fixed typos and spellings

src/benthic_base.F90

@@ -174,7 +174,7 @@ subroutine do_bottom(self,_ARGUMENTS_DO_BOTTOM_)
          if (self%resuspension) then
             ! The resuspension rate (1/d) is a linear function of shear stress (Pa)
             ! Prefactor "er" (1/d) can be interpreted as c*M/rho_sed*v_crit^2, with:
-            ! - c (1/m) = ratio between tracer concentration at the sediment surface and sediemnt-column-integrated tracer
+            ! - c (1/m) = ratio between tracer concentration at the sediment surface and sediment-column-integrated tracer
             !   (e.g., c=100 for an exponential profile with penetration depth of 1 cm)
             ! - M = the erosion rate in g*s/m4 (Puls & Suendermann 1990: M=100)
             ! - rho_sed = dry mass of sediment per total volume at the sediment surface. This is grain density (2650 kg/m3 for quartz) multiplied by (1-porosity)

src/benthic_column.F90

@@ -65,12 +65,12 @@ subroutine initialize(self,configunit)
       ! Create bioturbation submodel and provide it with parameters
       ! Currently the bioturbation logic must be separate from type_ersem_benthic_column to avoid circular dependencies.
       ! This is because type_ersem_benthic_column provides the max column depth, which is used to compute food for
-      ! benthic fauna, which in turn results in the aggrege biturbation/bioirrigation activity.
+      ! benthic fauna, which in turn results in the aggrege bioturbation/bioirrigation activity.
       allocate(bioturbation)
 
       ! Bioturbation
       call self%get_parameter(bioturbation%Etur,'Etur','m^2/d','basal bioturbation rate')
-      call self%get_parameter(bioturbation%mtur,'mtur','-','maximum relative turbation enhancement')
+      call self%get_parameter(bioturbation%mtur,'mtur','-','maximum relative bioturbation enhancement')
       call self%get_parameter(bioturbation%htur,'htur','mg C/m^2/d','Michaelis-Menten constant for bioturbation')
       call self%get_parameter(bioturbation%dtur,'dtur','m','bioturbation depth')
 

src/benthic_column_dissolved_matter.F90

@@ -406,13 +406,13 @@ subroutine process_constituent(self,_ARGUMENTS_DO_BOTTOM_,info)
          ! Constraints: diffusion of the residual across bottom of benthic column must be zero (i.e., zero gradient), and at the surface of the benthic
          ! column the concentration of the residual must equal zero (i.e., equilibrium holds at the very surface of the column).
          ! Since we do not know anything about the processes responsible for the residual, let's assume their contribution
-         ! in the past was a constant production or destruction per unit sediment volume thoughout the entire column.
+         ! in the past was a constant production or destruction per unit sediment volume throughout the entire column.
          ! That is, production (#/m^2/d) in the three layers was P_int*d1/d3, P_int(d2-d1)/d3, P_int(d3-d2)/d3.
          ! If we would know P_int, we could supply those rates along with zero surface concentration to "compute_equilibrium_profile"
          ! to derive the residual profile. By checking the equations in compute_equilibrium_profile, we can verify that the resulting bottom concentration
          ! and layer integral are both proportional to P_int. Thus, can can simply supply d1, d2-d1, d3-d2 to
          ! "compute_equilibrium_profile", and find the additional scale factor P_int/d3 by demanding that the sum of layer integrals is
-         ! equal to the known residual mass. That is, P_int/d3 equals the ratio of residual mass to the sum of normalized layer integrals
+         ! equal to the known residual mass. That is, P_int/d3 equals the ratio of residual mass to the sum of normalised layer integrals
          ! computed for layer production terms d1, d2-d1, d3-d2. As we are assuming the residual profile was previously an equilibrium
          ! profile, the necessary depth-integrated production rate P_int must equal the exchange across the surface, i.e., diffusivity*gradient.
          ! Thus, we can now simply add the P_int as a additional surface exchange term, accounting for the move towards equilibrium.

src/benthic_column_particulate_matter.F90

@@ -152,7 +152,7 @@ module ersem_benthic_column_particulate_matter
 !                              = D C0/z_mean
 !
 ! However, we KNOW that diffusion witin the column should not affect the mass integral. Why is this then non-zero?
-! The reason for this is that we have not accounted for the no-flux boundary conditions. As a result, we are implicity
+! The reason for this is that we have not accounted for the no-flux boundary conditions. As a result, we are implicitly
 ! using a non-zero inward flux at the surface that is determined by the gradient:
 !
 !   -D d/dz C(0) = D C0/z_mean exp(-z/z_mean) = D C0/z_mean
@@ -650,7 +650,7 @@ subroutine layer_initialize_constituent(self,info,name,units,long_name,remin,q10
 
       ! Register the only diagnostic for this constituent: mass integrated over desired depth interval.
       ! This diagnostic acts like a state variable, so that other models can provides sinks and sources.
-      ! These are converted by the "change_processor" submodel into appropriate changes in colmn-integrated mass and penetration depth.
+      ! These are converted by the "change_processor" submodel into appropriate changes in column-integrated mass and penetration depth.
       call self%register_diagnostic_variable(info%id_local,name,units//'/m^2',long_name, &
          act_as_state_variable=.true.,domain=domain_bottom,output=output_none,source=source_do_bottom)
       call self%add_to_aggregate_variable(aggregate_target,info%id_local,aggregate_scale_factor)
@@ -958,11 +958,11 @@ real(rk) function partQ( d_pen, d_top, d_bot, d_max )
       if ( d_pen>0._rk ) then
          ! Penetration depth > 0: integrate idealized [exponential] distribution over desired depth interval.
 
-         ! Compute normalization factor: integral of exponential distribution from surface to bottom of column.
+         ! Compute normalisation factor: integral of exponential distribution from surface to bottom of column.
          ! This interval must by definition contain 100 % of the modelled mass.
          norm = 1._rk - exp(-d_max/d_pen)
 
-         ! Compute integral of exponential over desired depth interval and normalize to obtain fraction between 0 and 1.
+         ! Compute integral of exponential over desired depth interval and normalise to obtain fraction between 0 and 1.
          partQ = (exp(-d_top1/d_pen) - exp(-d_bot1/d_pen)) / norm
       else
          ! Penetration depth = 0 (or < 0, but that's an artefact): all mass in surface layer of zero thickness.

src/benthic_fauna.F90

@@ -174,7 +174,7 @@ subroutine initialize(self,configunit)
       end do
 
       ! Set food-source-specific assimilation inefficiency.
-      ! (fraction of ingested frood going to faeces)
+      ! (fraction of ingested food going to faeces)
       do ifood=1,self%nfood
          write (index,'(i0)') ifood
          call self%get_parameter(foodispom,'food'//trim(index)//'ispom','','food source '//trim(index)//' is detritus',default=.false.)

src/benthic_nitrogen_cycle.F90

@@ -65,7 +65,7 @@ subroutine initialize(self,configunit)
       call self%get_parameter(self%xn2,   'xn2','mol O_2/mol N','oxygen demand fulfilled by reduction of nitrate to dinitrogen gas')
       call self%get_parameter(self%hM3G4,'hM3G4','mmol N/m^3','Michaelis-Menten constant for nitrate limitation of denitrification')
 
-      ! Create our own state avriable for dinitrogen gas
+      ! Create our own state variable for dinitrogen gas
       ! (only to track its total production, which can then be considered in nitrogen mass balance)
       call self%register_state_variable(self%id_G4n,'G4n','mmol N/m^2','dinitrogen gas')
       call self%add_to_aggregate_variable(standard_variables%total_nitrogen,self%id_G4n)
@@ -80,7 +80,7 @@ subroutine initialize(self,configunit)
       call self%register_diagnostic_variable(self%id_jM3G4n,'jM3G4n','mmol N/m^2/d','layer 2 de-nitrification flux',source=source_do_bottom)
 
       ! Create a child model that provides a K6 diagnostic. Other models (e.g., anaerobic bacteria) can attach to that to provide it with sink/source terms.
-      ! In turn, these are then picked up by this model (type_ersem_benthic_nitrogen_cycle) and translated into chnages in NO3 and O2.
+      ! In turn, these are then picked up by this model (type_ersem_benthic_nitrogen_cycle) and translated into changes in NO3 and O2.
       allocate(child)
       call self%add_child(child,'K6_calculator',configunit=configunit)
       call child%register_diagnostic_variable(child%id_K6,'K6','mmol O_2/m^2','oxygen debt due to anaerobic respiration',act_as_state_variable=.true.,output=output_none,domain=domain_bottom,source=source_none)

src/carbonate.F90

@@ -57,14 +57,14 @@ subroutine initialize(self,configunit)
          call self%register_state_variable(self%id_TA,'TA','mmol/m^3','total alkalinity',2300._rk,minimum=1.e-4_rk, &
             standard_variable=standard_variables%alkalinity_expressed_as_mole_equivalent)
       else
-         ! Total alkalinity is a diagnostic variable, parameterized as function of salinity and temperature.
+         ! Total alkalinity is a diagnostic variable, parameterised as function of salinity and temperature.
          ! since ERSEM22.11 Total alkalinity is expressed in mmol/m3 instead of umol/kg
          call self%register_diagnostic_variable(self%id_TA_diag,'TA','mmol/m^3','total alkalinity', act_as_state_variable=.true., &
             standard_variable=standard_variables%alkalinity_expressed_as_mole_equivalent)
 
          call self%get_parameter(iswbioalk,'iswbioalk','','use bioalkalinity (0: off, 1: on)',default=1,minimum=0,maximum=1)
          if (iswbioalk==1) then
-            ! Register state variable to track "bioalkalinity", i.e., the difference between parameterized
+            ! Register state variable to track "bioalkalinity", i.e., the difference between parameterised
             ! and actual alkalinity that is created by biogeochemical processes modifying alkalinity.
             ! since ERSEM22.11 bioalkalinity is expressed in mmol/m3 instead of umol/kg
             call self%register_state_variable(self%id_bioalk,'bioalk','mmol/m^3','bioalkalinity')
@@ -171,7 +171,7 @@ subroutine do(self,_ARGUMENTS_DO_)
 
          ! Calculate total alkalinity
          if (self%iswtalk/=5) then
-            ! Alkalinity is parameterized as function of salinity and temperature.
+            ! Alkalinity is parameterised as function of salinity and temperature.
             TA = approximate_alkalinity(self%iswtalk,ETW,X1X)
             ! Approximate alkalinity is still in umol kg-1 due to empirical regression
             ! therefore now need to be converted  in mmol m-3
@@ -248,7 +248,7 @@ subroutine do_surface(self,_ARGUMENTS_DO_SURFACE_)
          wnd = max(wnd, 0.0_rk)
 
          if (self%iswtalk/=5) then
-            ! Alkalinity is parameterized as function of salinity and temperature.
+            ! Alkalinity is parameterised as function of salinity and temperature.
             TA = approximate_alkalinity(self%iswtalk,T,S)
             ! Approximate alkalinity is still in umol kg-1 due to empirical regression
             ! therefore now need to be converted  in mmol m-3
@@ -563,7 +563,7 @@ END SUBROUTINE CO2SET
 ! !DESCRIPTION:
 !  TODO - check this.
 !
-! ROUTINE TO CARRY OUT CO2 CALCULATIONS WITH 2 FIXED PARAMETERS ACCORDI
+! ROUTINE TO CARRY OUT CO2 CALCULATIONS WITH 2 FIXED PARAMETERS ACCORDING TO
 ! THE EQUATIONS GIVEN BY PARKS(1969) AND SKIRROW (1975)
 ! WITH ADDITIONS FOR INCLUDING BORON IF BORON=.TRUE.
 !\\
@@ -600,7 +600,7 @@ SUBROUTINE CO2CLC(k0co2,k1co2,k2co2,kb,ICALC,BORON,BTOT,ctot,TA,pH,PCO2,H2CO3,HC
 !  CONDITIONS DO NOT ALLOW FOR CONVERGENCE (IN 3D MODEL THIS IS
 !  LIKELY TO OCCUR NEAR LOW SALINITY REGIONS) THE MODEL WILL
 !  BE STUCK IN THE LOOP.  TO AVOID THIS A CONVERGENCE CONDITION
-!  IS PUT IN PLACE TO SET A FLAGG OF -99 IN THE PH VAR FOR NON CONVEGENCE.
+!  IS PUT IN PLACE TO SET A FLAG OF -99 IN THE PH VAR FOR NON CONVERGENCE.
 !  THE MODEL IS THEN ALLOWED TO CONTINUE. 'COUNTER, C_SW,C_CHECK' ARE
 !  THE LOCAL VARS USED.
 ! C_SW = condition of convergence 0=yes, 1= no
@@ -654,8 +654,8 @@ SUBROUTINE CO2CLC(k0co2,k1co2,k2co2,kb,ICALC,BORON,BTOT,ctot,TA,pH,PCO2,H2CO3,HC
 ! SET COUNTER UPDATE.
             COUNTER=COUNTER+1
 
-! CHECK IF CONVERGENCE HAS OCCURED IN THE NUMBER OF
-! ACCEPTABLE ITTERATIONS.
+! CHECK IF CONVERGENCE HAS OCCURRED IN THE NUMBER OF
+! ACCEPTABLE ITERATIONS.
             if(counter.ge.c_check)then
 !!        IF(MASTER)THEN
 !!! LOG FILE TO SHOW WHEN AND WHERE NON CONVERGENCE OCCURS.

src/dvm_upper_lower_boundaries.F90

@@ -4,7 +4,7 @@
 ! For diel vertical migration of migrating plankton. Calculates an upper and 
 ! lower boundary in the water column, between which the migrator is able to 
 ! be present. Boundaries depend on light levels which can be set by the user
-! or defaul to a maximum light level of -6.5 log W m-2 and a minimum light 
+! or default to a maximum light level of -6.5 log W m-2 and a minimum light 
 ! level of -15 log W m-2
 !
 ! Adapted from code written by Caglar Yumruktepe (NERSC), available at: 
@@ -56,7 +56,7 @@ subroutine initialize(self, configunit)
         call self%get_parameter( self%lower_light,'lower_light','log W m-2','light level for lower isolume',default=-15._rk)
 
         call self%get_parameter(self%nprey,'nprey','','number of prey types',default=1)
-        call self%get_parameter(self%divide_food_by,'divide_food_by','','a likely concentration (e.g. half saturation constant) to normalize food',default=40.0_rk)
+        call self%get_parameter(self%divide_food_by,'divide_food_by','','a likely concentration (e.g. half saturation constant) to normalise food',default=40.0_rk)
         call self%register_diagnostic_variable(self%id_migrator_food,'migrator_food','mmol C/m^3','food availability for the migrators', act_as_state_variable=.true., missing_value=0.0_rk, source=source_do)
         ! Get prey-specific coupling links.
         allocate(self%id_prey(self%nprey))

src/mesozooplankton.F90

@@ -340,7 +340,7 @@ subroutine do(self,_ARGUMENTS_DO_)
             ! Specific mortality (1/d): background mortality + mortality due to oxygen limitation.
             sd = self%sd + (1._rk - eO2)*self%sdo
 
-            ! Compute abolute mortality (mg C/m3/d) from specific mortality and biomass.
+            ! Compute absolute mortality (mg C/m3/d) from specific mortality and biomass.
             rd = sd*cP
 
             ! Assimilation inefficiency (dimensionless):

src/oxygen.F90

@@ -5,7 +5,7 @@ module ersem_oxygen
 ! exchange of oxygen across the water surface.
 
 ! Note: negative oxygen concentrations are permitted.
-! These reflect an oygen debt (e.g., presence of H2S)
+! These reflect an oxygen debt (e.g., presence of H2S)
 ! In this case, oxygen saturation will be zero (not negative!),
 ! while apparent oxygen utilization will still be the difference
 ! between saturation concentration and [negative] oxygen concentration.

src/primary_producer.F90

@@ -55,7 +55,7 @@ module ersem_primary_producer
       type (type_diagnostic_variable_id) :: id_lD      ! Cell-bound calcite - used by calcifiers only
       type (type_diagnostic_variable_id) :: id_O3L2c   ! Calcification
       type (type_diagnostic_variable_id) :: id_fPIRPc,id_fPIRPn,id_fPIRPp,id_fPIRPs  ! Total loss to Particulate detritus
-      type (type_diagnostic_variable_id) :: id_fPIR1c,id_fPIR1n,id_fPIR1p ! Total loss to labile dissovled detritus
+      type (type_diagnostic_variable_id) :: id_fPIR1c,id_fPIR1n,id_fPIR1p ! Total loss to labile dissolved detritus
       type (type_diagnostic_variable_id) :: id_fPIR2c  ! Total loss to non-labile dissovled detritus
       type (type_diagnostic_variable_id) :: id_iNI
 
@@ -437,7 +437,7 @@ subroutine do(self,_ARGUMENTS_DO_)
 
             ! Calculate nutrient limitation impact on rain ratio:
             t=max(0._rk,ETW)  ! this is to avoid funny values of rain ratio when ETW ~ -2 degrees
-            RainR = RainR * min((1._rk-iNp),iNn) * (t/(2._rk+t)) !* max(1.,P2c(I)/2.) removd as P2 is a broad class not just calicifiers
+            RainR = RainR * min((1._rk-iNp),iNn) * (t/(2._rk+t)) !* max(1.,P2c(I)/2.) removed as P2 is a broad class not just calicifiers
             RainR = max(RainR,0.005_rk)
 
             ! Compute virtual calcite attached to live cells. It is virtual in the sense that it has not been subtracted
@@ -539,7 +539,7 @@ subroutine do(self,_ARGUMENTS_DO_)
 
          ! Net nitrogen uptake
 
-         ! maximum acheivable uptake of nitrate  (mmol N m-3 d-1)
+         ! maximum achievable uptake of nitrate  (mmol N m-3 d-1)
          rumn3 = self%qun3 * N3nP * c
 
          ! Maximum achievable uptake of ammonium (mmol N m-3 d-1)