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Run without population file #379

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Run without population file #379

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2229973
set grid width from height when it is first set
galactic-src Jun 7, 2020
60f9ecd
Sane grid initialisation if not supplying population density file
galactic-src Jun 7, 2020
a2e0608
Incorporate final iteration of population allocation into loop
galactic-src Jun 7, 2020
55424d1
Only sanity check adunit value if simulating P.DoAdUnits is set
galactic-src Jun 7, 2020
5ed0d21
supply grid width and height cell counts as parameters in the absence…
galactic-src Jun 10, 2020
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9 changes: 8 additions & 1 deletion src/CovidSim.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -519,7 +519,13 @@ void ReadParams(char* ParamFile, char* PreParamFile)
P.NumNonExtinctRealisations = P.NumRealisations;
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum number of cases defining small outbreak", "%i", (void*) & (P.SmallEpidemicCases), 1, 1, 0)) P.SmallEpidemicCases = -1;

P.NC = -1;
if (P.DoHeteroDensity) {
P.NC = -1;
} else {
GetInputParameter(ParamFile_dat, PreParamFile_dat, "Number of cells wide", "%i", (void*) & (P.ncw), 1, 1, 0);
GetInputParameter(ParamFile_dat, PreParamFile_dat, "Number of cells high", "%i", (void*) & (P.nch), 1, 1, 0);
P.NC = P.ncw * P.nch;
}
GetInputParameter(ParamFile_dat, PreParamFile_dat, "Number of micro-cells per spatial cell width", "%i", (void*) & (P.NMCL), 1, 1, 0);
//added parameter to reset seeds after every run
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Reset seeds for every run", "%i", (void*) & (P.ResetSeeds), 1, 1, 0)) P.ResetSeeds = 0;
Expand Down Expand Up @@ -1266,6 +1272,7 @@ void ReadParams(char* ParamFile, char* PreParamFile)
P.SpatialBoundingBox[2] = P.SpatialBoundingBox[3] = 1.0;
}
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Grid size", "%lf", (void*) & (P.in_cells_.width_), 1, 1, 0)) P.in_cells_.width_ = 1.0 / 120.0;
P.in_cells_.height_ = P.in_cells_.width_;
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Use long/lat coord system", "%i", (void*) & (P.DoUTM_coords), 1, 1, 0)) P.DoUTM_coords = 1;
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Bitmap scale", "%lf", (void*) & (P.BitmapScale), 1, 1, 0)) P.BitmapScale = 1.0;
if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Bitmap y:x aspect scaling", "%lf", (void*) & (P.BitmapAspectScale), 1, 1, 0)) P.BitmapAspectScale = 1.0;
Expand Down
60 changes: 27 additions & 33 deletions src/SetupModel.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,6 @@ void SetupModel(char* DensityFile, char* NetworkFile, char* SchoolFile, char* Re
if (!P.DoSpecifyPop) P.PopSize = (int)s2;
}

P.in_cells_.height_ = P.in_cells_.width_;
P.SpatialBoundingBox[0] = floor(P.SpatialBoundingBox[0] / P.in_cells_.width_) * P.in_cells_.width_;
P.SpatialBoundingBox[1] = floor(P.SpatialBoundingBox[1] / P.in_cells_.height_) * P.in_cells_.height_;
P.SpatialBoundingBox[2] = ceil(P.SpatialBoundingBox[2] / P.in_cells_.width_) * P.in_cells_.width_;
Expand All @@ -151,32 +150,26 @@ void SetupModel(char* DensityFile, char* NetworkFile, char* SchoolFile, char* Re
P.SpatialBoundingBox[2] = P.SpatialBoundingBox[0] + P.in_degrees_.width_;
P.SpatialBoundingBox[3] = P.SpatialBoundingBox[1] + P.in_degrees_.height_;
P.NC = P.ncw * P.nch;
fprintf(stderr, "Adjusted bounding box = (%lg, %lg)- (%lg, %lg)\n", P.SpatialBoundingBox[0], P.SpatialBoundingBox[1], P.SpatialBoundingBox[2], P.SpatialBoundingBox[3]);
fprintf(stderr, "Number of cells = %i (%i x %i)\n", P.NC, P.ncw, P.nch);
fprintf(stderr, "Population size = %i \n", P.PopSize);
if (P.in_degrees_.width_ > 180) {
fprintf(stderr, "WARNING: Width of bounding box > 180 degrees. Results may be inaccurate.\n");
}
if (P.in_degrees_.height_ > 90) {
fprintf(stderr, "WARNING: Height of bounding box > 90 degrees. Results may be inaccurate.\n");
}
s = 1;
P.DoPeriodicBoundaries = 0;
}
else
{
P.ncw = P.nch = (int)sqrt((double)P.NC);
P.NC = P.ncw * P.nch;
fprintf(stderr, "Number of cells adjusted to be %i (%i^2)\n", P.NC, P.ncw);
s = floor(sqrt((double)P.PopSize));
P.SpatialBoundingBox[0] = P.SpatialBoundingBox[1] = 0;
P.SpatialBoundingBox[2] = P.SpatialBoundingBox[3] = s;
P.PopSize = (int)(s * s);
fprintf(stderr, "Population size adjusted to be %i (%lg^2)\n", P.PopSize, s);
P.in_degrees_.width_ = P.in_degrees_.height_ = s;
P.in_cells_.width_ = P.in_degrees_.width_ / ((double)P.ncw);
P.in_cells_.height_ = P.in_degrees_.height_ / ((double)P.nch);
P.SpatialBoundingBox[2] = P.in_degrees_.width_ = P.ncw * P.in_cells_.width_;
P.SpatialBoundingBox[3] = P.in_degrees_.height_ = P.nch * P.in_cells_.height_;
}

fprintf(stderr, "Adjusted bounding box = (%lg, %lg)- (%lg, %lg)\n", P.SpatialBoundingBox[0], P.SpatialBoundingBox[1], P.SpatialBoundingBox[2], P.SpatialBoundingBox[3]);
fprintf(stderr, "Number of cells = %i (%i x %i)\n", P.NC, P.ncw, P.nch);
fprintf(stderr, "Population size = %i \n", P.PopSize);
if (P.in_degrees_.width_ > 180) {
fprintf(stderr, "WARNING: Width of bounding box > 180 degrees. Results may be inaccurate.\n");
}
if (P.in_degrees_.height_ > 90) {
fprintf(stderr, "WARNING: Height of bounding box > 90 degrees. Results may be inaccurate.\n");
}

P.NMC = P.NMCL * P.NMCL * P.NC;
fprintf(stderr, "Number of microcells = %i\n", P.NMC);
P.scalex = P.BitmapScale;
Expand Down Expand Up @@ -998,24 +991,25 @@ void SetupPopulation(char* SchoolFile, char* RegDemogFile)
fprintf(stderr, "Population size reset from %i to %i\n", i, P.PopSize);
}
t = 1.0;
for (int i = m = 0; i < (P.NMC - 1); i++)
for (int i = m = 0; i < P.NMC; i++)
{
s = mcell_dens[i] / maxd / t;
if (s > 1.0) s = 1.0;
m += (Mcells[i].n = (int)ignbin_mt((int32_t)(P.PopSize - m), s, 0));
t -= mcell_dens[i] / maxd;
if (i == P.NMC-1) {
Mcells[P.NMC - 1].n = P.PopSize - m;
} else {
s = mcell_dens[i] / maxd / t;
if (s > 1.0) s = 1.0;
m += (Mcells[i].n = (int)ignbin_mt((int32_t)(P.PopSize - m), s, 0));
t -= mcell_dens[i] / maxd;
}

if (Mcells[i].n > 0) {
P.NMCP++;
if (mcell_adunits[i] < 0) ERR_CRITICAL_FMT("Cell %i has adunits < 0 (indexing AdUnits)\n", i);
AdUnits[mcell_adunits[i]].n += Mcells[i].n;
if (P.DoAdUnits) {
if (mcell_adunits[i] < 0) ERR_CRITICAL_FMT("Cell %i has adunits < 0 (indexing AdUnits)\n", i);
AdUnits[mcell_adunits[i]].n += Mcells[i].n;
}
}
}
Mcells[P.NMC - 1].n = P.PopSize - m;
if (Mcells[P.NMC - 1].n > 0)
{
P.NMCP++;
AdUnits[mcell_adunits[P.NMC - 1]].n += Mcells[P.NMC - 1].n;
}

free(mcell_dens);
free(mcell_num);
Expand Down