osiris-utils 1.1.6__py3-none-any.whl → 1.1.8__py3-none-any.whl

examples/example_data/MS/run-info

@@ -0,0 +1,132 @@
+build_info = {
+  "version": "4.4.4-293-g983d5d2-dirty",
+  "branch": "dev",
+  "dimensions": "1",
+  "precision": "DOUBLE",
+  "build_type": "production",
+  "system": "macosx-m1.gnu",
+  "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",
+    "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__",
+    "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": """
+simulation
+{
+	random_seed = 0,
+	wall_clock_limit = "23:50:00",
+	wall_clock_check = 2000,
+	wall_clock_checkpoint = .true.,
+}
+
+node_conf
+{
+	node_number(1:1) = 4,
+	if_periodic(1:1) = .true.,
+}
+
+grid
+{
+	nx_p(1:1) = 500,
+	coordinates = "cartesian",
+}
+
+time_step
+{
+	dt = 0.0099,
+	ndump = 1,
+}
+
+restart
+{
+	if_restart = .false.,
+}
+
+space
+{
+	xmin(1:1) = 0.,
+	xmax(1:1) = 5.0,
+	if_move(1:1) = .false.,
+}
+
+time
+{
+	tmin = 0.0d0,
+	tmax = 2.5,
+}
+
+el_mag_fld
+{
+}
+
+emf_bound
+{
+	type(1:2,1) = "open", "open",
+}
+
+diag_emf
+{
+	ndump_fac = 1,
+	ndump_fac_ene_int = 1,
+    reports  = "e3",
+}
+
+particles
+{
+	interpolation = "linear",
+	num_species = 1,
+}
+
+species
+{
+	name = "electrons",
+	num_par_max = 2048,
+	rqm = -1.0,
+	num_par_x(1:1) = 64,
+}
+
+udist
+{
+	uth_type = "thermal",
+	uth(1:3) = 0.01, 0.01, 0.01,
+}
+
+profile
+{
+	density = 1,
+	profile_type = "uniform",
+}
+
+spe_bound
+{
+}
+
+diag_species
+{
+	ndump_fac_ene = 1,
+	ndump_fac_temp = 1,
+	ndump_fac = 1,
+
+	reports = "charge",
+  	rep_udist = "vfl1", "T11",
+}
+
+smooth
+{
+}
+
+diag_current
+{
+}
+
+
+"""
+}

examples/example_data/TIMINGS/timings-final

@@ -0,0 +1,31 @@
+  Iterations =          253
+  
+                                  Event             Avg [s]             Min [s]             Max [s]
+------------------------------------------------------------------------------
+                                   loop        0.151565E+01        0.151549E+01        0.151575E+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
+               dynlb reshape simulation        0.000000E+00        0.000000E+00        0.000000E+00
+   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
+                      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
+                           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
+                         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

examples/example_data/run-info

@@ -0,0 +1,132 @@
+build_info = {
+  "version": "4.4.4-293-g983d5d2-dirty",
+  "branch": "dev",
+  "dimensions": "1",
+  "precision": "DOUBLE",
+  "build_type": "production",
+  "system": "macosx-m1.gnu",
+  "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",
+    "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__",
+    "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": """
+simulation
+{
+	random_seed = 0,
+	wall_clock_limit = "23:50:00",
+	wall_clock_check = 2000,
+	wall_clock_checkpoint = .true.,
+}
+
+node_conf
+{
+	node_number(1:1) = 4,
+	if_periodic(1:1) = .true.,
+}
+
+grid
+{
+	nx_p(1:1) = 500,
+	coordinates = "cartesian",
+}
+
+time_step
+{
+	dt = 0.0099,
+	ndump = 1,
+}
+
+restart
+{
+	if_restart = .false.,
+}
+
+space
+{
+	xmin(1:1) = 0.,
+	xmax(1:1) = 5.0,
+	if_move(1:1) = .false.,
+}
+
+time
+{
+	tmin = 0.0d0,
+	tmax = 2.5,
+}
+
+el_mag_fld
+{
+}
+
+emf_bound
+{
+	type(1:2,1) = "open", "open",
+}
+
+diag_emf
+{
+	ndump_fac = 1,
+	ndump_fac_ene_int = 1,
+    reports  = "e3",
+}
+
+particles
+{
+	interpolation = "linear",
+	num_species = 1,
+}
+
+species
+{
+	name = "electrons",
+	num_par_max = 2048,
+	rqm = -1.0,
+	num_par_x(1:1) = 64,
+}
+
+udist
+{
+	uth_type = "thermal",
+	uth(1:3) = 0.01, 0.01, 0.01,
+}
+
+profile
+{
+	density = 1,
+	profile_type = "uniform",
+}
+
+spe_bound
+{
+}
+
+diag_species
+{
+	ndump_fac_ene = 1,
+	ndump_fac_temp = 1,
+	ndump_fac = 1,
+
+	reports = "charge",
+  	rep_udist = "vfl1", "T11",
+}
+
+smooth
+{
+}
+
+diag_current
+{
+}
+
+
+"""
+}

examples/example_data/thermal.1d

@@ -0,0 +1,108 @@
+simulation
+{
+	random_seed = 0,
+	wall_clock_limit = "23:50:00",
+	wall_clock_check = 2000,
+	wall_clock_checkpoint = .true.,
+}
+
+node_conf
+{
+	node_number(1:1) = 4,
+	if_periodic(1:1) = .true.,
+}
+
+grid
+{
+	nx_p(1:1) = 500,
+	coordinates = "cartesian",
+}
+
+time_step
+{
+	dt = 0.0099,
+	ndump = 1,
+}
+
+restart
+{
+	if_restart = .false.,
+}
+
+space
+{
+	xmin(1:1) = 0.,
+	xmax(1:1) = 5.0,
+	if_move(1:1) = .false.,
+}
+
+time
+{
+	tmin = 0.0d0,
+	tmax = 2.5,
+}
+
+el_mag_fld
+{
+}
+
+emf_bound
+{
+	type(1:2,1) = "open", "open",
+}
+
+diag_emf
+{
+	ndump_fac = 1,
+	ndump_fac_ene_int = 1,
+    reports  = "e3",
+}
+
+particles
+{
+	interpolation = "linear",
+	num_species = 1,
+}
+
+species
+{
+	name = "electrons",
+	num_par_max = 2048,
+	rqm = -1.0,
+	num_par_x(1:1) = 64,
+}
+
+udist
+{
+	uth_type = "thermal",
+	uth(1:3) = 0.01, 0.01, 0.01,
+}
+
+profile
+{
+	density = 1,
+	profile_type = "uniform",
+}
+
+spe_bound
+{
+}
+
+diag_species
+{
+	ndump_fac_ene = 1,
+	ndump_fac_temp = 1,
+	ndump_fac = 1,
+
+	reports = "charge",
+  	rep_udist = "vfl1", "T11",
+}
+
+smooth
+{
+}
+
+diag_current
+{
+}
+

examples/quick_start.ipynb

@@ -0,0 +1,82 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a652da90",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\"\"\"\n",
+    "Quick demonstration of osiris_utils:\n",
+    "• opens an OSIRIS simulation directory\n",
+    "• plots Ez field at t = 2000\n",
+    "Run with:  python examples/quick_start.py  <PATH_TO_RUN>\n",
+    "\"\"\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "03f2004e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "from pathlib import Path\n",
+    "import matplotlib.pyplot as plt\n",
+    "import osiris_utils as ou"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f1682a2f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sim_path = Path(sys.argv[1]) if len(sys.argv) > 1 else Path(\"example_data/thermal.1d\")\n",
+    "sim = ou.Simulation(sim_path)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d82e0b9d",
+   "metadata": {
+    "lines_to_next_cell": 2
+   },
+   "outputs": [],
+   "source": [
+    "# grab Ez diagnostic\n",
+    "ez = sim[\"e3\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "be1db274",
+   "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",
+    "plt.xlabel(ez.axis[0][\"plot_label\"])\n",
+    "plt.ylabel(f\"${ez.units}$\")\n",
+    "plt.legend()\n",
+    "plt.tight_layout()\n",
+    "plt.show()"
+   ]
+  }
+ ],
+ "metadata": {
+  "jupytext": {
+   "cell_metadata_filter": "-all",
+   "formats": "ipynb,py",
+   "main_language": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

examples/quick_start.py

@@ -0,0 +1,41 @@
+# ---
+# jupyter:
+#   jupytext:
+#     cell_metadata_filter: -all
+#     formats: ipynb,py:light
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.5'
+#       jupytext_version: 1.17.2
+# ---
+
+"""
+Quick demonstration of osiris_utils:
+• opens an OSIRIS simulation directory
+• plots Ez field at t = 2000
+Run with:  python examples/quick_start.py  <PATH_TO_RUN>
+"""
+
+import sys
+from pathlib import Path
+
+import matplotlib.pyplot as plt
+
+import osiris_utils as ou
+
+sim_path = Path(sys.argv[1]) if len(sys.argv) > 1 else Path("example_data/thermal.1d")
+sim = ou.Simulation(sim_path)
+
+# grab Ez diagnostic
+ez = sim["e3"]
+
+
+# plot Ez field at iteration 220
+plt.plot(ez.x, ez[220], label=f"${ez.label}$")
+plt.title(rf"${ez.label}$ at t = {ez.time(220)[0]} $[{ez.time(220)[1]}]$")
+plt.xlabel(ez.axis[0]["plot_label"])
+plt.ylabel(f"${ez.units}$")
+plt.legend()
+plt.tight_layout()
+plt.show()

osiris_utils/__init__.py

@@ -1,34 +1,93 @@
-from .utils import (
-    time_estimation,
-    filesize_estimation,
-    transverse_average,
-    integrate,
-    save_data,
-    read_data,
-    courant2D,
+from importlib import metadata as _meta
+
+try:
+    # Use the version that was baked into the wheel / sdist at build time
+    __version__: str = _meta.version(__name__)
+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,
+    OsirisHIST,
+    OsirisRawFile,
+    OsirisTrackFile,
 )
-from .gui.gui import LAVA_Qt, LAVA
-from .data.data import OsirisGridFile, OsirisRawFile, OsirisData, OsirisHIST, OsirisTrackFile
-from .data.simulation import Simulation, Species_Handler
 from .data.diagnostic import Diagnostic
-
+from .data.simulation import Simulation, Species_Handler
 from .decks.decks import InputDeckIO
 from .decks.species import Specie
-
-from .postprocessing.postprocess import PostProcess
-from .postprocessing.derivative import Derivative_Simulation, Derivative_Diagnostic
-from .postprocessing.fft import FFT_Diagnostic, FastFourierTransform_Simulation
-
-from .postprocessing.mft_for_gridfile import MFT_Single
+from .postprocessing.derivative import Derivative_Diagnostic, Derivative_Simulation
+from .postprocessing.fft import FFT_Diagnostic, FFT_Simulation
+from .postprocessing.field_centering import (
+    FieldCentering_Diagnostic,
+    FieldCentering_Simulation,
+)
+from .postprocessing.heatflux_correction import (
+    HeatfluxCorrection_Diagnostic,
+    HeatfluxCorrection_Simulation,
+)
 from .postprocessing.mft import (
-    MeanFieldTheory_Simulation,
     MFT_Diagnostic,
     MFT_Diagnostic_Average,
     MFT_Diagnostic_Fluctuations,
+    MFT_Simulation,
+)
+from .postprocessing.mft_for_gridfile import MFT_Single
+from .postprocessing.postprocess import PostProcess
+from .postprocessing.pressure_correction import (
+    PressureCorrection_Diagnostic,
+    PressureCorrection_Simulation,
+)
+from .utils import (
+    courant2D,
+    filesize_estimation,
+    integrate,
+    read_data,
+    save_data,
+    time_estimation,
+    transverse_average,
 )
 
-from .postprocessing.field_centering import FieldCentering_Simulation, FieldCentering_Diagnostic
-
-from .postprocessing.pressure_correction import PressureCorrection_Simulation, PressureCorrection_Diagnostic
-
-from .postprocessing.heatflux_correction import HeatfluxCorrection_Simulation, HeatfluxCorrection_Diagnostic
+__all__ = [
+    # Data Singles
+    "OsirisGridFile",
+    "OsirisRawFile",
+    "OsirisData",
+    "OsirisHIST",
+    "OsirisTrackFile",
+    # Data Diagnostic and Simulation
+    "Simulation",
+    "Diagnostic",
+    "Species_Handler",
+    # Decks
+    "Specie",
+    "InputDeckIO",
+    # PostProcessing
+    "PostProcess",
+    "Derivative_Simulation",
+    "Derivative_Diagnostic",
+    "FFT_Diagnostic",
+    "FFT_Simulation",
+    "MFT_Simulation",
+    "MFT_Diagnostic",
+    "MFT_Diagnostic_Average",
+    "MFT_Diagnostic_Fluctuations",
+    "FieldCentering_Simulation",
+    "FieldCentering_Diagnostic",
+    "PressureCorrection_Simulation",
+    "PressureCorrection_Diagnostic",
+    "HeatfluxCorrection_Simulation",
+    "HeatfluxCorrection_Diagnostic",
+    # Single file MFT
+    "MFT_Single",
+    # Utilities
+    "time_estimation",
+    "filesize_estimation",
+    "transverse_average",
+    "integrate",
+    "save_data",
+    "read_data",
+    "courant2D",
+]