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Clang-Tidy
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@tomchapman
tomchapman committed Nov 26, 2023
1 parent 0492470 commit 12ead24
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Showing 3 changed files with 50 additions and 48 deletions.
2 changes: 1 addition & 1 deletion include/bout/coordinates.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -82,7 +82,7 @@ public:
const Field2D& zlength() const;

/// True if corrections for non-uniform mesh spacing should be included in operators
bool non_uniform;
bool non_uniform{};
/// 2nd-order correction for non-uniform meshes d/di(1/dx), d/di(1/dy) and d/di(1/dz)
FieldMetric d1_dx, d1_dy, d1_dz;

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2 changes: 1 addition & 1 deletion include/bout/msg_stack.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -201,7 +201,7 @@ private:
arguments and the optional arguments follow from there.
*/
#define TRACE(...) \
MsgStackItem CONCATENATE(msgTrace_, __LINE__)(__FILE__, __LINE__, __VA_ARGS__)
const MsgStackItem CONCATENATE(msgTrace_, __LINE__)(__FILE__, __LINE__, __VA_ARGS__)
#else
#define TRACE(...)
#endif
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94 changes: 48 additions & 46 deletions src/mesh/coordinates.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,6 @@

#include <bout/fft.hxx>

#include <bout/globals.hxx>

#include "parallel/fci.hxx"
#include "parallel/shiftedmetricinterp.hxx"

Expand All @@ -24,7 +22,6 @@
#include "bout/field3d.hxx"
#include "bout/geometry.hxx"
#include "bout/metricTensor.hxx"
#include "bout/utils.hxx"
#include <bout/bout_types.hxx>

// use anonymous namespace so this utility function is not available outside this file
Expand Down Expand Up @@ -265,10 +262,9 @@ Coordinates::FieldMetric Coordinates::getUnaligned(const std::string& name,
if (field.getDirectionY() == YDirectionType::Aligned
and transform->canToFromFieldAligned()) {
return transform->fromFieldAligned(field);
} else {
field.setDirectionY(YDirectionType::Standard);
return field;
}
field.setDirectionY(YDirectionType::Standard);
return field;
}

Coordinates::FieldMetric Coordinates::getUnalignedAtLocationAndFillGuards(
Expand All @@ -278,7 +274,7 @@ Coordinates::FieldMetric Coordinates::getUnalignedAtLocationAndFillGuards(
ParallelTransform* pParallelTransform) {

auto field = getAtLocOrUnaligned(mesh, name, default_value, suffix, cell_location);
if (suffix == "") {
if (suffix.empty()) {
no_extra_interpolate = false;
pParallelTransform = transform.get();
}
Expand All @@ -297,10 +293,14 @@ Coordinates::Coordinates(Mesh* mesh, FieldMetric dx, FieldMetric dy, FieldMetric
FieldMetric IntShiftTorsion)
: dx(std::move(dx)), dy(std::move(dy)), dz(dz), ShiftTorsion(std::move(ShiftTorsion)),
IntShiftTorsion(std::move(IntShiftTorsion)), nz(mesh->LocalNz), localmesh(mesh),
location(CELL_CENTRE), differential_operators(DifferentialOperators(
mesh, this->IntShiftTorsion, location, dx, dy, dz)),
geometry(Geometry(J, Bxy, g11, g22, g33, g12, g13, g23, g_11, g_22, g_33, g_12,
g_13, g_23, differential_operators)) {}
location(CELL_CENTRE),
differential_operators(DifferentialOperators(mesh, this->IntShiftTorsion, location,
this->dx, this->dy, dz)),
geometry(Geometry(std::move(J), std::move(Bxy), std::move(g11), std::move(g22),
std::move(g33), std::move(g12), std::move(g13), std::move(g23),
std::move(g_11), std::move(g_22), std::move(g_33),
std::move(g_12), std::move(g_13), std::move(g_23),
differential_operators)) {}

Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
const Coordinates* coords_in, bool force_interpolate_from_centre)
Expand All @@ -323,10 +323,10 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
nz = mesh->LocalNz;

// Default to true in case staggered quantities are not read from file
bool extrapolate_x = true;
bool extrapolate_y = true;
const bool extrapolate_x = true;
const bool extrapolate_y = true;

if (coords_in && suffix != ""
if ((coords_in != nullptr) && !suffix.empty()
&& (force_interpolate_from_centre || !mesh->sourceHasVar("dx" + suffix))) {

// Interpolate fields from coords_in
Expand All @@ -349,8 +349,8 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
dz = localmesh->interpolateAndExtrapolate(coords_in->dz, location, true, true, false,
transform.get());

std::function<const FieldMetric(const FieldMetric)>
interpolateAndExtrapolate_function = [this](const FieldMetric component) {
std::function<const FieldMetric(const FieldMetric)> const
interpolateAndExtrapolate_function = [this](const FieldMetric& component) {
return localmesh->interpolateAndExtrapolate(component, location, true, true,
false, transform.get());
};
Expand Down Expand Up @@ -519,9 +519,9 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
// More robust to extrapolate derived quantities directly, rather than
// deriving from extrapolated covariant metric components

std::function<const FieldMetric(const FieldMetric)>
std::function<const FieldMetric(const FieldMetric)> const
interpolateAndExtrapolate_function = [this, extrapolate_y, extrapolate_x](
const FieldMetric component) {
const FieldMetric& component) {
return localmesh->interpolateAndExtrapolate(
component, location, extrapolate_x, extrapolate_y, false, transform.get());
};
Expand All @@ -541,7 +541,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
"\tWARNING: Jacobian 'J_{:s}' not found. Calculating from metric tensor\n",
suffix);
setJ(Jcalc);
} catch (BoutException) {
} catch (BoutException&) {
setJ(localmesh->interpolateAndExtrapolate(J(), location, extrapolate_x,
extrapolate_y, false, transform.get()));

Expand Down Expand Up @@ -570,7 +570,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
"Calculating from metric tensor\n",
suffix);
setBxy(Bcalc);
} catch (BoutException) {
} catch (BoutException&) {
setBxy(localmesh->interpolateAndExtrapolate(Bxy(), location, extrapolate_x,
extrapolate_y, false, transform.get()));
output_warn.write("\tMaximum difference in Bxy is {:e}\n", max(abs(Bxy() - Bcalc)));
Expand All @@ -580,7 +580,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
bout::checkFinite(Bxy(), "Bxy" + suffix, "RGN_NOCORNERS");
bout::checkPositive(Bxy(), "Bxy" + suffix, "RGN_NOCORNERS");

if (getAtLoc(mesh, ShiftTorsion, "ShiftTorsion", suffix, location)) {
if (getAtLoc(mesh, ShiftTorsion, "ShiftTorsion", suffix, location) != 0) {
output_warn.write("\tWARNING: No Torsion specified for zShift. "
"Derivatives may not be correct\n");
ShiftTorsion = 0.0;
Expand All @@ -592,7 +592,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,

if (mesh->IncIntShear) {
checkStaggeredGet(mesh, "IntShiftTorsion", suffix);
if (mesh->get(IntShiftTorsion, "IntShiftTorsion" + suffix, 0.0, false)) {
if (mesh->get(IntShiftTorsion, "IntShiftTorsion" + suffix, 0.0, false) != 0) {
output_warn.write("\tWARNING: No Integrated torsion specified\n");
IntShiftTorsion = 0.0;
}
Expand All @@ -608,7 +608,7 @@ Coordinates::Coordinates(Mesh* mesh, Options* options, const CELL_LOC loc,
}

void Coordinates::outputVars(Options& output_options) {
Timer time("io");
Timer const time("io");
const std::string loc_string =
(location == CELL_CENTRE) ? "" : "_" + toString(location);

Expand Down Expand Up @@ -758,17 +758,18 @@ int Coordinates::calculateGeometry(bool recalculate_staggered,

OPTION(Options::getRoot(), non_uniform, true);

Coordinates::FieldMetric d2x(localmesh), d2y(localmesh),
d2z(localmesh); // d^2 x / d i^2
Coordinates::FieldMetric d2x(localmesh);
Coordinates::FieldMetric d2y(localmesh);
Coordinates::FieldMetric const d2z(localmesh); // d^2 x / d i^2

// Read correction for non-uniform meshes
std::string suffix = getLocationSuffix(location);
std::string const suffix = getLocationSuffix(location);
if (location == CELL_CENTRE
or (!force_interpolate_from_centre and localmesh->sourceHasVar("dx" + suffix))) {
bool extrapolate_x = not localmesh->sourceHasXBoundaryGuards();
bool extrapolate_y = not localmesh->sourceHasYBoundaryGuards();
bool const extrapolate_x = not localmesh->sourceHasXBoundaryGuards();
bool const extrapolate_y = not localmesh->sourceHasYBoundaryGuards();

if (localmesh->get(d2x, "d2x" + suffix, 0.0, false, location)) {
if (localmesh->get(d2x, "d2x" + suffix, 0.0, false, location) != 0) {
output_warn.write("\tWARNING: differencing quantity 'd2x' not found. "
"Calculating from dx\n");
d1_dx = bout::derivatives::index::DDX(1. / dx); // d/di(1/dx)
Expand All @@ -785,7 +786,7 @@ int Coordinates::calculateGeometry(bool recalculate_staggered,
d1_dx = -d2x / (dx * dx);
}

if (localmesh->get(d2y, "d2y" + suffix, 0.0, false, location)) {
if (localmesh->get(d2y, "d2y" + suffix, 0.0, false, location) != 0) {
output_warn.write("\tWARNING: differencing quantity 'd2y' not found. "
"Calculating from dy\n");
d1_dy = DDY(1. / dy); // d/di(1/dy)
Expand Down Expand Up @@ -822,7 +823,7 @@ int Coordinates::calculateGeometry(bool recalculate_staggered,
d1_dz = 0;
#endif
} else {
if (localmesh->get(d2x, "d2x", 0.0, false)) {
if (localmesh->get(d2x, "d2x", 0.0, false) != 0) {
output_warn.write("\tWARNING: differencing quantity 'd2x' not found. "
"Calculating from dx\n");
d1_dx = bout::derivatives::index::DDX(1. / dx); // d/di(1/dx)
Expand All @@ -838,7 +839,7 @@ int Coordinates::calculateGeometry(bool recalculate_staggered,
d1_dx = -d2x / (dx * dx);
}

if (localmesh->get(d2y, "d2y", 0.0, false)) {
if (localmesh->get(d2y, "d2y", 0.0, false) != 0) {
output_warn.write("\tWARNING: differencing quantity 'd2y' not found. "
"Calculating from dy\n");
d1_dy = DDY(1. / dy); // d/di(1/dy)
Expand Down Expand Up @@ -1055,10 +1056,10 @@ void Coordinates::jacobian() {
TRACE("Geometry::jacobian");
try {

const auto j = geometry.recalculateJacobian();
const auto jacobian = geometry.recalculateJacobian();
// More robust to extrapolate derived quantities directly, rather than
// deriving from extrapolated covariant metric components
geometry.setJ(localmesh->interpolateAndExtrapolate(j, location, extrapolate_x,
geometry.setJ(localmesh->interpolateAndExtrapolate(jacobian, location, extrapolate_x,
extrapolate_y, false));

const auto Bxy = geometry.recalculateBxy();
Expand All @@ -1074,7 +1075,7 @@ void Coordinates::jacobian() {
namespace {
// Utility function for fixing up guard cells of zShift
void fixZShiftGuards(Field2D& zShift) {
auto localmesh = zShift.getMesh();
auto* localmesh = zShift.getMesh();

// extrapolate into boundary guard cells if necessary
zShift = localmesh->interpolateAndExtrapolate(
Expand Down Expand Up @@ -1103,7 +1104,7 @@ void fixZShiftGuards(Field2D& zShift) {
} // namespace

void Coordinates::setParallelTransform(Options* options) {
auto ptoptions = options->getSection("paralleltransform");
auto* ptoptions = options->getSection("paralleltransform");

std::string ptstr;
ptoptions->get("type", ptstr, "identity");
Expand All @@ -1122,13 +1123,13 @@ void Coordinates::setParallelTransform(Options* options) {
Field2D zShift{localmesh};

// Read the zShift angle from the mesh
std::string suffix = getLocationSuffix(location);
std::string const suffix = getLocationSuffix(location);
if (localmesh->sourceHasVar("dx" + suffix)) {
// Grid file has variables at this location, so should be able to read
checkStaggeredGet(localmesh, "zShift", suffix);
if (localmesh->get(zShift, "zShift" + suffix, 0.0, false, location)) {
if (localmesh->get(zShift, "zShift" + suffix, 0.0, false, location) != 0) {
// No zShift variable. Try qinty in BOUT grid files
if (localmesh->get(zShift, "qinty" + suffix, 0.0, false, location)) {
if (localmesh->get(zShift, "qinty" + suffix, 0.0, false, location) != 0) {
// Failed to find either variable, cannot use ShiftedMetric
throw BoutException("Could not read zShift" + suffix + " from grid file");
}
Expand All @@ -1140,9 +1141,9 @@ void Coordinates::setParallelTransform(Options* options) {
"file.");
}
Field2D zShift_centre;
if (localmesh->get(zShift_centre, "zShift", 0.0, false)) {
if (localmesh->get(zShift_centre, "zShift", 0.0, false) != 0) {
// No zShift variable. Try qinty in BOUT grid files
if (localmesh->get(zShift_centre, "qinty", 0.0, false)) {
if (localmesh->get(zShift_centre, "qinty", 0.0, false) != 0) {
// Failed to find either variable, cannot use ShiftedMetric
throw BoutException("Could not read zShift from grid file");
}
Expand Down Expand Up @@ -1361,6 +1362,7 @@ Field3D Coordinates::Grad2_par2(const Field3D& f, CELL_LOC outloc,
// perpendicular Laplacian operator

#include <bout/invert_laplace.hxx> // Delp2 uses same coefficients as inversion code
#include <utility>

Coordinates::FieldMetric Coordinates::Delp2(const Field2D& f, CELL_LOC outloc,
bool UNUSED(useFFT)) {
Expand Down Expand Up @@ -1456,11 +1458,11 @@ FieldPerp Coordinates::Delp2(const FieldPerp& f, CELL_LOC outloc, bool useFFT) {

FieldPerp result{emptyFrom(f).setLocation(outloc)};

int jy = f.getIndex();
int const jy = f.getIndex();
result.setIndex(jy);

if (useFFT) {
int ncz = localmesh->LocalNz;
int const ncz = localmesh->LocalNz;

// Allocate memory
auto ft = Matrix<dcomplex>(localmesh->LocalNx, ncz / 2 + 1);
Expand Down Expand Up @@ -1644,12 +1646,12 @@ void Coordinates::checkContravariant() { geometry.checkContravariant(localmesh->

void Coordinates::setContravariantMetricTensor(MetricTensor metric_tensor,
const std::string& region) {
geometry.setContravariantMetricTensor(metric_tensor, location, region);
geometry.setContravariantMetricTensor(std::move(metric_tensor), location, region);
}

void Coordinates::setCovariantMetricTensor(MetricTensor metric_tensor,
const std::string& region) {
geometry.setCovariantMetricTensor(metric_tensor, location, region);
geometry.setCovariantMetricTensor(std::move(metric_tensor), location, region);
}

const FieldMetric& Coordinates::g_11() const { return geometry.g_11(); }
Expand Down Expand Up @@ -1682,7 +1684,7 @@ void Coordinates::setJ(BoutReal value, int x, int y) {

void Coordinates::setBxy(FieldMetric Bxy) {
//TODO: Calculate Bxy and check value is close
geometry.setBxy(Bxy);
geometry.setBxy(std::move(Bxy));
}

const MetricTensor& Coordinates::getContravariantMetricTensor() const {
Expand Down

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