add some more public definitions

PALEOtoolkit · Jan 14, 2025 · f825e34 · f825e34
1 parent d1529a7
commit f825e34
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Showing 4 changed files with 49 additions and 23 deletions.
diff --git a/src/PALEOboxes.jl b/src/PALEOboxes.jl
@@ -61,7 +61,7 @@ end
 
 @public AbstractCellRange, create_default_cellrange, CellRange, CellRangeColumns
 
-@public Reservoirs, Fluxes, FluxPerturb, Forcings, GridForcings, GridReactions
+@public Reservoirs, Fluxes, FluxPerturb, Forcings, GridForcings, GridReactions, VariableStats
 
 @public AbstractReaction, ReactionBase, get_reaction, set_model_geometry, register_methods!, register_dynamic_methods!,
     add_method_setup!, add_method_initialize!, add_method_do!, create_reaction
@@ -91,7 +91,7 @@ end
 @public AbstractReactionMethod, ReactionMethod
 @public add_method_setup_initialvalue_vars_default!, add_method_initialize_zero_vars_default!, add_method_do_totals_default!
 @public RateStoich, create_ratestoich_method, parse_number_name
-@public LinInterp, interp, value_ad, zero_ad
+@public LinInterp, interp, value_ad, zero_ad, smoothstepcubic
 
 @public AbstractField, Field, get_field, add_field!
 

diff --git a/src/reactioncatalog/Constants.jl b/src/reactioncatalog/Constants.jl
@@ -1,29 +1,53 @@
 module Constants
 
+using ...PALEOboxes: @public
+
+@public k_CtoK, k_molVolIdealGas, k_Rgas, k_Avogadro
+@public age_present_yr, k_solar_presentday, k_secpyr, k_secpday, k_daypyr, k_g_earth, k_SurfAreaEarth
+@public k_atmmixrN2, k_atmmixrO2
+@public STANDARD_ATOMIC_WEIGHTS
+
 # Physical constants
-const k_CtoK          = 273.15     # convert temperature in Celsius to Kelvin
-const k_molVolIdealGas= 22.4136    # l/mol  molar volume of ideal gas at STP (0C, 1 atm)
-const k_Rgas          = 8.3144621  # J/K/mol gas constant
-const k_Avogadro      = 6.0221409e23 # molecules mol-1
+"convert temperature in Celsius to Kelvin"
+const k_CtoK          = 273.15
+"l/mol  molar volume of ideal gas at STP (0C, 1 atm)"
+const k_molVolIdealGas= 22.4136  
+"J/K/mol gas constant"
+const k_Rgas          = 8.3144621
+"molecules mol-1"
+const k_Avogadro      = 6.0221409e23 
 
 # Earth system present-day constants
-const age_present_yr  = 4.5e9       # Age of Earth at present-day
-const k_solar_presentday  = 1368.0 # present-day solar insolation W/m^2
-const k_secpyr        = 3.15569e7  # present-day seconds per year
-const k_secpday       = 24.0*3600.0 # sec per day
-const k_daypyr        = k_secpyr/k_secpday  # days in a year
-const k_g_earth       = 9.80665     # gravitational field strength for Earth m/s^2
-const k_SurfAreaEarth = 5.101e14 # Earth surface area in m
-
-const pCO2atm0        = 280e-6     # ppm pre-industrial pCO2
-const k16_PANtoO      = 3.762      #
-const k18_oceanmass   = 1.397e21   # kg Ocean total mass
-const k_moles1atm     = 1.77e20    # Moles in 1 atm
-const k_preindCO2atm  = 280e-6     # pre-industrial pCO2 (atm)
+"Age of Earth at present-day"
+const age_present_yr  = 4.5e9
+"present-day solar insolation W/m^2"
+const k_solar_presentday  = 1368.0
+"present-day seconds per year"
+const k_secpyr        = 3.15569e7
+"sec per day"
+const k_secpday       = 24.0*3600.0
+"days in a year"
+const k_daypyr        = k_secpyr/k_secpday
+"gravitational field strength for Earth m/s^2"
+const k_g_earth       = 9.80665
+"Earth surface area in m^2"
+const k_SurfAreaEarth = 5.101e14
+
+"ppm pre-industrial pCO2"
+const pCO2atm0        = 280e-6
+# const k16_PANtoO      = 3.762      #
+"COPSE kg Ocean total mass"
+const k18_oceanmass   = 1.397e21
+"COPSE Moles in 1 atm"
+const k_moles1atm     = 1.77e20
+"pre-industrial pCO2 (atm)"
+const k_preindCO2atm  = 280e-6
 
 # Atmospheric composition from Sarmiento & Gruber (2006) Table 3.1.1 (which cites Weast & Astle 1982)
-const k_atmmixrN2    = 0.78084     # N2 atmospheric mixing ratio (moles / moles dry air)
-const k_atmmixrO2    = 0.20946     # O2 atmospheric mixing ratio (moles / moles dry air)
+"present day Earth N2 atmospheric mixing ratio (moles / moles dry air)"
+const k_atmmixrN2    = 0.78084
+"present day O2 atmospheric mixing ratio (moles / moles dry air)"
+const k_atmmixrO2    = 0.20946
 
 """
     STANDARD_ATOMIC_WEIGHTS

diff --git a/src/reactioncatalog/Fluxes.jl b/src/reactioncatalog/Fluxes.jl
@@ -39,7 +39,7 @@ import ...PALEOboxes as PB
 using ...PALEOboxes: @public
 
 import SparseArrays
-import LinearAlgebra # for I
+using LinearAlgebra: I
 
 using ..DocStrings
 
@@ -432,7 +432,7 @@ function prepare_do_transfer(m::PB.ReactionMethod, (input_vardata, output_vardat
         elseif rj.pars.transfer_matrix[] == "Identity"
             input_length == output_length || 
                 PB.infoerror(io, "$(PB.fullname(m)) Identity transfer_matrix but Variable lengths don't match (input, output) $(input_length) != $(output_length)")
-            rj.transfer_matrix_tr = SparseArrays.sparse(LinearAlgebra.I, input_length, output_length).*rj.pars.transfer_multiplier[]
+            rj.transfer_matrix_tr = SparseArrays.sparse(I, input_length, output_length).*rj.pars.transfer_multiplier[]
             println(io, "    using Identity transfer matrix * $(rj.pars.transfer_multiplier[])")
         elseif rj.pars.transfer_matrix[] == "Distribute"
             rj.transfer_matrix_tr = SparseArrays.sparse(ones(input_length, output_length)./output_length.*rj.pars.transfer_multiplier[])

diff --git a/src/reactioncatalog/VariableStats.jl b/src/reactioncatalog/VariableStats.jl
@@ -2,8 +2,10 @@
 module VariableStats
 
 import ...PALEOboxes as PB
+using ...PALEOboxes: @public
 using ..DocStrings
 
+@public ReactionSum, ReactionVectorSum, ReactionWeightedMean, ReactionAreaVolumeValInRange
 
 """
     ReactionSum, ReactionVectorSum