fix particle WOA inputs and some formatting. (#1367)

Exec/DevTests/ParticlesOverWoA/inputs

@@ -44,7 +44,7 @@ erf.check_int = 10 # number of timesteps between checkpoints
 # PLOTFILES
 erf.plot_file_1 = plt # prefix of plotfile name
 erf.plot_int_1 = 5 # number of timesteps between plotfiles
-erf.plot_vars_1 = density x_velocity y_velocity z_velocity pressure theta pres_hse dens_hse pert_pres pert_dens z_phys detJ dpdx dpdy pres_hse_x pres_hse_y tracer_particle_count
+erf.plot_vars_1 = density x_velocity y_velocity z_velocity pressure theta pres_hse dens_hse pert_pres pert_dens z_phys detJ dpdx dpdy pres_hse_x pres_hse_y tracer_particles_count
 
 # SOLVER CHOICE
 erf.use_gravity = true

Source/Particles/ERFPC.H

@@ -103,16 +103,16 @@ class ERFPC : public amrex::ParticleContainer< ERFParticlesRealIdx::ncomps,
  }
 
  /*! Initialize particles in domain */
- virtual void InitializeParticles(const std::unique_ptr<amrex::MultiFab>& a_ptr = nullptr);
+ virtual void InitializeParticles (const std::unique_ptr<amrex::MultiFab>& a_ptr = nullptr);
 
  /*! Evolve particles for one time step */
- virtual void EvolveParticles( int,
- amrex::Real,
- amrex::Vector<amrex::Vector<amrex::MultiFab>>&,
- const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& );
+ virtual void EvolveParticles ( int,
+  amrex::Real,
+  amrex::Vector<amrex::Vector<amrex::MultiFab>>&,
+  const amrex::Vector<std::unique_ptr<amrex::MultiFab>>& );
 
  /*! Get real-type particle attribute names */
- virtual amrex::Vector<std::string> varNames() const
+ virtual amrex::Vector<std::string> varNames () const
  {
  BL_PROFILE("ERFPCPC::varNames()");
  return {AMREX_D_DECL("xvel","yvel","zvel"),"mass"};
@@ -142,30 +142,30 @@ class ERFPC : public amrex::ParticleContainer< ERFParticlesRealIdx::ncomps,
  int m_ppc_init; /*!< initial number of particles per cell */
 
  /*! read inputs from file */
- virtual void readInputs();
+ virtual void readInputs ();
 
  /*! Default particle initialization */
- void initializeParticlesUniformDistribution(const std::unique_ptr<amrex::MultiFab>& a_ptr = nullptr);
+ void initializeParticlesUniformDistribution (const std::unique_ptr<amrex::MultiFab>& a_ptr = nullptr);
 
  /*! Uses midpoint method to advance particles using flow velocity. */
- void AdvectWithFlow( amrex::MultiFab*,
- int,
- amrex::Real,
- const std::unique_ptr<amrex::MultiFab>& );
+ void AdvectWithFlow ( amrex::MultiFab*,
+  int,
+  amrex::Real,
+  const std::unique_ptr<amrex::MultiFab>& );
 
  /*! Uses midpoint method to advance particles falling under gravity. */
- void AdvectWithGravity( int,
- amrex::Real,
- const std::unique_ptr<amrex::MultiFab>& );
+ void AdvectWithGravity ( int,
+  amrex::Real,
+  const std::unique_ptr<amrex::MultiFab>& );
 
  private:
 
  /*! Default particle initialization */
- void initializeParticlesDefault(const std::unique_ptr<amrex::MultiFab>& a_ptr = nullptr);
+ void initializeParticlesDefault (const std::unique_ptr<amrex::MultiFab>& a_ptr = nullptr);
  /*! Default initialization for tracer particles for WoA case (ref: AA) */
- void initializeParticlesDefaultTracersWoA(const std::unique_ptr<amrex::MultiFab>& a_ptr=nullptr);
+ void initializeParticlesDefaultTracersWoA (const std::unique_ptr<amrex::MultiFab>& a_ptr=nullptr);
  /*! Default initialization for hydro particles (ref: AA) */
- void initializeParticlesDefaultHydro(const std::unique_ptr<amrex::MultiFab>& a_ptr = nullptr);
+ void initializeParticlesDefaultHydro (const std::unique_ptr<amrex::MultiFab>& a_ptr = nullptr);
 
 };
 

Source/Particles/ERFPCEvolve.cpp

@@ -9,10 +9,10 @@
 using namespace amrex;
 
 /*! Evolve particles for one time step */
-void ERFPC::EvolveParticles( int a_lev,
- Real a_dt_lev,
- Vector<Vector<MultiFab>>& a_flow_vars,
- const Vector<std::unique_ptr<MultiFab>>& a_z_phys_nd )
+void ERFPC::EvolveParticles ( int a_lev,
+  Real a_dt_lev,
+  Vector<Vector<MultiFab>>& a_flow_vars,
+  const Vector<std::unique_ptr<MultiFab>>& a_z_phys_nd )
 {
  BL_PROFILE("ERFPCPC::EvolveParticles()");
 
@@ -28,10 +28,10 @@ void ERFPC::EvolveParticles( int a_lev,
 }
 
 /*! Uses midpoint method to advance particles using flow velocity. */
-void ERFPC::AdvectWithFlow( MultiFab* a_umac,
- int a_lev,
- Real a_dt,
- const std::unique_ptr<MultiFab>& a_z_height )
+void ERFPC::AdvectWithFlow ( MultiFab* a_umac,
+  int a_lev,
+  Real a_dt,
+  const std::unique_ptr<MultiFab>& a_z_height )
 {
  BL_PROFILE("ERFPCPC::AdvectWithUmac()");
  AMREX_ASSERT(OK(a_lev, a_lev, a_umac[0].nGrow()-1));
@@ -163,9 +163,9 @@ void ERFPC::AdvectWithFlow( MultiFab* a_umac,
  }
 }
 
-void ERFPC::AdvectWithGravity( int a_lev,
- Real a_dt,
- const std::unique_ptr<MultiFab>& a_z_height )
+void ERFPC::AdvectWithGravity ( int a_lev,
+  Real a_dt,
+  const std::unique_ptr<MultiFab>& a_z_height )
 {
  BL_PROFILE("ERFPC::AdvectWithGravity()");
  AMREX_ASSERT(a_lev >= 0 && a_lev < GetParticles().size());

Source/Particles/ERFPCInitializations.cpp

@@ -8,7 +8,7 @@
 using namespace amrex;
 
 /*! Read inputs from file */
-void ERFPC::readInputs()
+void ERFPC::readInputs ()
 {
  BL_PROFILE("ERFPC::readInputs");
 
@@ -30,7 +30,7 @@ void ERFPC::readInputs()
 }
 
 /*! Initialize particles in domain */
-void ERFPC::InitializeParticles(const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
+void ERFPC::InitializeParticles (const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
 {
  BL_PROFILE("ERFPC::initializeParticles");
 
@@ -48,7 +48,7 @@ void ERFPC::InitializeParticles(const std::unique_ptr<amrex::MultiFab>& a_height
 }
 
 /*! Default particle initialization */
-void ERFPC::initializeParticlesDefault(const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
+void ERFPC::initializeParticlesDefault (const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
 {
  BL_PROFILE(" ERFPC::initializeParticlesDefault");
 
@@ -60,7 +60,7 @@ void ERFPC::initializeParticlesDefault(const std::unique_ptr<amrex::MultiFab>& a
 }
 
 /*! Default initialization for tracer particles for WoA case (ref: AA) */
-void ERFPC::initializeParticlesDefaultTracersWoA(const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
+void ERFPC::initializeParticlesDefaultTracersWoA (const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
 {
  BL_PROFILE("ERFPC::initializeParticlesDefaultTracersWoA");
 
@@ -168,7 +168,7 @@ void ERFPC::initializeParticlesDefaultTracersWoA(const std::unique_ptr<amrex::Mu
 }
 
 /*! Default initialization for hydro particles (ref: AA) */
-void ERFPC::initializeParticlesDefaultHydro(const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
+void ERFPC::initializeParticlesDefaultHydro (const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
 {
  BL_PROFILE("ERFPC::initializeParticlesDefaultHydro");
 
@@ -277,7 +277,7 @@ void ERFPC::initializeParticlesDefaultHydro(const std::unique_ptr<amrex::MultiFa
 
 /*! Uniform distribution: the number of particles per grid cell is specified
  * by "initial_particles_per_cell", and they are randomly distributed. */
-void ERFPC::initializeParticlesUniformDistribution(const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
+void ERFPC::initializeParticlesUniformDistribution (const std::unique_ptr<amrex::MultiFab>& a_height_ptr)
 {
  BL_PROFILE("ERFPC::initializeParticlesUniformDistribution");
 

Source/Particles/ERFTracers.cpp

@@ -7,7 +7,7 @@
 using namespace amrex;
 
 /*! Read tracer and hydro particles parameters */
-void ERF::readTracersParams()
+void ERF::readTracersParams ()
 {
  ParmParse pp(pp_prefix);
 
@@ -28,8 +28,8 @@ void ERF::readTracersParams()
 }
 
 /*! Initialize tracer and hydro particles */
-void ERF::initializeTracers( ParGDBBase* a_gdb,
- const Vector<std::unique_ptr<MultiFab>>& a_z_phys_nd )
+void ERF::initializeTracers ( ParGDBBase* a_gdb,
+  const Vector<std::unique_ptr<MultiFab>>& a_z_phys_nd )
 {
  auto& namelist_unalloc( particleData.getNamesUnalloc() );
 
@@ -63,10 +63,10 @@ void ERF::initializeTracers( ParGDBBase* a_gdb,
 }
 
 /*! Evolve tracers and hydro particles for one time step*/
-void ERF::evolveTracers( int a_lev,
- Real a_dt_lev,
- Vector<Vector<MultiFab>>& a_vars_new,
- const Vector<std::unique_ptr<MultiFab>>& a_z_phys_nd )
+void ERF::evolveTracers ( int a_lev,
+  Real a_dt_lev,
+  Vector<Vector<MultiFab>>& a_vars_new,
+  const Vector<std::unique_ptr<MultiFab>>& a_z_phys_nd )
 {
  if (m_use_tracer_particles) {
  particleData[ERFParticleNames::tracers]->EvolveParticles( a_lev,

Source/Particles/ParticleData.H

@@ -28,7 +28,7 @@ class ParticleData
  public:
 
  /*! Constructor */
- ParticleData()
+ ParticleData ()
  {
  BL_PROFILE("ParticleData::ParticleData()");
  m_particle_species.clear();
@@ -37,7 +37,7 @@ class ParticleData
  }
 
  /*! Destructor */
- ~ParticleData()
+ ~ParticleData ()
  {
  BL_PROFILE("ParticleData::~ParticleData()");
  for (ParticlesNamesVector::size_type i = 0; i < m_namelist.size(); i++) {
@@ -50,7 +50,7 @@ class ParticleData
  }
 
  /*! Write checkpoint files */
- void Checkpoint( const std::string& a_fname )
+ void Checkpoint ( const std::string& a_fname )
  {
  BL_PROFILE("ParticleData::Checkpoint()");
  for (ParticlesNamesVector::size_type i = 0; i < m_namelist.size(); i++) {
@@ -61,7 +61,7 @@ class ParticleData
  }
 
  /*! Read from restart file */
- void Restart( amrex::ParGDBBase* a_gdb, const std::string& a_fname )
+ void Restart ( amrex::ParGDBBase* a_gdb, const std::string& a_fname )
  {
  BL_PROFILE("ParticleData::Restart()");
  AMREX_ASSERT(isEmpty());
@@ -75,7 +75,7 @@ class ParticleData
  }
 
  /*! Redistribute/rebalance particles data */
- inline void Redistribute()
+ inline void Redistribute ()
  {
  BL_PROFILE("ParticleData::Redistribute()");
  for (ParticlesNamesVector::size_type i = 0; i < m_namelist.size(); i++) {
@@ -84,7 +84,7 @@ class ParticleData
  }
 
  /*! Get species of a given name */
- inline ERFPC* GetSpecies( const std::string& a_name )
+ inline ERFPC* GetSpecies ( const std::string& a_name )
  {
  BL_PROFILE("ParticleData::GetSpecies()");
  ParticleSpeciesMap::iterator it (m_particle_species.find(a_name));
@@ -112,7 +112,7 @@ class ParticleData
  }
 
  /*! Get species of a given name (const version) */
- inline const ERFPC* GetSpecies( const std::string& a_name ) const
+ inline const ERFPC* GetSpecies ( const std::string& a_name ) const
  {
  BL_PROFILE("ParticleData::GetSpecies()");
  ParticleSpeciesMap::const_iterator it (m_particle_species.find(a_name));
@@ -140,7 +140,7 @@ class ParticleData
  }
 
  /*! Add a particle species to this container */
- inline void pushBack(const std::string& a_name,
+ inline void pushBack (const std::string& a_name,
  ERFPC* const a_pc )
  {
  BL_PROFILE("ParticleData::pushBack()");
@@ -150,36 +150,36 @@ class ParticleData
  }
 
  /*! Add a name; particle container will be initialized later */
- inline void addName(const std::string& a_name )
+ inline void addName (const std::string& a_name )
  {
  BL_PROFILE("ParticleData::addName()");
  m_namelist_unalloc.push_back(a_name);
  }
 
  /*! Returns list of names of particle species */
- inline const ParticlesNamesVector& getNames() const
+ inline const ParticlesNamesVector& getNames () const
  {
  BL_PROFILE("ParticleData::getNames()");
  return m_namelist;
  }
 
  /*! Returns list of names of particle species that are unallocated */
- inline ParticlesNamesList& getNamesUnalloc()
+ inline ParticlesNamesList& getNamesUnalloc ()
  {
  BL_PROFILE("ParticleData::getNamesUnalloc()");
  return m_namelist_unalloc;
  }
 
  /*! queries if containe has species of a certain name */
- inline bool contains( const std::string& a_name ) const
+ inline bool contains ( const std::string& a_name ) const
  {
  BL_PROFILE("ParticleData::contains()");
  ParticleSpeciesMap::const_iterator it (m_particle_species.find(a_name));
  return (it != m_particle_species.end());
  }
 
  /*! query if container is empty */
- inline bool isEmpty() const
+ inline bool isEmpty () const
  {
  BL_PROFILE("ParticleData::isEmpty()");
  return (m_particle_species.size() == 0);