Merge remote-tracking branch 'upstream/master'

.gitignore

@@ -1,4 +1,4 @@
-
+# VS
 *~
 *.xls
 x64
@@ -9,9 +9,17 @@ x64
 *.bin
 wpop_*.txt
 out/
-build
+build/
 build-*/
 build_*/
 .project
 *.vcxproj.user
 tests/*-output/
+
+# VScode
+.vscode/
+
+# Executables
+*.exe
+*.out
+*.app

data/admin_units/Russia_admin.txt

@@ -16,6 +16,11 @@
 [Fix population size at specified value]
 1
 
+[Longitude cut line]
+0.0
+# Russia goes from around 19 degrees to -170 dgrees longitude, so need
+# different cut line to default of -180.0
+
 [Number of countries to include]
 1
 

data/run_sample.py

@@ -83,6 +83,7 @@ def parse_args():
 united_states = [ "United_States" ]
 canada = [ "Canada" ]
 usa_territories = ["Alaska", "Hawaii", "Guam", "Virgin_Islands_US", "Puerto_Rico", "American_Samoa"]
+nigeria = ["Nigeria"]
 
 # Determine whether we need to build the tool or use a user supplied one:
 if args.covidsim is not None:
@@ -127,6 +128,8 @@ def parse_args():
     wpop_file_root = "usacan"
 elif args.country in usa_territories:
     wpop_file_root = "us_terr"
+elif args.country in nigeria:
+    wpop_file_root = "nga_adm1"
 else:
     wpop_file_root = "eur"
 
@@ -157,6 +160,8 @@ def parse_args():
 # Configure pre-parameter file.  This file doesn't change between runs:
 if args.country in united_states:
     pp_file = os.path.join(args.paramdir, "preUS_R0=2.0.txt")
+elif args.country in nigeria:
+    pp_file = os.path.join(args.paramdir, "preNGA_R0=2.0.txt")
 else:
     pp_file = os.path.join(args.paramdir, "preUK_R0=2.0.txt")
 if not os.path.exists(pp_file):

src/CMakeLists.txt

@@ -1,7 +1,12 @@
 # CMakeLists.txt for src directory
 
+# Set up the IDE
+set(MAIN_SRC_FILES CovidSim.cpp binio.cpp Rand.cpp Error.cpp Dist.cpp Kernels.cpp Bitmap.cpp SetupModel.cpp CalcInfSusc.cpp Sweep.cpp Update.cpp)
+set(MAIN_HDR_FILES CovidSim.h binio.h Rand.h Constants.h Country.h MachineDefines.h Error.h Dist.h Kernels.h Bitmap.h Model.h Param.h SetupModel.h ModelMacros.h InfStat.h CalcInfSusc.h Sweep.h Update.h)
+source_group(covidsim\\main FILES ${MAIN_SRC_FILES} ${MAIN_HDR_FILES})
+
 # CovidSim target
-add_executable(CovidSim CovidSim.cpp CovidSim.h binio.cpp binio.h Rand.cpp Rand.h Constants.h Country.h MachineDefines.h Error.cpp Error.h Dist.cpp Dist.h Kernels.cpp Kernels.h Bitmap.cpp Bitmap.h Model.h Param.h SetupModel.cpp SetupModel.h ModelMacros.h InfStat.h CalcInfSusc.cpp CalcInfSusc.h Sweep.cpp Sweep.h Update.cpp Update.h)
+add_executable(CovidSim ${MAIN_SRC_FILES} ${MAIN_HDR_FILES})
 target_include_directories(CovidSim PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 if(USE_OPENMP)
   target_link_libraries(CovidSim PUBLIC OpenMP::OpenMP_CXX)

src/Constants.h

@@ -1,8 +1,67 @@
 #ifndef COVIDSIM_CONSTANTS_H_INCLUDED_
 #define COVIDSIM_CONSTANTS_H_INCLUDED_
 
-#define PI 3.1415926535
-#define EARTHRADIUS 6366707.0
+/**
+ * Math constant defined as the ratio of a circle's circumference to its diameter.
+ *
+ * TODO: since all calculations using this constant are being automatically
+ * type-casted to double, should the precision be extended for more accuracy in
+ * the simulations?
+ *
+ * Eventually could be replaced with C++20's std::numbers::pi.
+ * https://en.cppreference.com/w/cpp/header/numbers
+ */
+constexpr double PI = 3.1415926535; // full double precision: 3.14159265358979323846
+
+/**
+ * An arc minute of latitude along any line of longitude in meters.
+ *
+ * Also known as the International Nautical Mile.
+ *
+ * @see https://en.wikipedia.org/wiki/Nautical_mile
+ */
+constexpr int NMI = 1852;
+
+/**
+ * The number of arc minutes in one degree.
+ *
+ * @see https://en.wikipedia.org/wiki/Minute_and_second_of_arc
+ */
+constexpr int ARCMINUTES_PER_DEGREE = 60;
+
+/**
+ * The number of degrees in a complete rotation.
+ *
+ * @see https://en.wikipedia.org/wiki/Turn_(angle)
+ */
+constexpr int DEGREES_PER_TURN = 360;
+
+/**
+ * The earth's circumference in meters.
+ *
+ * The units of cancellation:
+ *    meters/minute * minutes/degree * degrees = meters
+ */
+constexpr int EARTH_CIRCUMFERENCE = NMI * ARCMINUTES_PER_DEGREE * DEGREES_PER_TURN;
+
+/**
+ * The earth's diameter in meters.
+ */
+constexpr double EARTH_DIAMETER = EARTH_CIRCUMFERENCE / PI;
+
+/**
+ * The Earth's radius in meters.
+ *
+ * The previous hardcoded value used 6366707 which was derived from the
+ * following formula:
+ *
+ *     Earth's radius (m) = Earth's circumference / 2 * Pi
+ *
+ * where Earth's circumference can be derived with the following formula:
+ *
+ *     Earth's circumference (m) = NMI * ARCMINUTES_PER_DEGREE * DEGREES_PER_TURN
+ */
+constexpr double EARTHRADIUS = EARTH_DIAMETER / 2;
 
 #define OUTPUT_DIST_SCALE 1000
 #define MAX_PLACE_SIZE 20000

src/CovidSim.cpp

@@ -473,6 +473,9 @@ void ReadParams(char* ParamFile, char* PreParamFile)
 	if (!(ParamFile_dat = fopen(ParamFile, "rb"))) ERR_CRITICAL("Unable to open parameter file\n");
 	PreParamFile_dat = fopen(PreParamFile, "rb");
 	if (!(AdminFile_dat = fopen(AdunitFile, "rb"))) AdminFile_dat = ParamFile_dat;
+	if (!GetInputParameter2(ParamFile_dat, AdminFile_dat, "Longitude cut line", "%lf", (void*) & (P.LongitudeCutLine), 1, 1, 0)) {
+		P.LongitudeCutLine = -360.0;
+	}
 	AgeSuscScale = 1.0;
 		GetInputParameter(ParamFile_dat, PreParamFile_dat, "Update timestep", "%lf", (void*) & (P.TimeStep), 1, 1, 0);
 	GetInputParameter(ParamFile_dat, PreParamFile_dat, "Sampling timestep", "%lf", (void*) & (P.SampleStep), 1, 1, 0);

src/CovidSim.h

@@ -3,8 +3,6 @@
 
 #include "MachineDefines.h"
 
-#define KMP_LIBRARY throughput
-
 #include <limits.h>
 #include <stdio.h>
 #include <stdlib.h>

src/InfStat.h

@@ -15,16 +15,13 @@
 #define InfStat_Dead_WasSymp					-5				//// Dead was symptomatic
 #define InfStat_Dead							5				//// Dead (will use this for abs() values) so code reads correctly
 
-
-#define NUM_SYMPTO_SEVERITY_CLASSES 4
-
 // SeverityClass defintions / labels (numbers arbitrary but must be different to each other).
 #define Severity_Asymptomatic				-1		//// Flag value.
 #define Severity_Mild						0
 #define Severity_ILI						1
 #define Severity_SARI						2
 #define Severity_Critical					3
-#define Severity_RecoveringFromCritical		4		//// Recovering from Critical (not recovered yet). Not included in NUM_SYMPTO_SEVERITY_CLASSES but could change. Also doesn't count as person.Severity_Final
+#define Severity_RecoveringFromCritical		4		//// Recovering from Critical (not recovered yet).
 #define Severity_Dead						5		//// label to avoid double counting. Not sure you need.
 #define Severity_Recovered					6		//// label to avoid double counting. Not sure you need.
 

src/Model.h

@@ -90,7 +90,7 @@ typedef struct CONTACTEVENT {
 typedef struct POPVAR {
 
 	int S, L, I, R, D, cumI, cumR, cumD, cumC, cumTC, cumFC, cumDC, trigDC;
-	int H, cumH; //Added total and cumulative hospitalisation: ggilani 28/10/14
+	int cumH; //Added cumulative hospitalisation: ggilani 28/10/14
 	int CT, cumCT, CC, cumCC, DCT, cumDCT; //Added total and cumulative contact tracing: ggilani 15/06/17, and equivalents for digital contact tracing: ggilani 11/03/20
 	int cumC_country[MAX_COUNTRIES]; //added cumulative cases by country: ggilani 12/11/14
 	int cumHQ, cumAC, cumAA, cumAH, cumACS, cumAPC, cumAPA, cumAPCS;
@@ -147,7 +147,7 @@ typedef struct POPVAR {
 typedef struct RESULTS {
 
 	double t, S, L, I, R, D, incC, incTC, incFC, incI, incR, incD, incDC ;
-	double H, incH; //added total hospitalisation and incidence of hospitalisation: ggilani 28/10/14
+	double incH; //added incidence of hospitalisation: ggilani 28/10/14
 	double CT, incCT, CC, incCC, DCT, incDCT; //added total numbers being contact traced and incidence of contact tracing: ggilani 15/06/17, and for digital contact tracing: ggilani 11/03/20
 	double incC_country[MAX_COUNTRIES]; //added incidence of cases
 	double cumT, cumUT, cumTP, cumV, cumTmax, cumVmax, cumDC, extinct, cumVG; //added cumVG

src/Param.h

@@ -63,6 +63,7 @@ typedef struct PARAM {
 	long nextSetupSeed1, nextSetupSeed2; // The next RNG seeds to use when we need to reinitialise the RNG for setup
 	long nextRunSeed1, nextRunSeed2; // The next RNG seeds to use when we need to reinitialise the RNG for the model
 	int ResetSeeds,KeepSameSeeds, ResetSeedsPostIntervention, ResetSeedsFlag, TimeToResetSeeds;
+	double LongitudeCutLine; // Longitude to image earth is cut at to produce a flat map.  Default -360 degrees (effectively -180).  Use to ensure countries have a contiguous boundary
 	double SpatialBoundingBox[4], LocationInitialInfection[MAX_NUM_SEED_LOCATIONS][2], InitialInfectionsAdminUnitWeight[MAX_NUM_SEED_LOCATIONS], TimeStepsPerDay;
 	double FalsePositiveRate, FalsePositivePerCapitaIncidence, FalsePositiveAgeRate[NUM_AGE_GROUPS];
 	double latent_icdf[CDF_RES + 1], infectious_icdf[CDF_RES + 1], infectious_prof[INFPROF_RES + 1], infectiousness[MAX_INFECTIOUS_STEPS];