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io.cu
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io.cu
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/**
* @author Christoph Schaefer [email protected] and Thomas I. Maindl
*
* @section LICENSE
* Copyright (c) 2019 Christoph Schaefer
*
* This file is part of miluphcuda.
*
* miluphcuda 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.
*
* miluphcuda 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 miluphcuda. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "io.h"
#include "timeintegration.h"
#include "pressure.h"
#include <libconfig.h>
#include "aneos.h"
#if HDF5IO
#include <hdf5.h>
#endif
int currentDiskIO = FALSE;
extern pthread_t fileIOthread;
extern double startTime;
extern double Smin;
extern double alphamin;
extern double emin;
extern double rhomin;
extern double damagemin;
extern double betamin;
extern double alpha_epspormin;
extern double epsilon_vmin;
File inputFile;
/*! \brief
Reading the material properties using libconfig.
\param pointer to config file
\return nothing
*/
void loadConfigFromFile(char *configFile)
{
config_init(¶m.config);
if (!config_read_file(¶m.config, configFile)) {
fprintf(stderr, "Error reading config file %s.\n", configFile);
config_destroy(¶m.config);
exit(1);
}
}
void set_integration_parameters()
{
FILE *f;
char line[1024];
char *name;
char *value;
char *fn = "pc_values.dat";
const char s[] = " = ";
int found = FALSE;
f = fopen(fn,"r");
if (f == NULL){
if (param.integrator_type == MONAGHAN_PC || param.integrator_type == EULER_PC) {
fprintf(stderr, "Can't open file %s!\n", fn);
exit(1);
}
} else {
found = TRUE;
}
Smin = rhomin = emin = alphamin = betamin = damagemin = alpha_epspormin = epsilon_vmin = 1e99;
if (found) {
while (fgets(line, sizeof(line), f)) {
/* comments start with # */
if (line[0] == '#') continue;
name = strtok(line, s);
value = strtok(NULL, s);
if (!strcmp(name, "Smin")) {
Smin = atof(value);
}
else if (!strcmp(name, "rhomin")) {
rhomin = atof(value);
}
else if (!strcmp(name, "emin")) {
emin = atof(value);
}
else if (!strcmp(name, "alphamin")) {
alphamin = atof(value);
}
else if (!strcmp(name, "betamin")) {
betamin = atof(value);
}
else if (!strcmp(name, "damagemin")) {
damagemin = atof(value);
}
else if (!strcmp(name, "alpha_epspormin")) {
alpha_epspormin = atof(value);
}
else if (!strcmp(name, "epsilon_vmin")) {
epsilon_vmin = atof(value);
}
}
fclose (f);
}
if (param.verbose && (param.integrator_type == MONAGHAN_PC || param.integrator_type == EULER_PC)) {
fprintf(stdout, "Using following values for the predictor corrector integrator:\n");
#if SOLID
fprintf(stdout, "Smin:\t\t\t %e\n", Smin);
#endif
#if INTEGRATE_ENERGY
fprintf(stdout, "emin:\t\t\t %e\n", emin);
#endif
#if INTEGRATE_DENSITY
fprintf(stdout, "rhomin:\t\t\t %e\n", rhomin);
#endif
#if FRAGMENTATION
fprintf(stdout, "damagemin:\t\t %e\n", damagemin);
#endif
#if PALPHA_POROSITY
fprintf(stdout, "alphamin:\t\t %e\n", alphamin);
#endif
#if INVISCID_SPH
fprintf(stdout, "betamin:\t\t %e\n", betamin);
#endif
#if EPSALPHA_POROSITY
fprintf(stdout, "alpha_epspormin:\t\t %e\n", alpha_epspormin);
fprintf(stdout, "epsilon_vmin:\t\t %e\n", epsilon_vmin);
#endif
fprintf(stdout, "These values (if not 1e99) are taken from file <pc_values.dat>.\n");
}
}
/* set some initial values */
void init_values(void)
{
int i;
int matId;
if (param.verbose) {
printf("initialising material constants and copying them to the gpu\n");
}
transferMaterialsToGPU();
for (i = 0; i < numberOfParticles; i++) {
matId = p_host.materialId[i];
#if PALPHA_POROSITY
p_host.cs[i] = cs_porous[matId];
#else
p_host.cs[i] = sqrt(bulk_modulus[matId]/till_rho_0[matId]);
#endif
#if !READ_INITIAL_SML_FROM_PARTICLE_FILE
if (!(p_host.h[i] > 0)) {
p_host.h[i] = sml[matId];
}
#endif
}
}
// read in particle from start file
void read_particles_from_file(File inputFile) {
int my_anop;
int i;
int d;
int c;
#if SOLID || NAVIER_STOKES
int e;
#endif
/*int rc = 1;*/
char h5filename[256];
char h5massfilename[256];
char massfilename[256];
FILE *massfile;
double h5time;
double *x;
int *ix;
#if HDF5IO
/* hdf5 related stuff */
hid_t file_id;
hid_t x_id, v_id, m_id, mtype_id;
#if INTEGRATE_DENSITY
hid_t rho_id;
#endif
#if INTEGRATE_ENERGY
hid_t e_id;
#endif
hid_t time_id;
#if VARIABLE_SML || READ_INITIAL_SML_FROM_PARTICLE_FILE
hid_t sml_id;
#endif
hid_t dspace;
#if FRAGMENTATION
hid_t noaf_id, damage_id;
hid_t activation_thresholds_id;
hid_t maxnof_id;
int nofi;
int maxnof;
double *ax;
#endif
#if GRAVITATING_POINT_MASSES
hid_t rmin_id;
hid_t rmax_id;
#endif
#if JC_PLASTICITY
hid_t ep_id, T_id;
#endif
#if SOLID
hid_t S_id;
#endif
#if NAVIER_STOKES
hid_t Tshear_id;
#endif
#if PALPHA_POROSITY
hid_t p_id;
hid_t alpha_id;
#if SOLID
#if FRAGMENTATION
hid_t damage_porjutzi_id;
#endif
#endif
#endif
#if SIRONO_POROSITY
hid_t K_id;
hid_t rho_0prime_id;
hid_t rho_c_plus_id;
hid_t rho_c_minus_id;
hid_t compressive_strength_id;
hid_t tensile_strength_id;
hid_t flag_rho_0prime_id;
hid_t flag_plastic_id;
hid_t shear_strength_id;
#endif
#if EPSALPHA_POROSITY
hid_t alpha_epspor_id;
hid_t epsilon_v_id;
#endif
herr_t status;
/* filename extension is .h5 */
strcpy(massfilename, inputFile.name);
strcat(massfilename, ".mass");
strcpy(h5filename, inputFile.name);
strcpy(h5massfilename, inputFile.name);
strcat(h5filename, ".h5");
strcat(h5massfilename, ".mass.h5");
#endif
// set start timestep from input filename
const char* ext;
ext = strrchr(inputFile.name, '.');
if (!ext) {
printf("could not get start timestep from filename. make sure to name the file *.1234 or something like this");
exit(1);
} else {
sscanf(ext+1, "%04d", &startTimestep);
printf("set start timestep to %d\n", startTimestep);
}
#if HDF5IO
if (param.hdf5input) {
printf("reading particle data from hdf5 file: %s.h5\n", inputFile.name);
#if GRAVITATING_POINT_MASSES
printf("reading pointmass data from hdf5 file: %s.mass.h5\n", inputFile.name);
#endif
file_id = H5Fopen (h5filename, H5F_ACC_RDONLY, H5P_DEFAULT);
if (file_id < 0) {
fprintf(stderr, "********************** Error opening file %s\n", h5filename);
exit(1);
} else {
fprintf(stdout, "Using hdf5 input file %s\n", h5filename);
}
/* open the dataset for the positions */
x_id = H5Dopen(file_id, "/x", H5P_DEFAULT);
if (x_id < 0) {
fprintf(stderr, "Could not find locations in hdf5 file. Exiting.\n");
}
/* determine number of particles stored in hdf5 file */
dspace = H5Dget_space(x_id);
const int ndims = H5Sget_simple_extent_ndims(dspace);
hsize_t dims[ndims];
H5Sget_simple_extent_dims(dspace, dims, NULL);
my_anop = dims[0];
fprintf(stdout, "Reading data for %d particles.\n", my_anop);
/* allocate space for my_anop particles */
/* read positions */
x = (double *) malloc(sizeof(double) * my_anop * DIM);
status = H5Dread(x_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(x_id);
for (i = 0, d = 0; i < my_anop; i++, d += DIM) {
p_host.x[i] = x[d];
#if DIM > 1
p_host.y[i] = x[d+1];
#if DIM == 3
p_host.z[i] = x[d+2];
#endif
#endif
}
/* read velocities */
v_id = H5Dopen(file_id, "/v", H5P_DEFAULT);
if (v_id < 0) {
fprintf(stderr, "Could not find velocities in hdf5 file. Exiting.\n");
exit(1);
}
status = H5Dread(v_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(v_id);
for (i = 0, d = 0; i < my_anop; i++, d += DIM) {
p_host.vx[i] = x[d];
#if DIM > 1
p_host.vy[i] = x[d+1];
#if DIM == 3
p_host.vz[i] = x[d+2];
#endif
#endif
}
free(x);
/* read simulation time */
time_id = H5Dopen(file_id, "/time", H5P_DEFAULT);
if (time_id < 0) {
fprintf(stderr, "Could not find time in hdf5 file. Exiting.\n");
exit(1);
}
status = H5Dread(time_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &h5time);
status = H5Dclose(time_id);
fprintf(stdout, "Current time: %g\n", h5time);
startTime = h5time;
/* read mass */
/* mass */
dims[0] = my_anop;
dims[1] = 1;
x = (double * ) malloc(sizeof(double) * my_anop);
m_id = H5Dopen(file_id, "/m", H5P_DEFAULT);
if (m_id < 0) {
fprintf(stderr, "Could not find mass information in hdf5 file. Exiting\n");
exit(1);
}
status = H5Dread(m_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(m_id);
for (i = 0; i < my_anop; i++) {
p_host.m[i] = x[i];
}
free(x);
#if PALPHA_POROSITY
/* read alpha_jutzi */
dims[0] = my_anop;
dims[1] = 1;
alpha_id = H5Dopen(file_id, "/alpha_jutzi", H5P_DEFAULT);
if (alpha_id < 0) {
fprintf(stderr, "Could not find alpha_jutzi information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(alpha_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(alpha_id);
for (i = 0; i < my_anop; i++) {
p_host.alpha_jutzi[i] = x[i];
}
free(x);
/* read pressure */
p_id = H5Dopen(file_id, "/p", H5P_DEFAULT);
if (p_id < 0) {
fprintf(stderr, "Could not find pressure information in hdf5 file. Exiting\n");
exit(1);
} else {
fprintf(stdout, "Reading actual pressure data to pressure_old on the device.\n");
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(p_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(p_id);
for (i = 0; i < my_anop; i++) {
p_host.pold[i] = x[i];
}
free(x);
#if FRAGMENTATION
/* damage_porjutzi */
damage_porjutzi_id = H5Dopen(file_id, "/DIM_root_of_damage_porjutzi", H5P_DEFAULT);
if (damage_porjutzi_id < 0) {
fprintf(stderr, "Could not find damage_porjutzi information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(damage_porjutzi_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(damage_porjutzi_id);
for (i = 0; i < my_anop; i++) {
p_host.damage_porjutzi[i] = x[i];
}
free(x);
#endif
#endif
#if SIRONO_POROSITY
/* read rho_c_plus */
rho_c_plus_id = H5Dopen(file_id, "/rho_c_plus", H5P_DEFAULT);
if (rho_c_plus_id < 0) {
fprintf(stderr, "Could not find rho_c_plus information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(rho_c_plus_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(rho_c_plus_id);
for (i = 0; i < my_anop; i++) {
p_host.rho_c_plus[i] = x[i];
}
free(x);
/* read rho_c_minus */
rho_c_minus_id = H5Dopen(file_id, "/rho_c_minus", H5P_DEFAULT);
if (rho_c_minus_id < 0) {
fprintf(stderr, "Could not find rho_c_minus information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(rho_c_minus_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(rho_c_minus_id);
for (i = 0; i < my_anop; i++) {
p_host.rho_c_minus[i] = x[i];
}
free(x);
/* read bulk modulus */
K_id = H5Dopen(file_id, "/K", H5P_DEFAULT);
if (K_id < 0) {
fprintf(stderr, "Could not find bulk modulus information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(K_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(K_id);
for (i = 0; i < my_anop; i++) {
p_host.K[i] = x[i];
}
free(x);
/* read rho_0prime */
rho_0prime_id = H5Dopen(file_id, "/rho_0prime", H5P_DEFAULT);
if (rho_0prime_id < 0) {
fprintf(stderr, "Could not find rho_0prime information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(rho_0prime_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(rho_0prime_id);
for (i = 0; i < my_anop; i++) {
p_host.rho_0prime[i] = x[i];
}
free(x);
/* read compressive_strength */
compressive_strength_id = H5Dopen(file_id, "/compressive_strength", H5P_DEFAULT);
if (compressive_strength_id < 0) {
fprintf(stderr, "Could not find compressive_strength information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(compressive_strength_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(compressive_strength_id);
for (i = 0; i < my_anop; i++) {
p_host.compressive_strength[i] = x[i];
}
free(x);
/* read tensile_strength */
tensile_strength_id = H5Dopen(file_id, "/tensile_strength", H5P_DEFAULT);
if (tensile_strength_id < 0) {
fprintf(stderr, "Could not find tensile_strength information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(tensile_strength_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(tensile_strength_id);
for (i = 0; i < my_anop; i++) {
p_host.tensile_strength[i] = x[i];
}
free(x);
/* read shear_strength */
shear_strength_id = H5Dopen(file_id, "/shear_strength", H5P_DEFAULT);
if (shear_strength_id < 0) {
fprintf(stderr, "Could not find shear_strength information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(shear_strength_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(shear_strength_id);
for (i = 0; i < my_anop; i++) {
p_host.shear_strength[i] = x[i];
}
free(x);
/* read flag_rho_0prime */
flag_rho_0prime_id = H5Dopen(file_id, "/flag_rho_0prime", H5P_DEFAULT);
if (flag_rho_0prime_id < 0) {
fprintf(stderr, "Could not flag_rho_0prime information in hdf5 file. Exiting\n");
exit(1);
}
ix = (int *) malloc(sizeof(int) * my_anop);
if (!(ix)) {
fprintf(stderr, "Cannot allocate enough memory.\n");
exit(1);
}
status = H5Dread(flag_rho_0prime_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, ix);
status = H5Dclose(flag_rho_0prime_id);
for (i = 0; i < my_anop; i++) {
p_host.flag_rho_0prime[i] = ix[i];
}
free(ix);
/* read flag_plastic */
flag_plastic_id = H5Dopen(file_id, "/flag_plastic", H5P_DEFAULT);
if (flag_plastic_id < 0) {
fprintf(stderr, "Could not flag_plastic information in hdf5 file. Exiting\n");
exit(1);
}
ix = (int *) malloc(sizeof(int) * my_anop);
status = H5Dread(flag_plastic_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, ix);
status = H5Dclose(flag_plastic_id);
for (i = 0; i < my_anop; i++) {
p_host.flag_plastic[i] = ix[i];
}
free(ix);
#endif
#if EPSALPHA_POROSITY
/* read alpha_epspor */
alpha_epspor_id = H5Dopen(file_id, "/alpha_epspor", H5P_DEFAULT);
if (alpha_epspor_id < 0) {
fprintf(stderr, "Could not find alpha_epspor information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(alpha_epspor_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(alpha_epspor_id);
for (i = 0; i < my_anop; i++) {
p_host.alpha_epspor[i] = x[i];
}
free(x);
/* read epsilon_v */
epsilon_v_id = H5Dopen(file_id, "/epsilon_v", H5P_DEFAULT);
if (epsilon_v_id < 0) {
fprintf(stderr, "Could not find epsilon_v information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(epsilon_v_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(epsilon_v_id);
for (i = 0; i < my_anop; i++) {
p_host.epsilon_v[i] = x[i];
}
free(x);
#endif
#if VARIABLE_SML || READ_INITIAL_SML_FROM_PARTICLE_FILE
/* read sml */
sml_id = H5Dopen(file_id, "/sml", H5P_DEFAULT);
if (sml_id < 0) {
fprintf(stderr, "Could not find smoothing length information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(sml_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(sml_id);
for (i = 0; i < my_anop; i++) {
p_host.h[i] = x[i];
}
free(x);
#endif
#if INTEGRATE_DENSITY
/* density */
rho_id = H5Dopen(file_id, "/rho", H5P_DEFAULT);
if (rho_id < 0) {
fprintf(stderr, "Could not find density information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(rho_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(rho_id);
for (i = 0; i < my_anop; i++) {
p_host.rho[i] = x[i];
}
free(x);
#endif
#if INTEGRATE_ENERGY
/* internal energy */
e_id = H5Dopen(file_id, "/e", H5P_DEFAULT);
if (e_id < 0) {
fprintf(stderr, "Could not find energy information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(e_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(e_id);
for (i = 0; i < my_anop; i++) {
p_host.e[i] = x[i];
}
free(x);
#endif
/* material types */
mtype_id = H5Dopen(file_id, "/material_type", H5P_DEFAULT);
if (mtype_id < 0) {
fprintf(stderr, "Could not material type information in hdf5 file. Exiting\n");
exit(1);
}
ix = (int *) malloc(sizeof(int) * my_anop);
if (!(ix)) {
fprintf(stderr, "Cannot allocate enough memory.\n");
exit(1);
}
status = H5Dread(mtype_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, ix);
status = H5Dclose(mtype_id);
for (i = 0; i < my_anop; i++) {
p_host.materialId[i] = ix[i];
}
free(ix);
#if JC_PLASTICITY
/* plastic strain */
ep_id = H5Dopen(file_id, "/ep", H5P_DEFAULT);
if (ep_id < 0) {
fprintf(stderr, "Could not find plastic strain information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(ep_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(ep_id);
for (i = 0; i < my_anop; i++) {
p_host.ep[i] = x[i];
}
free(x);
/* temperature */
T_id = H5Dopen(file_id, "/T", H5P_DEFAULT);
if (T_id < 0) {
fprintf(stderr, "Could not find temperature information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(T_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(T_id);
for (i = 0; i < my_anop; i++) {
p_host.T[i] = x[i];
}
free(x);
#endif
#if FRAGMENTATION
/* number of activated flaws */
noaf_id = H5Dopen(file_id, "/number_of_activated_flaws", H5P_DEFAULT);
if (noaf_id < 0) {
fprintf(stderr, "Could not find number of activated flaws information in hdf5 file. Exiting\n");
exit(1);
}
ix = (int *) malloc(sizeof(int) * my_anop);
status = H5Dread(noaf_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, ix);
status = H5Dclose(noaf_id);
for (i = 0; i < my_anop; i++) {
p_host.numActiveFlaws[i] = ix[i];
}
free(ix);
/* damage */
damage_id = H5Dopen(file_id, "/DIM_root_of_damage_tensile", H5P_DEFAULT);
if (damage_id < 0) {
fprintf(stderr, "Could not find tensile damage information in hdf5 file. Exiting\n");
exit(1);
}
x = (double * ) malloc(sizeof(double) * my_anop);
status = H5Dread(damage_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(damage_id);
for (i = 0; i < my_anop; i++) {
p_host.d[i] = x[i];
}
free(x);
/* now the activation thresholds */
/* read max number of activation threshold */
maxnof_id = H5Dopen(file_id, "/maximum_number_of_flaws", H5P_DEFAULT);
if (maxnof_id < 0) {
fprintf(stderr, "Could not find maximum number of flaws in hdf5 file. Exiting.\n");
exit(1);
}
status = H5Dread(maxnof_id, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &maxnof);
status = H5Dclose(maxnof_id);
fprintf(stdout, "Maximum number of activation thresholds for a particle in the data is %d\n", maxnof);
/* now read the activation thresholds */
dims[0] = my_anop;
dims[1] = maxnof;
x = (double *) malloc(sizeof(double) * my_anop * maxnof);
if (!x) {
fprintf(stderr, "Cannot allocate enough memory.\n");
exit(1);
}
activation_thresholds_id = H5Dopen(file_id, "/activation_thresholds", H5P_DEFAULT);
if (activation_thresholds_id < 0) {
fprintf(stderr, "Could not find activation thresholds in hdf5 file. Exiting.\n");
exit(1);
}
status = H5Dread(activation_thresholds_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(activation_thresholds_id);
ax = (double *) malloc(sizeof(double) * maxnof);
for (i = 0; i < my_anop; i++) {
nofi = 0;
while (x[i*maxnof + nofi] > 0 && nofi < maxnof) {
ax[nofi] = x[i*maxnof + nofi];
nofi++;
}
p_host.numFlaws[i] = nofi;
for (d = 0; d < nofi; d++) {
p_host.flaws[i*MAX_NUM_FLAWS+d] = ax[d];
}
}
free(ax);
free(x);
#endif
#if NAVIER_STOKES
/* deviatoric stresses */
x = (double *) malloc(sizeof(double) * my_anop * DIM * DIM);
dims[0] = my_anop;
dims[1] = DIM*DIM;
Tshear_id = H5Dopen(file_id, "/viscous_shear_stress", H5P_DEFAULT);
if (Tshear_id < 0) {
fprintf(stderr, "Could not find viscous_shear_stress information in hdf5 file. Exiting\n");
exit(1);
}
status = H5Dread(Tshear_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(Tshear_id);
for (i = 0; i < my_anop; i++) {
for (d = 0; d < DIM; d++) {
for (e = 0; e < DIM; e++) {
p_host.Tshear[i*DIM*DIM+d*DIM+e] = x[i*DIM*DIM + d*DIM + e];
}
}
}
free(x);
#endif
#if SOLID
/* deviatoric stresses */
x = (double *) malloc(sizeof(double) * my_anop * DIM * DIM);
dims[0] = my_anop;
dims[1] = DIM*DIM;
S_id = H5Dopen(file_id, "/deviatoric_stress", H5P_DEFAULT);
if (S_id < 0) {
fprintf(stderr, "Could not find stress information in hdf5 file. Exiting\n");
exit(1);
}
status = H5Dread(S_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(S_id);
for (i = 0; i < my_anop; i++) {
for (d = 0; d < DIM; d++) {
for (e = 0; e < DIM; e++) {
p_host.S[i*DIM*DIM+d*DIM+e] = x[i*DIM*DIM + d*DIM + e];
}
}
}
free(x);
#endif
H5Fclose(file_id);
#if GRAVITATING_POINT_MASSES
file_id = H5Fopen (h5massfilename, H5F_ACC_RDONLY, H5P_DEFAULT);
if (file_id < 0) {
fprintf(stderr, "********************** Error opening file %s\n", h5massfilename);
exit(1);
} else {
fprintf(stdout, "Using hdf5 input file %s\n", h5massfilename);
}
/* open the dataset for the positions */
x_id = H5Dopen(file_id, "/x", H5P_DEFAULT);
if (x_id < 0) {
fprintf(stderr, "Could not find locations in hdf5 file. Exiting.\n");
}
/* determine number of particles stored in hdf5 file */
dspace = H5Dget_space(x_id);
const int mndims = H5Sget_simple_extent_ndims(dspace);
hsize_t mdims[mndims];
H5Sget_simple_extent_dims(dspace, mdims, NULL);
my_anop = mdims[0];
fprintf(stdout, "Reading data for %d pointmasses.\n", my_anop);
/* allocate space for my_anop particles */
/* read positions */
x = (double *) malloc(sizeof(double) * my_anop * DIM);
status = H5Dread(x_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(x_id);
for (i = 0, d = 0; i < my_anop; i++, d += DIM) {
pointmass_host.x[i] = x[d];
#if DIM > 1
pointmass_host.y[i] = x[d+1];
#if DIM == 3
pointmass_host.z[i] = x[d+2];
#endif
#endif
}
/* read velocities */
v_id = H5Dopen(file_id, "/v", H5P_DEFAULT);
if (v_id < 0) {
fprintf(stderr, "Could not find velocities in hdf5 file. Exiting.\n");
exit(1);
}
status = H5Dread(v_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(v_id);
for (i = 0, d = 0; i < my_anop; i++, d += DIM) {
pointmass_host.vx[i] = x[d];
#if DIM > 1
pointmass_host.vy[i] = x[d+1];
#if DIM == 3
pointmass_host.vz[i] = x[d+2];
#endif
#endif
}
/* read mass */
/* mass */
dims[0] = my_anop;
dims[1] = 1;
free(x);
x = (double * ) malloc(sizeof(double) * my_anop);
m_id = H5Dopen(file_id, "/m", H5P_DEFAULT);
if (m_id < 0) {
fprintf(stderr, "Could not find mass information in hdf5 file. Exiting\n");
exit(1);
}
status = H5Dread(m_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(m_id);
for (i = 0; i < my_anop; i++) {
pointmass_host.m[i] = x[i];
}
rmin_id = H5Dopen(file_id, "/rmin", H5P_DEFAULT);
if (rmin_id < 0) {
fprintf(stderr, "Could not find rmin information in hdf5 file. Exiting\n");
exit(1);
}
status = H5Dread(rmin_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(rmin_id);
for (i = 0; i < my_anop; i++) {
pointmass_host.rmin[i] = x[i];
}
rmax_id = H5Dopen(file_id, "/rmax", H5P_DEFAULT);
if (rmax_id < 0) {
fprintf(stderr, "Could not find rmax information in hdf5 file. Exiting\n");
exit(1);
}
status = H5Dread(rmax_id, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, x);
status = H5Dclose(rmax_id);
for (i = 0; i < my_anop; i++) {
pointmass_host.rmax[i] = x[i];
}
free(x);
H5Fclose(file_id);
#endif
if (param.verbose) {
fprintf(stdout, "%d\n", status);
}
}
#endif
#if FRAGMENTATION
maxNumFlaws_host = MAX_NUM_FLAWS;
#endif
int columns;
char iotmp[256];
if (!param.hdf5input) {
for (i = 0; i < numberOfParticles; i++) {
// read in coordinates
columns = 0;
if (!fscanf(inputFile.data, "%s", &iotmp))
fprintf(stderr, "could not read x-position from input file\n");
p_host.x[i] = atof(iotmp);
columns++;
#if DIM > 1
if (!fscanf(inputFile.data, "%s", &iotmp))
fprintf(stderr, "could not read y-position from input file\n");
p_host.y[i] = atof(iotmp);
columns++;