Spectra 3d

cmake/report.cmake

@@ -146,7 +146,7 @@ printchoices(
   ON
   "${Green}"
   VENDOR_SORT_REPORT
-  44)
+  46)
 printchoices(
   "Debug mode"
   "DEBUG"
@@ -234,6 +234,9 @@ string(
   "  - DEVICES [${Magenta}Kokkos_ENABLE_***${ColorReset}]:              "
   "${Kokkos_DEVICES}"
   "\n"
+  "  "
+  ${VENDOR_SORT_REPORT}
+  "\n"
   "  > Multi-node specs"
   " ${Dim}[requires mpi=ON]${ColorReset}"
   "\n"
@@ -255,9 +258,6 @@ string(
   "    "
   "- Deposit drift [${Magenta}team_policy_drift${ColorReset}]:      "
   ${team_policy_drift}
-  "\n"
-  "    "
-  ${VENDOR_SORT_REPORT}
   "\n")
 
 string(

dependencies.py

@@ -8,7 +8,6 @@
 from dataclasses import dataclass, field
 from typing import Callable, List, Optional, Tuple
 
-
 # ============================
 # colors: edit these
 # ============================
@@ -54,7 +53,7 @@ class Settings:
 
     # versions
     kokkos_version: str = "5.2.1"
-    adios2_version: str = "2.11.0"
+    adios2_version: str = "2.12.1"
 
     # options
     kokkos_backend: str = "cpu"
@@ -135,7 +134,9 @@ def InstallKokkosScriptModfile(settings: Settings) -> tuple[str, str]:
             [f"module load {module}" for module in settings.module_loads]
         )
         src_path = os.path.join(prefix, "src", "kokkos")
-        install_path = os.path.join(prefix, "kokkos", version, backend, arch.lower() if arch else "")
+        install_path = os.path.join(
+            prefix, "kokkos", version, backend, arch.lower() if arch else ""
+        )
         if os.path.exists(install_path) and not settings.overwrite:
             raise FileExistsError(
                 f"Kokkos install path {install_path} already exists and overwrite is disabled"
@@ -300,7 +301,7 @@ def InstallNt2pyScript(settings: Settings) -> str:
     },
     "stellar": {"module_loads": []},
     "perlmutter": {
-        "module_loads": ["gpu/1.0"],
+        "module_loads": ["gpu/1.0", "python/3.14-26.8.1"],
         "kokkos_backend": "cuda",
         "kokkos_arch": "AMPERE80",
         "extra_kokkos_flags": [
@@ -313,17 +314,19 @@ def InstallNt2pyScript(settings: Settings) -> str:
         ],
     },
     "lumi": {
-        "module_loads": ["PrgEnv-cray", "cray-mpich", "craype-accel-amd-gfx90a", "rocm"],
+        "module_loads": [
+            "PrgEnv-cray",
+            "cray-mpich",
+            "craype-accel-amd-gfx90a",
+            "rocm",
+        ],
         "kokkos_backend": "hip",
         "kokkos_arch": "AMD_GFX90A",
         "extra_kokkos_flags": [
             "CMAKE_CXX_COMPILER=hipcc",
             "AMDGPU_TARGETS=gfx90a",
         ],
-        "extra_adios2_flags": [
-            "CMAKE_CXX_COMPILER=CC",
-            "CMAKE_C_COMPILER=cc"
-        ]
+        "extra_adios2_flags": ["CMAKE_CXX_COMPILER=CC", "CMAKE_C_COMPILER=cc"],
     },
     "frontier": {"module_loads": []},
     "aurora": {"module_loads": []},
@@ -366,7 +369,7 @@ def on_install_confirmed(settings: Settings) -> None:
                 "modules",
                 "kokkos",
                 settings.kokkos_version,
-                settings.kokkos_backend, 
+                settings.kokkos_backend,
                 settings.kokkos_arch.strip().lower(),
             )
             os.makedirs(os.path.dirname(kokkos_modfile_file), exist_ok=True)
@@ -1089,14 +1092,18 @@ def toggle(k: str):
 
     def menu_cluster(self) -> Tuple[str, str, List[MenuItem]]:
         def choose(name: str):
-            print ("CALLING:", name)
+            print("CALLING:", name)
             apply_preset(self.s, name)
             self.push("custom")
 
         return (
             "cluster-specific",
             "pick a preset:",
-            [MenuItem(cluster, "apply preset", on_enter=lambda c=cluster: choose(c)) for cluster in list(PRESETS.keys())] + [MenuItem("back", "", on_enter=self.pop)],
+            [
+                MenuItem(cluster, "apply preset", on_enter=lambda c=cluster: choose(c))
+                for cluster in list(PRESETS.keys())
+            ]
+            + [MenuItem("back", "", on_enter=self.pop)],
         )
 
     def get_menu(self) -> Tuple[str, str, List[MenuItem]]:

input.example.toml

@@ -627,10 +627,14 @@
     #   @type: bool
     #   @default: true
     log_bins = ""
-    # Number of bins for the spectra output
+    # Number of energy bins for the spectra output
     #   @type: uint [> 0]
     #   @default: 200
-    n_bins = ""
+    num_energy_bins = ""
+    # Number of spatial bins for the spectra output
+    #  @type: array<uint> [size 1 :->: 3]
+    #  @default: [1, 1, 1]
+    num_spatial_bins = ""
     # Number of timesteps between spectra outputs
     #   @type: uint
     #   @default: 0

pgens/shock/shock.toml

@@ -40,35 +40,38 @@
     maxnpart = 2e7
 
 [setup]
-  drift_ux    = 0.15         # speed towards the wall [c]
-  temperature = 0.168        # temperature of maxwell distribution [kB T / (m_i c^2)]
-  temperature_ratio = 1.0    # temperature ratio of electrons to protons
-  Bmag = 1.0                 # magnetic field strength as fraction of magnetisation
-  Btheta = 63.0              # magnetic field angle in the plane
-  Bphi = 0.0                 # magnetic field angle out of plane
-  filling_fraction = 0.99     # fraction of the shock piston filled with plasma
-  injector_velocity = 0.0    # speed of injector [c]
-  injection_start = 0.0      # start time of moving injector
+  drift_ux            = 0.15  # speed towards the wall [c]
+  temperature         = 0.168 # temperature of maxwell distribution [kB T / (m_i c^2)]
+  temperature_ratio   = 1.0   # temperature ratio of electrons to protons
+  Bmag                = 1.0   # magnetic field strength as fraction of magnetisation
+  Btheta              = 63.0  # magnetic field angle in the plane
+  Bphi                = 0.0   # magnetic field angle out of plane
+  filling_fraction    = 0.99  # fraction of the shock piston filled with plasma
+  injector_velocity   = 0.0   # speed of injector [c]
+  injection_start     = 0.0   # start time of moving injector
   injection_frequency = 100
 
 [output]
   interval_time = 1000.0
   format        = "BPFile"
-  
+
   [output.fields]
     quantities = ["N", "B", "E"]
 
   [output.particles]
     enable = true
-    stride = 10 
+    stride = 10
 
   [output.spectra]
-    enable = false
+    enable           = true
+    e_min            = 1e-2
+    e_max            = 1e1
+    log_bins         = true
+    num_spatial_bins = [40, 3, 1]
 
 [diagnostics]
   log_level = "WARNING"
-  blocking_timers = true
 
 [checkpoint]
   interval = 10000
-  keep = 1
+  keep     = 2

src/framework/domain/io/init.cpp

@@ -93,7 +93,9 @@ namespace ntt {
     for (const auto& sp : species_params()) {
       spectra_species.push_back(sp.index());
     }
-    g_writer.defineSpectraOutputs(spectra_species);
+    const auto num_spatial_bins = params.template get<std::vector<size_t>>(
+      "output.spectra.num_spatial_bins");
+    g_writer.defineSpectraOutputs(spectra_species, num_spatial_bins);
     for (const auto& type : { "fields", "particles", "spectra" }) {
       g_writer.addTracker(type,
                           params.template get<timestep_t>(