Merge branch 'SubExp' testing out merging

scenarios/ebola/both_run.in

@@ -61,7 +61,7 @@
 
 [Contact tracing and vaccination]			
 	Start_Time_Contact_Tracing	1	999
-	Start_Time_Self_Isolation	1	999
+	Start_Time_Self_Isolation	1	999g
 	Vaccine_Probability_Susceptible	1	0.95
 	Latent_Vaccinated_One_Minimum_Time	1	5
 	Latent_Vaccinated_One_Maximum_Time	1	7

scenarios/ebola/both_setup.in

@@ -2,7 +2,7 @@
 	dblHexagonWidth	1	0.001	[radians]
 	intNoMaximalNodes	1	1
 	dblMaxSpatialNeighbours	1	100
-	blNetworkDumpFile	0	FALSE
+	blNetworkDumpFile	0	TRUE
 	intBlockSizeInUnitsOfPointers	1	4096
 
 [Household setup]			
@@ -13,7 +13,7 @@
 [Workplace setup]			
 	dblPropColleguesInNetwork	1	0.1
 	dblAverageWorkplaceSize	1	1000
-	strWorkplaceDensityFile	0 	../../data/bikoroSmallAscii.asc [../data/Uniform_0_to_199]
+	strWorkplaceDensityFile	0       ../../data/bikoroSmallAscii.asc [../data/Uniform_0_to_199]
 	dblDistanceAllWorkplacesHistDx	1	10
 	dblDistanceAllWorkplacesGridDx	1	5
 	intMCMCMaxSamplesInMillions	1	0

scenarios/ebola/ebola_build_alpha0to6.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+TOP="../../"
+BINDIR=$TOP"g++/"
+PARSTEM="both"
+BUILD="ebola_build.exe"
+RUN="ebola_run.exe"
+
+OUTDIR="./output_MCMC/"
+NETDIR="./network/"
+OUTSTEM="ebola_pop_"
+
+$BINDIR$BUILD ${PARSTEM}_setup.in $NETDIR${OUTSTEM+"ebola_pop_alpha0"}  dblAverageHousehold   1	4	dblAverageWorkplaceSize 1	50	dblPropColleguesInNetwork 1	0.14										
+$BINDIR$BUILD ${PARSTEM}_setup.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"}  dblAverageHousehold    1	4	dblAverageWorkplaceSize 1	50	dblPropColleguesInNetwork 1	0.14	intMCMCMaxSamplesInMillions 1	210	Commute_Power_One_GZ 1	1	Commute_Power_One_HK 1	1	Commute_Change_Point_GZ 1	0.1	Commute_Change_Point_HK 1	0.1
+$BINDIR$BUILD ${PARSTEM}_setup.in $NETDIR${OUTSTEM+"ebola_pop_alpha2"}  dblAverageHousehold    1	4	dblAverageWorkplaceSize 1	50	dblPropColleguesInNetwork 1	0.14	intMCMCMaxSamplesInMillions 1	210	Commute_Power_One_GZ 1	2	Commute_Power_One_HK 1	2	Commute_Change_Point_GZ 1	0.1	Commute_Change_Point_HK 1	0.1
+$BINDIR$BUILD ${PARSTEM}_setup.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"}  dblAverageHousehold    1	4	dblAverageWorkplaceSize 1	50	dblPropColleguesInNetwork 1	0.14	intMCMCMaxSamplesInMillions 1	210	Commute_Power_One_GZ 1	3	Commute_Power_One_HK 1	3	Commute_Change_Point_GZ 1	0.1	Commute_Change_Point_HK 1	0.1
+$BINDIR$BUILD ${PARSTEM}_setup.in $NETDIR${OUTSTEM+"ebola_pop_alpha4"}  dblAverageHousehold    1	4	dblAverageWorkplaceSize 1	50	dblPropColleguesInNetwork 1	0.14	intMCMCMaxSamplesInMillions 1	210	Commute_Power_One_GZ 1	4	Commute_Power_One_HK 1	4	Commute_Change_Point_GZ 1	0.1	Commute_Change_Point_HK 1	0.1
+$BINDIR$BUILD ${PARSTEM}_setup.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"}  dblAverageHousehold   1	4	dblAverageWorkplaceSize 1	50	dblPropColleguesInNetwork 1	0.14	intMCMCMaxSamplesInMillions 1	210	Commute_Power_One_GZ 1	5	Commute_Power_One_HK 1	5	Commute_Change_Point_GZ 1	0.1	Commute_Change_Point_HK 1	0.1
+$BINDIR$BUILD ${PARSTEM}_setup.in $NETDIR${OUTSTEM+"ebola_pop_alpha6"}  dblAverageHousehold   1	4	dblAverageWorkplaceSize 1	50	dblPropColleguesInNetwork 1	0.14	intMCMCMaxSamplesInMillions 1	210	Commute_Power_One_GZ 1	6	Commute_Power_One_HK 1	6	Commute_Change_Point_GZ 1	0.1	Commute_Change_Point_HK 1	0.1

scenarios/ebola/ebola_run_alpha0to6.sh

@@ -0,0 +1,67 @@
+#!/bin/bash
+
+TOP="../../"
+BINDIR=$TOP"g++/"
+PARSTEM="both"
+BUILD="ebola_build.exe"
+RUN="ebola_run.exe"
+
+OUTDIR="./output/"
+NETDIR="./network/"
+OUTSTEM="ebola_pop_monrovia"
+
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha0"} ${OUTDIR}ebola_alpha0_1 R0_Network 1	2.71	0
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha0"} ${OUTDIR}ebola_alpha0_2  R0_Network 1	2.72	0
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha0"} ${OUTDIR}ebola_alpha0_3  R0_Network 1	2.73	0
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha0"} ${OUTDIR}ebola_alpha0_4  R0_Network 1	2.74	0
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha0"} ${OUTDIR}ebola_alpha0_5  R0_Network 1	2.745	0
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha0"} ${OUTDIR}ebola_alpha0_6  R0_Network 1	2.75	0
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha0"} ${OUTDIR}ebola_alpha0_7  R0_Network 1	2.76	0
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_8 R0_Network 1	2.67	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_9  R0_Network 1	2.68	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_10  R0_Network 1	2.69	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_11 R0_Network 1	2.7	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_12 R0_Network 1	2.71	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_13 R0_Network 1	2.72	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_14 R0_Network 1	2.73	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_15 R0_Network 1	2.74	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_16 R0_Network 1	2.75	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha1"} ${OUTDIR}ebola_alpha1_17 R0_Network 1	2.76	1
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha2"} ${OUTDIR}ebola_alpha2_18 R0_Network 1	2.71	2
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha2"} ${OUTDIR}ebola_alpha2_19 R0_Network 1	2.72	2
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha2"} ${OUTDIR}ebola_alpha2_20 R0_Network 1	2.73	2
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha2"} ${OUTDIR}ebola_alpha2_21 R0_Network 1	2.74	2
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha2"} ${OUTDIR}ebola_alpha2_22 R0_Network 1	2.75	2
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha2"} ${OUTDIR}ebola_alpha2_23 R0_Network 1	2.76	2
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"} ${OUTDIR}ebola_alpha3_24 R0_Network 1	2.71	3
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"} ${OUTDIR}ebola_alpha3_25 R0_Network 1	2.2	3
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"} ${OUTDIR}ebola_alpha3_26 R0_Network 1	2.73	3
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"} ${OUTDIR}ebola_alpha3_27 R0_Network 1	2.74	3
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"} ${OUTDIR}ebola_alpha3_28 R0_Network 1	2.75	3
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"} ${OUTDIR}ebola_alpha3_29 R0_Network 1	2.76	3
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"} ${OUTDIR}ebola_alpha3_30 R0_Network 1	2.77	3
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"} ${OUTDIR}ebola_alpha3_31 R0_Network 1	2.78	3
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha3"} ${OUTDIR}ebola_alpha3_32 R0_Network 1	2.79	3
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha4"} ${OUTDIR}ebola_alpha4_33 R0_Network 1	2.82	4
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha4"} ${OUTDIR}ebola_alpha4_34 R0_Network 1	2.83	4
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha4"} ${OUTDIR}ebola_alpha4_35 R0_Network 1	2.84	4
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha4"} ${OUTDIR}ebola_alpha4_36 R0_Network 1	2.85	4
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha4"} ${OUTDIR}ebola_alpha4_37 R0_Network 1	2.86	4
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha4"} ${OUTDIR}ebola_alpha4_38 R0_Network 1	2.87	4
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_39 R0_Network 1	2.84	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_40 R0_Network 1	2.85	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_41 R0_Network 1	2.86	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_42 R0_Network 1	2.87	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_43 R0_Network 1	2.88	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_44 R0_Network 1	2.89	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_45 R0_Network 1	2.9	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_46 R0_Network 1	2.91	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_47 R0_Network 1	2.92	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_48 R0_Network 1	2.93	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha5"} ${OUTDIR}ebola_alpha5_49 R0_Network 1	2.94	5
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha6"} ${OUTDIR}ebola_alpha6_50 R0_Network 1	2.95	6
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha6"} ${OUTDIR}ebola_alpha6_51 R0_Network 1	2.96	6
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha6"} ${OUTDIR}ebola_alpha6_52 R0_Network 1	2.97	6
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha6"} ${OUTDIR}ebola_alpha6_53 R0_Network 1	2.98	6
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha6"} ${OUTDIR}ebola_alpha6_54 R0_Network 1	2.99	6
+$BINDIR$RUN both_run.in $NETDIR${OUTSTEM+"ebola_pop_alpha6"} ${OUTDIR}ebola_alpha6_55 R0_Network 1	3	6