Merge branch '4.19-devel'

Author: TomGoffrey

.github/workflows/build_test.yml

@@ -19,7 +19,7 @@ jobs:
     if: github.event_name != 'pull_request_review' ||
         contains(github.event.pull_request.labels.*.name, 'auto-pr')
     # The type of runner that the job will run on
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
     strategy:
       matrix:
         include:
@@ -31,7 +31,7 @@ jobs:
           define: >-
             -DPER_SPECIES_WEIGHT -DZERO_CURRENT_PARTICLES -DNO_PARTICLE_PROBES
             -DPARTICLE_SHAPE_TOPHAT -DPARTICLE_ID -DPHOTONS -DTRIDENT_PHOTONS
-            -DBREMSSTRAHLUNG -DPARSER_DEBUG -DNO_IO -DCOLLISIONS_TEST
+            -DBREMSSTRAHLUNG -DPARSER_DEBUG -DNO_IO
             -DPER_PARTICLE_CHARGE_MASS -DPARSER_CHECKING -DNO_USE_ISATTY
             -DWORK_DONE_INTEGRATED -DHC_PUSH -DNO_MPI3 -DDECK_DEBUG
         - mode:
@@ -49,14 +49,10 @@ jobs:
 
     steps:
     - name: Install dependencies
-      run: sudo apt update &&
-           sudo apt install -y
-               python3-dev
-               python3-numpy
-               python3-nose
-               python3-matplotlib
-               libpython3-dev
-               mpich
+      run: |
+        sudo apt update &&
+        sudo apt install -y python3-dev python3-numpy python3-nose python3-matplotlib libpython3-dev openmpi-bin libopenmpi-dev
+        pip install sdfr
 
     - name: Checkout code
       uses: actions/checkout@v4

epoch1d/Makefile

@@ -234,10 +234,6 @@ DEFINES := $(DEFINE)
 # Don't generate any output at all. Useful for benchmarking.
 #DEFINES += $(D)NO_IO
 
-# Bypass the main simulation and only perform collision tests.
-# This flag should only ever be used for testing purposes.
-#DEFINES += $(D)COLLISIONS_TEST
-
 # Specify charge and mass per particle rather than per species.
 # This is a legacy option which will be removed soon.
 #DEFINES += $(D)PER_PARTICLE_CHARGE_MASS

epoch1d/src/boundary.F90

@@ -496,9 +496,9 @@ SUBROUTINE efield_bcs
     ! Perfectly conducting boundaries
     DO i = c_bd_x_min, c_bd_x_max, c_bd_x_max - c_bd_x_min
       IF (bc_field(i) == c_bc_conduct) THEN
-        CALL field_clamp_zero(ex, ng, c_stagger_ex, i)
-        CALL field_zero_gradient(ey, c_stagger_ey, i)
-        CALL field_zero_gradient(ez, c_stagger_ez, i)
+        CALL field_zero_gradient(ex, c_stagger_ex, i)
+        CALL field_clamp_zero(ey, ng, c_stagger_ey, i)
+        CALL field_clamp_zero(ez, ng, c_stagger_ez, i)
       END IF
     END DO
 
@@ -541,9 +541,9 @@ SUBROUTINE bfield_bcs(mpi_only)
     ! Perfectly conducting boundaries
     DO i = c_bd_x_min, c_bd_x_max, c_bd_x_max - c_bd_x_min
       IF (bc_field(i) == c_bc_conduct) THEN
-        CALL field_zero_gradient(bx, c_stagger_bx, i)
-        CALL field_clamp_zero(by, ng, c_stagger_by, i)
-        CALL field_clamp_zero(bz, ng, c_stagger_bz, i)
+        CALL field_clamp_zero(bx, ng, c_stagger_bx, i)
+        CALL field_zero_gradient(by, c_stagger_by, i)
+        CALL field_zero_gradient(bz, c_stagger_bz, i)
       END IF
     END DO
 

epoch1d/src/housekeeping/partlist.F90

@@ -58,9 +58,6 @@ SUBROUTINE set_partlist_size
 #if defined(PARTICLE_ID) || defined(PARTICLE_ID4)
     nvar = nvar+1
 #endif
-#ifdef COLLISIONS_TEST
-    nvar = nvar+1
-#endif
 #ifdef PHOTONS
     nvar = nvar+1
 #endif
@@ -444,10 +441,6 @@ SUBROUTINE pack_particle(array, a_particle)
     array(cpos) = REAL(a_particle%id, num)
     cpos = cpos+1
 #endif
-#ifdef COLLISIONS_TEST
-    array(cpos) = REAL(a_particle%coll_count, num)
-    cpos = cpos+1
-#endif
 #ifdef PHOTONS
     array(cpos) = a_particle%optical_depth
     cpos = cpos+1
@@ -523,10 +516,6 @@ SUBROUTINE unpack_particle(array, a_particle)
     a_particle%id = NINT(array(cpos),i8)
     cpos = cpos+1
 #endif
-#ifdef COLLISIONS_TEST
-    a_particle%coll_count = NINT(array(cpos))
-    cpos = cpos+1
-#endif
 #ifdef PHOTONS
     a_particle%optical_depth = array(cpos)
     cpos = cpos+1
@@ -585,9 +574,6 @@ SUBROUTINE init_particle(new_particle)
 #if defined(PARTICLE_ID) || defined(PARTICLE_ID4)
     new_particle%id = 0
 #endif
-#ifdef COLLISIONS_TEST
-    new_particle%coll_count = 0
-#endif
 #if defined(PHOTONS) || defined(BREMSSTRAHLUNG)
     ! This assigns an optical depth to newly created particle
     new_particle%particle_energy = 0.0_num

epoch1d/src/housekeeping/window.F90

@@ -216,6 +216,10 @@ SUBROUTINE insert_particles
           IF (npart_frac < random()) CYCLE
         END IF
         CALL create_particle(current)
+#ifdef PER_PARTICLE_CHARGE_MASS
+        current%mass = species%mass
+        current%charge = species%charge
+#endif
         current%part_pos = x0 + random() * dx
 
         IF (species%ic_df_type == c_ic_df_thermal) THEN

epoch1d/src/sdf_reader_example.f90

@@ -269,7 +269,7 @@ SUBROUTINE particles_for_rank(npart, rank, n_procs, npart_proc, start)
     ! Size per processor
     npart_proc_gen = npart / n_procs
 
-    IF (rank == n_procs) THEN
+    IF (rank == n_procs-1) THEN
       ! Last processor takes excess particles to make starts easier
       npart_proc = npart - MAX(npart_proc_gen * (n_procs - 1), 0_i8)
     ELSE

epoch1d/src/shared_data.F90

@@ -113,9 +113,6 @@ MODULE shared_data
 #elif PARTICLE_ID
     INTEGER(i8) :: id
 #endif
-#ifdef COLLISIONS_TEST
-    INTEGER :: coll_count
-#endif
 #ifdef WORK_DONE_INTEGRATED
     REAL(num) :: work_x
     REAL(num) :: work_y

epoch1d/tests/test_custom_stencils.py

@@ -23,7 +23,7 @@
 import numpy as np
 import matplotlib; matplotlib.use('Agg')
 import matplotlib.pyplot as plt
-import sdf
+import sdfr
 
 from . import SimTest
 
@@ -86,7 +86,7 @@ def setUpClass(cls):
             l = dumps.setdefault(solver, [])
             for dump in [osp.join(solver, '{:04d}.sdf'.format(i))
                          for i in range(8)]:
-                l.append(sdf.read(dump, dict=True))
+                l.append(sdfr.read(dump, dict=True))
 
     def test_createplot(self):
         if platform.system() == 'Darwin':

epoch1d/tests/test_landau.py

@@ -16,7 +16,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import sdf
+import sdfr
 import matplotlib; matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import unittest
@@ -25,20 +25,20 @@
 
 
 def showdatafields(sdffile):
-    data = sdf.read(sdffile, dict=True)
+    data = sdfr.read(sdffile, dict=True)
     print('Data fields present in "' + sdffile + '":')
     print(data.keys())
 
 
 def plotdump(sdffile, key, ax):
-    data = sdf.read(sdffile, dict=True)
+    data = sdfr.read(sdffile, dict=True)
     array = data[key].data
     ax.plot(array)
     ax.set_title(r'{:2.1f} ms'.format(data['Header']['time']*1e3))
 
 
 def plotdump2d(sdffile, key, ax):
-    data = sdf.read(sdffile, dict=True)
+    data = sdfr.read(sdffile, dict=True)
     if len(data[key].dims) == 3:
         array = data[key].data[:, :, 0]
     else:

epoch1d/tests/test_laser.py

@@ -16,7 +16,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import sdf
+import sdfr
 import matplotlib; matplotlib.use('Agg')
 import matplotlib.pyplot as plt
 import unittest
@@ -25,13 +25,13 @@
 
 
 def showdatafields(sdffile):
-    data = sdf.read(sdffile, dict=True)
+    data = sdfr.read(sdffile, dict=True)
     print('Data fields present in "' + sdffile + '":')
     print(data.keys())
 
 
 def plotdump(sdffile, key, ax):
-    data = sdf.read(sdffile, dict=True)
+    data = sdfr.read(sdffile, dict=True)
     array = data[key].data
     ax.plot(array)
     ax.set_title('{:2.1f} fs'.format(data['Header']['time']*1e15))
@@ -57,7 +57,7 @@ def createplots():
 class test_laser(SimTest):
 
     def totaleyassert(self, dump, val):
-        data = sdf.read(dump, dict=True)
+        data = sdfr.read(dump, dict=True)
         ey = data['Electric Field/Ey'].data**2
         eysum = np.sum(ey)
         test = np.isclose(eysum, val)