fix interpolation

README.md

@@ -71,3 +71,5 @@ If you want to skip the porting part, you can directly start from the `src/kokko
 ## Publications
 
 - SILVA-CUEVAS, J. J., ZYCH, M., PEYEN, K., et al. Towards a complete task-based implementation of a 3D Particle-In-Cell code: performance studies and benchmarks. Computer Physics Communications, 2025, p. 109647. https://doi.org/10.1016/j.cpc.2025.109647
+
+- KHOURY, E. E., LOBET, M., COLOMBET, L., BIGOT, J., PEYEN, K., SILVA-CUEVAS, J. J. Exploring C++ standard parallelism for GPU programming in a particle-in-cell application (preprint). 2025. HAL: [hal-05316488](https://hal.science/hal-05316488) — PDF: [HeteroPar_EuroPar.pdf](https://hal.science/hal-05316488v1/file/HeteroPar_EuroPar.pdf)

doc/python_tools.md

@@ -50,6 +50,24 @@ Note you have to source the activation script if you are in a new terminal (and
 
 </details>
 
+<details>
+
+<summary>
+And also with conda:
+</summary>
+
+```sh
+conda create -n minipic python=<x.y> pip -c conda-forge
+conda activate minipic
+```
+
+with `<x.y>` the version of Python.
+By instance, `python3.12`.
+Note you have to source the activation script if you are in a new terminal (and in a Slurm job).
+
+</details>
+
+
 ## `mini-run` command
 
 The `mini-run` command is used to build (mini)miniPIC for a selection of setups, to execute it and to validate its results.

libminipic/run.py

@@ -476,12 +476,13 @@ def run():
                     bench_dir,
                     "--setup",
                     setup,
+                    "--no-evaluate" if not evaluate else "",
                     "--threshold",
                     threshold,
                 ]
             )
 
-            validate_setup(bench_dir, setup, threshold)
+            validate_setup(bench_dir, setup=setup, evaluate=evaluate, threshold=threshold)
 
             # ____________________________________________________________________________
             # Read timers (json format)

libminipic/validate.py

@@ -41,6 +41,8 @@ def validate_setup(path, setup=None, evaluate=True, threshold=THRESHOLD):
     if not os.path.isdir("diags"):
         raise MissingFileMiniPICError(f"Directory diags is not in {path}")
 
+    print(evaluate, threshold)
+
     module.validate(evaluate=evaluate, threshold=threshold)
 
     print_success(f"Setup {setup} tested with success")

libminipic/validation/antenna.py

@@ -12,6 +12,9 @@
 
 def validate(evaluate=True, threshold=THRESHOLD):
 
+    # Get the name of the current file (without extension) to use as a label for the validation
+    validation_label = os.path.basename(__file__).split(".")[0]
+
     # ______________________________________________________________________
     # Check output files are created
 
@@ -33,25 +36,74 @@ def validate(evaluate=True, threshold=THRESHOLD):
         if not (os.path.exists("diags/" + file)):
             raise MissingFileMiniPICError(f"File {file} not generated")
 
+    # ______________________________________________________________________
+    # Reference database
+
+    references = {
+        "fields_final": [
+            600,
+            8.392314275494247e-06,
+            7.685688704219648e-08,
+            9.162999693074787e-04,
+            8.581201889410053e-06,
+            9.523643303672555e-04,
+            1.993340067202490e-34,
+            0.000000000000000e00,
+            0.000000000000000e00,
+            1.877328812863773e-37,
+        ],
+        "fields_3d": {
+            "Ex": [
+                0.0,
+                82.16528908415819,
+                344.34858930166956,
+                590.8495077993598,
+                557.1785762453475,
+                835.1262141764287,
+            ],
+            "Ey": [
+                0.0,
+                9.971267188545653,
+                38.4454341611614,
+                65.35670493378103,
+                59.67453062284768,
+                76.50264530492844,
+            ],
+            "Ez": [
+                0.0,
+                774.7241409632107,
+                3237.01821064664,
+                5666.167748229646,
+                6216.341002673892,
+                9765.210440891475,
+            ],
+            "Bx": [
+                0.0,
+                86.91713443298572,
+                355.1215926140225,
+                614.3956604220939,
+                634.2442079543871,
+                881.1441186493583,
+            ],
+            "By": [
+                0.0,
+                784.3391276892934,
+                3246.3762073832377,
+                5627.157839639507,
+                6428.848152848923,
+                9793.622315394427,
+            ],
+        },
+    }
+
     # ______________________________________________________________________
     # Check scalars
 
     print(" > Check scalars")
 
     # Check final scalar values for fields
 
-    reference_data = [
-        600,
-        8.392314275494247e-06,
-        7.685688704219648e-08,
-        9.162999693074787e-04,
-        8.581201889410053e-06,
-        9.523643303672555e-04,
-        1.993340067202490e-34,
-        0.000000000000000e00,
-        0.000000000000000e00,
-        1.877328812863773e-37,
-    ]
+    reference_data = references["fields_final"]
 
     with open("diags/fields.txt", "r") as f:
         lines = f.readlines()
@@ -112,55 +164,15 @@ def validate(evaluate=True, threshold=THRESHOLD):
             "By value in fields.txt is not correct",
         )
         # minipic_ci.evaluate(Bz, reference_data[6], 1e-2, 'relative', 'Bz value in fields.txt is not correct') ===> too small to be relevant
+    else:
+        references["fields_final"] = [iteration, Ex, Ey, Ez, Bx, By, Bz]
 
     # ______________________________________________________________________
     # Check field
 
     print(" > Check fields")
 
-    reference_data = {
-        "Ex": [
-            0.0,
-            82.16528908415819,
-            344.34858930166956,
-            590.8495077993598,
-            557.1785762453475,
-            835.1262141764287,
-        ],
-        "Ey": [
-            0.0,
-            9.971267188545653,
-            38.4454341611614,
-            65.35670493378103,
-            59.67453062284768,
-            76.50264530492844,
-        ],
-        "Ez": [
-            0.0,
-            774.7241409632107,
-            3237.01821064664,
-            5666.167748229646,
-            6216.341002673892,
-            9765.210440891475,
-        ],
-        "Bx": [
-            0.0,
-            86.91713443298572,
-            355.1215926140225,
-            614.3956604220939,
-            634.2442079543871,
-            881.1441186493583,
-        ],
-        "By": [
-            0.0,
-            784.3391276892934,
-            3246.3762073832377,
-            5627.157839639507,
-            6428.848152848923,
-            9793.622315394427,
-        ],
-        # 'Bz' : [0.0, 8.68335830083499e-14, 8.109979554106818e-13, 2.2881775959027207e-12, 3.4172712318143877e-12, 4.161059825829489e-12]
-    }
+    reference_data = references["fields_3d"]
 
     for field in reference_data.keys():
 
@@ -198,3 +210,22 @@ def validate(evaluate=True, threshold=THRESHOLD):
                     "relative",
                     "{} field not similar".format(field),
                 )
+        else:
+            references["fields_3d"][field] = new_data
+
+    # ______________________________________________________________________
+    # Write updated references to JSON file if not evaluating
+
+    if not evaluate:
+
+        import json
+
+        json_file_name = validation_label
+
+        with open(json_file_name, "w") as f:
+            json.dump(references, f, indent=4)
+        print(f" > New references written to {json_file_name}")
+
+        print(
+            " > New references: \n {}".format(json.dumps(references, indent=4))
+        )

libminipic/validation/antenna_heavy.py

@@ -12,6 +12,9 @@
 
 def validate(evaluate=True, threshold=THRESHOLD):
 
+    # Get the name of the current file (without extension) to use as a label for the validation
+    validation_label = os.path.basename(__file__).split(".")[0]
+
     # ______________________________________________________________________
     # Check output files are created
 
@@ -33,22 +36,51 @@ def validate(evaluate=True, threshold=THRESHOLD):
         if not (os.path.exists("diags/" + file)):
             raise MissingFileMiniPICError(f"File {file} not generated")
 
+    # ______________________________________________________________________
+    # Reference database
+
+    references = {
+        "fields_final": [
+            200,
+            1.178332626270596e-08,
+            1.121385881385788e-10,
+            1.372260141937414e-06,
+            1.217329509377536e-08,
+            1.397861526161067e-06,
+            5.139203602251246e-39,
+        ],
+        "fields_3d": {
+            "Ex": [
+                0.0,
+                78.55592092043187,
+            ],
+            "Ey": [
+                0.0,
+                9.5656799728717190,
+            ],
+            "Ez": [
+                0.0,
+                748.3567468708843,
+            ],
+            "Bx": [
+                0.0,
+                80.94553055070384,
+            ],
+            "By": [
+                0.0,
+                754.12940596242360,
+            ],
+        },
+    }
+
     # ______________________________________________________________________
     # Check scalars
 
     print(" > Check scalars")
 
     # Check final scalar values for fields
 
-    reference_data = [
-        200,
-        1.178332626270596e-08,
-        1.121385881385788e-10,
-        1.372260141937414e-06,
-        1.217329509377536e-08,
-        1.397861526161067e-06,
-        5.139203602251246e-39,
-    ]
+    reference_data = references["fields_final"]
 
     with open("diags/fields.txt", "r") as f:
         lines = f.readlines()
@@ -109,35 +141,15 @@ def validate(evaluate=True, threshold=THRESHOLD):
             "By value in fields.txt is not correct",
         )
         # minipic_ci.evaluate(Bz, reference_data[6], 1e-2, 'relative', 'Bz value in fields.txt is not correct') ===> too small to be relevant
+    else:
+        references["fields_final"] = [iteration, Ex, Ey, Ez, Bx, By, Bz]
 
     # ______________________________________________________________________
     # Check field
 
     print(" > Check fields")
 
-    reference_data = {
-        "Ex": [
-            0.0,
-            78.55592092043187,
-        ],
-        "Ey": [
-            0.0,
-            9.5656799728717190,
-        ],
-        "Ez": [
-            0.0,
-            748.3567468708843,
-        ],
-        "Bx": [
-            0.0,
-            80.94553055070384,
-        ],
-        "By": [
-            0.0,
-            754.12940596242360,
-        ],
-        # 'Bz' : [0.0, 8.68335830083499e-14, 8.109979554106818e-13, 2.2881775959027207e-12, 3.4172712318143877e-12, 4.161059825829489e-12]
-    }
+    reference_data = references["fields_3d"]
 
     for field in reference_data.keys():
 
@@ -178,3 +190,22 @@ def validate(evaluate=True, threshold=THRESHOLD):
                     "relative",
                     "{} field not similar".format(field),
                 )
+        else:
+            references["fields_3d"][field] = new_data
+
+    # ______________________________________________________________________
+    # Write updated references to JSON file if not evaluating
+
+    if not evaluate:
+        import json
+
+        json_file_name = validation_label
+
+        with open(json_file_name, "w") as f:
+            json.dump(references, f, indent=4)
+        print(f" > New references written to {json_file_name}")
+
+        print(
+            " > New references: \n {}".format(json.dumps(references, indent=4))
+        )
+