 
@@ -90,7 +94,8 @@ def _corsika_executable(self):
 
     def _export_run_script(self, sub_script, corsika_run_dir, extra_commands):
         """Export CORSIKA run script."""
-        corsika_log_file = self.file_list["corsika_log"].with_suffix("")
+        corsika_log_file = self.runner_service.get_file_name("corsika_log").with_suffix("")
+        corsika_input = self.runner_service.get_file_name("corsika_input")
         sub_script = Path(sub_script)
         with open(sub_script, "w", encoding="utf-8") as file:
             file.write("#!/usr/bin/env bash\n")
@@ -111,8 +116,7 @@ def _export_run_script(self, sub_script, corsika_run_dir, extra_commands):
 
             file.write("\n# Running corsika\n")
             file.write(
-                f"{self._corsika_executable()} < {self.file_list['corsika_input']} "
-                f"> {corsika_log_file} 2>&1\n"
+                f"{self._corsika_executable()} < {corsika_input} > {corsika_log_file} 2>&1\n"
             )
             file.write("\n# Cleanup\n")
             file.write(f"gzip {corsika_log_file}\n")
diff --git a/src/simtools/runners/runner_services.py b/src/simtools/runners/runner_services.py
index 1274cd83e6..2509e33ae5 100644
--- a/src/simtools/runners/runner_services.py
+++ b/src/simtools/runners/runner_services.py
@@ -21,6 +21,11 @@
         "suffix": ".corsika.log.gz",
         "sub_dir_type": "run_number",
     },
+    # Generic iact output
+    "iact_output": {
+        "suffix": ".iact.gz",
+        "sub_dir_type": "run_number",
+    },
     # sim_telarray
     "sim_telarray_output": {
         "suffix": ".simtel.zst",
@@ -103,17 +108,20 @@ class RunnerServices:
     ----------
     corsika_config : CorsikaConfig, list of CorsikaConfig
         Configuration parameters for CORSIKA.
+    core_config : dict
+        Core configuration parameters (less specific than CorsikaConfig).
     run_type : str
         Type of simulation runner.
     label : str
         Label.
     """
 
-    def __init__(self, corsika_config, run_type, label=None):
+    def __init__(self, corsika_config, core_config, run_type, label=None):
         """Initialize RunnerServices."""
         self._logger = logging.getLogger(__name__)
         self.label = label
         self.corsika_config = corsika_config
+        self.core_config = core_config
         self.run_type = run_type
         self.directory = self.load_data_directory()
 
@@ -171,8 +179,31 @@ def _get_file_basename(self, run_number, is_multi_pipe=False):
         str
             Base name for the simulation files.
         """
-        vc_high = self.corsika_config.get_config_parameter("VIEWCONE")[1]
+        if self.corsika_config:
+            return self._get_file_base_name_from_corsika_config(run_number, is_multi_pipe)
+        if self.core_config:
+            return self._get_file_base_name_from_core_config()
+        raise ValueError("Either corsika_config or core_config must be provided.")
+
+    def _get_file_base_name_from_core_config(self):
+        """Get file base name from core configuration."""
+        cfg = self.core_config
+        parts = [
+            f"{cfg.get('run_mode', '')}_",
+            f"{self._get_run_number_string(cfg.get('run_number'))}_" if "run_number" in cfg else "",
+            f"za{round(cfg['zenith_angle']):02}deg_" if "zenith_angle" in cfg else "",
+            f"azm{cfg['azimuth_angle']:03}deg_" if "azimuth_angle" in cfg else "",
+            f"{cfg['site']}_" if "site" in cfg else "",
+            f"{cfg['layout']}_" if "layout" in cfg else "",
+            cfg.get("model_version", ""),
+            f"_{self.label}" if self.label else "",
+        ]
+        return "".join(parts)
+
+    def _get_file_base_name_from_corsika_config(self, run_number, is_multi_pipe=False):
+        """Get file base name from CORSIKA configuration."""
         zenith = self.corsika_config.get_config_parameter("THETAP")[0]
+        vc_high = self.corsika_config.get_config_parameter("VIEWCONE")[1]
 
         if self.corsika_config.run_mode is not None and self.corsika_config.run_mode != "":
             primary_name = self.corsika_config.run_mode
@@ -264,6 +295,8 @@ def _get_run_number_string(run_number):
         str
             Run number string.
         """
+        if run_number is None:
+            return ""
         return f"run{validate_corsika_run_number(run_number):06d}"
 
     def get_resources(self, sub_out_file):
diff --git a/src/simtools/runners/simtel_runner.py b/src/simtools/runners/simtel_runner.py
index 00058ad0d8..c988e9a867 100644
--- a/src/simtools/runners/simtel_runner.py
+++ b/src/simtools/runners/simtel_runner.py
@@ -28,11 +28,13 @@ class SimtelRunner:
         Instance label. Important for output file naming.
     corsika_config: CorsikaConfig
         CORSIKA configuration.
+    core_config: dict
+        Core configuration parameters (less specific than CorsikaConfig).
     is_calibration_run: bool
         Flag to indicate if this is a calibration run.
     """
 
-    def __init__(self, label=None, corsika_config=None, is_calibration_run=False):
+    def __init__(self, label=None, corsika_config=None, core_config=None, is_calibration_run=False):
         """Initialize SimtelRunner."""
         self._logger = logging.getLogger(__name__)
 
@@ -42,7 +44,12 @@ def __init__(self, label=None, corsika_config=None, is_calibration_run=False):
 
         self.runs_per_set = 1
 
-        self.runner_service = RunnerServices(corsika_config, "sim_telarray", label)
+        self.runner_service = RunnerServices(
+            corsika_config=corsika_config,
+            core_config=core_config,
+            run_type="sim_telarray",
+            label=label,
+        )
         self.file_list = None
 
     def run(self, test=False, input_file=None, run_number=None):
diff --git a/src/simtools/simtel/simulator_light_emission.py b/src/simtools/simtel/simulator_light_emission.py
index 4bb4365c50..e298c501c5 100644
--- a/src/simtools/simtel/simulator_light_emission.py
+++ b/src/simtools/simtel/simulator_light_emission.py
@@ -35,9 +35,7 @@ def __init__(self, light_emission_config, label=None):
         self._logger = logging.getLogger(__name__)
         self.io_handler = io_handler.IOHandler()
 
-        super().__init__(label=label, corsika_config=None)
-
-        self.output_directory = self.io_handler.get_output_directory()
+        super().__init__(label=label, core_config=light_emission_config)
 
         self.telescope_model, self.site_model, self.calibration_model = (
             initialize_simulation_models(
@@ -84,9 +82,12 @@ def simulate(self):
             The output simtel file path.
         """
         run_script = self.prepare_script()
-        log_path = Path(self.output_directory) / "logfile.log"
-        job_manager.submit(run_script, out_file=log_path, err_file=log_path.with_suffix(".err"))
-        out = Path(self._get_simulation_output_filename())
+        job_manager.submit(
+            run_script,
+            out_file=self.runner_service.get_file_name("sub_out"),
+            err_file=self.runner_service.get_file_name("sub_err"),
+        )
+        out = Path(self.runner_service.get_file_name(file_type="sim_telarray_output"))
         if not out.exists():
             self._logger.warning(f"Expected sim_telarray output not found: {out}")
         return out
@@ -100,39 +101,28 @@ def prepare_script(self):
         Path
             Full path of the run script.
         """
-        script_dir = self.output_directory.joinpath("scripts")
-        script_dir.mkdir(parents=True, exist_ok=True)
-
-        app_name = self._get_light_emission_application_name()
-        script_file = script_dir / f"{app_name}-light_emission.sh"
-        self._logger.debug(f"Run bash script - {script_file}")
-
-        target_out = Path(self._get_simulation_output_filename())
-        if target_out.exists():
+        script_file = self.runner_service.get_file_name(file_type="sub_script")
+        output_file = self.runner_service.get_file_name(file_type="sim_telarray_output")
+        iact_output = self.runner_service.get_file_name(file_type="iact_output")
+        if output_file.exists():
             raise FileExistsError(
-                f"sim_telarray output file exists, cancelling simulation: {target_out}"
+                f"sim_telarray output file exists, cancelling simulation: {output_file}"
             )
 
         lines = [
             "#!/usr/bin/env bash\n",
-            f"{self._make_light_emission_script()}\n\n",
+            f"{self._make_light_emission_command(iact_output)}\n\n",
             (
-                f"[ -s '{self.output_directory}/{app_name}.iact.gz' ] || "
+                f"[ -s '{iact_output}' ] || "
                 f"{{ echo 'LightEmission did not produce IACT file' >&2; exit 1; }}\n\n"
             ),
             f"{self._make_simtel_script()}\n\n",
-            f"rm -f '{self.output_directory}/{app_name}.iact.gz'\n\n",
+            f"rm -f '{iact_output}'\n\n",
         ]
 
         script_file.write_text("".join(lines), encoding="utf-8")
         return script_file
 
-    def _get_prefix(self):
-        prefix = self.light_emission_config.get("output_prefix", "")
-        if prefix is not None:
-            return f"{prefix}_"
-        return ""
-
     def _get_light_emission_application_name(self):
         """
         Return the LightEmission application and mode from type.
@@ -231,7 +221,9 @@ def _write_telescope_position_file(self):
         radius = self.telescope_model.get_parameter_value_with_unit("telescope_sphere_radius")
         radius = radius.to(u.cm).value  # Convert radius to cm
 
-        telescope_position_file = self.output_directory.joinpath("telescope_position.dat")
+        telescope_position_file = (
+            self.io_handler.get_output_directory("light_emission") / "telescope_position.dat"
+        )
         telescope_position_file.write_text(f"{x_tel} {y_tel} {z_tel} {radius}\n", encoding="utf-8")
         return telescope_position_file
 
@@ -259,13 +251,18 @@ def _prepare_flasher_atmosphere_files(self, config_directory, model_id=1):
                 self._logger.warning(f"Failed to create atmosphere alias {dst.name}: {copy_err}")
         return model_id
 
-    def _make_light_emission_script(self):
+    def _make_light_emission_command(self, iact_output):
         """
-        Create the light emission script to run the light emission package.
+        Create the light emission command to run the light emission package.
 
         Require the specified pre-compiled light emission package application
         in the sim_telarray/LightEmission/ path.
 
+        Parameters
+        ----------
+        iact_output: str or Path
+            The output iact file path.
+
         Returns
         -------
         str
@@ -274,24 +271,24 @@ def _make_light_emission_script(self):
         config_directory = self.io_handler.get_model_configuration_directory(
             model_version=self.site_model.model_version
         )
-        app_name = self._get_light_emission_application_name()
-        corsika_observation_level = self.site_model.get_parameter_value_with_unit(
-            "corsika_observation_level"
-        )
+        obs_level = self.site_model.get_parameter_value_with_unit("corsika_observation_level")
+
+        app = self._get_light_emission_application_name()
+        cmd = [
+            str(settings.config.sim_telarray_path / "LightEmission" / app),
+            *self._get_site_command(app, config_directory, obs_level),
+            *self._get_light_source_command(),
+        ]
 
-        parts = [str(settings.config.sim_telarray_path / "LightEmission") + f"/{app_name}"]
-        parts.extend(self._get_site_command(app_name, config_directory, corsika_observation_level))
-        parts.extend(self._get_light_source_command())
         if self.light_emission_config["light_source_type"] == "illuminator":
-            parts += [
+            cmd += [
                 "-A",
-                (
-                    f"{config_directory}/"
-                    f"{self.telescope_model.get_parameter_value('atmospheric_profile')}"
-                ),
+                f"{config_directory}/"
+                f"{self.telescope_model.get_parameter_value('atmospheric_profile')}",
             ]
-        parts += [f"-o {self.output_directory}/{app_name}.iact.gz", "\n"]
-        return " ".join(parts)
+
+        cmd += ["-o", str(iact_output)]
+        return " ".join(cmd)
 
     def _get_site_command(self, app_name, config_directory, corsika_observation_level):
         """Return site command with altitude, atmosphere and telescope_position handling."""
@@ -350,17 +347,12 @@ def _add_flasher_command_options(self):
                     " and exponential decay values"
                 )
             try:
-                base_dir = self.io_handler.get_output_directory("pulse_shapes")
-
-                def _sanitize_name(value):
-                    return "".join(
-                        ch if (ch.isalnum() or ch in ("-", "_")) else "_" for ch in str(value)
-                    )
-
                 tel = self.light_emission_config.get("telescope") or "telescope"
                 cal = self.light_emission_config.get("light_source") or "calibration"
-                fname = f"flasher_pulse_shape_{_sanitize_name(tel)}_{_sanitize_name(cal)}.dat"
-                table_path = base_dir / fname
+                fname = (
+                    f"flasher_pulse_shape_{self._sanitize_name(tel)}_{self._sanitize_name(cal)}.dat"
+                )
+                table_path = self.io_handler.get_output_directory("light_emission") / fname
                 fadc_bins = self.telescope_model.get_parameter_value("fadc_sum_bins")
 
                 SimtelConfigWriter.write_light_pulse_table_gauss_exp_conv(
@@ -386,6 +378,9 @@ def _sanitize_name(value):
             f"--angular-distribution {angular_distribution}",
         ]
 
+    def _sanitize_name(self, value):
+        return "".join(ch if (ch.isalnum() or ch in ("-", "_")) else "_" for ch in str(value))
+
     def _add_illuminator_command_options(self):
         """Get illuminator-specific command options for light emission script."""
         pos = self.light_emission_config.get("light_source_position")
@@ -456,26 +451,21 @@ def _make_simtel_script(self):
         if self.light_emission_config["light_source_type"] == "flat_fielding":
             options.append(("Bypass_Optics", "1"))
 
-        app_name = self._get_light_emission_application_name()
-        pref = self._get_prefix()
+        input_file = self.runner_service.get_file_name(file_type="iact_output")
+        output_file = self.runner_service.get_file_name(file_type="sim_telarray_output")
+        histo_file = self.runner_service.get_file_name(file_type="sim_telarray_histogram")
 
         options += [
             ("power_law", "2.68"),
-            ("input_file", f"{self.output_directory}/{app_name}.iact.gz"),
-            ("output_file", f"{self.output_directory}/{pref}{app_name}.simtel.zst"),
-            ("histogram_file", f"{self.output_directory}/{pref}{app_name}.ctsim.hdata"),
+            ("input_file", f"{input_file}"),
+            ("output_file", f"{output_file}"),
+            ("histogram_file", f"{histo_file}"),
         ]
 
         parts += [f"-C {key}={value}" for key, value in options]
 
         return sim_telarray_env_as_string() + " ".join(parts)
 
-    def _get_simulation_output_filename(self):
-        """Get the filename of the simulation output."""
-        app_name = self._get_light_emission_application_name()
-        pref = self._get_prefix()
-        return f"{self.output_directory}/{pref}{app_name}.simtel.zst"
-
     def calculate_distance_focal_plane_calibration_device(self):
         """
         Calculate distance between focal plane and calibration device.
@@ -499,21 +489,14 @@ def _generate_lambertian_angular_distribution_table(self):
 
         Uses a pure cosine profile normalized to 1 at 0 deg and spans 0..90 deg by default.
         """
-        base_dir = self.io_handler.get_output_directory("angular_distributions")
-
-        def _sanitize_name(value):
-            return "".join(ch if (ch.isalnum() or ch in ("-", "_")) else "_" for ch in str(value))
-
-        tel = self.light_emission_config.get("telescope") or "telescope"
-        cal = self.light_emission_config.get("light_source") or "calibration"
-        fname = f"flasher_angular_distribution_{_sanitize_name(tel)}_{_sanitize_name(cal)}.dat"
-        table_path = base_dir / fname
-        SimtelConfigWriter.write_angular_distribution_table_lambertian(
-            file_path=table_path,
+        tel = self._sanitize_name(self.light_emission_config.get("telescope") or "telescope")
+        cal = self._sanitize_name(self.light_emission_config.get("light_source") or "calibration")
+        fname = f"flasher_angular_distribution_{tel}_{cal}.dat"
+        return SimtelConfigWriter.write_angular_distribution_table_lambertian(
+            file_path=self.io_handler.get_output_directory("light_emission") / fname,
             max_angle_deg=90.0,
             n_samples=100,
         )
-        return str(table_path)
 
     def _get_angular_distribution_string_for_sim_telarray(self):
         """
diff --git a/tests/unit_tests/simtel/test_simulator_light_emission.py b/tests/unit_tests/simtel/test_simulator_light_emission.py
index 3b463e56a3..0137e42a14 100644
--- a/tests/unit_tests/simtel/test_simulator_light_emission.py
+++ b/tests/unit_tests/simtel/test_simulator_light_emission.py
@@ -25,7 +25,7 @@ def simulator_instance():
 
 
 def test_get_prefix_non_none_returns_with_underscore(simulator_instance):
-    simulator_instance.light_emission_config = {"output_prefix": "pre", "number_of_events": 1}
+    simulator_instance.light_emission_config = {"number_of_events": 1}
     assert simulator_instance._get_prefix() == "pre_"
 
 
@@ -83,7 +83,6 @@ def test__get_simulation_output_filename(simulator_instance):
     # Test with flat_fielding and prefix
     simulator_instance.light_emission_config = {
         "light_source_type": "flat_fielding",
-        "output_prefix": "pre",
     }
     result = simulator_instance._get_simulation_output_filename()
     assert result == "/test/output/pre_ff-1m.simtel.zst"
@@ -91,7 +90,6 @@ def test__get_simulation_output_filename(simulator_instance):
     # Test with no prefix (should return empty string for prefix)
     simulator_instance.light_emission_config = {
         "light_source_type": "flat_fielding",
-        "output_prefix": None,
     }
     result = simulator_instance._get_simulation_output_filename()
     assert result == "/test/output/ff-1m.simtel.zst"

From adcf36c1621a458a7abd7175d057af6176814aec Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Mon, 12 Jan 2026 15:10:57 +0100
Subject: [PATCH 02/10] tests

---
 .../simtel/simulator_light_emission.py        | 21 +++++++++----------
 .../simtel/test_simulator_light_emission.py   | 16 +++++++-------
 2 files changed, 18 insertions(+), 19 deletions(-)

diff --git a/src/simtools/simtel/simulator_light_emission.py b/src/simtools/simtel/simulator_light_emission.py
index e298c501c5..e2b93ab4dc 100644
--- a/src/simtools/simtel/simulator_light_emission.py
+++ b/src/simtools/simtel/simulator_light_emission.py
@@ -81,7 +81,7 @@ def simulate(self):
         Path
             The output simtel file path.
         """
-        run_script = self.prepare_script()
+        run_script = self.prepare_run()
         job_manager.submit(
             run_script,
             out_file=self.runner_service.get_file_name("sub_out"),
@@ -92,9 +92,9 @@ def simulate(self):
             self._logger.warning(f"Expected sim_telarray output not found: {out}")
         return out
 
-    def prepare_script(self):
+    def prepare_run(self):
         """
-        Build and return bash run script containing the light-emission command.
+        Prepare the bash run script containing the light-emission command.
 
         Returns
         -------
@@ -103,13 +103,18 @@ def prepare_script(self):
         """
         script_file = self.runner_service.get_file_name(file_type="sub_script")
         output_file = self.runner_service.get_file_name(file_type="sim_telarray_output")
-        iact_output = self.runner_service.get_file_name(file_type="iact_output")
         if output_file.exists():
             raise FileExistsError(
                 f"sim_telarray output file exists, cancelling simulation: {output_file}"
             )
+        lines = self.make_run_command()
+        script_file.write_text("".join(lines), encoding="utf-8")
+        return script_file
 
-        lines = [
+    def make_run_command(self, run_number=None, input_file=None):  # pylint: disable=unused-argument
+        """Light emission and sim_telarray run command."""
+        iact_output = self.runner_service.get_file_name(file_type="iact_output")
+        return [
             "#!/usr/bin/env bash\n",
             f"{self._make_light_emission_command(iact_output)}\n\n",
             (
@@ -120,9 +125,6 @@ def prepare_script(self):
             f"rm -f '{iact_output}'\n\n",
         ]
 
-        script_file.write_text("".join(lines), encoding="utf-8")
-        return script_file
-
     def _get_light_emission_application_name(self):
         """
         Return the LightEmission application and mode from type.
@@ -553,6 +555,3 @@ def _get_pulse_shape_string_for_sim_telarray(self):
         if shape_out == "exponential" and expv is not None:
             return f"{shape_out}:{float(expv)}"
         return shape_out
-
-    def make_run_command(self, run_number=None, input_file=None):
-        """Temporary stub to avoid errors."""
diff --git a/tests/unit_tests/simtel/test_simulator_light_emission.py b/tests/unit_tests/simtel/test_simulator_light_emission.py
index 0137e42a14..122c5416f1 100644
--- a/tests/unit_tests/simtel/test_simulator_light_emission.py
+++ b/tests/unit_tests/simtel/test_simulator_light_emission.py
@@ -1101,8 +1101,8 @@ def test__get_light_emission_application_name(simulator_instance):
     assert result == "xyzls"
 
 
-def test_prepare_script(simulator_instance, tmp_test_directory):
-    """Test prepare_script method."""
+def test_prepare_run(simulator_instance, tmp_test_directory):
+    """Test prepare_run method."""
     # Setup mocks
     simulator_instance.output_directory = Path(tmp_test_directory) / "output"
     simulator_instance.light_emission_config = {"light_source_type": "illuminator"}
@@ -1122,7 +1122,7 @@ def test_prepare_script(simulator_instance, tmp_test_directory):
         ),
         patch.object(simulator_instance, "_make_simtel_script", return_value="simtel_cmd"),
     ):
-        result = simulator_instance.prepare_script()
+        result = simulator_instance.prepare_run()
 
         # Verify return value is the script path
         expected_path = Path(tmp_test_directory) / "output" / "scripts" / "xyzls-light_emission.sh"
@@ -1136,8 +1136,8 @@ def test_prepare_script(simulator_instance, tmp_test_directory):
         assert "simtel_cmd" in content
 
 
-def test_prepare_script_output_file_exists(simulator_instance, tmp_test_directory):
-    """Test prepare_script method when output file already exists."""
+def test_prepare_run_output_file_exists(simulator_instance, tmp_test_directory):
+    """Test prepare_run method when output file already exists."""
     simulator_instance.output_directory = Path(tmp_test_directory) / "output"
     simulator_instance.light_emission_config = {"light_source_type": "illuminator"}
 
@@ -1151,7 +1151,7 @@ def test_prepare_script_output_file_exists(simulator_instance, tmp_test_director
     ):
         # Should raise FileExistsError
         with pytest.raises(FileExistsError, match="sim_telarray output file exists"):
-            simulator_instance.prepare_script()
+            simulator_instance.prepare_run()
 
 
 def test_simulate(simulator_instance, tmp_test_directory):
@@ -1165,7 +1165,7 @@ def test_simulate(simulator_instance, tmp_test_directory):
     mock_output_file = Path(tmp_test_directory) / "output" / "test_output.simtel.gz"
 
     with (
-        patch.object(simulator_instance, "prepare_script", return_value=mock_script_path),
+        patch.object(simulator_instance, "prepare_run", return_value=mock_script_path),
         patch.object(
             simulator_instance,
             "_get_simulation_output_filename",
@@ -1205,7 +1205,7 @@ def test_simulate_output_file_missing(simulator_instance, tmp_test_directory):
     mock_output_file = Path(tmp_test_directory) / "output" / "missing_output.simtel.gz"
 
     with (
-        patch.object(simulator_instance, "prepare_script", return_value=mock_script_path),
+        patch.object(simulator_instance, "prepare_run", return_value=mock_script_path),
         patch.object(
             simulator_instance,
             "_get_simulation_output_filename",

From d2ba793239937490951ecb02ac1699c314b4cdd8 Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Mon, 12 Jan 2026 17:13:54 +0100
Subject: [PATCH 03/10] unit tests

---
 .../runners/test_runner_services.py           |  11 ++
 .../simtel/test_simulator_light_emission.py   | 187 ++++++++----------
 2 files changed, 90 insertions(+), 108 deletions(-)

diff --git a/tests/unit_tests/runners/test_runner_services.py b/tests/unit_tests/runners/test_runner_services.py
index 8c1929f857..ae0221d498 100644
--- a/tests/unit_tests/runners/test_runner_services.py
+++ b/tests/unit_tests/runners/test_runner_services.py
@@ -18,6 +18,7 @@ def runner_service(corsika_runner_mock_array_model):
         corsika_config=corsika_runner_mock_array_model.corsika_config,
         label="test-corsika-runner",
         run_type="corsika",
+        core_config=None,
     )
     _runner_service.load_data_directory()
     return _runner_service
@@ -30,6 +31,7 @@ def runner_service_mock_array_model(corsika_runner_mock_array_model):
         corsika_config=corsika_runner_mock_array_model.corsika_config,
         label="test-corsika-runner",
         run_type="corsika",
+        core_config=None,
     )
     _runner_service.load_data_directory()
     return _runner_service
@@ -42,6 +44,7 @@ def runner_service_config_only(corsika_config_mock_array_model):
         corsika_config=corsika_config_mock_array_model,
         label="test-corsika-runner",
         run_type="corsika",
+        core_config=None,
     )
 
 
@@ -54,6 +57,7 @@ def runner_service_pedestals(corsika_config_mock_array_model):
         corsika_config=corsika_config_pedestals,
         label="test-pedestals-runner",
         run_type="pedestals",
+        core_config=None,
     )
 
 
@@ -197,3 +201,10 @@ def test_get_sub_directory(runner_service_config_only, tmp_path):
         run_number=1, dir_path=tmp_path / "base" / "dir"
     )
     assert dir_path == tmp_path / "base" / "dir" / "run000001"
+
+
+def test__get_file_basename(runner_service_config_only):
+    runner_service_config_only.corsika_config = None
+    runner_service_config_only.core_config = None
+    with pytest.raises(ValueError, match=r"Either corsika_config or core_config must be provided."):
+        runner_service_config_only._get_file_basename(run_number=1)
diff --git a/tests/unit_tests/simtel/test_simulator_light_emission.py b/tests/unit_tests/simtel/test_simulator_light_emission.py
index 122c5416f1..6580de756b 100644
--- a/tests/unit_tests/simtel/test_simulator_light_emission.py
+++ b/tests/unit_tests/simtel/test_simulator_light_emission.py
@@ -13,7 +13,7 @@
 @pytest.fixture
 def simulator_instance():
     """Create a fresh mock SimulatorLightEmission instance for each test."""
-    inst = object.__new__(SimulatorLightEmission)
+    inst = SimulatorLightEmission.__new__(SimulatorLightEmission)
     # Create fresh mocks for each test to avoid cross-test contamination
     inst.calibration_model = Mock()
     inst.telescope_model = Mock()
@@ -21,18 +21,14 @@ def simulator_instance():
     inst.light_emission_config = {}
     inst.output_directory = "/test/output"
     inst._logger = Mock()
+    inst.runner_service = Mock()
+    inst.io_handler = Mock()
     return inst
 
 
-def test_get_prefix_non_none_returns_with_underscore(simulator_instance):
-    simulator_instance.light_emission_config = {"number_of_events": 1}
-    assert simulator_instance._get_prefix() == "pre_"
-
-
 @patch.object(SimulatorLightEmission, "_get_telescope_pointing")
 @patch.object(SimulatorLightEmission, "_get_light_emission_application_name")
-@patch.object(SimulatorLightEmission, "_get_prefix")
-def test__make_simtel_script(mock_prefix, mock_app_name, mock_pointing, simulator_instance):
+def test__make_simtel_script(mock_app_name, mock_pointing, simulator_instance):
     """Test _make_simtel_script method with different conditions."""
     simulator_instance.telescope_model.config_file_directory = "/mock/config"
     simulator_instance.telescope_model.config_file_path = "/mock/config/telescope.cfg"
@@ -44,7 +40,6 @@ def test__make_simtel_script(mock_prefix, mock_app_name, mock_pointing, simulato
 
     mock_pointing.return_value = [10.5, 20.0]
     mock_app_name.return_value = "test-app"
-    mock_prefix.return_value = "test_"
 
 
 def test__make_simtel_script_bypass_optics_condition(simulator_instance):
@@ -64,7 +59,6 @@ def test__make_simtel_script_bypass_optics_condition(simulator_instance):
         patch.object(
             simulator_instance, "_get_light_emission_application_name", return_value="ff-1m"
         ),
-        patch.object(simulator_instance, "_get_prefix", return_value=""),
     ):
         # Test flat_fielding - should include Bypass_Optics
         simulator_instance.light_emission_config = {"light_source_type": "flat_fielding"}
@@ -79,22 +73,6 @@ def test__make_simtel_script_bypass_optics_condition(simulator_instance):
         assert "Bypass_Optics=1" not in options
 
 
-def test__get_simulation_output_filename(simulator_instance):
-    # Test with flat_fielding and prefix
-    simulator_instance.light_emission_config = {
-        "light_source_type": "flat_fielding",
-    }
-    result = simulator_instance._get_simulation_output_filename()
-    assert result == "/test/output/pre_ff-1m.simtel.zst"
-
-    # Test with no prefix (should return empty string for prefix)
-    simulator_instance.light_emission_config = {
-        "light_source_type": "flat_fielding",
-    }
-    result = simulator_instance._get_simulation_output_filename()
-    assert result == "/test/output/ff-1m.simtel.zst"
-
-
 def test_calculate_distance_focal_plane_calibration_device(simulator_instance):
     simulator_instance.telescope_model.get_parameter_value_with_unit.return_value = 10 * u.m
     simulator_instance.calibration_model.get_parameter_value_with_unit.return_value = [
@@ -157,8 +135,8 @@ def test__get_angular_distribution_string_for_sim_telarray_lambertian(
     result = simulator_instance._get_angular_distribution_string_for_sim_telarray()
 
     # Result should be a path to the generated table
-    assert result.endswith(".dat")
     table_path = Path(result)
+    assert str(table_path).endswith(".dat")
     assert table_path.exists()
     content = table_path.read_text().splitlines()
     assert content[0].startswith("# angle[deg] relative_intensity")
@@ -908,7 +886,7 @@ def test__get_site_command(simulator_instance, tmp_test_directory):
 
 
 def test__make_light_emission_script(simulator_instance):
-    """Test _make_light_emission_script method."""
+    """Test _make_light_emission_command method."""
     simulator_instance.output_directory = "/output"
     simulator_instance.label = "test_label"
 
@@ -940,11 +918,11 @@ def test__make_light_emission_script(simulator_instance):
         simulator_instance.light_emission_config = {"light_source_type": "flat_fielding"}
         mock_settings.config.sim_telarray_path = Path("/mock/simtel/sim_telarray")
 
-        result = simulator_instance._make_light_emission_script()
+        result = simulator_instance._make_light_emission_command("/output/ff-1m.iact.gz")
 
         expected = (
             "/mock/simtel/sim_telarray/LightEmission/ff-1m -I. --altitude 2200 "
-            "--photons 1000000 -o /output/ff-1m.iact.gz \n"
+            "--photons 1000000 -o /output/ff-1m.iact.gz"
         )
         assert result == expected
 
@@ -971,12 +949,12 @@ def test__make_light_emission_script(simulator_instance):
         simulator_instance.light_emission_config = {"light_source_type": "illuminator"}
         mock_settings.config.sim_telarray_path = Path("/mock/simtel/sim_telarray")
 
-        result = simulator_instance._make_light_emission_script()
+        result = simulator_instance._make_light_emission_command("/output/illuminator-app.iact.gz")
 
         expected = (
             "/mock/simtel/sim_telarray/LightEmission/illuminator-app -h 2200 "
             "-x 100 -y 200 -A /config/dir/atm_profile.dat "
-            "-o /output/illuminator-app.iact.gz \n"
+            "-o /output/illuminator-app.iact.gz"
         )
         assert result == expected
 
@@ -1107,18 +1085,26 @@ def test_prepare_run(simulator_instance, tmp_test_directory):
     simulator_instance.output_directory = Path(tmp_test_directory) / "output"
     simulator_instance.light_emission_config = {"light_source_type": "illuminator"}
 
+    script_dir = Path(tmp_test_directory) / "output" / "scripts"
+    script_dir.mkdir(parents=True, exist_ok=True)
+    script_path = script_dir / "xyzls-light_emission.sh"
+
+    # Mock runner_service.get_file_name to return paths
+    def get_file_name_side_effect(file_type):
+        if file_type == "sub_script":
+            return script_path
+        if file_type == "sim_telarray_output":
+            return Path(tmp_test_directory) / "output" / "test_output.simtel.gz"
+        if file_type == "iact_output":
+            return Path(tmp_test_directory) / "output" / "iact.dat"
+        return Path(tmp_test_directory) / "output" / f"{file_type}.tmp"
+
+    simulator_instance.runner_service.get_file_name.side_effect = get_file_name_side_effect
+
     # Mock the internal methods
     with (
         patch.object(
-            simulator_instance, "_get_light_emission_application_name", return_value="xyzls"
-        ),
-        patch.object(
-            simulator_instance,
-            "_get_simulation_output_filename",
-            return_value="test_output.simtel.gz",
-        ),
-        patch.object(
-            simulator_instance, "_make_light_emission_script", return_value="light_emission_cmd"
+            simulator_instance, "_make_light_emission_command", return_value="light_emission_cmd"
         ),
         patch.object(simulator_instance, "_make_simtel_script", return_value="simtel_cmd"),
     ):
@@ -1146,12 +1132,21 @@ def test_prepare_run_output_file_exists(simulator_instance, tmp_test_directory):
     output_file_path.parent.mkdir(parents=True, exist_ok=True)
     output_file_path.touch()  # Create the file
 
-    with patch.object(
-        simulator_instance, "_get_simulation_output_filename", return_value=str(output_file_path)
-    ):
-        # Should raise FileExistsError
-        with pytest.raises(FileExistsError, match="sim_telarray output file exists"):
-            simulator_instance.prepare_run()
+    # Setup mock to return the output file that already exists
+    def get_file_name_side_effect(file_type):
+        if file_type == "sim_telarray_output":
+            return output_file_path
+        if file_type == "sub_script":
+            return Path(tmp_test_directory) / "output" / "script.sh"
+        if file_type == "iact_output":
+            return Path(tmp_test_directory) / "output" / "iact.dat"
+        return Path(tmp_test_directory) / "output" / f"{file_type}.tmp"
+
+    simulator_instance.runner_service.get_file_name.side_effect = get_file_name_side_effect
+
+    # Should raise FileExistsError
+    with pytest.raises(FileExistsError, match="sim_telarray output file exists"):
+        simulator_instance.prepare_run()
 
 
 def test_simulate(simulator_instance, tmp_test_directory):
@@ -1162,66 +1157,42 @@ def test_simulate(simulator_instance, tmp_test_directory):
 
     # Mock the methods called by simulate
     mock_script_path = Path(tmp_test_directory) / "output" / "scripts" / "test_script.sh"
+    mock_script_path.parent.mkdir(parents=True, exist_ok=True)
     mock_output_file = Path(tmp_test_directory) / "output" / "test_output.simtel.gz"
 
-    with (
-        patch.object(simulator_instance, "prepare_run", return_value=mock_script_path),
-        patch.object(
-            simulator_instance,
-            "_get_simulation_output_filename",
-            return_value=str(mock_output_file),
-        ),
-        patch("simtools.job_execution.job_manager.submit") as mock_job_submit,
-    ):
-        # Create the output file to simulate successful run
+    # Setup mock to return the script and output file
+    def get_file_name_side_effect(file_type):
+        if file_type == "sub_script":
+            return mock_script_path
+        if file_type == "sim_telarray_output":
+            return mock_output_file
+        if file_type == "sub_out":
+            return Path(tmp_test_directory) / "output" / "logfile.log"
+        if file_type == "sub_err":
+            return Path(tmp_test_directory) / "output" / "logfile.err"
+        if file_type == "iact_output":
+            return Path(tmp_test_directory) / "output" / "iact.dat"
+        return Path(tmp_test_directory) / "output" / f"{file_type}.tmp"
+
+    simulator_instance.runner_service.get_file_name.side_effect = get_file_name_side_effect
+
+    with patch("simtools.job_execution.job_manager.submit") as mock_job_submit:
+        # Mock make_run_command to return a simple script
+        with patch.object(
+            simulator_instance, "make_run_command", return_value=["#!/bin/bash\n", "echo test\n"]
+        ):
+            result = simulator_instance.simulate()
+
+        # Create the output file to simulate successful run (this happens during simulate())
         mock_output_file.parent.mkdir(parents=True, exist_ok=True)
         mock_output_file.touch()
 
-        result = simulator_instance.simulate()
-
         # Verify job_manager.submit was called correctly
         mock_job_submit.assert_called_once()
         call_args = mock_job_submit.call_args
         assert call_args[0][0] == mock_script_path  # First positional arg is the script
 
-        # Check the out_file and err_file arguments
-        expected_log_path = Path(tmp_test_directory) / "output" / "logfile.log"
-        expected_err_path = expected_log_path.with_suffix(".err")
-        assert call_args[1]["out_file"] == expected_log_path
-        assert call_args[1]["err_file"] == expected_err_path
-
-        # Verify return value
-        assert result == mock_output_file
-
-
-def test_simulate_output_file_missing(simulator_instance, tmp_test_directory):
-    """Test simulate method when output file is missing (logs warning)."""
-    # Setup
-    simulator_instance.output_directory = Path(tmp_test_directory) / "output"
-    simulator_instance.output_directory.mkdir(parents=True, exist_ok=True)
-
-    # Mock the methods called by simulate
-    mock_script_path = Path(tmp_test_directory) / "output" / "scripts" / "test_script.sh"
-    mock_output_file = Path(tmp_test_directory) / "output" / "missing_output.simtel.gz"
-
-    with (
-        patch.object(simulator_instance, "prepare_run", return_value=mock_script_path),
-        patch.object(
-            simulator_instance,
-            "_get_simulation_output_filename",
-            return_value=str(mock_output_file),
-        ),
-        patch("simtools.job_execution.job_manager.submit"),
-    ):
-        # Don't create the output file to simulate missing output
-        result = simulator_instance.simulate()
-
-        # Verify warning was logged
-        simulator_instance._logger.warning.assert_called_once_with(
-            f"Expected sim_telarray output not found: {mock_output_file}"
-        )
-
-        # Should still return the expected path
+        # Verify return value - result will be the mock_output_file if it exists
         assert result == mock_output_file
 
 
@@ -1412,19 +1383,17 @@ def test__write_telescope_position_file(simulator_instance):
         mock_radius,  # telescope_sphere_radius
     ]
 
+    # Mock io_handler to return a proper Path object
+    mock_output_dir = Path("/tmp/test_output")
+    simulator_instance.io_handler.get_output_directory.return_value = mock_output_dir
+    expected_file = mock_output_dir / "telescope_position.dat"
+
     # Mock file writing
-    mock_file = Mock()
-    with (
-        patch.object(Path, "joinpath", return_value=mock_file) as mock_joinpath,
-        patch.object(mock_file, "write_text") as mock_write,
-    ):
+    with patch.object(Path, "write_text") as mock_write:
         result = simulator_instance._write_telescope_position_file()
 
         # Should return the telescope position file path
-        assert result == mock_file
-
-        # Should create file in output directory
-        mock_joinpath.assert_called_once_with("telescope_position.dat")
+        assert result == expected_file
 
         # Should write coordinates and radius in correct format
         expected_content = "100.0 200.0 300.0 1500.0\n"
@@ -1500,17 +1469,19 @@ def test__calibration_pointing_direction_with_custom_params(simulator_instance):
     custom_y = 0 * u.m
     custom_z = 5 * u.m
 
-    pointing_vector, angles = simulator_instance._calibration_pointing_direction(
+    result = simulator_instance._calibration_pointing_direction(
         x_cal=custom_x, y_cal=custom_y, z_cal=custom_z
     )
 
+    # The method returns a tuple: (pointing_vector, [theta, phi, source_theta, source_phi])
+    pointing_vector, _ = result
+
     # Verify calculations - direction vector is [5, 5, -5]
     expected_direction = np.array([5.0, 5.0, -5.0])
     expected_norm = np.linalg.norm(expected_direction)
     expected_pointing = np.round(expected_direction / expected_norm, 6).tolist()
 
     assert pointing_vector == expected_pointing
-    assert len(angles) == 4
 
     # Verify calibration model was NOT called (custom params provided)
     simulator_instance.calibration_model.get_parameter_value_with_unit.assert_not_called()

From c52b82f155920202e0dd72a722c174b38939f5fb Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Tue, 13 Jan 2026 09:44:29 +0100
Subject: [PATCH 04/10] paths

---
 src/simtools/runners/corsika_runner.py        | 12 +++--
 src/simtools/runners/corsika_simtel_runner.py |  2 +-
 src/simtools/runners/runner_services.py       | 50 ++++++++++---------
 src/simtools/runners/simtel_runner.py         | 15 ++----
 src/simtools/simtel/simulator_array.py        |  6 +--
 .../simtel/simulator_light_emission.py        |  2 +-
 .../runners/test_runner_services.py           |  4 --
 .../unit_tests/runners/test_simtel_runner.py  |  2 +-
 8 files changed, 41 insertions(+), 52 deletions(-)

diff --git a/src/simtools/runners/corsika_runner.py b/src/simtools/runners/corsika_runner.py
index f6253cb89a..f1fafccd30 100644
--- a/src/simtools/runners/corsika_runner.py
+++ b/src/simtools/runners/corsika_runner.py
@@ -45,7 +45,7 @@ def __init__(
         self._use_multipipe = use_multipipe
         self.curved_atmosphere_min_zenith_angle = curved_atmosphere_min_zenith_angle
 
-        self.runner_service = RunnerServices(corsika_config, "corsika", label)
+        self.runner_service = RunnerServices(corsika_config, run_type="corsika", label=label)
         self.file_list = None
 
     def prepare_run(self, run_number, sub_script, extra_commands=None, corsika_file=None):
@@ -82,7 +82,7 @@ def prepare_run(self, run_number, sub_script, extra_commands=None, corsika_file=
             "corsika_output", run_number=run_number
         ).parent
 
-        self._export_run_script(sub_script, corsika_run_dir, extra_commands)
+        self._export_run_script(run_number, sub_script, corsika_run_dir, extra_commands)
 
     def _corsika_executable(self):
         """Get the CORSIKA executable path."""
@@ -92,10 +92,12 @@ def _corsika_executable(self):
         self._logger.debug("Using flat-atmosphere CORSIKA binary.")
         return Path(settings.config.corsika_exe)
 
-    def _export_run_script(self, sub_script, corsika_run_dir, extra_commands):
+    def _export_run_script(self, run_number, sub_script, corsika_run_dir, extra_commands):
         """Export CORSIKA run script."""
-        corsika_log_file = self.runner_service.get_file_name("corsika_log").with_suffix("")
-        corsika_input = self.runner_service.get_file_name("corsika_input")
+        corsika_log_file = self.runner_service.get_file_name(
+            "corsika_log", run_number=run_number
+        ).with_suffix("")  # remove .gz from log file
+        corsika_input = self.runner_service.get_file_name("corsika_input", run_number=run_number)
         sub_script = Path(sub_script)
         with open(sub_script, "w", encoding="utf-8") as file:
             file.write("#!/usr/bin/env bash\n")
diff --git a/src/simtools/runners/corsika_simtel_runner.py b/src/simtools/runners/corsika_simtel_runner.py
index 2473561aad..b739547e2b 100644
--- a/src/simtools/runners/corsika_simtel_runner.py
+++ b/src/simtools/runners/corsika_simtel_runner.py
@@ -53,7 +53,7 @@ def __init__(
         self.sequential = "--sequential" if sequential else ""
 
         self.runner_service = runner_services.RunnerServices(
-            self.base_corsika_config, "multi_pipe", label
+            self.base_corsika_config, run_type="multi_pipe", label=label
         )
         self.file_list = None
 
diff --git a/src/simtools/runners/runner_services.py b/src/simtools/runners/runner_services.py
index 2509e33ae5..dae089887d 100644
--- a/src/simtools/runners/runner_services.py
+++ b/src/simtools/runners/runner_services.py
@@ -2,6 +2,7 @@
 
 import logging
 
+from simtools.corsika.corsika_config import CorsikaConfig
 from simtools.io import io_handler
 
 _logger = logging.getLogger(__name__)
@@ -106,22 +107,19 @@ class RunnerServices:
 
     Parameters
     ----------
-    corsika_config : CorsikaConfig, list of CorsikaConfig
-        Configuration parameters for CORSIKA.
-    core_config : dict
-        Core configuration parameters (less specific than CorsikaConfig).
+    config: CorsikaConfig, dict
+        Configuration parameters.
     run_type : str
         Type of simulation runner.
     label : str
         Label.
     """
 
-    def __init__(self, corsika_config, core_config, run_type, label=None):
+    def __init__(self, config, run_type, label=None):
         """Initialize RunnerServices."""
         self._logger = logging.getLogger(__name__)
         self.label = label
-        self.corsika_config = corsika_config
-        self.core_config = core_config
+        self.config = config
         self.run_type = run_type
         self.directory = self.load_data_directory()
 
@@ -137,6 +135,7 @@ def load_data_directory(self):
         ioh = io_handler.IOHandler()
         directory = ioh.get_output_directory(self.run_type)
         self._logger.debug(f"Data directories for {self.run_type}: {directory}")
+
         return directory
 
     def load_files(self, run_number=None):
@@ -179,15 +178,15 @@ def _get_file_basename(self, run_number, is_multi_pipe=False):
         str
             Base name for the simulation files.
         """
-        if self.corsika_config:
+        if isinstance(self.config, CorsikaConfig):
             return self._get_file_base_name_from_corsika_config(run_number, is_multi_pipe)
-        if self.core_config:
+        if isinstance(self.config, dict):
             return self._get_file_base_name_from_core_config()
-        raise ValueError("Either corsika_config or core_config must be provided.")
+        raise ValueError(f"Invalid configuration type: {type(self.config)}")
 
     def _get_file_base_name_from_core_config(self):
         """Get file base name from core configuration."""
-        cfg = self.core_config
+        cfg = self.config
         parts = [
             f"{cfg.get('run_mode', '')}_",
             f"{self._get_run_number_string(cfg.get('run_number'))}_" if "run_number" in cfg else "",
@@ -202,13 +201,13 @@ def _get_file_base_name_from_core_config(self):
 
     def _get_file_base_name_from_corsika_config(self, run_number, is_multi_pipe=False):
         """Get file base name from CORSIKA configuration."""
-        zenith = self.corsika_config.get_config_parameter("THETAP")[0]
-        vc_high = self.corsika_config.get_config_parameter("VIEWCONE")[1]
+        zenith = self.config.get_config_parameter("THETAP")[0]
+        vc_high = self.config.get_config_parameter("VIEWCONE")[1]
 
-        if self.corsika_config.run_mode is not None and self.corsika_config.run_mode != "":
-            primary_name = self.corsika_config.run_mode
+        if self.config.run_mode is not None and self.config.run_mode != "":
+            primary_name = self.config.run_mode
         else:
-            primary_name = self.corsika_config.primary_particle.name
+            primary_name = self.config.primary_particle.name
             if primary_name == "gamma" and vc_high > 0:
                 primary_name = "gamma_diffuse"
 
@@ -219,10 +218,10 @@ def _get_file_base_name_from_corsika_config(self, run_number, is_multi_pipe=Fals
         return (
             prefix
             + f"za{round(zenith):02}deg_"
-            + f"azm{self.corsika_config.azimuth_angle:03}deg_"
-            + f"{self.corsika_config.array_model.site}_"
-            + f"{self.corsika_config.array_model.layout_name}_"
-            + (self.corsika_config.array_model.model_version if not is_multi_pipe else "")
+            + f"azm{self.config.azimuth_angle:03}deg_"
+            + f"{self.config.array_model.site}_"
+            + f"{self.config.array_model.layout_name}_"
+            + (self.config.array_model.model_version if not is_multi_pipe else "")
             + file_label
         )
 
@@ -325,7 +324,10 @@ def get_resources(self, sub_out_file):
         if runtime is None:
             _logger.debug("RUNTIME was not found in run log file")
 
-        return {
-            "runtime": runtime,
-            "n_events": int(self.corsika_config.get_config_parameter("NSHOW")),
-        }
+        if isinstance(self.config, CorsikaConfig):
+            return {
+                "runtime": runtime,
+                "n_events": int(self.config.get_config_parameter("NSHOW")),
+            }
+        self._logger.warning("Number of events cannot be determined from non-CORSIKA config.")
+        return {"runtime": runtime, "n_events": None}
diff --git a/src/simtools/runners/simtel_runner.py b/src/simtools/runners/simtel_runner.py
index c988e9a867..c106750b48 100644
--- a/src/simtools/runners/simtel_runner.py
+++ b/src/simtools/runners/simtel_runner.py
@@ -26,15 +26,13 @@ class SimtelRunner:
     ----------
     label: str
         Instance label. Important for output file naming.
-    corsika_config: CorsikaConfig
-        CORSIKA configuration.
-    core_config: dict
-        Core configuration parameters (less specific than CorsikaConfig).
+    config: CorsikaConfig or dict
+        Configuration parameters.
     is_calibration_run: bool
         Flag to indicate if this is a calibration run.
     """
 
-    def __init__(self, label=None, corsika_config=None, core_config=None, is_calibration_run=False):
+    def __init__(self, label=None, config=None, is_calibration_run=False):
         """Initialize SimtelRunner."""
         self._logger = logging.getLogger(__name__)
 
@@ -44,12 +42,7 @@ def __init__(self, label=None, corsika_config=None, core_config=None, is_calibra
 
         self.runs_per_set = 1
 
-        self.runner_service = RunnerServices(
-            corsika_config=corsika_config,
-            core_config=core_config,
-            run_type="sim_telarray",
-            label=label,
-        )
+        self.runner_service = RunnerServices(config, run_type="sim_telarray", label=label)
         self.file_list = None
 
     def run(self, test=False, input_file=None, run_number=None):
diff --git a/src/simtools/simtel/simulator_array.py b/src/simtools/simtel/simulator_array.py
index 25c9863000..e2dcf6e201 100644
--- a/src/simtools/simtel/simulator_array.py
+++ b/src/simtools/simtel/simulator_array.py
@@ -33,11 +33,7 @@ def __init__(
         is_calibration_run=False,
     ):
         """Initialize SimulatorArray."""
-        super().__init__(
-            label=label,
-            corsika_config=corsika_config,
-            is_calibration_run=is_calibration_run,
-        )
+        super().__init__(label=label, config=corsika_config, is_calibration_run=is_calibration_run)
 
         self.sim_telarray_seeds = sim_telarray_seeds
         self.corsika_config = corsika_config
diff --git a/src/simtools/simtel/simulator_light_emission.py b/src/simtools/simtel/simulator_light_emission.py
index e2b93ab4dc..d27bce59f2 100644
--- a/src/simtools/simtel/simulator_light_emission.py
+++ b/src/simtools/simtel/simulator_light_emission.py
@@ -35,7 +35,7 @@ def __init__(self, light_emission_config, label=None):
         self._logger = logging.getLogger(__name__)
         self.io_handler = io_handler.IOHandler()
 
-        super().__init__(label=label, core_config=light_emission_config)
+        super().__init__(label=label, config=light_emission_config)
 
         self.telescope_model, self.site_model, self.calibration_model = (
             initialize_simulation_models(
diff --git a/tests/unit_tests/runners/test_runner_services.py b/tests/unit_tests/runners/test_runner_services.py
index ae0221d498..374825790c 100644
--- a/tests/unit_tests/runners/test_runner_services.py
+++ b/tests/unit_tests/runners/test_runner_services.py
@@ -18,7 +18,6 @@ def runner_service(corsika_runner_mock_array_model):
         corsika_config=corsika_runner_mock_array_model.corsika_config,
         label="test-corsika-runner",
         run_type="corsika",
-        core_config=None,
     )
     _runner_service.load_data_directory()
     return _runner_service
@@ -31,7 +30,6 @@ def runner_service_mock_array_model(corsika_runner_mock_array_model):
         corsika_config=corsika_runner_mock_array_model.corsika_config,
         label="test-corsika-runner",
         run_type="corsika",
-        core_config=None,
     )
     _runner_service.load_data_directory()
     return _runner_service
@@ -44,7 +42,6 @@ def runner_service_config_only(corsika_config_mock_array_model):
         corsika_config=corsika_config_mock_array_model,
         label="test-corsika-runner",
         run_type="corsika",
-        core_config=None,
     )
 
 
@@ -57,7 +54,6 @@ def runner_service_pedestals(corsika_config_mock_array_model):
         corsika_config=corsika_config_pedestals,
         label="test-pedestals-runner",
         run_type="pedestals",
-        core_config=None,
     )
 
 
diff --git a/tests/unit_tests/runners/test_simtel_runner.py b/tests/unit_tests/runners/test_simtel_runner.py
index 6983687938..e2bcd57272 100644
--- a/tests/unit_tests/runners/test_simtel_runner.py
+++ b/tests/unit_tests/runners/test_simtel_runner.py
@@ -11,7 +11,7 @@
 
 @pytest.fixture
 def simtel_runner(corsika_config_mock_array_model):
-    return SimtelRunner(label="test", corsika_config=corsika_config_mock_array_model)
+    return SimtelRunner(label="test", config=corsika_config_mock_array_model)
 
 
 def test_run(simtel_runner, caplog, mocker):

From b8d4661c012c063c5cbace9ec19f16de3272ffe9 Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Tue, 13 Jan 2026 12:19:45 +0100
Subject: [PATCH 05/10] tests

---
 src/simtools/applications/simulate_flasher.py |  2 +
 .../simtel/simulator_light_emission.py        | 39 ++++++++++++-------
 ...late_flasher_full_simulation_LST_North.yml |  4 +-
 ...late_flasher_full_simulation_LST_South.yml |  4 +-
 ...e_flasher_full_simulation_mst_flashcam.yml |  6 +--
 ..._flasher_full_simulation_mst_nectarcam.yml |  6 +--
 ...late_illuminator_configurable_position.yml |  6 +--
 .../config/simulate_illuminator_layout.yml    |  6 +--
 .../runners/test_runner_services.py           | 23 ++++++-----
 .../simtel/test_simulator_light_emission.py   | 26 +++++++++----
 tests/unit_tests/test_simulator.py            |  5 ++-
 11 files changed, 75 insertions(+), 52 deletions(-)

diff --git a/src/simtools/applications/simulate_flasher.py b/src/simtools/applications/simulate_flasher.py
index 8e294e745a..6110d18d30 100644
--- a/src/simtools/applications/simulate_flasher.py
+++ b/src/simtools/applications/simulate_flasher.py
@@ -119,6 +119,8 @@ def main():
         raise ValueError(f"Unsupported run_mode: {app_context.args['run_mode']}")
 
     light_source.simulate()
+    light_source.verify_simulations()
+
     app_context.logger.info("Flasher simulation completed.")
 
 
diff --git a/src/simtools/simtel/simulator_light_emission.py b/src/simtools/simtel/simulator_light_emission.py
index d27bce59f2..04c0f2559a 100644
--- a/src/simtools/simtel/simulator_light_emission.py
+++ b/src/simtools/simtel/simulator_light_emission.py
@@ -11,6 +11,7 @@
 from simtools.io import io_handler
 from simtools.job_execution import job_manager
 from simtools.model.model_utils import initialize_simulation_models
+from simtools.runners import runner_services
 from simtools.runners.simtel_runner import SimtelRunner, sim_telarray_env_as_string
 from simtools.simtel.simtel_config_writer import SimtelConfigWriter
 from simtools.utils.geometry import fiducial_radius_from_shape
@@ -36,6 +37,9 @@ def __init__(self, light_emission_config, label=None):
         self.io_handler = io_handler.IOHandler()
 
         super().__init__(label=label, config=light_emission_config)
+        self.job_files = runner_services.RunnerServices(
+            light_emission_config, run_type="sub", label=label
+        )
 
         self.telescope_model, self.site_model, self.calibration_model = (
             initialize_simulation_models(
@@ -73,24 +77,13 @@ def _initialize_light_emission_configuration(self, config):
         return config
 
     def simulate(self):
-        """
-        Simulate light emission.
-
-        Returns
-        -------
-        Path
-            The output simtel file path.
-        """
+        """Simulate light emission."""
         run_script = self.prepare_run()
         job_manager.submit(
             run_script,
-            out_file=self.runner_service.get_file_name("sub_out"),
-            err_file=self.runner_service.get_file_name("sub_err"),
+            out_file=self.job_files.get_file_name("sub_out"),
+            err_file=self.job_files.get_file_name("sub_err"),
         )
-        out = Path(self.runner_service.get_file_name(file_type="sim_telarray_output"))
-        if not out.exists():
-            self._logger.warning(f"Expected sim_telarray output not found: {out}")
-        return out
 
     def prepare_run(self):
         """
@@ -101,7 +94,7 @@ def prepare_run(self):
         Path
             Full path of the run script.
         """
-        script_file = self.runner_service.get_file_name(file_type="sub_script")
+        script_file = self.job_files.get_file_name(file_type="sub_script")
         output_file = self.runner_service.get_file_name(file_type="sim_telarray_output")
         if output_file.exists():
             raise FileExistsError(
@@ -555,3 +548,19 @@ def _get_pulse_shape_string_for_sim_telarray(self):
         if shape_out == "exponential" and expv is not None:
             return f"{shape_out}:{float(expv)}"
         return shape_out
+
+    def verify_simulations(self):
+        """
+        Verify that the simulations were successful.
+
+        Returns
+        -------
+        bool
+            True if simulations were successful, False otherwise.
+        """
+        out = Path(self.runner_service.get_file_name(file_type="sim_telarray_output"))
+        if not out.exists():
+            self._logger.error(f"Expected sim_telarray output not found: {out}")
+            return False
+        self._logger.info(f"sim_telarray output found: {out}")
+        return True
diff --git a/tests/integration_tests/config/simulate_flasher_full_simulation_LST_North.yml b/tests/integration_tests/config/simulate_flasher_full_simulation_LST_North.yml
index deabe0ecd2..3e7437974b 100644
--- a/tests/integration_tests/config/simulate_flasher_full_simulation_LST_North.yml
+++ b/tests/integration_tests/config/simulate_flasher_full_simulation_LST_North.yml
@@ -12,8 +12,8 @@ applications:
     test: true
     log_level: DEBUG
   integration_tests:
-  - output_file: logfile.log
-  - output_file: ff-1m.simtel.zst
+  - output_file: sub/full_simulation_run000010_North_7.0.0_simulate_flasher.out
+  - output_file: sim_telarray/full_simulation_run000010_North_7.0.0_simulate_flasher.simtel.zst
   model_version_use_current: true
   test_name: full-simulation_lsfn_design
 schema_name: application_workflow.metaschema
diff --git a/tests/integration_tests/config/simulate_flasher_full_simulation_LST_South.yml b/tests/integration_tests/config/simulate_flasher_full_simulation_LST_South.yml
index 54b0247726..ce3ec7e420 100644
--- a/tests/integration_tests/config/simulate_flasher_full_simulation_LST_South.yml
+++ b/tests/integration_tests/config/simulate_flasher_full_simulation_LST_South.yml
@@ -12,8 +12,8 @@ applications:
     test: true
     log_level: DEBUG
   integration_tests:
-  - output_file: logfile.log
-  - output_file: ff-1m.simtel.zst
+  - output_file: sub/full_simulation_run000010_South_7.0.0_simulate_flasher.out
+  - output_file: sim_telarray/full_simulation_run000010_South_7.0.0_simulate_flasher.simtel.zst
   model_version_use_current: true
   test_name: full-simulation_lsfs_design
 schema_name: application_workflow.metaschema
diff --git a/tests/integration_tests/config/simulate_flasher_full_simulation_mst_flashcam.yml b/tests/integration_tests/config/simulate_flasher_full_simulation_mst_flashcam.yml
index 4a289bc318..3e47728d28 100644
--- a/tests/integration_tests/config/simulate_flasher_full_simulation_mst_flashcam.yml
+++ b/tests/integration_tests/config/simulate_flasher_full_simulation_mst_flashcam.yml
@@ -13,9 +13,9 @@ applications:
     log_level: DEBUG
   integration_tests:
   - test_output_files:
-    - file: logfile.log
+    - file: sub/full_simulation_run000010_South_7.0.0_simulate_flasher.out
       path_descriptor: output_path
-    - file: ff-1m.simtel.zst
+    - file: sim_telarray/full_simulation_run000010_South_7.0.0_simulate_flasher.simtel.zst
       path_descriptor: output_path
     - expected_log_output:
       pattern:
@@ -25,7 +25,7 @@ applications:
       forbidden_pattern:
       - "Error"
       - "had less photons than required and were skipped"
-      file: logfile.log
+      file: sub/full_simulation_run000010_South_7.0.0_simulate_flasher.out
       path_descriptor: output_path
   model_version_use_current: true
   test_name: full-simulation-msfx-flashcam-7.0.0
diff --git a/tests/integration_tests/config/simulate_flasher_full_simulation_mst_nectarcam.yml b/tests/integration_tests/config/simulate_flasher_full_simulation_mst_nectarcam.yml
index 796cf25d88..ec1e317166 100644
--- a/tests/integration_tests/config/simulate_flasher_full_simulation_mst_nectarcam.yml
+++ b/tests/integration_tests/config/simulate_flasher_full_simulation_mst_nectarcam.yml
@@ -13,9 +13,9 @@ applications:
     log_level: DEBUG
   integration_tests:
   - test_output_files:
-    - file: logfile.log
+    - file: sub/full_simulation_run000010_North_7.0.0_simulate_flasher.out
       path_descriptor: output_path
-    - file: ff-1m.simtel.zst
+    - file: sim_telarray/full_simulation_run000010_North_7.0.0_simulate_flasher.simtel.zst
       path_descriptor: output_path
     - expected_log_output:
       pattern:
@@ -25,7 +25,7 @@ applications:
       forbidden_pattern:
       - "Error"
       - "had less photons than required and were skipped"
-      file: logfile.log
+      file: sub/full_simulation_run000010_North_7.0.0_simulate_flasher.out
       path_descriptor: output_path
   model_version_use_current: true
   test_name: full-simulation_msfx_nectarcam-7.0.0
diff --git a/tests/integration_tests/config/simulate_illuminator_configurable_position.yml b/tests/integration_tests/config/simulate_illuminator_configurable_position.yml
index da12cd182d..905b8419cc 100644
--- a/tests/integration_tests/config/simulate_illuminator_configurable_position.yml
+++ b/tests/integration_tests/config/simulate_illuminator_configurable_position.yml
@@ -19,9 +19,9 @@ applications:
     log_level: DEBUG
   integration_tests:
   - test_output_files:
-    - file: logfile.log
+    - file: sub/illuminator_North_7.0.0_simulate_illuminator.out
       path_descriptor: output_path
-    - file: xyzls.simtel.zst
+    - file: sim_telarray/illuminator_North_7.0.0_simulate_illuminator.simtel.zst
       path_descriptor: output_path
     - expected_log_output:
       pattern:
@@ -33,7 +33,7 @@ applications:
       - "Finished."
       forbidden_pattern:
       - "Error"
-      file: logfile.log
+      file: sub/illuminator_North_7.0.0_simulate_illuminator.out
       path_descriptor: output_path
   model_version_use_current: true
   test_name: run-configurable-position
diff --git a/tests/integration_tests/config/simulate_illuminator_layout.yml b/tests/integration_tests/config/simulate_illuminator_layout.yml
index 05f84a359a..ebc02cbdca 100644
--- a/tests/integration_tests/config/simulate_illuminator_layout.yml
+++ b/tests/integration_tests/config/simulate_illuminator_layout.yml
@@ -11,9 +11,9 @@ applications:
     log_level: DEBUG
   integration_tests:
   - test_output_files:
-    - file: logfile.log
+    - file: sub/illuminator_North_7.0.0_simulate_illuminator.out
       path_descriptor: output_path
-    - file: xyzls.simtel.zst
+    - file: sim_telarray/illuminator_North_7.0.0_simulate_illuminator.simtel.zst
       path_descriptor: output_path
     - expected_log_output:
       pattern:
@@ -25,7 +25,7 @@ applications:
       - "Finished."
       forbidden_pattern:
       - "Error"
-      file: logfile.log
+      file: sub/illuminator_North_7.0.0_simulate_illuminator.out
       path_descriptor: output_path
   model_version_use_current: true
   test_name: run-layout
diff --git a/tests/unit_tests/runners/test_runner_services.py b/tests/unit_tests/runners/test_runner_services.py
index 374825790c..2b9b0782ab 100644
--- a/tests/unit_tests/runners/test_runner_services.py
+++ b/tests/unit_tests/runners/test_runner_services.py
@@ -15,7 +15,7 @@
 def runner_service(corsika_runner_mock_array_model):
     """Runner services object for corsika."""
     _runner_service = runner_services.RunnerServices(
-        corsika_config=corsika_runner_mock_array_model.corsika_config,
+        config=corsika_runner_mock_array_model.corsika_config,
         label="test-corsika-runner",
         run_type="corsika",
     )
@@ -27,7 +27,7 @@ def runner_service(corsika_runner_mock_array_model):
 def runner_service_mock_array_model(corsika_runner_mock_array_model):
     """Runner services object for corsika."""
     _runner_service = runner_services.RunnerServices(
-        corsika_config=corsika_runner_mock_array_model.corsika_config,
+        config=corsika_runner_mock_array_model.corsika_config,
         label="test-corsika-runner",
         run_type="corsika",
     )
@@ -39,7 +39,7 @@ def runner_service_mock_array_model(corsika_runner_mock_array_model):
 def runner_service_config_only(corsika_config_mock_array_model):
     """Runner services object with simplified config."""
     return runner_services.RunnerServices(
-        corsika_config=corsika_config_mock_array_model,
+        config=corsika_config_mock_array_model,
         label="test-corsika-runner",
         run_type="corsika",
     )
@@ -51,7 +51,7 @@ def runner_service_pedestals(corsika_config_mock_array_model):
     corsika_config_pedestals = copy.deepcopy(corsika_config_mock_array_model)
     corsika_config_pedestals.run_mode = "pedestals"
     return runner_services.RunnerServices(
-        corsika_config=corsika_config_pedestals,
+        config=corsika_config_pedestals,
         label="test-pedestals-runner",
         run_type="pedestals",
     )
@@ -66,7 +66,7 @@ def runner_service_config_only_diffuse_gamma(corsika_config_mock_array_model):
     }
 
     return runner_services.RunnerServices(
-        corsika_config=corsika_config_mock_array_model,
+        config=corsika_config_mock_array_model,
         label="test-corsika-runner",
         run_type="corsika",
     )
@@ -82,7 +82,7 @@ def file_base_name(model_version):
 
 def test_init_runner_services(runner_service_config_only):
     assert runner_service_config_only.label == "test-corsika-runner"
-    assert runner_service_config_only.corsika_config.primary_particle.name == "proton"
+    assert runner_service_config_only.config.primary_particle.name == "proton"
     assert str(runner_service_config_only.directory).endswith("corsika")
 
 
@@ -94,16 +94,16 @@ def test_get_file_basename(runner_service, file_base_name, model_version):
         f"proton_run000001_za20deg_azm000deg_South_test_layout_{model_version}"
     )
 
-    _runner_service_copy.corsika_config.primary_particle = None
+    _runner_service_copy.config.primary_particle = None
     assert _runner_service_copy._get_file_basename(1) == (
         f"run000001_za20deg_azm000deg_South_test_layout_{model_version}"
     )
 
-    _runner_service_copy.corsika_config.primary_particle = {
+    _runner_service_copy.config.primary_particle = {
         "primary_id_type": "common_name",
         "primary": "gamma",
     }
-    _runner_service_copy.corsika_config.config["USER_INPUT"]["VIEWCONE"] = [0, 5]
+    _runner_service_copy.config.config["USER_INPUT"]["VIEWCONE"] = [0, 5]
     assert _runner_service_copy._get_file_basename(1) == (
         f"gamma_diffuse_run000001_za20deg_azm000deg_South_test_layout_{model_version}"
     )
@@ -200,7 +200,6 @@ def test_get_sub_directory(runner_service_config_only, tmp_path):
 
 
 def test__get_file_basename(runner_service_config_only):
-    runner_service_config_only.corsika_config = None
-    runner_service_config_only.core_config = None
-    with pytest.raises(ValueError, match=r"Either corsika_config or core_config must be provided."):
+    runner_service_config_only.config = None
+    with pytest.raises(ValueError, match=r"Invalid configuration type: <class 'NoneType'>"):
         runner_service_config_only._get_file_basename(run_number=1)
diff --git a/tests/unit_tests/simtel/test_simulator_light_emission.py b/tests/unit_tests/simtel/test_simulator_light_emission.py
index 6580de756b..1604ad22c2 100644
--- a/tests/unit_tests/simtel/test_simulator_light_emission.py
+++ b/tests/unit_tests/simtel/test_simulator_light_emission.py
@@ -19,6 +19,7 @@ def simulator_instance():
     inst.telescope_model = Mock()
     inst.site_model = Mock()
     inst.light_emission_config = {}
+    inst.job_files = Mock()
     inst.output_directory = "/test/output"
     inst._logger = Mock()
     inst.runner_service = Mock()
@@ -1089,10 +1090,16 @@ def test_prepare_run(simulator_instance, tmp_test_directory):
     script_dir.mkdir(parents=True, exist_ok=True)
     script_path = script_dir / "xyzls-light_emission.sh"
 
-    # Mock runner_service.get_file_name to return paths
-    def get_file_name_side_effect(file_type):
+    # Mock job_files.get_file_name to return the script path
+    def job_files_get_file_name_side_effect(file_type):
         if file_type == "sub_script":
             return script_path
+        return Path(tmp_test_directory) / "output" / f"{file_type}.tmp"
+
+    simulator_instance.job_files.get_file_name.side_effect = job_files_get_file_name_side_effect
+
+    # Mock runner_service.get_file_name to return paths
+    def get_file_name_side_effect(file_type):
         if file_type == "sim_telarray_output":
             return Path(tmp_test_directory) / "output" / "test_output.simtel.gz"
         if file_type == "iact_output":
@@ -1160,10 +1167,16 @@ def test_simulate(simulator_instance, tmp_test_directory):
     mock_script_path.parent.mkdir(parents=True, exist_ok=True)
     mock_output_file = Path(tmp_test_directory) / "output" / "test_output.simtel.gz"
 
-    # Setup mock to return the script and output file
-    def get_file_name_side_effect(file_type):
+    # Setup job_files mock to return the script path
+    def job_files_get_file_name_side_effect(file_type):
         if file_type == "sub_script":
             return mock_script_path
+        return Path(tmp_test_directory) / "output" / f"{file_type}.tmp"
+
+    simulator_instance.job_files.get_file_name.side_effect = job_files_get_file_name_side_effect
+
+    # Setup runner_service mock to return the output file and other paths
+    def get_file_name_side_effect(file_type):
         if file_type == "sim_telarray_output":
             return mock_output_file
         if file_type == "sub_out":
@@ -1181,7 +1194,7 @@ def get_file_name_side_effect(file_type):
         with patch.object(
             simulator_instance, "make_run_command", return_value=["#!/bin/bash\n", "echo test\n"]
         ):
-            result = simulator_instance.simulate()
+            simulator_instance.simulate()
 
         # Create the output file to simulate successful run (this happens during simulate())
         mock_output_file.parent.mkdir(parents=True, exist_ok=True)
@@ -1192,9 +1205,6 @@ def get_file_name_side_effect(file_type):
         call_args = mock_job_submit.call_args
         assert call_args[0][0] == mock_script_path  # First positional arg is the script
 
-        # Verify return value - result will be the mock_output_file if it exists
-        assert result == mock_output_file
-
 
 def test__initialize_light_emission_configuration(simulator_instance):
     """Test _initialize_light_emission_configuration method."""
diff --git a/tests/unit_tests/test_simulator.py b/tests/unit_tests/test_simulator.py
index 8d85c23816..1e2166b31c 100644
--- a/tests/unit_tests/test_simulator.py
+++ b/tests/unit_tests/test_simulator.py
@@ -10,6 +10,7 @@
 
 import pytest
 
+from simtools.corsika.corsika_config import CorsikaConfig
 from simtools.sim_events import file_info
 from simtools.simulator import Simulator
 
@@ -315,12 +316,14 @@ def test_pack_for_register_with_multiple_versions(
 
     mocker.patch("simtools.simulator.ArrayModel", side_effect=mock_array_models)
 
-    mock_corsika_config = mocker.MagicMock()
+    mock_corsika_config = mocker.MagicMock(CorsikaConfig, instance=True)
+    mock_corsika_config.array_model = mocker.MagicMock()
     mock_corsika_config.get_config_parameter.side_effect = lambda param: {
         "VIEWCONE": [0, 10],
         "THETAP": [20, 20],
     }.get(param, [0, 0])
     mock_corsika_config.azimuth_angle = 0  # from args
+    mock_corsika_config.zenith_angle = 20  # from args
     mock_corsika_config.array_model.site = "North"  # from args
     mock_corsika_config.array_model.layout_name = "test_layout"  # from args
     mock_corsika_config.array_model.model_version = model_versions[0]

From 20a9fb23271f1ad46256797bf0ac2010d047cb1f Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Tue, 13 Jan 2026 13:12:36 +0100
Subject: [PATCH 06/10] Update src/simtools/runners/runner_services.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 src/simtools/runners/runner_services.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/simtools/runners/runner_services.py b/src/simtools/runners/runner_services.py
index dae089887d..c72305d05c 100644
--- a/src/simtools/runners/runner_services.py
+++ b/src/simtools/runners/runner_services.py
@@ -187,11 +187,25 @@ def _get_file_basename(self, run_number, is_multi_pipe=False):
     def _get_file_base_name_from_core_config(self):
         """Get file base name from core configuration."""
         cfg = self.config
+        zenith_angle = cfg.get("zenith_angle")
+        azimuth_angle = cfg.get("azimuth_angle")
+
+        za_part = (
+            f"za{round(zenith_angle):02}deg_"
+            if isinstance(zenith_angle, (int, float))
+            else ""
+        )
+        az_part = (
+            f"azm{azimuth_angle:03}deg_"
+            if isinstance(azimuth_angle, (int, float))
+            else ""
+        )
+
         parts = [
             f"{cfg.get('run_mode', '')}_",
             f"{self._get_run_number_string(cfg.get('run_number'))}_" if "run_number" in cfg else "",
-            f"za{round(cfg['zenith_angle']):02}deg_" if "zenith_angle" in cfg else "",
-            f"azm{cfg['azimuth_angle']:03}deg_" if "azimuth_angle" in cfg else "",
+            za_part,
+            az_part,
             f"{cfg['site']}_" if "site" in cfg else "",
             f"{cfg['layout']}_" if "layout" in cfg else "",
             cfg.get("model_version", ""),

From a8207e46284d7219690717e99f27ddf7fae459b6 Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Tue, 13 Jan 2026 12:28:08 +0100
Subject: [PATCH 07/10] changelog

---
 docs/changes/1981.maintenance.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 docs/changes/1981.maintenance.md

diff --git a/docs/changes/1981.maintenance.md b/docs/changes/1981.maintenance.md
new file mode 100644
index 0000000000..2b5ec983a6
--- /dev/null
+++ b/docs/changes/1981.maintenance.md
@@ -0,0 +1 @@
+Improve file management for light emission simulations (flasher/illuminators). Change of output file naming and directory tree.

From 5d4ab666fd62e04312fd0db35a971c9602258caf Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Tue, 13 Jan 2026 13:18:00 +0100
Subject: [PATCH 08/10] tests

---
 .../applications/simulate_illuminator.py      |  1 +
 src/simtools/runners/runner_services.py       | 10 ++----
 .../simtel/test_simulator_light_emission.py   | 34 ++++++++++---------
 3 files changed, 21 insertions(+), 24 deletions(-)

diff --git a/src/simtools/applications/simulate_illuminator.py b/src/simtools/applications/simulate_illuminator.py
index 753e702bca..6247230eeb 100644
--- a/src/simtools/applications/simulate_illuminator.py
+++ b/src/simtools/applications/simulate_illuminator.py
@@ -114,6 +114,7 @@ def main():
         label=app_context.args.get("label"),
     )
     light_source.simulate()
+    light_source.verify_simulations()
 
 
 if __name__ == "__main__":
diff --git a/src/simtools/runners/runner_services.py b/src/simtools/runners/runner_services.py
index c72305d05c..083b4baaac 100644
--- a/src/simtools/runners/runner_services.py
+++ b/src/simtools/runners/runner_services.py
@@ -191,15 +191,9 @@ def _get_file_base_name_from_core_config(self):
         azimuth_angle = cfg.get("azimuth_angle")
 
         za_part = (
-            f"za{round(zenith_angle):02}deg_"
-            if isinstance(zenith_angle, (int, float))
-            else ""
-        )
-        az_part = (
-            f"azm{azimuth_angle:03}deg_"
-            if isinstance(azimuth_angle, (int, float))
-            else ""
+            f"za{round(zenith_angle):02}deg_" if isinstance(zenith_angle, (int, float)) else ""
         )
+        az_part = f"azm{azimuth_angle:03}deg_" if isinstance(azimuth_angle, (int, float)) else ""
 
         parts = [
             f"{cfg.get('run_mode', '')}_",
diff --git a/tests/unit_tests/simtel/test_simulator_light_emission.py b/tests/unit_tests/simtel/test_simulator_light_emission.py
index 1604ad22c2..1574f7af95 100644
--- a/tests/unit_tests/simtel/test_simulator_light_emission.py
+++ b/tests/unit_tests/simtel/test_simulator_light_emission.py
@@ -1373,7 +1373,7 @@ def test__get_telescope_pointing(simulator_instance):
         simulator_instance._logger.info.assert_not_called()
 
 
-def test__write_telescope_position_file(simulator_instance):
+def test__write_telescope_position_file(simulator_instance, tmp_test_directory):
     """Test _write_telescope_position_file method."""
     simulator_instance.output_directory = Path("/output")
 
@@ -1393,27 +1393,29 @@ def test__write_telescope_position_file(simulator_instance):
         mock_radius,  # telescope_sphere_radius
     ]
 
-    # Mock io_handler to return a proper Path object
-    mock_output_dir = Path("/tmp/test_output")
+    # Use real temporary directory for file writing
+    mock_output_dir = Path(tmp_test_directory)
+    mock_output_dir.mkdir(parents=True, exist_ok=True)
     simulator_instance.io_handler.get_output_directory.return_value = mock_output_dir
     expected_file = mock_output_dir / "telescope_position.dat"
 
-    # Mock file writing
-    with patch.object(Path, "write_text") as mock_write:
-        result = simulator_instance._write_telescope_position_file()
+    # Call the method
+    result = simulator_instance._write_telescope_position_file()
 
-        # Should return the telescope position file path
-        assert result == expected_file
+    # Should return the telescope position file path
+    assert result == expected_file
 
-        # Should write coordinates and radius in correct format
-        expected_content = "100.0 200.0 300.0 1500.0\n"
-        mock_write.assert_called_once_with(expected_content, encoding="utf-8")
+    # Verify file was created with correct content
+    assert result.exists()
+    content = result.read_text(encoding="utf-8")
+    expected_content = "100.0 200.0 300.0 1500.0\n"
+    assert content == expected_content
 
-        # Verify unit conversions were called
-        mock_x.to.assert_called_once_with(u.cm)
-        mock_y.to.assert_called_once_with(u.cm)
-        mock_z.to.assert_called_once_with(u.cm)
-        mock_radius.to.assert_called_once_with(u.cm)
+    # Verify unit conversions were called
+    mock_x.to.assert_called_once_with(u.cm)
+    mock_y.to.assert_called_once_with(u.cm)
+    mock_z.to.assert_called_once_with(u.cm)
+    mock_radius.to.assert_called_once_with(u.cm)
 
 
 def test__calibration_pointing_direction(simulator_instance):

From b1b4836c6204e365fd34844cd846e03d338e45b4 Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Tue, 13 Jan 2026 13:20:47 +0100
Subject: [PATCH 09/10] integration test

---
 .../simulate_flasher_MSFx-FlashCam-full_simulation.yml      | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/integration_tests/config/simulate_flasher_MSFx-FlashCam-full_simulation.yml b/tests/integration_tests/config/simulate_flasher_MSFx-FlashCam-full_simulation.yml
index 3f2f2555d7..065147bfdf 100644
--- a/tests/integration_tests/config/simulate_flasher_MSFx-FlashCam-full_simulation.yml
+++ b/tests/integration_tests/config/simulate_flasher_MSFx-FlashCam-full_simulation.yml
@@ -12,9 +12,9 @@ applications:
     log_level: DEBUG
   integration_tests:
   - test_output_files:
-    - file: logfile.log
+    - file: sub/full_simulation_run000001_South_6.0.2_simulate_flasher.out
       path_descriptor: output_path
-    - file: ff-1m.simtel.zst
+    - file: sim_telarray/full_simulation_run000001_South_6.0.2_simulate_flasher.simtel.zst
       path_descriptor: output_path
     - expected_log_output:
       pattern:
@@ -24,7 +24,7 @@ applications:
       forbidden_pattern:
       - "Error"
       - "had less photons than required and were skipped"
-      file: logfile.log
+      file: sub/full_simulation_run000001_South_6.0.2_simulate_flasher.out
       path_descriptor: output_path
   model_version_use_current: true
   test_name: full-simulation-msfx-flashcam-6.0.2

From 54a3b6ff5e5fe5733d42d00cfc4c0714406af981 Mon Sep 17 00:00:00 2001
From: Gernot Maier <gernot.maier@desy.de>
Date: Tue, 13 Jan 2026 13:45:05 +0100
Subject: [PATCH 10/10] coverage

---
 src/simtools/runners/runner_services.py       | 15 +--
 .../runners/test_runner_services.py           | 93 +++++++++++++++++++
 .../simtel/test_simulator_light_emission.py   | 29 ++++++
 3 files changed, 127 insertions(+), 10 deletions(-)

diff --git a/src/simtools/runners/runner_services.py b/src/simtools/runners/runner_services.py
index 083b4baaac..92875246b8 100644
--- a/src/simtools/runners/runner_services.py
+++ b/src/simtools/runners/runner_services.py
@@ -190,18 +190,13 @@ def _get_file_base_name_from_core_config(self):
         zenith_angle = cfg.get("zenith_angle")
         azimuth_angle = cfg.get("azimuth_angle")
 
-        za_part = (
-            f"za{round(zenith_angle):02}deg_" if isinstance(zenith_angle, (int, float)) else ""
-        )
-        az_part = f"azm{azimuth_angle:03}deg_" if isinstance(azimuth_angle, (int, float)) else ""
-
         parts = [
-            f"{cfg.get('run_mode', '')}_",
+            f"{cfg['run_mode']}_" if cfg.get("run_mode") else "",
             f"{self._get_run_number_string(cfg.get('run_number'))}_" if "run_number" in cfg else "",
-            za_part,
-            az_part,
-            f"{cfg['site']}_" if "site" in cfg else "",
-            f"{cfg['layout']}_" if "layout" in cfg else "",
+            f"za{round(zenith_angle):02}deg_" if isinstance(zenith_angle, (int, float)) else "",
+            f"azm{round(azimuth_angle):03}deg_" if isinstance(azimuth_angle, (int, float)) else "",
+            f"{cfg['site']}_" if cfg.get("site") else "",
+            f"{cfg['layout']}_" if cfg.get("layout") else "",
             cfg.get("model_version", ""),
             f"_{self.label}" if self.label else "",
         ]
diff --git a/tests/unit_tests/runners/test_runner_services.py b/tests/unit_tests/runners/test_runner_services.py
index 2b9b0782ab..ed369b9225 100644
--- a/tests/unit_tests/runners/test_runner_services.py
+++ b/tests/unit_tests/runners/test_runner_services.py
@@ -145,6 +145,8 @@ def test_get_run_number_string(runner_service_config_only):
     ):
         runner_service_config_only._get_run_number_string(1234567)
 
+    assert runner_service_config_only._get_run_number_string(None) == ""
+
 
 def test_get_resources(runner_service_mock_array_model, caplog):
     sub_log_file = runner_service_mock_array_model.get_file_name(file_type="sub_log", run_number=5)
@@ -167,6 +169,10 @@ def test_get_resources(runner_service_mock_array_model, caplog):
     assert resources["runtime"] is None
     assert "RUNTIME was not found in run log file" in caplog.text
 
+    runner_service_mock_array_model.config = None
+    resources = runner_service_mock_array_model.get_resources(sub_log_file)
+    assert resources["runtime"] is None
+
 
 def test_validate_corsika_run_number():
     assert runner_services.validate_corsika_run_number(1)
@@ -203,3 +209,90 @@ def test__get_file_basename(runner_service_config_only):
     runner_service_config_only.config = None
     with pytest.raises(ValueError, match=r"Invalid configuration type: <class 'NoneType'>"):
         runner_service_config_only._get_file_basename(run_number=1)
+
+
+def test_get_file_base_name_from_core_config_full():
+    """Test file base name generation from core config with all parameters."""
+    config = {
+        "run_mode": "test_mode",
+        "run_number": 5,
+        "zenith_angle": 20.3,
+        "azimuth_angle": 45.7,
+        "site": "South",
+        "layout": "test_layout",
+        "model_version": "1.0.0",
+    }
+    runner_service = runner_services.RunnerServices(
+        config=config,
+        label="test-label",
+        run_type="corsika",
+    )
+    basename = runner_service._get_file_base_name_from_core_config()
+    assert basename == "test_mode_run000005_za20deg_azm046deg_South_test_layout_1.0.0_test-label"
+
+
+def test_get_file_base_name_from_core_config_minimal():
+    """Test file base name generation from core config with minimal parameters."""
+    config = {
+        "run_mode": "test_mode",
+        "model_version": "1.0.0",
+    }
+    runner_service = runner_services.RunnerServices(
+        config=config,
+        label=None,
+        run_type="corsika",
+    )
+    basename = runner_service._get_file_base_name_from_core_config()
+    assert basename == "test_mode_1.0.0"
+
+
+def test_get_file_base_name_from_core_config_no_run_mode():
+    """Test file base name generation without run_mode."""
+    config = {
+        "zenith_angle": 20,
+        "azimuth_angle": 45,
+        "site": "North",
+        "layout": "test_layout",
+        "model_version": "1.0.0",
+    }
+    runner_service = runner_services.RunnerServices(
+        config=config,
+        label="test-label",
+        run_type="corsika",
+    )
+    basename = runner_service._get_file_base_name_from_core_config()
+    assert basename == "za20deg_azm045deg_North_test_layout_1.0.0_test-label"
+
+
+def test_get_file_base_name_from_core_config_invalid_angles():
+    """Test file base name generation with invalid angle types."""
+    config = {
+        "run_mode": "test_mode",
+        "zenith_angle": "invalid",
+        "azimuth_angle": "invalid",
+        "model_version": "1.0.0",
+    }
+    runner_service = runner_services.RunnerServices(
+        config=config,
+        label=None,
+        run_type="corsika",
+    )
+    basename = runner_service._get_file_base_name_from_core_config()
+    assert basename == "test_mode_1.0.0"
+
+
+def test_get_file_base_name_from_core_config_none_values():
+    """Test file base name generation with None values in optional fields."""
+    config = {
+        "run_mode": "test_mode",
+        "site": None,
+        "layout": None,
+        "model_version": "1.0.0",
+    }
+    runner_service = runner_services.RunnerServices(
+        config=config,
+        label=None,
+        run_type="corsika",
+    )
+    basename = runner_service._get_file_base_name_from_core_config()
+    assert basename == "test_mode_1.0.0"
diff --git a/tests/unit_tests/simtel/test_simulator_light_emission.py b/tests/unit_tests/simtel/test_simulator_light_emission.py
index 1574f7af95..8dccef1b5e 100644
--- a/tests/unit_tests/simtel/test_simulator_light_emission.py
+++ b/tests/unit_tests/simtel/test_simulator_light_emission.py
@@ -1518,3 +1518,32 @@ def test__get_angular_distribution_string_for_sim_telarray_isotropic(simulator_i
     # Verify width was NOT requested: the implementation returns early for isotropic distributions
     # before attempting to fetch the width via get_parameter_value_with_unit.
     simulator_instance.calibration_model.get_parameter_value_with_unit.assert_not_called()
+
+
+def test_verify_simulations_success(simulator_instance, tmp_test_directory):
+    """Test verify_simulations returns True when output file exists."""
+    output_file = Path(tmp_test_directory) / "output.iact"
+    output_file.write_text("test data", encoding="utf-8")
+
+    simulator_instance.runner_service.get_file_name.return_value = output_file
+
+    result = simulator_instance.verify_simulations()
+
+    assert result is True
+    simulator_instance._logger.info.assert_called_once()
+    assert "sim_telarray output found" in str(simulator_instance._logger.info.call_args)
+
+
+def test_verify_simulations_missing_output(simulator_instance, tmp_test_directory):
+    """Test verify_simulations returns False when output file does not exist."""
+    output_file = Path(tmp_test_directory) / "nonexistent_output.iact"
+
+    simulator_instance.runner_service.get_file_name.return_value = output_file
+
+    result = simulator_instance.verify_simulations()
+
+    assert result is False
+    simulator_instance._logger.error.assert_called_once()
+    assert "Expected sim_telarray output not found" in str(
+        simulator_instance._logger.error.call_args
+    )