Merge branch 'hotfix/4.17.15' into main

Warwick-Plasma · Feb 16, 2021 · bbc1c3f · bbc1c3f
2 parents 3245264 + c2eb131
commit bbc1c3f
Show file tree

Hide file tree

Showing 23 changed files with 50 additions and 173 deletions.
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -10,7 +10,7 @@ test_ubuntu_gfortran:
     - web
     - hook
   except:
-    - master
+    - main
     - wip/*
     - tag
   script:
@@ -27,7 +27,7 @@ test_ubuntu_intel:
     - web
     - hook
   except:
-    - master
+    - main
     - wip/*
     - tag
   script:
@@ -43,7 +43,7 @@ test_ubuntu_pgi:
     - web
     - hook
   except:
-    - master
+    - main
     - wip/*
     - tag
   script:
@@ -60,7 +60,7 @@ test_osx:
     - web
     - hook
   except:
-    - master
+    - main
     - wip/*
     - tag
   script:

diff --git a/SDF b/SDF
diff --git a/epoch1d/src/deck/deck_control_block.F90 b/epoch1d/src/deck/deck_control_block.F90
@@ -64,6 +64,7 @@ SUBROUTINE control_deck_initialise
     n_zeros_control = -1
     dlb_maximum_interval = 500
     dlb_force_interval = 2000
+    dlb_threshold = -1.0_num
     nx_global = -1
     particle_push_start_time = 0.0_num
     particle_migration_interval = 1

diff --git a/epoch1d/src/deck/deck_io_block.F90 b/epoch1d/src/deck/deck_io_block.F90
@@ -61,7 +61,7 @@ END SUBROUTINE io_deck_initialise
   SUBROUTINE io_deck_finalise
 
     INTEGER :: i, io, iu, n_zeros_estimate, n_dumps
-    REAL(num) :: dumps
+    REAL(num) :: dumps, dx
 #ifndef NO_IO
     CHARACTER(LEN=c_max_path_length) :: list_filename
 #endif
@@ -138,6 +138,12 @@ SUBROUTINE io_deck_finalise
           IF (io_block_list(i)%dt_snapshot > 0.0_num) THEN
             dumps = MAX(dumps, t_end / io_block_list(i)%dt_snapshot)
           END IF
+
+          ! This might fail if Debye length not resolved
+          IF (io_block_list(i)%nstep_snapshot > 0) THEN
+            dx = (x_max - x_min) / nx_global
+            dumps = MAX(dumps, t_end * c / dx / io_block_list(i)%nstep_snapshot)
+          END IF
         END DO
 
         n_dumps = FLOOR(dumps)

diff --git a/epoch1d/src/deck/deck_species_block.F90 b/epoch1d/src/deck/deck_species_block.F90
@@ -75,6 +75,7 @@ SUBROUTINE species_deck_initialise
       ALLOCATE(dumpmask_array(4))
       ALLOCATE(bc_particle_array(2*c_ndims,4))
       release_species = ''
+      release_species_list = ''
     END IF
 
   END SUBROUTINE species_deck_initialise

diff --git a/epoch1d/src/housekeeping/window.F90 b/epoch1d/src/housekeeping/window.F90
@@ -177,6 +177,8 @@ SUBROUTINE insert_particles
     DO ispecies = 1, n_species
       species => species_list(ispecies)
 
+      IF (species%background_species) CYCLE
+
       CALL create_empty_partlist(append_list)
       npart_per_cell = FLOOR(species%npart_per_cell, KIND=i8)
       npart_frac = species%npart_per_cell - npart_per_cell

diff --git a/epoch1d/src/pack.py b/epoch1d/src/pack.py
@@ -407,7 +407,7 @@ def print_integer_array(value):
     print_integer_array(0)
 else:
     if pack_git_diff_from_origin:
-        sp.call(["git diff origin/master > %s" % gitdiff], shell=True)
+        sp.call(["git diff origin/main > %s" % gitdiff], shell=True)
     else:
         sp.call(["git diff > %s" % gitdiff], shell=True)
     if os.path.getsize(gitdiff) != 0:

diff --git a/epoch1d/src/pack.sh b/epoch1d/src/pack.sh
@@ -300,7 +300,7 @@ cat >> $outfile <<EOF
 EOF
 else
   if [ $pack_git_diff_from_origin -ne 0 ]; then
-    git diff --exit-code origin/master > $gitdiff
+    git diff --exit-code origin/main > $gitdiff
   else
     git diff --exit-code > $gitdiff
   fi

diff --git a/epoch1d/src/physics_packages/collisions.F90 b/epoch1d/src/physics_packages/collisions.F90
@@ -966,9 +966,6 @@ SUBROUTINE intra_collisions_np(p_list, mass, charge, weight, &
     REAL(num), PARAMETER :: two_thirds = 2.0_num / 3.0_num
     REAL(num), PARAMETER :: pi_fac = &
                                 (4.0_num * pi / 3.0_num)**(1.0_num / 3.0_num)
-#ifndef PER_SPECIES_WEIGHT
-    REAL(num) :: w1, w2, wr, e1, e5, e2, e6
-#endif
     factor = 0.0_num
     np = 0.0_num
 
@@ -1132,29 +1129,6 @@ SUBROUTINE intra_collisions_np(p_list, mass, charge, weight, &
       p5 = (p3 + (gc_m1_vc * DOT_PRODUCT(vc, p3) + gm3 * gc) * vc) * c
       p6 = (p4 + (gc_m1_vc * DOT_PRODUCT(vc, p4) + gm4 * gc) * vc) * c
 
-#ifndef PER_SPECIES_WEIGHT
-      w1 = current%weight
-      w2 = impact%weight
-      wr = w1 / w2
-
-      ! Energies before and after collision.
-      ! Only required for weighted particle correction
-      e1 = c * SQRT(DOT_PRODUCT(p1, p1) + (m1 * c)**2)
-      e2 = c * SQRT(DOT_PRODUCT(p2, p2) + (m2 * c)**2)
-
-      e5 = c * SQRT(DOT_PRODUCT(p5, p5) + (m1 * c)**2)
-      e6 = c * SQRT(DOT_PRODUCT(p6, p6) + (m2 * c)**2)
-
-      ! Restore values of p1, p2
-      p1 = p1 * c
-      p2 = p2 * c
-
-      IF (wr > one_p_2eps) THEN
-        CALL weighted_particles_correction(w2 / w1, p1, p5, e1, e5, m1)
-      ELSE IF (wr < one_m_2eps) THEN
-        CALL weighted_particles_correction(w1 / w2, p2, p6, e2, e6, m2)
-      END IF
-#endif
       ! Update particle properties
       current%part_p = p5
       impact%part_p = p6
@@ -1438,7 +1412,7 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
     TYPE(particle), POINTER :: current, impact
     REAL(num) :: factor, np
     INTEGER(i8) :: icount, jcount, pcount, k
-    REAL(num) :: m1, m2, q1, q2, w1, w2
+    REAL(num) :: m1, m2, q1, q2
     REAL(num) :: ran1, ran2, s12, cosp, sinp, s_fac, v_rel
     REAL(num) :: sinp_cos, sinp_sin, s_prime, s_fac_prime
     REAL(num) :: a, a_inv, p_perp, p_tot, v_sq, gamma_rel_inv
@@ -1448,7 +1422,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
     REAL(num), DIMENSION(3,3) :: mat
     REAL(num) :: p_mag, p_mag2, fac, gc, vc_sq, wr
     REAL(num) :: gm1, gm2, gm3, gm4, gm, gc_m1_vc
-    REAL(num) :: e1, e5, e2, e6
     REAL(num), PARAMETER :: pi4_eps2_c4 = 4.0_num * pi * epsilon0**2 * c**4
     REAL(num), PARAMETER :: two_thirds = 2.0_num / 3.0_num
     REAL(num), PARAMETER :: pi_fac = &
@@ -1506,9 +1479,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
       m2 = mass2
       q1 = charge1
       q2 = charge2
-      w1 = weight1
-      w2 = weight2
-      wr = w1 / w2
 
       current => p_list1%head
       impact => p_list2%head
@@ -1525,11 +1495,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
         q1 = current%charge
         q2 = impact%charge
 #endif
-#ifndef PER_SPECIES_WEIGHT
-        w1 = current%weight
-        w2 = impact%weight
-        wr = w1 / w2
-#endif
 
         p1 = current%part_p / c
         p2 = impact%part_p / c
@@ -1557,10 +1522,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
         v1 = p1 / gm1
         v2 = p2 / gm2
 
-        ! Pre-collision energies
-        e1 = c * SQRT(DOT_PRODUCT(p1, p1) + (m1 * c)**2)
-        e2 = c * SQRT(DOT_PRODUCT(p2, p2) + (m2 * c)**2)
-
         ! Velocity of centre-of-momentum (COM) reference frame
         vc = (p1 + p2) / gm
         vc_sq = DOT_PRODUCT(vc, vc)
@@ -1642,19 +1603,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
         p5 = (p3 + (gc_m1_vc * DOT_PRODUCT(vc, p3) + gm3 * gc) * vc) * c
         p6 = (p4 + (gc_m1_vc * DOT_PRODUCT(vc, p4) + gm4 * gc) * vc) * c
 
-        e5 = c * SQRT(DOT_PRODUCT(p5, p5) + (m1 * c)**2)
-        e6 = c * SQRT(DOT_PRODUCT(p6, p6) + (m2 * c)**2)
-
-        ! Restore values of p1, p2
-        p1 = p1 * c
-        p2 = p2 * c
-
-        IF (wr > one_p_2eps) THEN
-          CALL weighted_particles_correction(w2 / w1, p1, p5, e1, e5, m1)
-        ELSE IF (wr < one_m_2eps) THEN
-          CALL weighted_particles_correction(w1 / w2, p2, p6, e2, e6, m2)
-        END IF
-
         ! Update particle properties
         current%part_p = p5
         impact%part_p = p6

diff --git a/epoch2d/src/deck/deck_control_block.F90 b/epoch2d/src/deck/deck_control_block.F90
@@ -64,6 +64,7 @@ SUBROUTINE control_deck_initialise
     n_zeros_control = -1
     dlb_maximum_interval = 500
     dlb_force_interval = 2000
+    dlb_threshold = -1.0_num
     nx_global = -1
     ny_global = -1
     particle_push_start_time = 0.0_num

diff --git a/epoch2d/src/deck/deck_io_block.F90 b/epoch2d/src/deck/deck_io_block.F90
@@ -61,7 +61,7 @@ END SUBROUTINE io_deck_initialise
   SUBROUTINE io_deck_finalise
 
     INTEGER :: i, io, iu, n_zeros_estimate, n_dumps
-    REAL(num) :: dumps
+    REAL(num) :: dumps, dx
 #ifndef NO_IO
     CHARACTER(LEN=c_max_path_length) :: list_filename
 #endif
@@ -138,6 +138,13 @@ SUBROUTINE io_deck_finalise
           IF (io_block_list(i)%dt_snapshot > 0.0_num) THEN
             dumps = MAX(dumps, t_end / io_block_list(i)%dt_snapshot)
           END IF
+
+          ! This might fail if Debye length not resolved
+          IF (io_block_list(i)%nstep_snapshot > 0) THEN
+            dx = (x_max - x_min) / nx_global
+            dx = MIN(dx, (y_max - y_min) / ny_global)
+            dumps = MAX(dumps, t_end * c / dx / io_block_list(i)%nstep_snapshot)
+          END IF
         END DO
 
         n_dumps = FLOOR(dumps)

diff --git a/epoch2d/src/deck/deck_species_block.F90 b/epoch2d/src/deck/deck_species_block.F90
@@ -75,6 +75,7 @@ SUBROUTINE species_deck_initialise
       ALLOCATE(dumpmask_array(4))
       ALLOCATE(bc_particle_array(2*c_ndims,4))
       release_species = ''
+      release_species_list = ''
     END IF
 
   END SUBROUTINE species_deck_initialise

diff --git a/epoch2d/src/housekeeping/window.F90 b/epoch2d/src/housekeeping/window.F90
@@ -213,6 +213,8 @@ SUBROUTINE insert_particles
     DO ispecies = 1, n_species
       species => species_list(ispecies)
 
+      IF (species%background_species) CYCLE
+
       CALL create_empty_partlist(append_list)
       npart_per_cell = FLOOR(species%npart_per_cell, KIND=i8)
       npart_frac = species%npart_per_cell - npart_per_cell

diff --git a/epoch2d/src/pack.py b/epoch2d/src/pack.py
@@ -407,7 +407,7 @@ def print_integer_array(value):
     print_integer_array(0)
 else:
     if pack_git_diff_from_origin:
-        sp.call(["git diff origin/master > %s" % gitdiff], shell=True)
+        sp.call(["git diff origin/main > %s" % gitdiff], shell=True)
     else:
         sp.call(["git diff > %s" % gitdiff], shell=True)
     if os.path.getsize(gitdiff) != 0:

diff --git a/epoch2d/src/pack.sh b/epoch2d/src/pack.sh
@@ -300,7 +300,7 @@ cat >> $outfile <<EOF
 EOF
 else
   if [ $pack_git_diff_from_origin -ne 0 ]; then
-    git diff --exit-code origin/master > $gitdiff
+    git diff --exit-code origin/main > $gitdiff
   else
     git diff --exit-code > $gitdiff
   fi

diff --git a/epoch2d/src/physics_packages/collisions.F90 b/epoch2d/src/physics_packages/collisions.F90
@@ -981,9 +981,6 @@ SUBROUTINE intra_collisions_np(p_list, mass, charge, weight, &
     REAL(num), PARAMETER :: two_thirds = 2.0_num / 3.0_num
     REAL(num), PARAMETER :: pi_fac = &
                                 (4.0_num * pi / 3.0_num)**(1.0_num / 3.0_num)
-#ifndef PER_SPECIES_WEIGHT
-    REAL(num) :: w1, w2, wr, e1, e5, e2, e6
-#endif
     factor = 0.0_num
     np = 0.0_num
 
@@ -1147,29 +1144,6 @@ SUBROUTINE intra_collisions_np(p_list, mass, charge, weight, &
       p5 = (p3 + (gc_m1_vc * DOT_PRODUCT(vc, p3) + gm3 * gc) * vc) * c
       p6 = (p4 + (gc_m1_vc * DOT_PRODUCT(vc, p4) + gm4 * gc) * vc) * c
 
-#ifndef PER_SPECIES_WEIGHT
-      w1 = current%weight
-      w2 = impact%weight
-      wr = w1 / w2
-
-      ! Energies before and after collision.
-      ! Only required for weighted particle correction
-      e1 = c * SQRT(DOT_PRODUCT(p1, p1) + (m1 * c)**2)
-      e2 = c * SQRT(DOT_PRODUCT(p2, p2) + (m2 * c)**2)
-
-      e5 = c * SQRT(DOT_PRODUCT(p5, p5) + (m1 * c)**2)
-      e6 = c * SQRT(DOT_PRODUCT(p6, p6) + (m2 * c)**2)
-
-      ! Restore values of p1, p2
-      p1 = p1 * c
-      p2 = p2 * c
-
-      IF (wr > one_p_2eps) THEN
-        CALL weighted_particles_correction(w2 / w1, p1, p5, e1, e5, m1)
-      ELSE IF (wr < one_m_2eps) THEN
-        CALL weighted_particles_correction(w1 / w2, p2, p6, e2, e6, m2)
-      END IF
-#endif
       ! Update particle properties
       current%part_p = p5
       impact%part_p = p6
@@ -1453,7 +1427,7 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
     TYPE(particle), POINTER :: current, impact
     REAL(num) :: factor, np
     INTEGER(i8) :: icount, jcount, pcount, k
-    REAL(num) :: m1, m2, q1, q2, w1, w2
+    REAL(num) :: m1, m2, q1, q2
     REAL(num) :: ran1, ran2, s12, cosp, sinp, s_fac, v_rel
     REAL(num) :: sinp_cos, sinp_sin, s_prime, s_fac_prime
     REAL(num) :: a, a_inv, p_perp, p_tot, v_sq, gamma_rel_inv
@@ -1463,7 +1437,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
     REAL(num), DIMENSION(3,3) :: mat
     REAL(num) :: p_mag, p_mag2, fac, gc, vc_sq, wr
     REAL(num) :: gm1, gm2, gm3, gm4, gm, gc_m1_vc
-    REAL(num) :: e1, e5, e2, e6
     REAL(num), PARAMETER :: pi4_eps2_c4 = 4.0_num * pi * epsilon0**2 * c**4
     REAL(num), PARAMETER :: two_thirds = 2.0_num / 3.0_num
     REAL(num), PARAMETER :: pi_fac = &
@@ -1521,9 +1494,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
       m2 = mass2
       q1 = charge1
       q2 = charge2
-      w1 = weight1
-      w2 = weight2
-      wr = w1 / w2
 
       current => p_list1%head
       impact => p_list2%head
@@ -1540,11 +1510,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
         q1 = current%charge
         q2 = impact%charge
 #endif
-#ifndef PER_SPECIES_WEIGHT
-        w1 = current%weight
-        w2 = impact%weight
-        wr = w1 / w2
-#endif
 
         p1 = current%part_p / c
         p2 = impact%part_p / c
@@ -1572,10 +1537,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
         v1 = p1 / gm1
         v2 = p2 / gm2
 
-        ! Pre-collision energies
-        e1 = c * SQRT(DOT_PRODUCT(p1, p1) + (m1 * c)**2)
-        e2 = c * SQRT(DOT_PRODUCT(p2, p2) + (m2 * c)**2)
-
         ! Velocity of centre-of-momentum (COM) reference frame
         vc = (p1 + p2) / gm
         vc_sq = DOT_PRODUCT(vc, vc)
@@ -1657,19 +1618,6 @@ SUBROUTINE inter_collisions_np(p_list1, p_list2, mass1, mass2, &
         p5 = (p3 + (gc_m1_vc * DOT_PRODUCT(vc, p3) + gm3 * gc) * vc) * c
         p6 = (p4 + (gc_m1_vc * DOT_PRODUCT(vc, p4) + gm4 * gc) * vc) * c
 
-        e5 = c * SQRT(DOT_PRODUCT(p5, p5) + (m1 * c)**2)
-        e6 = c * SQRT(DOT_PRODUCT(p6, p6) + (m2 * c)**2)
-
-        ! Restore values of p1, p2
-        p1 = p1 * c
-        p2 = p2 * c
-
-        IF (wr > one_p_2eps) THEN
-          CALL weighted_particles_correction(w2 / w1, p1, p5, e1, e5, m1)
-        ELSE IF (wr < one_m_2eps) THEN
-          CALL weighted_particles_correction(w1 / w2, p2, p6, e2, e6, m2)
-        END IF
-
         ! Update particle properties
         current%part_p = p5
         impact%part_p = p6

diff --git a/epoch3d/src/deck/deck_control_block.F90 b/epoch3d/src/deck/deck_control_block.F90
@@ -64,6 +64,7 @@ SUBROUTINE control_deck_initialise
     n_zeros_control = -1
     dlb_maximum_interval = 500
     dlb_force_interval = 2000
+    dlb_threshold = -1.0_num
     nx_global = -1
     ny_global = -1
     nz_global = -1