Merge pull request QMCPACK#3489 from prckent/ppconvertcmakeclean

Fix ppconvert memory bugs and enable in testing

README.md

@@ -166,7 +166,7 @@ make -j 8
                          and use float and double for CUDA base and full precision.
      ENABLE_CUDA         ON/OFF(default). Enable CUDA code path for NVIDIA GPU acceleration.
                          Production quality for AFQMC. Pre-production quality for real-space.
-                         Use CUDA_ARCH, default sm_70, to set the actual GPU architecture.
+                         Use CMAKE_CUDA_ARCHITECTURES, default 70, to set the actual GPU architecture.
      ENABLE_OFFLOAD      ON/OFF(default). Experimental feature. Enable OpenMP target offload for GPU acceleration.
      ENABLE_TIMERS       ON(default)/OFF. Enable fine-grained timers. Timers are on by default but at level coarse
                          to avoid potential slowdown in tiny systems.

src/QMCTools/ppconvert/src/CMakeLists.txt

@@ -4,8 +4,8 @@ add_subdirectory(common)
 
 target_sources(
   ppconvert
-  PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/CubicSpline.cc" "${CMAKE_CURRENT_SOURCE_DIR}/ParseCommand.cc"
-          "${CMAKE_CURRENT_SOURCE_DIR}/XMLWriterClass2.cc" "${CMAKE_CURRENT_SOURCE_DIR}/NLPPClass.cc"
-          "${CMAKE_CURRENT_SOURCE_DIR}/ParserClass.cc")
+  PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/CubicSpline.cc" "${CMAKE_CURRENT_SOURCE_DIR}/ParseCommand.cc"
+         "${CMAKE_CURRENT_SOURCE_DIR}/XMLWriterClass2.cc" "${CMAKE_CURRENT_SOURCE_DIR}/NLPPClass.cc"
+         "${CMAKE_CURRENT_SOURCE_DIR}/ParserClass.cc")
 
 target_link_libraries(ppconvert common platform_LA)

src/QMCTools/ppconvert/src/NLPPClass.cc

@@ -2130,7 +2130,7 @@ PseudoClass::CalcProjector(std::string refstate, int lchannel)
     atom.RadialWFs(i).Energy = -0.5;
   }
   // Define a grid for solving
-  OptimalGrid *grid = new OptimalGrid(PseudoCharge, PotentialGrid.End());
+  std::shared_ptr<Grid> grid = std::make_shared<OptimalGrid>(PseudoCharge, PotentialGrid.End());
   atom.SetGrid (grid);
   // Set the potential
   atom.SetBarePot (this);

src/QMCTools/ppconvert/src/XMLWriterClass2.cc

@@ -150,7 +150,7 @@ XMLWriterClass::StartElement(std::string name)
 {
   int level = Elements.size();
 
-  XMLElement* elem = new XMLElement(name, level);
+  auto elem = std::make_shared<XMLElement>(name, level);
   if (level > 0)
     Elements.back()->AddElement (elem);
   Elements.push_back(elem);
@@ -175,7 +175,7 @@ XMLWriterClass::FullEndElement()
 bool
 XMLWriterClass::WriteAttribute (std::string name, std::string content)
 {
-  XMLAttribute *attr = new XMLAttribute (name, content);
+  auto attr = std::make_shared<XMLAttribute>(name, content);
   Elements.back()->AddAttribute (attr);
   return true;
 }
@@ -189,7 +189,7 @@ XMLWriterClass::WriteAttribute (std::string name, double val, bool scientific)
     content << std::setprecision(14);
   }
   content << val;
-  XMLAttribute *attr = new XMLAttribute (name, content.str());
+  auto attr = std::make_shared<XMLAttribute>(name, content.str());
   Elements.back()->AddAttribute (attr);
   return true;
 }
@@ -199,7 +199,7 @@ XMLWriterClass::WriteAttribute (std::string name, int val)
 {
   std::stringstream content;
   content << val;
-  XMLAttribute *attr = new XMLAttribute (name, content.str());
+  auto attr = std::make_shared<XMLAttribute>(name, content.str());
   Elements.back()->AddAttribute (attr);
   return true;
 }
@@ -223,7 +223,7 @@ bool
 XMLWriterClass::WriteElement (std::string name, std::vector<double> data)
 {
   int level = Elements.size();
-  XMLElement *elem = new XMLElement (name, level);
+  auto elem = std::make_shared<XMLElement>(name, level);
   elem->AddContent (data);
   if (level > 0)
     Elements.back()->AddElement (elem);

src/QMCTools/ppconvert/src/XMLWriterClass2.h

@@ -19,6 +19,7 @@
 #include <iostream>
 #include <fstream>
 #include <sstream>
+#include <memory> // std::shared_ptr
 
 
 class XMLAttribute
@@ -38,8 +39,8 @@ class XMLAttribute
 
 class XMLElement
 {
-  std::vector<XMLAttribute*> Attributes;
-  std::vector<XMLElement*> Children;
+  std::vector<std::shared_ptr<XMLAttribute>> Attributes;
+  std::vector<std::shared_ptr<XMLElement>> Children;
   std::string Name, Content;
   int Level;
   void Indent(std::ostream& out);
@@ -49,9 +50,9 @@ class XMLElement
 
   inline int GetLevel() { return Level; }
 
-  void AddElement(XMLElement* elem) { Children.push_back(elem); }
+  void AddElement(std::shared_ptr<XMLElement>& elem) { Children.push_back(elem); }
 
-  void AddAttribute(XMLAttribute* attr) { Attributes.push_back(attr); }
+  void AddAttribute(std::shared_ptr<XMLAttribute>& attr) { Attributes.push_back(attr); }
 
   void AddContent(std::string content) { Content += content; }
 
@@ -70,7 +71,7 @@ class XMLElement
 class XMLWriterClass
 {
 private:
-  std::vector<XMLElement*> Elements;
+  std::vector<std::shared_ptr<XMLElement>> Elements;
   void Write();
   std::ofstream Out;
 

src/QMCTools/ppconvert/src/common/AtomBase.h

@@ -18,6 +18,8 @@
 
 #include "RadialWF.h"
 
+#include <memory> // std::shared_ptr
+
 typedef enum
 {
   DFTType,
@@ -28,7 +30,7 @@ typedef enum
 class Atom
 {
 protected:
-  Grid* grid;
+  std::shared_ptr<Grid> grid;
 
 public:
   Array<RadialWF, 1> RadialWFs;
@@ -38,8 +40,8 @@ class Atom
   virtual void Solve()                                                                        = 0;
   virtual void Write(IOSectionClass& out)                                                     = 0;
   virtual void Read(IOSectionClass& in)                                                       = 0;
-  virtual void SetGrid(Grid* newGrid)                                                         = 0;
-  inline Grid* GetGrid() { return grid; }
+  virtual void SetGrid(std::shared_ptr<Grid>& newGrid)                                        = 0;
+  inline Grid* GetGrid() { return grid.get(); }
   inline double NumElecs();
   virtual void SetBarePot(Potential* pot) = 0;
 };

src/QMCTools/ppconvert/src/common/CMakeLists.txt

@@ -2,7 +2,7 @@ add_library(common EXCLUDE_FROM_ALL "")
 
 target_sources(
   common
-  PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/GKIntegration.cc
+  PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/GKIntegration.cc
           ${CMAKE_CURRENT_SOURCE_DIR}/CoulombPot.cc
           ${CMAKE_CURRENT_SOURCE_DIR}/NLPP.cc
           ${CMAKE_CURRENT_SOURCE_DIR}/DFTAtom.cc
@@ -19,6 +19,3 @@ target_sources(
           ${CMAKE_CURRENT_SOURCE_DIR}/PotentialBase.cc
           ${CMAKE_CURRENT_SOURCE_DIR}/IOASCII.cc
           ${CMAKE_CURRENT_SOURCE_DIR}/Functionals.cc)
-
-target_include_directories(common PUBLIC ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR}/blitz
-                                         ${CMAKE_CURRENT_SOURCE_DIR}/blitz/array)

src/QMCTools/ppconvert/src/common/CubicSplineCommon.h

@@ -39,7 +39,7 @@ class CubicSplineCommon
 
 public:
   int NumParams;
-  Grid* grid;
+  std::shared_ptr<Grid> grid;
   /// The values of the derivative of the represented function on the
   /// boundary.  If each value is greater that 1e30, we compute
   /// boundary conditions assuming that the second derivative is zero at
@@ -61,7 +61,7 @@ class CubicSplineCommon
 
   /// Initialize the cubic spline.  See notes about start and end
   /// deriv above.
-  inline void Init(Grid* NewGrid, Array<double, 1> NewYs, double startderiv, double endderiv)
+  inline void Init(std::shared_ptr<Grid>& NewGrid, Array<double, 1> NewYs, double startderiv, double endderiv)
   {
     StartDeriv = startderiv;
     EndDeriv   = endderiv;
@@ -82,17 +82,17 @@ class CubicSplineCommon
 
   /// Simplified form which assumes that the second derivative at both
   /// boundaries are zero.
-  inline void Init(Grid* NewGrid, Array<double, 1> NewYs) { Init(NewGrid, NewYs, 5.0e30, 5.0e30); }
+  inline void Init(std::shared_ptr<Grid>& NewGrid, Array<double, 1> NewYs) { Init(NewGrid, NewYs, 5.0e30, 5.0e30); }
 
   /// Simplified constructor.
-  inline CubicSplineCommon(Grid* NewGrid, Array<double, 1> NewYs)
+  inline CubicSplineCommon(std::shared_ptr<Grid>& NewGrid, Array<double, 1> NewYs)
   {
     StartDeriv = EndDeriv = 5.0e30;
     Init(NewGrid, NewYs, 5.0e30, 5.0e30);
   }
 
   /// Full constructor.
-  inline CubicSplineCommon(Grid* NewGrid, Array<double, 1> NewYs, double startderiv, double endderiv)
+  inline CubicSplineCommon(std::shared_ptr<Grid>& NewGrid, Array<double, 1> NewYs, double startderiv, double endderiv)
   {
     Init(NewGrid, NewYs, startderiv, endderiv);
     Update();

src/QMCTools/ppconvert/src/common/DFTAtom.cc

@@ -102,7 +102,7 @@ void DFTAtom::UpdateExCorr()
 }
 
 
-void DFTAtom::SetGrid(Grid *newgrid)
+void DFTAtom::SetGrid(std::shared_ptr<Grid>& newgrid)
 {
   grid = newgrid;
   int N = grid->NumPoints;

src/QMCTools/ppconvert/src/common/DFTAtom.h

@@ -48,7 +48,7 @@ class DFTAtom : public Atom
   double SolveIter();
   void Write(IOSectionClass& out) override;
   void Read(IOSectionClass& in) override;
-  void SetGrid(Grid* newGrid) override;
+  void SetGrid(std::shared_ptr<Grid>& newGrid) override;
   void SetBarePot(Potential* pot) override;
 
   inline double rho(double r) { return ChargeDensity(r); }

src/QMCTools/ppconvert/src/common/GeneralPot.cc

@@ -70,9 +70,3 @@ GeneralPot::GeneralPot() : PotGrid(NULL)
 {
 
 }
-
-GeneralPot::~GeneralPot()
-{
-  if (PotGrid != NULL)
-    delete PotGrid;
-}

src/QMCTools/ppconvert/src/common/GeneralPot.h

@@ -22,7 +22,7 @@
 class GeneralPot : public Potential
 {
 protected:
-  Grid* PotGrid;
+  std::shared_ptr<Grid> PotGrid;
   CubicSplineCommon PotSpline;
   double Z;
 
@@ -34,7 +34,7 @@ class GeneralPot : public Potential
   void Write(IOSectionClass& out) override;
   void Read(IOSectionClass& in) override;
   GeneralPot();
-  ~GeneralPot();
+  ~GeneralPot() = default;
 };
 
 #endif

src/QMCTools/ppconvert/src/common/Grid.h

@@ -630,31 +630,31 @@ class ClusterGrid : public Grid
 };
 
 
-inline Grid* ReadGrid(IOSectionClass& inSection)
+inline std::shared_ptr<Grid> ReadGrid(IOSectionClass& inSection)
 {
   std::string Type;
   assert(inSection.ReadVar("Type", Type));
 
-  Grid* newGrid;
+  std::shared_ptr<Grid> newGrid;
   if (Type == "Linear")
-    newGrid = new LinearGrid;
+    newGrid = std::make_shared<LinearGrid>();
   else if (Type == "General")
-    newGrid = new GeneralGrid;
+    newGrid = std::make_shared<GeneralGrid>();
   else if (Type == "Optimal")
-    newGrid = new OptimalGrid;
+    newGrid = std::make_shared<OptimalGrid>();
   else if (Type == "Optimal2")
-    newGrid = new OptimalGrid2;
+    newGrid = std::make_shared<OptimalGrid2>();
   else if (Type == "Log")
-    newGrid = new LogGrid;
+    newGrid = std::make_shared<LogGrid>();
   else if (Type == "Cluster")
-    newGrid = new ClusterGrid;
+    newGrid = std::make_shared<ClusterGrid>();
   else
   {
     std::cerr << "Unrecognized Grid type " << Type << "\n";
     exit(1);
   }
   newGrid->Read(inSection);
-  return (newGrid);
+  return newGrid;
 }
 
 

src/QMCTools/ppconvert/src/common/NLPP.cc

@@ -23,7 +23,7 @@ NLPPClass::IsNonlocal()
 }
 
 void 
-ChannelPotential::Read(IOSectionClass &in, Grid *grid)
+ChannelPotential::Read(IOSectionClass &in, std::shared_ptr<Grid>& grid)
 {
   assert (in.ReadVar("l", l));
   assert (in.ReadVar("n_principal", n_principal));
@@ -232,7 +232,7 @@ ChannelPotential::SetupProjector (double G_max, double G_FFT)
   zeta(0) = ProjectorNorm * DeltaV(0)*u(1.0e-8)*1.0e8;
   for (int i=1; i<grid.NumPoints; i++) 
     zeta(i) = ProjectorNorm * DeltaV(i)*u(i)/grid(i);
-  zeta_r.Init (&grid, zeta);
+  zeta_r.Init (u.grid, zeta);
 
   // Compute zeta(q)
   Job = ZETA_Q;
@@ -242,15 +242,16 @@ ChannelPotential::SetupProjector (double G_max, double G_FFT)
     qCurrent = qGrid(i);
     zeta(i) = integrator.Integrate(0.0, grid.End, 1.0e-12);
   }
-  zeta_q.Init (&qGrid, zeta);
+  std::shared_ptr<Grid> qGridSharedPtr(&qGrid);
+  zeta_q.Init (qGridSharedPtr, zeta);
 
 
   double gamma = G_FFT - G_max;
   // Zero out zeta_q above gamma;
   Array<double,1> chi_q_data(qGrid.NumPoints);
   for (int i=0; i<qGrid.NumPoints; i++) 
     chi_q_data(i) = (qGrid(i) >= gamma) ? 0.0 : zeta_q(i);
-  chi_q.Init  (&qGrid, chi_q_data);  
+  chi_q.Init  (qGridSharedPtr, chi_q_data);
 
   // Now for the magic:  We adjust chi_q between G_max and gamma so
   // that the real-space oscillations outside R0 are damped out
@@ -316,7 +317,7 @@ ChannelPotential::SetupProjector (double G_max, double G_FFT)
     rCurrent = grid(i);
     chi_r_data(i) = integrator.Integrate(0.0, gamma, 1.0e-10);
   }
-  chi_r.Init (&grid, chi_r_data);
+  chi_r.Init (u.grid, chi_r_data);
 
   // Finally, check to see if chi_r is small outside R0
   Job = CHECK_CHI_R;

src/QMCTools/ppconvert/src/common/NLPP.h

@@ -63,7 +63,7 @@ class ChannelPotential
   inline double operator()(double x);
 
   void SetupProjector(double G_max, double G_FFT);
-  void Read(IOSectionClass& in, Grid* grid);
+  void Read(IOSectionClass& in, std::shared_ptr<Grid>& grid);
   void Write(IOSectionClass& out);
 };
 
@@ -77,7 +77,7 @@ class NLPPClass : public Potential
   double Zion;
   int AtomicNumber;
   std::string Symbol;
-  Grid* PotentialGrid;
+  std::shared_ptr<Grid> PotentialGrid;
 
 public:
   // General accessor functions

src/QMCTools/ppconvert/src/common/PotentialBase.h

@@ -22,6 +22,7 @@ using namespace IO;
 class Potential
 {
 public:
+  virtual ~Potential() = default;
   // Optional member functions -- if you're not a pseudoHamiltonian,
   // you do not need to define these
   virtual bool IsPH();

src/QMCTools/ppconvert/src/common/RadialWF.cc

@@ -369,7 +369,7 @@ RadialWF::CountNodes()
 }
 
 void 
-RadialWF::SetGrid(Grid *newgrid)
+RadialWF::SetGrid(std::shared_ptr<Grid>& newgrid)
 {
   grid = newgrid;
   int N = grid->NumPoints;

src/QMCTools/ppconvert/src/common/RadialWF.h

@@ -33,7 +33,7 @@ class RadialWF
   Potential* pot;
 
 public:
-  Grid* grid;
+  std::shared_ptr<Grid> grid;
   CubicSplineCommon u, dudr;
   int n, l, CoreNodes;
   double Energy, Occupancy, Weight;
@@ -49,7 +49,7 @@ class RadialWF
   double LogDerivative();
   void Solve(double tolerance = 1.0e-8);
   void Normalize();
-  void SetGrid(Grid* newgrid);
+  void SetGrid(std::shared_ptr<Grid>& newgrid);
   void SetPotential(Potential* newPot);
   Potential* GetPotential();
   void Write(IOSectionClass& out);

src/QMCTools/ppconvert/src/common/SplinePot.cc

@@ -60,7 +60,7 @@ double SplinePot::d2Vdr2(double r)
 void SplinePot::Read(IOSectionClass &in)
 {
   assert(in.OpenSection("Grid"));
-  Grid *grid = ReadGrid(in);
+  auto grid = ReadGrid(in);
   in.CloseSection(); // "Grid" 
   Array<double,1> data;
   assert(in.ReadVar("SplineData", data));