update and merge air travel code

.gitignore

@@ -4,3 +4,5 @@ docs/doxyhtml
 docs/doxyxml
 docs/exaepi-doxygen-web.tag.xml
 docs/amrex-doxygen-web.tag.xml
+.vscode
+.build

CMakeLists.txt

@@ -5,6 +5,9 @@ project( ExaEpi
    #VERSION  ${AMREX_PKG_VERSION}
    )
 
+# Defines a DEBUG symbol for use in the code
+add_compile_options("$<$<CONFIG:DEBUG>:-DDEBUG>")
+
 set( CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake )
 
 set(AMReX_PARTICLES       ON)
@@ -72,3 +75,4 @@ foreach (_subdir IN LISTS AMREX_AGENT_SUBDIRS)
       add_subdirectory(${_dir})
    endforeach ()
 endforeach ()
+

docs/source/usage/utilities.rst

@@ -36,11 +36,11 @@ Data is either written as an ``int`` or a ``real``.
 
   - Real data:
 
-    - ``incubation_period``: (currently misleadingly named) Latent period length, i.e. time between exposure and infectiousness.
+    - ``latent_period``: Latent period length, i.e. time between exposure and infectiousness.
 
     - ``infectious_period``: Infections period length, i.e. time during which agent can spread disease
 
-    - ``symptomdev_period``: Symptom development period length (known as incubation period in some contexts), i.e. time between exposure and symptoms appearing.
+    - ``incubation_period``: Symptom development period length (known as incubation period in some contexts), i.e. time between exposure and symptoms appearing.
 
 - Every day (time-varying)
 

etc/plot_infected.ipynb

@@ -22,11 +22,11 @@
     "never = []\n",
     "with open(\"agent_data/run_9_cases.out\") as f:\n",
     "    for line in f:\n",
-    "        if line.startswith(\"Never infected: \"):\n",
+    "        if line.startswith(\"Susceptible: \"):\n",
     "            never.append(int(line.strip().split()[-1]))\n",
     "        if line.startswith(\"Infected: \"):\n",
     "            infected.append(int(line.strip().split()[1]))\n",
-    "        if line.startswith(\"Immune: \"):\n",
+    "        if line.startswith(\"Recovered: \"):\n",
     "            immune.append(int(line.strip().split()[1]))"
    ]
   },
@@ -53,7 +53,7 @@
     "ax = plt.gca()\n",
     "ax.set_xlabel(\"Day\")\n",
     "ax.set_ylabel(\"Number\")\n",
-    "plt.legend((\"Never infected\", \"Infected\", \"Immune\"))\n",
+    "plt.legend((\"Susceptible\", \"Infected\", \"Recovered\"))\n",
     "\n",
     "plt.savefig(\"infected_9_cases\")"
    ]

src/AgentContainer.H

@@ -34,7 +34,7 @@ class AgentContainer
     using PType = ParticleType;
     using PTileType = ParticleTileType;
     using PTDType = PTileType::ParticleTileDataType;
-    using IntModel = InteractionModel<PCType,PTileType,PTDType,PType>;
+    using IntModel = InteractionModel<PCType, PTDType, PType>;
 
     using MFPtr = std::unique_ptr<MultiFab>;
     using MFPtrVec = std::vector<MFPtr>;
@@ -45,7 +45,8 @@ public:
                     const amrex::DistributionMapping & a_dmap,
                     const amrex::BoxArray            & a_ba,
                     const int                        & a_num_diseases,
-                    const std::vector<std::string>   & a_disease_names);
+                    const std::vector<std::string>   & a_disease_names,
+                    const bool                       fast);
 
     void morningCommute(amrex::MultiFab&);
 
@@ -57,19 +58,17 @@ public:
 
     void interactNight(amrex::MultiFab&);
 
-    void interactRandomTravel(amrex::MultiFab&, AgentContainer& on_travel_pc);
+    void moveAirTravel (const amrex::iMultiFab& unit_mf, AirTravelFlow& air, DemographicData& demo);
 
-    void interactAirTravel(amrex::MultiFab&, AgentContainer& on_travel_pc);
+    void setAirTravel (const iMultiFab& unit_mf, AirTravelFlow& air, DemographicData& demo);
 
     void moveAgentsRandomWalk ();
 
-    void moveRandomTravel ();
-    void moveAirTravel (const amrex::iMultiFab& unit_mf, AirTravelFlow& air, DemographicData& demo);
-    void setAirTravel (const iMultiFab& unit_mf, AirTravelFlow& air, DemographicData& demo);
+    void moveRandomTravel (const amrex::Real random_travel_prob);
 
-    void returnRandomTravel (const AgentContainer& on_travel_pc);
+    void returnRandomTravel ();
 
-    void returnAirTravel (const AgentContainer& on_travel_pc);
+    void returnAirTravel ();
 
     void updateStatus (MFPtrVec&);
 
@@ -83,12 +82,12 @@ public:
 
     std::array<amrex::Long, 9> getTotals (const int);
 
+    int getMaxGroup(const int group_idx);
+
     void moveAgentsToWork ();
 
     void moveAgentsToHome ();
 
-    amrex::DenseBins<PType>* getBins(const std::pair<int,int>& a_idx, const std::string& a_mod_name);
-
     /*! \brief Return flag indicating if agents are at work */
     inline bool isAtWork() const {
         return m_at_work;
@@ -164,25 +163,17 @@ protected:
     std::vector<DiseaseParm*> m_h_parm;    /*!< Disease parameters */
     std::vector<DiseaseParm*> m_d_parm;    /*!< Disease parameters (GPU device) */
 
-    /*! Map of home bins (of agents) indexed by MultiFab iterator and tile index;
-        see AgentContainer::interactAgentsHomeWork() */
-    std::map<std::pair<int, int>, amrex::DenseBins<PType> > m_bins_home;
-    /*! Map of work bins (of agents) indexed by MultiFab iterator and tile index;
-        see AgentContainer::interactAgentsHomeWork() */
-    std::map<std::pair<int, int>, amrex::DenseBins<PType> > m_bins_work;
-    /*! Map of air and random travel bins (of agents) indexed by MultiFab iterator and tile index;
-        see AgentContainer::interactAgentsRandom() */
-    std::map<std::pair<int, int>, amrex::DenseBins<PType> > m_bins_travel;
-
-    std::map<std::string,IntModel*> m_interactions; /*!< Map of interaction models */
-    std::unique_ptr<HospitalModel<PCType,PTileType,PTDType,PType>> m_hospital; /*!< hospital model */
+    std::map<std::string, IntModel*> m_interactions; /*!< Map of interaction models */
+    std::unique_ptr<HospitalModel<PCType, PTDType, PType>> m_hospital; /*!< hospital model */
 
     /*! Flag to indicate if agents are at work */
     bool m_at_work;
 
     /*! Disease status update model */
     DiseaseStatus<PCType,PTileType,PTDType,PType> m_disease_status;
 
+    Array<int, IntIdx::nattribs> max_attribute_values;
+
     /*! \brief queries if a given interaction type (model) is available */
     inline bool haveInteractionModel( const std::string& a_mod_name ) const {
         return (m_interactions.find(a_mod_name) != m_interactions.end());