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eles_pris.cpp
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/*!
* \file eles_pris.cpp
* \author - Original code: HiFiLES Aerospace Computing Laboratory (ACL)
* Aero/Astro Department. Stanford University.
* - Current development: Weiqi Shen
* University of Florida
*
* High Fidelity Large Eddy Simulation (HiFiLES) Code.
*
* HiFiLES is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* HiFiLES is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with HiFiLES. If not, see <http://www.gnu.org/licenses/>.
*/
#include <iomanip>
#include <iostream>
#include <cmath>
#include "../include/global.h"
#include "../include/eles_pris.h"
#include "../include/cubature_1d.h"
#include "../include/cubature_tri.h"
#include "../include/cubature_quad.h"
#include "../include/cubature_pris.h"
using namespace std;
// #### constructors ####
// default constructor
eles_pris::eles_pris()
{
}
// #### methods ####
void eles_pris::setup_ele_type_specific()
{
#ifndef _MPI
cout << "Initializing pris" << endl;
#endif
ele_type=3;
n_dims=3;
if (run_input.equation==0)
n_fields=5;
else if (run_input.equation==1)
n_fields=1;
else
FatalError("Equation not supported");
if (run_input.RANS==1)
n_fields++;
n_inters_per_ele=5;
length.setup(5);
n_upts_per_ele=(order+2)*(order+1)*(order+1)/2;
upts_type_pri_tri = run_input.upts_type_pri_tri;
upts_type_pri_1d = run_input.upts_type_pri_1d;
set_loc_upts();
set_vandermonde_tri();
set_vandermonde3D();
//set shock capturing arrays
if(run_input.shock_cap)
{
if (run_input.shock_det == 0) //persson
calc_norm_basis();
else
FatalError("Shock detector not implmented.");
if (run_input.shock_cap == 1) //exp filter
set_exp_filter();
else
FatalError("Shock capturing method not implmented.");
}
set_inters_cubpts();
set_volume_cubpts(order, loc_volume_cubpts, weight_volume_cubpts);
set_opp_volume_cubpts(loc_volume_cubpts, opp_volume_cubpts);
n_ppts_per_ele=(p_res+1)*(p_res)*(p_res)/2;
n_peles_per_ele=( (p_res-1)*(p_res-1)*(p_res-1) );
n_verts_per_ele = 6;
set_loc_ppts();
set_opp_p();
//de-aliasing by over-integration
if (run_input.over_int)
set_over_int();
n_fpts_per_inter.setup(5);
n_fpts_per_inter(0)=(order+2)*(order+1)/2;
n_fpts_per_inter(1)=(order+2)*(order+1)/2;
n_fpts_per_inter(2)=(order+1)*(order+1);
n_fpts_per_inter(3)=(order+1)*(order+1);
n_fpts_per_inter(4)=(order+1)*(order+1);
n_fpts_per_ele=3*(order+1)*(order+1)+(order+2)*(order+1);
// Check consistency between tet-pri interface
if (upts_type_pri_tri != run_input.fpts_type_tet)
FatalError("upts_type_pri_tri != fpts_type_tet");
// Check consistency between hex-pri interface
if (upts_type_pri_1d != run_input.upts_type_hexa)
FatalError("upts_type_pri_1d != upts_type_hexa");
set_tloc_fpts();
set_tnorm_fpts();
set_opp_0(run_input.sparse_pri);
set_opp_1(run_input.sparse_pri);
set_opp_2(run_input.sparse_pri);
set_opp_3(run_input.sparse_pri);
if(viscous)
{
// Compute hex filter matrix
//if(LES_filter) compute_filter_upts();
set_opp_4(run_input.sparse_pri);
set_opp_5(run_input.sparse_pri);
set_opp_6(run_input.sparse_pri);
temp_grad_u.setup(n_fields,n_dims);
}
temp_u.setup(n_fields);
temp_f.setup(n_fields,n_dims);
}
void eles_pris::set_connectivity_plot()
{
int vertex_0, vertex_1, vertex_2, vertex_3, vertex_4, vertex_5;
int count = 0;
int temp = (p_res) * (p_res + 1) / 2; //number of pts each 1d layer
for (int l = 0; l < p_res - 1; ++l)
{ // level 1d
for (int j = 0; j < p_res - 1; ++j)
{ // level_tri
for (int k = 0; k < p_res - j - 1; ++k)
{ // starting pt
vertex_0 = k + (j * (p_res + 1)) - ((j * (j + 1)) / 2) + l * temp;
vertex_1 = vertex_0 + 1;
vertex_2 = k + ((j + 1) * (p_res + 1)) - (((j + 1) * (j + 2)) / 2) + l * temp;
vertex_3 = vertex_0 + temp;
vertex_4 = vertex_1 + temp;
vertex_5 = vertex_2 + temp;
connectivity_plot(0, count) = vertex_0;
connectivity_plot(1, count) = vertex_1;
connectivity_plot(2, count) = vertex_2;
connectivity_plot(3, count) = vertex_3;
connectivity_plot(4, count) = vertex_4;
connectivity_plot(5, count) = vertex_5;
count++;
}
}
}
for (int l = 0; l < p_res - 1; ++l)
{
for (int j = 0; j < p_res - 2; ++j)
{
for (int k = 0; k < p_res - j - 2; ++k)
{
vertex_0 = k + 1 + (j * (p_res)) - ((j * (j - 1)) / 2) + l * temp;
vertex_1 = vertex_0 + p_res - j;
vertex_2 = vertex_1 - 1;
vertex_3 = vertex_0 + temp;
vertex_4 = vertex_1 + temp;
vertex_5 = vertex_2 + temp;
connectivity_plot(0, count) = vertex_0;
connectivity_plot(1, count) = vertex_1;
connectivity_plot(2, count) = vertex_2;
connectivity_plot(3, count) = vertex_3;
connectivity_plot(4, count) = vertex_4;
connectivity_plot(5, count) = vertex_5;
count++;
}
}
}
}
// set location of solution points in standard element
void eles_pris::set_loc_upts(void)
{
loc_upts.setup(n_dims,n_upts_per_ele);
n_upts_tri = (order+1)*(order+2)/2;
n_upts_1d = order+1;
loc_upts_pri_1d.setup(n_upts_1d);
loc_upts_pri_tri.setup(2,n_upts_tri);
cubature_1d cub_1d(upts_type_pri_1d,order);
cubature_tri cub_tri(upts_type_pri_tri,order);
for (int i = 0; i < n_upts_1d;i++)
loc_upts_pri_1d(i) = cub_1d.get_r(i);
for (int i=0;i<n_upts_tri;i++) {
loc_upts_pri_tri(0,i) = cub_tri.get_r(i);
loc_upts_pri_tri(1,i) = cub_tri.get_s(i);
}
// Now set loc_upts
for (int i=0;i<n_upts_1d;i++) {
for (int j=0;j<n_upts_tri;j++) {
loc_upts(0,n_upts_tri*i+j) = loc_upts_pri_tri(0,j);
loc_upts(1,n_upts_tri*i+j) = loc_upts_pri_tri(1,j);
loc_upts(2,n_upts_tri*i+j) = loc_upts_pri_1d(i);
}
}
}
// set location of flux points in standard element
void eles_pris::set_tloc_fpts(void)
{
tloc_fpts.setup(n_dims,n_fpts_per_ele);
hf_array<double> loc_tri_fpts( (order+1)*(order+2)/2,2);
loc_1d_fpts.setup(order+1);
cubature_1d cub_1d(upts_type_pri_1d,order);
cubature_tri cub_tri(upts_type_pri_tri,order);
for (int i = 0; i < n_fpts_per_inter(0); i++)
{
loc_tri_fpts(i, 0) = cub_tri.get_r(i);
loc_tri_fpts(i, 1) = cub_tri.get_s(i);
}
for (int i = 0; i < order + 1; i++)
loc_1d_fpts(i) = cub_1d.get_r(i);
// Now need to map these points on faces of prisms
// Inter 0
for (int i=0;i<n_fpts_per_inter(0);i++)
{
tloc_fpts(0,i) = loc_tri_fpts(i,1);//note need to notice
tloc_fpts(1,i) = loc_tri_fpts(i,0);
tloc_fpts(2,i) = -1.;
}
// Inter 1
for (int i=0;i<n_fpts_per_inter(1);i++)
{
tloc_fpts(0,n_fpts_per_inter(0)+i) = loc_tri_fpts(i,0);
tloc_fpts(1,n_fpts_per_inter(0)+i) = loc_tri_fpts(i,1);
tloc_fpts(2,n_fpts_per_inter(0)+i) = 1.;
}
// Inters 2,3,4
int offset = n_fpts_per_inter(0)*2;
for (int face=0;face<3;face++) {
for (int i=0;i<order+1;i++) {
for (int j=0;j<order+1;j++) {
if (face==0) {
tloc_fpts(0,offset+face*(order+1)*(order+1)+i*(order+1)+j) = loc_1d_fpts(j);
tloc_fpts(1,offset+face*(order+1)*(order+1)+i*(order+1)+j) = -1;;
}
else if (face==1) {
tloc_fpts(0,offset+face*(order+1)*(order+1)+i*(order+1)+j) = loc_1d_fpts(order-j);//x from r to l
tloc_fpts(1,offset+face*(order+1)*(order+1)+i*(order+1)+j) = loc_1d_fpts(j);//y from bot to up
}
else if (face==2) {
tloc_fpts(0,offset+face*(order+1)*(order+1)+i*(order+1)+j) = -1.;
tloc_fpts(1,offset+face*(order+1)*(order+1)+i*(order+1)+j) = loc_1d_fpts(order-j);;
}
tloc_fpts(2,offset+face*(order+1)*(order+1)+i*(order+1)+j) = loc_1d_fpts(i);
}
}
}
}
void eles_pris::set_inters_cubpts(void)
{
n_cubpts_per_inter.setup(n_inters_per_ele);
loc_inters_cubpts.setup(n_inters_per_ele);
weight_inters_cubpts.setup(n_inters_per_ele);
tnorm_inters_cubpts.setup(n_inters_per_ele);
cubature_tri cub_tri(0,order);
cubature_quad cub_quad(0,order);
int n_cubpts_tri = cub_tri.get_n_pts();
int n_cubpts_quad = cub_quad.get_n_pts();
for (int i=0;i<n_inters_per_ele;i++)
{
if (i==0 || i==1) {
n_cubpts_per_inter(i) = n_cubpts_tri;
}
else if (i==2 || i==3 || i==4) {
n_cubpts_per_inter(i) = n_cubpts_quad;
}
}
for (int i=0;i<n_inters_per_ele;i++) {
loc_inters_cubpts(i).setup(n_dims,n_cubpts_per_inter(i));
weight_inters_cubpts(i).setup(n_cubpts_per_inter(i));
tnorm_inters_cubpts(i).setup(n_dims,n_cubpts_per_inter(i));
for (int j=0;j<n_cubpts_per_inter(i);j++) {
if (i==0) {
loc_inters_cubpts(i)(0,j)=cub_tri.get_r(j);
loc_inters_cubpts(i)(1,j)=cub_tri.get_s(j);
loc_inters_cubpts(i)(2,j)=-1.;
}
else if (i==1) {
loc_inters_cubpts(i)(0,j)=cub_tri.get_r(j);
loc_inters_cubpts(i)(1,j)=cub_tri.get_s(j);
loc_inters_cubpts(i)(2,j)=1.;
}
else if (i==2) {
loc_inters_cubpts(i)(0,j)=cub_quad.get_r(j);
loc_inters_cubpts(i)(1,j)=-1.;
loc_inters_cubpts(i)(2,j)=cub_quad.get_s(j);
}
else if (i==3) {
loc_inters_cubpts(i)(0,j)=cub_quad.get_r(j);
loc_inters_cubpts(i)(1,j)=-cub_quad.get_r(j);
loc_inters_cubpts(i)(2,j)=cub_quad.get_s(j);
}
else if (i==4) {
loc_inters_cubpts(i)(0,j)=-1.;
loc_inters_cubpts(i)(1,j)=cub_quad.get_r(j);
loc_inters_cubpts(i)(2,j)=cub_quad.get_s(j);
}
if (i==0 || i==1)
weight_inters_cubpts(i)(j) = cub_tri.get_weight(j);
else if (i==2 || i==3 || i==4)
weight_inters_cubpts(i)(j) = cub_quad.get_weight(j);
if (i==0) {
tnorm_inters_cubpts(i)(0,j)= 0.;
tnorm_inters_cubpts(i)(1,j)= 0.;
tnorm_inters_cubpts(i)(2,j)= -1.;
}
else if (i==1) {
tnorm_inters_cubpts(i)(0,j)= 0.;
tnorm_inters_cubpts(i)(1,j)= 0.;
tnorm_inters_cubpts(i)(2,j)= 1.;
}
else if (i==2) {
tnorm_inters_cubpts(i)(0,j)= 0.;
tnorm_inters_cubpts(i)(1,j)= -1.;
tnorm_inters_cubpts(i)(2,j)= 0.;
}
else if (i==3) {
tnorm_inters_cubpts(i)(0,j)= 1./sqrt(2.);
tnorm_inters_cubpts(i)(1,j)= 1./sqrt(2.);
tnorm_inters_cubpts(i)(2,j)= 0.;
}
else if (i==4) {
tnorm_inters_cubpts(i)(0,j)= -1.;
tnorm_inters_cubpts(i)(1,j)= 0.;
tnorm_inters_cubpts(i)(2,j)= 0.;
}
}
}
set_opp_inters_cubpts();
}
void eles_pris::set_volume_cubpts(int in_order, hf_array<double> &out_loc_volume_cubpts, hf_array<double> &out_weight_volume_cubpts)
{
cubature_pris cub_pri(0, 0, in_order);
int n_cubpts_per_ele_pri = cub_pri.get_n_pts();
out_loc_volume_cubpts.setup(n_dims, n_cubpts_per_ele_pri);
out_weight_volume_cubpts.setup(n_cubpts_per_ele_pri);
for (int i = 0; i < n_cubpts_per_ele_pri; i++)
{
out_loc_volume_cubpts(0, i) = cub_pri.get_r(i);
out_loc_volume_cubpts(1, i) = cub_pri.get_s(i);
out_loc_volume_cubpts(2, i) = cub_pri.get_t(i);
out_weight_volume_cubpts(i) = cub_pri.get_weight(i);
}
}
// Compute the surface jacobian determinant on a face
double eles_pris::compute_inter_detjac_inters_cubpts(int in_inter,hf_array<double> d_pos)
{
double output = 0.;
double xr, xs, xt;
double yr, ys, yt;
double zr, zs, zt;
double temp0,temp1,temp2;
xr = d_pos(0,0);
xs = d_pos(0,1);
xt = d_pos(0,2);
yr = d_pos(1,0);
ys = d_pos(1,1);
yt = d_pos(1,2);
zr = d_pos(2,0);
zs = d_pos(2,1);
zt = d_pos(2,2);
double xu=0.;
double yu=0.;
double zu=0.;
double xv=0.;
double yv=0.;
double zv=0.;
// From calculus, for a surface parameterized by two parameters
// u and v, than jacobian determinant is
//
// || (xu i + yu j + zu k) cross ( xv i + yv j + zv k) ||
if (in_inter==0) // u=r, v=s
{
xu = xr;
yu = yr;
zu = zr;
xv = xs;
yv = ys;
zv = zs;
}
else if (in_inter==1) // u=s, v=s
{
xu = xr;
yu = yr;
zu = zr;
xv = xs;
yv = ys;
zv = zs;
}
else if (in_inter==2) //u=r, v=t
{
xu = xr;
yu = yr;
zu = zr;
xv = xt;
yv = yt;
zv = zt;
}
else if (in_inter==3) //r=u,t=v,s=1-u
{
xu = xr-xs;
yu = yr-ys;
zu = zr-zs;
xv = xt;
yv = yt;
zv = zt;
}
else if (in_inter==4) //u=s,v=t
{
xu = xs;
yu = ys;
zu = zs;
xv = xt;
yv = yt;
zv = zt;
}
temp0 = yu*zv-zu*yv;
temp1 = zu*xv-xu*zv;
temp2 = xu*yv-yu*xv;
output = sqrt(temp0*temp0+temp1*temp1+temp2*temp2);
return output;
}
// set location of plot points in standard element
void eles_pris::set_loc_ppts(void)
{
int i,j,k,index;
loc_ppts.setup(3,p_res*(p_res+1)/2*p_res);
for(k=0;k<p_res;k++)//z index
{
for(j=0;j<p_res;j++)//y index
{
for(i=0;i<p_res-j;i++)//x index
{
index = (p_res*(p_res+1)/2)*k + (i+(j*(p_res+1))-((j*(j+1))/2));/*|2\ bottom to up
//|0_1\*/
loc_ppts(0,index)=-1.0+((2.0*i)/(1.0*(p_res-1)));
loc_ppts(1,index)=-1.0+((2.0*j)/(1.0*(p_res-1)));
loc_ppts(2,index)=-1.0+((2.0*k)/(1.0*(p_res-1)));
}
}
}
}
// set location of shape points in standard element
/*
void eles_pris::set_loc_spts(void)
{
// fill in
}
*/
// set transformed normal at flux points
void eles_pris::set_tnorm_fpts(void)
{
tnorm_fpts.setup(n_dims,n_fpts_per_ele);
int fpt = -1;
for (int i=0;i<n_inters_per_ele;i++)
{
for (int j=0;j<n_fpts_per_inter(i);j++)
{
fpt++;
if (i==0) {
tnorm_fpts(0,fpt) = 0.;
tnorm_fpts(1,fpt) = 0.;
tnorm_fpts(2,fpt) = -1.;
}
else if (i==1) {
tnorm_fpts(0,fpt) = 0.;
tnorm_fpts(1,fpt) = 0.;
tnorm_fpts(2,fpt) = 1.;
}
else if (i==2) {
tnorm_fpts(0,fpt) = 0.;
tnorm_fpts(1,fpt) = -1.;
tnorm_fpts(2,fpt) = 0.;
}
else if (i==3) {
tnorm_fpts(0,fpt) = 1./sqrt(2.);
tnorm_fpts(1,fpt) = 1./sqrt(2.);
tnorm_fpts(2,fpt) = 0.;
}
else if (i==4) {
tnorm_fpts(0,fpt) = -1.;
tnorm_fpts(1,fpt) = 0.;
tnorm_fpts(2,fpt) = 0.;
}
}
}
//cout << "tnorm_fpts" << endl;
//tnorm_fpts.print();
}
//#### helper methods ####
// initialize the vandermonde matrix
void eles_pris::set_vandermonde_tri()
{
vandermonde_tri.setup(n_upts_tri,n_upts_tri);
// create the vandermonde matrix
for (int i=0;i<n_upts_tri;i++)
for (int j=0;j<n_upts_tri;j++)
vandermonde_tri(i,j) = eval_dubiner_basis_2d(loc_upts_pri_tri(0,i),loc_upts_pri_tri(1,i),j,order);
// Store its inverse
inv_vandermonde_tri = inv_array(vandermonde_tri);
}
void eles_pris::set_vandermonde3D(void)
{
vandermonde.setup(n_upts_per_ele, n_upts_per_ele);
hf_array<double> loc(n_dims);
// create the vandermonde matrix
for (int i = 0; i < n_upts_per_ele; i++)
{
loc(0) = loc_upts(0, i);
loc(1) = loc_upts(1, i);
loc(2) = loc_upts(2, i);
for (int j = 0; j < n_upts_per_ele; j++)
{
vandermonde(i, j) = eval_pris_basis_hierarchical(j, loc, order);
}
}
// Store its inverse
inv_vandermonde = inv_array(vandermonde);
}
void eles_pris::set_exp_filter(void)
{
exp_filter.setup(n_upts_per_ele, n_upts_per_ele);
exp_filter.initialize_to_zero();
int i, j, k, l, mode;
double eta_rs,eta_t;
double eta_c= (double)run_input.expf_cutoff / (double)(order);
mode = 0;
for (l = 0; l < 2 * order + 1; l++) //sum of x,y,z mode
{
for (k = 0; k < l + 1; k++) //k<=sum
{
for (j = 0; j < l - k + 1; j++) //j<=sum-k
{
i = l - k - j;
if (k <= order && i + j <= order)
{
eta_rs = (double)(i + j) / (double)(order);
eta_t = (double)(k) / (double)(order);
exp_filter(mode, mode) = 1.;
if (eta_rs > eta_c)
exp_filter(mode, mode) *= exp(-run_input.expf_fac * pow((eta_rs - eta_c) / (1. - eta_c), run_input.expf_order));
if (eta_t > eta_c)
exp_filter(mode, mode) *= exp(-run_input.expf_fac * pow((eta_t - eta_c) / (1. - eta_c), run_input.expf_order));
mode++;
}
}
}
}
exp_filter = mult_arrays(exp_filter, inv_vandermonde);
exp_filter = mult_arrays(vandermonde, exp_filter);
}
void eles_pris::calc_norm_basis(void)
{
int n1, n2, n3;
double norm3;
norm_basis_persson.setup(n_upts_per_ele);
for (int i = 0; i < n_upts_per_ele; i++)
{
get_pris_basis_index(i, order, n1, n2, n3);
norm3 = 2.0 / (2.0 * n3 + 1.0);
norm_basis_persson(i) = norm3;
}
}
//detect shock use persson's method
void eles_pris::shock_det_persson(void)
{
hf_array<double> temp_modal(n_upts_per_ele); //store modal value
int x, y, z;
for (int ic = 0; ic < n_eles; ic++)
{
if (run_input.shock_det_field == 0) //density
{
//step 1. convert to modal value
#if defined _ACCELERATE_BLAS || defined _MKL_BLAS || defined _STANDARD_BLAS
cblas_dgemv(CblasColMajor, CblasNoTrans, n_upts_per_ele, n_upts_per_ele, 1.0, inv_vandermonde.get_ptr_cpu(), n_upts_per_ele, disu_upts(0).get_ptr_cpu(0, ic, 0), 1, 0.0, temp_modal.get_ptr_cpu(), 1);
#else
dgemm(n_upts_per_ele, 1, n_upts_per_ele, 1.0, 0.0, inv_vandermonde.get_ptr_cpu(), disu_upts(0).get_ptr_cpu(0, ic, 0), temp_modal.get_ptr_cpu());
#endif
}
else if (run_input.shock_det_field == 1) //total energy
{
//step 1. convert to modal value
#if defined _ACCELERATE_BLAS || defined _MKL_BLAS || defined _STANDARD_BLAS
cblas_dgemv(CblasColMajor, CblasNoTrans, n_upts_per_ele, n_upts_per_ele, 1.0, inv_vandermonde.get_ptr_cpu(), n_upts_per_ele, disu_upts(0).get_ptr_cpu(0, ic, n_dims+1), 1, 0.0, temp_modal.get_ptr_cpu(), 1);
#else
dgemm(n_upts_per_ele, 1, n_upts_per_ele, 1.0, 0.0, inv_vandermonde.get_ptr_cpu(), disu_upts(0).get_ptr_cpu(0, ic, n_dims+1), temp_modal.get_ptr_cpu());
#endif
}
else
{
FatalError("Unsupported shock capturing field.")
}
//step 2. perform inplace \hat{u}^2 store in temp_modal
#if defined _ACCELERATE_BLAS || defined _MKL_BLAS || defined _STANDARD_BLAS
vdSqr(n_upts_per_ele, temp_modal.get_ptr_cpu(), temp_modal.get_ptr_cpu());
#else
transform(temp_modal.get_ptr_cpu(), temp_modal.get_ptr_cpu(n_upts_per_ele), temp_modal.get_ptr_cpu(), [](double x) { return x * x; });
#endif
//step 3. use Parseval's theorem to calculate (u-u_n,u-u_n)
sensor(ic) = 0;
for (int j = 0; j < n_upts_per_ele; j++)
{
get_pris_basis_index(j, order, x, y, z);
if (x + y == order || z == order)
sensor(ic) += temp_modal(j) * norm_basis_persson(j);
}
//step 4. use Parseval's theorem to calculate (u,u), and calculate ((u-u_n,u-u_n)/(u,u))
#if defined _ACCELERATE_BLAS || defined _MKL_BLAS || defined _STANDARD_BLAS
sensor(ic) /= cblas_ddot(n_upts_per_ele, norm_basis_persson.get_ptr_cpu(), 1, temp_modal.get_ptr_cpu(), 1);
#else
sensor(ic) /= inner_product(norm_basis_persson.get_ptr_cpu(), norm_basis_persson.get_ptr_cpu(n_upts_per_ele), temp_modal.get_ptr_cpu(), 0.);
#endif
}
}
// initialize the vandermonde matrix
void eles_pris::set_vandermonde_tri_restart()
{
vandermonde_tri_rest.setup(n_upts_tri_rest,n_upts_tri_rest);
// create the vandermonde matrix
for (int i=0;i<n_upts_tri_rest;i++)
for (int j=0;j<n_upts_tri_rest;j++)
vandermonde_tri_rest(i,j) = eval_dubiner_basis_2d(loc_upts_pri_tri_rest(0,i),loc_upts_pri_tri_rest(1,i),j,order_rest);
// Store its inverse
inv_vandermonde_tri_rest = inv_array(vandermonde_tri_rest);
}
int eles_pris::read_restart_info_ascii(ifstream& restart_file)
{
string str;
// Move to triangle element
while(1) {
getline(restart_file,str);
if (str=="PRIS") break;
if (restart_file.eof()) return 0;
}
getline(restart_file,str);
restart_file >> order_rest;
getline(restart_file,str);
getline(restart_file,str);
restart_file >> n_upts_per_ele_rest;
getline(restart_file,str);
getline(restart_file,str);
restart_file >> n_upts_tri_rest;
getline(restart_file,str);
getline(restart_file,str);
loc_upts_pri_1d_rest.setup(order_rest+1);
loc_upts_pri_tri_rest.setup(2,n_upts_tri_rest);
for (int i=0;i<order_rest+1;i++) {
restart_file >> loc_upts_pri_1d_rest(i);
}
getline(restart_file,str);
getline(restart_file,str);
for (int i=0;i<n_upts_tri_rest;i++) {
for (int j=0;j<2;j++) {
restart_file >> loc_upts_pri_tri_rest(j,i);
}
}
set_vandermonde_tri_restart();
set_opp_r();
return 1;
}
#ifdef _HDF5
void eles_pris::read_restart_info_hdf5(hid_t &restart_file, int in_rest_order)
{
hid_t dataset_id, plist_id, memspace_id, dataspace_id;
hsize_t count; // number of blocks
hsize_t offset; // start
//open dataset
dataset_id = H5Dopen2(restart_file, "PRIS", H5P_DEFAULT);
if (dataset_id < 0)
FatalError("Cannot find pris property");
plist_id = H5Pcreate(H5P_DATASET_XFER);
#ifdef _MPI
//set collective read
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
#endif
if (n_eles)
{
order_rest = in_rest_order;
n_upts_per_ele_rest = (order_rest + 2) * (order_rest + 1) * (order_rest + 1) / 2;
n_upts_tri_rest = (order_rest + 1) * (order_rest + 2) / 2;
loc_upts_pri_1d_rest.setup(order_rest + 1);
loc_upts_pri_tri_rest.setup(2, n_upts_tri_rest);
//read data
offset = 0;
count = order_rest + 1;
memspace_id = H5Screate_simple(1, &count, NULL); //row major: n_eles by n_upts_per_ele_rest* n_fields
dataspace_id = H5Dget_space(dataset_id);
if (H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET, &offset, NULL, &count, NULL) < 0)
FatalError("Failed to get hyperslab");
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, memspace_id, dataspace_id, plist_id, loc_upts_pri_1d_rest.get_ptr_cpu()); //read 1d
H5Sclose(memspace_id);
offset = order_rest + 1;
count = 2 * n_upts_tri_rest;
memspace_id = H5Screate_simple(1, &count, NULL); //row major: n_eles by n_upts_per_ele_rest* n_fields
if (H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET, &offset, NULL, &count, NULL) < 0)
FatalError("Failed to get hyperslab");
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, memspace_id, dataspace_id, plist_id, loc_upts_pri_tri_rest.get_ptr_cpu()); //read tri
H5Sclose(memspace_id);
H5Sclose(dataspace_id);
set_vandermonde_tri_restart();
set_opp_r();
}
#ifdef _MPI
else //read empty
{
dataspace_id = H5Dget_space(dataset_id);
H5Sselect_none(dataspace_id);
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, dataspace_id, dataspace_id, plist_id, NULL);
H5Dread(dataset_id, H5T_NATIVE_DOUBLE, dataspace_id, dataspace_id, plist_id, NULL);
H5Sclose(dataspace_id);
}
#endif
//close objects
H5Pclose(plist_id);
H5Dclose(dataset_id);
}
#endif
#ifndef _HDF5
void eles_pris::write_restart_info_ascii(ofstream& restart_file)
{
restart_file << "PRIS" << endl;
restart_file << "Order" << endl;
restart_file << order << endl;
restart_file << "Number of solution points per prismatic element" << endl;
restart_file << n_upts_per_ele << endl;
restart_file << "Number of solution points in triangle" << endl;
restart_file << n_upts_tri << endl;
restart_file << "Location of solution points in 1D" << endl;
for (int i=0;i<order+1;i++) {
restart_file << loc_upts_pri_1d(i) << " ";
}
restart_file << endl;
restart_file << "Location of solution points in triangle" << endl;
for (int i=0;i<n_upts_tri;i++) {
for (int j=0;j<2;j++) {
restart_file << loc_upts_pri_tri(j,i) << " ";
}
restart_file << endl;
}
}
#endif
#ifdef _HDF5
void eles_pris::write_restart_info_hdf5(hid_t &restart_file)
{
hid_t dataset_id, plist_id, dataspace_id, memspace_id;
hsize_t count, offset;
hsize_t dim = run_input.order + 1 + 2 * (run_input.order + 1) * (run_input.order + 2) / 2;
//create PRIS dataset
dataspace_id = H5Screate_simple(1, &dim, NULL);
dataset_id = H5Dcreate2(restart_file, "PRIS", H5T_NATIVE_DOUBLE, dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
plist_id = H5Pcreate(H5P_DATASET_XFER);
#ifdef _MPI
//set collective read
H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
#endif
//write loc_upts_pri_1d and loc_upts_pri_tri
if (n_eles)
{
offset = 0;
count = order + 1;
memspace_id = H5Screate_simple(1, &count, NULL);
if (H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET, &offset, NULL, &count, NULL) < 0)
FatalError("Failed to get hyperslab");
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, memspace_id, dataspace_id, plist_id, loc_upts_pri_1d.get_ptr_cpu());
H5Sclose(memspace_id);
offset = order + 1;
count = 2 * (order + 1) * (order + 2) / 2;
memspace_id = H5Screate_simple(1, &count, NULL);
if (H5Sselect_hyperslab(dataspace_id, H5S_SELECT_SET, &offset, NULL, &count, NULL) < 0)
FatalError("Failed to get hyperslab");
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, memspace_id, dataspace_id, plist_id, loc_upts_pri_tri.get_ptr_cpu());
H5Sclose(memspace_id);
}
#ifdef _MPI
else
{
H5Sselect_none(dataspace_id);
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, dataspace_id, dataspace_id, plist_id, NULL);
H5Dwrite(dataset_id, H5T_NATIVE_DOUBLE, dataspace_id, dataspace_id, plist_id, NULL);
}
#endif
H5Pclose(plist_id);
H5Dclose(dataset_id);
H5Sclose(dataspace_id);
}
#endif
void eles_pris::set_over_int(void)
{
//initialize over integration cubature points
set_volume_cubpts(run_input.over_int_order, loc_over_int_cubpts, weight_over_int_cubpts);
//set interpolation matrix from solution points to over integration cubature points
set_opp_volume_cubpts(loc_over_int_cubpts, opp_over_int_cubpts);
//set projection matrix from over integration cubature points to modal coefficients
temp_u_over_int_cubpts.setup(loc_over_int_cubpts.get_dim(1), n_fields);
temp_u_over_int_cubpts.initialize_to_zero();
temp_tdisf_over_int_cubpts.setup(loc_over_int_cubpts.get_dim(1), n_fields, n_dims);
hf_array<double> loc(n_dims);
hf_array<double> temp_proj(n_upts_per_ele, loc_over_int_cubpts.get_dim(1));
//step 1. nodal to L2 projected modal \hat{u_i}=\int{\phi_i*\l_j}=>\phi_i(j)*w(j)
int n1, n2, n3;
double norm3;
for (int i = 0; i < n_upts_per_ele; i++)
{
get_pris_basis_index(i, order, n1, n2, n3);
norm3 = 2.0 / (2.0 * n3 + 1.0);
for (int j = 0; j < loc_over_int_cubpts.get_dim(1); j++)
{
loc(0) = loc_over_int_cubpts(0, j);
loc(1) = loc_over_int_cubpts(1, j);
loc(2) = loc_over_int_cubpts(2, j);
temp_proj(i, j) = eval_pris_basis_hierarchical(i, loc, order) / norm3 * weight_over_int_cubpts(j);
}
}
//multiply modal coefficient by vandermonde matrix to get over_int_filter
over_int_filter = mult_arrays(vandermonde, temp_proj);
}
// evaluate nodal basis
double eles_pris::eval_nodal_basis(int in_index, hf_array<double> in_loc)
{
double oned_nodal_basis_at_loc;
double tri_nodal_basis_at_loc;
int index_tri = in_index%n_upts_tri;
int index_1d = in_index/n_upts_tri;
// 1. First evaluate the triangular nodal basis at loc(0) and loc(1)
// First evaluate the normalized Dubiner basis at position in_loc
hf_array<double> dubiner_basis_at_loc(n_upts_tri);
for (int i=0;i<n_upts_tri;i++)
dubiner_basis_at_loc(i) = eval_dubiner_basis_2d(in_loc(0),in_loc(1),i,order);
// From Hesthaven, equation 3.3, V^T * l = P, or l = (V^-1)^T P
tri_nodal_basis_at_loc = 0.;
for (int i=0;i<n_upts_tri;i++)
tri_nodal_basis_at_loc += inv_vandermonde_tri(i,index_tri)*dubiner_basis_at_loc(i);
// 2. Now evaluate the 1D lagrange basis at loc(2)
oned_nodal_basis_at_loc = eval_lagrange(in_loc(2),index_1d,loc_upts_pri_1d);
return (tri_nodal_basis_at_loc*oned_nodal_basis_at_loc);
}
// evaluate nodal basis for restart