Merge pull request #22 from Mistra-UEA/master

Sync with Mistra-UEA (2 Oct 2020)

param/param_jjb1

@@ -61,4 +61,7 @@ else
     echo "The executable does not exist, installation aborted" && exit 1
 fi
 
-echo " -- End of param script -- "
+# Move output files in OUTDIR
+mv fort.* *.out *.nc rst*.dat $OUTDIR
+
+echo " -- End of param script (end of the run) -- "

src/Makefile

@@ -65,7 +65,7 @@ global_params.o global_params.mod: global_params.f90 Makefile
 	rm -f global_params.mod
 	$(FC) $(CFLAGS) -c $<
 
-common_modules.o gas_common.mod: common_modules.f global_params.mod Makefile
+common_modules.o gas_common.mod: common_modules.f90 global_params.mod Makefile
 	rm -f gas_common.mod
 	$(FC) $(CFLAGS) -c $<
 
@@ -114,7 +114,7 @@ utils.o: utils.f90 config.mod file_unit.mod gas_common.mod global_params.mod \
 	Makefile
 	$(FC) $(CFLAGS) -o $(@F) -c $<
 
-str.o: str.f config.mod constants.mod gas_common.mod global_params.mod Makefile
+str.o: str.f90 config.mod constants.mod gas_common.mod global_params.mod Makefile
 	$(FC) $(CFLAGS) -o $(@F) -c $<
 
 radinit.o: radinit.f90 config.mod constants.mod file_unit.mod global_params.mod precision.mod Makefile

src/activity.f90

@@ -389,8 +389,8 @@ subroutine calpar(Iflag,NC,NA,T,b0,b1,C0,C1,omega,xs)
   integer,       intent(in) :: Iflag(NC,NA)
 
 ! Array arguments with intent(out):
-  real(kind=dp), dimension(nc,na), intent(out) :: b0, b1
-  real(kind=dp), dimension(nc,na), intent(out) :: c0, c1
+  real(kind=dp), intent(out) :: b0(nc,na), b1(nc,na)
+  real(kind=dp), intent(out) :: c0(nc,na), c1(nc,na)
 
   real(kind=dp), intent(out) :: omega(nc,na)
   real(kind=dp), intent(out) :: xs(11)

src/common_modules.f90

@@ -0,0 +1,140 @@
+!
+! Copyright 2016-2017 Josue Bock
+!
+! Licensed under the EUPL, Version 1.1 only (the "Licence");
+!
+! You may not use this work except in compliance with the Licence.
+! You may obtain a copy of the Licence at:
+!   https://joinup.ec.europa.eu/software/page/eupl
+!
+! Unless required by applicable law or agreed to in writing,
+! software distributed under the Licence is distributed on an
+! "AS IS" basis, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
+! either express or implied.
+!
+! See the Licence for the specific language governing permissions
+! and limitations under the Licence.
+
+
+! In this file are all modules which replace old common block
+
+module gas_common
+
+! Description :
+! -----------
+!    gas_common holds the variables related to gas phase species
+
+! Author :
+! ------
+!    Josué Bock
+
+! Modifications :
+! -------------
+!  26-Sep-2020   Josue Bock   Fortran 90 conversion (straightforward)
+
+! == End of header =============================================================
+
+
+! Declarations :
+! ------------
+! Modules used:
+
+  USE global_params, ONLY : &
+! Imported Parameters:
+       n
+
+  USE precision, ONLY : &
+! Imported Parameters:
+       dp
+
+  implicit none
+
+  save
+
+! GASES (non radical)
+  ! Numbers of gas species
+  integer :: j1                             ! Number of non radical gases actually used
+  integer :: j1_br, j1_cl, j1_iod, j1_halo  ! Number of brominated / chlorinated / ...  gases
+
+  ! Indexes
+  integer, allocatable :: ind_gas (:)        ! User defined index for non radical gas species
+  integer, allocatable :: ind_gas_rev (:)    ! revert old hard coded indexes. Should disappear soon...
+  integer, allocatable :: ind_gas_br  (:,:)  ! Same for halogenated species:
+  integer, allocatable :: ind_gas_cl  (:,:)  !   - first column holds stoechiometric nb
+!  integer, allocatable :: ind_gas_iod (:,:)  !   - second column holds the (compressed) index
+
+  ! Logical
+  logical, allocatable :: gas_is_halo (:)    ! True is halogenated (Br, Cl, I) gas. Used to initialise differently these gases.
+
+  ! Names
+  character(len=12),  allocatable :: gas_name (:)
+  character(len=100), allocatable :: gas_name_long (:)
+
+  ! Data:
+  !   - molar mass of non radical gas [kg/mol]
+  real (kind=dp), allocatable :: gas_mass (:)
+  !   - concentration of non radical gas [mol/m3]
+  real (kind=dp), allocatable :: s1 (:,:)
+  !   - user defined initial concentrations at ground and top level [ppb]
+  real (kind=dp), allocatable :: s1_init_grd(:)
+  real (kind=dp), allocatable :: s1_init_top(:)
+  !   - ground emission of the gas []
+  real (kind=dp), allocatable :: es1 (:)
+  real (kind=dp), allocatable :: vg (:)
+
+! Conversion tables, gas species
+  ! KPP to Mistra: in Mistra order
+  integer, allocatable :: gas_k2m_g (:)
+  integer, allocatable :: gas_k2m_a (:)
+  integer, allocatable :: gas_k2m_t (:)
+  ! Mistra to KPP: in KPP order
+  integer, allocatable :: gas_m2k_g (:,:)
+  integer, allocatable :: gas_m2k_a (:,:)
+  integer, allocatable :: gas_m2k_t (:,:)
+
+
+
+! RADICALS (gas phase)
+  ! Numbers of radical species
+  integer :: j5                            ! Number of radicals actually used
+  integer :: j5_br, j5_cl, j5_iod, j5_halo ! Number of brominated / chlorinated / ...  radicals
+
+  ! Indexes
+  integer, allocatable :: ind_rad (:)        ! User defined index for radical species
+  integer, allocatable :: ind_rad_br  (:,:)  ! Same for halogenated species:
+  integer, allocatable :: ind_rad_cl  (:,:)  !   - first column holds stoechiometric nb
+!  integer, allocatable :: ind_rad_iod (:,:)  !   - second column holds the (compressed) index
+
+  ! Logical
+!  logical, allocatable :: rad_is_halo (:)
+
+  ! Names
+  character(len=12),  allocatable :: rad_name (:)
+  character(len=100), allocatable :: rad_name_long (:)
+
+  ! Data:
+  !   - molar mass of radical [kg/mol]
+  real (kind=dp), allocatable :: rad_mass (:)
+  !   - concentration of radical [mol/m3]
+  real (kind=dp), allocatable :: s3 (:,:)
+
+! Conversion tables, raedical species
+  ! KPP to Mistra: in Mistra order
+  integer, allocatable :: rad_k2m_g (:)
+  integer, allocatable :: rad_k2m_a (:)
+  integer, allocatable :: rad_k2m_t (:)
+  ! Mistra to KPP: in KPP order
+  integer, allocatable :: rad_m2k_g (:,:)
+  integer, allocatable :: rad_m2k_a (:,:)
+  integer, allocatable :: rad_m2k_t (:,:)
+
+
+! FIXED species which are exchanged
+  integer, parameter :: j4 = 1
+  real (kind=dp) :: fix_mass(j4)
+  data fix_mass /32.d-3/
+
+  real (kind=dp), allocatable :: vmean_init(:)
+  real (kind=dp), allocatable :: vmean(:,:)
+
+end module gas_common