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Support for ensemble of pencil structure factor multifabs for the surface chemistry in do_2D mode #186

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Support for ensemble of pencil structure factor multifabs for the surface chemistry in do_2D mode #186

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dd4503c
enable ensemble of pencil structure factors for surface coverage in d…
ajnonaka Feb 18, 2025
59325aa
fix do_2D surfCov SF names
ajnonaka Feb 18, 2025
d8460be
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ajnonaka Feb 18, 2025
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118 changes: 92 additions & 26 deletions src_compressible_stag/main_driver.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -265,8 +265,8 @@ void main_driver(const char* argv)
}
}
}
if (do_2D and n_ads_spec>0 and ads_wall_dir == 2) {
Abort("do_2D with n_ads_spec>0 requires ads_wall_dir != 2");
if (do_2D and n_ads_spec>0 and ads_wall_dir != 1) {
Abort("do_2D with n_ads_spec>0 requires ads_wall_dir = 1");
}
if (do_1D and n_ads_spec>0 and ads_wall_dir != 0) {
Abort("do_1D with n_ads_spec>0 requires ads_wall_dir = 0");
Expand Down Expand Up @@ -353,6 +353,9 @@ void main_driver(const char* argv)
// Structure factor for surface coverage slice
// these are enabled if n_ads_spec > 0 and assumes the k=0 plane is the slice of interest
StructFact structFactSurfCov;
// Vector of structure factors for pencils of surface coverage for 2D simulation
// these are enabled if do_2D (this mode assumes that ads_wall_dir=1)
Vector < StructFact > structFactSurfCovPencil;

// for structure factor analysis of flattened MultiFabs
// (slices, vertical averages, arrays of flattened MFs, surface coverage)
Expand All @@ -364,7 +367,7 @@ void main_driver(const char* argv)
Vector < StructFact > structFactPrimPencil;
Vector < StructFact > structFactConsPencil;

// for structure factor analysis of pencil MultiFabs
// for structure factor analysis of pencil MultiFabs (either do_1D mode or do_2D with n_ads_spec>0)
BoxArray ba_pencil;
DistributionMapping dmap_pencil;

Expand Down Expand Up @@ -806,8 +809,24 @@ void main_driver(const char* argv)
// don't do structure factors of surface if there is only 1 cell
int surfCov_has_multiple_cells = 1;
if (n_ads_spec > 0) {
if (n_cells[(ads_wall_dir+1)%3] == 1 && n_cells[(ads_wall_dir+2)%3] == 1) {
if (do_1D) {
// for do_1D each pencil has a single cell for surface coverage
// so don't take structure factors
surfCov_has_multiple_cells = 0;
} else if (do_2D) {
// for do_2D if there is is only 1 cell in x then each slab is
// actually a pencil with a single cell for surface coverage,
// so don't take structure factors
if (n_cells[0] == 1) {
surfCov_has_multiple_cells = 0;
}
} else {
// for full 3D simulations if n_cells=1 in both of the non-ads_wall_dir directions
// the surface coverage is only a single cell
// so don't take structure factors
if (n_cells[(ads_wall_dir+1)%3] == 1 && n_cells[(ads_wall_dir+2)%3] == 1) {
surfCov_has_multiple_cells = 0;
}
}
}

Expand Down Expand Up @@ -861,19 +880,11 @@ void main_driver(const char* argv)

if (n_ads_spec > 0 && surfCov_has_multiple_cells) {

MultiFab Flattened; // flattened multifab defined below

// we are only calling ExtractSlice here to obtain
// a built version of Flattened so can obtain what we need to build the
// structure factor and geometry objects for flattened data
// assume surface covered is stored in the "k" direction in the k=0 coordinate.
int surfcov_plane = 0;
int surfcov_structVars = n_ads_spec;
int surfcov_nPairs = surfcov_structVars*(surfcov_structVars+1)/2;
int surfcov_nPairs = n_ads_spec*(n_ads_spec+1)/2;

Vector< std::string > surfcov_var_names;
surfcov_var_names.resize(surfcov_structVars);
for (int d=0; d<surfcov_structVars; d++) {
surfcov_var_names.resize(n_ads_spec);
for (int d=0; d<n_ads_spec; d++) {
x = "surfCov";
x += (48+d);
surfcov_var_names[d] = x;
Expand All @@ -883,12 +894,40 @@ void main_driver(const char* argv)
for (int d=0; d<surfcov_var_scaling.size(); ++d) {
surfcov_var_scaling[d] = 1.;
}

ExtractSlice(surfcov, Flattened, ads_wall_dir, surfcov_plane, 0, surfcov_structVars);
BoxArray ba_surfcov = Flattened.boxArray();
const DistributionMapping& dmap_surfcov = Flattened.DistributionMap();

structFactSurfCov.define(ba_surfcov,dmap_surfcov,surfcov_var_names,surfcov_var_scaling);
if (do_2D) {

MultiFab pencil;

// we are only calling ExtractXPencil here to obtain
// a built version of pencil so can obtain what we need to build the
// structure factor objects for pencil data
ExtractXPencil(prim, pencil, 0, 0, 0, 1);

ba_pencil = pencil.boxArray();
dmap_pencil = pencil.DistributionMap();

// each plane in z will have an x-pencil on the low-y face
structFactSurfCovPencil.resize(n_cells[2]);

for (int i = 0; i < n_cells[2]; ++i) {
structFactSurfCovPencil[i].define(ba_pencil,dmap_pencil,surfcov_var_names,surfcov_var_scaling);
}

} else {

MultiFab Flattened; // flattened multifab defined below

// we are only calling ExtractSlice here to obtain
// a built version of Flattened so can obtain what we need to build the
// structure factor and geometry objects for flattened data
// assume surface covered is stored in the "k" direction in the k=0 coordinate.
ExtractSlice(surfcov, Flattened, ads_wall_dir, 0, 0, 1);
BoxArray ba_surfcov = Flattened.boxArray();
const DistributionMapping& dmap_surfcov = Flattened.DistributionMap();

structFactSurfCov.define(ba_surfcov,dmap_surfcov,surfcov_var_names,surfcov_var_scaling);
}
}

if (do_1D) {
Expand Down Expand Up @@ -1438,11 +1477,21 @@ void main_driver(const char* argv)
} // if (project_dir >= 0)

if (n_ads_spec > 0 && surfCov_has_multiple_cells) {
int surfcov_plane = 0;
int surfcov_structVars = n_ads_spec;
MultiFab Flattened; // flattened multifab defined below
ExtractSlice(surfcov, Flattened, ads_wall_dir, surfcov_plane, 0, surfcov_structVars);
structFactSurfCov.FortStructure(Flattened);

if (do_2D) {

MultiFab pencil;

for (int i=0; i<n_cells[2]; ++i) {
ExtractXPencil(surfcov, pencil, 0, i, 0, n_ads_spec);
structFactSurfCovPencil[i].FortStructure(pencil);
}

} else {
MultiFab Flattened; // flattened multifab defined below
ExtractSlice(surfcov, Flattened, ads_wall_dir, 0, 0, n_ads_spec);
structFactSurfCov.FortStructure(Flattened);
}
}

if (do_1D) {
Expand Down Expand Up @@ -1523,7 +1572,24 @@ void main_driver(const char* argv)
}

if (n_ads_spec > 0 && surfCov_has_multiple_cells) {
structFactSurfCov.WritePlotFile(step,time,"plt_SF_surfcov");

if (do_2D) {

MultiFab surfcov_mag, surfcov_realimag;
surfcov_mag.define(ba_pencil,dmap_pencil,structFactSurfCovPencil[0].get_ncov(),0);
for (int i=0; i<n_cells[2]; ++i) {
structFactSurfCovPencil[i].AddToExternal(surfcov_mag,surfcov_realimag);
}
Real ncellsinv = 1.0/n_cells[2];
surfcov_mag.mult(ncellsinv);
surfcov_realimag.mult(ncellsinv);

WritePlotFilesSF_1D(surfcov_mag,surfcov_realimag,step,time,
structFactSurfCovPencil[0].get_names(),"plt_SF_surfcov_1D");

} else {
structFactSurfCov.WritePlotFile(step,time,"plt_SF_surfcov");
}
}

if (do_1D) {
Expand Down
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