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Your Name 2012-03-29 15:55:08 -04:00
commit 2932240daf
7 changed files with 138 additions and 63 deletions
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7
sample/Hartmann_Matrix.txt Normal file
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@ -0,0 +1,7 @@
6
14.8253 -6.4243 7.8746 -1.2498 10.2733 10.2733
-6.4243 15.1024 -1.1155 -0.2761 -8.2117 -8.2117
7.8746 -1.1155 51.8519 -23.3482 12.5902 12.5902
-1.2498 -0.2761 -23.3482 22.7962 -9.8958 -9.8958
10.2733 -8.2117 12.5902 -9.8958 21.0656 21.0656
10.2733 -8.2117 12.5902 -9.8958 21.0656 21.0656

31
sample/testEskow.cpp
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@ -1,3 +1,4 @@
#include <fstream>
#include <cstring>
#include <iostream>
#include <iomanip>
@ -26,25 +27,39 @@ struct MatrixOp
}
};
int main()
int main(int argc, char **argv)
{
MatrixOp M;
double norm_E;
ifstream fi(argv[1]);
ofstream f("eskowed.txt");
CholeskyEskow<double,MatrixOp> chol;
M.N = 6;
fi >> M.N;
M.M.resize(M.N*M.N);
memcpy(&M.M[0], &Hartmann_Matrix[0][0], sizeof(double)*36);
CholeskyEskow::cholesky_eskow(M, M.N, norm_E);
for (int i = 0; i < M.N; i++)
{
for (int j = 0; j < M.N; j++)
{
cout << setprecision(25) << M(i,j) << " ";
fi >> M(i,j);
if (j > i)
M(i,j) =0;
}
cout << endl;
}
chol.cholesky(M, M.N, norm_E);
for (int i = 0; i < M.N; i++)
{
for (int j = 0; j < M.N; j++)
{
if (j > i)
f << "0 ";
else
f << setprecision(25) << M(i,j) << " ";
}
f << endl;
}
return 0;
}

94
src/eskow.hpp
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@ -7,24 +7,49 @@
/* Implementation of Schnabel & Eskow, 1999, Vol. 9, No. 4, pp. 1135-148, SIAM J. OPTIM. */
namespace CholeskyEskow
template<typename T, typename A>
class CholeskyEskow
{
private:
static const bool verbose_eskow = true;
T tau, tau_bar, mu;
void print_matrix(A& m, int N)
{
using std::cout;
using std::endl;
using std::setprecision;
if (verbose_eskow)
{
for (int i = 0; i < N; i++)
{
for (int j = 0; j < N; j++)
{
cout.width(6);
cout << setprecision(5) << m(i,j) << " ";
}
cout << endl;
}
cout << endl;
}
}
template<typename T, typename A>
T max_diag(A& m, int j, int N)
{
T maxval = m(j,j);
T maxval = std::abs(m(j,j));
for (int k = j+1; k < N; k++)
{
maxval = std::max(maxval, m(k,k));
maxval = std::max(maxval, std::abs(m(k,k)));
}
return maxval;
}
template<typename T, typename A>
void minmax_diag(A& m, int j, int N, T& minval, T& maxval, int& i_min, int& i_max)
{
i_min = i_max = j;
minval = maxval = m(j,j);
for (int k = j+1; k < N; k++)
@ -35,34 +60,30 @@ namespace CholeskyEskow
for (int k = j; k < N; k++)
{
if (m(k,k) == minval)
if (m(k,k) == minval && i_min < 0)
i_min = k;
if (m(k,k) == maxval)
if (m(k,k) == maxval && i_max < 0)
i_max = k;
}
}
template<typename T, typename A>
void swap_rows(A& m, int N, int i0, int i1)
{
for (int r = 0; r < N; r++)
std::swap(m(r,i0), m(r,i1));
}
template<typename T, typename A>
void swap_cols(A& m, int N, int i0, int i1)
{
for (int c = 0; c < N; c++)
std::swap(m(i0,c), m(i1,c));
}
template<typename T>
T square(T x)
{
return x*x;
}
template<typename T, typename A>
T min_row(A& m, int j, int N)
{
T a = 1/m(j,j);
@ -70,13 +91,12 @@ namespace CholeskyEskow
for (int i = j+2; i < N; i++)
{
v = std::max(v, m(i, i) - square(m(i,j))*a);
v = std::min(v, m(i, i) - square(m(i,j))*a);
}
return v;
}
template<typename T>
int g_max(const std::vector<T>& g, int j, int N)
{
T a = g[j];
@ -93,37 +113,45 @@ namespace CholeskyEskow
return k;
}
template<typename T, typename A>
void cholesky_eskow(A& m, int N, T& norm_E)
public:
CholeskyEskow()
{
tau = std::pow(mach_epsilon<T>(), 1./3);
tau_bar = std::pow(mach_epsilon<T>(), 2./3);
mu=0.1;
}
void cholesky(A& m, int N, T& norm_E)
{
T tau_bar = std::pow(mach_epsilon<T>(), 2./3);
T tau = std::pow(mach_epsilon<T>(), 1./3);
T mu = 0.1;
bool phaseone = true;
T gamma = max_diag<T,A>(m, 0, N);
T gamma = max_diag(m, 0, N);
int j;
norm_E = 0;
for (j = 0; j < N && phaseone; j++)
{
T minval, maxval;
int i_min, i_max;
minmax_diag<T,A>(m, j, N, minval, maxval, i_min, i_max);
print_matrix(m, N);
minmax_diag(m, j, N, minval, maxval, i_min, i_max);
if (maxval < tau_bar*gamma || minval < -mu*maxval)
{
phaseone = false;
break;
}
if (i_max != j)
if (i_max != j)
{
swap_cols<T,A>(m, N, i_max, j);
swap_rows<T,A>(m, N, i_max, j);
std::cout << "Have to swap i=" << i_max << " and j=" << j << std::endl;
swap_cols(m, N, i_max, j);
swap_rows(m, N, i_max, j);
}
if (min_row<T,A>(m, j, N) < -mu*gamma)
if (min_row(m, j, N) < -mu*gamma)
{
phaseone = false;
break;
@ -135,7 +163,7 @@ namespace CholeskyEskow
for (int i = j+1; i < N; i++)
{
m(i,j) /= L_jj;
for (int k = j+1; k < i; k++)
for (int k = j+1; k <= i; k++)
m(i,k) -= m(i,j)*m(k,j);
}
}
@ -151,9 +179,10 @@ namespace CholeskyEskow
if (!phaseone && j < (N-1))
{
std::cout << "Phase two ! (j=" << j << ")" << std::endl;
int k = j-1;
std::vector<T> g(N);
@ -173,12 +202,15 @@ namespace CholeskyEskow
int i = g_max(g, j, N);
T norm_j;
print_matrix(m, N);
if (i != j)
{
swap_cols<T,A>(m, N, i, j);
swap_rows<T,A>(m, N, i, j);
swap_cols(m, N, i, j);
swap_rows(m, N, i, j);
}
for (int i = j+1; j < N; j++)
{
norm_j += std::abs(m(i,j));
@ -208,7 +240,7 @@ namespace CholeskyEskow
for (int i = j+1; i < N; i++)
{
m(i,j) /= L_jj;
for (int k = j+1; k < i; k++)
for (int k = j+1; k <= i; k++)
m(i,k) -= m(i,j)*m(k,j);
}
}

26
src/h5_readFlash.cpp
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@ -179,13 +179,13 @@ void h5_read_flash3_particles (H5File* file,
int* totalparticles,
int* localnp,
int* particle_offset,
float pos1[],
float pos2[],
float pos3[],
float vel1[],
float vel2[],
float vel3[],
int id[])
float *pos1,
float *pos2,
float *pos3,
float *vel1,
float *vel2,
float *vel3,
int *id)
{
herr_t status;
@ -339,15 +339,27 @@ void h5_read_flash3_particles (H5File* file,
/* convert buffer into particle struct */
if (id) {
for(p=0; p < (pcount); p++) {
id[p+poffset] = (int) *(partBuffer+iptag-1+p*numProps);
} }
if (pos1 && pos2 && pos3) {
for(p=0; p < (pcount); p++) {
pos1[p+poffset] = (float) *(partBuffer+ipx-1+p*numProps);
pos2[p+poffset] = (float) *(partBuffer+ipy-1+p*numProps);
pos3[p+poffset] = (float) *(partBuffer+ipz-1+p*numProps);
}
}
if (vel1 && vel2 && vel3) {
for(p=0; p < (pcount); p++) {
vel1[p+poffset] = (float) *(partBuffer+ipvx-1+p*numProps);
vel2[p+poffset] = (float) *(partBuffer+ipvy-1+p*numProps);
vel3[p+poffset] = (float) *(partBuffer+ipvz-1+p*numProps);
}
}
memspace.close();
//status = H5Sclose(memspace);

14
src/h5_readFlash.hpp
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@ -23,13 +23,13 @@ void h5_read_flash3_particles (H5File* file,
int* totalparticles,
int* localnp,
int* particle_offset,
float pos1[],
float pos2[],
float pos3[],
float vel1[],
float vel2[],
float vel3[],
int id[]);
float *pos1,
float *pos2,
float *pos3,
float *vel1,
float *vel2,
float *vel3,
int *id);
void h5_read_flash3_header_info(H5File* file,
double* time, /* simulation time */

23
src/loadFlash.cpp
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@ -51,29 +51,36 @@ SimuData *CosmoTool::loadFlashMulti(const char *fname, int id, int loadflags)
data->Omega_Lambda = omegalambda;
// particle data
for (int i = 0; i < 3; i++) {
data->Pos[i] = new float[data->NumPart];
if (data->Pos[i] == 0) {
delete data;
if (loadflags& NEED_POSITION) {
for (int i = 0; i < 3; i++) {
data->Pos[i] = new float[data->NumPart];
if (data->Pos[i] == 0) {
delete data;
return 0;
}
}
} }
if (loadflags &NEED_VELOCITY) {
for (int i = 0; i < 3; i++) {
data->Vel[i] = new float[data->NumPart];
if (data->Vel[i] == 0) {
delete data;
return 0;
}
}
} }
if (loadflags & NEED_GADGET_ID) {
data->Id = new int[data->NumPart];
if (data->Id == 0) {
delete data;
return 0;
}
}
int offset = 0;
if (loadflags &(NEED_GADGET_ID|NEED_POSITION|NEED_VELOCITY))
h5_read_flash3_particles(&file, &npart, &npart, &offset,
data->Pos[0], data->Pos[1], data->Pos[2],
data->Vel[0], data->Vel[1], data->Vel[2],
@ -81,8 +88,8 @@ SimuData *CosmoTool::loadFlashMulti(const char *fname, int id, int loadflags)
for (int i = 0; i < 3; i++) {
for (int n = 0; n < data->NumPart; n++) {
data->Pos[i][n] = data->Pos[i][n] * data->Hubble / kpc2cm;
data->Vel[i][n] = data->Vel[i][n] * data->Hubble / km2cm;
if (loadflags& NEED_POSITION) data->Pos[i][n] = data->Pos[i][n] * data->Hubble / kpc2cm;
if (loadflags&NEED_VELOCITY) data->Vel[i][n] = data->Vel[i][n] * data->Hubble / km2cm;
}
}

6
src/mach.hpp
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@ -1,5 +1,7 @@
#ifndef __MACHINE_INFORMATION_HPP
#define __MACHINE_INFORMATION_HPP
#ifndef __COSMO_MACHINE_TEST_HPP
#define __COSMO_MACHINE_TEST_HPP
#include <iostream>
template<typename T>
T mach_epsilon()