From 2203297777b7eaa075c9b7bc7bc72b830015a96e Mon Sep 17 00:00:00 2001
From: kdorheim <kalyn.dorheim@pnnl.gov>
Date: Mon, 4 Nov 2024 17:44:37 -0500
Subject: [PATCH 1/7] use more conservative code to define a constant

---
 src/ch4_component.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/ch4_component.cpp b/src/ch4_component.cpp
index d20c920e6..36af4d43a 100644
--- a/src/ch4_component.cpp
+++ b/src/ch4_component.cpp
@@ -165,7 +165,7 @@ void CH4Component::run(const double runToDate) {
         << std::endl;
 
 // Permafrost thaw produces CH4 emissions
-#define PG_C_TO_TG_CH4 (1000.0 * 16.04 / 12.01)
+    const double PG_C_TO_TG_CH4 (1000.0 * 16.04 / 12.01);
     const double rh_ch4 =
         core->sendMessage(M_GETDATA, D_RH_CH4).value(U_PGC_YR) * PG_C_TO_TG_CH4;
 

From a46e14e1243f3849e27eb2f08a2dd18a47afe47b Mon Sep 17 00:00:00 2001
From: kdorheim <kalyn.dorheim@pnnl.gov>
Date: Wed, 6 Nov 2024 13:03:28 -0500
Subject: [PATCH 2/7] increase the version index so that it is easier to keep
 track of errors in the gcam coupling

---
 DESCRIPTION             |  2 +-
 NEWS.md                 |  4 ++++
 inst/include/h_util.hpp |  2 +-
 src/oh_component.cpp    | 10 +++++++++-
 4 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b0feeb110..b92616faa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: hector
 Title: The Hector Simple Climate Model
-Version: 3.2.0
+Version: 3.3.0.9999999
 Authors@R: c(person("Kalyn", "Dorheim", 
 	        email = "kalyn.dorheim@pnnl.gov",
 	        role = c("aut", "cre"),
diff --git a/NEWS.md b/NEWS.md
index 101ca4ef9..56bac6059 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# hector 3.3.0.9999999
+
+* under development for the H2 integration, increasing the version index though will be ensure that the right version of hector is being run with gcam
+
 # hector 3.2.0 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10698028.svg)](https://doi.org/10.5281/zenodo.10698028)
 * Correct aerosol forcing coefficients based on Zelinka et al. (2023)
diff --git a/inst/include/h_util.hpp b/inst/include/h_util.hpp
index 11f4c7d56..57d7c8f67 100644
--- a/inst/include/h_util.hpp
+++ b/inst/include/h_util.hpp
@@ -26,7 +26,7 @@
  * \brief The model version number to be included in logs and outputs.
  * \note  Manually update the git tag to match this.
  */
-#define MODEL_VERSION "3.2.0"
+#define MODEL_VERSION "3.3.0.9999999"
 
 #define OUTPUT_DIRECTORY "output/"
 
diff --git a/src/oh_component.cpp b/src/oh_component.cpp
index 418f7ee2c..811a54112 100644
--- a/src/oh_component.cpp
+++ b/src/oh_component.cpp
@@ -149,6 +149,8 @@ void OHComponent::run(const double runToDate) {
   unitval current_nox = NOX_emissions.get(runToDate);
   unitval current_co = CO_emissions.get(runToDate);
   unitval current_nmvoc = NMVOC_emissions.get(runToDate);
+  unitval current_h2 = H2_emissions.get(runToDate);
+
 
   // get this from CH4 component, this is last year's value
   const double previous_ch4 =
@@ -169,7 +171,13 @@ void OHComponent::run(const double runToDate) {
         CNMVOC *
         ((1.0 * +current_nmvoc) -
          NMVOC_emissions.get(NMVOC_emissions.firstdate()).value(U_TG_NMVOC));
-    toh = a + b + c + d;
+    const double e =
+          (-0.00044625) *
+          ((1.0 * +current_h2) -
+           H2_emissions.get(H2_emissions.firstdate()).value(U_TG_H2));
+      
+      
+    toh = a + b + c + d + e;
     H_LOG(logger, Logger::DEBUG)
         << "Year " << runToDate << " toh = " << toh << std::endl;
   }

From ec1511ff1eb341f8cdc2b4244fe6fd548bf12e4b Mon Sep 17 00:00:00 2001
From: kdorheim <kalyn.dorheim@pnnl.gov>
Date: Wed, 6 Nov 2024 13:59:40 -0500
Subject: [PATCH 3/7] implement the H2 coeff for the OH componet as something
 that can be read in from teh ini file

---
 inst/include/component_data.hpp   | 1 +
 inst/include/oh_component.hpp     | 2 ++
 inst/input/hector_ssp119.ini      | 1 +
 inst/input/hector_ssp126.ini      | 2 ++
 inst/input/hector_ssp245.ini      | 2 ++
 inst/input/hector_ssp370.ini      | 2 ++
 inst/input/hector_ssp434.ini      | 2 ++
 inst/input/hector_ssp460.ini      | 2 ++
 inst/input/hector_ssp534-over.ini | 2 ++
 inst/input/hector_ssp585.ini      | 2 ++
 src/oh_component.cpp              | 5 ++++-
 11 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/inst/include/component_data.hpp b/inst/include/component_data.hpp
index f22b6c2c5..e2766a459 100644
--- a/inst/include/component_data.hpp
+++ b/inst/include/component_data.hpp
@@ -281,6 +281,7 @@
 #define D_COEFFICENT_CH4 "CCH4"
 #define D_COEFFICENT_NMVOC "CNMVOC"
 #define D_COEFFICENT_CO "CCO"
+#define D_COEFFICENT_H2 "CH2"
 #define D_EMISSIONS_H2 "H2_emissions"
 
 
diff --git a/inst/include/oh_component.hpp b/inst/include/oh_component.hpp
index 7c39d7623..4b022bc8f 100644
--- a/inst/include/oh_component.hpp
+++ b/inst/include/oh_component.hpp
@@ -71,6 +71,8 @@ class OHComponent : public IModelComponent {
   double CNMVOC; // coefficent for NMVOC
   double CNOX;   // coefficent for NOX
   double CCH4;   // coefficent for CH4
+  double CH2;   // coefficent for CH4
+
 
   // logger
   Logger logger;
diff --git a/inst/input/hector_ssp119.ini b/inst/input/hector_ssp119.ini
index 4a226a9fd..dca52ea81 100644
--- a/inst/input/hector_ssp119.ini
+++ b/inst/input/hector_ssp119.ini
@@ -138,6 +138,7 @@ CNOX=0.0042			; coefficent for NOX
 CCO=-0.000105		; coefficent for CO
 CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
 CCH4=-0.32			; coefficent for CH4
+CH2=-0.00044625 ; coefficent for H2
 
 ;------------------------------------------------------------------------
 [ozone]
diff --git a/inst/input/hector_ssp126.ini b/inst/input/hector_ssp126.ini
index 1b2e92698..7be816dd3 100644
--- a/inst/input/hector_ssp126.ini
+++ b/inst/input/hector_ssp126.ini
@@ -137,6 +137,8 @@ CNOX=0.0042			; coefficent for NOX
 CCO=-0.000105		; coefficent for CO
 CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
 CCH4=-0.32			; coefficent for CH4
+CH2=-0.00044625 ; coefficent for H2
+
 
 ;------------------------------------------------------------------------
 [ozone]
diff --git a/inst/input/hector_ssp245.ini b/inst/input/hector_ssp245.ini
index 30667b965..f44837eaa 100644
--- a/inst/input/hector_ssp245.ini
+++ b/inst/input/hector_ssp245.ini
@@ -138,6 +138,8 @@ CNOX=0.0042			; coefficent for NOX
 CCO=-0.000105		; coefficent for CO
 CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
 CCH4=-0.32			; coefficent for CH4
+CH2=-0.00044625 ; coefficent for H2
+
 
 ;------------------------------------------------------------------------
 [ozone]
diff --git a/inst/input/hector_ssp370.ini b/inst/input/hector_ssp370.ini
index 8f70ff60c..80aa3a484 100644
--- a/inst/input/hector_ssp370.ini
+++ b/inst/input/hector_ssp370.ini
@@ -138,6 +138,8 @@ CNOX=0.0042			; coefficent for NOX
 CCO=-0.000105		; coefficent for CO
 CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
 CCH4=-0.32			; coefficent for CH4
+CH2=-0.00044625 ; coefficent for H2
+
 
 ;------------------------------------------------------------------------
 [ozone]
diff --git a/inst/input/hector_ssp434.ini b/inst/input/hector_ssp434.ini
index bd810229e..532a9e8f1 100644
--- a/inst/input/hector_ssp434.ini
+++ b/inst/input/hector_ssp434.ini
@@ -138,6 +138,8 @@ CNOX=0.0042			; coefficent for NOX
 CCO=-0.000105		; coefficent for CO
 CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
 CCH4=-0.32			; coefficent for CH4
+CH2=-0.00044625 ; coefficent for H2
+
 
 ;------------------------------------------------------------------------
 [ozone]
diff --git a/inst/input/hector_ssp460.ini b/inst/input/hector_ssp460.ini
index 02231d1b1..acffa23cf 100644
--- a/inst/input/hector_ssp460.ini
+++ b/inst/input/hector_ssp460.ini
@@ -138,6 +138,8 @@ CNOX=0.0042			; coefficent for NOX
 CCO=-0.000105		; coefficent for CO
 CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
 CCH4=-0.32			; coefficent for CH4
+CH2=-0.00044625 ; coefficent for H2
+
 
 ;------------------------------------------------------------------------
 [ozone]
diff --git a/inst/input/hector_ssp534-over.ini b/inst/input/hector_ssp534-over.ini
index 278fbc646..68cd577fd 100644
--- a/inst/input/hector_ssp534-over.ini
+++ b/inst/input/hector_ssp534-over.ini
@@ -138,6 +138,8 @@ CNOX=0.0042			; coefficent for NOX
 CCO=-0.000105		; coefficent for CO
 CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
 CCH4=-0.32			; coefficent for CH4
+CH2=-0.00044625 ; coefficent for H2
+
 
 ;------------------------------------------------------------------------
 [ozone]
diff --git a/inst/input/hector_ssp585.ini b/inst/input/hector_ssp585.ini
index 9051bcb93..9abb26ea1 100644
--- a/inst/input/hector_ssp585.ini
+++ b/inst/input/hector_ssp585.ini
@@ -137,6 +137,8 @@ CNOX=0.0042			; coefficent for NOX
 CCO=-0.000105		; coefficent for CO
 CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
 CCH4=-0.32			; coefficent for CH4
+CH2=-0.00044625 ; coefficent for H2
+
 
 ;------------------------------------------------------------------------
 [ozone]
diff --git a/src/oh_component.cpp b/src/oh_component.cpp
index 811a54112..0f0be81a1 100644
--- a/src/oh_component.cpp
+++ b/src/oh_component.cpp
@@ -117,6 +117,9 @@ void OHComponent::setData(const string &varName, const message_data &data) {
     } else if (varName == D_COEFFICENT_NOX) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CNOX = data.getUnitval(U_UNDEFINED);
+    } else if (varName == D_COEFFICENT_H2) {
+      H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
+      CH2 = data.getUnitval(U_UNDEFINED);
     } else {
       H_THROW("Unknown variable name while parsing " + getComponentName() +
               ": " + varName);
@@ -172,7 +175,7 @@ void OHComponent::run(const double runToDate) {
         ((1.0 * +current_nmvoc) -
          NMVOC_emissions.get(NMVOC_emissions.firstdate()).value(U_TG_NMVOC));
     const double e =
-          (-0.00044625) *
+         CH2 *
           ((1.0 * +current_h2) -
            H2_emissions.get(H2_emissions.firstdate()).value(U_TG_H2));
       

From 42479b7473e63349bab49c2fbfc0b06f23f17a71 Mon Sep 17 00:00:00 2001
From: kdorheim <kalyn.dorheim@pnnl.gov>
Date: Mon, 11 Nov 2024 13:13:01 -0500
Subject: [PATCH 4/7] saving wip

---
 R/RcppExports.R               |  7 +++++++
 inst/include/oh_component.hpp |  2 +-
 src/RcppExports.cpp           | 11 +++++++++++
 src/oh_component.cpp          | 10 ++++++++--
 src/rcpp_constants.cpp        |  6 ++++++
 5 files changed, 33 insertions(+), 3 deletions(-)

diff --git a/R/RcppExports.R b/R/RcppExports.R
index e4a7bde03..1f34d9d42 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -4,6 +4,9 @@
 #' @describeIn emissions Emissions hydrogen gas (\code{"Tg H2"})
 NULL
 
+#' @describeIn oh coefficent for the h2 emissions
+NULL
+
 #' @describeIn msgtype Message type for retrieving data from a component
 #' @keywords internal
 GETDATA <- function() {
@@ -1571,6 +1574,10 @@ HEAT_FLUX <- function() {
     .Call('_hector_HEAT_FLUX', PACKAGE = 'hector')
 }
 
+COEFF_H2 <- function() {
+    .Call('_hector_COEFF_H2', PACKAGE = 'hector')
+}
+
 newcore_impl <- function(inifile, loglevel, suppresslogging, name) {
     .Call('_hector_newcore_impl', PACKAGE = 'hector', inifile, loglevel, suppresslogging, name)
 }
diff --git a/inst/include/oh_component.hpp b/inst/include/oh_component.hpp
index 4b022bc8f..f9fc20b2d 100644
--- a/inst/include/oh_component.hpp
+++ b/inst/include/oh_component.hpp
@@ -71,7 +71,7 @@ class OHComponent : public IModelComponent {
   double CNMVOC; // coefficent for NMVOC
   double CNOX;   // coefficent for NOX
   double CCH4;   // coefficent for CH4
-  double CH2;   // coefficent for CH4
+  unitval CH2;   // coefficent for CH4
 
 
   // logger
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
index fd1b82e30..9ade15016 100644
--- a/src/RcppExports.cpp
+++ b/src/RcppExports.cpp
@@ -2627,6 +2627,16 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
+// COEFF_H2
+String COEFF_H2();
+RcppExport SEXP _hector_COEFF_H2() {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    rcpp_result_gen = Rcpp::wrap(COEFF_H2());
+    return rcpp_result_gen;
+END_RCPP
+}
 // newcore_impl
 Environment newcore_impl(String inifile, int loglevel, bool suppresslogging, String name);
 RcppExport SEXP _hector_newcore_impl(SEXP inifileSEXP, SEXP loglevelSEXP, SEXP suppressloggingSEXP, SEXP nameSEXP) {
@@ -3035,6 +3045,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_hector_FLUX_MIXED", (DL_FUNC) &_hector_FLUX_MIXED, 0},
     {"_hector_FLUX_INTERIOR", (DL_FUNC) &_hector_FLUX_INTERIOR, 0},
     {"_hector_HEAT_FLUX", (DL_FUNC) &_hector_HEAT_FLUX, 0},
+    {"_hector_COEFF_H2", (DL_FUNC) &_hector_COEFF_H2, 0},
     {"_hector_newcore_impl", (DL_FUNC) &_hector_newcore_impl, 4},
     {"_hector_shutdown", (DL_FUNC) &_hector_shutdown, 1},
     {"_hector_reset", (DL_FUNC) &_hector_reset, 2},
diff --git a/src/oh_component.cpp b/src/oh_component.cpp
index 0f0be81a1..f53965364 100644
--- a/src/oh_component.cpp
+++ b/src/oh_component.cpp
@@ -57,12 +57,15 @@ void OHComponent::init(Core *coreptr) {
 
   // Inform core what data we can provide
   core->registerCapability(D_LIFETIME_OH, getComponentName());
+  core->registerCapability(D_COEFFICENT_H2, getComponentName());
   // Register inputs accepted.  Note that more than one component
   // can accept an input
   core->registerInput(D_EMISSIONS_CO, getComponentName());
   core->registerInput(D_EMISSIONS_NMVOC, getComponentName());
   core->registerInput(D_EMISSIONS_NOX, getComponentName());
   core->registerInput(D_EMISSIONS_H2, getComponentName());
+  core->registerInput(D_COEFFICENT_H2, getComponentName());
+
 
 }
 
@@ -178,8 +181,8 @@ void OHComponent::run(const double runToDate) {
          CH2 *
           ((1.0 * +current_h2) -
            H2_emissions.get(H2_emissions.firstdate()).value(U_TG_H2));
-      
-      
+
+
     toh = a + b + c + d + e;
     H_LOG(logger, Logger::DEBUG)
         << "Year " << runToDate << " toh = " << toh << std::endl;
@@ -212,6 +215,9 @@ unitval OHComponent::getData(const std::string &varName, const double date) {
     H_ASSERT(date != Core::undefinedIndex(),
              "Date required for NMVOC emissions");
     returnval = NMVOC_emissions.get(date);
+  } else if (varName == D_COEFFICENT_H2) {
+      H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for ECS");
+     returnval = CH2;
   } else if (varName == D_EMISSIONS_H2) {
       H_ASSERT(date != Core::undefinedIndex(), "Date required for H2 emissions");
       returnval = H2_emissions.get(date);
diff --git a/src/rcpp_constants.cpp b/src/rcpp_constants.cpp
index 9b566bf32..fbd22ab57 100644
--- a/src/rcpp_constants.cpp
+++ b/src/rcpp_constants.cpp
@@ -1503,3 +1503,9 @@ String FLUX_INTERIOR() { return D_FLUX_INTERIOR; }
 //' @export
 // [[Rcpp::export]]
 String HEAT_FLUX() { return D_HEAT_FLUX; }
+
+
+//' @describeIn oh coefficent for the h2 emissions
+ //' @export
+ // [[Rcpp::export]]
+ String COEFF_H2() { return D_COEFFICENT_H2; }

From 8ed3f3e78f6dd6b0cf15d03a530a9a4ad776e833 Mon Sep 17 00:00:00 2001
From: kdorheim <kalyn.dorheim@pnnl.gov>
Date: Tue, 26 Nov 2024 18:41:47 -0500
Subject: [PATCH 5/7] Correct warning message

---
 src/oh_component.cpp | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/oh_component.cpp b/src/oh_component.cpp
index f53965364..29dbaee18 100644
--- a/src/oh_component.cpp
+++ b/src/oh_component.cpp
@@ -103,8 +103,8 @@ void OHComponent::setData(const string &varName, const message_data &data) {
       H_ASSERT(data.date != Core::undefinedIndex(), "date required");
       NMVOC_emissions.set(data.date, data.getUnitval(U_TG_NMVOC));
     } else if (varName == D_EMISSIONS_H2) {
-        H_ASSERT(data.date != Core::undefinedIndex(), "date required");
-        H2_emissions.set(data.date, data.getUnitval(U_TG_H2));
+      H_ASSERT(data.date != Core::undefinedIndex(), "date required");
+      H2_emissions.set(data.date, data.getUnitval(U_TG_H2));
     } else if (varName == D_INITIAL_LIFETIME_OH) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       TOH0 = data.getUnitval(U_YRS);
@@ -216,11 +216,11 @@ unitval OHComponent::getData(const std::string &varName, const double date) {
              "Date required for NMVOC emissions");
     returnval = NMVOC_emissions.get(date);
   } else if (varName == D_COEFFICENT_H2) {
-      H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for ECS");
-     returnval = CH2;
+    H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for H2 coefficent");
+    returnval = CH2 ;
   } else if (varName == D_EMISSIONS_H2) {
-      H_ASSERT(date != Core::undefinedIndex(), "Date required for H2 emissions");
-      returnval = H2_emissions.get(date);
+    H_ASSERT(date != Core::undefinedIndex(), "Date required for H2 emissions");
+    returnval = H2_emissions.get(date);
   } else {
     H_THROW("Caller is requesting unknown variable: " + varName);
   }

From 95b31964c1ab4fabd067371cad17abdace0aa582 Mon Sep 17 00:00:00 2001
From: kdorheim <kalyn.dorheim@pnnl.gov>
Date: Mon, 2 Dec 2024 15:52:18 -0500
Subject: [PATCH 6/7] feedback from ben

---
 src/ch4_component.cpp    |  2 +-
 src/oh_component.cpp     |  4 ++--
 tests/testthat/test-h2.R | 17 +++++++++--------
 3 files changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/ch4_component.cpp b/src/ch4_component.cpp
index 36af4d43a..5abf7c924 100644
--- a/src/ch4_component.cpp
+++ b/src/ch4_component.cpp
@@ -165,7 +165,7 @@ void CH4Component::run(const double runToDate) {
         << std::endl;
 
 // Permafrost thaw produces CH4 emissions
-    const double PG_C_TO_TG_CH4 (1000.0 * 16.04 / 12.01);
+    #define PG_C_TO_TG_CH4 (1000.0 * 16.04 / 12.01);
     const double rh_ch4 =
         core->sendMessage(M_GETDATA, D_RH_CH4).value(U_PGC_YR) * PG_C_TO_TG_CH4;
 
diff --git a/src/oh_component.cpp b/src/oh_component.cpp
index 29dbaee18..b57047859 100644
--- a/src/oh_component.cpp
+++ b/src/oh_component.cpp
@@ -177,13 +177,13 @@ void OHComponent::run(const double runToDate) {
         CNMVOC *
         ((1.0 * +current_nmvoc) -
          NMVOC_emissions.get(NMVOC_emissions.firstdate()).value(U_TG_NMVOC));
-    const double e =
+    const double f =
          CH2 *
           ((1.0 * +current_h2) -
            H2_emissions.get(H2_emissions.firstdate()).value(U_TG_H2));
 
 
-    toh = a + b + c + d + e;
+    toh = a + b + c + d + f;
     H_LOG(logger, Logger::DEBUG)
         << "Year " << runToDate << " toh = " << toh << std::endl;
   }
diff --git a/tests/testthat/test-h2.R b/tests/testthat/test-h2.R
index 07d5466d1..30039f4d6 100644
--- a/tests/testthat/test-h2.R
+++ b/tests/testthat/test-h2.R
@@ -25,9 +25,9 @@ test_that("tau ", {
 
 test_that("H2 emissions ", {
 
-    # Check to make sure that can fetch and set the H2 emissions although
-    # at this point changing the emissions will have no impact on
-    # [ch4] dynamics but in the future it should...
+    # Check to make sure that can fetch and set the H2 emissions and
+    # that the effects of adding some H2 emissions change thigns
+    # now that we have the CH4 indrect effects implement.
 
     hc <- newcore(ini)
     run(hc)
@@ -45,12 +45,13 @@ test_that("H2 emissions ", {
 
     diff <- abs(out$value - out2$value)
 
-    # As of now the [CH4] and tau oh should not change
-    expect_equal(mean(diff[out$variable == CONCENTRATIONS_CH4()]), 0)
-    expect_equal(mean(diff[out$variable == LIFETIME_OH()]), 0)
+    # Now we do expect to see changes in CH4 concentrations in response
+    # to H2 emissions
+    expect_gt(mean(diff[out$variable == CONCENTRATIONS_CH4()]), 0)
+    expect_gt(mean(diff[out$variable == LIFETIME_OH()]), 0)
 
-    # But if we can change the H2 emissions we should see a difference in
-    # H2 emissions between the two new runs!
+    # Since we are working off of some default H2 emissions = 0, then
+    # changing the H2 emissions we should see a difference.
     expect_equal(mean(diff[out$variable == EMISSIONS_H2()]), new_val)
 
     })

From 7058e568252f00e111725ed8d75fbbfee58ff9e1 Mon Sep 17 00:00:00 2001
From: kdorheim <kalyn.dorheim@pnnl.gov>
Date: Wed, 4 Dec 2024 13:36:31 -0500
Subject: [PATCH 7/7] address response to pr 758

---
 R/RcppExports.R                    |  2 +-
 inst/include/component_data.hpp    | 10 +++++-----
 inst/include/oh_component.hpp      | 10 +++++-----
 inst/input/hector_ssp119.ini       | 10 +++++-----
 inst/input/hector_ssp126.ini       | 10 +++++-----
 inst/input/hector_ssp245.ini       | 10 +++++-----
 inst/input/hector_ssp370.ini       | 10 +++++-----
 inst/input/hector_ssp434.ini       | 16 ++++++++--------
 inst/input/hector_ssp460.ini       | 16 ++++++++--------
 inst/input/hector_ssp534-over.ini  | 10 +++++-----
 inst/input/hector_ssp585.ini       | 10 +++++-----
 src/oh_component.cpp               | 30 +++++++++++++++---------------
 src/rcpp_constants.cpp             |  4 ++--
 tests/testthat/input/luc_pulse.ini |  8 ++++----
 14 files changed, 78 insertions(+), 78 deletions(-)

diff --git a/R/RcppExports.R b/R/RcppExports.R
index 1f34d9d42..d269dff1d 100644
--- a/R/RcppExports.R
+++ b/R/RcppExports.R
@@ -4,7 +4,7 @@
 #' @describeIn emissions Emissions hydrogen gas (\code{"Tg H2"})
 NULL
 
-#' @describeIn oh coefficent for the h2 emissions
+#' @describeIn oh coefficient for the h2 emissions
 NULL
 
 #' @describeIn msgtype Message type for retrieving data from a component
diff --git a/inst/include/component_data.hpp b/inst/include/component_data.hpp
index e2766a459..595d271b9 100644
--- a/inst/include/component_data.hpp
+++ b/inst/include/component_data.hpp
@@ -277,11 +277,11 @@
 // oh component
 #define D_LIFETIME_OH "TAU_OH"
 #define D_INITIAL_LIFETIME_OH "TOH0"
-#define D_COEFFICENT_NOX "CNOX"
-#define D_COEFFICENT_CH4 "CCH4"
-#define D_COEFFICENT_NMVOC "CNMVOC"
-#define D_COEFFICENT_CO "CCO"
-#define D_COEFFICENT_H2 "CH2"
+#define D_COEFFICIENT_NOX "CNOX"
+#define D_COEFFICIENT_CH4 "CCH4"
+#define D_COEFFICIENT_NMVOC "CNMVOC"
+#define D_COEFFICIENT_CO "CCO"
+#define D_COEFFICIENT_H2 "CH2"
 #define D_EMISSIONS_H2 "H2_emissions"
 
 
diff --git a/inst/include/oh_component.hpp b/inst/include/oh_component.hpp
index f9fc20b2d..ab916f21b 100644
--- a/inst/include/oh_component.hpp
+++ b/inst/include/oh_component.hpp
@@ -67,11 +67,11 @@ class OHComponent : public IModelComponent {
   unitval M0;   // initial CH4 concentration
   unitval TOH0; // preindustrial OH lifetime
 
-  double CCO;    // coefficent for CO
-  double CNMVOC; // coefficent for NMVOC
-  double CNOX;   // coefficent for NOX
-  double CCH4;   // coefficent for CH4
-  unitval CH2;   // coefficent for CH4
+  double CCO;    // coefficient for CO
+  double CNMVOC; // coefficient for NMVOC
+  double CNOX;   // coefficient for NOX
+  double CCH4;   // coefficient for CH4
+  unitval CH2;   // coefficient for CH4
 
 
   // logger
diff --git a/inst/input/hector_ssp119.ini b/inst/input/hector_ssp119.ini
index dca52ea81..e3ad719f9 100644
--- a/inst/input/hector_ssp119.ini
+++ b/inst/input/hector_ssp119.ini
@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 ;------------------------------------------------------------------------
 [ozone]
diff --git a/inst/input/hector_ssp126.ini b/inst/input/hector_ssp126.ini
index 7be816dd3..0373b3b9b 100644
--- a/inst/input/hector_ssp126.ini
+++ b/inst/input/hector_ssp126.ini
@@ -133,11 +133,11 @@ NMVOC_emissions=csv:tables/ssp126_emiss-constraints_rf.csv   ; emissions time se
 H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time series
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------
diff --git a/inst/input/hector_ssp245.ini b/inst/input/hector_ssp245.ini
index f44837eaa..976a76619 100644
--- a/inst/input/hector_ssp245.ini
+++ b/inst/input/hector_ssp245.ini
@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------
diff --git a/inst/input/hector_ssp370.ini b/inst/input/hector_ssp370.ini
index 80aa3a484..855a88c5d 100644
--- a/inst/input/hector_ssp370.ini
+++ b/inst/input/hector_ssp370.ini
@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------
diff --git a/inst/input/hector_ssp434.ini b/inst/input/hector_ssp434.ini
index 532a9e8f1..79f73bb15 100644
--- a/inst/input/hector_ssp434.ini
+++ b/inst/input/hector_ssp434.ini
@@ -37,7 +37,7 @@ preind_interdeep_c=37100	; intermediate and deep ocean C, IPCC AR6 Figure 5.12
 atmos_co2=590.33	; initial atmospheric carbon pool Pg C of CO2 size used in spin up, consistent with C0
 C0=277.15			; preindustrial CO2 from table 7.SM.1 IPCC AR6; CO2 radiative forcing is calibrated to this value
 npp_flux0=56.2		; preindustrial net primary production, Pg C/yr from Ito et al. 2011
-;pf.npp_flux0=5.6	; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978 
+;pf.npp_flux0=5.6	; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978
 ;nonpf.npp_flux0=50.6
 
 veg_c=550			; initial vegetation pool, Pg C
@@ -73,7 +73,7 @@ f_litterd=0.98		; Fraction of litter flux to detritus (balance to soil)
 ;nonpf.f_litterd=0.98
 
 ; Anthropogenic contributions: emissions, direct air carbon capture and storage, and land use change, Pg C/yr
-ffi_emissions=csv:tables/ssp434_emiss-constraints_rf.csv	
+ffi_emissions=csv:tables/ssp434_emiss-constraints_rf.csv
 daccs_uptake=csv:tables/ssp434_emiss-constraints_rf.csv
 luc_emissions=csv:tables/ssp434_emiss-constraints_rf.csv
 luc_uptake=csv:tables/ssp434_emiss-constraints_rf.csv
@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------
@@ -236,7 +236,7 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp434_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				
+[HFC4310_halocarbon]
 ; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
diff --git a/inst/input/hector_ssp460.ini b/inst/input/hector_ssp460.ini
index acffa23cf..287e2a950 100644
--- a/inst/input/hector_ssp460.ini
+++ b/inst/input/hector_ssp460.ini
@@ -37,7 +37,7 @@ preind_interdeep_c=37100	; intermediate and deep ocean C, IPCC AR6 Figure 5.12
 atmos_co2=590.33	; initial atmospheric carbon pool Pg C of CO2 size used in spin up, consistent with C0
 C0=277.15			; preindustrial CO2 from table 7.SM.1 IPCC AR6; CO2 radiative forcing is calibrated to this value
 npp_flux0=56.2		; preindustrial net primary production, Pg C/yr from Ito et al. 2011
-;pf.npp_flux0=5.6	; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978 
+;pf.npp_flux0=5.6	; cf. Figure 3 in Chen et al. 2017 10.1088/1748-9326/aa8978
 ;nonpf.npp_flux0=50.6
 
 veg_c=550			; initial vegetation pool, Pg C
@@ -73,7 +73,7 @@ f_litterd=0.98		; Fraction of litter flux to detritus (balance to soil)
 ;nonpf.f_litterd=0.98
 
 ; Anthropogenic contributions: emissions, direct air carbon capture and storage, and land use change, Pg C/yr
-ffi_emissions=csv:tables/ssp460_emiss-constraints_rf.csv	
+ffi_emissions=csv:tables/ssp460_emiss-constraints_rf.csv
 daccs_uptake=csv:tables/ssp460_emiss-constraints_rf.csv
 luc_emissions=csv:tables/ssp460_emiss-constraints_rf.csv
 luc_uptake=csv:tables/ssp460_emiss-constraints_rf.csv
@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time se
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------
@@ -236,7 +236,7 @@ delta_HFC32=0.0 				; tropospheric adjustments scalar unitless (7.3.2.4 IPCC AR6
 molarMass=52.0					; grams
 HFC32_emissions=csv:tables/ssp460_emiss-constraints_rf.csv
 
-[HFC4310_halocarbon]				
+[HFC4310_halocarbon]
 ; This is equivalent to HFC-43-10mee
 tau=17.0					; lifetime in years (Table 7.SM.7 IPPC AR6)
 rho_HFC4310=0.000357				; radiative efficiencies W/m2/ppt (Table 7.SM.7 IPPC AR6)
diff --git a/inst/input/hector_ssp534-over.ini b/inst/input/hector_ssp534-over.ini
index 68cd577fd..203633c2f 100644
--- a/inst/input/hector_ssp534-over.ini
+++ b/inst/input/hector_ssp534-over.ini
@@ -134,11 +134,11 @@ H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv           ; emissions ti
 
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------
diff --git a/inst/input/hector_ssp585.ini b/inst/input/hector_ssp585.ini
index 9abb26ea1..1aca8f4fa 100644
--- a/inst/input/hector_ssp585.ini
+++ b/inst/input/hector_ssp585.ini
@@ -133,11 +133,11 @@ NMVOC_emissions=csv:tables/ssp585_emiss-constraints_rf.csv   ; emissions time se
 H2_emissions=csv:tables/ssp119_emiss-constraints_rf.csv      ; emissions time series
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105		; coefficent for CO
-CNMVOC=-0.000315	; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
-CH2=-0.00044625 ; coefficent for H2
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105		; coefficient for CO
+CNMVOC=-0.000315	; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
+CH2=-0.00044625 ; coefficient for H2 TODO-H2
 
 
 ;------------------------------------------------------------------------
diff --git a/src/oh_component.cpp b/src/oh_component.cpp
index b57047859..9d9fe19aa 100644
--- a/src/oh_component.cpp
+++ b/src/oh_component.cpp
@@ -57,14 +57,14 @@ void OHComponent::init(Core *coreptr) {
 
   // Inform core what data we can provide
   core->registerCapability(D_LIFETIME_OH, getComponentName());
-  core->registerCapability(D_COEFFICENT_H2, getComponentName());
+  core->registerCapability(D_COEFFICIENT_H2, getComponentName());
   // Register inputs accepted.  Note that more than one component
   // can accept an input
   core->registerInput(D_EMISSIONS_CO, getComponentName());
   core->registerInput(D_EMISSIONS_NMVOC, getComponentName());
   core->registerInput(D_EMISSIONS_NOX, getComponentName());
   core->registerInput(D_EMISSIONS_H2, getComponentName());
-  core->registerInput(D_COEFFICENT_H2, getComponentName());
+  core->registerInput(D_COEFFICIENT_H2, getComponentName());
 
 
 }
@@ -108,19 +108,19 @@ void OHComponent::setData(const string &varName, const message_data &data) {
     } else if (varName == D_INITIAL_LIFETIME_OH) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       TOH0 = data.getUnitval(U_YRS);
-    } else if (varName == D_COEFFICENT_CH4) {
+    } else if (varName == D_COEFFICIENT_CH4) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CCH4 = data.getUnitval(U_UNDEFINED);
-    } else if (varName == D_COEFFICENT_CO) {
+    } else if (varName == D_COEFFICIENT_CO) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CCO = data.getUnitval(U_UNDEFINED);
-    } else if (varName == D_COEFFICENT_NMVOC) {
+    } else if (varName == D_COEFFICIENT_NMVOC) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CNMVOC = data.getUnitval(U_UNDEFINED);
-    } else if (varName == D_COEFFICENT_NOX) {
+    } else if (varName == D_COEFFICIENT_NOX) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CNOX = data.getUnitval(U_UNDEFINED);
-    } else if (varName == D_COEFFICENT_H2) {
+    } else if (varName == D_COEFFICIENT_H2) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
       CH2 = data.getUnitval(U_UNDEFINED);
     } else {
@@ -162,28 +162,28 @@ void OHComponent::run(const double runToDate) {
   const double previous_ch4 =
       core->sendMessage(M_GETDATA, D_CH4_CONC, oldDate).value(U_PPBV_CH4);
 
+  // toh is a sum of coefficients in an exponential representation of OH lifetime
   double toh = 0.0;
   if (previous_ch4 != M0) // if we are not at the first time
   {
-    const double a =
+    const double toh_ch4 =
         CCH4 * ((1.0 * log(previous_ch4)) - log(M0.value(U_PPBV_CH4)));
-    const double b =
+    const double toh_nox =
         CNOX * ((1.0 * current_nox) -
                 NOX_emissions.get(NOX_emissions.firstdate()).value(U_TG_N));
-    const double c =
+    const double toh_co =
         CCO * ((1.0 * +current_co) -
                CO_emissions.get(CO_emissions.firstdate()).value(U_TG_CO));
-    const double d =
+    const double toh_nmvoc =
         CNMVOC *
         ((1.0 * +current_nmvoc) -
          NMVOC_emissions.get(NMVOC_emissions.firstdate()).value(U_TG_NMVOC));
-    const double f =
+    const double toh_h2 =
          CH2 *
           ((1.0 * +current_h2) -
            H2_emissions.get(H2_emissions.firstdate()).value(U_TG_H2));
 
-
-    toh = a + b + c + d + f;
+    toh = toh_ch4 + toh_nox + toh_co + toh_nmvoc + toh_h2;
     H_LOG(logger, Logger::DEBUG)
         << "Year " << runToDate << " toh = " << toh << std::endl;
   }
@@ -215,7 +215,7 @@ unitval OHComponent::getData(const std::string &varName, const double date) {
     H_ASSERT(date != Core::undefinedIndex(),
              "Date required for NMVOC emissions");
     returnval = NMVOC_emissions.get(date);
-  } else if (varName == D_COEFFICENT_H2) {
+  } else if (varName == D_COEFFICIENT_H2) {
     H_ASSERT(date == Core::undefinedIndex(), "Date not allowed for H2 coefficent");
     returnval = CH2 ;
   } else if (varName == D_EMISSIONS_H2) {
diff --git a/src/rcpp_constants.cpp b/src/rcpp_constants.cpp
index fbd22ab57..1850f9a92 100644
--- a/src/rcpp_constants.cpp
+++ b/src/rcpp_constants.cpp
@@ -1505,7 +1505,7 @@ String FLUX_INTERIOR() { return D_FLUX_INTERIOR; }
 String HEAT_FLUX() { return D_HEAT_FLUX; }
 
 
-//' @describeIn oh coefficent for the h2 emissions
+//' @describeIn oh coefficient for the h2 emissions
  //' @export
  // [[Rcpp::export]]
- String COEFF_H2() { return D_COEFFICENT_H2; }
+ String COEFF_H2() { return D_COEFFICIENT_H2; }
diff --git a/tests/testthat/input/luc_pulse.ini b/tests/testthat/input/luc_pulse.ini
index 98a3c2e45..0fe761ef5 100644
--- a/tests/testthat/input/luc_pulse.ini
+++ b/tests/testthat/input/luc_pulse.ini
@@ -112,10 +112,10 @@ CO_emissions=csv:luc_pulse_tables.csv      ; emissions time series
 NMVOC_emissions=csv:luc_pulse_tables.csv   ; emissions time series
 
 TOH0=6.6			; inital OH lifetime (years)
-CNOX=0.0042			; coefficent for NOX
-CCO=-0.000105			; coefficent for CO
-CNMVOC=-0.000315		; coefficent for NMVOC (non methane VOC)
-CCH4=-0.32			; coefficent for CH4
+CNOX=0.0042			; coefficient for NOX
+CCO=-0.000105			; coefficient for CO
+CNMVOC=-0.000315		; coefficient for NMVOC (non methane VOC)
+CCH4=-0.32			; coefficient for CH4
 
 ;------------------------------------------------------------------------
 [ozone]