Bug fixes and other adjustments from comparison to Epicast

docs/source/usage/how_to_run.rst

@@ -88,8 +88,15 @@ The following are inputs for the overall simulation:
     Number of days shelter-in-place is in effect.
 * ``agent.shelter_compliance`` (`float`, default ``0.95``)
     Fraction of agents that comply with shelter-in-place order.
-* ``agent.symptomatic_withdraw_compliance`` (`float`, default: ``0.95``)
-    Compliance rate for agents withdrawing when they have symptoms. Should be 0.0 to 1.0. Set it to 0 if not using withdrawal.
+* ``agent.symptomatic_withdraw_compliance_0`` (`float`, default: ``0.3 0.3 0.3 0.3 0.3 0.3``)
+    Compliance rate for agents withdrawing on day 0 when they have symptoms, per age groups u5, 6-17, 18-29, 30-49, 50-64, 64+.
+    Should be 0.0 to 1.0. Set it to 0 if not using withdrawal.
+* ``agent.symptomatic_withdraw_compliance_1`` (`float`, default: ``0.8 0.6 0.5 0.5 0.5 0.5``)
+    Compliance rate for agents withdrawing on day 1 when they have symptoms, per age groups u5, 6-17, 18-29, 30-49, 50-64, 64+.
+    Should be 0.0 to 1.0. Set it to 0 if not using withdrawal.
+* ``agent.symptomatic_withdraw_compliance_2`` (`float`, default: ``0.9 0.8 0.7 0.7 0.7 0.7``)
+    Compliance rate for agents withdrawing on day 2 when they have symptoms, per age groups u5, 6-17, 18-29, 30-49, 50-64, 64+.
+    Should be 0.0 to 1.0. Set it to 0 if not using withdrawal.
 * ``agent.child_compliance`` (`float`, default ``0.95``)
     Compliance rate for children when schools are closed. This reduces the probability of transmission within
     neighborhood clusters, neighborhoods and communities.
@@ -98,11 +105,8 @@ The following are inputs for the overall simulation:
 * ``agent.student_teacher_ratio`` (`list of int`, default: ``0 15 15 15 15 15``)
     This option sets the desired student-teacher ratio for school levels (none, college, high, middle, elementary, daycare).
     The first entry is ignored and should always be set to 0. This option is only used with ``ic_type = census``.
-* ``agent.max_box_size`` (`integer`, default ``16`` or ``500`` or ``100``)
-    This option sets the maximum box size used for MPI domain decomposition. If set to
-    ``16``, for example, for ``ic_type = census``, the domain will be broken up into boxes of `16^2` communities, and
-    these boxes will be assigned to different MPI ranks / GPUs.
-    The default for ``ictype = census`` is 16, and for ``ic_type = urbanpop`` it is 500 when using GPUs, and 100 otherwise.
+* ``agent.max_box_size`` (`integer`, default ``16``)
+    This option sets the maximum box size used for MPI domain decomposition.
 * ``diag.output_filename`` (`string`, default ``output.dat`` for a single disease,
     ``diag.output_[disease name].dat`` for multiple diseases)
     Filename for the output data; the number of list elements must be the same as ``agent.number_of_diseases``.

examples/inputs.defaults

@@ -45,8 +45,10 @@ agent.shelter_start = -1
 agent.shelter_length = 0
 # The compliance rate for shelter-in-place, i.e. the probability of an agent actually sheltering.
 agent.shelter_compliance = 0.95
-# The probability of an agent withdrawing when first becoming symptomatic.
-agent.symptomatic_withdraw_compliance = 0.95
+# The probability of an agent withdrawing on day 0, day 1 and day 2 for age groups u5, 5-17, 18-29, 30-49, 50-64, 65+
+agent.symptomatic_withdraw_compliance_day_0 = 0.3 0.3 0.3 0.3 0.3 0.3
+agent.symptomatic_withdraw_compliance_day_1 = 0.8 0.6 0.5 0.5 0.5 0.5
+agent.symptomatic_withdraw_compliance_day_2 = 0.9 0.8 0.7 0.7 0.7 0.7
 # The compliance rate for children when schools are closed. This reduces the probability of transmission in the neighborhood.
 agent.child_compliance = 0.5
 # A factor for increasing transmission by children within households when schools are closed.
@@ -55,12 +57,7 @@ agent.child_HH_closure = 2
 # This is only used for the census data.
 agent.student_teacher_ratio = 0 15 15 15 15 15
 # The maximum grid size used for MPI domain decomposition. Adjusting this can change the computation time and load balance.
-# if ic_type is census
-# agent.max_box_size = 16
-# if ic_type is urbanpop and using GPUs
-# agent.max_box_size = 500
-# if ic_type is urbanpop and not using GPUs
-# agent.max_box_size = 100
+agent.max_box_size = 16
 
 # A list of file names, one per disease, each one of which will be the output for the counts of the statuses for that disease.
 # defalut for one disease
@@ -112,8 +109,12 @@ disease.hospital_delay_length_alpha = 1.0
 # Beta parameter for the hospital_delay length Gamma distribution. The hospital_delay length is the length in days after developing symptoms that agents seek treatment.
 disease.hospital_delay_length_beta = 1.0
 
-# Number of days in hospital for the age groups under 50, 50 to 64 and over 64.
-disease.hospitalization_days = 3 8 7
+# Number of days in hospital for age groups 0-4, 5-17, 18-29, 30-49, 50-64, 64+
+disease.hospitalization_days = 3 3 3 3 8 7
+# Alpha parameter for days in hospital Gamma distribution, for age groups 0-4, 5-17, 18-29, 30-49, 50-64, 64+
+disease.hospitalization_days_alpha = 1.33 1.33 1.33 1.33 0.5 0.57
+# Beta parameter for days in hospital Gamma distribution, for age groups 0-4, 5-17, 18-29, 30-49, 50-64, 64+
+disease.hospitalization_days_beta = 1.5 1.5 1.5 1.5 4.0 3.5
 
 # Transmission probabilites at the community level, for both work and home locations,
 # for the age groups 0-4, 5-17, 18-29, 30-49, 50-64, 64+

examples/inputs.nm

@@ -1,32 +1,16 @@
-# settings for the census input type
-# agent.ic_type = "census"
-agent.census_filename = "../CensusData/NM_TX_2010.dat"
-agent.workerflow_filename = "../CensusData/US-wf.bin"
-
-# settings for the urbanpop input type
-# agent.ic_type = "urbanpop"
-agent.urbanpop_filename = "../UrbanPop/NM_35/urbanpop_nm"
+# The input data file for urbanpop ic_type. Do not include the extension. There must be two files, with extensions .csv and .idx.
+agent.ic_type = "urbanpop"
+agent.urbanpop_filename = "data/UrbanPop/urbanpop_nm"
 
 agent.nsteps = 70
-#agent.seed = 11
+agent.plot_int = -1
 
-disease.initial_case_type = "file"
-disease.case_filename = "../CaseData/nm-july4.cases"
+agent.aggregated_diag_int = -1
 
-# agent.number_of_diseases = 2
-# agent.disease_names = "covid" "flu"
+agent.seed = 0
 
-# disease.initial_case_type = "random" "random"
-# disease.num_initial_cases = 1000
+diag.output_filename = output_nm.dat
 
-# setting these results in simulations with similar outcomes between UrbanPop and Census
-# disease.hospitalization_days = 6 6 6
-# disease.CHR = 0.1 0.1 0.1 0.1 0.1 0.1
-# disease.CIC = 0.3 0.3 0.3 0.3 0.3 0.3
-# disease.CVE = 0.15 0.15 0.15 0.15 0.15 0.15
-# disease.hospCVF = 0 0 0 0 0 0
-# disease.icuCVF = 0 0 0 0 0 0.0
-# disease.ventCVF = 0.3 0.3 0.3 0.3 0.3 0.3
+disease.initial_case_type = "file"
+disease.case_filename = "data/CaseData/nm-july4.cases"
 
-# disease_flu.num_initial_cases = 100
-# disease_flu.p_trans = 0.3

src/AgentContainer.H

@@ -77,6 +77,8 @@ class AgentContainer : public amrex::ParticleContainer<0, 0, RealIdx::nattribs,
 
     std::array<amrex::Long, OutputStatus::nattribs> getTotals(const int);
 
+    std::array<amrex::Long, AgeGroups::total> getNewStatusByAge(const int a_d, const int output_status);
+
     int getMaxGroup(const int group_idx);
 
     void moveAgentsToWork();
@@ -97,9 +99,6 @@ class AgentContainer : public amrex::ParticleContainer<0, 0, RealIdx::nattribs,
     /*! \brief Return the number of diseases */
     inline int numDiseases () const { return m_num_diseases; }
 
-    /*! \brief return the symptomatic withdrawal compliance */
-    inline amrex::Real symptomaticWithdrawCompliance () const { return m_symptomatic_withdraw_compliance; }
-
     void printStudentTeacherCounts() const;
 
     void printAgeGroupCounts() const;
@@ -108,18 +107,27 @@ class AgentContainer : public amrex::ParticleContainer<0, 0, RealIdx::nattribs,
     /// Used only for Census data. A ratio for each school type: none, college, high, middle, elem, daycare
     amrex::GpuArray<int, SchoolType::total> m_student_teacher_ratio = {0, 15, 15, 15, 15, 15};
 
+    /*!< Symptomatic withdrawal compliance rate, day 0, AgeGroups u5, 5-17, 18-29, 30-49, 50-64, 65+*/
+    amrex::GpuArray<amrex::Real, AgeGroups::total> m_symptomatic_withdraw_compliance_day_0 = {0.3_rt, 0.3_rt, 0.3_rt,
+                                                                                              0.3_rt, 0.3_rt, 0.3_rt};
+    /*!< Symptomatic withdrawal compliance rate, day 1 */
+    amrex::GpuArray<amrex::Real, AgeGroups::total> m_symptomatic_withdraw_compliance_day_1 = {0.8_rt, 0.7_rt, 0.5_rt,
+                                                                                              0.5_rt, 0.5_rt, 0.5_rt};
+    /*!< Symptomatic withdrawal compliance rate, day 2 */
+    amrex::GpuArray<amrex::Real, AgeGroups::total> m_symptomatic_withdraw_compliance_day_2 = {0.9_rt, 0.8_rt, 0.7_rt,
+                                                                                              0.7_rt, 0.7_rt, 0.7_rt};
+
     int m_num_diseases; /*!< Number of diseases */
 
     amrex::iMultiFab comm_mf;
 
     short ic_type;
 
   protected:
-    amrex::Real m_shelter_compliance = 0.95_rt;              /*!< Shelter-in-place compliance rate */
-    amrex::Real m_symptomatic_withdraw_compliance = 0.95_rt; /*!< Symptomatic withdrawal compliance rate */
+    amrex::Real m_shelter_compliance = 0.95_rt; /*!< Shelter-in-place compliance rate */
 
-    std::vector<DiseaseParm*> m_h_parm;                      /*!< Disease parameters */
-    std::vector<DiseaseParm*> m_d_parm;                      /*!< Disease parameters (GPU device) */
+    std::vector<DiseaseParm*> m_h_parm;         /*!< Disease parameters */
+    std::vector<DiseaseParm*> m_d_parm;         /*!< Disease parameters (GPU device) */
 
     std::unique_ptr<DiseaseCouplingParm<PTDType>> m_disease_coupling;