/// <summary>
/// returns global unique indices which correlate to a certain sub-set of ...
/// <list type="bullet">
/// <item>the mappings's basis (<paramref name="mapping"/>, <see cref="UnsetteledCoordinateMapping.BasisS"/>).</item>
/// <item>species (<paramref name="_SpcIds"/>).</item>
/// <item>cells (<paramref name="cm"/>).</item>
/// </list>
/// </summary>
/// <param name="mapping">
/// the mapping
/// </param>
/// <param name="Fields">
/// determines which fields should be in the sub-vector-indices-list
/// </param>
/// <param name="_SpcIds">
/// determines which species should be in the sub-vector-indices-list; null indicates all species.
/// </param>
/// <param name="cm">
/// determines which cells should be in the sub-vector-indices-list; null indicates all cells.
/// </param>
/// <param name="regions">
/// Determines which XDG-coordinate belongs to which species.
/// </param>
/// <param name="presenceTest">
/// if true, cells where some species has zero measure are excluded from the sub-vector-indices-list.
/// </param>
/// <param name="drk">
/// a cell-agglomeration object: if null, ignored; if provided,
/// cells which are eliminated by the agglomeration are excluded from the sub-vector-indices-list
/// </param>
/// <returns>a list of global (over all MPI processes) unique indices.</returns>
static public int[] GetSubvectorIndices(this UnsetteledCoordinateMapping mapping, LevelSetTracker.LevelSetRegions regions, int[] Fields,
ICollection <SpeciesId> _SpcIds = null, CellMask cm = null, bool presenceTest = true, MultiphaseCellAgglomerator drk = null)
{
#region Check Arguments
// =========
SpeciesId[] SpcIds = null;
if (_SpcIds == null)
{
// take all species, if arg is null
SpcIds = regions.SpeciesIdS.ToArray();
}
else
{
SpcIds = _SpcIds.ToArray();
}
if (SpcIds.Length <= 0)
{
// return will be empty for no species
return(new int[0]);
}
#endregion
#region collect cells which are excluded by agglomeration
// =================================================
int[][] ExcludeLists;
if (drk != null)
{
ExcludeLists = new int[regions.SpeciesIdS.Count][]; // new Dictionary<SpeciesId, int[]>();
foreach (var id in SpcIds)
{
int[] ExcludeList = drk.GetAgglomerator(id).AggInfo.AgglomerationPairs.Select(pair => pair.jCellSource).ToArray();
Array.Sort(ExcludeList);
ExcludeLists[id.cntnt - LevelSetTracker.___SpeciesIDOffest] = ExcludeList;
}
}
else
{
ExcludeLists = null;
}
#endregion
#region determine over which cells we want to loop
// ==========================================
CellMask loopCells;
if ((new HashSet <SpeciesId>(regions.SpeciesIdS)).SetEquals(new HashSet <SpeciesId>(SpcIds)))
{
if (cm == null)
{
loopCells = CellMask.GetFullMask(regions.GridDat);
}
else
{
loopCells = cm;
}
}
else
{
loopCells = regions.GetSpeciesMask(SpcIds[0]);
for (int i = 1; i < SpcIds.Length; i++)
{
loopCells = loopCells.Intersect(regions.GetSpeciesMask(SpcIds[i]));
}
if (cm != null)
{
loopCells = loopCells.Intersect(cm);
}
}
#endregion
#region build list
// ==========
var R = new List <int>();
// which basis is XDG?
var _BasisS = mapping.BasisS.ToArray();
XDGBasis[] _XBasisS = new XDGBasis[_BasisS.Length];
for (int i = 0; i < _BasisS.Length; i++)
{
_XBasisS[i] = _BasisS[i] as XDGBasis;
}
Tuple <int, SpeciesId>[] iSpcS = new Tuple <int, SpeciesId> [SpcIds.Length];
int KK;
int Len_iSpcS = iSpcS.Length;
int[] ExcludeListsPointer = new int[regions.SpeciesIdS.Count];
// loop over cells?
foreach (int jCell in loopCells.ItemEnum)
{
int NoOfSpc = regions.GetNoOfSpecies(jCell);
#region
//
// in cell 'jCell', for each species in 'SpcIds' ...
// * is the species present in 'jCell'?
// * what is the species index in 'jCell'?
// * we also have to consider that due to agglomeration, the respective cut-cell for the species might have been agglomerated.
// so we determine
// * 'KK' is the number of species (from 'SpcIds') which is actually present and not agglomerated in 'jCell'
// * for i in (0 ... KK-1), iSpcS[i] is a tuple of (Species-index-in-cell, SpeciesID)
//
// yes, the following code sucks:
KK = 0;
for (int k = 0; k < Len_iSpcS; k++) // loop over all species (provided as argument)...
{
SpeciesId id = SpcIds[k];
int __iSpcS = regions.GetSpeciesIndex(id, jCell);
if (__iSpcS >= 0)
{
// species index is non-negative, so indices for the species are allocated ...
if (!presenceTest || regions.IsSpeciesPresentInCell(id, jCell))
{
// species is also present (i.e. has a greater-than-zero measure ...
if (drk == null)
{
// no agglomeration exclution
iSpcS[KK] = new Tuple <int, SpeciesId>(__iSpcS, id);
KK++;
}
else
{
int q = id.cntnt - LevelSetTracker.___SpeciesIDOffest;
var el = ExcludeLists[q];
while (ExcludeListsPointer[q] < el.Length &&
el[ExcludeListsPointer[q]] < jCell)
{
ExcludeListsPointer[q]++;
}
Debug.Assert(ExcludeListsPointer[q] >= el.Length || el[ExcludeListsPointer[q]] >= jCell);
if (ExcludeListsPointer[q] >= el.Length || el[ExcludeListsPointer[q]] != jCell)
{
// cell is also not agglomerated ...
iSpcS[KK] = new Tuple <int, SpeciesId>(__iSpcS, id);
KK++;
}
}
}
}
}
if (KK > 1)
{
Array.Sort <Tuple <int, SpeciesId> >(iSpcS, 0, KK, new ilPSP.FuncComparer <Tuple <int, SpeciesId> >((a, b) => a.Item1 - b.Item1));
}
// --------- esc (end of sucking code)
#endregion
for (int k = 0; k < KK; k++) // loop over species in cell
{
int iSpc = iSpcS[k].Item1;
for (int i = 0; i < Fields.Length; i++)
{
int iField = Fields[i];
if (_XBasisS[iField] == null)
{
int N = _BasisS[iField].GetLength(jCell);
int i0 = mapping.LocalUniqueCoordinateIndex(iField, jCell, 0);
for (int n = 0; n < N; n++)
{
R.Add(i0 + n);
}
}
else
{
int N = _XBasisS[iField].DOFperSpeciesPerCell;
int i0 = mapping.LocalUniqueCoordinateIndex(iField, jCell, 0) + iSpc * N;
for (int n = 0; n < N; n++)
{
R.Add(i0 + n);
}
}
}
}
}
#endregion
return(R.ToArray());
}
void Setup_Frame2Full()
{
//if (FrameMap.Rank == 0)
// Debugger.Launch();
//csMPI.Raw.Barrier(csMPI.Raw._COMM.WORLD);
//FrameMap.GridDat.Cells.NoOfLocalUpdatedCells
int L = FrameMap.LocalLength;
Frame2Full_Lookup = new int[L];
Basis[] BasisS = FullMap.BasisS.ToArray();
XDGBasis[] XBasisS = new XDGBasis[BasisS.Length];
for (int i = 0; i < BasisS.Length; i++)
{
XBasisS[i] = BasisS[i] as XDGBasis;
}
var GridDat = this.FullMap.GridDat;
Frame2Full_Lookup = new int[L];
Frame2Full_Lookup.SetAll(int.MinValue);
int Jup = FrameMap.GridDat.iLogicalCells.NoOfLocalUpdatedCells;
int Jtot = FrameMap.GridDat.iLogicalCells.NoOfCells;
int G = BasisS.Length;
for (int j = 0; j < Jup; j++) // loop over all cells ...
{
int NoOfSpc = m_Regions.GetNoOfSpecies(j);
int iSpc = m_Regions.GetSpeciesIndex(m_spcId, j);
for (int g = 0; g < G; g++) // loop over all basises
{
Basis b = BasisS[g];
XDGBasis xb = XBasisS[g];
bool b_is_XDGbasis = (xb != null);
int n0, N;
if (b_is_XDGbasis)
{
if (iSpc < 0)
{
n0 = int.MaxValue;
N = int.MinValue;
}
else
{
N = xb.DOFperSpeciesPerCell;
n0 = N * iSpc;
}
}
else
{
n0 = 0;
N = b.GetLength(j);
}
if (N >= 0)
{
int iFull = (int)FullMap.GlobalUniqueCoordinateIndex(g, j, n0);
int iLoc = FrameMap.LocalUniqueCoordinateIndex(g, j, 0);
for (int n = 0; n < N; n++)
{
Frame2Full_Lookup[iLoc + n] = iFull + n;
Debug.Assert(Frame2Full_Lookup[iLoc + n] < 0 || FullMap.IsInLocalRange(Frame2Full_Lookup[iLoc + n]));
}
}
}
}
#if DEBUG
var _Frame2Full_Lookup = new int[L];
for (int iLoc = 0; iLoc < L; iLoc++) // loop over all indices of the frame...
{
int j, g, n;
FrameMap.LocalFieldCoordinateIndex(iLoc, out g, out j, out n);
int NoOfSpc = m_Regions.GetNoOfSpecies(j);
Basis b = BasisS[g];
XDGBasis xb = XBasisS[g];
bool b_is_XDGbasis = (xb != null);
int iSpc = m_Regions.GetSpeciesIndex(m_spcId, j);
if (b_is_XDGbasis)
{
if (iSpc < 0)
{
_Frame2Full_Lookup[iLoc] = int.MinValue;
}
else
{
int Nsep = xb.DOFperSpeciesPerCell;
_Frame2Full_Lookup[iLoc] = (int)(FullMap.GlobalUniqueCoordinateIndex(g, j, iSpc * Nsep + n));
}
}
else
{
_Frame2Full_Lookup[iLoc] = (int)(FullMap.GlobalUniqueCoordinateIndex(g, j, n));
}
Debug.Assert(_Frame2Full_Lookup[iLoc] == Frame2Full_Lookup[iLoc]);
}
for (int l = 0; l < L; l++)
{
Debug.Assert(Frame2Full_Lookup[l] < 0 || FullMap.IsInLocalRange(Frame2Full_Lookup[l]));
}
#endif
/*
* if (m_supportExternal) {
* int[] PeerProcess = GridDat.Parallel.ProcessesToReceiveFrom;
* int TT = PeerProcess.Length;
* int DOFperCell = FrameMap.MaxTotalNoOfCoordinatesPerCell;
*
* ExtRangeStart = new int[TT];
* ExtRangeLen = new int[TT];
* ExtRangeTrafo = new int[TT][];
*
* for(int tt = 0; tt < TT; tt++) {
* int otherRank = PeerProcess[tt];
* int jFristCell = GridDat.Parallel.m_RcvCommListsInsertIndex[otherRank];
* int Jrank = GridDat.Parallel.m_RcvCommListsNoOfItems[otherRank];
*
*
* int offset = (int)(FrameMap.GlobalUniqueCoordinateIndex(0, jFristCell, 0));
* ExtRangeStart[tt] = offset;
* ExtRangeLen[tt] = Jrank*DOFperCell;
*
*
* ExtRangeTrafo[tt] = new int[ExtRangeLen[tt]];
* ExtRangeTrafo[tt].SetAll(int.MinValue);
*
* for (int j = 0; j < Jrank; j++) { // loop over all external cells that this process receives from 'otherRank' ...
* int jCell = j + jFristCell;
* Debug.Assert(jCell >= Jup);
* Debug.Assert(jCell < Jtot);
* ReducedRegionCode rrc;
* int NoOfSpc = m_lsTrk.GetNoOfSpecies(jCell, out rrc);
* int iSpc = m_lsTrk.GetSpeciesIndexFromId(rrc, m_spcId);
*
* for (int g = 0; g < G; g++) { // loop over all basises
* Basis b = BasisS[g];
* XDGBasis xb = XBasisS[g];
* bool b_is_XDGbasis = (xb != null);
*
* int n0, N;
* if (b_is_XDGbasis) {
* if (iSpc < 0) {
* n0 = int.MaxValue;
* N = int.MinValue;
* } else {
* N = xb.DOFperSpeciesPerCell;
* n0 = N*iSpc;
* }
* } else {
* n0 = 0;
* N = b.GetLength(j);
* }
*
* if (N >= 0) {
* int iFull = (int)(FullMap.GlobalUniqueCoordinateIndex(g, jCell, n0));
* int iFrame = (int)(FrameMap.GlobalUniqueCoordinateIndex(g, jCell, 0));
*
* for (int n = 0; n < N; n++) {
* ExtRangeTrafo[tt][iFrame + n - offset] = iFull + n;
* }
* }
* }
* }
* }
* }
*/
{
int NoOfSpc = this.m_Regions.SpeciesIdS.Count;
int N_frame = this.FrameMap.MaxTotalNoOfCoordinatesPerCell;
var FramBasisS = this.FrameMap.BasisS.ToArray();
var FullBasisS = this.FullMap.BasisS.ToArray();
int[] NBs = FramBasisS.Select(b => b.Length).ToArray();
int[] NBf = FullBasisS.Select(b => b.MaximalLength).ToArray();
Debug.Assert(NBf.Length == NBs.Length);
for (int i = 0; i < NBf.Length; i++)
{
Debug.Assert(NBf[i] % NBs[i] == 0);
}
bool[] XBasis = FullBasisS.Select(b => b is XDGBasis).ToArray();
this.IndexTrafoWithinCell = new int[NoOfSpc, this.FrameMap.MaxTotalNoOfCoordinatesPerCell];
for (int iSpc = 0; iSpc < NoOfSpc; iSpc++) // loop over all possible species indices
{
int n_frame = 0;
int n_full = 0;
for (int ifld = 0; ifld < NBs.Length; ifld++) // loop over all basises in the mapping
{
if (XBasis[ifld])
{
for (int n = 0; n < NBs[ifld]; n++)
{
this.IndexTrafoWithinCell[iSpc, n_frame + n] = n_full + iSpc * NBs[ifld] + n;
}
}
else
{
for (int n = 0; n < NBs[ifld]; n++)
{
this.IndexTrafoWithinCell[iSpc, n_frame + n] = n_full + n;
}
}
n_frame += NBs[ifld];
n_full += NBf[ifld];
}
}
}
}
///// <summary>
///// cached inverse mass-matrix blocks for cut-cells
///// </summary>
//Dictionary<SpeciesId, MassMatrixFactory.MassMatrixBlockContainer> InverseMassBlocks;
/// <summary>
/// computes the mass matrices for a given mapping and accumulates the mass matrix to some other matrix.
/// </summary>
public void AccMassMatrix <T>(T M, UnsetteledCoordinateMapping mapping, IDictionary <SpeciesId, IEnumerable <double> > _alpha, bool inverse = false)
where T : IMutableMatrixEx //
{
using (new FuncTrace()) {
var _basisS = mapping.BasisS.ToArray();
var ctx = _basisS[0].GridDat;
int J = ctx.iLogicalCells.NoOfLocalUpdatedCells;
//if (VariableAgglomerationSwitch == null) {
// VariableAgglomerationSwitch = new bool[mapping.BasisS.Count];
// VariableAgglomerationSwitch.SetAll(true);
//} else {
// if (VariableAgglomerationSwitch.Length != mapping.BasisS.Count)
// throw new ArgumentException();
//}
//if(VariableAgglomerationSwitch.Any() && (agg == null)) {
// throw new ArgumentException("Cell Agglomerator is required.");
//}
if (!M.RowPartitioning.EqualsPartition(mapping))
{
throw new ArgumentException("Mismatch in row mapping.");
}
if (!M.ColPartition.EqualsPartition(mapping))
{
throw new ArgumentException("Mismatch in column mapping.");
}
if (!_alpha.Keys.IsSubsetOf(this.AvailableSpecies))
{
throw new ArgumentException("trying to obtain mass matrix for species that is not supported by this factory.");
}
foreach (var __alpha in _alpha.Values)
{
if (__alpha.Count() != _basisS.Length)
{
throw new ArgumentException("Number of alpha's must match number of variables/fields in mapping.");
}
}
LevelSetTracker.LevelSetRegions regions = null;// XDGSpaceMetrics.LevelSetRegions;
// compute the Mass-Blocks for the cut cells...
// --------------------------------------------
int _MaxDeg = _basisS.Max(b => b.Degree);
var RequestedSpecies = _alpha.Keys;
UpdateBlocks(_MaxDeg, RequestedSpecies);
Dictionary <SpeciesId, MassMatrixBlockContainer>[] invBlocks = null;
if (inverse)
{
invBlocks = GetInverseMassMatrixBlocks(RequestedSpecies, mapping.BasisS.Select(b => b.Degree).ToArray());
//VariableAgglomerationSwitch = new bool[VariableAgglomerationSwitch.Length];
//VariableAgglomerationSwitch.SetAll(true); // we already took care about this in the 'GetInverseMassMatrixBlocks'
}
// set the matrix
// --------------
for (int fld = 0; fld < _basisS.Length; fld++) // loop over Variables in mapping...
// loop over species...
{
foreach (var species in _alpha.Keys)
{
double alpha = _alpha[species].ElementAt(fld);
int[] jSub2jCell = this.MassBlocks[species].jSub2jCell;
if (alpha != 0.0)
{
// properties of the basis
XDGBasis Xbasis = _basisS[fld] as XDGBasis;
Basis nonXbasis;
Basis basis = _basisS[fld];
if (Xbasis != null)
{
nonXbasis = Xbasis.NonX_Basis;
regions = Xbasis.Tracker.Regions; // compute species indices with respect to **actual** regions !!!!
//if (!object.ReferenceEquals(Xbasis.Tracker, this.XDGSpaceMetrics.))
// throw new ArgumentException();
}
else
{
nonXbasis = _basisS[fld];
}
int N = nonXbasis.Length;
// get Mass-Matrix subblock
MultidimensionalArray Mass;
if (!inverse)
{
Mass = this.MassBlocks[species].MassMatrixBlocks;
}
else
{
Mass = invBlocks[fld][species].MassMatrixBlocks;
Debug.Assert(Mass.GetLength(1) == N);
Debug.Assert(Mass.GetLength(2) == N);
}
// set diagonal element 1.0 in all cells of the subgrid
// (later, we subtract 1.0 from the diagonal in cut cells)
var speciesMask = XDGSpaceMetrics.LevelSetRegions.GetSpeciesMask(species);
{
foreach (int jCell in speciesMask.ItemEnum)
{
int iSpc = 0;
if (Xbasis != null)
{
int NoOfSpc = regions.GetNoOfSpecies(jCell);
iSpc = regions.GetSpeciesIndex(species, jCell);
}
int n0 = mapping.GlobalUniqueCoordinateIndex(fld, jCell, N * iSpc);
for (int n = 0; n < N; n++)
{
M[n0 + n, n0 + n] += alpha;
}
}
}
// now, set then Non-Identity blocks in the cut cells
var speciesBitMask = speciesMask.GetBitMask();
{
int JSUB = jSub2jCell.Length;
for (int jsub = 0; jsub < JSUB; jsub++) // loop over cut cells
{
int jCell = jSub2jCell[jsub];
if (!speciesBitMask[jCell])
{
continue;
}
int iSpc = 0;
if (Xbasis != null)
{
int NoOfSpc = regions.GetNoOfSpecies(jCell);
iSpc = regions.GetSpeciesIndex(species, jCell);
}
var MassSub = Mass.ExtractSubArrayShallow(new int[] { jsub, 0, 0 }, new int[] { jsub - 1, N - 1, N - 1 });
//MultidimensionalArray MassSub;
//if (VariableAgglomerationSwitch[fld] || (Mass_B4Agglom[jsub] == null)) {
// // block with agglomeration
// MassSub = Mass.ExtractSubArrayShallow(new int[] { jsub, 0, 0 }, new int[] { jsub - 1, N - 1, N - 1 });
//} else {
// // block without agglomeration
// Debug.Assert(VariableAgglomerationSwitch[fld] == false);
// Debug.Assert(Mass_B4Agglom[jsub] != null);
// MassSub = Mass_B4Agglom[jsub].ExtractSubArrayShallow(new int[] { 0, 0 }, new int[] { N - 1, N - 1 });
//}
int i0 = mapping.GlobalUniqueCoordinateIndex(fld, jCell, N * iSpc);
for (int n = 0; n < N; n++) // loop over rows (within block)
{
for (int m = 0; m < N; m++) // loop over columns (within block)
{
M[i0 + n, i0 + m] += alpha * MassSub[n, m] - (m == n ? alpha : 0.0);
}
}
}
}
}
}
}
//// cell-aglomeration
//// -----------------
//if (inverse == true)
// //throw new ApplicationException("todo: double-check with agglomeration");
// Console.WriteLine("todo: double-check with agglomeration");
//this.m_agglomerator.ManipulateMassMatrix_Mk2(M, mapping);
}
}