Change default behavior of picmi.FieldDiagnostic and picmi.ParticleDi…

…agnostic & fix CI tests (ECP-WarpX#4317) * Do not write particles with `FieldDiagnostic` Do not write fields with `ParticleDiagnostic Update implementation Revert "Update implementation" This reverts commit 77b473f. Use syntax with argvattrs Correct typo Force writing of species Add function that can replace existing attributes Revert "Revert "Update implementation"" This reverts commit d946fe6. Correct syntax typo [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci Revert "Revert "Revert "Update implementation""" This reverts commit 69092be. Generalization for backtransformed diagnostics Update lab-frame diagnostics Update 1D CI case Fix additional merge errors Remove particle diagnostic Add particle diagnostic where needed Use latest PICMI version Handle the case when species is None Add missing `add_diagnostic` calls * Update 1D ion beam case Fixed CI: plasma_lens Fixed CI: LoadExternalField Fixed CI: Python_reduced_diags_loadbalancecosts_timers Clean up * Fixed CI: Python_ionization, Ohm Solver * Clean up: removed jx, jy, jz * More fixes in Ohm solver's CIs * Placed species in squire brackets * Wrtie FieldDiagnostics in CI: Python_prev_positions * Do not specify datalist in test --------- Co-authored-by: Remi Lehe <[email protected]>
dpgrote · Oct 11, 2023 · 419d47a · 419d47a
1 parent b71b89c
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diff --git a/Docs/requirements.txt b/Docs/requirements.txt
@@ -11,7 +11,7 @@ docutils>=0.17.1
 
 # PICMI API docs
 # note: keep in sync with version in ../requirements.txt
-picmistandard==0.26.0
+picmistandard==0.28.0
 # for development against an unreleased PICMI version, use:
 # picmistandard @ git+https://github.com/picmi-standard/picmi.git#subdirectory=PICMI_Python
 

diff --git a/Examples/Physics_applications/capacitive_discharge/PICMI_inputs_1d.py b/Examples/Physics_applications/capacitive_discharge/PICMI_inputs_1d.py
@@ -324,6 +324,12 @@ def setup_run(self):
         else:
             file_prefix = 'Python_background_mcc_1d_tridiag_plt'
 
+        particle_diag = picmi.ParticleDiagnostic(
+            name='diag1',
+            period=0,
+            write_dir='.',
+            warpx_file_prefix=file_prefix
+        )
         field_diag = picmi.FieldDiagnostic(
             name='diag1',
             grid=self.grid,
@@ -332,6 +338,7 @@ def setup_run(self):
             write_dir='.',
             warpx_file_prefix=file_prefix
         )
+        self.sim.add_diagnostic(particle_diag)
         self.sim.add_diagnostic(field_diag)
 
     def _get_rho_ions(self):

diff --git a/Examples/Physics_applications/capacitive_discharge/PICMI_inputs_2d.py b/Examples/Physics_applications/capacitive_discharge/PICMI_inputs_2d.py
@@ -312,6 +312,12 @@ def solve(self):
 # diagnostics
 ##########################
 
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = diagnostic_intervals,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_background_mcc_plt'
+)
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
@@ -345,6 +351,7 @@ def solve(self):
     )
 )
 
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 
 ##########################

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_1d.py
@@ -79,6 +79,11 @@
 
 # Diagnostics
 diag_field_list = ['B', 'E', 'J', 'rho']
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 100,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_LaserAcceleration_1d_plt')
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
@@ -108,6 +113,7 @@
     injection_method = laser_antenna)
 
 # Add diagnostics
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 
 # Write input file that can be used to run with the compiled version

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_2d.py
@@ -112,6 +112,11 @@
 
 # Diagnostics
 diag_field_list = ['B', 'E', 'J', 'rho']
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 200,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_LaserAccelerationMR_plt')
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
@@ -145,6 +150,7 @@
     injection_method = laser_antenna)
 
 # Add diagnostics
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 
 # Write input file that can be used to run with the compiled version

diff --git a/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py b/Examples/Physics_applications/laser_acceleration/PICMI_inputs_3d.py
@@ -110,6 +110,11 @@
 
 # Diagnostics
 diag_field_list = ['B', 'E', 'J', 'rho']
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 100,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_LaserAcceleration_plt')
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
@@ -144,6 +149,7 @@
     injection_method = laser_antenna)
 
 # Add diagnostics
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 
 # Write input file that can be used to run with the compiled version

diff --git a/Examples/Tests/LoadExternalField/PICMI_inputs_3d.py b/Examples/Tests/LoadExternalField/PICMI_inputs_3d.py
@@ -87,10 +87,19 @@
 ######### DIAGNOSTICS ###########
 #################################
 
+particle_diag = picmi.ParticleDiagnostic(
+        name='diag1',
+        period=300,
+        species=[ions],
+        data_list = ['ux', 'uy', 'uz', 'x', 'y', 'z', 'weighting'],
+        write_dir='.',
+        warpx_file_prefix='Python_LoadExternalField3D_plt'
+        )
 field_diag = picmi.FieldDiagnostic(
         name='diag1',
         grid=grid,
         period=300,
+        data_list = ['Bx', 'By', 'Bz', 'Ex', 'Ey', 'Ez', 'Jx', 'Jy', 'Jz'],
         write_dir='.',
         warpx_file_prefix='Python_LoadExternalField3D_plt'
         )
@@ -121,6 +130,7 @@
         )
 
 sim.add_diagnostic(field_diag)
+sim.add_diagnostic(particle_diag)
 
 #################################
 ##### SIMULATION EXECUTION ######

diff --git a/Examples/Tests/collision/PICMI_inputs_2d.py b/Examples/Tests/collision/PICMI_inputs_2d.py
@@ -106,6 +106,12 @@
 ######### DIAGNOSTICS ###########
 #################################
 
+particle_diag = picmi.ParticleDiagnostic(
+    name='diag1',
+    period=10,
+    write_dir='.',
+    warpx_file_prefix='Python_collisionXZ_plt'
+)
 field_diag = picmi.FieldDiagnostic(
     name='diag1',
     grid=grid,
@@ -140,6 +146,7 @@
     )
 )
 
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 
 #################################

diff --git a/Examples/Tests/electrostatic_dirichlet_bc/PICMI_inputs_2d.py b/Examples/Tests/electrostatic_dirichlet_bc/PICMI_inputs_2d.py
@@ -58,6 +58,12 @@
 # diagnostics
 ##########################
 
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 4,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_dirichletbc_plt'
+)
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
@@ -79,6 +85,7 @@
     verbose = 0
 )
 
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 
 ##########################

diff --git a/Examples/Tests/electrostatic_sphere_eb/PICMI_inputs_3d.py b/Examples/Tests/electrostatic_sphere_eb/PICMI_inputs_3d.py
@@ -70,6 +70,12 @@
 # diagnostics
 ##########################
 
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 1,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_ElectrostaticSphereEB_plt'
+)
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
@@ -102,6 +108,7 @@
     warpx_field_gathering_algo='momentum-conserving'
 )
 
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 sim.add_diagnostic(reduced_diag)
 sim.add_diagnostic(reduced_diag_one_eighth)

diff --git a/Examples/Tests/embedded_boundary_python_api/PICMI_inputs_EB_API.py b/Examples/Tests/embedded_boundary_python_api/PICMI_inputs_EB_API.py
@@ -58,6 +58,12 @@
 # diagnostics
 ##########################
 
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 1,
+    write_dir = '.',
+    warpx_file_prefix = "embedded_boundary_python_API_plt"
+)
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
@@ -78,6 +84,7 @@
     verbose = 1
 )
 
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 
 sim.initialize_inputs()

diff --git a/Examples/Tests/ionization/PICMI_inputs_2d.py b/Examples/Tests/ionization/PICMI_inputs_2d.py
@@ -84,10 +84,18 @@
     cfl = 0.999)
 
 # Diagnostics
-diag = picmi.FieldDiagnostic(
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 10000,
+    species = [electrons, ions],
+    data_list = ['ux', 'uy', 'uz', 'x', 'y', 'weighting'],
+    write_dir = '.',
+    warpx_file_prefix = 'Python_ionization_plt')
+field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
     period = 10000,
+    data_list = ['Bx', 'By', 'Bz', 'Ex', 'Ey', 'Ez', 'Jx', 'Jy', 'Jz'],
     write_dir = '.',
     warpx_file_prefix = 'Python_ionization_plt')
 
@@ -115,7 +123,8 @@
     injection_method = laser_antenna)
 
 # Add diagnostics
-sim.add_diagnostic(diag)
+sim.add_diagnostic(particle_diag)
+sim.add_diagnostic(field_diag)
 
 # Write input file that can be used to run with the compiled version
 sim.write_input_file(file_name = 'inputs_2d_picmi')

diff --git a/Examples/Tests/magnetostatic_eb/PICMI_inputs_3d.py b/Examples/Tests/magnetostatic_eb/PICMI_inputs_3d.py
@@ -113,6 +113,12 @@
 # diagnostics
 ##########################
 
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 1,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_magnetostatic_eb_3d_plt'
+)
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
@@ -140,6 +146,7 @@
 
 sim.add_species(beam, layout=beam_layout, initialize_self_field=True)
 
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 
 ##########################

diff --git a/Examples/Tests/magnetostatic_eb/PICMI_inputs_rz.py b/Examples/Tests/magnetostatic_eb/PICMI_inputs_rz.py
@@ -110,6 +110,12 @@
 # diagnostics
 ##########################
 
+particle_diag = picmi.ParticleDiagnostic(
+    name = 'diag1',
+    period = 1,
+    write_dir = '.',
+    warpx_file_prefix = 'Python_magnetostatic_eb_rz_plt'
+)
 field_diag = picmi.FieldDiagnostic(
     name = 'diag1',
     grid = grid,
@@ -137,6 +143,7 @@
 
 sim.add_species(beam, layout=beam_layout, initialize_self_field=True)
 
+sim.add_diagnostic(particle_diag)
 sim.add_diagnostic(field_diag)
 
 ##########################

diff --git a/Examples/Tests/ohm_solver_EM_modes/PICMI_inputs.py b/Examples/Tests/ohm_solver_EM_modes/PICMI_inputs.py
@@ -21,7 +21,10 @@
 
 comm = mpi.COMM_WORLD
 
-simulation = picmi.Simulation(verbose=0)
+simulation = picmi.Simulation(
+    warpx_serialize_initial_conditions=True,
+    verbose=0
+)
 # make a shorthand for simulation.extension since we use it a lot
 sim_ext = simulation.extension
 
@@ -256,6 +259,15 @@ def setup_run(self):
             self.output_file_name = 'perp_field_data.txt'
 
         if self.test:
+            particle_diag = picmi.ParticleDiagnostic(
+                name='field_diag',
+                period=self.total_steps,
+                write_dir='.',
+                warpx_file_prefix='Python_ohms_law_solver_EM_modes_1d_plt',
+                # warpx_format = 'openpmd',
+                # warpx_openpmd_backend = 'h5'
+            )
+            simulation.add_diagnostic(particle_diag)
             field_diag = picmi.FieldDiagnostic(
                 name='field_diag',
                 grid=self.grid,

diff --git a/Examples/Tests/ohm_solver_ion_Landau_damping/PICMI_inputs.py b/Examples/Tests/ohm_solver_ion_Landau_damping/PICMI_inputs.py
@@ -20,7 +20,9 @@
 
 comm = mpi.COMM_WORLD
 
-simulation = picmi.Simulation(verbose=0)
+simulation = picmi.Simulation(
+    warpx_serialize_initial_conditions=True,
+    verbose=0)
 # make a shorthand for simulation.extension since we use it a lot
 sim_ext = simulation.extension
 
@@ -216,11 +218,21 @@ def setup_run(self):
         callbacks.installafterstep(self.text_diag)
 
         if self.test:
+            particle_diag = picmi.ParticleDiagnostic(
+                name='diag1',
+                period=100,
+                write_dir='.',
+                species=[self.ions],
+                data_list = ['ux', 'uy', 'uz', 'x', 'y', 'weighting'],
+                warpx_file_prefix=f'Python_ohms_law_solver_landau_damping_{self.dim}d_plt',
+            )
+            simulation.add_diagnostic(particle_diag)
             field_diag = picmi.FieldDiagnostic(
-                name='field_diag',
+                name='diag1',
                 grid=self.grid,
                 period=100,
                 write_dir='.',
+                data_list = ['Bx', 'By', 'Bz', 'Ex', 'Ey', 'Ez', 'Jx', 'Jy', 'Jz'],
                 warpx_file_prefix=f'Python_ohms_law_solver_landau_damping_{self.dim}d_plt',
             )
             simulation.add_diagnostic(field_diag)

diff --git a/Examples/Tests/ohm_solver_ion_beam_instability/PICMI_inputs.py b/Examples/Tests/ohm_solver_ion_beam_instability/PICMI_inputs.py
@@ -21,7 +21,9 @@
 
 comm = mpi.COMM_WORLD
 
-simulation = picmi.Simulation(verbose=0)
+simulation = picmi.Simulation(
+    warpx_serialize_initial_conditions=True,
+    verbose=0)
 # make a shorthand for simulation.extension since we use it a lot
 sim_ext = simulation.extension
 
@@ -256,10 +258,20 @@ def setup_run(self):
         callbacks.installafterstep(self.text_diag)
 
         if self.test:
+            part_diag = picmi.ParticleDiagnostic(
+                name='diag1',
+                period=1250,
+                species=[self.ions, self.beam_ions],
+                data_list = ['ux', 'uy', 'uz', 'x', 'weighting'],
+                write_dir='.',
+                warpx_file_prefix='Python_ohms_law_solver_ion_beam_1d_plt',
+            )
+            simulation.add_diagnostic(part_diag)
             field_diag = picmi.FieldDiagnostic(
-                name='field_diag',
+                name='diag1',
                 grid=self.grid,
                 period=1250,
+                data_list = ['Bx', 'By', 'Bz', 'Ex', 'Ey', 'Ez', 'Jx', 'Jy', 'Jz'],
                 write_dir='.',
                 warpx_file_prefix='Python_ohms_law_solver_ion_beam_1d_plt',
             )