Add example jupyter notebook and dataset

PlasmaFAIR · Nov 15, 2024 · 1491918 · 1491918
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diff --git a/tutorials/base_tutorial.ipynb b/tutorials/base_tutorial.ipynb
diff --git a/tutorials/base_tutorial_dataset_1d/0000.sdf b/tutorials/base_tutorial_dataset_1d/0000.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0001.sdf b/tutorials/base_tutorial_dataset_1d/0001.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0002.sdf b/tutorials/base_tutorial_dataset_1d/0002.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0003.sdf b/tutorials/base_tutorial_dataset_1d/0003.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0004.sdf b/tutorials/base_tutorial_dataset_1d/0004.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0005.sdf b/tutorials/base_tutorial_dataset_1d/0005.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0006.sdf b/tutorials/base_tutorial_dataset_1d/0006.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0007.sdf b/tutorials/base_tutorial_dataset_1d/0007.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0008.sdf b/tutorials/base_tutorial_dataset_1d/0008.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0009.sdf b/tutorials/base_tutorial_dataset_1d/0009.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0010.sdf b/tutorials/base_tutorial_dataset_1d/0010.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0011.sdf b/tutorials/base_tutorial_dataset_1d/0011.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0012.sdf b/tutorials/base_tutorial_dataset_1d/0012.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0013.sdf b/tutorials/base_tutorial_dataset_1d/0013.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0014.sdf b/tutorials/base_tutorial_dataset_1d/0014.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0015.sdf b/tutorials/base_tutorial_dataset_1d/0015.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0016.sdf b/tutorials/base_tutorial_dataset_1d/0016.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0017.sdf b/tutorials/base_tutorial_dataset_1d/0017.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0018.sdf b/tutorials/base_tutorial_dataset_1d/0018.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0019.sdf b/tutorials/base_tutorial_dataset_1d/0019.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0020.sdf b/tutorials/base_tutorial_dataset_1d/0020.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0021.sdf b/tutorials/base_tutorial_dataset_1d/0021.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0022.sdf b/tutorials/base_tutorial_dataset_1d/0022.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0023.sdf b/tutorials/base_tutorial_dataset_1d/0023.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0024.sdf b/tutorials/base_tutorial_dataset_1d/0024.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0025.sdf b/tutorials/base_tutorial_dataset_1d/0025.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0026.sdf b/tutorials/base_tutorial_dataset_1d/0026.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0027.sdf b/tutorials/base_tutorial_dataset_1d/0027.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0028.sdf b/tutorials/base_tutorial_dataset_1d/0028.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0029.sdf b/tutorials/base_tutorial_dataset_1d/0029.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0030.sdf b/tutorials/base_tutorial_dataset_1d/0030.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0031.sdf b/tutorials/base_tutorial_dataset_1d/0031.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0032.sdf b/tutorials/base_tutorial_dataset_1d/0032.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0033.sdf b/tutorials/base_tutorial_dataset_1d/0033.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0034.sdf b/tutorials/base_tutorial_dataset_1d/0034.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0035.sdf b/tutorials/base_tutorial_dataset_1d/0035.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0036.sdf b/tutorials/base_tutorial_dataset_1d/0036.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0037.sdf b/tutorials/base_tutorial_dataset_1d/0037.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0038.sdf b/tutorials/base_tutorial_dataset_1d/0038.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0039.sdf b/tutorials/base_tutorial_dataset_1d/0039.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/0040.sdf b/tutorials/base_tutorial_dataset_1d/0040.sdf
diff --git a/tutorials/base_tutorial_dataset_1d/deck.status b/tutorials/base_tutorial_dataset_1d/deck.status
@@ -0,0 +1,343 @@
+ EPOCH1D v4.19.3   v4.19.3-24-gaafed395-dirty 1729856095.720           
+
+Deck state:  1
+
+ Beginning "constant" block
+
+ 	Element nel=1.750208573569848e+22 handled OK
+ 	Element intens=1.2142321215274375e+22 handled OK
+ 	Element omega=2.0 * pi * c / (1.0e-6) handled OK
+ 	Element den_crit=critical(omega) handled OK
+ 	Element scale=3.5e-06 handled OK
+ 	Element den_max=5.0 * den_crit handled OK
+ 	Element den_maxpoint=4e-05 handled OK
+ 	Element den_contrast=1.0 handled OK
+ 	Element amax=1.0 handled OK
+
+ Ending "constant" block
+
+ Beginning "control" block
+
+ 	Element nx=1024*1.5 handled OK
+ 	Element nparticles=1024*2 * 64 handled OK
+ 	Element nsteps=-1 handled OK
+ 	Element t_end=2e-13 handled OK
+ 	Element x_min=-1e-05 handled OK
+ 	Element x_max=2e-05 handled OK
+ 	Element dt_multiplier=0.8 handled OK
+
+ Ending "control" block
+
+ Beginning "qed" block
+
+ 	Element use_qed=F handled OK
+ 	Element qed_start_time=0 handled OK
+ 	Element produce_photons=F handled OK
+ 	Element photon_energy_min=50 * kev handled OK
+ 	Element produce_pairs=F handled OK
+ 	Element photon_dynamics=F handled OK
+
+ Ending "qed" block
+
+ Beginning "collisions" block
+
+ 	Element use_collisions=T handled OK
+ 	Element coulomb_log=auto handled OK
+ 	Element collide=all handled OK
+
+ Ending "collisions" block
+
+ Beginning "boundaries" block
+
+ 	Element bc_x_min=simple_laser handled OK
+ 	Element bc_x_max=simple_laser handled OK
+ 	Element bc_x_max_field=simple_outflow handled OK
+ 	Element bc_x_max_particle=reflect handled OK
+
+ Ending "boundaries" block
+
+ Beginning "species" block
+
+ 	Element name=Electron handled OK
+ 	Element fraction=0.5 handled OK
+ 	Element dump=T handled OK
+ 	Element temperature=0 handled OK
+ 	Element number_density=if (x gt 0e-6, nel * 1.0e6, 0) handled OK
+ 	Element number_density_min=1 handled OK
+ 	Element identify=electron handled OK
+
+ Ending "species" block
+
+ Beginning "species" block
+
+ 	Element name=Ion handled OK
+ 	Element fraction=0.5 handled OK
+ 	Element dump=T handled OK
+ 	Element number_density=number_density(Electron) handled OK
+ 	Element temperature=temperature_x(Electron) handled OK
+ 	Element number_density_min=1 handled OK
+ 	Element identify=proton handled OK
+
+ Ending "species" block
+
+ Beginning "species" block
+
+ 	Element name=Photon handled OK
+ 	Element nparticles=0 handled OK
+ 	Element dump=T handled OK
+ 	Element identify=photon handled OK
+
+ Ending "species" block
+
+ Beginning "species" block
+
+ 	Element name=Positron handled OK
+ 	Element nparticles=0 handled OK
+ 	Element dump=T handled OK
+ 	Element identify=positron handled OK
+
+ Ending "species" block
+
+ Beginning "output_global" block
+
+ 	Element force_final_to_be_restartable=T handled OK
+
+ Ending "output_global" block
+
+ Beginning "output" block
+
+ 	Element name=normal handled OK
+ 	Element use_offset_grid=F handled OK
+ 	Element dt_snapshot=5e-15 handled OK
+ 	Element particles=never handled OK
+ 	Element px=never handled OK
+ 	Element py=never handled OK
+ 	Element pz=never handled OK
+ 	Element vx=never handled OK
+ 	Element vy=never handled OK
+ 	Element vz=never handled OK
+ 	Element charge=never handled OK
+ 	Element mass=never handled OK
+ 	Element particle_weight=never handled OK
+ 	Element species_id=never handled OK
+ 	Element grid=always handled OK
+ 	Element ex=always handled OK
+ 	Element ey=always handled OK
+ 	Element ez=always handled OK
+ 	Element bx=always handled OK
+ 	Element by=always handled OK
+ 	Element bz=always handled OK
+ 	Element jx=always handled OK
+ 	Element jy=always handled OK
+ 	Element jz=never handled OK
+ 	Element average_particle_energy=always + species handled OK
+ 	Element mass_density=never + species handled OK
+ 	Element charge_density=never handled OK
+ 	Element number_density=always + species handled OK
+ 	Element temperature=never + species handled OK
+ 	Element distribution_functions=always handled OK
+ 	Element particle_probes=never handled OK
+ 	Element absorption=always handled OK
+ 	Element total_energy_sum=always + species handled OK
+
+ Ending "output" block
+
+ Beginning "laser" block
+
+ 	Element boundary=x_min handled OK
+ 	Element intensity=intens * 1.0e4 handled OK
+ 	Element omega=omega handled OK
+ 	Element polarisation=0.0 handled OK
+ 	Element phase=0.0 handled OK
+ 	Element t_profile=gauss(time, 40.0e-15, 30.0e-15) handled OK
+ 	Element t_start=0.0 handled OK
+ 	Element t_end=end handled OK
+
+ Ending "laser" block
+
+ Beginning "dist_fn" block
+
+ 	Element name=px_py handled OK
+ 	Element ndims=2 handled OK
+ 	Element dumpmask=always handled OK
+ 	Element direction1=dir_px handled OK
+ 	Element direction2=dir_py handled OK
+ 	Element range1=(-1.5e-21, 1.5e-21) handled OK
+ 	Element range2=(-1.5e-21, 1.5e-21) handled OK
+ 	Element resolution1=200 handled OK
+ 	Element resolution2=200 handled OK
+ 	Element include_species=Photon handled OK
+
+ Ending "dist_fn" block
+
+Deck state:  2
+
+ Beginning "constant" block
+
+ 	Element nel=1.750208573569848e+22 handled OK
+ 	Element intens=1.2142321215274375e+22 handled OK
+ 	Element omega=2.0 * pi * c / (1.0e-6) handled OK
+ 	Element den_crit=critical(omega) handled OK
+ 	Element scale=3.5e-06 handled OK
+ 	Element den_max=5.0 * den_crit handled OK
+ 	Element den_maxpoint=4e-05 handled OK
+ 	Element den_contrast=1.0 handled OK
+ 	Element amax=1.0 handled OK
+
+ Ending "constant" block
+
+ Beginning "control" block
+
+ 	Element nx=1024*1.5 handled OK
+ 	Element nparticles=1024*2 * 64 handled OK
+ 	Element nsteps=-1 handled OK
+ 	Element t_end=2e-13 handled OK
+ 	Element x_min=-1e-05 handled OK
+ 	Element x_max=2e-05 handled OK
+ 	Element dt_multiplier=0.8 handled OK
+
+ Ending "control" block
+
+ Beginning "qed" block
+
+ 	Element use_qed=F handled OK
+ 	Element qed_start_time=0 handled OK
+ 	Element produce_photons=F handled OK
+ 	Element photon_energy_min=50 * kev handled OK
+ 	Element produce_pairs=F handled OK
+ 	Element photon_dynamics=F handled OK
+
+ Ending "qed" block
+
+ Beginning "collisions" block
+
+ 	Element use_collisions=T handled OK
+ 	Element coulomb_log=auto handled OK
+ 	Element collide=all handled OK
+
+ Ending "collisions" block
+
+ Beginning "boundaries" block
+
+ 	Element bc_x_min=simple_laser handled OK
+ 	Element bc_x_max=simple_laser handled OK
+ 	Element bc_x_max_field=simple_outflow handled OK
+ 	Element bc_x_max_particle=reflect handled OK
+
+ Ending "boundaries" block
+
+ Beginning "species" block
+
+ 	Element name=Electron handled OK
+ 	Element fraction=0.5 handled OK
+ 	Element dump=T handled OK
+ 	Element temperature=0 handled OK
+ 	Element number_density=if (x gt 0e-6, nel * 1.0e6, 0) handled OK
+ 	Element number_density_min=1 handled OK
+ 	Element identify=electron handled OK
+
+ Ending "species" block
+
+ Beginning "species" block
+
+ 	Element name=Ion handled OK
+ 	Element fraction=0.5 handled OK
+ 	Element dump=T handled OK
+ 	Element number_density=number_density(Electron) handled OK
+ 	Element temperature=temperature_x(Electron) handled OK
+ 	Element number_density_min=1 handled OK
+ 	Element identify=proton handled OK
+
+ Ending "species" block
+
+ Beginning "species" block
+
+ 	Element name=Photon handled OK
+ 	Element nparticles=0 handled OK
+ 	Element dump=T handled OK
+ 	Element identify=photon handled OK
+
+ Ending "species" block
+
+ Beginning "species" block
+
+ 	Element name=Positron handled OK
+ 	Element nparticles=0 handled OK
+ 	Element dump=T handled OK
+ 	Element identify=positron handled OK
+
+ Ending "species" block
+
+ Beginning "output_global" block
+
+ 	Element force_final_to_be_restartable=T handled OK
+
+ Ending "output_global" block
+
+ Beginning "output" block
+
+ 	Element name=normal handled OK
+ 	Element use_offset_grid=F handled OK
+ 	Element dt_snapshot=5e-15 handled OK
+ 	Element particles=never handled OK
+ 	Element px=never handled OK
+ 	Element py=never handled OK
+ 	Element pz=never handled OK
+ 	Element vx=never handled OK
+ 	Element vy=never handled OK
+ 	Element vz=never handled OK
+ 	Element charge=never handled OK
+ 	Element mass=never handled OK
+ 	Element particle_weight=never handled OK
+ 	Element species_id=never handled OK
+ 	Element grid=always handled OK
+ 	Element ex=always handled OK
+ 	Element ey=always handled OK
+ 	Element ez=always handled OK
+ 	Element bx=always handled OK
+ 	Element by=always handled OK
+ 	Element bz=always handled OK
+ 	Element jx=always handled OK
+ 	Element jy=always handled OK
+ 	Element jz=never handled OK
+ 	Element average_particle_energy=always + species handled OK
+ 	Element mass_density=never + species handled OK
+ 	Element charge_density=never handled OK
+ 	Element number_density=always + species handled OK
+ 	Element temperature=never + species handled OK
+ 	Element distribution_functions=always handled OK
+ 	Element particle_probes=never handled OK
+ 	Element absorption=always handled OK
+ 	Element total_energy_sum=always + species handled OK
+
+ Ending "output" block
+
+ Beginning "laser" block
+
+ 	Element boundary=x_min handled OK
+ 	Element intensity=intens * 1.0e4 handled OK
+ 	Element omega=omega handled OK
+ 	Element polarisation=0.0 handled OK
+ 	Element phase=0.0 handled OK
+ 	Element t_profile=gauss(time, 40.0e-15, 30.0e-15) handled OK
+ 	Element t_start=0.0 handled OK
+ 	Element t_end=end handled OK
+
+ Ending "laser" block
+
+ Beginning "dist_fn" block
+
+ 	Element name=px_py handled OK
+ 	Element ndims=2 handled OK
+ 	Element dumpmask=always handled OK
+ 	Element direction1=dir_px handled OK
+ 	Element direction2=dir_py handled OK
+ 	Element range1=(-1.5e-21, 1.5e-21) handled OK
+ 	Element range2=(-1.5e-21, 1.5e-21) handled OK
+ 	Element resolution1=200 handled OK
+ 	Element resolution2=200 handled OK
+ 	Element include_species=Photon handled OK
+
+ Ending "dist_fn" block
+
+ Initial conditions complete and valid.
diff --git a/tutorials/base_tutorial_dataset_1d/epoch1d.dat b/tutorials/base_tutorial_dataset_1d/epoch1d.dat
@@ -0,0 +1,45 @@
+ EPOCH1D v4.19.3   v4.19.3-24-gaafed395-dirty 1729856095.720           
+
+ Loaded 65536 particles of species "Electron"
+ Loaded 65536 particles of species "Ion"
+Wrote normal ,           0000.sdf at time  0.2606E-16 and iteration       0
+Wrote normal ,           0001.sdf at time  0.5003E-14 and iteration      96
+Wrote normal ,           0002.sdf at time  0.1001E-13 and iteration     192
+Wrote normal ,           0003.sdf at time  0.1501E-13 and iteration     288
+Wrote normal ,           0004.sdf at time  0.2001E-13 and iteration     384
+Wrote normal ,           0005.sdf at time  0.2502E-13 and iteration     480
+Wrote normal ,           0006.sdf at time  0.3002E-13 and iteration     576
+Wrote normal ,           0007.sdf at time  0.3502E-13 and iteration     672
+Wrote normal ,           0008.sdf at time  0.4003E-13 and iteration     768
+Wrote normal ,           0009.sdf at time  0.4503E-13 and iteration     864
+Wrote normal ,           0010.sdf at time  0.5003E-13 and iteration     960
+Wrote normal ,           0011.sdf at time  0.5504E-13 and iteration    1056
+Wrote normal ,           0012.sdf at time  0.6004E-13 and iteration    1152
+Wrote normal ,           0013.sdf at time  0.6504E-13 and iteration    1248
+Wrote normal ,           0014.sdf at time  0.7005E-13 and iteration    1344
+Wrote normal ,           0015.sdf at time  0.7505E-13 and iteration    1440
+Wrote normal ,           0016.sdf at time  0.8000E-13 and iteration    1535
+Wrote normal ,           0017.sdf at time  0.8501E-13 and iteration    1631
+Wrote normal ,           0018.sdf at time  0.9001E-13 and iteration    1727
+Wrote normal ,           0019.sdf at time  0.9501E-13 and iteration    1823
+Wrote normal ,           0020.sdf at time  0.1000E-12 and iteration    1919
+Wrote normal ,           0021.sdf at time  0.1050E-12 and iteration    2015
+Wrote normal ,           0022.sdf at time  0.1100E-12 and iteration    2111
+Wrote normal ,           0023.sdf at time  0.1150E-12 and iteration    2207
+Wrote normal ,           0024.sdf at time  0.1200E-12 and iteration    2303
+Wrote normal ,           0025.sdf at time  0.1250E-12 and iteration    2399
+Wrote normal ,           0026.sdf at time  0.1300E-12 and iteration    2495
+Wrote normal ,           0027.sdf at time  0.1350E-12 and iteration    2591
+Wrote normal ,           0028.sdf at time  0.1400E-12 and iteration    2687
+Wrote normal ,           0029.sdf at time  0.1450E-12 and iteration    2783
+Wrote normal ,           0030.sdf at time  0.1501E-12 and iteration    2879
+Wrote normal ,           0031.sdf at time  0.1550E-12 and iteration    2974
+Wrote normal ,           0032.sdf at time  0.1600E-12 and iteration    3070
+Wrote normal ,           0033.sdf at time  0.1650E-12 and iteration    3166
+Wrote normal ,           0034.sdf at time  0.1700E-12 and iteration    3262
+Wrote normal ,           0035.sdf at time  0.1750E-12 and iteration    3358
+Wrote normal ,           0036.sdf at time  0.1800E-12 and iteration    3454
+Wrote normal ,           0037.sdf at time  0.1850E-12 and iteration    3550
+Wrote normal ,           0038.sdf at time  0.1900E-12 and iteration    3646
+Wrote normal ,           0039.sdf at time  0.1950E-12 and iteration    3742
+Wrote restart,           0040.sdf at time  0.2000E-12 and iteration    3838