Merge branch 'hotfix/4.17.16' into main

.github/workflows/build_test.yml

@@ -0,0 +1,72 @@
+name: CI
+
+# Controls when the action will run.
+on:
+  push:
+    branches: [ main, '*-devel' ]
+  pull_request:
+    branches: [ main, '*-devel' ]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build_and_test:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        include:
+        - mode: debug
+          flag: -b
+          define:
+        - mode: debug
+          flag: -b
+          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
+            -DPER_PARTICLE_CHARGE_MASS -DPARSER_CHECKING -DNO_USE_ISATTY
+            -DWORK_DONE_INTEGRATED -DHC_PUSH -DNO_MPI3 -DDECK_DEBUG
+        - mode:
+          flag:
+          define:
+
+    env:
+      COMPILER: gfortran
+      MPIPROCS: 2
+      MODE: ${{ matrix.mode }}
+      DEFINE: ${{ matrix.define }}
+
+    steps:
+      - name: Install dependencies
+        run: sudo apt update &&
+             sudo apt install -y
+                 python3-dev
+                 python3-numpy
+                 python3-nose
+                 python3-matplotlib
+                 libpython3-dev
+                 mpich
+
+      - name: Checkout code
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
+          fetch-depth: 0
+
+      - name: Merge branch
+        if: github.event_name == 'pull_request'
+        run: git config user.email "[email protected]" &&
+             git config user.name "test" &&
+             git checkout -b $GITHUB_HEAD_REF $GITHUB_SHA &&
+             git checkout -b $GITHUB_BASE_REF origin/$GITHUB_BASE_REF &&
+             git merge --no-ff $GITHUB_HEAD_REF
+
+      - name: Cleanup
+        run: cd epoch1d && make cleanall &&
+             cd ../epoch2d && make cleanall &&
+             cd ../epoch3d && make cleanall
+
+      - name: Compile and run tests
+        run: ./scripts/run-tests-epoch-all.sh ${{ matrix.flag }}

epoch1d/Makefile

@@ -147,7 +147,7 @@ endif
 # ARCHER (also works for HECToR)
 # ========
 ifeq ($(strip $(COMPILER)),archer)
-  FFLAGS = -O3
+  FFLAGS = -O3 -hipa2
   ifeq ($(strip $(MODE)),debug)
     FFLAGS = -O0 -g -ea -ec -eC -eD -eI -en -hfp_trap -Ktrap=fp -m0 -M1438,7413
   endif

epoch1d/src/constants.F90

@@ -103,6 +103,27 @@ MODULE constants
   INTEGER, PARAMETER :: c_err_io_error = 2**15
   INTEGER, PARAMETER :: c_err_bad_setup = 2**16
   INTEGER, PARAMETER :: c_err_window = 2**17
+  INTEGER, PARAMETER :: c_err_max = 17
+
+  CHARACTER(LEN=*), PARAMETER :: c_err_char(0:c_err_max) = (/ &
+      'unknown_block           ', &
+      'unknown_element         ', &
+      'preset_element          ', &
+      'preset_element_use_later', &
+      'bad_value               ', &
+      'missing_elements        ', &
+      'terminate               ', &
+      'required_element_not_set', &
+      'pp_options_missing      ', &
+      'bad_array_length        ', &
+      'other                   ', &
+      'warn_bad_value          ', &
+      'generic_warning         ', &
+      'generic_error           ', &
+      'pp_options_wrong        ', &
+      'io_error                ', &
+      'bad_setup               ', &
+      'window                  '/)
 
   INTEGER, PARAMETER :: c_ds_first = 1
   INTEGER, PARAMETER :: c_ds_last = 2
@@ -293,9 +314,23 @@ MODULE constants
   INTEGER, PARAMETER :: c_pt_species = 9
   INTEGER, PARAMETER :: c_pt_subset = 10
   INTEGER, PARAMETER :: c_pt_default_constant = 11
+  INTEGER, PARAMETER :: c_pt_max = 11
   INTEGER, PARAMETER :: c_pt_bad = 1024
   INTEGER, PARAMETER :: c_pt_null = 1025
 
+  CHARACTER(LEN=*), PARAMETER :: c_pt_char(c_pt_max) = (/ &
+      'variable        ', &
+      'constant        ', &
+      'operator        ', &
+      'function        ', &
+      'parenthesis     ', &
+      'separator       ', &
+      'character       ', &
+      'deck_constant   ', &
+      'species         ', &
+      'subset          ', &
+      'default_constant'/)
+
   ! Opcode constants
   INTEGER, PARAMETER :: c_opcode_plus = 1
   INTEGER, PARAMETER :: c_opcode_minus = 2

epoch1d/src/deck/deck.F90

@@ -538,6 +538,7 @@ RECURSIVE SUBROUTINE read_deck(filename, first_call, deck_state_in)
       deck_values(2)%value = ''
       slen = 1
       line = 1
+      deck_line_number = '0'
       column = 0
 
       ! Use non-advancing IO to pop characters off the deck file one at a time
@@ -558,6 +559,7 @@ RECURSIVE SUBROUTINE read_deck(filename, first_call, deck_state_in)
           got_eof = .TRUE.
           column = 0
           line = line + 1
+          CALL integer_as_string(line - 1, deck_line_number)
         ELSE
           got_eor = .FALSE.
           column = column + 1
@@ -667,6 +669,7 @@ RECURSIVE SUBROUTINE read_deck(filename, first_call, deck_state_in)
           END IF
           continuation = .FALSE.
           line = line + 1
+          CALL integer_as_string(line - 1, deck_line_number)
           column = 0
         END IF
 
@@ -678,6 +681,7 @@ RECURSIVE SUBROUTINE read_deck(filename, first_call, deck_state_in)
               io = io_units(iu)
               WRITE(io,*)
               WRITE(io,*) '*** ERROR ***'
+              WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
               IF (flip > 1) THEN
                 WRITE(io,*) 'Whilst reading ',TRIM(deck_values(1)%value) &
                     // ' = ' // TRIM(deck_values(2)%value(1:pos-1))
@@ -847,6 +851,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
             io = io_units(iu)
             WRITE(io,*)
             WRITE(io,*) '*** WARNING ***'
+            WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
             WRITE(io,*) 'The block "' // TRIM(value) &
                 // '" cannot be set because'
             WRITE(io,*) 'the code has not been compiled with the correct ' &
@@ -861,6 +866,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
             io = io_units(iu)
             WRITE(io,*)
             WRITE(io,*) '*** WARNING ***'
+            WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
             WRITE(io,*) 'The block "' // TRIM(value) &
                 // '" cannot be set because'
             WRITE(io,*) 'the code has not been compiled with the correct ' &
@@ -875,6 +881,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
             io = io_units(iu)
             WRITE(io,*)
             WRITE(io,*) '*** WARNING ***'
+            WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
             WRITE(io,*) 'Unknown block "' // TRIM(value) &
                 // '" in input deck, ignoring', deck_state
           END DO
@@ -903,6 +910,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
         WRITE(du,*)
         IF (err_count /= 0) THEN
           WRITE(du,*) '*** WARNING ***'
+          WRITE(du,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(du,*) 'Block "' // TRIM(ADJUSTL(value)) // '" contains errors'
           WRITE(du,*)
         END IF
@@ -919,6 +927,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** ERROR ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Value "' // TRIM(value) // '" in element "' &
               // TRIM(element) // '" is invalid and cannot be parsed.'
           WRITE(io,*) 'Code will terminate'
@@ -947,6 +956,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Unrecognised element "' // TRIM(element) &
               // '" in input deck.'
           WRITE(io,*) 'Code will continue to run, but behaviour is undefined'
@@ -960,6 +970,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Element "' // TRIM(element) &
               // '" is set multiple times in this deck.'
           WRITE(io,*) 'Code will continue using first value in deck'
@@ -973,6 +984,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Element "' // TRIM(element) &
               // '" is set multiple times in this deck.'
           WRITE(io,*) 'Code will continue using last value in deck'
@@ -986,6 +998,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** ERROR ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Value "' // TRIM(value) // '" in element "' &
               // TRIM(element) // '" is'
           WRITE(io,*) 'invalid or could not be parsed. Code will terminate.'
@@ -1000,6 +1013,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Value "' // TRIM(value) // '" in element "' &
               // TRIM(element) // '" is'
           WRITE(io,*) 'invalid or could not be parsed. Code will use', &
@@ -1015,6 +1029,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** ERROR ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Value "' // TRIM(value) // '" in element "' &
               // TRIM(element) // '" cannot be'
           WRITE(io,*) 'set because a prerequisite element "' &
@@ -1031,6 +1046,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'The element "' // TRIM(element) // '" of block "' &
               // TRIM(current_block_name) // '" cannot be set'
           WRITE(io,*) 'because the code has not been compiled with the ' &
@@ -1048,6 +1064,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) TRIM(extended_error_string)
           WRITE(io,*)
         END DO
@@ -1059,6 +1076,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** ERROR ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) TRIM(extended_error_string)
           WRITE(io,*)
         END DO
@@ -1071,6 +1089,7 @@ SUBROUTINE handle_deck_element(element, value, errcode_deck)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** ERROR ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'You have managed to find an impossible situation in ' &
               // 'this code.'
           WRITE(io,*) 'Good for you. Just because of that, the code will ' &

epoch1d/src/deck/deck_constant_block.f90

@@ -115,6 +115,7 @@ FUNCTION constant_block_handle_element(element, value) RESULT(errcode)
         DO iu = 1, nio_units ! Print to stdout and to file
           io = io_units(iu)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'The constant block variable "' // TRIM(element) &
               // '" conflicts with a'
           WRITE(io,*) 'built-in constant name. It will be ignored.'

epoch1d/src/deck/deck_dist_fn_block.f90

@@ -167,6 +167,7 @@ FUNCTION dist_fn_block_handle_element(element, value) RESULT(errcode)
           DO iu = 1, nio_units ! Print to stdout and to file
             io = io_units(iu)
             WRITE(io,*) '*** ERROR ***'
+            WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
             WRITE(io,*) 'Distribution functions can only be 1D, 2D or 3D'
           END DO
         END IF
@@ -277,6 +278,7 @@ FUNCTION dist_fn_block_handle_element(element, value) RESULT(errcode)
             DO iu = 1, nio_units ! Print to stdout and to file
               io = io_units(iu)
               WRITE(io,*) '*** ERROR ***'
+              WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
               WRITE(io,*) 'Unable to apply dist_fn to non existant species ', &
                   ispecies
             END DO

epoch1d/src/deck/deck_injector_block.f90

@@ -99,6 +99,7 @@ FUNCTION injector_block_handle_element(element, value) RESULT(errcode)
         DO iu = 1, nio_units ! Print to stdout and to file
           io = io_units(iu)
           WRITE(io,*) '*** ERROR ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Cannot set injector properties before boundary is set'
         END DO
         CALL abort_code(c_err_required_element_not_set)

epoch1d/src/deck/deck_io_block.F90

@@ -329,6 +329,7 @@ FUNCTION io_block_handle_element(element, value) RESULT(errcode)
             DO iu = 1, nio_units ! Print to stdout and to file
               io = io_units(iu)
               WRITE(io,*) '*** ERROR ***'
+              WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
               WRITE(io,*) 'Cannot have multiple "rolling_restart" blocks.'
             END DO
           END IF
@@ -387,6 +388,7 @@ FUNCTION io_block_handle_element(element, value) RESULT(errcode)
         DO iu = 1, nio_units ! Print to stdout and to file
           io = io_units(iu)
           WRITE(io,*) '*** ERROR ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'The "extended_io_file" option is no longer supported.'
           WRITE(io,*) 'Please use the "import" directive instead'
         END DO
@@ -433,6 +435,7 @@ FUNCTION io_block_handle_element(element, value) RESULT(errcode)
             DO iu = 1, nio_units ! Print to stdout and to file
               io = io_units(iu)
               WRITE(io,*) '*** ERROR ***'
+              WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
               WRITE(io,*) 'Output block "' // TRIM(value) &
                   // '" already defined.'
             END DO
@@ -728,6 +731,7 @@ FUNCTION io_block_handle_element(element, value) RESULT(errcode)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Element "' // TRIM(ADJUSTL(element)) &
               // '" not ', 'allowed in an unnamed output block.'
           WRITE(io,*) 'It has been ignored.'
@@ -740,6 +744,7 @@ FUNCTION io_block_handle_element(element, value) RESULT(errcode)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Element "' // TRIM(ADJUSTL(element)) &
               // '" not ', 'allowed in a named output block.'
           WRITE(io,*) 'It has been ignored.'
@@ -752,6 +757,7 @@ FUNCTION io_block_handle_element(element, value) RESULT(errcode)
           io = io_units(iu)
           WRITE(io,*)
           WRITE(io,*) '*** WARNING ***'
+          WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
           WRITE(io,*) 'Element "' // TRIM(ADJUSTL(element)) &
               // '" should be moved to ', 'an "output_global" block.'
           WRITE(io,*) 'Its value will be applied to all output blocks.'
@@ -841,6 +847,7 @@ FUNCTION io_block_handle_element(element, value) RESULT(errcode)
             DO iu = 1, nio_units ! Print to stdout and to file
               io = io_units(iu)
               WRITE(io,*) '*** WARNING ***'
+              WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
               WRITE(io,*) 'Attempting to set per species property for "' &
                   // TRIM(element) // '" which'
               WRITE(io,*) 'does not support this property. Ignoring.'
@@ -889,6 +896,7 @@ FUNCTION io_block_handle_element(element, value) RESULT(errcode)
             DO iu = 1, nio_units ! Print to stdout and to file
               io = io_units(iu)
               WRITE(io,*) '*** WARNING ***'
+              WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
               WRITE(io,*) 'Attempting to set average property for "' &
                   // TRIM(element) // '" which'
               WRITE(io,*) 'does not support this property. Ignoring.'
@@ -907,6 +915,7 @@ FUNCTION io_block_handle_element(element, value) RESULT(errcode)
               DO iu = 1, nio_units ! Print to stdout and to file
                 io = io_units(iu)
                 WRITE(io,*) '*** WARNING ***'
+                WRITE(io,*) 'Input deck line number ', TRIM(deck_line_number)
                 WRITE(io,*) 'Error occurred whilst assigning the averaging ', &
                     'dumpmask of the variable'
                 WRITE(io,*) '"' // TRIM(element) &