HRESULT CDataBlockStore::AddData(const void *pNewData, UINT bufferSize, UINT *pCurOffset)
{
HRESULT hr = S_OK;
if (bufferSize == 0)
{
if (pCurOffset)
{
*pCurOffset = 0;
}
goto lExit;
}
if (!m_pFirst)
{
VN( m_pFirst = NEW CDataBlock() );
if (m_IsAligned)
{
m_pFirst->EnableAlignment();
}
m_pLast = m_pFirst;
}
if (pCurOffset)
*pCurOffset = m_Size + m_Offset;
VH( m_pLast->AddData(pNewData, bufferSize, &m_pLast) );
m_Size += bufferSize;
lExit:
return hr;
}
BOOL grmWriteFile( HANDLE * ph, LPTSTR lpb )
{
HANDLE h = 0;
DWORD dwi, dww;
dwi = dww = 0;
if( ph && lpb )
{
dwi = strlen(lpb);
h = *ph;
}
if( ( VH(h) ) &&
( dwi ) )
{
if( ( WriteFile(h,lpb,dwi,&dww,NULL) ) &&
( dwi == dww ) )
{
// success
}
else
{
CloseHandle(h);
h = (HANDLE)-1;
*ph = h;
dww = 0;
}
}
return( (BOOL)dww );
}
Variant StreamMessageFactory::GetUserControlStream(uint16_t operation, uint32_t streamId) {
Variant result;
VH(result, HT_FULL, 2, 0, 0, RM_HEADER_MESSAGETYPE_USRCTRL,
0, true);
M_USRCTRL_TYPE(result) = (uint16_t) operation;
M_USRCTRL_TYPE_STRING(result) =
RTMPProtocolSerializer::GetUserCtrlTypeString(operation);
M_USRCTRL_STREAMID(result) = streamId;
return result;
}
_Use_decl_annotations_
HRESULT CDataBlock::AddData(const void *pvNewData, uint32_t bufferSize, CDataBlock **ppBlock)
{
HRESULT hr = S_OK;
uint32_t bytesToCopy;
const uint8_t *pNewData = (const uint8_t*) pvNewData;
if (m_maxSize == 0)
{
// This is a brand new DataBlock, fill it up
m_maxSize = std::max<uint32_t>(8192, bufferSize);
VN( m_pData = new uint8_t[m_maxSize] );
}
assert(m_pData == AlignToPowerOf2(m_pData, c_DataAlignment));
bytesToCopy = std::min(m_maxSize - m_size, bufferSize);
memcpy(m_pData + m_size, pNewData, bytesToCopy);
pNewData += bytesToCopy;
if (m_IsAligned)
{
assert(m_size == AlignToPowerOf2(m_size, c_DataAlignment));
m_size += AlignToPowerOf2(bytesToCopy, c_DataAlignment);
}
else
{
m_size += bytesToCopy;
}
bufferSize -= bytesToCopy;
*ppBlock = this;
if (bufferSize != 0)
{
assert(nullptr == m_pNext); // make sure we're not overwriting anything
// Couldn't fit all data into this block, spill over into next
VN( m_pNext = new CDataBlock() );
if (m_IsAligned)
{
m_pNext->EnableAlignment();
}
VH( m_pNext->AddData(pNewData, bufferSize, ppBlock) );
}
lExit:
return hr;
}
HRESULT CDataBlock::AddData(const void *pvNewData, UINT bufferSize, CDataBlock **ppBlock)
{
HRESULT hr = S_OK;
UINT bytesToCopy;
const BYTE *pNewData = (const BYTE*) pvNewData;
if (m_maxSize == 0)
{
// This is a brand new DataBlock, fill it up
m_maxSize = max(8192, bufferSize);
VN( m_pData = NEW BYTE[m_maxSize] );
}
D3DXASSERT(m_pData == AlignToPowerOf2(m_pData, c_DataAlignment));
bytesToCopy = min(m_maxSize - m_size, bufferSize);
memcpy(m_pData + m_size, pNewData, bytesToCopy);
pNewData += bytesToCopy;
if (m_IsAligned)
{
D3DXASSERT(m_size == AlignToPowerOf2(m_size, c_DataAlignment));
m_size += AlignToPowerOf2(bytesToCopy, c_DataAlignment);
}
else
{
m_size += bytesToCopy;
}
bufferSize -= bytesToCopy;
*ppBlock = this;
if (bufferSize != 0)
{
D3DXASSERT(NULL == m_pNext); // make sure we're not overwriting anything
// Couldn't fit all data into this block, spill over into next
VN( m_pNext = NEW CDataBlock() );
if (m_IsAligned)
{
m_pNext->EnableAlignment();
}
VH( m_pNext->AddData(pNewData, bufferSize, ppBlock) );
}
lExit:
return hr;
}
Variant StreamMessageFactory::GetFlexStreamSend(uint32_t channelId,
uint32_t streamId, double timeStamp, bool isAbsolute, string function,
Variant ¶meters) {
Variant result;
VH(result, HT_FULL, channelId, timeStamp, 0,
RM_HEADER_MESSAGETYPE_FLEXSTREAMSEND, streamId, isAbsolute);
result[RM_FLEXSTREAMSEND][RM_FLEXSTREAMSEND_UNKNOWNBYTE] = (uint8_t) 0;
result[RM_FLEXSTREAMSEND][RM_FLEXSTREAMSEND_PARAMS][(uint32_t) 0] = function;
FOR_MAP(parameters, string, Variant, i) {
result[RM_FLEXSTREAMSEND][RM_FLEXSTREAMSEND_PARAMS][
result[RM_FLEXSTREAMSEND][RM_FLEXSTREAMSEND_PARAMS].MapSize()] = MAP_VAL(i);
}
void MultiplyAdjoint
( int maxRank, std::complex<Real> alpha,
const Dense<std::complex<Real> >& A,
const Dense<std::complex<Real> >& B,
LowRank<std::complex<Real> >& C )
{
#ifndef RELEASE
CallStackEntry entry("hmat_tools::MultiplyAdjoint (F := D D^H)");
#endif
typedef std::complex<Real> Scalar;
const int m = A.Height();
const int n = B.Height();
const int minDim = std::min( m, n );
const int r = std::min( minDim, maxRank );
// C.U := alpha A B^H
MultiplyAdjoint( alpha, A, B, C.U );
// Get the economic SVD of C.U, C.U = U Sigma V^H, overwriting C.U with U.
Vector<Real> s( minDim );
Dense<Scalar> VH( minDim, n );
const int lwork = lapack::SVDWorkSize( m, n );
std::vector<Scalar> work( lwork );
std::vector<Real> rwork( 5*minDim );
lapack::SVD
( 'O', 'S', m, n, C.U.Buffer(), C.U.LDim(),
s.Buffer(), 0, 1, VH.Buffer(), VH.LDim(),
&work[0], lwork, &rwork[0] );
// Truncate the SVD in-place
C.U.Resize( m, r );
s.Resize( r );
VH.Resize( r, n );
C.V.SetType( GENERAL ); C.V.Resize( n, r );
// Put (Sigma V^H)^T = (V^H)^T Sigma into C.V
const int VHLDim = VH.LDim();
for( int j=0; j<r; ++j )
{
const Real sigma = s.Get(j);
Scalar* RESTRICT VCol = C.V.Buffer(0,j);
const Scalar* RESTRICT VHRow = VH.LockedBuffer(j,0);
for( int i=0; i<n; ++i )
VCol[i] = sigma*VHRow[i*VHLDim];
}
}
BOOL grmCloseFile( HANDLE * ph )
{
HANDLE h = 0;
BOOL bRet = FALSE;
if( ph )
h = *ph;
if( VH(h) )
{
if( CloseHandle(h) )
bRet = TRUE;
}
h = 0;
if( ph )
*ph = h;
return bRet;
}
void LatticeDefGrad<EvalT, Traits>::
evaluateFields(typename Traits::EvalData workset)
{
// Compute LatticeDefGrad tensor from displacement gradient
for (int cell=0; cell < workset.numCells; ++cell)
{
for (int qp=0; qp < numQPs; ++qp)
{
for (int i=0; i < numDims; ++i)
{
for (int j=0; j < numDims; ++j)
{
latticeDefGrad(cell,qp,i,j) = defgrad(cell,qp,i,j);
}
}
JH(cell,qp) = J(cell,qp);
}
}
// Since Intrepid will later perform calculations on the entire workset size
// and not just the used portion, we must fill the excess with reasonable
// values. Leaving this out leads to inversion of 0 tensors.
for (int cell=workset.numCells; cell < worksetSize; ++cell)
for (int qp=0; qp < numQPs; ++qp)
for (int i=0; i < numDims; ++i)
latticeDefGrad(cell,qp,i,i) = 1.0;
if (weightedAverage)
{
ScalarT Jbar, wJbar, vol;
for (int cell=0; cell < workset.numCells; ++cell)
{
Jbar = 0.0;
vol = 0.0;
for (int qp=0; qp < numQPs; ++qp)
{
Jbar += weights(cell,qp) * std::log( 1 + VH(cell,qp)*(Ctotal(cell,qp) - CtotalRef(cell,qp)) );
vol += weights(cell,qp);
}
Jbar /= vol;
// Jbar = std::exp(Jbar);
for (int qp=0; qp < numQPs; ++qp)
{
for (int i=0; i < numDims; ++i)
{
for (int j=0; j < numDims; ++j)
{
wJbar = std::exp( (1-alpha) * Jbar +
alpha * std::log( 1 + VH(cell,qp)*(Ctotal(cell,qp) - CtotalRef(cell,qp))));
latticeDefGrad(cell,qp,i,j) *= std::pow( wJbar ,-1./3. );
}
}
JH(cell,qp) *= wJbar;
}
}
} else {
for (int cell=0; cell < workset.numCells; ++cell)
{
for (int qp=0; qp < numQPs; ++qp)
{
JH(cell,qp) *= (1 + VH(cell,qp)*(Ctotal(cell,qp) - CtotalRef(cell,qp)));
for (int i=0; i < numDims; ++i)
{
for (int j=0; j < numDims; ++j)
{
latticeDefGrad(cell,qp,i,j) *= std::pow(JH(cell,qp) ,-1./3. );
}
}
}
}
}
}
int tester(const std::string &root_name)
{
std::vector<std::string> species_str_list;
species_str_list.push_back( "N2" );
species_str_list.push_back( "O2" );
species_str_list.push_back( "N" );
species_str_list.push_back( "O" );
species_str_list.push_back( "NO" );
species_str_list.push_back( "C" );
species_str_list.push_back( "C2" );
species_str_list.push_back( "CN" );
species_str_list.push_back( "CH4" );
species_str_list.push_back( "CH3" );
species_str_list.push_back( "H" );
unsigned int n_species = species_str_list.size();
Antioch::ChemicalMixture<Scalar> chem_mixture( species_str_list );
Antioch::ReactionSet<Scalar> reaction_set( chem_mixture );
Antioch::read_reaction_set_data_xml<Scalar>( root_name + "/test_parsing.xml", true, reaction_set );
//photochemistry set here
std::vector<Scalar> hv,lambda;
std::ifstream solar_flux(root_name + "/solar_flux.dat");
std::string line;
//// the unit management here is tedious and useless, but it's got
// all the steps, if ever someone needs a reference
getline(solar_flux,line);
Antioch::Units<Scalar> solar_wave("nm");
Antioch::Units<Scalar> solar_irra("W/m2/nm");
Antioch::Units<Scalar> i_unit = solar_irra - (Antioch::Constants::Planck_constant_unit<Scalar>() + Antioch::Constants::light_celerity_unit<Scalar>() - solar_wave); //photons.s-1 = irradiance/(h*c/lambda)
i_unit += Antioch::Units<Scalar>("nm"); //supress bin in unit calculations
while(!solar_flux.eof())
{
Scalar l,i,di;
solar_flux >> l >> i >> di;
hv.push_back(i /(Antioch::Constants::Planck_constant<Scalar>() * Antioch::Constants::light_celerity<Scalar>() / l) // irr/(h*c/lambda): power -> number of photons.s-1
* i_unit.get_SI_factor()); //SI for cs, keep nm for bin
lambda.push_back(l * solar_wave.factor_to_some_unit("nm")); //nm
if(lambda.size() == 796)break;
}
solar_flux.close();
std::vector<Scalar> CH4_s,CH4_lambda;
std::ifstream CH4_file(root_name + "/CH4_hv_cs.dat");
Scalar T = 2000.L;
Scalar Tr = 1.;
Antioch::Units<Scalar> unitA_m1("kmol/m3/s"),unitA_0("s-1"),unitA_1("m3/kmol/s"),unitA_2("m6/kmol2/s");
Scalar Rcal = Antioch::Constants::R_universal<Scalar>() * Antioch::Constants::R_universal_unit<Scalar>().factor_to_some_unit("cal/mol/K");
getline(CH4_file,line);
Antioch::Units<Scalar> cs_input("cm2");
Antioch::Units<Scalar> lambda_input("ang");
Scalar factor_cs = cs_input.get_SI_factor() / lambda_input.factor_to_some_unit("nm");
while(!CH4_file.eof())
{
Scalar l,s;
CH4_file >> l >> s;
CH4_s.push_back(s * factor_cs);
CH4_lambda.push_back(l * lambda_input.factor_to_some_unit("nm"));
if(CH4_s.size() == 137)break;
}
CH4_file.close();
Antioch::ParticleFlux<std::vector<Scalar> > photons(lambda,hv);
Antioch::KineticsConditions<Scalar,std::vector<Scalar> > conditions(T);
//
// Molar densities
std::vector<Scalar> molar_densities(n_species,5e-4);
Scalar tot_dens((Scalar)n_species * 5e-4);
///Elementary, + Kooij - Arrhenius conversion tested
std::vector<Scalar> k;
Scalar A,beta,Ea,D;
// N2 -> 2 N
A = 7e18 * unitA_0.get_SI_factor();
beta = -1.6;
k.push_back(HE(T,A,beta));
// O2 -> 2 O
A = 2e18 * unitA_0.get_SI_factor();
D = -5e-3;
k.push_back(Bert(T,A,D));
//NO -> N + O
A = 5e12 * unitA_0.get_SI_factor();
Ea = 149943.0;
k.push_back(Arrh(T,A,Ea,Rcal));
beta = 0.42;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal));
//N2 + O -> NO + N
A = 5.7e9 * unitA_1.get_SI_factor();
beta = 0.42;
k.push_back(BHE(T,A,beta,D));
//NO + O -> NO + N
A = 8.4e9 * unitA_1.get_SI_factor();
beta = 0.4;
Ea = 38526.0;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal));
k.push_back(Arrh(T,A,Ea,Rcal));
//C2 -> 2 C
A = 3.7e11 * unitA_0.get_SI_factor();
beta = -0.42;
// Ea = 138812.8; // cal/mol
Ea = 69900; // K
k.push_back(Kooij(T,A,beta,Ea,Tr,Scalar(1)));
//CN -> C + N
A = 2.5e11 * unitA_0.get_SI_factor();
beta = 0.40;
Ea = 174240.9;
D = 0.05;
k.push_back(VH(T,A,beta,Ea,D,Tr,Rcal));
///Duplicate
Scalar A2,beta2,Ea2,D2,A3,beta3,Ea3,D3,A4,Ea4;
// N2 -> 2 N
A = 7e18 * unitA_0.get_SI_factor();
beta = -1.6;
A2 = 5e17 * unitA_0.get_SI_factor();
beta2 = 0.5;
A3 = 3e18 * unitA_0.get_SI_factor();
beta3 = -0.6;
k.push_back(HE(T,A,beta) + HE(T,A2,beta2) + HE(T,A3,beta3));
// O2 -> 2 O
A = 2e18 * unitA_0.get_SI_factor();
D = -5e-2;
A2 = 2e+16 * unitA_0.get_SI_factor();
D2 = 0.003;
k.push_back(Bert(T,A,D) + Bert(T,A2,D2));
// NO -> N + O
A = 5e+12 * unitA_0.get_SI_factor();
Ea = 149943.0;
A2 = 3.5e+10 * unitA_0.get_SI_factor();
Ea2 = 1943.0;
A3 = 1.5e+8 * unitA_0.get_SI_factor();
Ea3 = 149.0;
A4 = 5.5e+8 * unitA_0.get_SI_factor();
Ea4 = 943.0;
k.push_back(Arrh(T,A,Ea,Rcal) + Arrh(T,A2,Ea2,Rcal) + Arrh(T,A3,Ea3,Rcal) + Arrh(T,A4,Ea4,Rcal));
// N2 + O -> NO + N
A = 5.7e+9 * unitA_1.get_SI_factor();
beta = 0.42;
D = -5e-3;
A2 = 7e+7 * unitA_1.get_SI_factor();
beta2 = 0.5;
D2 = 2.5e-5;
k.push_back(BHE(T,A,beta,D) + BHE(T,A2,beta2,D2));
//NO + O -> NO + N
A = 8.4e+09 * unitA_1.get_SI_factor();
beta = 0.40;
Ea = 38526.0;
A2 = 4e+07 * unitA_1.get_SI_factor();
beta2 = 0.50;
Ea2 = 40500.0;
A3 = 5e+10 * unitA_1.get_SI_factor();
beta3 = 0.10;
Ea3 = 15000.0;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) + Kooij(T,A2,beta2,Ea2,Tr,Rcal) + Kooij(T,A3,beta3,Ea3,Tr,Rcal));
//C2 -> 2 C
A = 3.7e+11 * unitA_0.get_SI_factor();
beta = -0.42;
Ea = 138812.8;
A2 = 5.0e+10 * unitA_0.get_SI_factor();
beta2 = 1.32;
Ea2 = 150500.8;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) + Kooij(T,A2,beta2,Ea2,Tr,Rcal));
//CN -> C + N
A = 2.5e+11 * unitA_0.get_SI_factor();
beta = 0.40;
D = -5e-3;
Ea = 174240.9;
A2 = 5e+10 * unitA_0.get_SI_factor();
beta2 = 0.50;
D2 = -1.5e-2;
Ea2 = 4240.9;
A3 = 3.2e+10 * unitA_0.get_SI_factor();
beta3 = 1.20;
D3 = -2.5e-5;
Ea3 = 174.9;
k.push_back(VH(T,A,beta,Ea,D,Tr,Rcal) + VH(T,A2,beta2,Ea2,D2,Tr,Rcal) + VH(T,A3,beta3,Ea3,D3,Tr,Rcal));
//three body
// N2 -> 2 N
A = 7e18 * unitA_1.get_SI_factor();
beta = -1.6;
Ea = 149943.0;
k.push_back(HE(T,A,beta) * (Scalar(n_species) - 2. + 4.2857 + 4.2857) * 5e-4);
// O2 -> 2 O
A = 2e18 * unitA_1.get_SI_factor();
D = -5e-3;
k.push_back(Bert(T,A,D) * (Scalar(n_species) - 2. + 5.0 + 5.0) * 5e-4);
//NO -> N + O
A = 5e12 * unitA_1.get_SI_factor();
k.push_back(Arrh(T,A,Ea,Rcal) * (Scalar(n_species) - 3. + 22.0 + 22.0 + 22.0) * 5e-4);
//N2 + O -> NO + N
A = 5.7e9 * unitA_2.get_SI_factor();
beta = 0.42;
D = -5e-3;
k.push_back(BHE(T,A,beta,D) * (Scalar(n_species) - 3. + 22.0 + 22.0 + 22.0) * 5e-4);
//NO + O -> NO + N
A = 8.4e9 * unitA_2.get_SI_factor();
beta = 0.4;
Ea = 38526.0;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) * (Scalar(n_species) - 3. + 22.0 + 22.0 + 22.0) * 5e-4);
//C2 -> 2 C
A = 3.7e11 * unitA_1.get_SI_factor();
beta = -0.42;
Ea = 138812.8;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) * Scalar(n_species) * 5e-4);
//CN -> C + N
A = 2.5e11 * unitA_1.get_SI_factor();
beta = 0.40;
Ea = 729372.4;
D = 5e-3;
k.push_back(VH(T,A,beta,Ea,D,Tr,Rcal) * Scalar(n_species) * 5e-4);
///Lindemann Falloff
// falloff is k(T,[M]) = k0*[M]/(1 + [M]*k0/kinf) * F = k0 * ([M]^-1 + k0 * kinf^-1)^-1 * F
// F = 1
// N2 -> 2 N
A = 7e18 * unitA_1.get_SI_factor();
beta = -1.6;
A2 = 5e15 * unitA_0.get_SI_factor();
beta2 = 0.5;
k.push_back(HE(T,A,beta) / (1./tot_dens + HE(T,A,beta)/HE(T,A2,beta2)) );
// O2 -> 2 O
A = 5e17 * unitA_1.get_SI_factor();
D = -2.5e-5;
A2 = 2e18 * unitA_0.get_SI_factor();
D2 = -5e-3;
k.push_back(Bert(T,A,D) / (1./tot_dens + Bert(T,A,D)/Bert(T,A2,D2)) );
//NO -> N + O
A = 5.e+12 * unitA_1.get_SI_factor();
Ea = 149943.0;
A2 = 3e+15 * unitA_0.get_SI_factor();
Ea2 = 200000.0;
k.push_back(Arrh(T,A,Ea,Rcal) / (1./tot_dens + Arrh(T,A,Ea,Rcal)/Arrh(T,A2,Ea2,Rcal)) );
//N2 + O -> NO + N
A = 5e+9 * unitA_2.get_SI_factor();
beta = 0.6;
D = -5e-4;
A2 = 5.7e+9 * unitA_1.get_SI_factor();
beta2 = -0.42;
D2 = -5e-3;
k.push_back(BHE(T,A,beta,D) / (1./tot_dens + BHE(T,A,beta,D)/BHE(T,A2,beta2,D2)) );
//NO + O -> NO + N
A = 8.4e+09 * unitA_2.get_SI_factor();
beta = 0.40;
Ea = 38526.0;
A2 = 8.4e+05 * unitA_1.get_SI_factor();
beta2 = 0.02;
Ea2 = 3526.0;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) / (1./tot_dens + Kooij(T,A,beta,Ea,Tr,Rcal)/Kooij(T,A2,beta2,Ea2,Tr,Rcal)) );
//C2 -> 2 C
A = 3.7e+11 * unitA_1.get_SI_factor();
beta = -0.42;
Ea = 138812.8;
A2 = 3.7e+12 * unitA_0.get_SI_factor();
beta2 = -0.52;
Ea2 = 135000.8;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) / (1./tot_dens + Kooij(T,A,beta,Ea,Tr,Rcal)/Kooij(T,A2,beta2,Ea2,Tr,Rcal)) );
//CN -> C + N
A = 5e+10 * unitA_1.get_SI_factor();
beta = -0.10;
D = 1.5e-3;
Ea = 150240.9;
A2 = 2.5e+11 * unitA_0.get_SI_factor();
beta2 = 0.40;
D2 = -0.005;
Ea2 = 174240.9;
k.push_back(VH(T,A,beta,Ea,D,Tr,Rcal) / (1./tot_dens + VH(T,A,beta,Ea,D,Tr,Rcal)/VH(T,A2,beta2,Ea2,D2,Tr,Rcal)) );
//Troe falloff
//falloff is k(T,[M]) = k0*[M]/(1 + [M]*k0/kinf) * F = k0 * ([M]^-1 + k0 * kinf^-1)^-1 * F
// F is complicated...
Scalar Pr,k0,kinf;
Scalar Fc,alpha,T1,T2,T3;
alpha = 0.562;
T1 = 5836;
T2 = 8552;
T3 = 91;
Fc = FcentTroe(T,alpha,T3,T1,T2);
// N2 -> 2 N
A = 7.e+18 * unitA_1.get_SI_factor();
beta = -1.6;
A2 = 5.e+15 * unitA_0.get_SI_factor();
beta2 = 0.5;
k0 = HE(T,A,beta);
kinf = HE(T,A2,beta2);
Pr = tot_dens * k0/kinf;
k.push_back(k0 / (1./tot_dens + k0/kinf) * FTroe(Fc,Pr));
// O2 -> 2 O
A = 5e17 * unitA_1.get_SI_factor();
D = -2.5e-5;
A2 = 2e18 * unitA_0.get_SI_factor();
D2 = -5e-3;
k0 = Bert(T,A,D);
kinf = Bert(T,A2,D2);
Pr = tot_dens * k0/kinf;
k.push_back(k0 / (1./tot_dens + k0/kinf) * FTroe(Fc,Pr));
//NO -> N + O
A = 5.e+12 * unitA_1.get_SI_factor();
Ea = 149943.0;
A2 = 3e+15 * unitA_0.get_SI_factor();
Ea2 = 200000.0;
k0 = Arrh(T,A,Ea,Rcal);
kinf = Arrh(T,A2,Ea2,Rcal);
Pr = tot_dens * k0/kinf;
k.push_back(k0 / (1./tot_dens + k0/kinf) * FTroe(Fc,Pr));
//N2 + O -> NO + N
A = 5e+9 * unitA_2.get_SI_factor();
beta = 0.6;
D = -5e-4;
A2 = 5.7e+9 * unitA_1.get_SI_factor();
beta2 = -0.42;
D2 = -5e-3;
k0 = BHE(T,A,beta,D);
kinf = BHE(T,A2,beta2,D2);
Pr = tot_dens * k0/kinf;
k.push_back(k0 / (1./tot_dens + k0/kinf) * FTroe(Fc,Pr));
//NO + O -> NO + N
A = 8.4e+09 * unitA_2.get_SI_factor();
beta = 0.40;
Ea = 38526.0;
A2 = 8.4e+05 * unitA_1.get_SI_factor();
beta2 = 0.02;
Ea2 = 3526.0;
k0 = Kooij(T,A,beta,Ea,Tr,Rcal);
kinf = Kooij(T,A2,beta2,Ea2,Tr,Rcal);
Pr = tot_dens * k0/kinf;
k.push_back(k0 / (1./tot_dens + k0/kinf) * FTroe(Fc,Pr));
//C2 -> 2 C
A = 3.7e+11 * unitA_1.get_SI_factor();
beta = -0.42;
Ea = 138812.8;
A2 = 3.7e+12 * unitA_0.get_SI_factor();
beta2 = -0.52;
Ea2 = 135000.8;
k0 = Kooij(T,A,beta,Ea,Tr,Rcal);
kinf = Kooij(T,A2,beta2,Ea2,Tr,Rcal);
Pr = tot_dens * k0/kinf;
k.push_back(k0 / (1./tot_dens + k0/kinf) * FTroe(Fc,Pr));
//CN -> C + N
A = 5e+10 * unitA_1.get_SI_factor();
beta = -0.10;
D = 1.5e-3;
Ea = 150240.9;
A2 = 2.5e+11 * unitA_0.get_SI_factor();
beta2 = 0.40;
D2 = -0.005;
Ea2 = 174240.9;
k0 = VH(T,A,beta,Ea,D,Tr,Rcal);
kinf = VH(T,A2,beta2,Ea2,D2,Tr,Rcal);
Pr = tot_dens * k0/kinf;
k.push_back(k0 / (1./tot_dens + k0/kinf) * FTroe(Fc,Pr));
//
//photochemistry
k.push_back(k_photo(lambda,hv,CH4_lambda,CH4_s));
conditions.add_particle_flux(photons,k.size()-1);
//Constant
k.push_back(2.5e11);
const Scalar tol = (std::numeric_limits<Scalar>::epsilon() < 1e-17L)?
std::numeric_limits<Scalar>::epsilon() * 5000:
std::numeric_limits<Scalar>::epsilon() * 100;
int return_flag(0);
for(unsigned int ir = 0; ir < k.size(); ir++)
{
const Antioch::Reaction<Scalar> * reac = &reaction_set.reaction(ir);
if(std::abs(k[ir] - reac->compute_forward_rate_coefficient(molar_densities,conditions))/k[ir] > tol)
{
std::cout << *reac << std::endl;
std::cout << std::scientific << std::setprecision(16)
<< "Error in kinetics comparison\n"
<< "reaction #" << ir << "\n"
<< "temperature: " << T << " K" << "\n"
<< "theory: " << k[ir] << "\n"
<< "calculated: " << reac->compute_forward_rate_coefficient(molar_densities,conditions) << "\n"
<< "relative error = " << std::abs(k[ir] - reac->compute_forward_rate_coefficient(molar_densities,conditions))/k[ir] << "\n"
<< "tolerance = " << tol
<< std::endl;
return_flag = 1;
}
}
return return_flag;
}
SVDInfo ScaLAPACKHelper
( const AbstractDistMatrix<F>& APre,
AbstractDistMatrix<F>& UPre,
AbstractDistMatrix<Base<F>>& sPre,
AbstractDistMatrix<F>& V,
const SVDCtrl<Base<F>>& ctrl )
{
DEBUG_CSE
AssertScaLAPACKSupport();
SVDInfo info;
#ifdef EL_HAVE_SCALAPACK
typedef Base<F> Real;
DistMatrix<F,MC,MR,BLOCK> A( APre );
DistMatrixWriteProxy<Real,Real,STAR,STAR> sProx(sPre);
DistMatrixWriteProxy<F,F,MC,MR,BLOCK> UProx(UPre);
auto& s = sProx.Get();
auto& U = UProx.Get();
const int m = A.Height();
const int n = A.Width();
const int k = Min(m,n);
auto approach = ctrl.bidiagSVDCtrl.approach;
if( approach == THIN_SVD || approach == COMPACT_SVD )
{
Zeros( U, m, k );
DistMatrix<F,MC,MR,BLOCK> VH( A.Grid() );
Zeros( VH, k, n );
s.Resize( k, 1 );
auto descA = FillDesc( A );
auto descU = FillDesc( U );
auto descVH = FillDesc( VH );
scalapack::SVD
( m, n,
A.Buffer(), descA.data(),
s.Buffer(),
U.Buffer(), descU.data(),
VH.Buffer(), descVH.data() );
const bool compact = ( approach == COMPACT_SVD );
if( compact )
{
const Real twoNorm = ( k==0 ? Real(0) : s.Get(0,0) );
const Real thresh =
bidiag_svd::APosterioriThreshold
( m, n, twoNorm, ctrl.bidiagSVDCtrl );
Int rank = k;
for( Int j=0; j<k; ++j )
{
if( s.Get(j,0) <= thresh )
{
rank = j;
break;
}
}
s.Resize( rank, 1 );
U.Resize( m, rank );
VH.Resize( rank, n );
}
Adjoint( VH, V );
}
else
LogicError
("Only Thin and Compact singular value options currently supported");
#endif
return info;
}
int tester(const std::string &input_name)
{
std::vector<std::string> species_str_list;
species_str_list.push_back( "N2" );
species_str_list.push_back( "O2" );
species_str_list.push_back( "N" );
species_str_list.push_back( "O" );
species_str_list.push_back( "NO" );
species_str_list.push_back( "C" );
species_str_list.push_back( "C2" );
species_str_list.push_back( "CN" );
unsigned int n_species = species_str_list.size();
Antioch::ChemicalMixture<Scalar> chem_mixture( species_str_list );
Antioch::ReactionSet<Scalar> reaction_set( chem_mixture );
Antioch::read_reaction_set_data_xml<Scalar>( input_name, true, reaction_set );
Scalar T = 2000.L;
Scalar Tr = 1.;
Scalar Rcal = 1.9858775;
// Molar densities
std::vector<Scalar> molar_densities(n_species,5e-4);
///Elementary, + Kooij - Arrhenius conversion tested
std::vector<Scalar> k;
Scalar A,beta,Ea,D;
A = 7e18;
beta = -1.6;
k.push_back(HE(T,A,beta));
A = 2e18;
D = -5e-3;
k.push_back(Bert(T,A,D));
A = 5e12;
Ea = 149943.0;
k.push_back(Arrh(T,A,Ea,Rcal));
beta = 0.42;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal));
A = 5.7e9;
beta = 0.42;
k.push_back(BHE(T,A,beta,D));
A = 8.4e9;
beta = 0.4;
Ea = 38526.0;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal));
k.push_back(Arrh(T,A,Ea,Rcal));
A = 3.7e11;
beta = -0.42;
Ea = 138812.8;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal));
A = 2.5e11;
beta = 0.40;
Ea = 174240.9;
D = 0.05;
k.push_back(VH(T,A,beta,Ea,D,Tr,Rcal));
///Duplicate
Scalar A2,beta2,Ea2,D2,A3,beta3,Ea3,D3,A4,Ea4;
A = 7e18;
beta = -1.6;
A2 = 5e17;
beta2 = 0.5;
A3 = 3e18;
beta3 = -0.6;
k.push_back(HE(T,A,beta) + HE(T,A2,beta2) + HE(T,A3,beta3));
A = 2e18;
D = -5e-2;
A2 = 2e+16;
D2 = 0.003;
k.push_back(Bert(T,A,D) + Bert(T,A2,D2));
A = 5e+12;
Ea = 149943.0;
A2 = 3.5e+10;
Ea2 = 1943.0;
A3 = 1.5e+8;
Ea3 = 149.0;
A4 = 5.5e+8;
Ea4 = 943.0;
k.push_back(Arrh(T,A,Ea,Rcal) + Arrh(T,A2,Ea2,Rcal) + Arrh(T,A3,Ea3,Rcal) + Arrh(T,A4,Ea4,Rcal));
A = 5.7e+9;
beta = 0.42;
D = -5e-3;
A2 = 7e+7;
beta2 = 0.5;
D2 = 2.5e-5;
k.push_back(BHE(T,A,beta,D) + BHE(T,A2,beta2,D2));
A = 8.4e+09;
beta = 0.40;
Ea = 38526.0;
A2 = 4e+07;
beta2 = 0.50;
Ea2 = 40500.0;
A3 = 5e+10;
beta3 = 0.10;
Ea3 = 15000.0;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) + Kooij(T,A2,beta2,Ea2,Tr,Rcal) + Kooij(T,A3,beta3,Ea3,Tr,Rcal));
A = 3.7e+11;
beta = -0.42;
Ea = 138812.8;
A2 = 5.0e+10;
beta2 = 1.32;
Ea2 = 150500.8;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) + Kooij(T,A2,beta2,Ea2,Tr,Rcal));
A = 2.5e+11;
beta = 0.40;
D = -5e-3;
Ea = 174240.9;
A2 = 5e+10;
beta2 = 0.50;
D2 = -1.5e-2;
Ea2 = 4240.9;
A3 = 3.2e+10;
beta3 = 1.20;
D3 = -2.5e-5;
Ea3 = 174.9;
k.push_back(VH(T,A,beta,Ea,D,Tr,Rcal) + VH(T,A2,beta2,Ea2,D2,Tr,Rcal) + VH(T,A3,beta3,Ea3,D3,Tr,Rcal));
//three body
A = 7e18;
beta = -1.6;
Ea = 149943.0;
k.push_back(HE(T,A,beta) * (Scalar(n_species) - 2. + 4.2857 + 4.2857) * 5e-4);
A = 2e18;
D = -5e-3;
k.push_back(Bert(T,A,D) * (Scalar(n_species) - 2. + 5.0 + 5.0) * 5e-4);
A = 5e12;
k.push_back(Arrh(T,A,Ea,Rcal) * (Scalar(n_species) - 3. + 22.0 + 22.0 + 22.0) * 5e-4);
A = 5.7e9;
beta = 0.42;
D = -5e-3;
k.push_back(BHE(T,A,beta,D) * (Scalar(n_species) - 3. + 22.0 + 22.0 + 22.0) * 5e-4);
A = 8.4e9;
beta = 0.4;
Ea = 38526.0;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) * (Scalar(n_species) - 3. + 22.0 + 22.0 + 22.0) * 5e-4);
A = 3.7e11;
beta = -0.42;
Ea = 138812.8;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) * Scalar(n_species) * 5e-4);
A = 2.5e11;
beta = 0.40;
Ea = 729372.4;
D = 5e-3;
k.push_back(VH(T,A,beta,Ea,D) * Scalar(n_species) * 5e-4);
///Lindemann Falloff
// falloff is k(T,[M]) = k0*[M]/(1 + [M]*k0/kinf) * F = k0 * ([M]^-1 + k0 * kinf^-1)^-1 * F
// F = 1
A = 7e18;
beta = -1.6;
A2 = 5e15;
beta2 = 0.5;
k.push_back(HE(T,A,beta) / (1./4e-3 + HE(T,A,beta)/HE(T,A2,beta2)) );
A = 5e17;
D = -2.5e-5;
A2 = 2e18;
D2 = -5e-3;
k.push_back(Bert(T,A,D) / (1./4e-3 + Bert(T,A,D)/Bert(T,A2,D2)) );
A = 5.e+12;
Ea = 149943.0;
A2 = 3e+15;
Ea2 = 200000.0;
k.push_back(Arrh(T,A,Ea,Rcal) / (1./4e-3 + Arrh(T,A,Ea,Rcal)/Arrh(T,A2,Ea2,Rcal)) );
A = 5e+9;
beta = 0.6;
D = -5e-4;
A2 = 5.7e+9;
beta2 = -0.42;
D2 = -5e-3;
k.push_back(BHE(T,A,beta,D) / (1./4e-3 + BHE(T,A,beta,D)/BHE(T,A2,beta2,D2)) );
A = 8.4e+09;
beta = 0.40;
Ea = 38526.0;
A2 = 8.4e+05;
beta2 = 0.02;
Ea2 = 3526.0;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) / (1./4e-3 + Kooij(T,A,beta,Ea,Tr,Rcal)/Kooij(T,A2,beta2,Ea2,Tr,Rcal)) );
A = 3.7e+11;
beta = -0.42;
Ea = 138812.8;
A2 = 3.7e+12;
beta2 = -0.52;
Ea2 = 135000.8;
k.push_back(Kooij(T,A,beta,Ea,Tr,Rcal) / (1./4e-3 + Kooij(T,A,beta,Ea,Tr,Rcal)/Kooij(T,A2,beta2,Ea2,Tr,Rcal)) );
A = 5e+10;
beta = -0.10;
D = 1.5e-3;
Ea = 150240.9;
A2 = 2.5e+11;
beta2 = 0.40;
D2 = -0.005;
Ea2 = 174240.9;
k.push_back(VH(T,A,beta,Ea,D,Tr,Rcal) / (1./4e-3 + VH(T,A,beta,Ea,D,Tr,Rcal)/VH(T,A2,beta2,Ea2,D2,Tr,Rcal)) );
//Troe falloff
//falloff is k(T,[M]) = k0*[M]/(1 + [M]*k0/kinf) * F = k0 * ([M]^-1 + k0 * kinf^-1)^-1 * F
// F is complicated...
Scalar Pr,k0,kinf;
Scalar Fc,alpha,T1,T2,T3;
alpha = 0.562;
T1 = 5836;
T2 = 8552;
T3 = 91;
Fc = FcentTroe(T,alpha,T3,T1,T2);
A = 7.e+18;
beta = -1.6;
A2 = 5.e+15;
beta2 = 0.5;
k0 = HE(T,A,beta);
kinf = HE(T,A2,beta2);
Pr = 4e-3 * k0/kinf;
k.push_back(k0 / (1./4e-3 + k0/kinf) * FTroe(Fc,Pr));
A = 5e17;
D = -2.5e-5;
A2 = 2e18;
D2 = -5e-3;
k0 = Bert(T,A,D);
kinf = Bert(T,A2,D2);
Pr = 4e-3 * k0/kinf;
k.push_back(k0 / (1./4e-3 + k0/kinf) * FTroe(Fc,Pr));
A = 5.e+12;
Ea = 149943.0;
A2 = 3e+15;
Ea2 = 200000.0;
k0 = Arrh(T,A,Ea,Rcal);
kinf = Arrh(T,A2,Ea2,Rcal);
Pr = 4e-3 * k0/kinf;
k.push_back(k0 / (1./4e-3 + k0/kinf) * FTroe(Fc,Pr));
A = 5e+9;
beta = 0.6;
D = -5e-4;
A2 = 5.7e+9;
beta2 = -0.42;
D2 = -5e-3;
k0 = BHE(T,A,beta,D);
kinf = BHE(T,A2,beta2,D2);
Pr = 4e-3 * k0/kinf;
k.push_back(k0 / (1./4e-3 + k0/kinf) * FTroe(Fc,Pr));
A = 8.4e+09;
beta = 0.40;
Ea = 38526.0;
A2 = 8.4e+05;
beta2 = 0.02;
Ea2 = 3526.0;
k0 = Kooij(T,A,beta,Ea,Tr,Rcal);
kinf = Kooij(T,A2,beta2,Ea2,Tr,Rcal);
Pr = 4e-3 * k0/kinf;
k.push_back(k0 / (1./4e-3 + k0/kinf) * FTroe(Fc,Pr));
A = 3.7e+11;
beta = -0.42;
Ea = 138812.8;
A2 = 3.7e+12;
beta2 = -0.52;
Ea2 = 135000.8;
k0 = Kooij(T,A,beta,Ea,Tr,Rcal);
kinf = Kooij(T,A2,beta2,Ea2,Tr,Rcal);
Pr = 4e-3 * k0/kinf;
k.push_back(k0 / (1./4e-3 + k0/kinf) * FTroe(Fc,Pr));
A = 5e+10;
beta = -0.10;
D = 1.5e-3;
Ea = 150240.9;
A2 = 2.5e+11;
beta2 = 0.40;
D2 = -0.005;
Ea2 = 174240.9;
k0 = VH(T,A,beta,Ea,D,Tr,Rcal);
kinf = VH(T,A2,beta2,Ea2,D2,Tr,Rcal);
Pr = 4e-3 * k0/kinf;
k.push_back(k0 / (1./4e-3 + k0/kinf) * FTroe(Fc,Pr));
const Scalar tol = std::numeric_limits<Scalar>::epsilon() * 100;
int return_flag(0);
for(unsigned int ir = 0; ir < k.size(); ir++)
{
const Antioch::Reaction<Scalar> * reac = &reaction_set.reaction(ir);
if(std::abs(k[ir] - reac->compute_forward_rate_coefficient(molar_densities,T))/k[ir] > tol)
{
std::cout << std::scientific << std::setprecision(16)
<< "Error in kinetics comparison\n"
<< "reaction #: " << ir << "\n"
<< "theory: " << k[ir] << "\n"
<< "calculated: " << reac->compute_forward_rate_coefficient(molar_densities,T) << "\n"
<< "relative error = " << std::abs(k[ir] - reac->compute_forward_rate_coefficient(molar_densities,T))/k[ir] << "\n"
<< "tolerance = " << tol
<< std::endl;
return_flag = 1;
}
}
return return_flag;
}
int Pseudoinverse(
size_t m, size_t n,
const doublecomplex *A, size_t lda,
doublecomplex *P, size_t ldp
){
integer info;
CMat Acopy(Eigen::Map<const CMat,Eigen::Unaligned,Eigen::OuterStride<> >(A, m, n, Eigen::OuterStride<>(lda)));
Eigen::Map<CMat,Eigen::Unaligned,Eigen::OuterStride<> > mP(P, n, m, Eigen::OuterStride<>(ldp));
if(m >= n){ // tall case
RVec S(n);
CMat VH(n,n);
doublecomplex dum;
integer lwork = -1;
RVec rwork(5*n);
zgesvd_(
"O","A", m,n, Acopy.data(), Acopy.outerStride(),
S.data(), NULL, m, VH.data(), VH.outerStride(),
&dum, lwork, rwork.data(), &info
);
lwork = (integer)dum.real();
CVec work(lwork);
zgesvd_(
"O","A", m,n, Acopy.data(), Acopy.outerStride(),
S.data(), NULL, m, VH.data(), VH.outerStride(),
work.data(), lwork, rwork.data(), &info
);
mP = Acopy.adjoint();
{
double threshold = 2 * std::numeric_limits<double>::epsilon() * S[0];
for(size_t i = 0; i < n; ++i){
if(S[i] < threshold){
break;
}
S[i] = 1./S[i];
}
}
mP = VH.adjoint() * S.asDiagonal() * mP;
}else{ // wide case
RVec S(m);
CMat U(m,m);
doublecomplex dum;
integer lwork = -1;
RVec rwork(5*m);
zgesvd_(
"A","O", m,n, Acopy.data(), Acopy.outerStride(),
S.data(), U.data(), U.outerStride(), NULL, m,
&dum, lwork, rwork.data(), &info
);
lwork = (integer)dum.real();
CVec work(lwork);
zgesvd_(
"A","O", m,n, Acopy.data(), Acopy.outerStride(),
S.data(), U.data(), U.outerStride(), NULL, m,
work.data(), lwork, rwork.data(), &info
);
mP = Acopy.adjoint();
{
double threshold = 2 * std::numeric_limits<double>::epsilon() * S[0];
for(size_t i = 0; i < m; ++i){
if(S[i] < threshold){
break;
}
S[i] = 1./S[i];
}
}
mP = mP * S.asDiagonal() * U.adjoint();
}
return info;
}
