void GridPatchCSGLL::ComputeVorticityDivergence(
int iDataIndex
) {
// Physical constants
const PhysicalConstants & phys = m_grid.GetModel().GetPhysicalConstants();
// Working data
DataArray4D<double> & dataState =
GetDataState(iDataIndex, DataLocation_Node);
if (dataState.GetSize(0) < 2) {
_EXCEPTIONT(
"Insufficient components for vorticity calculation");
}
// Get the alpha and beta components of vorticity
DataArray3D<double> dataUa;
dataUa.SetSize(
dataState.GetSize(1),
dataState.GetSize(2),
dataState.GetSize(3));
DataArray3D<double> dataUb;
dataUb.SetSize(
dataState.GetSize(1),
dataState.GetSize(2),
dataState.GetSize(3));
dataUa.AttachToData(&(dataState[0][0][0][0]));
dataUb.AttachToData(&(dataState[1][0][0][0]));
// Compute the radial component of the curl of the velocity field
ComputeCurlAndDiv(dataUa, dataUb);
}
void Grid::ReduceInterpolate(
const DataArray1D<double> & dAlpha,
const DataArray1D<double> & dBeta,
const DataArray1D<int> & iPatch,
DataType eDataType,
DataLocation eDataLocation,
bool fInterpAllVariables,
DataArray3D<double> & dInterpData,
bool fIncludeReferenceState,
bool fConvertToPrimitive
) const {
// Check interpolation data array size
if ((dAlpha.GetRows() != dBeta.GetRows()) ||
(dAlpha.GetRows() != iPatch.GetRows())
) {
_EXCEPTIONT("Inconsistency in vector lengths.");
}
if ((eDataType == DataType_Tracers) &&
(m_model.GetEquationSet().GetTracers() == 0)
) {
_EXCEPTIONT("Unable to Interpolate with no tracers.");
}
// Check interpolation data array size
if ((eDataType == DataType_State) &&
(dInterpData.GetRows() != m_model.GetEquationSet().GetComponents())
) {
_EXCEPTIONT("InterpData dimension mismatch (0)");
}
if ((eDataType == DataType_Tracers) &&
(dInterpData.GetRows() != m_model.GetEquationSet().GetTracers())
) {
_EXCEPTIONT("InterpData dimension mismatch (0)");
}
if ((eDataType == DataType_Topography) &&
(dInterpData.GetRows() != 1)
) {
_EXCEPTIONT("InterpData dimension mismatch (0)");
}
if ((eDataType == DataType_Vorticity) &&
(dInterpData.GetRows() != 1)
) {
_EXCEPTIONT("InterpData dimension mismatch (0)");
}
if ((eDataType == DataType_Divergence) &&
(dInterpData.GetRows() != 1)
) {
_EXCEPTIONT("InterpData dimension mismatch (0)");
}
if ((eDataType == DataType_Temperature) &&
(dInterpData.GetRows() != 1)
) {
_EXCEPTIONT("InterpData dimension mismatch (0)");
}
if ((eDataLocation == DataLocation_None) &&
(dInterpData.GetColumns() != 1)
) {
_EXCEPTIONT("InterpData dimension mismatch (1)");
}
if ((eDataLocation == DataLocation_Node) &&
(dInterpData.GetColumns() != GetRElements())
) {
_EXCEPTIONT("InterpData dimension mismatch (1)");
}
if ((eDataLocation == DataLocation_REdge) &&
(dInterpData.GetColumns() != GetRElements() + 1)
) {
_EXCEPTIONT("InterpData dimension mismatch (1)");
}
if (dInterpData.GetSubColumns() != dAlpha.GetRows()) {
_EXCEPTIONT("InterpData dimension mismatch (2)");
}
// Zero the interpolated data
dInterpData.Zero();
// Interpolate state data
for (int n = 0; n < m_vecActiveGridPatches.size(); n++) {
m_vecActiveGridPatches[n]->InterpolateData(
dAlpha, dBeta, iPatch,
eDataType,
eDataLocation,
fInterpAllVariables,
dInterpData,
fIncludeReferenceState,
fConvertToPrimitive);
}
#ifdef USE_MPI
// Perform an Reduce operation to combine all data
int nRank;
MPI_Comm_rank(MPI_COMM_WORLD, &nRank);
if (nRank == 0) {
MPI_Reduce(
MPI_IN_PLACE,
&(dInterpData[0][0][0]),
dInterpData.GetRows()
* dInterpData.GetColumns()
* dInterpData.GetSubColumns(),
MPI_DOUBLE,
MPI_SUM,
0,
MPI_COMM_WORLD);
} else {
MPI_Reduce(
&(dInterpData[0][0][0]),
NULL,
dInterpData.GetRows()
* dInterpData.GetColumns()
* dInterpData.GetSubColumns(),
MPI_DOUBLE,
MPI_SUM,
0,
MPI_COMM_WORLD);
}
#endif
}
void ExchangeBuffer::Unpack(
DataArray3D<double> & data
) {
const size_t sAElements = data.GetSize(0);
const size_t sBElements = data.GetSize(1);
const size_t sRElements = data.GetSize(2);
// Index for halo elements along boundary
int ixBoundaryBegin;
int ixBoundaryEnd;
int ixABoundaryBegin;
int ixABoundaryEnd;
int ixBBoundaryBegin;
int ixBBoundaryEnd;
// Unpack data from right
if (m_dir == Direction_Right) {
ixBoundaryBegin = sAElements - m_sHaloElements;
ixBoundaryEnd = sAElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixBoundaryEnd - ixBoundaryBegin)
* (m_ixSecond - m_ixFirst);
if (m_ixRecvBuffer + nTotalValues > m_dRecvBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in RecvBuffer for operation.");
}
// Unpack data
for (int i = ixBoundaryEnd-1; i >= ixBoundaryBegin; i--) {
for (int j = m_ixFirst; j < m_ixSecond; j++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
data(i,j,k) =
m_dRecvBuffer[m_ixRecvBuffer + k];
}
m_ixRecvBuffer += sRElements;
}
}
// Unpack data from top
} else if (m_dir == Direction_Top) {
ixBoundaryBegin = sBElements - m_sHaloElements;
ixBoundaryEnd = sBElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixBoundaryEnd - ixBoundaryBegin)
* (m_ixSecond - m_ixFirst);
if (m_ixRecvBuffer + nTotalValues > m_dRecvBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in RecvBuffer for operation.");
}
// Unpack data
for (int j = ixBoundaryEnd-1; j >= ixBoundaryBegin; j--) {
for (int i = m_ixFirst; i < m_ixSecond; i++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
data(i,j,k) =
m_dRecvBuffer[m_ixRecvBuffer + k];
}
m_ixRecvBuffer += sRElements;
}
}
// Unpack data from left
} else if (m_dir == Direction_Left) {
ixBoundaryBegin = 0;
ixBoundaryEnd = m_sHaloElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixBoundaryEnd - ixBoundaryBegin)
* (m_ixSecond - m_ixFirst);
if (m_ixRecvBuffer + nTotalValues > m_dRecvBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in RecvBuffer for operation.");
}
// Unpack data
for (int i = ixBoundaryBegin; i < ixBoundaryEnd; i++) {
for (int j = m_ixFirst; j < m_ixSecond; j++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
data(i,j,k) =
m_dRecvBuffer[m_ixRecvBuffer + k];
}
m_ixRecvBuffer += sRElements;
}
}
// Unpack data from bottom
} else if (m_dir == Direction_Bottom) {
ixBoundaryBegin = 0;
ixBoundaryEnd = m_sHaloElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixBoundaryEnd - ixBoundaryBegin)
* (m_ixSecond - m_ixFirst);
if (m_ixRecvBuffer + nTotalValues > m_dRecvBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in RecvBuffer for operation.");
}
// Unpack data
for (int j = ixBoundaryBegin; j < ixBoundaryEnd; j++) {
for (int i = m_ixFirst; i < m_ixSecond; i++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
data(i,j,k) =
m_dRecvBuffer[m_ixRecvBuffer + k];
}
m_ixRecvBuffer += sRElements;
}
}
// Unpack data from top-right
} else if (m_dir == Direction_TopRight) {
ixABoundaryBegin = m_ixFirst + 1;
ixABoundaryEnd = m_ixFirst + m_sHaloElements + 1;
ixBBoundaryBegin = m_ixSecond + 1;
ixBBoundaryEnd = m_ixSecond + m_sHaloElements + 1;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixABoundaryEnd - ixABoundaryBegin)
* (ixBBoundaryEnd - ixBBoundaryBegin);
if (m_ixRecvBuffer + nTotalValues > m_dRecvBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in RecvBuffer for operation.");
}
// Unpack data
for (int j = ixBBoundaryEnd-1; j >= ixBBoundaryBegin; j--) {
for (int i = ixABoundaryEnd-1; i >= ixABoundaryBegin; i--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
data(i,j,k) =
m_dRecvBuffer[m_ixRecvBuffer + k];
}
m_ixRecvBuffer += sRElements;
}
}
// Unpack data from top-left
} else if (m_dir == Direction_TopLeft) {
ixABoundaryBegin = m_ixFirst - m_sHaloElements;
ixABoundaryEnd = m_ixFirst;
ixBBoundaryBegin = m_ixSecond + 1;
ixBBoundaryEnd = m_ixSecond + m_sHaloElements + 1;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixABoundaryEnd - ixABoundaryBegin)
* (ixBBoundaryEnd - ixBBoundaryBegin);
if (m_ixRecvBuffer + nTotalValues > m_dRecvBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in RecvBuffer for operation.");
}
// Unpack data
for (int j = ixBBoundaryEnd-1; j >= ixBBoundaryBegin; j--) {
for (int i = ixABoundaryBegin; i < ixABoundaryEnd; i++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
data(i,j,k) =
m_dRecvBuffer[m_ixRecvBuffer + k];
}
m_ixRecvBuffer += sRElements;
}
}
// Unpack data from bottom-left
} else if (m_dir == Direction_BottomLeft) {
ixABoundaryBegin = m_ixFirst - m_sHaloElements;
ixABoundaryEnd = m_ixFirst;
ixBBoundaryBegin = m_ixSecond - m_sHaloElements;
ixBBoundaryEnd = m_ixSecond;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixABoundaryEnd - ixABoundaryBegin)
* (ixBBoundaryEnd - ixBBoundaryBegin);
if (m_ixRecvBuffer + nTotalValues > m_dRecvBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in RecvBuffer for operation.");
}
// Unpack data
for (int j = ixBBoundaryBegin; j < ixBBoundaryEnd; j++) {
for (int i = ixABoundaryBegin; i < ixABoundaryEnd; i++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
data(i,j,k) =
m_dRecvBuffer[m_ixRecvBuffer + k];
}
m_ixRecvBuffer += sRElements;
}
}
// Unpack data from bottom-right
} else if (m_dir == Direction_BottomRight) {
ixABoundaryBegin = m_ixFirst + 1;
ixABoundaryEnd = m_ixFirst + m_sHaloElements + 1;
ixBBoundaryBegin = m_ixSecond - m_sHaloElements;
ixBBoundaryEnd = m_ixSecond;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixABoundaryEnd - ixABoundaryBegin)
* (ixBBoundaryEnd - ixBBoundaryBegin);
if (m_ixRecvBuffer + nTotalValues > m_dRecvBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in RecvBuffer for operation.");
}
// Unpack data
for (int j = ixBBoundaryBegin; j < ixBBoundaryEnd; j++) {
for (int i = ixABoundaryEnd-1; i >= ixABoundaryBegin; i--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
data(i,j,k) =
m_dRecvBuffer[m_ixRecvBuffer + k];
}
m_ixRecvBuffer += sRElements;
}
}
// Invalid direction
} else {
_EXCEPTIONT("Invalid direction");
}
}
void ExchangeBuffer::Pack(
const DataArray3D<double> & data
) {
const size_t sAElements = data.GetSize(0);
const size_t sBElements = data.GetSize(1);
const size_t sRElements = data.GetSize(2);
// Check matrix bounds
if (((m_dir == Direction_Right) || (m_dir == Direction_Left)) &&
(m_ixSecond > sBElements)
) {
_EXCEPTIONT("GridData / ExteriorNeighbor inconsistency.");
}
if (((m_dir == Direction_Top) || (m_dir == Direction_Bottom)) &&
(m_ixSecond > sAElements)
) {
_EXCEPTIONT("GridData / ExteriorNeighbor inconsistency.");
}
// Index for halo elements along boundary
int ixBoundaryBegin;
int ixBoundaryEnd;
int ixABoundaryBegin;
int ixABoundaryEnd;
int ixBBoundaryBegin;
int ixBBoundaryEnd;
// Maximum index for radial elements
int nVarRElements;
// Pack data to send right
if (m_dir == Direction_Right) {
ixBoundaryBegin = sAElements - 2 * m_sHaloElements;
ixBoundaryEnd = sAElements - m_sHaloElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixBoundaryEnd - ixBoundaryBegin)
* (m_ixSecond - m_ixFirst);
if (m_ixSendBuffer + nTotalValues > m_dSendBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in SendBuffer for operation.");
}
// Pack the SendBuffer
if (m_fReverseDirection) {
for (int i = ixBoundaryBegin; i < ixBoundaryEnd; i++) {
for (int j = m_ixSecond-1; j >= m_ixFirst; j--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
} else {
for (int i = ixBoundaryBegin; i < ixBoundaryEnd; i++) {
for (int j = m_ixFirst; j < m_ixSecond; j++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
}
// Pack data to send topward
} else if (m_dir == Direction_Top) {
ixBoundaryBegin = sBElements - 2 * m_sHaloElements;
ixBoundaryEnd = sBElements - m_sHaloElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixBoundaryEnd - ixBoundaryBegin)
* (m_ixSecond - m_ixFirst);
if (m_ixSendBuffer + nTotalValues > m_dSendBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in SendBuffer for operation.");
}
// Pack the SendBuffer
if (m_fReverseDirection) {
for (int j = ixBoundaryBegin; j < ixBoundaryEnd; j++) {
for (int i = m_ixSecond-1; i >= m_ixFirst; i--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
} else {
for (int j = ixBoundaryBegin; j < ixBoundaryEnd; j++) {
for (int i = m_ixFirst; i < m_ixSecond; i++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
}
// Pack data to send left
} else if (m_dir == Direction_Left) {
ixBoundaryBegin = m_sHaloElements;
ixBoundaryEnd = 2 * m_sHaloElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixBoundaryEnd - ixBoundaryBegin)
* (m_ixSecond - m_ixFirst);
if (m_ixSendBuffer + nTotalValues > m_dSendBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in SendBuffer for operation.");
}
// Pack the SendBuffer
if (m_fReverseDirection) {
for (int i = ixBoundaryEnd-1; i >= ixBoundaryBegin; i--) {
for (int j = m_ixSecond-1; j >= m_ixFirst; j--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
} else {
for (int i = ixBoundaryEnd-1; i >= ixBoundaryBegin; i--) {
for (int j = m_ixFirst; j < m_ixSecond; j++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
}
// Pack data to send bottomward
} else if (m_dir == Direction_Bottom) {
ixBoundaryBegin = m_sHaloElements;
ixBoundaryEnd = 2 * m_sHaloElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixBoundaryEnd - ixBoundaryBegin)
* (m_ixSecond - m_ixFirst);
if (m_ixSendBuffer + nTotalValues > m_dSendBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in SendBuffer for operation.");
}
// Pack the SendBuffer
if (m_fReverseDirection) {
for (int j = ixBoundaryEnd-1; j >= ixBoundaryBegin; j--) {
for (int i = m_ixSecond-1; i >= m_ixFirst; i--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
} else {
for (int j = ixBoundaryEnd-1; j >= ixBoundaryBegin; j--) {
for (int i = m_ixFirst; i < m_ixSecond; i++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
}
// Pack data to send toprightward
} else if (m_dir == Direction_TopRight) {
ixABoundaryBegin = m_ixFirst - m_sHaloElements + 1;
ixABoundaryEnd = m_ixFirst + 1;
ixBBoundaryBegin = m_ixSecond - m_sHaloElements + 1;
ixBBoundaryEnd = m_ixSecond + 1;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixABoundaryEnd - ixABoundaryBegin)
* (ixBBoundaryEnd - ixBBoundaryBegin);
if (m_ixSendBuffer + nTotalValues > m_dSendBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in SendBuffer for operation.");
}
// Pack the SendBuffer
if (m_fReverseDirection) {
for (int i = ixABoundaryBegin; i < ixABoundaryEnd; i++) {
for (int j = ixBBoundaryBegin; j < ixBBoundaryEnd; j++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
} else {
for (int j = ixBBoundaryBegin; j < ixBBoundaryEnd; j++) {
for (int i = ixABoundaryBegin; i < ixABoundaryEnd; i++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
}
// Pack data to send topleftward
} else if (m_dir == Direction_TopLeft) {
ixABoundaryBegin = m_ixFirst;
ixABoundaryEnd = m_ixFirst + m_sHaloElements;
ixBBoundaryBegin = m_ixSecond - m_sHaloElements + 1;
ixBBoundaryEnd = m_ixSecond + 1;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixABoundaryEnd - ixABoundaryBegin)
* (ixBBoundaryEnd - ixBBoundaryBegin);
if (m_ixSendBuffer + nTotalValues > m_dSendBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in SendBuffer for operation.");
}
// Pack the SendBuffer
if (m_fReverseDirection) {
for (int i = ixABoundaryEnd-1; i >= ixABoundaryBegin; i--) {
for (int j = ixBBoundaryBegin; j < ixBBoundaryEnd; j++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
} else {
for (int j = ixBBoundaryBegin; j < ixBBoundaryEnd; j++) {
for (int i = ixABoundaryEnd-1; i >= ixABoundaryBegin; i--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
}
// Pack data to send bottomleftward
} else if (m_dir == Direction_BottomLeft) {
ixABoundaryBegin = m_ixFirst;
ixABoundaryEnd = m_ixFirst + m_sHaloElements;
ixBBoundaryBegin = m_ixSecond;
ixBBoundaryEnd = m_ixSecond + m_sHaloElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixABoundaryEnd - ixABoundaryBegin)
* (ixBBoundaryEnd - ixBBoundaryBegin);
if (m_ixSendBuffer + nTotalValues > m_dSendBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in SendBuffer for operation.");
}
// Pack the SendBuffer
if (m_fReverseDirection) {
for (int i = ixABoundaryEnd-1; i >= ixABoundaryBegin; i--) {
for (int j = ixBBoundaryEnd-1; j >= ixBBoundaryBegin; j--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
} else {
for (int j = ixBBoundaryEnd-1; j >= ixBBoundaryBegin; j--) {
for (int i = ixABoundaryEnd-1; i >= ixABoundaryBegin; i--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
}
// Pack data to send bottomrightward
} else if (m_dir == Direction_BottomRight) {
ixABoundaryBegin = m_ixFirst - m_sHaloElements + 1;
ixABoundaryEnd = m_ixFirst + 1;
ixBBoundaryBegin = m_ixSecond;
ixBBoundaryEnd = m_ixSecond + m_sHaloElements;
// Check that sufficient data remains in send buffer
int nTotalValues =
sRElements
* (ixABoundaryEnd - ixABoundaryBegin)
* (ixBBoundaryEnd - ixBBoundaryBegin);
if (m_ixSendBuffer + nTotalValues > m_dSendBuffer.GetRows()) {
_EXCEPTIONT("Insufficient space in SendBuffer for operation.");
}
// Pack the SendBuffer
if (m_fReverseDirection) {
for (int i = ixABoundaryBegin; i < ixABoundaryEnd; i++) {
for (int j = ixBBoundaryEnd-1; j >= ixBBoundaryBegin; j--) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
} else {
for (int j = ixBBoundaryEnd-1; j >= ixBBoundaryBegin; j--) {
for (int i = ixABoundaryBegin; i < ixABoundaryEnd; i++) {
#pragma simd
for (int k = 0; k < sRElements; k++) {
m_dSendBuffer[m_ixSendBuffer + k] =
data(i,j,k);
}
m_ixSendBuffer += sRElements;
}
}
}
// Invalid direction
} else {
_EXCEPTIONT("Invalid direction");
}
}
int main(int argc, char ** argv) {
MPI_Init(&argc, &argv);
NcError error(NcError::silent_nonfatal);
try {
// Input filename
std::string strInputFile;
// Output filename
std::string strOutputFile;
// Separate topography file
std::string strTopographyFile;
// List of variables to extract
std::string strVariables;
// Extract geopotential height
bool fGeopotentialHeight;
// Pressure levels to extract
std::string strPressureLevels;
// Height levels to extract
std::string strHeightLevels;
// Extract variables at the surface
bool fExtractSurface;
// Extract total energy
bool fExtractTotalEnergy;
// Parse the command line
BeginCommandLine()
CommandLineString(strInputFile, "in", "");
CommandLineString(strOutputFile, "out", "");
CommandLineString(strVariables, "var", "");
CommandLineBool(fGeopotentialHeight, "output_z");
CommandLineBool(fExtractTotalEnergy, "output_energy");
CommandLineString(strPressureLevels, "p", "");
CommandLineString(strHeightLevels, "z", "");
CommandLineBool(fExtractSurface, "surf");
ParseCommandLine(argc, argv);
EndCommandLine(argv)
AnnounceBanner();
// Check command line arguments
if (strInputFile == "") {
_EXCEPTIONT("No input file specified");
}
if (strOutputFile == "") {
_EXCEPTIONT("No output file specified");
}
if (strVariables == "") {
_EXCEPTIONT("No variables specified");
}
// Parse variable string
std::vector< std::string > vecVariableStrings;
ParseVariableList(strVariables, vecVariableStrings);
// Check variables
if (vecVariableStrings.size() == 0) {
_EXCEPTIONT("No variables specified");
}
// Parse pressure level string
std::vector<double> vecPressureLevels;
ParseLevelArray(strPressureLevels, vecPressureLevels);
int nPressureLevels = (int)(vecPressureLevels.size());
for (int k = 0; k < nPressureLevels; k++) {
if (vecPressureLevels[k] <= 0.0) {
_EXCEPTIONT("Non-positive pressure values not allowed");
}
}
// Parse height level string
std::vector<double> vecHeightLevels;
ParseLevelArray(strHeightLevels, vecHeightLevels);
int nHeightLevels = (int)(vecHeightLevels.size());
// Check pressure levels
if ((nPressureLevels == 0) &&
(nHeightLevels == 0) &&
(!fExtractSurface)
) {
_EXCEPTIONT("No pressure / height levels to process");
}
// Open input file
AnnounceStartBlock("Loading input file");
NcFile ncdf_in(strInputFile.c_str(), NcFile::ReadOnly);
if (!ncdf_in.is_valid()) {
_EXCEPTION1("Unable to open file \"%s\" for reading",
strInputFile.c_str());
}
// Load time array
Announce("Time");
NcVar * varTime = ncdf_in.get_var("time");
if (varTime == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"time\"",
strInputFile.c_str());
}
int nTime = varTime->get_dim(0)->size();
DataArray1D<double> dTime(nTime);
varTime->set_cur((long)0);
varTime->get(&(dTime[0]), nTime);
// Load latitude array
Announce("Latitude");
NcVar * varLat = ncdf_in.get_var("lat");
if (varLat == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"lat\"",
strInputFile.c_str());
}
int nLat = varLat->get_dim(0)->size();
DataArray1D<double> dLat(nLat);
varLat->set_cur((long)0);
varLat->get(&(dLat[0]), nLat);
// Load longitude array
Announce("Longitude");
NcVar * varLon = ncdf_in.get_var("lon");
if (varLon == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"lon\"",
strInputFile.c_str());
}
int nLon = varLon->get_dim(0)->size();
DataArray1D<double> dLon(nLon);
varLon->set_cur((long)0);
varLon->get(&(dLon[0]), nLon);
// Load level array
Announce("Level");
NcVar * varLev = ncdf_in.get_var("lev");
if (varLev == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"lev\"",
strInputFile.c_str());
}
int nLev = varLev->get_dim(0)->size();
DataArray1D<double> dLev(nLev);
varLev->set_cur((long)0);
varLev->get(&(dLev[0]), nLev);
// Load level interface array
Announce("Interface");
NcVar * varILev = ncdf_in.get_var("ilev");
int nILev = 0;
DataArray1D<double> dILev;
if (varILev == NULL) {
Announce("Warning: Variable \"ilev\" not found");
} else {
nILev = varILev->get_dim(0)->size();
if (nILev != nLev + 1) {
_EXCEPTIONT("Variable \"ilev\" must have size lev+1");
}
dILev.Allocate(nILev);
varILev->set_cur((long)0);
varILev->get(&(dILev[0]), nILev);
}
// Load topography
Announce("Topography");
NcVar * varZs = ncdf_in.get_var("Zs");
if (varZs == NULL) {
_EXCEPTION1("File \"%s\" does not contain variable \"Zs\"",
strInputFile.c_str());
}
DataArray2D<double> dZs(nLat, nLon);
varZs->set_cur((long)0, (long)0);
varZs->get(&(dZs[0][0]), nLat, nLon);
AnnounceEndBlock("Done");
// Open output file
AnnounceStartBlock("Constructing output file");
NcFile ncdf_out(strOutputFile.c_str(), NcFile::Replace);
if (!ncdf_out.is_valid()) {
_EXCEPTION1("Unable to open file \"%s\" for writing",
strOutputFile.c_str());
}
CopyNcFileAttributes(&ncdf_in, &ncdf_out);
// Output time array
Announce("Time");
NcDim * dimOutTime = ncdf_out.add_dim("time");
NcVar * varOutTime = ncdf_out.add_var("time", ncDouble, dimOutTime);
varOutTime->set_cur((long)0);
varOutTime->put(&(dTime[0]), nTime);
CopyNcVarAttributes(varTime, varOutTime);
// Output pressure array
NcDim * dimOutP = NULL;
NcVar * varOutP = NULL;
if (nPressureLevels > 0) {
Announce("Pressure");
dimOutP = ncdf_out.add_dim("p", nPressureLevels);
varOutP = ncdf_out.add_var("p", ncDouble, dimOutP);
varOutP->set_cur((long)0);
varOutP->put(&(vecPressureLevels[0]), nPressureLevels);
}
// Output height array
NcDim * dimOutZ = NULL;
NcVar * varOutZ = NULL;
if (nHeightLevels > 0) {
Announce("Height");
dimOutZ = ncdf_out.add_dim("z", nHeightLevels);
varOutZ = ncdf_out.add_var("z", ncDouble, dimOutZ);
varOutZ->set_cur((long)0);
varOutZ->put(&(vecHeightLevels[0]), nHeightLevels);
}
// Output latitude and longitude array
Announce("Latitude");
NcDim * dimOutLat = ncdf_out.add_dim("lat", nLat);
NcVar * varOutLat = ncdf_out.add_var("lat", ncDouble, dimOutLat);
varOutLat->set_cur((long)0);
varOutLat->put(&(dLat[0]), nLat);
CopyNcVarAttributes(varLat, varOutLat);
Announce("Longitude");
NcDim * dimOutLon = ncdf_out.add_dim("lon", nLon);
NcVar * varOutLon = ncdf_out.add_var("lon", ncDouble, dimOutLon);
varOutLon->set_cur((long)0);
varOutLon->put(&(dLon[0]), nLon);
CopyNcVarAttributes(varLon, varOutLon);
// Output topography
Announce("Topography");
NcVar * varOutZs = ncdf_out.add_var(
"Zs", ncDouble, dimOutLat, dimOutLon);
varOutZs->set_cur((long)0, (long)0);
varOutZs->put(&(dZs[0][0]), nLat, nLon);
AnnounceEndBlock("Done");
// Done
AnnounceEndBlock("Done");
// Load all variables
Announce("Loading variables");
std::vector<NcVar *> vecNcVar;
for (int v = 0; v < vecVariableStrings.size(); v++) {
vecNcVar.push_back(ncdf_in.get_var(vecVariableStrings[v].c_str()));
if (vecNcVar[v] == NULL) {
_EXCEPTION1("Unable to load variable \"%s\" from file",
vecVariableStrings[v].c_str());
}
}
// Physical constants
Announce("Initializing thermodynamic variables");
NcAtt * attEarthRadius = ncdf_in.get_att("earth_radius");
double dEarthRadius = attEarthRadius->as_double(0);
NcAtt * attRd = ncdf_in.get_att("Rd");
double dRd = attRd->as_double(0);
NcAtt * attCp = ncdf_in.get_att("Cp");
double dCp = attCp->as_double(0);
double dGamma = dCp / (dCp - dRd);
NcAtt * attP0 = ncdf_in.get_att("P0");
double dP0 = attP0->as_double(0);
double dPressureScaling = dP0 * std::pow(dRd / dP0, dGamma);
NcAtt * attZtop = ncdf_in.get_att("Ztop");
double dZtop = attZtop->as_double(0);
// Input data
DataArray3D<double> dataIn(nLev, nLat, nLon);
DataArray3D<double> dataInt(nILev, nLat, nLon);
// Output data
DataArray2D<double> dataOut(nLat, nLon);
// Pressure in column
DataArray1D<double> dataColumnP(nLev);
// Height in column
DataArray1D<double> dataColumnZ(nLev);
DataArray1D<double> dataColumnIZ(nILev);
// Column weights
DataArray1D<double> dW(nLev);
DataArray1D<double> dIW(nILev);
// Loop through all times, pressure levels and variables
AnnounceStartBlock("Interpolating");
// Add energy variable
NcVar * varEnergy;
if (fExtractTotalEnergy) {
varEnergy = ncdf_out.add_var("TE", ncDouble, dimOutTime);
}
// Create output pressure variables
std::vector<NcVar *> vecOutNcVarP;
if (nPressureLevels > 0) {
for (int v = 0; v < vecVariableStrings.size(); v++) {
vecOutNcVarP.push_back(
ncdf_out.add_var(
vecVariableStrings[v].c_str(), ncDouble,
dimOutTime, dimOutP, dimOutLat, dimOutLon));
// Copy attributes
CopyNcVarAttributes(vecNcVar[v], vecOutNcVarP[v]);
}
}
// Create output height variables
std::vector<NcVar *> vecOutNcVarZ;
if (nHeightLevels > 0) {
for (int v = 0; v < vecVariableStrings.size(); v++) {
std::string strVarName = vecVariableStrings[v];
if (nPressureLevels > 0) {
strVarName += "z";
}
vecOutNcVarZ.push_back(
ncdf_out.add_var(
strVarName.c_str(), ncDouble,
dimOutTime, dimOutZ, dimOutLat, dimOutLon));
// Copy attributes
CopyNcVarAttributes(vecNcVar[v], vecOutNcVarZ[v]);
}
}
// Create output surface variable
std::vector<NcVar *> vecOutNcVarS;
if (fExtractSurface) {
for (int v = 0; v < vecVariableStrings.size(); v++) {
std::string strVarName = vecVariableStrings[v];
strVarName += "S";
vecOutNcVarS.push_back(
ncdf_out.add_var(
strVarName.c_str(), ncDouble,
dimOutTime, dimOutLat, dimOutLon));
// Copy attributes
CopyNcVarAttributes(vecNcVar[v], vecOutNcVarS[v]);
}
}
// Loop over all times
for (int t = 0; t < nTime; t++) {
char szAnnounce[256];
sprintf(szAnnounce, "Time %i", t);
AnnounceStartBlock(szAnnounce);
// Rho
DataArray3D<double> dataRho(nLev, nLat, nLon);
NcVar * varRho = ncdf_in.get_var("Rho");
if (varRho == NULL) {
_EXCEPTIONT("Unable to load variable \"Rho\" from file");
}
varRho->set_cur(t, 0, 0, 0);
varRho->get(&(dataRho[0][0][0]), 1, nLev, nLat, nLon);
// Pressure
DataArray3D<double> dataP(nLev, nLat, nLon);
if (nPressureLevels != 0) {
NcVar * varP = ncdf_in.get_var("P");
if (varP == NULL) {
_EXCEPTIONT("Unable to load variable \"P\" from file");
}
varP->set_cur(t, 0, 0, 0);
varP->get(&(dataP[0][0][0]), 1, nLev, nLat, nLon);
}
/*
// Populate pressure array
if (nPressureLevels > 0) {
// Calculate pointwise pressure
for (int k = 0; k < nLev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataP[k][i][j] = dPressureScaling
* exp(log(dataRho[k][i][j] * dataP[k][i][j]) * dGamma);
}
}
}
}
*/
// Height everywhere
DataArray3D<double> dataZ(nLev, nLat, nLon);
DataArray3D<double> dataIZ;
if (nILev != 0) {
dataIZ.Allocate(nILev, nLat, nLon);
}
// Populate height array
if ((nHeightLevels > 0) || (fGeopotentialHeight)) {
for (int k = 0; k < nLev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataZ[k][i][j] = dZs[i][j] + dLev[k] * (dZtop - dZs[i][j]);
}
}
}
for (int k = 0; k < nILev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataIZ[k][i][j] = dZs[i][j] + dILev[k] * (dZtop - dZs[i][j]);
}
}
}
}
// Loop through all pressure levels and variables
for (int v = 0; v < vecNcVar.size(); v++) {
bool fOnInterfaces = false;
// Load in the data array
vecNcVar[v]->set_cur(t, 0, 0, 0);
if (vecNcVar[v]->get_dim(1)->size() == nLev) {
vecNcVar[v]->get(&(dataIn[0][0][0]), 1, nLev, nLat, nLon);
Announce("%s (n)", vecVariableStrings[v].c_str());
} else if (vecNcVar[v]->get_dim(1)->size() == nILev) {
vecNcVar[v]->get(&(dataInt[0][0][0]), 1, nILev, nLat, nLon);
fOnInterfaces = true;
Announce("%s (i)", vecVariableStrings[v].c_str());
} else {
_EXCEPTION1("Variable \"%s\" has invalid level dimension",
vecVariableStrings[v].c_str());
}
// At the physical surface
if (fExtractSurface) {
if (fOnInterfaces) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
dataOut[i][j] = dataInt[0][i][j];
}
}
} else {
int kBegin = 0;
int kEnd = 3;
PolynomialInterp::LagrangianPolynomialCoeffs(
3, dLev, dW, 0.0);
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataIn[k][i][j];
}
}
}
}
// Write variable
vecOutNcVarS[v]->set_cur(t, 0, 0);
vecOutNcVarS[v]->put(&(dataOut[0][0]), 1, nLat, nLon);
}
// Loop through all pressure levels
for (int p = 0; p < nPressureLevels; p++) {
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Store column pressure
for (int k = 0; k < nLev; k++) {
dataColumnP[k] = dataP[k][i][j];
}
// Find weights
int kBegin = 0;
int kEnd = 0;
// On a pressure surface
InterpolationWeightsLinear(
vecPressureLevels[p],
dataColumnP,
kBegin,
kEnd,
dW);
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataIn[k][i][j];
}
}
}
// Write variable
vecOutNcVarP[v]->set_cur(t, p, 0, 0);
vecOutNcVarP[v]->put(&(dataOut[0][0]), 1, 1, nLat, nLon);
}
// Loop through all height levels
for (int z = 0; z < nHeightLevels; z++) {
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Find weights
int kBegin = 0;
int kEnd = 0;
// Interpolate from levels to z surfaces
if (!fOnInterfaces) {
for (int k = 0; k < nLev; k++) {
dataColumnZ[k] = dataZ[k][i][j];
}
InterpolationWeightsLinear(
vecHeightLevels[z],
dataColumnZ,
kBegin,
kEnd,
dW);
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataIn[k][i][j];
}
// Interpolate from interfaces to z surfaces
} else {
for (int k = 0; k < nILev; k++) {
dataColumnIZ[k] = dataIZ[k][i][j];
}
InterpolationWeightsLinear(
vecHeightLevels[z],
dataColumnIZ,
kBegin,
kEnd,
dIW);
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dIW[k] * dataInt[k][i][j];
}
}
}
}
// Write variable
vecOutNcVarZ[v]->set_cur(t, z, 0, 0);
vecOutNcVarZ[v]->put(&(dataOut[0][0]), 1, 1, nLat, nLon);
}
}
// Output geopotential height
if (fGeopotentialHeight) {
Announce("Geopotential height");
// Output variables
NcVar * varOutZ;
NcVar * varOutZs;
if (nPressureLevels > 0) {
varOutZ = ncdf_out.add_var(
"PHIZ", ncDouble, dimOutTime, dimOutP, dimOutLat, dimOutLon);
}
if (fExtractSurface) {
varOutZs = ncdf_out.add_var(
"PHIZS", ncDouble, dimOutTime, dimOutLat, dimOutLon);
}
// Interpolate onto pressure levels
for (int p = 0; p < nPressureLevels; p++) {
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
int kBegin = 0;
int kEnd = 0;
for (int k = 0; k < nLev; k++) {
dataColumnP[k] = dataP[k][i][j];
}
InterpolationWeightsLinear(
vecPressureLevels[p],
dataColumnP,
kBegin,
kEnd,
dW);
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataZ[k][i][j];
}
}
}
// Write variable
varOutZ->set_cur(t, p, 0, 0);
varOutZ->put(&(dataOut[0][0]), 1, 1, nLat, nLon);
}
// Interpolate onto the physical surface
if (fExtractSurface) {
int kBegin = 0;
int kEnd = 3;
PolynomialInterp::LagrangianPolynomialCoeffs(
3, dLev, dW, 0.0);
// Loop thorugh all latlon indices
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
// Interpolate in the vertical
dataOut[i][j] = 0.0;
for (int k = kBegin; k < kEnd; k++) {
dataOut[i][j] += dW[k] * dataZ[k][i][j];
}
}
}
// Write variable
varOutZs->set_cur(t, 0, 0);
varOutZs->put(&(dataOut[0][0]), 1, nLat, nLon);
}
}
// Extract total energy
if (fExtractTotalEnergy) {
Announce("Total Energy");
// Zonal velocity
DataArray3D<double> dataU(nLev, nLat, nLon);
NcVar * varU = ncdf_in.get_var("U");
varU->set_cur(t, 0, 0, 0);
varU->get(&(dataU[0][0][0]), 1, nLev, nLat, nLon);
// Meridional velocity
DataArray3D<double> dataV(nLev, nLat, nLon);
NcVar * varV = ncdf_in.get_var("V");
varV->set_cur(t, 0, 0, 0);
varV->get(&(dataV[0][0][0]), 1, nLev, nLat, nLon);
// Vertical velocity
DataArray3D<double> dataW(nLev, nLat, nLon);
NcVar * varW = ncdf_in.get_var("W");
varW->set_cur(t, 0, 0, 0);
varW->get(&(dataW[0][0][0]), 1, nLev, nLat, nLon);
// Calculate total energy
double dTotalEnergy = 0.0;
double dElementRefArea =
dEarthRadius * dEarthRadius
* M_PI / static_cast<double>(nLat)
* 2.0 * M_PI / static_cast<double>(nLon);
for (int k = 0; k < nLev; k++) {
for (int i = 0; i < nLat; i++) {
for (int j = 0; j < nLon; j++) {
double dKineticEnergy =
0.5 * dataRho[k][i][j] *
( dataU[k][i][j] * dataU[k][i][j]
+ dataV[k][i][j] * dataV[k][i][j]
+ dataW[k][i][j] * dataW[k][i][j]);
double dInternalEnergy =
dataP[k][i][j] / (dGamma - 1.0);
dTotalEnergy +=
(dKineticEnergy + dInternalEnergy)
* std::cos(M_PI * dLat[i] / 180.0) * dElementRefArea
* (dZtop - dZs[i][j]) / static_cast<double>(nLev);
}
}
}
// Put total energy into file
varEnergy->set_cur(t);
varEnergy->put(&dTotalEnergy, 1);
}
AnnounceEndBlock("Done");
}
AnnounceEndBlock("Done");
} catch(Exception & e) {
Announce(e.ToString().c_str());
}
// Finalize MPI
MPI_Finalize();
}
void GridCartesianGLL::ApplyDSS(
int iDataUpdate,
DataType eDataType
) {
// Exchange data between nodes
Exchange(eDataType, iDataUpdate);
// Post-process velocities across panel edges and
// perform direct stiffness summation (DSS)
for (int n = 0; n < GetActivePatchCount(); n++) {
GridPatchCartesianGLL * pPatch =
dynamic_cast<GridPatchCartesianGLL*>(GetActivePatch(n));
const PatchBox & box = pPatch->GetPatchBox();
// Patch-specific quantities
int nElementCountA = pPatch->GetElementCountA();
int nElementCountB = pPatch->GetElementCountB();
// Apply panel transforms to velocity data
if (eDataType == DataType_State) {
pPatch->TransformHaloVelocities(iDataUpdate);
}
if (eDataType == DataType_TopographyDeriv) {
pPatch->TransformTopographyDeriv();
}
// Loop through all components associated with this DataType
int nComponents;
if (eDataType == DataType_State) {
nComponents = m_model.GetEquationSet().GetComponents();
} else if (eDataType == DataType_Tracers) {
nComponents = m_model.GetEquationSet().GetTracers();
} else if (eDataType == DataType_Vorticity) {
nComponents = 1;
} else if (eDataType == DataType_Divergence) {
nComponents = 1;
} else if (eDataType == DataType_TopographyDeriv) {
nComponents = 2;
} else {
_EXCEPTIONT("Invalid DataType");
}
// Apply BC only to state DSS
if (eDataType == DataType_State) {
pPatch->ApplyBoundaryConditions(iDataUpdate, DataType_State, n);
}
// Perform Direct Stiffness Summation (DSS)
for (int c = 0; c < nComponents; c++) {
// Obtain the array of working data
int nRElements = GetRElements();
DataArray3D<double> pDataUpdate;
if ((eDataType == DataType_State) &&
(GetVarLocation(c) == DataLocation_REdge)
) {
nRElements++;
}
if (eDataType == DataType_TopographyDeriv) {
nRElements = 2;
}
pDataUpdate.SetSize(
nRElements,
box.GetATotalWidth(),
box.GetBTotalWidth());
// State data
if (eDataType == DataType_State) {
DataArray4D<double> & dState =
pPatch->GetDataState(iDataUpdate, GetVarLocation(c));
pDataUpdate.AttachToData(&(dState[c][0][0][0]));
// Tracer data
} else if (eDataType == DataType_Tracers) {
DataArray4D<double> & dTracers =
pPatch->GetDataTracers(iDataUpdate);
pDataUpdate.AttachToData(&(dTracers[c][0][0][0]));
// Vorticity data
} else if (eDataType == DataType_Vorticity) {
DataArray3D<double> & dVorticity =
pPatch->GetDataVorticity();
pDataUpdate.AttachToData(&(dVorticity[0][0][0]));
// Divergence data
} else if (eDataType == DataType_Divergence) {
DataArray3D<double> & dDivergence =
pPatch->GetDataDivergence();
pDataUpdate.AttachToData(&(dDivergence[0][0][0]));
// Topographic derivative data
} else if (eDataType == DataType_TopographyDeriv) {
DataArray3D<double> & dTopographyDeriv =
pPatch->GetTopographyDeriv();
pDataUpdate.AttachToData(&(dTopographyDeriv[0][0][0]));
}
// Averaging DSS across patch boundaries
for (int k = 0; k < nRElements; k++) {
// Average in the alpha direction
for (int a = 0; a <= nElementCountA; a++) {
int iA = a * m_nHorizontalOrder + box.GetHaloElements();
// Averaging done at the corners of the panel
int jBegin = box.GetBInteriorBegin()-1;
int jEnd = box.GetBInteriorEnd()+1;
// Perform averaging across edge of patch
for (int j = jBegin; j < jEnd; j++) {
pDataUpdate[k][iA][j] = 0.5 * (
+ pDataUpdate[k][iA ][j]
+ pDataUpdate[k][iA-1][j]);
pDataUpdate[k][iA-1][j] = pDataUpdate[k][iA][j];
}
}
// Average in the beta direction
for (int b = 0; b <= nElementCountB; b++) {
int iB = b * m_nHorizontalOrder + box.GetHaloElements();
// Averaging done at the corners of the panel
int iBegin = box.GetAInteriorBegin()-1;
int iEnd = box.GetAInteriorEnd()+1;
for (int i = iBegin; i < iEnd; i++) {
pDataUpdate[k][i][iB] = 0.5 * (
+ pDataUpdate[k][i][iB ]
+ pDataUpdate[k][i][iB-1]);
pDataUpdate[k][i][iB-1] = pDataUpdate[k][i][iB];
}
}
}
}
}
}
void GridPatchCSGLL::InterpolateData(
DataType eDataType,
const DataArray1D<double> & dREta,
const DataArray1D<double> & dAlpha,
const DataArray1D<double> & dBeta,
const DataArray1D<int> & iPatch,
DataArray3D<double> & dInterpData,
DataLocation eOnlyVariablesAt,
bool fIncludeReferenceState,
bool fConvertToPrimitive
) {
if ((dAlpha.GetRows() != dBeta.GetRows()) ||
(dAlpha.GetRows() != iPatch.GetRows())
) {
_EXCEPTIONT("Point vectors must have equivalent length.");
}
// Vector for storage interpolated points
DataArray1D<double> dAInterpCoeffs(m_nHorizontalOrder);
DataArray1D<double> dBInterpCoeffs(m_nHorizontalOrder);
DataArray1D<double> dADiffCoeffs(m_nHorizontalOrder);
DataArray1D<double> dBDiffCoeffs(m_nHorizontalOrder);
DataArray1D<double> dAInterpPt(m_nHorizontalOrder);
// Physical constants
const PhysicalConstants & phys = m_grid.GetModel().GetPhysicalConstants();
// Perform interpolation on all variables
int nComponents = 0;
int nRElements = m_grid.GetRElements();
// Discretization type
Grid::VerticalDiscretization eVerticalDiscType =
m_grid.GetVerticalDiscretization();
// State Data: Perform interpolation on all variables
if (eDataType == DataType_State) {
nComponents = m_datavecStateNode[0].GetSize(0);
nRElements = m_grid.GetRElements() + 1;
// Tracer Data: Perform interpolation on all variables
} else if (eDataType == DataType_Tracers) {
nComponents = m_datavecTracers[0].GetSize(0);
// Topography Data
} else if (eDataType == DataType_Topography) {
nComponents = 1;
nRElements = 1;
// Vorticity Data
} else if (eDataType == DataType_Vorticity) {
nComponents = 1;
// Divergence Data
} else if (eDataType == DataType_Divergence) {
nComponents = 1;
// Temperature Data
} else if (eDataType == DataType_Temperature) {
nComponents = 1;
// Surface Pressure Data
} else if (eDataType == DataType_SurfacePressure) {
nComponents = 1;
nRElements = 1;
// 2D User Data
} else if (eDataType == DataType_Auxiliary2D) {
nComponents = m_dataUserData2D.GetSize(0);
nRElements = 1;
} else {
_EXCEPTIONT("Invalid DataType");
}
// Buffer storage in column
DataArray1D<double> dColumnDataOut(dREta.GetRows());
// Loop through all components
for (int c = 0; c < nComponents; c++) {
DataLocation eDataLocation = DataLocation_Node;
if (eDataType == DataType_State) {
eDataLocation = m_grid.GetVarLocation(c);
// Exclude variables not at the specified DataLocation
if ((eOnlyVariablesAt != DataLocation_None) &&
(eOnlyVariablesAt != eDataLocation)
) {
continue;
}
// Adjust RElements depending on state data location
if (eDataLocation == DataLocation_Node) {
nRElements = m_grid.GetRElements();
} else if (eDataLocation == DataLocation_REdge) {
nRElements = m_grid.GetRElements() + 1;
} else {
_EXCEPTIONT("Invalid DataLocation");
}
}
// Vertical interpolation operator
LinearColumnInterpFEM opInterp;
if (nRElements != 1) {
// Finite element interpolation
if (eVerticalDiscType ==
Grid::VerticalDiscretization_FiniteElement
) {
if (eDataLocation == DataLocation_Node) {
opInterp.Initialize(
LinearColumnInterpFEM::InterpSource_Levels,
m_nVerticalOrder,
m_grid.GetREtaLevels(),
m_grid.GetREtaInterfaces(),
dREta);
} else if (eDataLocation == DataLocation_REdge) {
opInterp.Initialize(
LinearColumnInterpFEM::InterpSource_Interfaces,
m_nVerticalOrder,
m_grid.GetREtaLevels(),
m_grid.GetREtaInterfaces(),
dREta);
} else {
_EXCEPTIONT("Invalid DataLocation");
}
// Finite volume interpolation
} else if (
eVerticalDiscType ==
Grid::VerticalDiscretization_FiniteVolume
) {
if (eDataLocation == DataLocation_Node) {
opInterp.Initialize(
LinearColumnInterpFEM::InterpSource_Levels,
1,
m_grid.GetREtaLevels(),
m_grid.GetREtaInterfaces(),
dREta);
} else if (eDataLocation == DataLocation_REdge) {
opInterp.Initialize(
LinearColumnInterpFEM::InterpSource_Interfaces,
1,
m_grid.GetREtaLevels(),
m_grid.GetREtaInterfaces(),
dREta);
} else {
_EXCEPTIONT("Invalid DataLocation");
}
// Invalid vertical discretization type
} else {
_EXCEPTIONT("Invalid VerticalDiscretization");
}
} else {
opInterp.InitializeIdentity(1);
}
// Buffer storage in column
DataArray1D<double> dColumnData(nRElements);
// Get a pointer to the 3D data structure
DataArray3D<double> pData;
DataArray3D<double> pDataRef;
pData.SetSize(
nRElements,
m_box.GetATotalWidth(),
m_box.GetBTotalWidth());
pDataRef.SetSize(
nRElements,
m_box.GetATotalWidth(),
m_box.GetBTotalWidth());
if (eDataType == DataType_State) {
if (eDataLocation == DataLocation_Node) {
pData.AttachToData(&(m_datavecStateNode[0][c][0][0][0]));
pDataRef.AttachToData(&(m_dataRefStateNode[c][0][0][0]));
} else if (eDataLocation == DataLocation_REdge) {
pData.AttachToData(&(m_datavecStateREdge[0][c][0][0][0]));
pDataRef.AttachToData(&(m_dataRefStateREdge[c][0][0][0]));
} else {
_EXCEPTIONT("Invalid DataLocation");
}
} else if (eDataType == DataType_Tracers) {
pData.AttachToData(&(m_datavecTracers[0][c][0][0][0]));
} else if (eDataType == DataType_Topography) {
pData.AttachToData(&(m_dataTopography[0][0]));
} else if (eDataType == DataType_Vorticity) {
pData.AttachToData(&(m_dataVorticity[0][0][0]));
} else if (eDataType == DataType_Divergence) {
pData.AttachToData(&(m_dataDivergence[0][0][0]));
} else if (eDataType == DataType_Temperature) {
pData.AttachToData(&(m_dataTemperature[0][0][0]));
} else if (eDataType == DataType_SurfacePressure) {
pData.AttachToData(&(m_dataSurfacePressure[0][0]));
} else if (eDataType == DataType_Auxiliary2D) {
pData.AttachToData(&(m_dataUserData2D[c][0][0]));
}
// Loop throught all points
for (int i = 0; i < dAlpha.GetRows(); i++) {
// Element index
if (iPatch[i] != GetPatchIndex()) {
continue;
}
// Verify point lies within domain of patch
const double Eps = 1.0e-10;
if ((dAlpha[i] < m_dAEdge[m_box.GetAInteriorBegin()] - Eps) ||
(dAlpha[i] > m_dAEdge[m_box.GetAInteriorEnd()] + Eps) ||
(dBeta[i] < m_dBEdge[m_box.GetBInteriorBegin()] - Eps) ||
(dBeta[i] > m_dBEdge[m_box.GetBInteriorEnd()] + Eps)
) {
_EXCEPTIONT("Point out of range");
}
// Determine finite element index
int iA =
(dAlpha[i] - m_dAEdge[m_box.GetAInteriorBegin()])
/ GetElementDeltaA();
int iB =
(dBeta[i] - m_dBEdge[m_box.GetBInteriorBegin()])
/ GetElementDeltaB();
// Bound the index within the element
if (iA < 0) {
iA = 0;
}
if (iA >= (m_box.GetAInteriorWidth() / m_nHorizontalOrder)) {
iA = m_box.GetAInteriorWidth() / m_nHorizontalOrder - 1;
}
if (iB < 0) {
iB = 0;
}
if (iB >= (m_box.GetBInteriorWidth() / m_nHorizontalOrder)) {
iB = m_box.GetBInteriorWidth() / m_nHorizontalOrder - 1;
}
iA = m_box.GetHaloElements() + iA * m_nHorizontalOrder;
iB = m_box.GetHaloElements() + iB * m_nHorizontalOrder;
// Compute interpolation coefficients
PolynomialInterp::LagrangianPolynomialCoeffs(
m_nHorizontalOrder,
&(m_dAEdge[iA]),
dAInterpCoeffs,
dAlpha[i]);
PolynomialInterp::LagrangianPolynomialCoeffs(
m_nHorizontalOrder,
&(m_dBEdge[iB]),
dBInterpCoeffs,
dBeta[i]);
// Perform interpolation on all levels
for (int k = 0; k < nRElements; k++) {
dColumnData[k] = 0.0;
// Rescale vertical velocity
const int WIx = 3;
if ((c == WIx) && (fConvertToPrimitive)) {
if (m_grid.GetVarLocation(WIx) == DataLocation_REdge) {
for (int m = 0; m < m_nHorizontalOrder; m++) {
for (int n = 0; n < m_nHorizontalOrder; n++) {
dColumnData[k] +=
dAInterpCoeffs[m]
* dBInterpCoeffs[n]
* pData[k][iA+m][iB+n]
/ m_dataDerivRREdge[k][iA][iB][2];
}
}
} else {
for (int m = 0; m < m_nHorizontalOrder; m++) {
for (int n = 0; n < m_nHorizontalOrder; n++) {
dColumnData[k] +=
dAInterpCoeffs[m]
* dBInterpCoeffs[n]
* pData[k][iA+m][iB+n]
/ m_dataDerivRNode[k][iA][iB][2];
}
}
}
} else {
for (int m = 0; m < m_nHorizontalOrder; m++) {
for (int n = 0; n < m_nHorizontalOrder; n++) {
dColumnData[k] +=
dAInterpCoeffs[m]
* dBInterpCoeffs[n]
* pData[k][iA+m][iB+n];
}
}
}
// Do not include the reference state
if ((eDataType == DataType_State) &&
(!fIncludeReferenceState)
) {
for (int m = 0; m < m_nHorizontalOrder; m++) {
for (int n = 0; n < m_nHorizontalOrder; n++) {
dColumnData[k] -=
dAInterpCoeffs[m]
* dBInterpCoeffs[n]
* pDataRef[k][iA+m][iB+n];
}
}
}
}
// Interpolate vertically
opInterp.Apply(
&(dColumnData[0]),
&(dColumnDataOut[0]));
// Store data
for (int k = 0; k < dREta.GetRows(); k++) {
dInterpData[c][k][i] = dColumnDataOut[k];
}
}
}
// Convert to primitive variables
if ((eDataType == DataType_State) && (fConvertToPrimitive)) {
for (int i = 0; i < dAlpha.GetRows(); i++) {
if (iPatch[i] != GetPatchIndex()) {
continue;
}
for (int k = 0; k < dREta.GetRows(); k++) {
double dUalpha =
dInterpData[0][k][i] / phys.GetEarthRadius();
double dUbeta =
dInterpData[1][k][i] / phys.GetEarthRadius();
CubedSphereTrans::CoVecTransRLLFromABP(
tan(dAlpha[i]),
tan(dBeta[i]),
GetPatchBox().GetPanel(),
dUalpha,
dUbeta,
dInterpData[0][k][i],
dInterpData[1][k][i]);
}
}
}
}