floating_t Pyramid::calculate_link(const Node& node, const Node& desc,
spectral_distance_meassure_t spec_dst) const
{
using std::exp;
using std::isfinite;
using std::isinf;
if (link(node, desc) == 0.l
/* || 1./util::condition(value2(desc)) < 1e-6*/) {
return 0.l;
}
const auto beta_spec = -0.01;
const auto beta_vari = -0.01;
const auto beta_spat = -0.01;
auto spec_term = exp(beta_spec * spec_dst(node, desc));
auto spat_term = exp(beta_spat * spatial_distance(node, desc));
auto vari_term = exp(beta_vari * var(desc));
auto result = spec_term * vari_term * spat_term;
assert(isfinite(spec_term));
assert(isfinite(vari_term));
assert(isfinite(spat_term));
assert(isfinite(result));
return result;
}
EIGEN_STRONG_INLINE const Scalar operator() (const Scalar& a, const Scalar& b) const {
using std::isfinite;
if (isfinite(a) && isfinite(b)) return a + b;
if (isfinite(a)) return a;
if (isfinite(b)) return b;
return a + b;
}
/**
* \brief TODO
*/
static double
trunc_estim_param_bisec(const double mean, const double tol){
double lambda_low = mean-1;
double lambda_high = mean;
double lambda_mid = mean - 0.5;
double diff = std::numeric_limits<double>::max();
double prev_val = std::numeric_limits<double>::max();
while(movement(lambda_high, lambda_low) > tol &&
diff > tol){
lambda_mid = (lambda_low + lambda_high)/2;
const double mid_val = lambda_score_funct(mean, lambda_mid);
if (mid_val < 0) lambda_low = lambda_mid;
else lambda_high = lambda_mid;
diff = fabs((prev_val - mid_val)/std::max(mid_val, prev_val));
prev_val = mid_val;
}
if (!(isfinite(lambda_mid))) {
stringstream ss;
ss << "Zero-truncated Poisson parameter estimation failed. Reason: "
<< "got non-finite value for lambda";
throw DistributionException(ss.str());
}
return lambda_mid;
}
T invoke(I& integrand, P const& point)
{
using std::isfinite;
hep::projector<T> projector(this, point);
// call the integrand function with the supplied point. Distributions
// are generated here
T value = integrand.function()(point, projector);
if (value != T())
{
value *= point.weight();
if (isfinite(value))
{
accumulate(sums_[0], sums_[1], compensations_[0], value);
++finite_calls_[0];
}
else
{
value = T();
}
++non_zero_calls_[0];
}
return value;
}
/**
* \brief ZTP probability mass function in log space
*/
double
ZeroTruncatedPoisson::loglikelihood(const double y) const {
if (y==0) {
stringstream ss;
ss << "Zero-truncated Poisson log-likelihood calculation failed. Reason: "
<< "log-likelihood is undefined for response of 0";
throw DistributionException(ss.str());
}
// we're going to cast y from double to size_t, but be careful doing it..
double intpart;
if ((y < 0) || (!(modf(y, &intpart) == 0.0))) {
stringstream ss;
ss << "evaluating ZTNB PDF value at " << y << " failed. "
<< "Reason: " << y << " is not a non-negative integer";
throw DistributionException(ss.str());
}
double res = (-this->lambda + (y*log(this->lambda)) -
gsl_sf_lnfact(size_t(y))) - log(1-exp(-this->lambda));
if (!(isfinite(res))) {
stringstream ss;
ss << "Zero-truncated Poisson log-likelihood calculation failed. Reason: "
<< "got non-finite value for response of " << y << " with "
<< "distribution parameters of " << this->toString();
throw DistributionException(ss.str());
}
return res;
}
T invoke(I& integrand, P const& point)
{
using std::isfinite;
// call the integrand function with the supplied point. No distributions
// are generated here
T value = integrand.function()(point);
if (value != T())
{
value *= point.weight();
if (isfinite(value))
{
accumulate(sums_[0], sums_[1], sums_[2], value);
++finite_calls_;
}
else
{
value = T();
}
++non_zero_calls_;
}
return value;
}
int luaV_tostring (lua_State *L, StkId obj) {
if (!ttisnumber(obj))
return 0;
else {
char s[LUAI_MAXNUMBER2STR];
lua_Number n = nvalue(obj);
// SPRING -- synced safety change
// -- need a custom number formatter?
if (isfinite(n)) {
lua_number2str(s, n);
}
else {
if (isnan(n)) {
strcpy(s, "nan");
}
else {
const int inf_type = isinf(n);
if (inf_type == 1) {
strcpy(s, "+inf");
} else if (inf_type == -1) {
strcpy(s, "-inf");
} else {
strcpy(s, "weird_number");
}
}
}
setsvalue2s(L, obj, luaS_new(L, s));
return 1;
}
}
void add_to_2d_distribution(std::size_t index, T x, T y, T value)
{
using std::isfinite;
if (!isfinite(value))
{
return;
}
// TODO: index might be larger than the than allowed; throw?
auto const parameters = parameters_.at(index);
T const shifted_x = x - parameters.x_min();
if (shifted_x < T())
{
// point is outside the binning range
return;
}
T const shifted_y = y - parameters.y_min();
if (shifted_y < T())
{
// point is outside the binning range
return;
}
std::size_t const bin_x = shifted_x / parameters.bin_size_x();
if (bin_x >= parameters.bins_x())
{
// point is right of the range that we are binning
return;
}
std::size_t const bin_y = shifted_y / parameters.bin_size_y();
if (bin_y >= parameters.bins_y())
{
return;
}
std::size_t const new_index = indices_.at(index) + 2 * (bin_y *
parameters.bins_x() + bin_x);
accumulate(
sums_.at(new_index),
sums_.at(new_index + 1),
compensations_.at(new_index / 2),
value
);
// FIXME: if this function is called more than once, the values are
// incorrect
++non_zero_calls_.at(new_index / 2);
++finite_calls_.at(new_index / 2);
}
void print_nonfinite(const FloatType& x, const Node& node, const Node& dst)
{
using namespace std;
if (!isfinite(x)) {
cerr << endl
<< util::RED << "Non-finite weight " << x << "\tfrom " << node
<< "\tto " << dst << util::RESET << flush;
}
}
void print_nonfinite(const FloatType& x, const Node& node)
{
using namespace std;
if (!isfinite(x)) {
cerr << endl
<< util::RED << "Non-finite element " << x << "\tat " << node
<< util::RESET << flush;
}
}
bool TestExpDalpha(const MatrixXd& expDalpha) {
for (int j = 0; j < expDalpha.cols(); j++) {
for (int i = 0; i < expDalpha.rows(); i++) {
if (isfinite(expDalpha(i, j)) == 0) {
return false;
}
}
}
return true;
}
// check 3 term recurrence to avoid non-positive elements
// truncate if non-positive element found
static void
check_three_term_relation(vector<double> &a,
vector<double> &b){
// first entry is zero! Abort
if(a[0] <= 0.0){
a.clear();
b.clear();
}
for(size_t i = 0; i < b.size(); i++){
if(b[i] <= 0.0 || !isfinite(b[i])
|| a[i + 1] <= 0.0 || !isfinite(a[i + 1])){
b.resize(i);
a.resize(i + 1);
break;
}
}
}
/**
* \brief randomize the parameters for this distribution. In the case of the
* ZTP this just selects a random value for lambda between 0 and
* MAX_RANDOM_LAMBDA
*/
void
ZeroTruncatedPoisson::randomise() {
this->lambda = (rand() / double(RAND_MAX)) * MAX_RANDOM_LAMBDA;
if (!(isfinite(this->lambda))) {
stringstream ss;
ss << "Randomizing zero-truncated Poisson failed. Reason: "
<< "got non-finite value for lambda";
throw DistributionException(ss.str());
}
}
void DPmatrix::compute_Pr_sum_all_paths()
{
const int I = size1()-1;
const int J = size2()-1;
double total = 0.0;
for(int state1=0;state1<nstates();state1++)
total += (*this)(I,J,state1)*GQ(state1,endstate());
Pr_total = pow(efloat_t(2.0),scale(I,J)) * total;
assert(not isnan(log(Pr_total)) and isfinite(log(Pr_total)));
}
void TestExpDalpha(const MatrixXd& D, MatrixXd& alpha, MatrixXd& expDalpha) {
for (int j = 0; j < expDalpha.cols(); j++) {
for (int i = 0; i < expDalpha.rows(); i++) {
if (isfinite(expDalpha(i, j)) == 0 ||
expDalpha(i, j) > MAX_EXPDALPHA_VAL ||
expDalpha(i, j) <-MAX_EXPDALPHA_VAL) {
alpha.block(0, j, alpha.rows(), 1).noalias() = MatrixXd::Zero(alpha.rows(), 1);
expDalpha.block(0, j, expDalpha.rows(), 1).noalias() = MatrixXd::Identity(expDalpha.rows(), 1);
break;
}
}
}
}
void ConvolvedSpikeTrain::UpdateExponentialVectors() {
if (size > 0) {
for (unsigned int i=0; i<size; ++i) {
exp_pos[i] = exp((long double)(spikes[i]/tau));
exp_neg[i] = exp((long double)(-spikes[i]/tau));
}
/* Check if any over/underflow occurred while calculating the
* exponentials */
if (tau!=0 && (exp_neg.front()==0 || !isfinite(exp_pos.back()))) {
throw overflow_error("tau is too small compared to the spike times. Please use a larger value for tau, or shorter spike trains.");
}
}
}
void DPmatrixConstrained::compute_Pr_sum_all_paths()
{
const int I = size1()-1;
const int J = size2()-1;
double total = 0.0;
for(int s1=0;s1<states(J).size();s1++) {
int S1 = states(J)[s1];
total += (*this)(I,J,S1)*GQ(S1,endstate());
}
Pr_total = pow(efloat_t(2.0),scale(I,J)) * total;
assert(not isnan(log(Pr_total)) and isfinite(log(Pr_total)));
}
bool
Modification::isFinite() const
{
return isfinite(m_transform.sx) &&
isfinite(m_transform.shy) &&
isfinite(m_transform.shx) &&
isfinite(m_transform.sy) &&
isfinite(m_transform.tx) &&
isfinite(m_transform.ty);
}
/****
* \brief Set the parameters for this zero-truncated Poisson distribution
* \param params a vector with only a single value in it, which is the value
* of lambda
* \throws DistributionException if more than one value is given in params
*/
void
ZeroTruncatedPoisson::setParams(const vector<double>& params) {
if (params.size() != 1) {
stringstream ss;
ss << "Setting parameters for zero-truncated Poisson failed. Reason: "
<< "expected one parameters (lambda), but instead we got "
<< params.size() << " parameters";
throw DistributionException(ss.str());
}
if (!(isfinite(params[0]))) {
stringstream ss;
ss << "Setting parameters for zero-truncated Poisson failed. Reason: "
<< "supplied parameter value for lambda was non-finite";
throw DistributionException(ss.str());
}
this->lambda = params[0];
}
/**
* \brief read this NegativeBinomial distribution from the provided XML object
* \throws DistributionException if the XML object does not define the mean
* and alpha tags
* \todo throw exception if root tag is incorrectly named
*/
void
ZeroTruncatedPoisson::load(const SimpleXML& xml) {
vector<SimpleXML> meanX = xml.getChildren("lambda");
if (meanX.size() != 1) {
stringstream ss;
ss << "loading zero-truncated Poisson from XML object " << endl
<< xml.toString() << endl << " failed. Reason: expected a single child "
<< "tag of type <mean> -- didn't find it";
throw DistributionException(ss.str());
}
std::stringstream ss1, ss2;
ss1 << meanX[0].getData();
ss1 >> this->lambda;
if (!(isfinite(this->lambda))) {
stringstream ss;
ss << "Loading zero-truncated Poisson failed. Reason: "
<< "got non-finite value for lambda";
throw DistributionException(ss.str());
}
}
floating_t Pyramid::calculate_var(const Node& node,
spectral_distance_meassure_t spec_dst) const
{
using accumulators::extract::sum;
using common::descs;
using accumulators::sum_acc;
using std::isfinite;
auto acc = sum_acc<floating_t>{};
const auto node_norm = calculate_norm(node);
for (const auto& desc : descs(node)) {
if (link(node, desc) == 0. // skip deterministic descs
/* ||1./util::condition(value2(desc)) < 1e-6*/) {
continue;
}
else {
acc(spec_dst(node, desc) * calculate_weight(node, desc, node_norm));
}
}
auto result = sum(acc);
assert(isfinite(result));
return result;
}
void Ip2_ViscElMat_ViscElMat_ViscElPhys::Calculate_ViscElMat_ViscElMat_ViscElPhys(const shared_ptr<Material>& b1, const shared_ptr<Material>& b2, const shared_ptr<Interaction>& interaction, shared_ptr<ViscElPhys> phys) {
ViscElMat* mat1 = static_cast<ViscElMat*>(b1.get());
ViscElMat* mat2 = static_cast<ViscElMat*>(b2.get());
Real mass1 = 1.0;
Real mass2 = 1.0;
if ((isfinite(mat1->kn) and not (isfinite(mat2->kn))) or
(isfinite(mat2->kn) and not (isfinite(mat1->kn))) or
(isfinite(mat1->ks) and not (isfinite(mat2->ks))) or
(isfinite(mat2->ks) and not (isfinite(mat1->ks))) or
(isfinite(mat1->cn) and not (isfinite(mat2->cn))) or
(isfinite(mat2->cn) and not (isfinite(mat1->cn))) or
(isfinite(mat1->cs) and not (isfinite(mat2->cs))) or
(isfinite(mat2->cs) and not (isfinite(mat1->cs))) or
(isfinite(mat1->tc) and not (isfinite(mat2->tc))) or
(isfinite(mat2->tc) and not (isfinite(mat1->tc))) or
(isfinite(mat1->en) and not (isfinite(mat2->en))) or
(isfinite(mat2->en) and not (isfinite(mat1->en))) or
(isfinite(mat1->et) and not (isfinite(mat2->et))) or
(isfinite(mat2->et) and not (isfinite(mat1->et)))) {
throw runtime_error("Both materials should have the same defined set of variables e.g. tc, ks etc.!");
}
mass1 = Body::byId(interaction->getId1())->state->mass;
mass2 = Body::byId(interaction->getId2())->state->mass;
if (mass1 == 0.0 and mass2 > 0.0) {
mass1 = mass2;
} else if (mass2 == 0.0 and mass1 > 0.0) {
mass2 = mass1;
}
// See [Pournin2001, just below equation (19)]
const Real massR = mass1*mass2/(mass1+mass2);
GenericSpheresContact* sphCont=YADE_CAST<GenericSpheresContact*>(interaction->geom.get());
Real R1=sphCont->refR1>0?sphCont->refR1:sphCont->refR2;
Real R2=sphCont->refR2>0?sphCont->refR2:sphCont->refR1;
Real kn1 = 0.0; Real kn2 = 0.0;
Real cn1 = 0.0; Real cn2 = 0.0;
Real ks1 = 0.0; Real ks2 = 0.0;
Real cs1 = 0.0; Real cs2 = 0.0;
if (((isfinite(mat1->tc)) and (isfinite(mat1->en)) and (isfinite(mat1->et))) or ((tc) and (en) and (et))) {
//Set parameters according to [Pournin2001]
const Real Tc = (tc) ? (*tc)(mat1->id,mat2->id) : (mat1->tc+mat2->tc)/2.0;
const Real En = (en) ? (*en)(mat1->id,mat2->id) : (mat1->en+mat2->en)/2.0;
const Real Et = (et) ? (*et)(mat1->id,mat2->id) : (mat1->et+mat2->et)/2.0;
// Factor 2 at the end of each expression is necessary, because we calculate
// individual kn1, kn2, ks1, ks2 etc., because kn1 = 2*kn, ks1 = 2*ks
// http://www.mail-archive.com/[email protected]/msg08778.html
kn1 = kn2 = 1/Tc/Tc * ( Mathr::PI*Mathr::PI + pow(log(En),2) )*massR*2;
cn1 = cn2 = -2.0 /Tc * log(En)*massR*2;
ks1 = ks2 = 2.0/7.0 /Tc/Tc * ( Mathr::PI*Mathr::PI + pow(log(Et),2) )*massR*2;
cs1 = cs2 = -4.0/7.0 /Tc * log(Et)*massR*2;
// ^^^
// It seems to be an error in [Pournin2001] (22) Eq.4, missing factor 2
// Thanks to Dominik Boemer for pointing this out
// http://www.mail-archive.com/[email protected]/msg08741.html
if (std::abs(cn1) <= Mathr::ZERO_TOLERANCE ) cn1=0;
if (std::abs(cn2) <= Mathr::ZERO_TOLERANCE ) cn2=0;
if (std::abs(cs1) <= Mathr::ZERO_TOLERANCE ) cs1=0;
if (std::abs(cs2) <= Mathr::ZERO_TOLERANCE ) cs2=0;
} else if ((isfinite(mat1->kn)) and (isfinite(mat1->ks)) and (isfinite(mat1->cn)) and (isfinite(mat1->cs))) {
//Set parameters explicitly
kn1 = mat1->kn;
kn2 = mat2->kn;
ks1 = mat1->ks;
ks2 = mat2->ks;
cn1 = mat1->cn;
cn2 = mat2->cn;
cs1 = mat1->cs;
cs2 = mat2->cs;
} else {
//Set parameters on the base of young modulus
kn1 = 2*mat1->young*R1;
kn2 = 2*mat2->young*R2;
ks1 = kn1*mat1->poisson;
ks2 = kn2*mat2->poisson;
if ((isfinite(mat1->cn)) and (isfinite(mat1->cs))) {
cn1 = mat1->cn;
cn2 = mat2->cn;
cs1 = mat1->cs;
cs2 = mat2->cs;
}
else if( isfinite(mat1->en) and isfinite(mat1->et)) {
const Real En = (en) ? (*en)(mat1->id,mat2->id) : (mat1->en+mat2->en)/2.0;
cn1 = cn2 = 2.0*find_cn_from_en(En, massR,contactParameterCalculation(kn1,kn2),interaction);
cs1 = cs2 = 0;
}
}
const Real mR1 = mat1->mR; const Real mR2 = mat2->mR;
const int mRtype1 = mat1->mRtype; const int mRtype2 = mat2->mRtype;
phys->kn = contactParameterCalculation(kn1,kn2);
phys->ks = contactParameterCalculation(ks1,ks2);
phys->cn = contactParameterCalculation(cn1,cn2);
phys->cs = contactParameterCalculation(cs1,cs2);
if ((mR1>0) or (mR2>0)) {
phys->mR = 2.0/( ((mR1>0)?1/mR1:0) + ((mR2>0)?1/mR2:0) );
} else {
phys->mR = 0;
}
if (frictAngle) {
phys->tangensOfFrictionAngle = std::tan((*frictAngle)(mat1->id,mat2->id));
} else {
phys->tangensOfFrictionAngle = std::tan(std::min(mat1->frictionAngle, mat2->frictionAngle));
}
phys->shearForce = Vector3r(0,0,0);
if ((mRtype1 != mRtype2) or (mRtype1>2) or (mRtype2>2) or (mRtype1<1) or (mRtype2<1) ) {
throw runtime_error("mRtype should be equal for both materials and have the values 1 or 2!");
} else {
phys->mRtype = mRtype1;
}
#ifdef YADE_SPH
if (mat1->SPHmode and mat2->SPHmode) {
phys->SPHmode=true;
phys->mu=(mat1->mu+mat2->mu);
phys->h=(mat1->h+mat2->h)/2.0;
}
phys->kernelFunctionCurrentPressure = returnKernelFunction (mat1->KernFunctionPressure, mat2->KernFunctionPressure, Grad);
phys->kernelFunctionCurrentVisco = returnKernelFunction (mat1->KernFunctionVisco, mat2->KernFunctionVisco, Lapl);
#endif
}