void read_cladistic_tensor(std::ifstream& inFile,
RealTensor& F,
StateTreeVector& S)
{
g_lineNumber = 0;
inFile >> F;
F.setLabels(inFile);
std::string line;
gm::getline(inFile, line);
S = StateTreeVector(F.n(), StateTree(F.k()));
for (int c = 0; c < F.n(); ++c)
{
try
{
inFile >> S[c];
}
catch (std::runtime_error& e)
{
std::cerr << "State tree file. " << getLineNumber() << e.what() << std::endl;
exit(1);
}
}
}
void NonlinearNeoHookeCurrentConfig::calculate_stress()
{
double mu = E / (2.0 * (1.0 + nu));
double lambda = E * nu / ((1 + nu) * (1 - 2 * nu));
Real detF = F.det();
RealTensor Ft = F.transpose();
RealTensor C = Ft * F;
RealTensor b = F * Ft;
RealTensor identity;
identity(0, 0) = 1.0; identity(1, 1) = 1.0; identity(2, 2) = 1.0;
RealTensor invC = C.inverse();
S = 0.5 * lambda * (detF * detF - 1) * invC + mu * (identity - invC);
tau = (F * S) * Ft;
sigma = 1/detF * tau;
}
void NonlinearNeoHookeCurrentConfig::init_for_qp(VectorValue<Gradient> & grad_u, unsigned int qp) {
this->current_qp = qp;
F.zero();
S.zero();
{
RealTensor invF;
invF.zero();
for (unsigned int i = 0; i < 3; ++i)
for (unsigned int j = 0; j < 3; ++j) {
invF(i, j) += libmesh_real(grad_u(i)(j));
}
F.add(inv(invF));
libmesh_assert_greater (F.det(), -TOLERANCE);
}
if (this->calculate_linearized_stiffness) {
this->calculate_tangent();
}
this->calculate_stress();
}
void NoisyCnaEnumerate::fixTrunk(const RealTensor& F_ub,
const StateTreeVector& S,
const StlIntVector& mapNewCharToOldChar,
const StlIntVector& mapOldCharToNewChar,
RootedCladisticNoisyAncestryGraph& G)
{
const int m = F_ub.m();
const int k = F_ub.k();
const int n = F_ub.n();
typedef std::set<IntPair> IntPairSet;
IntPairSet truncalCharacters;
for (int c = 0; c < n; ++c)
{
std::cerr << "Character " << _M(0, mapNewCharToOldChar[c]).characterLabel() << " (" << mapNewCharToOldChar[c] << ") : ";
S[c].writeEdgeList(std::cerr);
std::cerr << std::endl;
bool truncal = true;
int mutation_i = -1;
for (int p = 0; p < m; ++p)
{
double ccf = 0;
for (int i = 0; i < k; ++i)
{
if (!S[c].isPresent(i))
continue;
const auto& xyz = _M.stateToTriple(i);
if (xyz._z >= 1)
{
ccf += F_ub(i, p, c);
const auto& pi_xyz = _M.stateToTriple(S[c].parent(i));
if (pi_xyz._z == 0 && xyz._z == 1)
{
mutation_i = i;
}
}
}
ccf /= _purityValues[p];
if (g_tol.less(ccf, 1))
{
truncal = false;
break;
}
}
if (truncal)
{
assert(mutation_i != -1);
const StateTree& S_c = S[c];
truncalCharacters.insert(IntPair(c, mutation_i));
while ((mutation_i = S_c.parent(mutation_i)) != 0)
{
truncalCharacters.insert(IntPair(c, mutation_i));
}
}
}
std::cerr << "Truncal:" << std::endl;
for (auto ci : truncalCharacters)
{
auto xyz = _M.stateToTriple(ci.second);
std::cerr << _M(0, mapNewCharToOldChar[ci.first]).characterLabel()
<< " , (" << xyz._x << "," << xyz._y << "," << xyz._z << ")" << std::endl;
}
Digraph::Node monoClonalRoot = G.collapse(truncalCharacters);
G.makeMonoclonal(monoClonalRoot);
}
