tools/mech_converter.py no longer creates ro2-rates.f90, which needs adding in at compilation time. Instead, it creates mechanism.ro2, which is read in at run-time. This commit contains all the changes to the testing and reference outputs to match this change.

Author: Sam Cox

src/atchem2.f90

@@ -198,6 +198,9 @@ end subroutine FCVFUN
   write (*, '(A, I0)') ' Species requiring detailed rate output (number of species found): ', size( detailedRatesSpeciesName )
   write (*,*)
 
+  ! Read in the numbers of RO2 species from mechanism.ro2
+  call readRO2species()
+
   ! Read in and set solver parameters
   call set_solver_parameters( getParametersFromFile( trim( param_dir ) // "/solver.parameters" ) )
   write (*,*)

src/dataStructures.f90

@@ -236,6 +236,7 @@ module env_vars_mod
   real(kind=DP), allocatable :: envVarX (:,:), envVarY (:,:)
   integer(kind=NPI), allocatable :: envVarNumberOfPoints(:)
   real(kind=DP) :: ro2
+  integer(kind=NPI), allocatable :: ro2Numbers(:)
 
 end module env_vars_mod
 

src/inputFunctions.f90

@@ -1326,6 +1326,41 @@ subroutine readSpeciesConstraints( t, y )
     return
   end subroutine readSpeciesConstraints
 
+  ! ----------------------------------------------------------------- !
+  ! Read in the contents of model/configuration/ro2-rates.list and add
+  ! its contents to the variable ro2Numbers
+  subroutine readRO2species()
+    use types_mod
+    use env_vars_mod, only : ro2Numbers
+    use storage_mod, only : maxFilepathLength
+    use directories_mod, only : param_dir
+    implicit none
+
+    integer(kind=NPI) :: j, numberOfRO2Species
+    character(len=maxFilepathLength) :: fileLocation
+
+    write (*, '(A)') ' Reading ro2 numbers from mechanism.ro2...'
+    fileLocation=trim( param_dir ) // '/mechanism.ro2'
+
+    ! Read in ro2 species numbers from model/configuration/mechanism.ro2
+    ! to ro2Numbers
+
+    call inquire_or_abort( fileLocation, 'readSpecies()')
+    numberOfRO2Species = count_lines_in_file( fileLocation, .true. )
+    allocate(ro2Numbers(numberOfRO2Species))
+
+    open (10, file=fileLocation) ! input file
+    ! skip first line
+    read (10,*)
+    do j = 1, numberOfRO2Species
+      read (10,*) ro2Numbers(j)
+    end do
+    close (10, status='keep')
+    write (*, '(A)') ' Finished reading ro2 numbers.'
+
+    return
+  end subroutine readRO2species
+
   ! ----------------------------------------------------------------- !
   ! Given a filename, count the number of lines. Optional argument
   ! skip_first_line_in ignores the first line if it exists.

src/outputFunctions.f90

@@ -24,13 +24,19 @@ module output_functions_mod
   ! Returns the sum of all ro2 species' concentrations
   pure function ro2Sum( y ) result ( ro2 )
     use types_mod
+    use env_vars_mod, only : ro2Numbers
     implicit none
 
     real(kind=DP), intent(in) :: y(*)
     real(kind=DP) :: ro2
+    integer(kind=NPI) :: i
 
-    include './gen/ro2-rates.f90'
-
+    ro2 = 0.0_DP
+    if ( size( ro2Numbers ) > 0 ) then
+      do i = 1, size( ro2Numbers )
+        ro2 = ro2 + y(ro2Numbers(i))
+      end do
+    end if
     return
   end function ro2Sum
 

src/solverFunctions.f90

@@ -244,7 +244,7 @@ subroutine mechanism_rates( t, y, p )
         j(constrainedPhotoNumbers(i)) = photoRateAtT
       end do
     end if
-
+    !TODO: is this necessary a second time?
     ro2 = ro2sum( y )
 
     include './gen/mechanism-rate-coefficients.f90'

tools/mech_converter.py

@@ -221,24 +221,20 @@ def convert(input_file, output_dir, mc_dir, mcm_dir):
 
         # loop over RO2 and write the necessary line to mechanism-rate-coefficients.f90, using the species number of the RO2
         print 'adding RO2 to src/gen/ro2-rates.f90'
-        with open(os.path.join(output_dir, 'ro2-rates.f90'), 'w') as ro2_file:
-            ro2_file.write("""! Note that this file is generated by tools/mech_converter.py
-! based upon the file tools/mcm_example.fac
-! Any manual edits to this file will be overwritten when
-! calling tools/mech_converter.py
-
-ro2 = 0.00e+00_DP\n""")
+        with open(os.path.join(mc_dir, 'mechanism.ro2'), 'w') as ro2_file:
+            ro2_file.write("""! Note that this file is generated by tools/mech_converter.py based upon the file tools/mcm_example.fac. Any manual edits to this file will be overwritten when calling tools/mech_converter.py
+""")
 
             for ro2List_i in ro2List:
                 for speciesNumber, y in zip(range(1, len(speciesList) + 1), speciesList):
                     if ro2List_i.strip() == y.strip():
-                        ro2_file.write('ro2 = ro2 + y(' + str(speciesNumber) + ')!' + ro2List_i.strip() + '\n')
+                        ro2_file.write(str(speciesNumber) + ' !' + ro2List_i.strip() + '\n')
                         # Exit loop early if species found
                         break
                         # This code only executes if the break is NOT called, i.e. if the loop runs to completion without the RO2 being
                         # found in the species list
                 else:
-                    ro2_file.write('\t ! error RO2 not in mechanism: ' + ro2List_i + '\n')
+                    ro2_file.write('0 ! error RO2 not in mechanism: ' + ro2List_i + '\n')
 
 
     coeffSpeciesList = ['N2', 'O2', 'M', 'RH', 'H2O', 'DEC', 'BLH', 'DILUTE', 'JFAC', 'ROOFOPEN']

travis/run_tests.sh

@@ -137,24 +137,6 @@ $this_file_failures"
     elif [ $exitcode -eq 1 ]; then
       this_test_failures="$this_test_failures
 
-$this_file_failures"
-    else
-      echo 'Numdiff gave an error. Aborting.'
-      exit 1
-    fi
-  done
-
-  # Apply numdiff to ro2-rates.f90.cmp, a special case. If the numdiff gives differences,
-  # then add the numdiff output to $this_test_failures via $this_file_failures,.
-  for filename in $TESTS_DIR/$test/ro2-rates.f90.cmp; do
-    echo 'Checking' $filename
-    this_file_failures=$(test_output_file src/gen/ro2-rates.f90 $filename)
-    exitcode=$?
-    if [ $exitcode -eq 0 ]; then
-      continue
-    elif [ $exitcode -eq 1 ]; then
-      this_test_failures="$this_test_failures
-
 $this_file_failures"
     else
       echo 'Numdiff gave an error. Aborting.'

travis/tests/.gitignore

@@ -4,6 +4,7 @@
 */output/instantaneousRates/*
 */model/configuration/mechanism.prod
 */model/configuration/mechanism.reac
+*/model/configuration/mechanism.ro2
 */model/configuration/mechanism.species
 testsuite.log
 

travis/tests/firstorder/firstorder.out.cmp

@@ -41,6 +41,8 @@ AtChem2 v1.1-dev
  Finished reading which species require detailed rate output.
  Species requiring detailed rate output (number of species found): 2
 
+ Reading ro2 numbers from mechanism.ro2...
+ Finished reading ro2 numbers.
  Reading solver parameters from file...
  ------------------
  Solver parameters:

travis/tests/firstorder/model/configuration/mechanism.ro2.cmp

@@ -0,0 +1 @@
+! Note that this file is generated by tools/mech_converter.py based upon the file tools/mcm_example.fac. Any manual edits to this file will be overwritten when calling tools/mech_converter.py