Add cell volume and areas

include/bout/coordinates.hxx

@@ -3,16 +3,16 @@
  *
  * ChangeLog
  * =========
- * 
+ *
  * 2014-11-10 Ben Dudson <bd512@york.ac.uk>
  *    * Created by separating metric from Mesh
  *
- * 
+ *
  **************************************************************************
  * Copyright 2014-2025 BOUT++ contributors
  *
  * Contact: Ben Dudson, dudson2@llnl.gov
- * 
+ *
  * This file is part of BOUT++.
  *
  * BOUT++ is free software: you can redistribute it and/or modify
@@ -38,6 +38,7 @@
 #include <bout/field2d.hxx>
 #include <bout/field3d.hxx>
 #include <bout/paralleltransform.hxx>
+#include <optional>
 
 class Mesh;
 
@@ -102,6 +103,149 @@ public:
   /// Covariant metric tensor
   FieldMetric g_11, g_22, g_33, g_12, g_13, g_23;
 
+  /// get g_22 at the cell faces;
+  const FieldMetric& g_22_ylow() const;
+  const FieldMetric& g_22_yhigh() const;
+  FieldMetric& g_22_ylow();
+  FieldMetric& g_22_yhigh();
+  /// get Jxz at the cell faces or cell centre
+  const FieldMetric& Jxz_ylow() const {
+    if (!_jxz_ylow.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_ylow;
+  }
+  const FieldMetric& Jxz_yhigh() const {
+    if (!_jxz_yhigh.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_yhigh;
+  }
+  const FieldMetric& Jxz() const {
+    if (!_jxz_centre.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_centre;
+  }
+  FieldMetric& Jxz_ylow() {
+    if (!_jxz_ylow.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_ylow;
+  }
+  FieldMetric& Jxz_yhigh() {
+    if (!_jxz_yhigh.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_yhigh;
+  }
+  FieldMetric& Jxz() {
+    if (!_jxz_centre.has_value()) {
+      _compute_Jxz_cell_faces();
+    }
+    return *_jxz_centre;
+  }
+  // Cell Areas
+  const FieldMetric& cell_area_xlow() const {
+    if (!_cell_area_xlow.has_value()) {
+      _compute_cell_area_x();
+    }
+    return *_cell_area_xlow;
+  }
+  const FieldMetric& cell_area_xhigh() const {
+    if (!_cell_area_xhigh.has_value()) {
+      _compute_cell_area_x();
+    }
+    return *_cell_area_xhigh;
+  }
+  const FieldMetric& cell_area_ylow() const {
+    if (!_cell_area_ylow.has_value()) {
+      _compute_cell_area_y();
+    }
+    return *_cell_area_ylow;
+  }
+  const FieldMetric& cell_area_yhigh() const {
+    if (!_cell_area_yhigh.has_value()) {
+      _compute_cell_area_y();
+    }
+    return *_cell_area_yhigh;
+  }
+  const FieldMetric& cell_area_zlow() const {
+    if (!_cell_area_zlow.has_value()) {
+      _compute_cell_area_z();
+    }
+    return *_cell_area_zlow;
+  }
+  const FieldMetric& cell_area_zhigh() const {
+    if (!_cell_area_zhigh.has_value()) {
+      _compute_cell_area_z();
+    }
+    return *_cell_area_zhigh;
+  }
+  FieldMetric& cell_area_xlow() {
+    if (!_cell_area_xlow.has_value()) {
+      _compute_cell_area_x();
+    }
+    return *_cell_area_xlow;
+  }
+  FieldMetric& cell_area_xhigh() {
+    if (!_cell_area_xhigh.has_value()) {
+      _compute_cell_area_x();
+    }
+    return *_cell_area_xhigh;
+  }
+  FieldMetric& cell_area_ylow() {
+    if (!_cell_area_ylow.has_value()) {
+      _compute_cell_area_y();
+    }
+    return *_cell_area_ylow;
+  }
+  FieldMetric& cell_area_yhigh() {
+    if (!_cell_area_yhigh.has_value()) {
+      _compute_cell_area_y();
+    }
+    return *_cell_area_yhigh;
+  }
+  FieldMetric& cell_area_zlow() {
+    if (!_cell_area_zlow.has_value()) {
+      _compute_cell_area_z();
+    }
+    return *_cell_area_zlow;
+  }
+  FieldMetric& cell_area_zhigh() {
+    if (!_cell_area_zhigh.has_value()) {
+      _compute_cell_area_z();
+    }
+    return *_cell_area_zhigh;
+  }
+  // Cell Volume
+  const FieldMetric& cell_volume() const {
+    if (!_cell_volume.has_value()) {
+      _compute_cell_volume();
+    }
+    return *_cell_volume;
+  }
+  FieldMetric& cell_volume() {
+    if (!_cell_volume.has_value()) {
+      _compute_cell_volume();
+    }
+    return *_cell_volume;
+  }
+
+private:
+  mutable std::optional<FieldMetric> _g_22_ylow, _g_22_yhigh;
+  mutable std::optional<FieldMetric> _jxz_ylow, _jxz_yhigh, _jxz_centre;
+  mutable std::optional<FieldMetric> _cell_area_xlow, _cell_area_xhigh;
+  mutable std::optional<FieldMetric> _cell_area_ylow, _cell_area_yhigh;
+  mutable std::optional<FieldMetric> _cell_area_zlow, _cell_area_zhigh;
+  mutable std::optional<FieldMetric> _cell_volume;
+  void _compute_Jxz_cell_faces() const;
+  void _compute_cell_area_x() const;
+  void _compute_cell_area_y() const;
+  void _compute_cell_area_z() const;
+  void _compute_cell_volume() const;
+
+public:
   /// Christoffel symbol of the second kind (connection coefficients)
   FieldMetric G1_11, G1_22, G1_33, G1_12, G1_13, G1_23;
   FieldMetric G2_11, G2_22, G2_33, G2_12, G2_13, G2_23;
@@ -256,10 +400,10 @@ private:
 class TokamakCoordinates : public Coordinates {
 public:
   TokamakCoordinates(Mesh *mesh) : Coordinates(mesh) {
-    
+
   }
 private:
-  
+
 };
 */
 

include/bout/field2d.hxx

@@ -275,6 +275,9 @@ public:
 
   int size() const override { return nx * ny; }
 
+  Field2D& asField3DParallel() { return *this; }
+  const Field2D& asField3DParallel() const { return *this; }
+
 private:
   /// Internal data array. Handles allocation/freeing of memory
   Array<BoutReal> data;

src/mesh/coordinates.cxx

@@ -1878,7 +1878,7 @@ Field2D Coordinates::Laplace_perpXY([[maybe_unused]] const Field2D& A,
 
 const Coordinates::FieldMetric& Coordinates::invSg() const {
   if (invSgCache == nullptr) {
-    auto ptr = std::make_unique<FieldMetric>();
+    auto ptr = std::make_unique<Coordinates::FieldMetric>();
     (*ptr) = 1.0 / sqrt(g_22);
     invSgCache = std::move(ptr);
   }
@@ -1898,7 +1898,7 @@ Coordinates::Grad2_par2_DDY_invSg(CELL_LOC outloc, const std::string& method) co
   invSgCache->applyParallelBoundary("parallel_neumann_o2");
 
   // cache
-  auto ptr = std::make_unique<FieldMetric>();
+  auto ptr = std::make_unique<Coordinates::FieldMetric>();
   *ptr = DDY(*invSgCache, outloc, method) * invSg();
   Grad2_par2_DDY_invSgCache[method] = std::move(ptr);
   return *Grad2_par2_DDY_invSgCache[method];
@@ -2007,3 +2007,130 @@ void Coordinates::checkContravariant() {
     }
   }
 }
+
+const Coordinates::FieldMetric& Coordinates::g_22_ylow() const {
+  if (_g_22_ylow.has_value()) {
+    return *_g_22_ylow;
+  }
+  _g_22_ylow.emplace(emptyFrom(g_22));
+  //_g_22_ylow->setLocation(CELL_YLOW);
+  auto* mesh = Bxy.getMesh();
+  if (Bxy.isFci()) {
+    if (mesh->get(_g_22_ylow.value(), "g_22_cell_ylow", 0.0, false) != 0) {
+      throw BoutException("The grid file does not contain `g_22_cell_ylow`.");
+    }
+  } else {
+    ASSERT0(mesh->ystart > 0);
+    BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
+      _g_22_ylow.value()[i] = SQ(0.5 * (sqrt(g_22[i]) + sqrt(g_22[i.ym()])));
+    }
+  }
+  return g_22_ylow();
+}
+
+const Coordinates::FieldMetric& Coordinates::g_22_yhigh() const {
+  if (_g_22_yhigh.has_value()) {
+    return *_g_22_yhigh;
+  }
+  _g_22_yhigh.emplace(emptyFrom(g_22));
+  //_g_22_yhigh->setLocation(CELL_YHIGH);
+  auto* mesh = Bxy.getMesh();
+  if (Bxy.isFci()) {
+    if (mesh->get(_g_22_yhigh.value(), "g_22_cell_yhigh", 0.0, false) != 0) {
+      throw BoutException("The grid file does not contain `g_22_cell_yhigh`.");
+    }
+  } else {
+    ASSERT0(mesh->ystart > 0);
+    BOUT_FOR(i, g_22.getRegion("RGN_NOY")) {
+      _g_22_yhigh.value()[i] = SQ(0.5 * (sqrt(g_22[i]) + sqrt(g_22[i.yp()])));
+    }
+  }
+  return g_22_yhigh();
+}
+
+void Coordinates::_compute_Jxz_cell_faces() const {
+  _jxz_centre.emplace(sqrt(g_11 * g_33 - SQ(g_13)));
+  _jxz_ylow.emplace(emptyFrom(_jxz_centre.value()));
+  //_jxz_ylow->setLocation(CELL_YLOW);
+  _jxz_yhigh.emplace(emptyFrom(_jxz_centre.value()));
+  //_jxz_yhigh->setLocation(CELL_YHIGH);
+  auto* mesh = _jxz_centre->getMesh();
+  if (Bxy.isFci()) {
+    Coordinates::FieldMetric By_c;
+    Coordinates::FieldMetric By_h;
+    Coordinates::FieldMetric By_l;
+    if (mesh->get(By_c, "By", 0.0, false, CELL_CENTRE) != 0) {
+      throw BoutException("The grid file does not contain `By`.");
+    }
+    if (mesh->get(By_l, "By_cell_ylow", 0.0, false) != 0) {
+      throw BoutException("The grid file does not contain `By_cell_ylow`.");
+    }
+    if (mesh->get(By_h, "By_cell_yhigh", 0.0, false) != 0) {
+      throw BoutException("The grid file does not contain `By_cell_yhigh`.");
+    }
+    BOUT_FOR(i, By_c.getRegion("RGN_NOY")) {
+      (*_jxz_ylow)[i] = By_c[i] / By_l[i] * (*_jxz_centre)[i];
+      (*_jxz_yhigh)[i] = By_c[i] / By_h[i] * (*_jxz_centre)[i];
+    }
+  } else {
+    ASSERT0(mesh->ystart > 0);
+    BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOY")) {
+      (*_jxz_ylow)[i] = 0.5 * ((*_jxz_centre)[i] + (*_jxz_centre)[i.ym()]);
+      (*_jxz_yhigh)[i] = 0.5 * ((*_jxz_centre)[i] + (*_jxz_centre)[i.yp()]);
+    }
+  }
+}
+
+void Coordinates::_compute_cell_area_x() const {
+  const auto area_centre = sqrt(g_22 * g_33 - SQ(g_23)) * dy * dz;
+  _cell_area_xlow.emplace(emptyFrom(area_centre));
+  _cell_area_xhigh.emplace(emptyFrom(area_centre));
+  // We cannot setLocation, as that would trigger the computation of staggered
+  // metrics.
+  auto* mesh = Bxy.getMesh();
+  ASSERT0(mesh->xstart > 0);
+  BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOX")) {
+    (*_cell_area_xlow)[i] = 0.5 * (area_centre[i] + area_centre[i.xm()]);
+    (*_cell_area_xhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.xp()]);
+  }
+}
+
+void Coordinates::_compute_cell_area_y() const {
+  Jxz();
+  if (_jxz_centre->isFci()) {
+    ASSERT3(isUniform(dx, true, "RGN_ALL"));
+    ASSERT2(isUniform(dx, false, "RGN_ALL"));
+    ASSERT3(isUniform(dz, true, "RGN_ALL"));
+    ASSERT2(isUniform(dz, false, "RGN_ALL"));
+    _cell_area_ylow.emplace(*_jxz_ylow * dx * dz);
+    _cell_area_yhigh.emplace(*_jxz_yhigh * dx * dz);
+  } else {
+    // Field aligned
+    const auto area_centre = sqrt(g_11 * g_33 - SQ(g_13)) * dx * dz;
+    _cell_area_ylow.emplace(emptyFrom(area_centre));
+    _cell_area_yhigh.emplace(emptyFrom(area_centre));
+    // We cannot setLocation, as that would trigger the computation of staggered
+    // metrics.
+    auto* mesh = Bxy.getMesh();
+    ASSERT0(mesh->ystart > 0);
+    BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOY")) {
+      (*_cell_area_ylow)[i] = 0.5 * (area_centre[i] + area_centre[i.ym()]);
+      (*_cell_area_yhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.yp()]);
+    }
+  }
+}
+
+void Coordinates::_compute_cell_area_z() const {
+  const auto area_centre = sqrt(g_11 * g_22 - SQ(g_12)) * dx * dy;
+  _cell_area_zlow.emplace(emptyFrom(area_centre));
+  _cell_area_zhigh.emplace(emptyFrom(area_centre));
+  // We cannot setLocation, as that would trigger the computation of staggered
+  // metrics.
+  //ASSERT0(mesh->zstart > 0);
+  BOUT_FOR(i, _jxz_centre->getRegion("RGN_NOZ")) {
+    (*_cell_area_zlow)[i] = 0.5 * (area_centre[i] + area_centre[i.zm()]);
+    (*_cell_area_zhigh)[i] = 0.5 * (area_centre[i] + area_centre[i.zp()]);
+  }
+}
+
+void Coordinates::_compute_cell_volume() const { _cell_volume.emplace(J * dx * dy * dz); }