osiris-utils 1.2.1__py3-none-any.whl → 1.2.3__py3-none-any.whl

examples/example_data/MS/run-info

@@ -1,6 +1,6 @@
 build_info = {
-  "version": "4.4.4-293-g983d5d2-dirty",
-  "branch": "dev",
+  "version": "4.4.4-308-g6600aee",
+  "branch": "boost-quant",
   "dimensions": "1",
   "precision": "DOUBLE",
   "build_type": "production",
@@ -8,16 +8,16 @@ build_info = {
   "build_tool": "make",
   "build_flags": {
     "FPP"  :"/opt/homebrew/bin/mpicc -C -E -x assembler-with-cpp -D__HAS_MPI_IN_PLACE__ -D_OPENMP -DHDF5",
-    "FPPF" :"-DP_X_DIM=1 -DOS_REV=\"4.4.4-293-g983d5d2-dirty\" -DFORTRANSINGLEUNDERSCORE -DPRECISION_DOUBLE -DENABLE_RAD -DENABLE_TILES -DENABLE_PGC -DENABLE_QED -DENABLE_SHEAR -DENABLE_CYLMODES -DENABLE_QEDCYL -DENABLE_RADCYL -DENABLE_OVERDENSE -DENABLE_OVERDENSE_CYL -DENABLE_NEUTRAL_SPIN -DENABLE_XXFEL -DENABLE_GR",
+    "FPPF" :"-DP_X_DIM=1 -DOS_REV=\"4.4.4-308-g6600aee\" -DFORTRANSINGLEUNDERSCORE -DPRECISION_DOUBLE -DENABLE_RAD -DENABLE_TILES -DENABLE_PGC -DENABLE_QED -DENABLE_SHEAR -DENABLE_CYLMODES -D1 -DENABLE_RADCYL -DENABLE_OVERDENSE -DENABLE_OVERDENSE_CYL -DENABLE_NEUTRAL_SPIN -DENABLE_XXFEL -DENABLE_GR",
     "F90"  :"gfortran",
-    "F90F" :"-pipe -ffree-line-length-none -fno-range-check -lgcc_s.1.1 --openmp -Ofast -march=native -I/opt/homebrew/Cellar/open-mpi/5.0.7/include -Wl,-flat_namespace -I/opt/homebrew/Cellar/open-mpi/5.0.7/lib -I/usr/local/.hdf5/include",
-    "CF"   :"-Ofast -mcpu=apple-m1 -std=c99  -DFORTRANSINGLEUNDERSCORE -DPRECISION_DOUBLE -D__MACH_TIMER__",
+    "F90F" :"-pipe -ffree-line-length-none -fno-range-check -lgcc_s.1.1 --openmp -O3 -ffast-math -march=native -I/opt/homebrew/Cellar/open-mpi/5.0.7/include -Wl,-flat_namespace -I/opt/homebrew/Cellar/open-mpi/5.0.7/lib -I/usr/local/.hdf5/include",
+    "CF"   :"-O3 -ffast-math -mcpu=apple-m1 -std=c99 -DFORTRANSINGLEUNDERSCORE -DPRECISION_DOUBLE -D__MACH_TIMER__",
     "cc"   :"/opt/homebrew/bin/mpicc ",
     "LDF"  :" -L/usr/local/.hdf5/lib -lhdf5_fortran -lhdf5 -lz -lm -I/opt/homebrew/Cellar/open-mpi/5.0.7/include -Wl,-flat_namespace -I/opt/homebrew/Cellar/open-mpi/5.0.7/lib -L/opt/homebrew/Cellar/open-mpi/5.0.7/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi ",
    }
 }
 run_info = {
-  "input_deck_crc":         3871076978.,
+  "input_deck_crc":         4166345302.,
   "input_deck": """
 simulation
 {
@@ -42,7 +42,7 @@ grid
 time_step
 {
 	dt = 0.0099,
-	ndump = 1,
+	ndump = 20,
 }
 
 restart

examples/example_data/TIMINGS/timings-final

@@ -2,7 +2,7 @@
   
                                   Event             Avg [s]             Min [s]             Max [s]
 ------------------------------------------------------------------------------
-                                   loop        0.151565E+01        0.151549E+01        0.151575E+01
+                                   loop        0.800285E-01        0.800185E-01        0.800373E-01
            dynamic load balance (total)        0.000000E+00        0.000000E+00        0.000000E+00
                      dynlb get int load        0.000000E+00        0.000000E+00        0.000000E+00
                        dynlb get new lb        0.000000E+00        0.000000E+00        0.000000E+00
@@ -10,22 +10,22 @@
    dynlb reshape simulation (particles)        0.000000E+00        0.000000E+00        0.000000E+00
        dynlb reshape simulation (grids)        0.000000E+00        0.000000E+00        0.000000E+00
             writing restart information        0.000000E+00        0.000000E+00        0.000000E+00
-                       load diagnostics        0.779896E-04        0.569583E-04        0.107500E-03
+                       load diagnostics        0.755208E-05        0.495833E-05        0.131667E-04
                       dynlb sum up load        0.000000E+00        0.000000E+00        0.000000E+00
-                    update emf boundary        0.171758E-01        0.356096E-02        0.561896E-01
-                           field solver        0.123370E-02        0.896000E-03        0.187450E-02
+                    update emf boundary        0.129557E-02        0.629333E-03        0.201988E-02
+                           field solver        0.240823E-03        0.230583E-03        0.258333E-03
                            field smooth        0.000000E+00        0.000000E+00        0.000000E+00
                         psi calculation        0.000000E+00        0.000000E+00        0.000000E+00
-                        EMF diagnostics        0.199701E+00        0.171400E+00        0.269367E+00
-           electric current diagnostics        0.251250E-04        0.148333E-04        0.436667E-04
-                         current smooth        0.271562E-04        0.187083E-04        0.392917E-04
-                update current boundary        0.343694E-01        0.933750E-03        0.545176E-01
-                        advance deposit        0.859551E-01        0.820932E-01        0.930120E-01
+                        EMF diagnostics        0.841009E-02        0.781517E-02        0.101309E-01
+           electric current diagnostics        0.280208E-05        0.225000E-05        0.333333E-05
+                         current smooth        0.821875E-05        0.295833E-05        0.138750E-04
+                update current boundary        0.393088E-02        0.301733E-02        0.536271E-02
+                        advance deposit        0.361144E-01        0.351665E-01        0.371676E-01
                          reduce current        0.000000E+00        0.000000E+00        0.000000E+00
-               update particle boundary        0.376471E-01        0.834267E-02        0.616104E-01
-                      cathode injection        0.838542E-05        0.595833E-05        0.101667E-04
-                      neutral injection        0.448958E-05        0.370833E-05        0.545833E-05
-                   particle diagnostics        0.113437E+01        0.112332E+01        0.114122E+01
-                  particle sort (total)        0.358918E-02        0.230400E-02        0.731125E-02
-                particle sort, gen. idx        0.633365E-03        0.556000E-03        0.691708E-03
-     particle sort, rearrange particles        0.292353E-02        0.162496E-02        0.663883E-02
+               update particle boundary        0.824873E-02        0.790433E-02        0.859958E-02
+                      cathode injection        0.221875E-05        0.200000E-05        0.245833E-05
+                      neutral injection        0.177083E-05        0.150000E-05        0.216667E-05
+                   particle diagnostics        0.208982E-01        0.208554E-01        0.209608E-01
+                  particle sort (total)        0.587302E-03        0.580708E-03        0.592500E-03
+                particle sort, gen. idx        0.291010E-03        0.287958E-03        0.296417E-03
+     particle sort, rearrange particles        0.279417E-03        0.268958E-03        0.287000E-03

examples/example_data/run-info

@@ -1,6 +1,6 @@
 build_info = {
-  "version": "4.4.4-293-g983d5d2-dirty",
-  "branch": "dev",
+  "version": "4.4.4-308-g6600aee",
+  "branch": "boost-quant",
   "dimensions": "1",
   "precision": "DOUBLE",
   "build_type": "production",
@@ -8,16 +8,16 @@ build_info = {
   "build_tool": "make",
   "build_flags": {
     "FPP"  :"/opt/homebrew/bin/mpicc -C -E -x assembler-with-cpp -D__HAS_MPI_IN_PLACE__ -D_OPENMP -DHDF5",
-    "FPPF" :"-DP_X_DIM=1 -DOS_REV=\"4.4.4-293-g983d5d2-dirty\" -DFORTRANSINGLEUNDERSCORE -DPRECISION_DOUBLE -DENABLE_RAD -DENABLE_TILES -DENABLE_PGC -DENABLE_QED -DENABLE_SHEAR -DENABLE_CYLMODES -DENABLE_QEDCYL -DENABLE_RADCYL -DENABLE_OVERDENSE -DENABLE_OVERDENSE_CYL -DENABLE_NEUTRAL_SPIN -DENABLE_XXFEL -DENABLE_GR",
+    "FPPF" :"-DP_X_DIM=1 -DOS_REV=\"4.4.4-308-g6600aee\" -DFORTRANSINGLEUNDERSCORE -DPRECISION_DOUBLE -DENABLE_RAD -DENABLE_TILES -DENABLE_PGC -DENABLE_QED -DENABLE_SHEAR -DENABLE_CYLMODES -D1 -DENABLE_RADCYL -DENABLE_OVERDENSE -DENABLE_OVERDENSE_CYL -DENABLE_NEUTRAL_SPIN -DENABLE_XXFEL -DENABLE_GR",
     "F90"  :"gfortran",
-    "F90F" :"-pipe -ffree-line-length-none -fno-range-check -lgcc_s.1.1 --openmp -Ofast -march=native -I/opt/homebrew/Cellar/open-mpi/5.0.7/include -Wl,-flat_namespace -I/opt/homebrew/Cellar/open-mpi/5.0.7/lib -I/usr/local/.hdf5/include",
-    "CF"   :"-Ofast -mcpu=apple-m1 -std=c99  -DFORTRANSINGLEUNDERSCORE -DPRECISION_DOUBLE -D__MACH_TIMER__",
+    "F90F" :"-pipe -ffree-line-length-none -fno-range-check -lgcc_s.1.1 --openmp -O3 -ffast-math -march=native -I/opt/homebrew/Cellar/open-mpi/5.0.7/include -Wl,-flat_namespace -I/opt/homebrew/Cellar/open-mpi/5.0.7/lib -I/usr/local/.hdf5/include",
+    "CF"   :"-O3 -ffast-math -mcpu=apple-m1 -std=c99 -DFORTRANSINGLEUNDERSCORE -DPRECISION_DOUBLE -D__MACH_TIMER__",
     "cc"   :"/opt/homebrew/bin/mpicc ",
     "LDF"  :" -L/usr/local/.hdf5/lib -lhdf5_fortran -lhdf5 -lz -lm -I/opt/homebrew/Cellar/open-mpi/5.0.7/include -Wl,-flat_namespace -I/opt/homebrew/Cellar/open-mpi/5.0.7/lib -L/opt/homebrew/Cellar/open-mpi/5.0.7/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi ",
    }
 }
 run_info = {
-  "input_deck_crc":         3871076978.,
+  "input_deck_crc":         4166345302.,
   "input_deck": """
 simulation
 {
@@ -42,7 +42,7 @@ grid
 time_step
 {
 	dt = 0.0099,
-	ndump = 1,
+	ndump = 20,
 }
 
 restart

examples/example_data/thermal.1d

@@ -21,7 +21,7 @@ grid
 time_step
 {
 	dt = 0.0099,
-	ndump = 1,
+	ndump = 20,
 }
 
 restart

examples/quick_start.ipynb

@@ -48,7 +48,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "sim_path = Path(sys.argv[1]) if len(sys.argv) > 1 else Path(\"example_data/thermal.1d\")\n",
+    "sim_path = \"example_data/thermal.1d\"\n",
     "sim = ou.Simulation(sim_path)"
    ]
   },
@@ -72,9 +72,9 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# plot Ez field at iteration 220\n",
-    "plt.plot(ez.x, ez[220], label=f\"${ez.label}$\")\n",
-    "plt.title(rf\"${ez.label}$ at t = {ez.time(220)[0]} $[{ez.time(220)[1]}]$\")\n",
+    "# plot Ez field at iteration 10\n",
+    "plt.plot(ez.x, ez[10], label=f\"${ez.label}$\")\n",
+    "plt.title(rf\"${ez.label}$ at t = {ez.time(10)[0]} $[{ez.time(10)[1]}]$\")\n",
     "plt.xlabel(ez.axis[0][\"plot_label\"])\n",
     "plt.ylabel(f\"${ez.units}$\")\n",
     "plt.legend()\n",
@@ -89,8 +89,22 @@
    "formats": "ipynb,py",
    "main_language": "python"
   },
+  "kernelspec": {
+   "display_name": "plasma",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.14.2"
   }
  },
  "nbformat": 4,

osiris_utils/__init__.py

@@ -9,7 +9,6 @@ except _meta.PackageNotFoundError:  # package is being run from a checkout
     # Fallback for `pip install -e .` or direct source use
     __version__ = "0.0.0.dev0"
 
-
 from .data.data import (
     OsirisData,
     OsirisGridFile,

osiris_utils/data/data.py

@@ -186,7 +186,7 @@ class OsirisGridFile(OsirisData):
         Field label/name (LaTeX formatted, e.g., r'$E_x$')
     """
 
-    def __init__(self, filename, data_slice: slice | None = None):
+    def __init__(self, filename, data_slice: slice | None = None, load_data: bool = True):
         super().__init__(filename)
 
         variable_key = self._get_variable_key(self._file)
@@ -195,12 +195,14 @@ class OsirisGridFile(OsirisData):
         self._label = self._file.attrs["LABEL"][0].decode("utf-8")
         self._FFTdata = None
 
-        data = np.array(self._file[variable_key][:]) if data_slice is None else np.array(self._file[variable_key][data_slice])
+        # Use dataset.shape to obtain sizes without loading full data when possible
+        dset = self._file[variable_key]
 
         axis = list(self._file["AXIS"].keys())
         if len(axis) == 1:
             self._grid = self._file["AXIS/" + axis[0]][()]
-            self._nx = len(data)
+            # nx for 1D is dataset length along its only axis
+            self._nx = dset.shape[0]
             self._dx = (self.grid[1] - self.grid[0]) / self.nx
             self._x = np.arange(self.grid[0], self.grid[1], self.dx)
         else:
@@ -208,15 +210,14 @@ class OsirisGridFile(OsirisData):
             for ax in axis:
                 grid.append(self._file["AXIS/" + ax][()])
             self._grid = np.array(grid)
-            self._nx = self._file[variable_key][()].transpose().shape
+            # use dataset.shape to avoid reading the whole dataset
+            # dataset stored may need transpose to match expected ordering; preserve shape only
+            self._nx = tuple(dset.shape[::-1]) if len(dset.shape) > 1 else (dset.shape[0],)
             self._dx = (self.grid[:, 1] - self.grid[:, 0]) / self.nx
 
-            # There's an issue when the dimension is 3 and we want to plot a 2D phasespace. I believe this
-            # is a problem for all cases where the dim != dim_of_phasespace
             try:
                 self._x = [np.arange(self.grid[i, 0], self.grid[i, 1], self.dx[i]) for i in range(self.dim)]
-            except Exception as e:
-                print(f"Error occurred while creating spatial coordinates: {e}")
+            except Exception:
                 self._x = [np.arange(self.grid[i, 0], self.grid[i, 1], self.dx[i]) for i in range(1)]
 
         self._axis = []
@@ -226,12 +227,30 @@ class OsirisGridFile(OsirisData):
                 "units": self._file["AXIS/" + ax].attrs["UNITS"][0].decode("utf-8"),
                 "long_name": self._file["AXIS/" + ax].attrs["LONG_NAME"][0].decode("utf-8"),
                 "type": self._file["AXIS/" + ax].attrs["TYPE"][0].decode("utf-8"),
-                "plot_label": rf'${self._file["AXIS/" + ax].attrs["LONG_NAME"][0].decode("utf-8")}$'
-                + rf'$[{self._file["AXIS/" + ax].attrs["UNITS"][0].decode("utf-8")}]$',
+                "plot_label": rf'${self._file["AXIS/" + ax].attrs["LONG_NAME"][0].decode("utf-8")}$' + rf'$[{self._file["AXIS/" + ax].attrs["UNITS"][0].decode("utf-8")}]$',
             }
             self._axis.append(axis_data)
 
-        self._data = np.ascontiguousarray(data.T)
+        # Only load data if explicitly requested. Otherwise keep a placeholder so metadata-only
+        # initializations are cheap for large files.
+        if load_data:
+            # Handle partial slicing by padding with (slice(None),)
+            if data_slice is not None:
+                if not isinstance(data_slice, tuple):
+                    data_slice = (data_slice,)
+
+                # Check if we need to pad
+                ndims = len(dset.shape)
+                if len(data_slice) < ndims:
+                    data_slice = data_slice + (slice(None),) * (ndims - len(data_slice))
+
+            # data slice should be transposed to match data storage order [x, y, z] to [z, y, x]
+            data_slice = data_slice[::-1] if data_slice is not None and len(dset.shape) > 1 else data_slice
+
+            data = np.array(dset[:]) if data_slice is None else np.array(dset[data_slice])
+            self._data = np.ascontiguousarray(data.T)
+        else:
+            self._data = None
 
         self._close_file()
 
@@ -361,12 +380,10 @@ class OsirisRawFile(OsirisData):
     def __init__(self, filename):
         super().__init__(filename)
 
-        self._grid = np.array(
-            [
-                self._file["SIMULATION"].attrs["XMIN"],
-                self._file["SIMULATION"].attrs["XMAX"],
-            ]
-        ).T
+        self._grid = np.array([
+            self._file["SIMULATION"].attrs["XMIN"],
+            self._file["SIMULATION"].attrs["XMAX"],
+        ]).T
 
         self._quants = [byte.decode("utf-8") for byte in self._file.attrs["QUANTS"][:]]
         units_list = [byte.decode("utf-8") for byte in self._file.attrs["UNITS"][:]]
@@ -529,12 +546,10 @@ class OsirisTrackFile(OsirisData):
     def __init__(self, filename):
         super().__init__(filename)
 
-        self._grid = np.array(
-            [
-                self._file["SIMULATION"].attrs["XMIN"],
-                self._file["SIMULATION"].attrs["XMAX"],
-            ]
-        ).T
+        self._grid = np.array([
+            self._file["SIMULATION"].attrs["XMIN"],
+            self._file["SIMULATION"].attrs["XMAX"],
+        ]).T
 
         self._quants = [byte.decode("utf-8") for byte in self._file.attrs["QUANTS"][1:]]
         units_list = [byte.decode("utf-8") for byte in self._file.attrs["UNITS"][1:]]
@@ -598,17 +613,7 @@ class OsirisTrackFile(OsirisData):
 
     def __str__(self):
         # write me a template to print with the name, label, units, iter, grid, nx, dx, axis, dt, dim in a logical way
-        return (
-            rf"{self.name}"
-            + "\n"
-            + f"Iteration: {self.iter}"
-            + "\n"
-            + f"Grid: {self.grid}"
-            + "\n"
-            + f"dx: {self.dx}"
-            + "\n"
-            + f"Dimensions: {self.dim}D"
-        )
+        return rf"{self.name}" + "\n" + f"Iteration: {self.iter}" + "\n" + f"Grid: {self.grid}" + "\n" + f"dx: {self.dx}" + "\n" + f"Dimensions: {self.dim}D"
 
     def __array__(self):
         return np.asarray(self.data)