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, 54 insertions, 51 deletions

diff --git a/Python/pywarpx/picmi.py b/Python/pywarpx/picmi.py
index 9fe0b0781..86ffad728 100644
--- a/Python/pywarpx/picmi.py
+++ b/Python/pywarpx/picmi.py
@@ -502,8 +502,6 @@ class LaserAntenna(picmistandard.PICMI_LaserAntenna):
 class Simulation(picmistandard.PICMI_Simulation):
     def init(self, kw):
 
-        self.plot_int = kw.pop('warpx_plot_int', None)
-        self.plot_file = kw.pop('warpx_plot_file', None)
         self.current_deposition_algo = kw.pop('warpx_current_deposition_algo', None)
         self.charge_deposition_algo = kw.pop('warpx_charge_deposition_algo', None)
         self.field_gathering_algo = kw.pop('warpx_field_gathering_algo', None)
@@ -531,8 +529,6 @@ class Simulation(picmistandard.PICMI_Simulation):
             pywarpx.warpx.gamma_boost = self.gamma_boost
             pywarpx.warpx.boost_direction = None
 
-        pywarpx.amr.plot_int = self.plot_int
-        pywarpx.amr.plot_file = self.plot_file
         pywarpx.algo.current_deposition = self.current_deposition_algo
         pywarpx.algo.charge_deposition = self.charge_deposition_algo
         pywarpx.algo.field_gathering = self.field_gathering_algo
@@ -610,40 +606,59 @@ class Simulation(picmistandard.PICMI_Simulation):
 # ----------------------------
 
 
-class FieldDiagnostic(picmistandard.PICMI_FieldDiagnostic):
+class _WarpX_FieldDiagnostic(picmistandard.PICMI_FieldDiagnostic):
     def init(self, kw):
 
         self.plot_raw_fields = kw.pop('warpx_plot_raw_fields', None)
         self.plot_raw_fields_guards = kw.pop('warpx_plot_raw_fields_guards', None)
         self.plot_finepatch = kw.pop('warpx_plot_finepatch', None)
         self.plot_crsepatch = kw.pop('warpx_plot_crsepatch', None)
+        self.format = kw.pop('warpx_format', 'plotfile')
+        self.openpmd_backend = kw.pop('warpx_openpmd_backend', None)
+        self.file_prefix = kw.pop('warpx_file_prefix', None)
 
     def initialize_inputs(self):
-        # --- For now, the period must be the same as plot_int if set
-        pywarpx.amr.check_consistency('plot_int', self.period, 'The period must be the same for all simulation frame diagnostics')
-        pywarpx.amr.plot_int = self.period
+        self.diagnostics_number = len(pywarpx.Diagnostics.diagnostics_list) + 1
+
+        # --- This a placeholder until the name attribute is added to the picmi standard
+        name = getattr(self, 'name', None)
+        if name is None:
+            self.name = 'diag{}'.format(self.diagnostics_number)
+
+        self.diagnostic = pywarpx.Bucket.Bucket(self.name)
+        pywarpx.diagnostics.diags_names.append(self.name)
+        pywarpx.Diagnostics.diagnostics_list.append(self.diagnostic)
+
+        self.diagnostic.diag_type = 'Full'
+        self.diagnostic.format = self.format
+        self.diagnostic.openpmd_backend = self.openpmd_backend
+        self.diagnostic.period = self.period
+        self.diagnostic.diag_lo = self.lower_bound
+        self.diagnostic.diag_hi = self.upper_bound
+        self.diagnostic.coarsening_ratio = (np.array(self.grid.number_of_cells)/np.array(self.number_of_cells)).astype(int)
+        self.diagnostic.fields_to_plot = set()
 
         for dataname in self.data_list:
             if dataname == 'E':
-                pywarpx.warpx.add_field_to_plot('Ex')
-                pywarpx.warpx.add_field_to_plot('Ey')
-                pywarpx.warpx.add_field_to_plot('Ez')
+                self.diagnostic.fields_to_plot.add('Ex')
+                self.diagnostic.fields_to_plot.add('Ey')
+                self.diagnostic.fields_to_plot.add('Ez')
             elif dataname == 'B':
-                pywarpx.warpx.add_field_to_plot('Bx')
-                pywarpx.warpx.add_field_to_plot('By')
-                pywarpx.warpx.add_field_to_plot('Bz')
+                self.diagnostic.fields_to_plot.add('Bx')
+                self.diagnostic.fields_to_plot.add('By')
+                self.diagnostic.fields_to_plot.add('Bz')
             elif dataname == 'J':
-                pywarpx.warpx.add_field_to_plot('jx')
-                pywarpx.warpx.add_field_to_plot('jy')
-                pywarpx.warpx.add_field_to_plot('jz')
-            elif dataname in ['Ex', 'Ey', 'Ez', 'Bx', 'By', 'Bz', 'rho', 'F', 'proc_number']:
-                pywarpx.warpx.add_field_to_plot(dataname)
+                self.diagnostic.fields_to_plot.add('jx')
+                self.diagnostic.fields_to_plot.add('jy')
+                self.diagnostic.fields_to_plot.add('jz')
+            elif dataname in ['Ex', 'Ey', 'Ez', 'Bx', 'By', 'Bz', 'rho', 'F', 'proc_number', 'part_per_cell']:
+                self.diagnostic.fields_to_plot.add(dataname)
             elif dataname in ['Jx', 'Jy', 'Jz']:
-                pywarpx.warpx.add_field_to_plot(dataname.lower())
+                self.diagnostic.fields_to_plot.add(dataname.lower())
             elif dataname == 'dive':
-                pywarpx.warpx.add_field_to_plot('divE')
+                self.diagnostic.fields_to_plot.add('divE')
             elif dataname == 'divb':
-                pywarpx.warpx.add_field_to_plot('divB')
+                self.diagnostic.fields_to_plot.add('divB')
             elif dataname == 'raw_fields':
                 self.plot_raw_fields = 1
             elif dataname == 'raw_fields_guards':
@@ -653,36 +668,31 @@ class FieldDiagnostic(picmistandard.PICMI_FieldDiagnostic):
             elif dataname == 'crsepatch':
                 self.plot_crsepatch = 1
 
-        pywarpx.warpx.plot_raw_fields = self.plot_raw_fields
-        pywarpx.warpx.plot_raw_fields_guards = self.plot_raw_fields_guards
+        self.diagnostic.plot_raw_fields = self.plot_raw_fields
+        self.diagnostic.plot_raw_fields_guards = self.plot_raw_fields_guards
+        self.diagnostic.plot_finepatch = self.plot_finepatch
+        self.diagnostic.plot_crsepatch = self.plot_crsepatch
 
-        pywarpx.warpx.check_consistency('plot_finepatch', self.plot_finepatch, 'The fine patch flag must be the same for all simulation frame field diagnostics')
-        pywarpx.warpx.check_consistency('plot_crsepatch', self.plot_crsepatch, 'The coarse patch flag must be the same for all simulation frame field diagnostics')
-        pywarpx.warpx.plot_finepatch = self.plot_finepatch
-        pywarpx.warpx.plot_crsepatch = self.plot_crsepatch
+        if self.write_dir is not None or self.file_prefix is not None:
+            write_dir = (self.write_dir or 'diags')
+            file_prefix = (self.file_prefix or self.name)
+            self.diagnostic.file_prefix = write_dir + '/' + file_prefix
 
-        if self.write_dir is not None:
-            plot_file = self.write_dir + '/plotfiles/plt'
-            pywarpx.amr.check_consistency('plot_file', plot_file, 'The plot directory must be the same for all simulation frame diagnostics')
-            pywarpx.amr.plot_file = plot_file
 
-class ElectrostaticFieldDiagnostic(picmistandard.PICMI_ElectrostaticFieldDiagnostic):
-    def initialize_inputs(self):
-        # --- For now, the period must be the same as plot_int if set
-        pywarpx.amr.check_consistency('plot_int', self.period, 'The period must be the same for all simulation frame diagnostics')
-        pywarpx.amr.plot_int = self.period
+class FieldDiagnostic(_WarpX_FieldDiagnostic, picmistandard.PICMI_FieldDiagnostic):
+    pass
 
-        if self.write_dir is not None:
-            plot_file = self.write_dir + '/plotfiles/plt'
-            pywarpx.amr.check_consistency('plot_file', plot_file, 'The plot directory must be the same for all simulation frame diagnostics')
-            pywarpx.amr.plot_file = plot_file
+
+class ElectrostaticFieldDiagnostic(_WarpX_FieldDiagnostic, picmistandard.PICMI_ElectrostaticFieldDiagnostic):
+    def initialize_inputs(self):
+        if 'phi' in self.data_list:
+            # --- phi is not supported by WarpX, but is in the default data_list
+            self.data_list.remove('phi')
+        _WarpX_FieldDiagnostic.initialize_inputs(self)
 
 
 class ParticleDiagnostic(picmistandard.PICMI_ParticleDiagnostic):
     def initialize_inputs(self):
-        # --- For now, the period must be the same as plot_int if set
-        pywarpx.amr.check_consistency('plot_int', self.period, 'The period must be the same for all simulation frame diagnostics')
-        pywarpx.amr.plot_int = self.period
 
         plot_vars = set()
         for dataname in self.data_list:
@@ -704,8 +714,6 @@ class ParticleDiagnostic(picmistandard.PICMI_ParticleDiagnostic):
                 plot_vars.add('Bz')
             elif dataname in ['ux', 'uy', 'uz', 'Ex', 'Ey', 'Ez', 'Bx', 'By', 'Bz']:
                 plot_vars.add(dataname)
-            elif dataname in ['part_per_cell', 'part_per_grid', 'part_per_proc']:
-                pywarpx.warpx.add_field_to_plot(dataname)
 
         if plot_vars:
             species = self.species
@@ -715,11 +723,6 @@ class ParticleDiagnostic(picmistandard.PICMI_ParticleDiagnostic):
                 for var in plot_vars:
                     specie.species.plot_vars.add(var)
 
-        if self.write_dir is not None:
-            plot_file = self.write_dir + '/plotfiles/plt'
-            pywarpx.amr.check_consistency('plot_file', plot_file, 'The plot directory must be the same for all simulation frame diagnostics')
-            pywarpx.amr.plot_file = plot_file
-
 
 # ----------------------------
 # Lab frame diagnostics