def _calcValueIn(self, eps, P):
alpha = self._getArray().copy()
inline._runInline("""
if (fabs(P[i]) < eps) {
P[i] = eps;
}
alpha[i] = 0.5;
if (P[i] > 10.) {
alpha[i] = (P[i] - 1.) / P[i];
} else if (10. >= P[i] && P[i] > eps) {
double tmp = (1. - P[i] / 10.);
double tmpSqr = tmp * tmp;
alpha[i] = ((P[i] - 1.) + tmpSqr*tmpSqr*tmp) / P[i];
} else if (-eps > P[i] && P[i] >= -10.) {
double tmp = (1. + P[i] / 10.);
double tmpSqr = tmp * tmp;
alpha[i] = (tmpSqr*tmpSqr*tmp - 1.) / P[i];
} else if (P[i] < -10.) {
alpha[i] = -1. / P[i];
}
""",
alpha = alpha, eps = eps, P = P,
ni = self.mesh._getNumberOfFaces()
)
return self._makeValue(value = alpha)
def _calcValue(self):
eps = self.eps
P = self.P.numericValue
alpha = self._array.copy()
inline._runInline("""
if (fabs(P[i]) < eps) {
P[i] = eps;
}
alpha[i] = 0.5;
if (P[i] > 10.) {
alpha[i] = (P[i] - 1.) / P[i];
} else if (10. >= P[i] && P[i] > eps) {
double tmp = (1. - P[i] / 10.);
double tmpSqr = tmp * tmp;
alpha[i] = ((P[i] - 1.) + tmpSqr*tmpSqr*tmp) / P[i];
} else if (-eps > P[i] && P[i] >= -10.) {
double tmp = (1. + P[i] / 10.);
double tmpSqr = tmp * tmp;
alpha[i] = (tmpSqr*tmpSqr*tmp - 1.) / P[i];
} else if (P[i] < -10.) {
alpha[i] = -1. / P[i];
}
""",
alpha = alpha, eps = eps, P = P,
ni = len(P.flat)
)
return self._makeValue(value = alpha)
def _areaProjections(self):
areaProjections = numerix.zeros((2, self.numberOfFaces), 'd')
inline._runInline(
"""
if (i < nx) {
areaProjections[i + 1 * ni] = faceAreas[i] * faceNormals[i + 1 * ni];
} else if (i < Nhor) {
areaProjections[i + 1 * ni] = faceAreas[i] * faceNormals[i + 1 * ni];
} else if ( (i - Nhor) % (nx + 1) == 0 ) {
areaProjections[i + 0 * ni] = faceAreas[i] * faceNormals[i + 0 * ni];
} else {
areaProjections[i + 0 * ni] = faceAreas[i] * faceNormals[i + 0 * ni];
}
""",
dx=float(self.dx), # horrible hack to get around
dy=float(
self.dy), # http://www.scipy.org/scipy/scipy/ticket/496
nx=self.nx,
Nhor=self.numberOfHorizontalFaces,
areaProjections=areaProjections,
ni=self.numberOfFaces,
faceNormals=self.faceNormals,
faceAreas=self._faceAreas)
return areaProjections
def _explicitBuildMatrixInline_(self, oldArray, id1, id2, b, coeffMatrix, mesh, interiorFaces, dt, weight):
oldArrayId1, oldArrayId2 = self._getOldAdjacentValues(oldArray, id1, id2, dt)
coeff = numerix.array(self._getGeomCoeff(oldArray))
Nfac = mesh.numberOfFaces
cell1Diag = numerix.zeros((Nfac,), 'd')
cell1Diag[:] = weight['cell 1 diag']
cell1OffDiag = numerix.zeros((Nfac,), 'd')
cell1OffDiag[:] = weight['cell 1 offdiag']
cell2Diag = numerix.zeros((Nfac,), 'd')
cell2Diag[:] = weight['cell 2 diag']
cell2OffDiag = numerix.zeros((Nfac,), 'd')
cell2OffDiag[:] = weight['cell 2 offdiag']
inline._runInline("""
long int faceID = faceIDs[i];
long int cellID1 = id1[i];
long int cellID2 = id2[i];
b[cellID1] += -coeff[faceID] * (cell1Diag[faceID] * oldArrayId1[i] + cell1OffDiag[faceID] * oldArrayId2[i]);
b[cellID2] += -coeff[faceID] * (cell2Diag[faceID] * oldArrayId2[i] + cell2OffDiag[faceID] * oldArrayId1[i]);
""", oldArrayId1 = numerix.array(oldArrayId1),
oldArrayId2 = numerix.array(oldArrayId2),
id1 = id1,
id2 = id2,
b = b,
cell1Diag = cell1Diag,
cell1OffDiag = cell1OffDiag,
cell2Diag = cell2Diag,
cell2OffDiag = cell2OffDiag,
coeff = coeff,
faceIDs = interiorFaces,
ni = len(interiorFaces))
def _calcValueInline(self):
NCells = self.mesh.numberOfCells
ids = self.mesh.cellFaceIDs
val = self._array.copy()
inline._runInline("""
int i;
for(i = 0; i < numberOfCells; i++)
{
int j;
value[i] = 0.;
for(j = 0; j < numberOfCellFaces; j++)
{
// cellFaceIDs can be masked, which caused subtle and
// unreproduceable problems on OS X (who knows why not elsewhere)
long id = ids[i + j * numberOfCells];
if (id >= 0) {
value[i] += orientations[i + j * numberOfCells] * faceVariable[id];
}
}
value[i] = value[i] / cellVolume[i];
}
""",
numberOfCellFaces = self.mesh._maxFacesPerCell,
numberOfCells = NCells,
faceVariable = self.faceVariable.numericValue,
ids = numerix.array(ids),
value = val,
orientations = numerix.array(self.mesh._cellToFaceOrientations),
cellVolume = numerix.array(self.mesh.cellVolumes))
return self._makeValue(value = val)
def _explicitBuildMatrixIn(self, oldArray, id1, id2, b, weightedStencilCoeff, mesh, interiorFaces, dt, weight):
oldArrayId1, oldArrayId2 = self._getOldAdjacentValues(oldArray, id1, id2, dt)
coeff = numerix.array(self._getGeomCoeff(mesh))
Nfac = mesh._getNumberOfFaces()
cell1Diag = numerix.zeros((Nfac,),'d')
cell1Diag[:] = weight['cell 1 diag']
cell1OffDiag = numerix.zeros((Nfac,),'d')
cell1OffDiag[:] = weight['cell 1 offdiag']
cell2Diag = numerix.zeros((Nfac,),'d')
cell2Diag[:] = weight['cell 2 diag']
cell2OffDiag = numerix.zeros((Nfac,),'d')
cell2OffDiag[:] = weight['cell 2 offdiag']
inline._runInline("""
long int faceID = faceIDs[i];
long int cellID1 = id1[i];
long int cellID2 = id2[i];
b[cellID1] += -coeff[faceID] * (cell1Diag[faceID] * oldArrayId1[i] + cell1OffDiag[faceID] * oldArrayId2[i]);
b[cellID2] += -coeff[faceID] * (cell2Diag[faceID] * oldArrayId2[i] + cell2OffDiag[faceID] * oldArrayId1[i]);
""",oldArrayId1 = numerix.array(oldArrayId1),
oldArrayId2 = numerix.array(oldArrayId2),
id1 = id1,
id2 = id2,
b = b,
cell1Diag = cell1Diag,
cell1OffDiag = cell1OffDiag,
cell2Diag = cell2Diag,
cell2OffDiag = cell2OffDiag,
coeff = coeff,
faceIDs = interiorFaces,
ni = len(interiorFaces))
def _calcValue(self):
eps = self.eps
P = self.P.numericValue
alpha = self._array.copy()
inline._runInline("""
if (fabs(P[i]) < eps) {
P[i] = eps;
}
alpha[i] = 0.5;
if (P[i] > 10.) {
alpha[i] = (P[i] - 1.) / P[i];
} else if (10. >= P[i] && P[i] > eps) {
double tmp = (1. - P[i] / 10.);
double tmpSqr = tmp * tmp;
alpha[i] = ((P[i] - 1.) + tmpSqr*tmpSqr*tmp) / P[i];
} else if (-eps > P[i] && P[i] >= -10.) {
double tmp = (1. + P[i] / 10.);
double tmpSqr = tmp * tmp;
alpha[i] = (tmpSqr*tmpSqr*tmp - 1.) / P[i];
} else if (P[i] < -10.) {
alpha[i] = -1. / P[i];
}
""",
alpha=alpha,
eps=eps,
P=P,
ni=len(P.flat))
return self._makeValue(value=alpha)
def _putAddIn(vector, ids, additionVector):
from fipy.tools import inline
inline._runInline("""
int ID = ids[i];
vector[ID] += additionVector[i];
""",
vector=vector, ids=ids, additionVector=numerix.array(additionVector),
ni = len(ids.flat))
def putAdd(vector, ids, additionVector):
""" This is a temporary replacement for Numeric.put as it was not doing
what we thought it was doing.
"""
inline._runInline("""
int ID = ids[i];
vector[ID] += additionVector[i];
""",
vector=vector,
ids=ids,
additionVector=numerix.array(additionVector),
ni = len(ids.flat))
def putAdd(vector, ids, additionVector):
""" This is a temporary replacement for Numeric.put as it was not doing
what we thought it was doing.
"""
inline._runInline("""
int ID = ids[i];
vector[ID] += additionVector[i];
""",
vector=vector,
ids=ids,
additionVector=numerix.array(additionVector),
ni=len(ids.flat))
def sqrtDot(a1, a2):
"""Return array of square roots of vector dot-products
for arrays a1 and a2 of vectors v1 and v2
Usually used with v1==v2 to return magnitude of v1.
"""
from fipy.tools.dimensions import physicalField
unit1 = unit2 = physicalField._unity
def dimensionlessUnmasked(a):
unit = physicalField._unity
mask = False
if _isPhysical(a):
unit = a.inBaseUnits().unit
a = a.numericValue
if MA.isMaskedArray(a):
mask = a.mask
a = a.filled(fill_value=1)
if not a.flags['C_CONTIGUOUS']:
a = a.copy('C')
return (a, unit, mask)
a1, unit1, mask1 = dimensionlessUnmasked(a1)
a2, unit2, mask2 = dimensionlessUnmasked(a2)
NJ, ni = NUMERIX.shape(a1)
result1 = NUMERIX.zeros((ni, ), 'd')
inline._runInline("""
int j;
result1[i] = 0.;
for (j = 0; j < NJ; j++)
{
result1[i] += a1[i + j * ni] * a2[i + j * ni];
}
result1[i] = sqrt(result1[i]);
""",
result1=result1,
a1=a1,
a2=a2,
ni=ni,
NJ=NJ)
if NUMERIX.any(mask1) or NUMERIX.any(mask2):
result1 = MA.array(result1, mask=NUMERIX.logical_or(mask1, mask2))
if unit1 != physicalField._unity or unit2 != physicalField._unity:
from fipy.tools.dimensions.physicalField import PhysicalField
result1 = PhysicalField(value=result, unit=(unit1 * unit2)**0.5)
return result1
def _calcValue_(self, alpha, id1, id2):
val = self._array.copy()
inline._runInline(self.modIn + """
int ID1 = id1[i];
int ID2 = id2[i];
double cell2 = var[ID2];
val[i] = mod(cell2 - var[ID1]) * alpha[i] + var[ID1];
""",var = self.var.numericValue,
val = val,
alpha = alpha,
id1 = id1, id2 = id2,
ni = self.mesh.numberOfFaces)
return self._makeValue(value = val)
def _calcValue_(self, alpha, id1, id2):
val = self._array.copy()
inline._runInline(self.modIn + """
int ID1 = id1[i];
int ID2 = id2[i];
double cell2 = var[ID2];
val[i] = mod(cell2 - var[ID1]) * alpha[i] + var[ID1];
""", var = self.var.numericValue,
val = val,
alpha = alpha,
id1 = id1, id2 = id2,
ni = self.mesh.numberOfFaces)
return self._makeValue(value = val)
def _calcValueIn(self, P):
alpha = self._getArray().copy()
inline._runInline("""
alpha[i] = 0.5;
if (P[i] > 0.) {
alpha[i] = 1.;
} else {
alpha[i] = 0.;
}
""",
alpha = alpha, P = P,
ni = self.mesh._getNumberOfFaces()
)
return self._makeValue(value = alpha)
def _calcValue(self):
P = self.P.numericValue
alpha = self._array.copy()
inline._runInline("""
alpha[i] = 0.5;
if (P[i] > 0.) {
alpha[i] = 1.;
} else {
alpha[i] = 0.;
}
""",
alpha=alpha, P=P,
ni = len(P.flat))
return self._makeValue(value=alpha)
def _createCellsIn(self):
cellFaceIDs = numerix.zeros((4, self.nx * self.ny))
inline._runInline("""
int ID = j * ni + i;
int NCELLS = ni * nj;
cellFaceIDs[ID + 0 * NCELLS] = ID;
cellFaceIDs[ID + 2 * NCELLS] = cellFaceIDs[ID + 0 * NCELLS] + ni;
cellFaceIDs[ID + 3 * NCELLS] = horizontalFaces + ID + j;
cellFaceIDs[ID + 1 * NCELLS] = cellFaceIDs[ID + 3 * NCELLS] + 1;
""",
horizontalFaces=self.numberOfHorizontalFaces,
cellFaceIDs=cellFaceIDs,
ni=self.nx,
nj=self.ny)
return cellFaceIDs
def sqrtDot(a1, a2):
"""Return array of square roots of vector dot-products
for arrays a1 and a2 of vectors v1 and v2
Usually used with v1==v2 to return magnitude of v1.
"""
from fipy.tools.dimensions import physicalField
unit1 = unit2 = physicalField._unity
def dimensionlessUnmasked(a):
unit = physicalField._unity
mask = False
if _isPhysical(a):
unit = a.inBaseUnits().unit
a = a.numericValue
if MA.isMaskedArray(a):
mask = a.mask
a = a.filled(fill_value=1)
if not a.flags['C_CONTIGUOUS']:
a = a.copy('C')
return (a, unit, mask)
a1, unit1, mask1 = dimensionlessUnmasked(a1)
a2, unit2, mask2 = dimensionlessUnmasked(a2)
NJ, ni = NUMERIX.shape(a1)
result1 = NUMERIX.zeros((ni,), 'd')
inline._runInline("""
int j;
result1[i] = 0.;
for (j = 0; j < NJ; j++)
{
result1[i] += a1[i + j * ni] * a2[i + j * ni];
}
result1[i] = sqrt(result1[i]);
""", result1=result1, a1=a1, a2=a2, ni=ni, NJ=NJ)
if NUMERIX.any(mask1) or NUMERIX.any(mask2):
result1 = MA.array(result1, mask=NUMERIX.logical_or(mask1, mask2))
if unit1 != physicalField._unity or unit2 != physicalField._unity:
from fipy.tools.dimensions.physicalField import PhysicalField
result1 = PhysicalField(value=result, unit=(unit1 * unit2)**0.5)
return result1
def _calcValue(self):
P = self.P.numericValue
alpha = self._array.copy()
inline._runInline("""
alpha[i] = 0.5;
if (P[i] > 0.) {
alpha[i] = 1.;
} else {
alpha[i] = 0.;
}
""",
alpha=alpha,
P=P,
ni=len(P.flat))
return self._makeValue(value=alpha)
def faceCellIDs(self):
faceCellIDs = numerix.zeros((2, self.numberOfFaces), 'l')
mask = numerix.zeros((2, self.numberOfFaces), 'l')
inline._runInline("""
int ID = j * ni + i;
int rowlength = ni * nj + Nhor + nj;
faceCellIDs[ID + 0 * rowlength] = ID - ni;
faceCellIDs[ID + 1 * rowlength] = ID;
faceCellIDs[ID + Nhor + j + 0 * rowlength] = ID - 1;
faceCellIDs[ID + Nhor + j + 1 * rowlength] = ID;
if (j == 0) {
faceCellIDs[ID + 0 * rowlength] = ID;
mask[ID + 1 * rowlength] = 1;
}
if (j == nj - 1) {
faceCellIDs[ID + ni + 0 * rowlength] = ID;
mask[ID + ni + 1 * rowlength] = 1;
}
if (i == 0) {
faceCellIDs[ID + Nhor + j + 0 * rowlength] = ID;
mask[ID + Nhor + j + 1 * rowlength] = 1;
}
if ( i == ni - 1 ) {
faceCellIDs[ID + Nhor + j + 1 + 0 * rowlength] = ID;
mask[ID + Nhor + j + 1 + 1 * rowlength] = 1;
}
""",
Nhor=self.numberOfHorizontalFaces,
mask=mask,
faceCellIDs=faceCellIDs,
ni=self.nx,
nj=self.ny)
return MA.masked_where(mask, faceCellIDs)
def faceCellIDs(self):
faceCellIDs = numerix.zeros((2, self.numberOfFaces), 'l')
mask = numerix.zeros((2, self.numberOfFaces), 'l')
inline._runInline("""
int ID = j * ni + i;
int rowlength = ni * nj + Nhor + nj;
faceCellIDs[ID + 0 * rowlength] = ID - ni;
faceCellIDs[ID + 1 * rowlength] = ID;
faceCellIDs[ID + Nhor + j + 0 * rowlength] = ID - 1;
faceCellIDs[ID + Nhor + j + 1 * rowlength] = ID;
if (j == 0) {
faceCellIDs[ID + 0 * rowlength] = ID;
mask[ID + 1 * rowlength] = 1;
}
if (j == nj - 1) {
faceCellIDs[ID + ni + 0 * rowlength] = ID;
mask[ID + ni + 1 * rowlength] = 1;
}
if (i == 0) {
faceCellIDs[ID + Nhor + j + 0 * rowlength] = ID;
mask[ID + Nhor + j + 1 * rowlength] = 1;
}
if ( i == ni - 1 ) {
faceCellIDs[ID + Nhor + j + 1 + 0 * rowlength] = ID;
mask[ID + Nhor + j + 1 + 1 * rowlength] = 1;
}
""",
Nhor=self.numberOfHorizontalFaces,
mask=mask,
faceCellIDs=faceCellIDs,
ni=self.nx,
nj=self.ny)
return MA.masked_where(mask, faceCellIDs)
def _buildMatrixIn(self, L, oldArray, b, dt, coeffVectors):
N = oldArray.getMesh().getNumberOfCells()
updatePyArray = numerix.zeros((N),'d')
inline._runInline("""
b[i] += oldArray[i] * oldCoeff[i] / dt;
b[i] += bCoeff[i];
updatePyArray[i] += newCoeff[i] / dt;
updatePyArray[i] += diagCoeff[i];
""",b=b,
oldArray=oldArray.getNumericValue(),
## oldArray=numerix.array(oldArray),
oldCoeff=numerix.array(coeffVectors['old value']),
bCoeff=numerix.array(coeffVectors['b vector']),
newCoeff=numerix.array(coeffVectors['new value']),
diagCoeff=numerix.array(coeffVectors['diagonal']),
updatePyArray=updatePyArray,
ni=len(updatePyArray),
dt=dt)
L.addAtDiagonal(updatePyArray)
def createCells(nx, ny, numFaces, numHorizFaces, numVertCols):
"""
cells = (f1, f2, f3, f4) going anticlock wise.
f1 etc. refer to the faces
"""
cellFaceIDs = numerix.zeros((4, nx * ny), 'l')
inline._runInline("""
int ID = j * ni + i;
int NCELLS = ni * nj;
cellFaceIDs[ID + 0 * NCELLS] = ID;
cellFaceIDs[ID + 2 * NCELLS] = cellFaceIDs[ID + 0 * NCELLS] + ni;
cellFaceIDs[ID + 3 * NCELLS] = horizontalFaces + ID + j;
cellFaceIDs[ID + 1 * NCELLS] = cellFaceIDs[ID + 3 * NCELLS] + 1;
""",
horizontalFaces=numHorizFaces,
cellFaceIDs=cellFaceIDs,
ni=nx,
nj=ny)
return cellFaceIDs
def createCells(nx, ny, numFaces, numHorizFaces, numVertCols):
"""
cells = (f1, f2, f3, f4) going anticlock wise.
f1 etc. refer to the faces
"""
cellFaceIDs = numerix.zeros((4, nx * ny), 'l')
inline._runInline("""
int ID = j * ni + i;
int NCELLS = ni * nj;
cellFaceIDs[ID + 0 * NCELLS] = ID;
cellFaceIDs[ID + 2 * NCELLS] = cellFaceIDs[ID + 0 * NCELLS] + ni;
cellFaceIDs[ID + 3 * NCELLS] = horizontalFaces + ID + j;
cellFaceIDs[ID + 1 * NCELLS] = cellFaceIDs[ID + 3 * NCELLS] + 1;
""",
horizontalFaces=numHorizFaces,
cellFaceIDs=cellFaceIDs,
ni=nx,
nj=ny)
return cellFaceIDs
def _getAreaProjectionsIn(self):
areaProjections = numerix.zeros((2, self.numberOfFaces), 'd')
inline._runInline("""
if (i < nx) {
areaProjections[i + 1 * ni] = -dx;
} else if (i < Nhor) {
areaProjections[i + 1 * ni] = dx;
} else if ( (i - Nhor) % (nx + 1) == 0 ) {
areaProjections[i + 0 * ni] = -dy;
} else {
areaProjections[i + 0 * ni] = dy;
}
""",
dx = float(self.dx), # horrible hack to get around
dy = float(self.dy), # http://www.scipy.org/scipy/scipy/ticket/496
nx = self.nx,
Nhor = self.numberOfHorizontalFaces,
areaProjections = areaProjections,
ni = self.numberOfFaces)
return areaProjections
def _adjacentCellIDs(self):
faceCellIDs0 = numerix.zeros(self.numberOfFaces, 'l')
faceCellIDs1 = numerix.zeros(self.numberOfFaces, 'l')
inline._runInline("""
int ID = j * ni + i;
faceCellIDs0[ID] = ID - ni;
faceCellIDs1[ID] = ID;
faceCellIDs0[ID + Nhor + j] = ID - 1;
faceCellIDs1[ID + Nhor + j] = ID;
if (j == 0) {
faceCellIDs0[ID] = ID;
}
if (j == nj - 1) {
faceCellIDs0[ID + ni] = ID;
faceCellIDs1[ID + ni] = ID;
}
if (i == 0) {
faceCellIDs0[ID + Nhor + j] = ID;
}
if ( i == ni - 1 ) {
faceCellIDs0[ID + Nhor + j + 1] = ID;
faceCellIDs1[ID + Nhor + j + 1] = ID;
}
""",
Nhor=self.numberOfHorizontalFaces,
faceCellIDs0=faceCellIDs0,
faceCellIDs1=faceCellIDs1,
ni=self.nx,
nj=self.ny)
return (faceCellIDs0, faceCellIDs1)
def _adjacentCellIDs(self):
faceCellIDs0 = numerix.zeros(self.numberOfFaces, 'l')
faceCellIDs1 = numerix.zeros(self.numberOfFaces, 'l')
inline._runInline("""
int ID = j * ni + i;
faceCellIDs0[ID] = ID - ni;
faceCellIDs1[ID] = ID;
faceCellIDs0[ID + Nhor + j] = ID - 1;
faceCellIDs1[ID + Nhor + j] = ID;
if (j == 0) {
faceCellIDs0[ID] = ID;
}
if (j == nj - 1) {
faceCellIDs0[ID + ni] = ID;
faceCellIDs1[ID + ni] = ID;
}
if (i == 0) {
faceCellIDs0[ID + Nhor + j] = ID;
}
if ( i == ni - 1 ) {
faceCellIDs0[ID + Nhor + j + 1] = ID;
faceCellIDs1[ID + Nhor + j + 1] = ID;
}
""",
Nhor=self.numberOfHorizontalFaces,
faceCellIDs0=faceCellIDs0,
faceCellIDs1=faceCellIDs1,
ni=self.nx,
nj=self.ny)
return (faceCellIDs0, faceCellIDs1)
def _calcValue_(self, alpha, id1, id2):
val = self._array.copy()
inline._runInline("""
int ID1 = id1[i];
int ID2 = id2[i];
double cell1 = var[ID1];
double cell2 = var[ID2];
if (cell1 < 0 || cell2 < 0) {
val[i] = 0;
} else {
val[i] = diffusionCoeff;
}
""",
var=numerix.array(self.var),
val=val,
id1=id1,
id2=id2,
diffusionCoeff=self.diffusionCoeff,
ni=self.mesh.numberOfFaces)
return self._makeValue(value=val)
def _buildMatrixInline_(self, L, oldArray, b, dt, coeffVectors):
oldArray = oldArray.value.ravel()
N = len(oldArray)
updatePyArray = numerix.zeros((N),'d')
dt = self._checkDt(dt)
inline._runInline("""
b[i] += oldArray[i] * oldCoeff[i] / dt;
b[i] += bCoeff[i];
updatePyArray[i] += newCoeff[i] / dt;
updatePyArray[i] += diagCoeff[i];
""",b=b,
oldArray=oldArray,
oldCoeff=coeffVectors['old value'].ravel(),
bCoeff=coeffVectors['b vector'].ravel(),
newCoeff=coeffVectors['new value'].ravel(),
diagCoeff=coeffVectors['diagonal'].ravel(),
updatePyArray=updatePyArray,
ni=len(updatePyArray),
dt=dt)
L.addAtDiagonal(updatePyArray)
def _buildMatrixInline_(self, L, oldArray, b, dt, coeffVectors):
oldArray = oldArray.value.ravel()
N = len(oldArray)
updatePyArray = numerix.zeros((N), 'd')
dt = self._checkDt(dt)
inline._runInline("""
b[i] += oldArray[i] * oldCoeff[i] / dt;
b[i] += bCoeff[i];
updatePyArray[i] += newCoeff[i] / dt;
updatePyArray[i] += diagCoeff[i];
""", b=b,
oldArray=oldArray,
oldCoeff=coeffVectors['old value'].ravel(),
bCoeff=coeffVectors['b vector'].ravel(),
newCoeff=coeffVectors['new value'].ravel(),
diagCoeff=coeffVectors['diagonal'].ravel(),
updatePyArray=updatePyArray,
ni=len(updatePyArray),
dt=dt)
L.addAtDiagonal(updatePyArray)
def _calcValue_(self, alpha, id1, id2):
val = self._array.copy()
inline._runInline("""
int ID1 = id1[i];
int ID2 = id2[i];
double cell1 = var[ID1];
double cell2 = var[ID2];
if (cell1 < 0 || cell2 < 0) {
val[i] = 0;
} else {
val[i] = diffusionCoeff;
}
""",
var = numerix.array(self.var),
val = val,
id1 = id1, id2 = id2,
diffusionCoeff = self.diffusionCoeff,
ni = self.mesh.numberOfFaces
)
return self._makeValue(value = val)
def _calcValueInline(self):
NCells = self.mesh.numberOfCells
ids = self.mesh.cellFaceIDs
val = self._array.copy()
inline._runInline("""
int i;
for(i = 0; i < numberOfCells; i++)
{
int j;
value[i] = 0.;
for(j = 0; j < numberOfCellFaces; j++)
{
// cellFaceIDs can be masked, which caused subtle and
// unreproduceable problems on OS X (who knows why not elsewhere)
long id = ids[i + j * numberOfCells];
if (id >= 0) {
value[i] += orientations[i + j * numberOfCells] * faceVariable[id];
}
}
value[i] = value[i] / cellVolume[i];
}
""",
numberOfCellFaces=self.mesh._maxFacesPerCell,
numberOfCells=NCells,
faceVariable=self.faceVariable.numericValue,
ids=numerix.array(ids),
value=val,
orientations=numerix.array(
self.mesh._cellToFaceOrientations),
cellVolume=numerix.array(self.mesh.cellVolumes))
return self._makeValue(value=val)
def _execInline(self, comment=None):
"""
Gets the stack from _getCstring() which calls _getRepresentation()
>>> (Variable((1,2,3,4)) * Variable((5,6,7,8)))._getCstring()
'(var0[i] * var1[i])'
>>> (Variable(((1,2),(3,4))) * Variable(((5,6),(7,8))))._getCstring()
'(var0[i + j * ni] * var1[i + j * ni])'
>>> (Variable((1,2)) * Variable((5,6)) * Variable((7,8)))._getCstring()
'((var00[i] * var01[i]) * var1[i])'
The following test was implemented due to a problem with
contiguous arrays. The `mesh.getCellCenters()[1]` command
introduces a non-contiguous array into the `Variable` and this
causes the inline routine to return senseless results.
>>> from fipy import Grid2D, CellVariable
>>> mesh = Grid2D(dx=1., dy=1., nx=2, ny=2)
>>> var = CellVariable(mesh=mesh, value=0.)
>>> Y = mesh.getCellCenters()[1]
>>> var.setValue(Y + 1.0)
>>> print var - Y
[ 1. 1. 1. 1.]
"""
from fipy.tools import inline
argDict = {}
string = self._getCstring(argDict=argDict, freshen=True) + ';'
try:
shape = self.opShape
except AttributeError:
shape = self.shape
dimensions = len(shape)
if dimensions == 0:
string = 'result[0] = ' + string
dim = ()
else:
string = 'result' + self._getCIndexString(shape) + ' = ' + string
ni = self.opShape[-1]
argDict['ni'] = ni
if dimensions == 1:
dim = (ni)
else:
nj = self.opShape[-2]
argDict['nj'] = nj
if dimensions == 2:
dim =(nj,ni)
elif dimensions == 3:
nk = self.opShape[-3]
dim = (nk,nj,ni)
argDict['nk'] = nk
else:
raise DimensionError, 'Impossible Dimensions'
## Following section makes sure that the result array has a
## valid typecode. If self.value is None then a typecode is
## assigned to the Variable by running the calculation without
## inlining. The non-inlined result is thus used the first
## time through.
if self.value is None and not hasattr(self, 'typecode'):
self.canInline = False
argDict['result'] = self.getValue()
self.canInline = True
self.typecode = numerix.obj2sctype(argDict['result'])
else:
if self.value is None:
if self.getsctype() == numerix.bool_:
argDict['result'] = numerix.empty(dim, numerix.int8)
else:
argDict['result'] = numerix.empty(dim, self.getsctype())
else:
argDict['result'] = self.value
resultShape = argDict['result'].shape
if resultShape == ():
argDict['result'] = numerix.reshape(argDict['result'], (1,))
inline._runInline(string, converters=None, comment=comment, **argDict)
if resultShape == ():
argDict['result'] = numerix.reshape(argDict['result'], resultShape)
return argDict['result']