void
LinearIsotropicMaterial::computeProperties()
{
for (_qp = 0; _qp < _qrule->n_points(); ++_qp)
{
Real alpha = computeAlpha();
_local_elasticity_tensor->calculate(_qp);
_elasticity_tensor[_qp] = *_local_elasticity_tensor;
SymmTensor strn(_grad_disp_x[_qp](0),
_grad_disp_y[_qp](1),
_grad_disp_z[_qp](2),
0.5 * (_grad_disp_x[_qp](1) + _grad_disp_y[_qp](0)),
0.5 * (_grad_disp_y[_qp](2) + _grad_disp_z[_qp](1)),
0.5 * (_grad_disp_z[_qp](0) + _grad_disp_x[_qp](2)));
// Add in Isotropic Thermal Strain
if (_has_temp)
{
Real isotropic_strain = alpha * (_temp[_qp] - _t_ref);
strn.addDiag(-isotropic_strain);
_d_strain_dT.zero();
_d_strain_dT.addDiag(-alpha);
}
SymmTensor strain(strn);
computeStress(strain, _stress[_qp]);
}
}
void
LinearIsotropicMaterial::computeProperties()
{
for (_qp=0; _qp < _qrule->n_points(); ++_qp)
{
Real alpha = computeAlpha();
_local_elasticity_tensor->calculate(_qp);
_elasticity_tensor[_qp] = *_local_elasticity_tensor;
SymmTensor strn( _grad_disp_x[_qp](0),
_grad_disp_y[_qp](1),
_grad_disp_z[_qp](2),
0.5*(_grad_disp_x[_qp](1)+_grad_disp_y[_qp](0)),
0.5*(_grad_disp_y[_qp](2)+_grad_disp_z[_qp](1)),
0.5*(_grad_disp_z[_qp](0)+_grad_disp_x[_qp](2)) );
// Add in Isotropic Thermal Strain
if (_has_temp)
{
Real isotropic_strain = alpha * (_temp[_qp] - _t_ref);
strn.addDiag( -isotropic_strain );
_d_strain_dT.zero();
_d_strain_dT.addDiag( -alpha );
}
SymmTensor v_strain(0);
SymmTensor dv_strain_dT(0);
for (unsigned int i(0); i < _volumetric_models.size(); ++i)
{
_volumetric_models[i]->modifyStrain(_qp, 1, v_strain, dv_strain_dT);
}
SymmTensor strain( v_strain );
strain *= _dt;
strain += strn;
dv_strain_dT *= _dt;
_d_strain_dT += dv_strain_dT;
computeStress(strain, _stress[_qp]);
}
}
string StringUtil::trimCopy(const string& str)
{
string strn(str);
trim(strn);
return strn;
}
string StringUtil::capitalizedCopy(const string& str)
{
string strn(str);
capitalized(strn);
return strn;
}
int phypp_main(int argc, char* argv[]) {
if (argc < 2) {
print("usage: make_shifts <ob_filter> [options]");
return 0;
}
vec1u exclude;
std::string helper;
read_args(argc-1, argv+1, arg_list(exclude, helper));
if (helper.empty()) {
error("please provide the name of (one of) the helper target you used to "
"calibrate the shifts (helper=...)");
return 1;
}
helper = tolower(helper);
std::string scis = argv[1];
vec1d cent_ra, cent_dec;
file::read_table("centroid_helper.txt", 0, cent_ra, cent_dec);
vec1u ids = uindgen(cent_ra.size())+1;
vec1u idex = where(is_any_of(ids, exclude));
inplace_remove(ids, idex);
inplace_remove(cent_ra, idex);
inplace_remove(cent_dec, idex);
std::ofstream cmb("combine.sof");
vec1d shx, shy;
vec1d x0, y0;
bool first_line = true;
uint_t nexp = 0;
for (uint_t i : range(ids)) {
std::string dir = scis+align_right(strn(ids[i]), 2, '0')+"/";
print(dir);
vec1s files = dir+file::list_files(dir+"sci_reconstructed*-sci.fits");
inplace_sort(files);
// Find out which exposures contain the helper target from which the
// shifts were calibrated
vec1u ignore;
for (uint_t k : range(files)) {
std::string f = files[k];
fits::generic_file fcubes(f);
vec1s arms(24);
bool badfile = false;
for (uint_t u : range(24)) {
if (!fcubes.read_keyword("ESO OCS ARM"+strn(u+1)+" NAME", arms[u])) {
note("ignoring invalid file '", f, "'");
note("missing keyword 'ESO OCS ARM"+strn(u+1)+" NAME'");
ignore.push_back(k);
badfile = true;
break;
}
}
if (badfile) continue;
arms = tolower(trim(arms));
vec1u ida = where(arms == helper);
if (ida.empty()) {
ignore.push_back(k);
} else if (x0.empty()) {
// Get astrometry of IFUs from first exposure
// NB: assumes the rotation is the same for all exposures,
// which is anyway what kmos_combine does later on.
fcubes.reach_hdu(ida[0]+1);
fits::wcs astro(fcubes.read_header());
fits::ad2xy(astro, cent_ra, cent_dec, x0, y0);
}
}
inplace_remove(files, ignore);
if (files.empty()) {
warning("folder ", dir, " does not contain any usable file");
continue;
}
for (std::string f : files) {
cmb << f << " COMMAND_LINE\n";
++nexp;
}
double dox = x0[0] - x0[i], doy = y0[0] - y0[i];
if (first_line) {
// Ommit first line which has, by definition, no offset
first_line = false;
} else {
shx.push_back(dox);
shy.push_back(doy);
}
if (file::exists(dir+"helpers/shifts.txt")) {
vec1d tx, ty;
file::read_table(dir+"helpers/shifts.txt", 0, tx, ty);
for (uint_t j : range(tx)) {
shx.push_back(dox+tx[j]);
shy.push_back(doy+ty[j]);
}
}
}
note("found ", nexp, " exposures");
cmb.close();
auto truncate_decimals = vectorize_lambda([](double v, uint_t nd) {
return long(v*e10(nd))/e10(nd);
});
shx = truncate_decimals(shx, 2);
shy = truncate_decimals(shy, 2);
file::write_table("shifts.txt", 10, shx, shy);
return 0;
}