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STY: astyle
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@aaronjridley
aaronjridley committed Nov 20, 2023
1 parent f0ba8ce commit 0003b19
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Showing 10 changed files with 135 additions and 105 deletions.
1 change: 1 addition & 0 deletions src/advance.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,7 @@ bool advance(Planets &planet,
// first

neutrals.calc_scale_height(gGrid);

if (didWork)
didWork = neutrals.set_bcs(gGrid, time, indices);

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22 changes: 11 additions & 11 deletions src/calc_neutral_derived.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -393,7 +393,7 @@ precision_t Neutrals::calc_dt_cubesphere(Grid grid) {
int64_t nAlts = grid.get_nAlts();
int64_t nXs = grid.get_nLons();
int64_t nYs = grid.get_nLats();

// dtx dty for reference coordinate system
arma_cube dtx(size(cMax_vcgc[0]));
arma_cube dty(size(cMax_vcgc[0]));
Expand All @@ -405,17 +405,17 @@ precision_t Neutrals::calc_dt_cubesphere(Grid grid) {
for (int iAlt = 0; iAlt < nAlts; iAlt++) {
// Conver cMax to contravariant velocity first
arma_mat u1 = sqrt(
cMax_vcgc[0].slice(iAlt) % grid.A11_inv_scgc.slice(iAlt) %
cMax_vcgc[0].slice(iAlt) % grid.A11_inv_scgc.slice(iAlt) +
cMax_vcgc[1].slice(iAlt) % grid.A12_inv_scgc.slice(iAlt) %
cMax_vcgc[1].slice(iAlt) % grid.A12_inv_scgc.slice(iAlt));
cMax_vcgc[0].slice(iAlt) % grid.A11_inv_scgc.slice(iAlt) %
cMax_vcgc[0].slice(iAlt) % grid.A11_inv_scgc.slice(iAlt) +
cMax_vcgc[1].slice(iAlt) % grid.A12_inv_scgc.slice(iAlt) %
cMax_vcgc[1].slice(iAlt) % grid.A12_inv_scgc.slice(iAlt));
arma_mat u2 = sqrt(
cMax_vcgc[0].slice(iAlt) % grid.A21_inv_scgc.slice(iAlt) %
cMax_vcgc[0].slice(iAlt) % grid.A21_inv_scgc.slice(iAlt) +
cMax_vcgc[1].slice(iAlt) % grid.A22_inv_scgc.slice(iAlt) %
cMax_vcgc[1].slice(iAlt) % grid.A22_inv_scgc.slice(iAlt));
dtx.slice(iAlt) = grid.drefx(iAlt) * dummy_1 / u1;
dty.slice(iAlt) = grid.drefy(iAlt) * dummy_1 / u2;
cMax_vcgc[0].slice(iAlt) % grid.A21_inv_scgc.slice(iAlt) %
cMax_vcgc[0].slice(iAlt) % grid.A21_inv_scgc.slice(iAlt) +
cMax_vcgc[1].slice(iAlt) % grid.A22_inv_scgc.slice(iAlt) %
cMax_vcgc[1].slice(iAlt) % grid.A22_inv_scgc.slice(iAlt));
dtx.slice(iAlt) = grid.drefx(iAlt) * dummy_1 / u1;
dty.slice(iAlt) = grid.drefy(iAlt) * dummy_1 / u2;
}

// simply some things, and just take the bulk value for now:
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151 changes: 79 additions & 72 deletions src/electrodynamics.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@


// -----------------------------------------------------------------------------
// Call (fortran) ionospheric electrodynamics if we enable this
// Call (fortran) ionospheric electrodynamics if we enable this
// in the cmake file
// -----------------------------------------------------------------------------

Expand All @@ -27,36 +27,40 @@ Electrodynamics::Electrodynamics(Times time) {
HaveFortranIe = false;
isSet = false;

#ifdef FORTRAN
// Initialize IE components (reading in the data files):
std::string ieDir = input.get_electrodynamics_dir();
int* ieDir_iArray = copy_string_to_int(ieDir);
std::string efield = input.get_potential_model();
std::string aurora = input.get_diffuse_auroral_model();
#ifdef FORTRAN
// Initialize IE components (reading in the data files):
std::string ieDir = input.get_electrodynamics_dir();
int* ieDir_iArray = copy_string_to_int(ieDir);
std::string efield = input.get_potential_model();
std::string aurora = input.get_diffuse_auroral_model();

if (efield.length() == 0 & aurora.length() == 0) {
HaveFortranIe = false;
if (efield.length() == 0 & aurora.length() == 0)
HaveFortranIe = false;

else {
int* efield_iArray = copy_string_to_int(efield);
int* aurora_iArray = copy_string_to_int(aurora);
ie_init_library(ieDir_iArray, efield_iArray, aurora_iArray, &iError);

if (iError > 0) {
report.print(0, "Error in setting fortran IE!");
IsOk = false;
} else {
int* efield_iArray = copy_string_to_int(efield);
int* aurora_iArray = copy_string_to_int(aurora);
ie_init_library(ieDir_iArray, efield_iArray, aurora_iArray, &iError);
if (iError > 0) {
report.print(0,"Error in setting fortran IE!");
IsOk = false;
} else {
HaveFortranIe = true;
isSet = true;
}
HaveFortranIe = true;
isSet = true;
}
isCompiled = true;
#else
isCompiled = false;
#endif
}

isCompiled = true;
#else
isCompiled = false;
#endif

// If we don't set IE through Fortran, then try to set it through a file:

if (!HaveFortranIe) {
std::string electrodynamics_file = input.get_electrodynamics_file();

if (electrodynamics_file.length() > 0 &
electrodynamics_file != "none") {
// This function sets HaveElectrodynamicsFile = true.
Expand All @@ -83,7 +87,7 @@ Electrodynamics::Electrodynamics(Times time) {
// -----------------------------------------------------------------------------

void Electrodynamics::set_all_indices_for_ie(Times time,
Indices &indices) {
Indices &indices) {
std::string function = "Electrodynamics::set_all_indices_for_ie";
static int iFunction = -1;
report.enter(function, iFunction);
Expand Down Expand Up @@ -111,17 +115,18 @@ void Electrodynamics::set_all_indices_for_ie(Times time,
std::cout << "sw v : " << iVx_ << " " << swv << "\n";
std::cout << "sw n : " << iN_ << " " << swn << "\n";
}
#ifdef FORTRAN
ie_set_time(&time_now);
ie_set_imfby(&imfby);
ie_set_imfbz(&imfbz);
ie_set_swv(&swv);
ie_set_swn(&swn);
ie_set_ae(&ae);
ie_set_au(&au);
ie_set_al(&al);
ie_set_hp_from_ae(&ae);
#endif

#ifdef FORTRAN
ie_set_time(&time_now);
ie_set_imfby(&imfby);
ie_set_imfbz(&imfbz);
ie_set_swv(&swv);
ie_set_swn(&swn);
ie_set_ae(&ae);
ie_set_au(&au);
ie_set_al(&al);
ie_set_hp_from_ae(&ae);
#endif

report.exit(function);
return;
Expand Down Expand Up @@ -154,60 +159,62 @@ bool Electrodynamics::update(Planets planet,
ions.eflux.zeros();
ions.avee.ones();

#ifdef FORTRAN
if (HaveFortranIe) {
report.print(3, "Using Fortran Electrodynamics!");
set_all_indices_for_ie(time, indices);

if (!IsAllocated) {
int nXs = gGrid.get_nX();
ie_set_nxs(&nXs);
int nYs = gGrid.get_nY();
ie_set_nys(&nYs);
int64_t iTotal = nXs * nYs;
mlt2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
lat2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
pot2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
eflux2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
avee2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
IsAllocated = true;
}
#ifdef FORTRAN

if (HaveFortranIe) {
report.print(3, "Using Fortran Electrodynamics!");
set_all_indices_for_ie(time, indices);

if (!IsAllocated) {
int nXs = gGrid.get_nX();
ie_set_nxs(&nXs);
int nYs = gGrid.get_nY();
ie_set_nys(&nYs);
int64_t iTotal = nXs * nYs;
mlt2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
lat2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
pot2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
eflux2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
avee2d = static_cast<float*>(malloc(iTotal * sizeof(float)));
IsAllocated = true;
}

int64_t nZs = gGrid.get_nZ();
int64_t iZ;
int64_t nZs = gGrid.get_nZ();
int64_t iZ;

int iError;
int iError;

for (iZ = 0; iZ < nZs; iZ++) {
copy_mat_to_array(gGrid.magLocalTime_scgc.slice(iZ), mlt2d, true);
copy_mat_to_array(gGrid.magLat_scgc.slice(iZ), lat2d, true);
for (iZ = 0; iZ < nZs; iZ++) {
copy_mat_to_array(gGrid.magLocalTime_scgc.slice(iZ), mlt2d, true);
copy_mat_to_array(gGrid.magLat_scgc.slice(iZ), lat2d, true);

ie_set_mlts(mlt2d, &iError);
ie_set_lats(lat2d, &iError);
ie_update_grid(&iError);
ie_set_mlts(mlt2d, &iError);
ie_set_lats(lat2d, &iError);
ie_update_grid(&iError);

ie_get_potential(pot2d, &iError);
copy_array_to_mat(pot2d, ions.potential_scgc.slice(iZ), true);
ie_get_potential(pot2d, &iError);
copy_array_to_mat(pot2d, ions.potential_scgc.slice(iZ), true);

if (iZ == nZs-1) {
ie_get_electron_diffuse_aurora(eflux2d, avee2d, &iError);
copy_array_to_mat(avee2d, ions.avee, true);
copy_array_to_mat(eflux2d, ions.eflux, true);
}
if (iZ == nZs - 1) {
ie_get_electron_diffuse_aurora(eflux2d, avee2d, &iError);
copy_array_to_mat(avee2d, ions.avee, true);
copy_array_to_mat(eflux2d, ions.eflux, true);
}
}
#endif
}

#endif

if (HaveElectrodynamicsFile) {
report.print(3, "Setting electrodynamics from file!");
auto electrodynamics_values =
get_electrodynamics(gGrid.magLat_scgc,
gGrid.magLocalTime_scgc);
gGrid.magLocalTime_scgc);
ions.potential_scgc = std::get<0>(electrodynamics_values);
ions.eflux = std::get<1>(electrodynamics_values);
ions.avee = std::get<2>(electrodynamics_values);
}
}
}

report.exit(function);
return true;
Expand Down
6 changes: 5 additions & 1 deletion src/exchange_messages_v2.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -602,10 +602,12 @@ void Grid::exchange(arma_cube &data, const bool pole_inverse) {
bool Neutrals::exchange(Grid &grid) {
// For each species, exchange if its DoAdvect is true
int64_t nGCs = grid.get_nGCs();

for (int i = 0; i < nSpecies; ++i) {
if (species[i].DoAdvect)
grid.exchange(species[i].density_scgc, false);
fill_corners(species[i].density_scgc, nGCs);

fill_corners(species[i].density_scgc, nGCs);
}

// Exchange temperature
Expand All @@ -617,7 +619,9 @@ bool Neutrals::exchange(Grid &grid) {
grid.exchange(velocity_vcgc[0], true);
grid.exchange(velocity_vcgc[1], true);
grid.exchange(velocity_vcgc[2], false);

for (int iDir = 0; iDir < 3; iDir++)
fill_corners(velocity_vcgc[iDir], nGCs);

return true;
}
2 changes: 2 additions & 0 deletions src/init_geo_grid.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -984,10 +984,12 @@ bool Grid::init_geo_grid(Quadtree quadtree,

// Calculate the radius (for spherical or non-spherical)
fill_grid_radius(planet);

// Correct the reference grid with correct length scale:
// (with R = actual radius)
if (input.get_is_cubesphere())
correct_xy_grid(planet);

// Calculate grid spacing
calc_grid_spacing(planet);
//calculate radial unit vector (for spherical or oblate planet)
Expand Down
8 changes: 4 additions & 4 deletions src/inputs.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -461,7 +461,7 @@ bool Inputs::get_euv_douse() {
}

// -----------------------------------------------------------------------
// Return the Electrodynamics Dir - this is where all of the
// Return the Electrodynamics Dir - this is where all of the
// files that are for the empirical models reside
// -----------------------------------------------------------------------

Expand All @@ -470,7 +470,7 @@ std::string Inputs::get_electrodynamics_north_file() {
}

// -----------------------------------------------------------------------
// Return the Electrodynamics Dir - this is where all of the
// Return the Electrodynamics Dir - this is where all of the
// files that are for the empirical models reside
// -----------------------------------------------------------------------

Expand All @@ -479,7 +479,7 @@ std::string Inputs::get_electrodynamics_south_file() {
}

// -----------------------------------------------------------------------
// Return the Electrodynamics Dir - this is where all of the
// Return the Electrodynamics Dir - this is where all of the
// files that are for the empirical models reside
// -----------------------------------------------------------------------

Expand All @@ -488,7 +488,7 @@ std::string Inputs::get_electrodynamics_file() {
}

// -----------------------------------------------------------------------
// Return the Electrodynamics Dir - this is where all of the
// Return the Electrodynamics Dir - this is where all of the
// files that are for the empirical models reside
// -----------------------------------------------------------------------

Expand Down
7 changes: 5 additions & 2 deletions src/neutrals.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -290,22 +290,25 @@ bool Neutrals::check_for_nonfinites() {
bool didWork = true;

isBad = !all_finite(density_scgc, "density_scgc");

if (isBad) {
report.error("non-finite found in neutral density!");
didWork = false;
}

isBad = !all_finite(temperature_scgc, "temperature_scgc");

if (isBad) {
report.error("non-finite found in neutral temperature!");
didWork = false;
}
}

isBad = !all_finite(velocity_vcgc, "velocity_vcgc");

if (isBad) {
report.error("non-finite found in neutral velocity!");
didWork = false;
}
}

return didWork;
}
Expand Down
7 changes: 5 additions & 2 deletions src/solver_gradients.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -11,13 +11,15 @@ std::vector<arma_cube> calc_gradient_vector(arma_cube value_scgc, Grid grid) {

std::vector<arma_cube> gradient_vcgc;

if (input.get_is_cubesphere()) {
if (input.get_is_cubesphere())
gradient_vcgc = calc_gradient_cubesphere(value_scgc, grid);
} else {

else {
gradient_vcgc.push_back(calc_gradient_lon(value_scgc, grid));
gradient_vcgc.push_back(calc_gradient_lat(value_scgc, grid));
gradient_vcgc.push_back(calc_gradient_alt(value_scgc, grid));
}

return gradient_vcgc;
}

Expand Down Expand Up @@ -215,6 +217,7 @@ std::vector<arma_cube> calc_gradient_cubesphere(arma_cube value, Grid grid) {
}
}
}

// We then use A transformation matrices to convert grad_xy to grad_latlon
// Ref -> Physical, we use A matrix
grad_lon.slice(iAlt) = grad_x_curr % grid.A11_inv_scgc.slice(
Expand Down
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