Halo finder

Exec/HaloFinder/CMakeLists.txt

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+set(_sources     Prob.cpp Prob_error.cpp)
+set(_input_files inputs inputs.summit inputs_gimlet_in_transit.dsc)
+list(APPEND _input_files inputs_nohydro.rt inputs.rt inputs.rt.garuda)
+list(APPEND _input_files 32.nyx 64sssss_20mpc.nyx TREECOOL_middle)
+list(APPEND _input_files ascent_actions_nohydro.yaml ascent_actions.yaml ascent_actions_slicefile.yaml)
+
+# setup_nyx_executable(_sources _input_files)
+nyx_setup_executable(_sources _input_files)
+
+unset(_sources)
+unset(_input_files)

Exec/HaloFinder/DarkMatterParticleContainer.H

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+
+#ifndef _DarkMatterParticleContainer_H_
+#define _DarkMatterParticleContainer_H_
+
+#include <NyxParticleContainer.H>
+
+class DarkMatterParticleContainer
+    : public NyxParticleContainer<1+AMREX_SPACEDIM>
+{
+public:
+    DarkMatterParticleContainer (amrex::Amr* amr)
+        : NyxParticleContainer<1+AMREX_SPACEDIM>(amr)
+    {
+      real_comp_names.clear();
+      real_comp_names.push_back("mass");
+      real_comp_names.push_back("xvel");
+      real_comp_names.push_back("yvel");
+      real_comp_names.push_back("zvel");
+    }
+
+    using MyParIter = amrex::ParIter<1+AMREX_SPACEDIM>;
+    using MyConstParIter = amrex::ParConstIter<1+AMREX_SPACEDIM>;
+
+    virtual ~DarkMatterParticleContainer () {}
+
+    void InitCosmo1ppcMultiLevel(amrex::MultiFab& mf, const amrex::Real disp_fac[], const amrex::Real vel_fac[],
+                                 const amrex::Real particleMass, int disp_idx, int vel_idx,
+                                 amrex::BoxArray &baWhereNot, int lev, int nlevs);
+
+    void AssignDensityAndVels (amrex::Vector<std::unique_ptr<amrex::MultiFab> >& mf, int lev_min = 0) const;
+
+    virtual void moveKickDrift (amrex::MultiFab& acceleration, int level, amrex::Real time,
+                                amrex::Real timestep,
+                                amrex::Real a_old = 1.0, amrex::Real a_half = 1.0, int where_width = 0, amrex::Real radius_inner = -1.e34, amrex::Real radius_outer = -1.e34);
+    virtual void moveKick      (amrex::MultiFab& acceleration, int level, amrex::Real time,
+                                amrex::Real timestep,
+                                amrex::Real a_new = 1.0, amrex::Real a_half = 1.0);
+
+    void InitFromBinaryMortonFile(const std::string& particle_directory, int nextra, int skip_factor);
+
+};
+
+AMREX_GPU_HOST_DEVICE AMREX_INLINE void update_dm_particle_single (amrex::ParticleContainer<1+AMREX_SPACEDIM, 0>::SuperParticleType&  p,
+                                                                   const int nc,
+                                                                   amrex::Array4<amrex::Real const> const& acc,
+                                                                   amrex::GpuArray<amrex::Real,AMREX_SPACEDIM> const& plo,
+                                                                   amrex::GpuArray<amrex::Real,AMREX_SPACEDIM> const& dxi,
+                                                                   const amrex::Real& dt, const amrex::Real& a_prev,
+                                                                   const amrex::Real& a_cur, const int& do_move);
+
+AMREX_GPU_HOST_DEVICE AMREX_INLINE void update_dm_particle_move_single (amrex::ParticleContainer<1+AMREX_SPACEDIM, 0>::SuperParticleType&  p,
+                                                                   const int nc,
+                                                                   amrex::Array4<amrex::Real const> const& acc,
+                                                                   amrex::GpuArray<amrex::Real,AMREX_SPACEDIM> const& plo,
+                                                                   amrex::GpuArray<amrex::Real,AMREX_SPACEDIM> const& dxi,
+                                                                   const amrex::Real& dt, const amrex::Real& a_prev,
+                                                                   const amrex::Real& a_cur, const int& do_move);
+
+AMREX_GPU_HOST_DEVICE AMREX_INLINE void store_dm_particle_single (amrex::ParticleContainer<1+AMREX_SPACEDIM, 0>::SuperParticleType&  p,
+                                                                  amrex::ParticleContainer<1+AMREX_SPACEDIM+6, 0>::SuperParticleType&  p2,
+                                                                  const int nc,
+                                                                  amrex::Array4<amrex::Real const> const& acc,
+                                                                  amrex::GpuArray<amrex::Real,AMREX_SPACEDIM> const& plo,
+                                                                  amrex::GpuArray<amrex::Real,AMREX_SPACEDIM> const& phi,
+                                                                  amrex::GpuArray<amrex::Real,AMREX_SPACEDIM> const& dxi,
+                                                                  const amrex::Real& dt, const amrex::Real& a_prev,
+                                                                  const amrex::Real& a_cur, const int& do_move, 
+																  const amrex::Real& radius_inner, 
+																  const amrex::Real& radius_outer, 
+																  int index, const bool is_file_write=false);
+
+#endif /* _DarkMatterParticleContainer_H_ */
+