A bit of cleanup

src/geometry/Geometry.cc

@@ -1,4 +1,4 @@
-/* Copyright (C) 2017, 2018, 2019, 2020 PISM Authors
+/* Copyright (C) 2017, 2018, 2019, 2020, 2021 PISM Authors
  *
  * This file is part of PISM.
  *
@@ -31,10 +31,10 @@
 
 namespace pism {
 
-Geometry::Geometry(IceGrid::ConstPtr grid)
+Geometry::Geometry(const IceGrid::ConstPtr &grid)
   // FIXME: ideally these fields should be "global", i.e. without ghosts.
   // (However this may increase communication costs...)
-  : m_stencil_width(grid->ctx()->config()->get_number("grid.max_stencil_width")),
+  : m_stencil_width(static_cast<int>(grid->ctx()->config()->get_number("grid.max_stencil_width"))),
     latitude(grid, "lat", WITHOUT_GHOSTS),
     longitude(grid, "lon", WITHOUT_GHOSTS),
     bed_elevation(grid, "topg", WITH_GHOSTS, m_stencil_width),

src/geometry/Geometry.hh

@@ -1,4 +1,4 @@
-/* Copyright (C) 2016, 2017, 2018, 2019, 2020 PISM Authors
+/* Copyright (C) 2016, 2017, 2018, 2019, 2020, 2021 PISM Authors
  *
  * This file is part of PISM.
  *
@@ -28,9 +28,9 @@ namespace pism {
 
 class Geometry {
 private:
-  const unsigned int m_stencil_width;
+  const int m_stencil_width;
 public:
-  Geometry(IceGrid::ConstPtr grid);
+  Geometry(const IceGrid::ConstPtr &grid);
 
   /*!
    * Ensures consistency of ice geometry by re-computing cell type, cell grounded fraction, and ice

src/icemodel/IceModel.cc

@@ -61,14 +61,15 @@
 
 namespace pism {
 
-IceModel::IceModel(IceGrid::Ptr grid, std::shared_ptr<Context> context)
+IceModel::IceModel(const IceGrid::Ptr &grid,
+                   const std::shared_ptr<Context> &context)
   : m_grid(grid),
     m_config(context->config()),
     m_ctx(context),
     m_sys(context->unit_system()),
     m_log(context->log()),
     m_time(context->time()),
-    m_wide_stencil(m_config->get_number("grid.max_stencil_width")),
+    m_wide_stencil(static_cast<int>(m_config->get_number("grid.max_stencil_width"))),
     m_output_global_attributes("PISM_GLOBAL", m_sys),
     m_run_stats("run_stats", m_sys),
     m_geometry(m_grid),
@@ -132,7 +133,7 @@ IceModel::IceModel(IceGrid::Ptr grid, std::shared_ptr<Context> context)
   auto surface_input_file = m_config->get_string("hydrology.surface_input.file");
   if (not surface_input_file.empty()) {
     ForcingOptions surface_input(*m_ctx, "hydrology.surface_input");
-    int buffer_size = m_config->get_number("input.forcing.buffer_size");
+    int buffer_size = static_cast<int>(m_config->get_number("input.forcing.buffer_size"));
 
     File file(m_grid->com, surface_input.filename, PISM_NETCDF3, PISM_READONLY);
 
@@ -163,9 +164,6 @@ void IceModel::reset_counters() {
 
 
 IceModel::~IceModel() {
-
-  delete m_beddef;
-
   delete m_btu;
   delete m_energy_model;
 }
@@ -243,7 +241,8 @@ void IceModel::allocate_storage() {
   {
     double fill_value = units::convert(m_sys, m_config->get_number("output.fill_value"),
                                        "m year-1", "m second-1");
-    double valid_range = units::convert(m_sys, 1e6, "m year-1", "m second-1");
+    const double huge_value = 1e6;
+    double valid_range = units::convert(m_sys, huge_value, "m year-1", "m second-1");
     // vel_bc
     m_ssa_dirichlet_bc_values.set_attrs("model_state",
                                         "X-component of the SSA velocity boundary conditions",
@@ -581,9 +580,8 @@ void IceModel::step(bool do_mass_continuity,
 
     // add removed icebergs to discharge due to calving
     {
-      IceModelVec2S
-        &old_H    = *m_work2d[0],
-        &old_Href = *m_work2d[1];
+      auto &old_H    = *m_work2d[0];
+      auto &old_Href = *m_work2d[1];
 
       {
         old_H.copy_from(m_geometry.ice_thickness);
@@ -619,11 +617,7 @@ void IceModel::step(bool do_mass_continuity,
                      current_time, m_dt);
     profiling.end("bed_deformation");
 
-    if (m_beddef->bed_elevation().state_counter() != topg_state_counter) {
-      m_new_bed_elevation = true;
-    } else {
-      m_new_bed_elevation = false;
-    }
+    m_new_bed_elevation = m_beddef->bed_elevation().state_counter() != topg_state_counter;
   } else {
     m_new_bed_elevation = false;
   }
@@ -772,7 +766,7 @@ void IceModel::run() {
   // This is needed to compute rates of change of the ice mass, volume, etc.
   {
     const double time = m_time->current();
-    for (auto d : m_ts_diagnostics) {
+    for (const auto &d : m_ts_diagnostics) {
       d.second->update(time, time);
     }
   }
@@ -827,11 +821,12 @@ void IceModel::run() {
   profiling.stage_end("time-stepping loop");
 
   if (stepcount >= 0) {
+    double count = stepcount;
     m_log->message(1,
                "count_time_steps:  run() took %d steps\n"
                "average dt = %.6f years\n",
                stepcount,
-               units::convert(m_sys, m_time->end() - m_time->start(), "seconds", "years")/(double)stepcount);
+               units::convert(m_sys, m_time->end() - m_time->start(), "seconds", "years") / count);
   }
 }
 
@@ -895,10 +890,6 @@ const ocean::OceanModel* IceModel::ocean_model() const {
   return m_ocean.get();
 }
 
-const bed::BedDef* IceModel::bed_model() const {
-  return m_beddef;
-}
-
 const energy::BedThermalUnit* IceModel::bedrock_thermal_model() const {
   return m_btu;
 }
@@ -934,17 +925,16 @@ void warn_about_missing(const Logger &log,
                         const std::set<std::string> &available,
                         bool stop) {
   std::vector<std::string> missing;
-  for (auto v : vars) {
+  for (const auto &v : vars) {
     if (available.find(v) == available.end()) {
       missing.push_back(v);
     }
   }
 
   if (not missing.empty()) {
     size_t N = missing.size();
-    const char
-      *ending = N > 1 ? "s" : "",
-      *verb   = N > 1 ? "are" : "is";
+    const char *ending = N > 1 ? "s" : "";
+    const char *verb   = N > 1 ? "are" : "is";
     if (stop) {
       throw RuntimeError::formatted(PISM_ERROR_LOCATION,
                                     "%s variable%s %s %s not available!\n"
@@ -954,14 +944,14 @@ void warn_about_missing(const Logger &log,
                                     join(missing, ",").c_str(),
                                     verb,
                                     set_join(available, ",\n- ").c_str());
-    } else {
-      log.message(2,
-                  "\nWARNING: %s variable%s %s %s not available!\n\n",
-                  type.c_str(),
-                  ending,
-                  join(missing, ",").c_str(),
-                  verb);
     }
+
+    log.message(2,
+                "\nWARNING: %s variable%s %s %s not available!\n\n",
+                type.c_str(),
+                ending,
+                join(missing, ",").c_str(),
+                verb);
   }
 }
 
@@ -977,7 +967,7 @@ void IceModel::prune_diagnostics() {
 
   // get the list of available diagnostics
   std::set<std::string> available;
-  for (auto d : m_diagnostics) {
+  for (const auto &d : m_diagnostics) {
     available.insert(d.first);
   }
 
@@ -995,7 +985,7 @@ void IceModel::prune_diagnostics() {
   requested = combine(requested, m_backup_vars);
 
   // de-allocate diagnostics that were not requested
-  for (auto v : available) {
+  for (const auto &v : available) {
     if (requested.find(v) == requested.end()) {
       m_diagnostics.erase(v);
     }
@@ -1007,7 +997,7 @@ void IceModel::prune_diagnostics() {
     // use all diagnostics
   } else {
     TSDiagnosticList diagnostics;
-    for (auto v : m_ts_vars) {
+    for (const auto &v : m_ts_vars) {
       if (m_ts_diagnostics.find(v) != m_ts_diagnostics.end()) {
         diagnostics[v] = m_ts_diagnostics[v];
       } else {
@@ -1033,12 +1023,12 @@ void IceModel::prune_diagnostics() {
  * Call this after prune_diagnostics() to avoid unnecessary work.
  */
 void IceModel::update_diagnostics(double dt) {
-  for (auto d : m_diagnostics) {
+  for (const auto &d : m_diagnostics) {
     d.second->update(dt);
   }
 
   const double time = m_time->current();
-  for (auto d : m_ts_diagnostics) {
+  for (const auto &d : m_ts_diagnostics) {
     d.second->update(time - dt, time);
   }
 }
@@ -1047,12 +1037,12 @@ void IceModel::update_diagnostics(double dt) {
  * Reset accumulators in diagnostics that compute time-averaged quantities.
  */
 void IceModel::reset_diagnostics() {
-  for (auto d : m_diagnostics) {
+  for (auto &d : m_diagnostics) {
     d.second->reset();
   }
 }
 
-IceModel::ThicknessChanges::ThicknessChanges(IceGrid::ConstPtr grid)
+IceModel::ThicknessChanges::ThicknessChanges(const IceGrid::ConstPtr &grid)
   : calving(grid, "thickness_change_due_to_calving", WITHOUT_GHOSTS),
     frontal_melt(grid, "thickness_change_due_to_frontal_melt", WITHOUT_GHOSTS),
     forced_retreat(grid, "thickness_change_due_to_forced_retreat", WITHOUT_GHOSTS) {

src/icemodel/IceModel.hh

@@ -110,7 +110,7 @@ class ScalarForcing;
 //! an ice sheet.
 class IceModel {
 public:
-  IceModel(IceGrid::Ptr g, std::shared_ptr<Context> context);
+  IceModel(const IceGrid::Ptr &grid, const std::shared_ptr<Context> &context);
 
   // the destructor must be virtual merely because some members are virtual
   virtual ~IceModel();
@@ -124,7 +124,7 @@ public:
   virtual void run();
 
   /** Advance the current PISM run to a specific time */
-  virtual void run_to(double time);
+  virtual void run_to(double run_end);
 
   virtual void save_results();
 
@@ -145,7 +145,6 @@ public:
   const stressbalance::StressBalance* stress_balance() const;
   const ocean::OceanModel* ocean_model() const;
   const frontalmelt::FrontalMelt* frontalmelt_model() const;
-  const bed::BedDef* bed_model() const;
   const energy::BedThermalUnit* bedrock_thermal_model() const;
   const energy::EnergyModel* energy_balance_model() const;
 
@@ -281,7 +280,7 @@ protected:
   std::shared_ptr<frontalmelt::FrontalMelt>   m_frontal_melt;
   std::shared_ptr<ocean::sea_level::SeaLevel> m_sea_level;
 
-  bed::BedDef *m_beddef;
+  std::shared_ptr<bed::BedDef> m_beddef;
 
   // state variables and some diagnostics/internals
 
@@ -381,7 +380,7 @@ protected:
   std::shared_ptr<stressbalance::StressBalance> m_stress_balance;
 
   struct ThicknessChanges {
-    ThicknessChanges(IceGrid::ConstPtr grid);
+    ThicknessChanges(const IceGrid::ConstPtr &grid);
 
     // calving during the last time step
     IceModelVec2S calving;

src/icemodel/initialization.cc

@@ -972,29 +972,29 @@ void IceModel::init_calving() {
 }
 
 void IceModel::allocate_bed_deformation() {
-  std::string model = m_config->get_string("bed_deformation.model");
-
-  if (m_beddef != NULL) {
+  if (m_beddef) {
     return;
   }
 
   m_log->message(2,
                  "# Allocating a bed deformation model...\n");
 
+  std::string model = m_config->get_string("bed_deformation.model");
+
   if (model == "none") {
-    m_beddef = new bed::Null(m_grid);
+    m_beddef = std::make_shared<bed::Null>(m_grid);
   }
   else if (model == "iso") {
-    m_beddef = new bed::PointwiseIsostasy(m_grid);
+    m_beddef = std::make_shared<bed::PointwiseIsostasy>(m_grid);
   }
   else if (model == "lc") {
-    m_beddef = new bed::LingleClark(m_grid);
+    m_beddef = std::make_shared<bed::LingleClark>(m_grid);
   }
   else if (model == "given") {
-    m_beddef = new bed::Given(m_grid);
+    m_beddef = std::make_shared<bed::Given>(m_grid);
   }
 
-  m_submodels["bed deformation"] = m_beddef;
+  m_submodels["bed deformation"] = m_beddef.get();
 }
 
 //! Read some runtime (command line) options and alter the