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Pass zShift to ShiftedMetric constructor (backwards compatible) #1413

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Merged
ZedThree merged 1 commit into from
Jan 7, 2019
Merged

Pass zShift to ShiftedMetric constructor (backwards compatible) #1413

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7 changes: 7 additions & 0 deletions include/bout/paralleltransform.hxx
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Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,10 @@ public:
class ShiftedMetric : public ParallelTransform {
public:
ShiftedMetric() = delete;
/// Read zShift from the mesh
ShiftedMetric(Mesh &mesh);
/// Use an existing zShift
ShiftedMetric(Mesh &mesh, Field2D zShift);

/*!
* Calculates the yup() and ydown() fields of f
Expand Down Expand Up @@ -182,6 +185,10 @@ private:
* @param[out] out A 1D array of length mesh.LocalNz, already allocated
*/
void shiftZ(const BoutReal *in, const std::vector<dcomplex> &phs, BoutReal *out);

/// Calculate and store the phases for to/from field aligned and for
/// the parallel slices using zShift
void cachePhases();
};


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90 changes: 50 additions & 40 deletions src/mesh/parallel/shiftedmetric.cxx
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Expand Up @@ -17,8 +17,7 @@

ShiftedMetric::ShiftedMetric(Mesh &m) : mesh(m), zShift(&m) {
// Read the zShift angle from the mesh

if(mesh.get(zShift, "zShift")) {
if (mesh.get(zShift, "zShift")) {
// No zShift variable. Try qinty in BOUT grid files
mesh.get(zShift, "qinty");
}
Expand All @@ -28,76 +27,87 @@ ShiftedMetric::ShiftedMetric(Mesh &m) : mesh(m), zShift(&m) {
bool twistshift = Options::root()["TwistShift"].withDefault(false);
bool shift_without_twist = Options::root()["ShiftWithoutTwist"].withDefault(false);
if (!twistshift and !shift_without_twist) {
throw BoutException("ShiftedMetric usually requires the option TwistShift=true\n"
throw BoutException(
"ShiftedMetric usually requires the option TwistShift=true\n"
" Set ShiftWithoutTwist=true to use ShiftedMetric without TwistShift");
}

//If we wanted to be efficient we could move the following cached phase setup
//into the relevant shifting routines (with static bool first protection)
//so that we only calculate the phase if we actually call a relevant shift
//routine -- however as we're only going to do this initialisation once I
//think it's cleaner to put it in the constructor here.
cachePhases();
}

ShiftedMetric::ShiftedMetric(Mesh &m, Field2D zShift_) : mesh(m), zShift(std::move(zShift_)) {
cachePhases();
}

//As we're attached to a mesh we can expect the z direction to
//not change once we've been created so precalculate the complex
//phases used in transformations
int nmodes = mesh.LocalNz/2 + 1;
void ShiftedMetric::cachePhases() {
// If we wanted to be efficient we could move the following cached phase setup
// into the relevant shifting routines (with static bool first protection)
// so that we only calculate the phase if we actually call a relevant shift
// routine -- however as we're only going to do this initialisation once I
// think it's cleaner to put it in the constructor here.

// As we're attached to a mesh we can expect the z direction to
// not change once we've been created so precalculate the complex
// phases used in transformations
int nmodes = mesh.LocalNz / 2 + 1;
BoutReal zlength = mesh.getCoordinates()->zlength();

//Allocate storage for complex intermediate
// Allocate storage for complex intermediate
cmplx.resize(nmodes);
std::fill(cmplx.begin(), cmplx.end(), 0.0);

//Allocate storage for our 3d vector structures.
//This could be made more succinct but this approach is fairly
//verbose --> transparent
// Allocate storage for our 3d vector structures.
// This could be made more succinct but this approach is fairly
// verbose --> transparent
fromAlignedPhs.resize(mesh.LocalNx);
toAlignedPhs.resize(mesh.LocalNx);

yupPhs.resize(mesh.LocalNx);
ydownPhs.resize(mesh.LocalNx);

for(int jx=0;jx<mesh.LocalNx;jx++){
for (int jx = 0; jx < mesh.LocalNx; jx++) {
fromAlignedPhs[jx].resize(mesh.LocalNy);
toAlignedPhs[jx].resize(mesh.LocalNy);

yupPhs[jx].resize(mesh.LocalNy);
ydownPhs[jx].resize(mesh.LocalNy);
for(int jy=0;jy<mesh.LocalNy;jy++){
for (int jy = 0; jy < mesh.LocalNy; jy++) {
fromAlignedPhs[jx][jy].resize(nmodes);
toAlignedPhs[jx][jy].resize(nmodes);

yupPhs[jx][jy].resize(nmodes);
ydownPhs[jx][jy].resize(nmodes);
}
}

//To/From field aligned phases
for(int jx=0;jx<mesh.LocalNx;jx++){
for(int jy=0;jy<mesh.LocalNy;jy++){
for(int jz=0;jz<nmodes;jz++) {
BoutReal kwave=jz*2.0*PI/zlength; // wave number is 1/[rad]
fromAlignedPhs[jx][jy][jz] = dcomplex(cos(kwave*zShift(jx,jy)) , -sin(kwave*zShift(jx,jy)));
toAlignedPhs[jx][jy][jz] = dcomplex(cos(kwave*zShift(jx,jy)) , sin(kwave*zShift(jx,jy)));

// To/From field aligned phases
for (int jx = 0; jx < mesh.LocalNx; jx++) {
for (int jy = 0; jy < mesh.LocalNy; jy++) {
for (int jz = 0; jz < nmodes; jz++) {
BoutReal kwave = jz * 2.0 * PI / zlength; // wave number is 1/[rad]
fromAlignedPhs[jx][jy][jz] =
dcomplex(cos(kwave * zShift(jx, jy)), -sin(kwave * zShift(jx, jy)));
toAlignedPhs[jx][jy][jz] =
dcomplex(cos(kwave * zShift(jx, jy)), sin(kwave * zShift(jx, jy)));
}
}
}

//Yup/Ydown phases -- note we don't shift in the boundaries/guards
for(int jx=0;jx<mesh.LocalNx;jx++){
for(int jy=mesh.ystart;jy<=mesh.yend;jy++){
BoutReal yupShift = zShift(jx,jy) - zShift(jx,jy+1);
BoutReal ydownShift = zShift(jx,jy) - zShift(jx,jy-1);

for(int jz=0;jz<nmodes;jz++) {
BoutReal kwave=jz*2.0*PI/zlength; // wave number is 1/[rad]

yupPhs[jx][jy][jz] = dcomplex(cos(kwave*yupShift) , -sin(kwave*yupShift));
ydownPhs[jx][jy][jz] = dcomplex(cos(kwave*ydownShift) , -sin(kwave*ydownShift));
// Yup/Ydown phases -- note we don't shift in the boundaries/guards
for (int jx = 0; jx < mesh.LocalNx; jx++) {
for (int jy = mesh.ystart; jy <= mesh.yend; jy++) {
BoutReal yupShift = zShift(jx, jy) - zShift(jx, jy + 1);
BoutReal ydownShift = zShift(jx, jy) - zShift(jx, jy - 1);

for (int jz = 0; jz < nmodes; jz++) {
BoutReal kwave = jz * 2.0 * PI / zlength; // wave number is 1/[rad]

yupPhs[jx][jy][jz] = dcomplex(cos(kwave * yupShift), -sin(kwave * yupShift));
ydownPhs[jx][jy][jz] =
dcomplex(cos(kwave * ydownShift), -sin(kwave * ydownShift));
}
}
}

}

/*!
Expand Down