Delete old diagnostics (#933)

* Create subsection for diags documentation in input parameters list

* Replace old diags with new ones IN DOC ONLY

* eol whitespace

* Check first CI test with new diags, before changing all of them

* use diags in all CI

* oops, had forgotten all examples except Tests/

* Updated picmi interface to use the new diagnostics

* fix bug in how field functors are initialized for diags

* fix bug: should always dump output at the end of simulation

* eol

* update test parameters in ini file

* Further fixes to picmi for new diagnostics

* Updates PICMI input files to use the new diagnostics

* avoid dumping final plotfile twoce

* update test to run with new diags

* fix typo introduced when fixing merge conflicts

* had accidentally removed the max_step here, so the run never ended on TravisCI

* Add Diagnostics.py for picmi with new diagnostics

* Adding m_ for member variables in new diags (#934)

* fixing bug to initialize CellCenterFunctor for Bx

* diag_name renamed to m_diag_name

* some more diag members made m_

* renaming member variable mf_avg to m_mf_output

* fixing m_mf_output to mf_dst in comments

* Python documentation updates (#936)

* Update Python documentation

* Added numpy as a requirement for the Python installation

* Cleaned EOL white space in Python documentation

* Add periodictable to the Python packages required

Co-Authored-By: Axel Huebl <axel.huebl@plasma.ninja>

* Added periodictable to required packages for pure Python version

Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>

* Add hostname to LoadBalanceCosts reduced diagnostic (#902)

* Add hostname to reduced diags

EOL

Fix rd loadbalancecosts test

AMREX_USE_MPI

EOL

move macro to source file

Review changes

eol

add GPU ID if running on GPU

eol

Typo in comment

use vectors to get rid of C-style memory management

Fix for test

eol

* Compute number of unique box data fields in analysis script

* analysis script

* Use amrex Tokenize to split string

* Update WarpXUtil.cpp

* Update WarpXUtil.H

* [mini] Add contact us section to documentation (#941)

* add contact us section to doc

* Update Docs/source/contact_us.rst

Co-Authored-By: L. Diana Amorim <LDianaAmorim@lbl.gov>

* Update Docs/source/contact_us.rst

Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>

* stop calling the old WritePlotFile functions

* fix new diags, problem with rho and PSATD and particle output variables

* remove more deprecated code for old diags

* Move checkpoint capability to new diagnostics

* error if user asks custom output for checkpoint

* eol

* some more old diags code deleted

* further cleaning

* eol

* further cleaning, make sure that WarpX compiles with USE_OPENPMD

* remove old diags parameters

* use new option to change the plotfile name

* typo

* do not need checkpoint files

* adapt to new option for checkpoint

* removed unread options as they make tests crash

* remove warpx_checkInt from the Python layer

* remove some more python wrappers

* add checkpoint capability with 2 diags in new output

* fix bug in MultiDiagnostics, and (should) fix checkpoint-restart test

* fix restart CI test

* avoid issue when writing the last plotfile twice

* dpgrote's fix for the Python tests

* update doc for diagnostics

* stop requesting ndiags, this is read from the list of diags

* awk to remove ndiags from all example input files

* Removed diagnostics.ndiags from picmi interface

Co-authored-by: Dave Grote <dpgrote@lbl.gov>
Co-authored-by: Dave Grote <grote1@llnl.gov>
Co-authored-by: Revathi  Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com>
Co-authored-by: Axel Huebl <axel.huebl@plasma.ninja>
Co-authored-by: Michael E Rowan <38045958+mrowan137@users.noreply.github.com>
Co-authored-by: L. Diana Amorim <LDianaAmorim@lbl.gov>

1 files changed, 7 insertions, 7 deletions

diff --git a/Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration.py b/Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration.py
index a1a8a0ba5..e958f99fd 100644
--- a/Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration.py
+++ b/Examples/Physics_applications/plasma_acceleration/PICMI_inputs_plasma_acceleration.py
@@ -46,21 +46,21 @@ plasma = picmi.Species(particle_type='electron', name='plasma', initial_distribu
 sim = picmi.Simulation(solver = solver,
                        max_steps = max_steps,
                        verbose = 1,
-                       warpx_plot_int = max_steps,
                        warpx_current_deposition_algo = 'esirkepov')
 
 sim.add_species(beam, layout=picmi.GriddedLayout(grid=grid, n_macroparticle_per_cell=number_per_cell_each_dim))
 sim.add_species(plasma, layout=picmi.GriddedLayout(grid=grid, n_macroparticle_per_cell=number_per_cell_each_dim))
 
 field_diag = picmi.FieldDiagnostic(grid = grid,
-                                    period = max_steps,
-                                    data_list = ['Ex', 'Ey', 'Ez', 'Jx', 'Jy', 'Jz', 'part_per_cell'],
-                                    write_dir = 'diags')
+                                   period = max_steps,
+                                   data_list = ['Ex', 'Ey', 'Ez', 'Jx', 'Jy', 'Jz', 'part_per_cell'],
+                                   write_dir = 'diags',
+                                   warpx_file_prefix = 'plotfiles/plt')
 
 part_diag = picmi.ParticleDiagnostic(period = max_steps,
-                                      species = [beam, plasma],
-                                      data_list = ['ux', 'uy', 'uz', 'weighting', 'Ex', 'Ey', 'Ez'],
-                                      write_dir = 'diags')
+                                     species = [beam, plasma],
+                                     data_list = ['ux', 'uy', 'uz', 'weighting', 'Ex', 'Ey', 'Ez'],
+                                     write_dir = 'diags')
 
 sim.add_diagnostic(field_diag)
 sim.add_diagnostic(part_diag)