final clang-format run

inst/include/component_data.hpp

@@ -346,8 +346,8 @@
 #define D_VEGC "veg_c"
 #define D_DETRITUSC "detritus_c"
 #define D_SOILC "soil_c"
-#define D_PERMAFROSTC           "permafrost_c"
-#define D_THAWEDPC              "thawedp_c"
+#define D_PERMAFROSTC "permafrost_c"
+#define D_THAWEDPC "thawedp_c"
 #define D_FFI_EMISSIONS "ffi_emissions"
 #define D_DACCS_UPTAKE "daccs_uptake"
 #define D_LUC_EMISSIONS "luc_emissions"
@@ -357,21 +357,21 @@
 #define D_Q10_RH "q10_rh"
 #define D_NPP "NPP"
 #define D_RH "RH"
-#define D_RH_DETRITUS           "rh_det"
-#define D_RH_SOIL               "rh_soil"
-#define D_RH_THAWEDP            "rh_thawedp"
+#define D_RH_DETRITUS "rh_det"
+#define D_RH_SOIL "rh_soil"
+#define D_RH_THAWEDP "rh_thawedp"
 #define D_F_NPPV "f_nppv"
 #define D_F_NPPD "f_nppd"
 #define D_F_LITTERD "f_litterd"
 #define D_NPP_FLUX0 "npp_flux0"
 #define D_BETA "beta"
 #define D_WARMINGFACTOR "warmingfactor"
-#define D_F_FROZEN              "f_frozen"
-#define D_RH_CH4                "rh_ch4"
-#define D_RH_CH4_FRAC           "rh_ch4_frac"
-#define D_PF_SIGMA              "pf_sigma"
-#define D_PF_MU                 "pf_mu"
-#define D_FPF_STATIC            "fpf_static"
+#define D_F_FROZEN "f_frozen"
+#define D_RH_CH4 "rh_ch4"
+#define D_RH_CH4_FRAC "rh_ch4_frac"
+#define D_PF_SIGMA "pf_sigma"
+#define D_PF_MU "pf_mu"
+#define D_FPF_STATIC "fpf_static"
 
 // Constraints
 #define D_CO2_CONSTRAIN "CO2_constrain"

inst/include/fluxpool.hpp

@@ -97,7 +97,7 @@ inline fluxpool::fluxpool(unitval v, unordered_map<string, double> pool_map,
   ctmap = pool_map;
   name = pool_name;
 
-  if(v < 0) {
+  if (v < 0) {
     H_ASSERT(v >= 0, "Flux and pool values may not be negative in " + name);
   }
 
@@ -118,7 +118,7 @@ inline fluxpool::fluxpool(unitval v, unordered_map<string, double> pool_map,
 inline void fluxpool::set(double v, unit_types u, bool track = false,
                           string pool_name = "?") {
   name = pool_name;
-  if(v < 0) {
+  if (v < 0) {
     H_ASSERT(v >= 0, "Flux and pool values may not be negative in " + name);
   }
   tracking = track;

inst/include/ocean_component.hpp

@@ -153,8 +153,9 @@ class OceanComponent : public CarbonCycleModel {
    *****************************************************************/
   // Ocean initial state
   unitval preind_C_surface; //!< Carbon in the preindustrial surface pool
-  unitval preind_C_ID;      //!< Carbon in the preindustrial intermediate and deep pool
-
+  unitval
+      preind_C_ID; //!< Carbon in the preindustrial intermediate and deep pool
+
   // Ocean boxes over time
   tvector<oceanbox> surfaceHL_tv;
   tvector<oceanbox> surfaceLL_tv;

inst/include/oceanbox.hpp

@@ -29,9 +29,9 @@
 
 // Mean absolute global tos temperature, preindustrial (deg C), this is used by
 // the ocean component which, requires absolute temperature to calculate ocean
-// chemistry, the CMIP6 multi model mean from 1850 - 1860. See Leeya Pressburger,
-// & Kalyn R. Dorheim. (2022). JGCRI/hector_cmip6data: v1.0 (v1.0). Zenodo.
-// https://doi.org/10.5281/zenodo.7304553
+// chemistry, the CMIP6 multi model mean from 1850 - 1860. See Leeya
+// Pressburger, & Kalyn R. Dorheim. (2022). JGCRI/hector_cmip6data: v1.0 (v1.0).
+// Zenodo. https://doi.org/10.5281/zenodo.7304553
 #define MEAN_TOS_TEMP 18
 
 namespace Hector {

inst/include/simpleNbox.hpp

@@ -267,8 +267,8 @@ class SimpleNbox : public CarbonCycleModel {
   double_stringmap pf_mu; //!< Mean for permafrost-temp model fit
   double_stringmap fpf_static; //!< Permafrost C non-labile fraction
   typedef std::map<std::string, boost::math::lognormal> lognormal_stringmap;
-  lognormal_stringmap pf_s;//!< Permafrost lognormal distribution
-  
+  lognormal_stringmap pf_s; //!< Permafrost lognormal distribution
+
   /*****************************************************************
    * Functions computing sub-elements of the carbon cycle
    *****************************************************************/
@@ -293,8 +293,10 @@ class SimpleNbox : public CarbonCycleModel {
      double time = Core::undefinedIndex()) const; //!< calculates RH for a biome
   fluxpool sum_rh(double time = Core::undefinedIndex())
       const; //!< calculates RH, global total
-  tuple<double, double, double> compute_pf_thaw_refreeze(string biome, fluxpool rh_co2, fluxpool rh_ch4) const;
-
+  tuple<double, double, double> compute_pf_thaw_refreeze(string biome,
+                                                         fluxpool rh_co2,
+                                                         fluxpool rh_ch4) const;
+
   /*****************************************************************
    * Private helper functions
    *****************************************************************/

inst/include/unitval.hpp

@@ -221,7 +221,7 @@ inline void unitval::set(double v, unit_types u, double err = 0.0) {
  *  Get value. Caller has to provide assumed units, as a check.
  */
 inline double unitval::value(unit_types u) const {
-  if(u != valUnits) {
+  if (u != valUnits) {
     H_ASSERT(u == valUnits, "variable is not of this type.  Expected: " +
                                 unitsName(valUnits) + "; got: " + unitsName(u));
   }

src/carbon-cycle-solver.cpp

@@ -71,7 +71,7 @@ unitval CarbonCycleSolver::sendMessage(const std::string &message,
 
   } else if (message == M_SETDATA) { //! Caller is requesting to set data
     // TODO: call setData below
- 
+
   } else { //! We don't handle any other messages
     H_THROW("Caller sent unknown message: " + message);
   }

src/ch4_component.cpp

@@ -95,11 +95,12 @@ void CH4Component::setData(const string &varName, const message_data &data) {
   try {
     if (varName == D_PREINDUSTRIAL_CH4) {
       H_ASSERT(data.date == Core::undefinedIndex(), "date not allowed");
-        if (data.getUnitval(U_PPBV_CH4).value(U_PPBV_CH4) != 731.41) {
-            H_LOG(logger, Logger::WARNING) << "Changing " << varName <<
-                " from default value; this is not recomended and may cause" <<
-                    " issues with RF CH4 calucation" << std::endl;
-        }
+      if (data.getUnitval(U_PPBV_CH4).value(U_PPBV_CH4) != 731.41) {
+        H_LOG(logger, Logger::WARNING)
+            << "Changing " << varName
+            << " from default value; this is not recomended and may cause"
+            << " issues with RF CH4 calucation" << std::endl;
+      }
       M0 = data.getUnitval(U_PPBV_CH4);
     } else if (varName == D_EMISSIONS_CH4) {
       H_ASSERT(data.date != Core::undefinedIndex(), "date required");
@@ -163,13 +164,15 @@ void CH4Component::run(const double runToDate) {
         << "Year " << runToDate << " current_toh = " << current_toh
         << std::endl;
 
-    // Permafrost thaw produces CH4 emissions
-    #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;
+// Permafrost thaw produces CH4 emissions
+#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;
 
     // Additional, background CH4 natural emissions
     const double ch4n = CH4N.value(U_TG_CH4);
-    const double emisTocon = (current_ch4em + rh_ch4 + ch4n) / UC_CH4.value(U_TG_PPBV);
+    const double emisTocon =
+        (current_ch4em + rh_ch4 + ch4n) / UC_CH4.value(U_TG_PPBV);
     const double previous_ch4 = CH4.get(oldDate);
 
     H_LOG(logger, Logger::DEBUG)

src/core.cpp

@@ -543,7 +543,7 @@ void Core::reset(double resetdate) {
   if (rerun_spinup) {
     prepareToRun();
     lastDate = getStartDate();
-  }  else {
+  } else {
     lastDate = resetdate;
   }
 }

src/csv_outputstream_visitor.cpp

@@ -196,14 +196,16 @@ void CSVOutputStreamVisitor::visit(SimpleNbox *c) {
                      c->final_rh[biome]);
       STREAM_UNITVAL(csvFile, c, biome + SNBOX_PARSECHAR + D_RH_CH4,
                      c->RH_ch4[biome]);
-     STREAM_UNITVAL(csvFile, c, biome + SNBOX_PARSECHAR + D_VEGC,
+      STREAM_UNITVAL(csvFile, c, biome + SNBOX_PARSECHAR + D_VEGC,
                      c->veg_c[biome]);
       STREAM_UNITVAL(csvFile, c, biome + SNBOX_PARSECHAR + D_DETRITUSC,
                      c->detritus_c[biome]);
       STREAM_UNITVAL(csvFile, c, biome + SNBOX_PARSECHAR + D_SOILC,
                      c->soil_c[biome]);
-      STREAM_UNITVAL( csvFile, c, biome + SNBOX_PARSECHAR + D_PERMAFROSTC, c->permafrost_c[ biome ] );
-      STREAM_UNITVAL( csvFile, c, biome + SNBOX_PARSECHAR + D_THAWEDPC, c->thawed_permafrost_c[ biome ] );
+      STREAM_UNITVAL(csvFile, c, biome + SNBOX_PARSECHAR + D_PERMAFROSTC,
+                     c->permafrost_c[biome]);
+      STREAM_UNITVAL(csvFile, c, biome + SNBOX_PARSECHAR + D_THAWEDPC,
+                     c->thawed_permafrost_c[biome]);
       STREAM_UNITVAL(csvFile, c, biome + SNBOX_PARSECHAR + D_F_FROZEN,
                      unitval(c->f_frozen[biome], U_UNITLESS));
       STREAM_UNITVAL(csvFile, c, biome + SNBOX_PARSECHAR + D_TEMPFERTD,

src/csv_tracking_visitor.cpp

@@ -116,8 +116,8 @@ void CSVFluxPoolVisitor::visit(SimpleNbox *c) {
     print_pool(c->veg_c[biome], cname);
     print_pool(c->detritus_c[biome], cname);
     print_pool(c->soil_c[biome], cname);
-    print_pool( c->permafrost_c[ biome ], cname );
-    print_pool( c->thawed_permafrost_c[ biome ], cname );
+    print_pool(c->permafrost_c[biome], cname);
+    print_pool(c->thawed_permafrost_c[biome], cname);
   }
 }
 

src/dependency_finder.cpp

@@ -12,7 +12,7 @@
  *
  */
 
-//#include <cassert>
+// #include <cassert>
 #include <algorithm>
 #include <limits>
 

src/dummy_model_component.cpp

@@ -74,7 +74,7 @@ unitval DummyModelComponent::sendMessage(const std::string &message,
 
   } else if (message == M_SETDATA) { //! Caller is requesting to set data
     // TODO: call setData below
-  
+
   } else { //! We don't handle any other messages
     H_THROW("Caller sent unknown message: " + message);
   }

src/h_interpolator.cpp

@@ -48,11 +48,11 @@ h_interpolator::~h_interpolator() { release_data(); }
  *  Release memory used by internal vars.
  */
 void h_interpolator::release_data() {
-  delete[](xdata); // free old memory, if necessary
-  delete[](ydata);
-  delete[](b_coef);
-  delete[](c_coef);
-  delete[](d_coef);
+  delete[] (xdata); // free old memory, if necessary
+  delete[] (ydata);
+  delete[] (b_coef);
+  delete[] (c_coef);
+  delete[] (d_coef);
 }
 
 //-----------------------------------------------------------------------