Tidy up some comments

The clangformat auto-applied patch produced some untidily formatted
comments.  This commit tidies up the ones I spotted.

src/Bitmap.cpp

@@ -10,9 +10,7 @@
 #include "Model.h"
 #include "Param.h"
 
-//// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** //// ****
-/////// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** / **** BITMAP
-///stuff.
+//// **** BITMAP stuff
 
 #ifdef _WIN32
 // HAVI avi;

src/CalcInfSusc.cpp

@@ -7,11 +7,11 @@
 #include "ModelMacros.h"
 #include "Param.h"
 
-//// Infectiousness functions (House, Place, Spatial, Person). Idea is that in addition to a
-///person's personal infectiousness, they have separate "infectiousnesses" for their house, place
-///and on other cells (spatial). / These functions consider one person only. A person has an
-///infectiousness that is independent of other people. Slightly different therefore than
-///susceptibility functions.
+/// Infectiousness functions (House, Place, Spatial, Person). Idea is that in addition to a
+/// person's personal infectiousness, they have separate "infectiousnesses" for their house, place
+/// and on other cells (spatial). / These functions consider one person only. A person has an
+/// infectiousness that is independent of other people. Slightly different therefore than
+/// susceptibility functions.
 double CalcHouseInf(int j, unsigned short int ts)
 {
 		return ((HOST_ISOLATED(j) && (Hosts[j].digitalContactTraced != 1))
@@ -54,11 +54,11 @@ double CalcPersonInf(int j, unsigned short int ts)
 					 fabs(Hosts[j].infectiousness) * P.infectiousness[ts - Hosts[j].latent_time - 1];
 }
 
-//// Susceptibility functions (House, Place, Spatial, Person). Similarly, idea is that in addition
-///to a person's personal susceptibility, they have separate "susceptibilities" for their house,
-///place and on other cells (spatial) / These functions consider two people. A person has a
-///susceptibility TO ANOTHER PERSON/infector. Slightly different therefore than infectiousness
-///functions.
+/// Susceptibility functions (House, Place, Spatial, Person). Similarly, idea is that in addition
+/// to a person's personal susceptibility, they have separate "susceptibilities" for their house,
+/// place and on other cells (spatial) / These functions consider two people. A person has a
+/// susceptibility TO ANOTHER PERSON/infector. Slightly different therefore than infectiousness
+/// functions.
 double CalcHouseSusc(int ai, unsigned short int ts, int infector, int tn)
 {
 		return CalcPersonSusc(ai, ts, infector, tn) *

src/Constants.h

@@ -97,7 +97,8 @@ const int NNA = 10;
 const int MIN_HOTELS_PER_AIRPORT = 20;
 const int HOTELS_PER_1000PASSENGER = 10;
 
-const int MAX_NUM_INTERVENTION_CHANGE_TIMES =
-		100; // may want to make this intervention-specifc, but keep simple for now.
+/// Max number of intervention changes possible.  May want to make this
+/// intervention-specific, but keep simple for now.
+const int MAX_NUM_INTERVENTION_CHANGE_TIMES = 100;
 
 #endif // COVIDSIM_CONSTANTS_H_INCLUDED_

src/Dist.cpp

@@ -11,7 +11,7 @@ double sinx[361], cosx[361], asin2sqx[1001];
 
 //// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** //// ****
 /////// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** / **** DISTANCE
-///FUNCTIONS (return distance-squared, which is input for every Kernel function) / **** //// ****
+/// FUNCTIONS (return distance-squared, which is input for every Kernel function) / **** //// ****
 /////// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** ////
 ///**** //// **** //// **** //// **** //// **** //// **** //// ****
 

src/InfStat.h

@@ -2,14 +2,14 @@
 #define COVIDSIM_INFSTAT_H_INCLUDED_
 
 //// Infection Status definitions / labels (generally positive value indicates asymptomatic
-///infection, / negative value indicates symptomatic infection).
+/// infection, / negative value indicates symptomatic infection).
 
 enum InfStat
 {
 
 		//// Note - DO NOT CHANGE these definitions without accounting for "Quarantined not Infected" /
 		//// "Quarantined not symptomatic" calculation: relies on value below being negative for
-		///symptomatic people.
+		/// symptomatic people.
 
 		//// Susceptible
 		InfStat_Susceptible = 0,
@@ -28,7 +28,7 @@ enum InfStat
 		//// InfStat_Recovered (will use this for abs() values) so code reads correctly
 		InfStat_Recovered = 3,
 		//// Immune at start of epidemic - used to model partially immune population. Distinct from
-		///recovered, who recovered during runtime. Doesn't take negative values.
+		/// recovered, who recovered during runtime. Doesn't take negative values.
 		InfStat_ImmuneAtStart = 4,
 		//// Dead was asymptomatic
 		InfStat_Dead_WasAsymp = 5,

src/Kernels.cpp

@@ -70,7 +70,7 @@ void InitKernel(double norm)
 
 //// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** //// ****
 /////// **** //// **** //// **** //// **** //// **** //// **** //// **** //// **** / **** KERNEL
-///DEFINITIONS
+/// DEFINITIONS
 
 double ExpKernel(double r2)
 {

src/Model.h

@@ -16,7 +16,7 @@
 #include "Models/Person.h"
 
 //// need to test that inequalities in IncubRecoverySweep can be replaced if you initialize to
-///USHRT_MAX, rather than zero. / need to output quantities by admin unit
+/// USHRT_MAX, rather than zero. / need to output quantities by admin unit
 
 #pragma pack(push, 2)
 
@@ -62,7 +62,7 @@ struct PopVar
 		int cumC_country[MAX_COUNTRIES]; // added cumulative cases by country: ggilani 12/11/14
 		int cumHQ, cumAC, cumAA, cumAH, cumACS, cumAPC, cumAPA, cumAPCS;
 		//// age specific versions of above variables. e.g. cumI is cumulative infections. cumIa is
-		///cumulative infections by age group.
+		/// cumulative infections by age group.
 		int cumIa[NUM_AGE_GROUPS], cumCa[NUM_AGE_GROUPS], cumDa[NUM_AGE_GROUPS];
 		int cumI_adunit[MAX_ADUNITS], cumC_adunit[MAX_ADUNITS], cumD_adunit[MAX_ADUNITS],
 				cumT_adunit[MAX_ADUNITS], cumH_adunit[MAX_ADUNITS],
@@ -94,9 +94,9 @@ struct PopVar
 		ContactEvent *dct_queue[MAX_ADUNITS]; // queues for digital contact tracing: ggilani 14/04/20
 		int ndct_queue[MAX_ADUNITS];					// queues for digital contact tracing: ggilani 10/03/20
 		int contact_dist[MAX_CONTACTS + 1];		// added this to store contact distribution: ggilani
-																				// 13/04/20
-		double *origin_dest[MAX_ADUNITS]; // added intermediate storage for calculation of
-																			// origin-destination matrix: ggilani 02/02/15
+																					// 13/04/20
+		double *origin_dest[MAX_ADUNITS];			// added intermediate storage for calculation of
+																					// origin-destination matrix: ggilani 02/02/15
 
 		///// Prevalence quantities (+ by admin unit)
 		int Mild, ILI, SARI, Critical, CritRecov, /*cumulative incidence*/ cumMild, cumILI, cumSARI,
@@ -232,7 +232,7 @@ struct Results
 		//// ii) RecordSample: add to incidence / Timeseries).
 		//// iii) SaveResults and SaveSummary results.
 		///// need to update these quantities in InitModel (DONE), Record Sample (DONE) (and of course
-		///places where you need to increment, decrement).
+		/// places where you need to increment, decrement).
 };
 
 // The offset (in number of doubles) of the first double field in Results.
@@ -356,9 +356,9 @@ extern AdminUnit AdUnits[MAX_ADUNITS];
 
 //// Time Series defs:
 //// TimeSeries is an array of type results, used to store (unsurprisingly) a time series of every
-///quantity in results. Mostly used in RecordSample. / TSMeanNE and TSVarNE are the mean and
-///variance of non-extinct time series. TSMeanE and TSVarE are the mean and variance of extinct time
-///series. TSMean and TSVar are pointers that point to either extinct or non-extinct.
+/// quantity in results. Mostly used in RecordSample. / TSMeanNE and TSVarNE are the mean and
+/// variance of non-extinct time series. TSMeanE and TSVarE are the mean and variance of extinct
+/// time series. TSMean and TSVar are pointers that point to either extinct or non-extinct.
 extern Results *TimeSeries, *TSMean, *TSVar, *TSMeanNE, *TSVarNE, *TSMeanE,
 		*TSVarE; //// TimeSeries used in RecordSample, RecordInfTypes, SaveResults. TSMean and TSVar
 

src/Models/Cell.h

@@ -14,7 +14,7 @@ struct Cell
 		int n, S, L, I, R, D, cumTC, S0, tot_treat, tot_vacc;
 		int *members, *susceptible, *latent,
 				*infected; //// pointers to people in cell. e.g. *susceptible identifies where the final
-									 ///susceptible member of cel is.
+									 /// susceptible member of cel is.
 		int *InvCDF;
 		float tot_prob, *cum_trans, *max_trans;
 		short int CurInterv[MAX_INTERVENTION_TYPES];

src/Models/Person.h

@@ -12,8 +12,8 @@ struct Person
 		int listpos;	// Goes up to at least MAX_SEC_REC, also used as a temp variable?
 
 		int PlaceLinks[NUM_PLACE_TYPES]; //// indexed by i) place type. Value is the number of that
-																		 ///place type (e.g. school no. 17; office no. 310 etc.)
-																		 ///Place[i][person->PlaceLinks[i]], can be up to P.Nplace[i]
+																		 /// place type (e.g. school no. 17; office no. 310 etc.)
+																		 /// Place[i][person->PlaceLinks[i]], can be up to P.Nplace[i]
 		float infectiousness, susc, ProbAbsent, ProbCare;
 
 		unsigned int esocdist_comply : 1;
@@ -28,8 +28,8 @@ struct Person
 		unsigned char num_treats;	 // set to 0 and tested < 2. but never modified?
 		Severity Severity_Current,
 				Severity_Final; //// Note we allow Severity_Final to take values: Severity_Mild,
-												///Severity_ILI, Severity_SARI, Severity_Critical (not e.g. Severity_Dead or
-												///Severity_RecoveringFromCritical)
+												/// Severity_ILI, Severity_SARI, Severity_Critical (not e.g. Severity_Dead
+												/// or Severity_RecoveringFromCritical)
 
 		unsigned short int PlaceGroupLinks[NUM_PLACE_TYPES]; // These can definitely get > 255
 		short int infect_type;															 // INFECT_TYPE_MASK
@@ -48,8 +48,8 @@ struct Person
 		unsigned short int recovery_or_death_time; // set in DoIncub function
 		unsigned short int SARI_time, Critical_time,
 				RecoveringFromCritical_time; //// /*mild_time, ILI_time,*/ Time of infectiousness onset same
-																		 ///for asymptomatic, Mild, and ILI infection so don't need
-																		 ///mild_time etc.
+																		 /// for asymptomatic, Mild, and ILI infection so don't need
+																		 /// mild_time etc.
 		unsigned short int treat_start_time, treat_stop_time,
 				vacc_start_time; //// set in TreatSweep function.
 		unsigned int digitalContactTraced : 1;
@@ -58,5 +58,5 @@ struct Person
 		unsigned short int dct_start_time, dct_end_time, dct_trigger_time,
 				dct_test_time; // digital contact tracing start and end time: ggilani 10/03/20
 		int ncontacts;		 // added this in to record total number of contacts each index case records:
-									 // ggilani 13/04/20
+											 // ggilani 13/04/20
 };

src/Param.h

@@ -267,29 +267,29 @@ struct Param
 																																 (enhanced) social distancing */
 		double SD_SpatialEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///SocDistSpatialEffectCurrent
+																						 /// SocDistSpatialEffectCurrent
 		double SD_HouseholdEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///SocDistHouseholdEffectCurrent
+																						 /// SocDistHouseholdEffectCurrent
 		double SD_PlaceEffects_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]
 																	 [NUM_PLACE_TYPES]; //// indexed by i) change time; ii) place
-																											///type;  //// time-varying equivalent of
-																											///SocDistPlaceEffectCurrent
+																											/// type;  //// time-varying equivalent of
+																											/// SocDistPlaceEffectCurrent
 		int SD_CellIncThresh_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent
-																																			///of SocDistCellIncThresh
+																																			/// of SocDistCellIncThresh
 
 		/**< enhanced	*/
 		double Enhanced_SD_SpatialEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///EnhancedSocDistSpatialEffectCurrent
+																						 /// EnhancedSocDistSpatialEffectCurrent
 		double Enhanced_SD_HouseholdEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///EnhancedSocDistHouseholdEffectCurrent
+																						 /// EnhancedSocDistHouseholdEffectCurrent
 		double
 				Enhanced_SD_PlaceEffects_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]
 																				 [NUM_PLACE_TYPES]; //// indexed by i) change time; ii)
-																														///place type;  time-varying equivalent
-																														///of EnhancedSocDistPlaceEffectCurrent
+																														/// place type;  time-varying equivalent
+																														/// of EnhancedSocDistPlaceEffectCurrent
 
 		int Num_CI_ChangeTimes;	 //// must be at most MAX_NUM_INTERVENTION_CHANGE_TIMES
 		int Num_HQ_ChangeTimes;	 //// must be at most MAX_NUM_INTERVENTION_CHANGE_TIMES
@@ -301,76 +301,77 @@ struct Param
 																																 case isolation */
 		double CI_SpatialAndPlaceEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///CaseIsolationEffectiveness
+																						 /// CaseIsolationEffectiveness
 		double CI_HouseholdEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES];										//// time-varying equivalent of
-																																///CaseIsolationHouseEffectiveness
+																																/// CaseIsolationHouseEffectiveness
 		double CI_Prop_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																																///CaseIsolationProp
-		double
-				CI_CellIncThresh_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent
-																																			///of
-																																			///CaseIsolation_CellIncThresh
+																																/// CaseIsolationProp
+		double CI_CellIncThresh_OverTime
+				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent
+																						 /// of
+																						 /// CaseIsolation_CellIncThresh
 
 		/**< HOUSEHOLD QUARANTINE	*/
 		double HQ_ChangeTimes[MAX_NUM_INTERVENTION_CHANGE_TIMES]; /**< change times for intensity of
 																																 household quarantine */
 		double
 				HQ_SpatialEffects_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent
-																																			 ///of
-																																			 ///HQuarantineSpatialEffect
+																																			 /// of
+																																			 /// HQuarantineSpatialEffect
 		double HQ_HouseholdEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of HQuarantineHouseEffect
 		double HQ_PlaceEffects_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]
 																	 [NUM_PLACE_TYPES]; //// indexed by i) change time; ii) place
-																											///type; time-varying equivalent of
-																											///HQuarantinePlaceEffect
+																											/// type; time-varying equivalent of
+																											/// HQuarantinePlaceEffect
 		double HQ_Individual_PropComply_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///HQuarantinePropIndivCompliant
+																						 /// HQuarantinePropIndivCompliant
 		double HQ_Household_PropComply_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///HQuarantinePropHouseCompliant
+																						 /// HQuarantinePropHouseCompliant
 		double
 				HQ_CellIncThresh_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent
-																																			///of HHQuar_CellIncThresh
+																																			/// of HHQuar_CellIncThresh
 
 		/**< PLACE CLOSURE	*/
 		double PC_ChangeTimes[MAX_NUM_INTERVENTION_CHANGE_TIMES]; /**< change times for intensity of
 																																 place closure */
 		double PC_SpatialEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///PlaceCloseSpatialRelContact
+																						 /// PlaceCloseSpatialRelContact
 		double PC_HouseholdEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///PlaceCloseHouseholdRelContact
+																						 /// PlaceCloseHouseholdRelContact
 		double PC_PlaceEffects_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]
 																	 [NUM_PLACE_TYPES]; //// indexed by i) change time; ii) place
-																											///type; //// time-varying equivalent of
-																											///PlaceCloseEffect
+																											/// type; //// time-varying equivalent of
+																											/// PlaceCloseEffect
 		double PC_PropAttending_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES][NUM_PLACE_TYPES];
 		int PC_IncThresh_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																																	///PlaceCloseIncTrig /
-																																	///PlaceCloseIncTrig1
+																																	/// PlaceCloseIncTrig /
+																																	/// PlaceCloseIncTrig1
 		double
 				PC_FracIncThresh_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent
-																																			///of PlaceCloseFracIncTrig
+																																			/// of PlaceCloseFracIncTrig
 		int PC_CellIncThresh_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent
-																																			///of PlaceCloseCellIncThresh
+																																			/// of PlaceCloseCellIncThresh
 		double PC_Durs_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																																///PlaceCloseDuration
+																																/// PlaceCloseDuration
 
 		/**< DIGITAL CONTACT TRACING	*/
 		double DCT_ChangeTimes[MAX_NUM_INTERVENTION_CHANGE_TIMES]; /**< change times for intensity of
 																																	digital contact tracing */
 		double DCT_SpatialAndPlaceEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///DCTCaseIsolationEffectiveness
+																						 /// DCTCaseIsolationEffectiveness
 		double DCT_HouseholdEffects_OverTime
 				[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																						 ///DCTCaseIsolationHouseEffectiveness
-		double DCT_Prop_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
-																																 ///ProportionDigitalContactsIsolate
+																						 /// DCTCaseIsolationHouseEffectiveness
+		double
+				DCT_Prop_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES]; //// time-varying equivalent of
+																															/// ProportionDigitalContactsIsolate
 		int DCT_MaxToTrace_OverTime[MAX_NUM_INTERVENTION_CHANGE_TIMES];
 
 		double KeyWorkerProphTimeStart, KeyWorkerProphDuration,
@@ -431,7 +432,7 @@ struct Param
 		int WindowToEvaluateTriggerAlert; // Number of days to accummulate cases/deaths before alert
 		int DoAlertTriggerAfterInterv;		// Alert trigger starts after interventions, i.e. were there
 																			// interventions before date specified in
-																	 // DateTriggerReached_CalTime / "Day of year trigger is reached"?
+		// DateTriggerReached_CalTime / "Day of year trigger is reached"?
 		int AlertTriggerAfterIntervThreshold; // initialized to CaseOrDeathThresholdBeforeAlert (i.e.
 																					// number cases or deaths accumulated before alert).
 
@@ -465,7 +466,7 @@ struct Param
 		int DoRecordInfEvents, MaxInfEvents, RecordInfEventsPerRun;
 		unsigned short int usHQuarantineHouseDuration, usVaccTimeToEfficacy,
 				usVaccTimeEfficacySwitch; //// us = unsigned short versions of their namesakes, multiplied
-																	///by P.TimeStepsPerDay
+																	/// by P.TimeStepsPerDay
 		unsigned short int usCaseIsolationDuration, usCaseIsolationDelay, usCaseAbsenteeismDuration,
 				usCaseAbsenteeismDelay, usAlignDum; // last is for 8 byte alignment