void Model_cell::run() {
if (this->timeCounter == 0 || ((this->timeCounter + 1) % trajOutputInterval == 0)) {
this->outputTrajectory(this->trajOs);
}
Eigen::MatrixXd randomDispMat;
randomDispMat.setRandom(3, numP);
calForces();
for (int i = 0; i < numP; i++) {
// cellInfo[i]->polarization.fill(-1);
// int oldIdx = particles[i]->meshFaceIdx;
// if (i == 146)
// std::cerr << "polarization"<<cellInfo[i]->polarization << std::endl;
particles[i]->vel = cellInfo[i]->polarization*polar_vel + particles[i]->F;
cellInfo[i]->polarization *= (1 - dt_ / tau);
cellInfo[i]->polarization += sqrt(2.0*sigma*dt_) * randomDispMat.col(i) + (beta * cellInfo[i]->inhibition)*dt_;
// for (int j = 0; j < 3; j++){
// if (std::isnan(cellInfo[i]->polarization[j])){
// std::cerr << "particle vel NaN at step" << this->timeCounter << "\t" << i << std::endl;
// std::cerr << particles[i]->r << std::endl;
// std::cerr << particles[i]->vel << std::endl;
// std::cerr << "polarization"<<cellInfo[i]->polarization << std::endl;
// std::cerr <<"force" <<particles[i]->F << std::endl;
// std::cerr << cellInfo[i]->inhibition << std::endl;
// std::cerr << randomDispMat.col(i) << std::endl;
// exit(1);
// }
// }
this->moveOnMesh(i);
}
this->timeCounter++;
}
void Model::run() {
if (this->timeCounter == 0 || ((this->timeCounter + 1) % trajOutputInterval == 0)) {
this->outputTrajectory(this->trajOs);
}
calForces();
Eigen::MatrixXd randomDispMat;
randomDispMat.setRandom(3,numP);
// omp_set_num_threads(1);
#pragma omp parallel default(shared)
{// std::cout << omp_get_num_threads() << std::endl;
#pragma omp for schedule(dynamic)
for (int i = 0; i < numP; i++) {
// Eigen::Vector3d velocity;
for (int j = 0; j < 3; j++){
// particles[i]->F(j) = 0.0;
particles[i]->vel(j) = diffusivity_t * particles[i]->F(j) + sqrt(2.0 * diffusivity_t/dt_) * randomDispMat(j,i);
}
// particles[i]->vel = velocity;
/* Obtain thread number */
// int tid = omp_get_thread_num();
// printf("Hello World from thread = %d\n", tid);
// std::cout << omp_get_num_threads() << std::endl;
// std::cout << numP << std::endl;
// std::cout << velocity << std::endl;
this->moveOnMesh(i);
}
}
// this->moveOnMesh_OMP();
this->timeCounter++;
}
void Model::run() {
if (this->timeCounter == 0 || ((this->timeCounter + 1) % trajOutputInterval == 0)) {
this->outputTrajectory(this->trajOs);
}
Eigen::MatrixXd randomDispMat;
randomDispMat.setRandom(3,numP);
calForces();
for (int i = 0; i < numP; i++) {
Eigen::Vector3d velocity;
for (int j = 0; j < 3; j++){
velocity(j) = diffusivity_t * particles[i]->F(j) + sqrt(2.0 * diffusivity_t/dt_) * randomDispMat(j,i);
}
this->moveOnMesh(i);
}
this->timeCounter++;
}
void IRLTest::generateData()
{
int num_active_features;
int num_data;
int num_samples_per_data;
double cost_noise_stddev;
num_features_ = 10;
num_active_features = 2;
num_data = 10;
num_samples_per_data = 10;
cost_noise_stddev = 0.1;
// generate random weights
real_weights_ = Eigen::VectorXd::Zero(num_features_);
real_weights_.head(num_active_features).setRandom();
data_.resize(num_data);
for (int i=0; i<num_data; ++i)
{
IRLData* d = new IRLData(num_features_);
Eigen::MatrixXd features = Eigen::MatrixXd::Zero(num_samples_per_data, num_features_);
Eigen::VectorXd target = Eigen::VectorXd::Zero(num_samples_per_data);
features.setRandom();
// compute w^t * phi
Eigen::VectorXd costs = features*real_weights_;
// add random noise to costs
costs += cost_noise_stddev * Eigen::VectorXd::Random(num_samples_per_data);
// set min cost target to 1
int min_index;
double min_cost = costs.minCoeff(&min_index);
target(min_index) = 1.0;
d->addSamples(features, target);
data_[i].reset(d);
}
real_weights_exist_ = true;
}