/* Counterpart for complex256 */
hid_t create_ieee_complex256(const char *byteorder) {
herr_t err = 0;
hid_t float_id, complex_id;
H5T_order_t h5order = H5Tget_order(H5T_NATIVE_LDOUBLE);
complex_id = H5Tcreate(H5T_COMPOUND, sizeof(npy_complex256));
float_id = H5Tcopy(H5T_NATIVE_LDOUBLE);
if (float_id < 0)
{
H5Tclose(complex_id);
return float_id;
}
if ((strcmp(byteorder, "little") == 0) && (h5order != H5T_ORDER_LE))
err = H5Tset_order(float_id, H5T_ORDER_LE);
else if ((strcmp(byteorder, "big") == 0) && (h5order != H5T_ORDER_BE))
err = H5Tset_order(float_id, H5T_ORDER_BE);
if (err < 0)
{
H5Tclose(complex_id);
return err;
}
H5Tinsert(complex_id, "r", HOFFSET(npy_complex256, real), float_id);
H5Tinsert(complex_id, "i", HOFFSET(npy_complex256, imag), float_id);
H5Tclose(float_id);
return complex_id;
}
/* This only works for datatypes that are not Complex. However,
these types should already been created with correct byteorder */
herr_t set_order(hid_t type_id, const char *byteorder) {
herr_t status=0;
if (! is_complex(type_id)) {
if (strcmp(byteorder, "little") == 0)
status = H5Tset_order(type_id, H5T_ORDER_LE);
else if (strcmp(byteorder, "big") == 0)
status = H5Tset_order(type_id, H5T_ORDER_BE);
else if (strcmp(byteorder, "irrelevant") == 0) {
/* Do nothing because 'irrelevant' doesn't require setting the
byteorder explicitely */
/* status = H5Tset_order(type_id, H5T_ORDER_NONE ); */
}
else {
fprintf(stderr, "Error: unsupported byteorder <%s>\n", byteorder);
status = -1;
}
}
return status;
}
static
void *tts_error_thread(void UNUSED *arg)
{
hid_t dataspace, datatype, dataset;
hsize_t dimsf[1]; /* dataset dimensions */
H5E_auto2_t old_error_cb;
void *old_error_client_data;
int value;
int ret;
/* preserve previous error stack handler */
H5Eget_auto2(H5E_DEFAULT, &old_error_cb, &old_error_client_data);
/* set each thread's error stack handler */
H5Eset_auto2(H5E_DEFAULT, error_callback, NULL);
/* define dataspace for dataset */
dimsf[0] = 1;
dataspace = H5Screate_simple(1, dimsf, NULL);
assert(dataspace >= 0);
/* define datatype for the data using native little endian integers */
datatype = H5Tcopy(H5T_NATIVE_INT);
assert(datatype >= 0);
H5Tset_order(datatype, H5T_ORDER_LE);
/* create a new dataset within the file */
dataset = H5Dcreate2(error_file, DATASETNAME, datatype, dataspace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if(dataset >= 0) { /* not an error */
value = WRITE_NUMBER;
H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &value);
H5Dclose(dataset);
} /* end if */
ret = H5Tclose(datatype);
assert(ret >= 0);
ret = H5Sclose(dataspace);
assert(ret >= 0);
/* turn our error stack handler off */
H5Eset_auto2(H5E_DEFAULT, old_error_cb, old_error_client_data);
return NULL;
}
int create_new_dataset(H5block *d){
hid_t file_id, dataset_id, dataspace_id, status, dcpl, datatype;
file_id = H5Fopen(d->name, H5F_ACC_RDWR, H5P_DEFAULT);
hsize_t dims[2];
dims[0] = d->x_index_dim;
dims[1] = d->y_index_dim;
dataspace_id = H5Screate_simple(2, dims, NULL);
datatype = H5Tcopy(H5T_NATIVE_FLOAT);
status = H5Tset_order(datatype, H5T_ORDER_LE);
char buffer[50];
sprintf(buffer, "/dset%ld", d->ticks);
dataset_id = H5Dcreate(file_id, buffer, datatype, dataspace_id, H5P_DEFAULT);
status = H5Dwrite(dataset_id, H5T_NATIVE_FLOAT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
d->field);
status = H5Dclose(dataset_id);
status = H5Tclose(datatype);
status = H5Sclose(dataspace_id);
status = H5Fclose(file_id);
}
int
write_data_to_hdf5_file (int nx, int ny, double **data, hid_t file)
{
hid_t dataset; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
dimsf[0] = nx;
dimsf[1] = ny;
dataspace = H5Screate_simple (RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian DOUBLE numbers.
*/
datatype = H5Tcopy (H5T_NATIVE_DOUBLE);
status = H5Tset_order (datatype, H5T_ORDER_LE);
/*
* Create a new dataset within the file using defined dataspace and
* datatype and default dataset creation properties.
*/
dataset = H5Dcreate (file, "Temperature", datatype, dataspace, H5P_DEFAULT);
/*
* Write the data to the dataset using default transfer properties.
*/
status = H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
/*
* Close/release resources.
*/
H5Sclose (dataspace);
H5Tclose (datatype);
H5Dclose (dataset);
return 0;
}
/*-------------------------------------------------------------------------
* Function: create_nbit_dsets_float
*
* Purpose: Create a dataset of FLOAT datatype with nbit filter
*
* Return: Success: 0
* Failure: -1
*
* Programmer: Raymond Lu
* 29 March 2011
*
* Modifications:
*
*-------------------------------------------------------------------------
*/
int
create_nbit_dsets_float(hid_t fid, hid_t fsid, hid_t msid)
{
hid_t dataset = -1; /* dataset handles */
hid_t datatype = -1;
hid_t dcpl = -1;
size_t precision, offset;
float data[NX][NY]; /* data to write */
float fillvalue = -2.2f;
hsize_t chunk[RANK] = {CHUNK0, CHUNK1};
int i, j;
/*
* Data and output buffer initialization.
*/
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = ((float)(i + j + 1))/3;
}
/*
* Create the dataset creation property list, add the Scale-Offset
* filter, set the chunk size, and set the fill value.
*/
if((dcpl = H5Pcreate(H5P_DATASET_CREATE)) < 0)
TEST_ERROR
if(H5Pset_nbit(dcpl) < 0)
TEST_ERROR
if(H5Pset_chunk(dcpl, RANK, chunk) < 0)
TEST_ERROR
if(H5Pset_fill_value(dcpl, H5T_NATIVE_FLOAT, &fillvalue) < 0)
TEST_ERROR
/* Define user-defined single-precision floating-point type for dataset.
* A 20-bit little-endian data type. */
if((datatype = H5Tcopy(H5T_IEEE_F32LE)) < 0)
TEST_ERROR
if(H5Tset_fields(datatype, (size_t)26, (size_t)20, (size_t)6, (size_t)7, (size_t)13) < 0)
TEST_ERROR
offset = 7;
if(H5Tset_offset(datatype,offset) < 0)
TEST_ERROR
precision = 20;
if(H5Tset_precision(datatype,precision) < 0)
TEST_ERROR
if(H5Tset_size(datatype, (size_t)4) < 0)
TEST_ERROR
if(H5Tset_ebias(datatype, (size_t)31) < 0)
TEST_ERROR
/*
* Create a new dataset within the file using defined dataspace,
* user-defined datatype, and default dataset creation properties.
*/
if((dataset = H5Dcreate2(fid, DATASETNAME22, datatype, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
/*
* Write the data to the dataset using default transfer properties.
*/
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
/* Close dataset */
if(H5Dclose(dataset) < 0)
TEST_ERROR
/* Now create a dataset with a big-endian type */
if(H5Tset_order(datatype, H5T_ORDER_BE) < 0)
TEST_ERROR
if((dataset = H5Dcreate2(fid, DATASETNAME23, datatype, fsid,
H5P_DEFAULT, dcpl, H5P_DEFAULT)) < 0)
TEST_ERROR
if(H5Dwrite(dataset, H5T_NATIVE_FLOAT, msid, fsid, H5P_DEFAULT, data) < 0)
TEST_ERROR
if(H5Dclose(dataset) < 0)
TEST_ERROR
/*
* Close/release resources.
*/
if(H5Pclose(dcpl) < 0)
TEST_ERROR
return 0;
error:
H5E_BEGIN_TRY {
H5Pclose(dcpl);
H5Dclose(dataset);
} H5E_END_TRY;
return -1;
}
int main(void)
{
SRB_Info srb_info={ NULL, /* Use the server name in ~/.srb/MdasEnv */
NULL, /* Use the server port number in
* ~/.srb/MdasEnv */
NULL, /* Use the password in ~/.srb/MdasAuth */
0, /* Using Unix storage system. */
0600, /* Open file for read and write for owner */
-1 /* default */
};
hid_t fapl =-1, file;
hid_t dataspace, datatype, dataset;
hsize_t dimsf[2];
herr_t status = 0;
int data[NX][NY]; /* data to write */
int i, j;
/*
* Data and output buffer initialization.
*/
for (j = 0; j < NX; j++) {
for (i = 0; i < NY; i++)
data[j][i] = i*i + j*j;
}
/*
* 0 1 4 9 16 25
* 1 2 5 10 17 26
* 4 5 8 13 20 29
* 9 10 13 18 25 34
* 16 17 20 25 32 41
*/
/* Create access property list and set the driver to GASS */
fapl = H5Pcreate (H5P_FILE_ACCESS);
if (fapl < 0) {
printf (" H5Pcreate failed. \n");
return -1;
}
status = H5Pset_fapl_srb (fapl, srb_info);
if (status < 0) {
printf ("H5Pset_fapl_gass failed. \n");
return -1;
}
/*
* Open an existing file using H5F_ACC_RDWR access,
* and srb file access properties.
*/
file = H5Fopen(fileName, H5F_ACC_RDWR, fapl);
if (file < 0) {
printf ("H5Fopen failed. \n");
return -1;
}
/*
* Describe the size of the array and create the data space for fixed
* size dataset.
*/
dimsf[0] = NX;
dimsf[1] = NY;
dataspace = H5Screate_simple(RANK, dimsf, NULL);
if (dataspace < 0) {
printf ("H5Screate failed. \n");
return -1;
}
/*
* Define datatype for the data in the file.
* We will store little endian INT numbers.
*/
datatype = H5Tcopy(H5T_NATIVE_INT);
if (datatype < 0) {
printf ("H5Tcopy failed. \n");
return -1;
}
status = H5Tset_order(datatype, H5T_ORDER_LE);
if (status < 0) {
printf ("H5Tset_order failed. \n");
return -1;
}
/*
* Create a new dataset within the file using defined dataspace and
* datatype and default dataset creation properties.
*/
dataset = H5Dcreate(file, DATASETNAME, datatype, dataspace,
H5P_DEFAULT);
if (dataset < 0) {
printf ("H5Dcreate failed. \n");
return -1;
}
/*
* Write the data to the dataset using default transfer properties.
*/
status = H5Dwrite(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
if (status < 0) {
printf ("H5Dwrite failed. \n");
return -1;
}
/*
* Close/release resources.
*/
H5Sclose(dataspace);
H5Tclose(datatype);
H5Dclose(dataset);
H5Fclose(file);
H5Pclose(fapl);
printf("Test finished!\n");
return 0;
}
int
output (Array3D < zone > grid, Array3D < zone > fx, Array3D < zone > fy,
int time, char *filename)
{
#ifdef USE_HDF5
hid_t file, dataset; /* file and dataset handles */
hid_t datatype, dataspace; /* handles */
hsize_t dimsf[2]; /* dataset dimensions */
herr_t status;
double data[nx][ny];
char *names[] =
{ "Density", "Velx", "Vely", "Velz", "Energy", "Bx", "By", "Bz" };
int ll = 0;
stringstream hdf5_stream_filename;
string hdf5_filename;
#endif
ofstream fout;
ofstream gout;
double gammam1 = gammag - 1;
double rl, ri;
double px;
double py;
double pz;
double pressure;
double bx;
double by;
double bz;
double bsquared;
double et, ul, vl, wl, ke, al;
int ii = 0;
int jj = 0;
int kk = 0;
char outputdir[50] = "output/";
// char filename[50] = "out_2d_";
stringstream s;
stringstream stream_filename;
stringstream stream_temp_b;
string str_file_tag;
string str_output_filename;
string str_input_filename;
double ki = 24296.3696;
double mp = 1.67262158;
double mpi = 1.0 / mp;
double nt = 0;
double nt2 = 0;
double temperature = 0;
s.clear ();
s.width (5);
s.fill ('0');
s << time;
s >> str_file_tag;
stream_filename.clear ();
stream_filename << outputdir << filename << str_file_tag;
stream_filename >> str_input_filename;
#ifdef USE_HDF5
hdf5_stream_filename << outputdir << "hdf5_" << filename << str_file_tag <<
".h5";
hdf5_stream_filename >> hdf5_filename;
file =
H5Fcreate (hdf5_filename.c_str (), H5F_ACC_TRUNC, H5P_DEFAULT,
H5P_DEFAULT);
for (ll = 0; ll < ne; ll++)
{
dimsf[0] = nx;
dimsf[1] = ny;
dataspace = H5Screate_simple (RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian DOUBLE numbers.
*/
datatype = H5Tcopy (H5T_NATIVE_DOUBLE);
status = H5Tset_order (datatype, H5T_ORDER_LE);
/*
* Create a new dataset within the file using defined dataspace and
* datatype and default dataset creation properties.
*/
dataset = H5Dcreate (file, names[ll], datatype, dataspace, H5P_DEFAULT);
for (jj = 0; jj < ny; jj++)
{
for (ii = 0; ii < nx; ii++)
data[ii][jj] = grid[ii][jj][kk].array[ll];
}
/*
* Write the data to the dataset using default transfer properties.
*/
status = H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
/*
* Close/release resources.
*/
H5Sclose (dataspace);
H5Tclose (datatype);
H5Dclose (dataset);
}
dimsf[0] = nx;
dimsf[1] = ny;
dataspace = H5Screate_simple (RANK, dimsf, NULL);
/*
* Define datatype for the data in the file.
* We will store little endian DOUBLE numbers.
*/
datatype = H5Tcopy (H5T_NATIVE_DOUBLE);
status = H5Tset_order (datatype, H5T_ORDER_LE);
/*
* Create a new dataset within the file using defined dataspace and
* datatype and default dataset creation properties.
*/
dataset = H5Dcreate (file, "Pressure", datatype, dataspace, H5P_DEFAULT);
for (jj = 0; jj < ny; jj++)
{
for (ii = 0; ii < nx; ii++)
{
rl = grid[ii][jj][kk] _MASS;
px = grid[ii][jj][kk] _MOMX;
py = grid[ii][jj][kk] _MOMY;
pz = grid[ii][jj][kk] _MOMZ;
et = grid[ii][jj][kk] _ENER;
bx = grid[ii][jj][kk] _B_X;
by = grid[ii][jj][kk] _B_Y;
bz = grid[ii][jj][kk] _B_Z;
ri = 1.0 / rl;
ul = px * ri;
vl = py * ri;
wl = pz * ri;
ke = 0.5 * rl * (ul * ul + vl * vl + wl * wl);
bsquared = bx * bx + by * by + bz * bz;
pressure = et - ke - 0.5 * bsquared;
pressure = pressure * gammam1;
al = sqrt (gammag * pressure * ri);
nt = 2 * mpi * rl;
nt2 = nt * nt;
temperature = ki * pressure / nt;
temperature = log10 (temperature);
data[ii][jj] = pressure;
}
}
/*
* Write the data to the dataset using default transfer properties.
*/
status = H5Dwrite (dataset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL,
H5P_DEFAULT, data);
/*
* Close/release resources.
*/
H5Sclose (dataspace);
H5Tclose (datatype);
H5Dclose (dataset);
H5Fclose (file);
#endif /* HDF5 or not */
fout.open (str_input_filename.c_str ());
if (!fout)
{
cerr << "unable to open file " << endl;
}
jj = 0;
// Determine Div B
Array2D < double >divb (nx, ny);
double bx1, bx2, by1, by2, bz1, bz2;
for (ii = 1; ii < nx - 2; ii++)
{
for (jj = 1; jj < ny - 2; jj++)
{
bx1 = (grid[ii][jj][kk] _B_X + grid[ii - 1][jj][kk] _B_X);
bx2 = (grid[ii + 1][jj][kk] _B_X + grid[ii][jj][kk] _B_X);
by1 = (grid[ii][jj][kk] _B_Y + grid[ii][jj - 1][kk] _B_Y);
by2 = (grid[ii][jj + 1][kk] _B_Y + grid[ii][jj][kk] _B_Y);
// bz1 = ( grid[ii ][jj ][kk ]_B_Z + grid[ii ][jj ][kk-1]_B_Z );
// bz2 = ( grid[ii ][jj ][kk+1]_B_Z + grid[ii ][jj ][kk ]_B_Z );
//divb = (1/delta_x)*(bx2- bx1 + by2 -by1 +bz2 -bz1);
divb[ii][jj] = (0.5 / delta_x) * (bx2 - bx1 + by2 - by1);
}
}
for (ii = 0; ii < nx; ii++)
{
for (jj = 0; jj < ny; jj++)
{
rl = grid[ii][jj][kk] _MASS;
px = grid[ii][jj][kk] _MOMX;
py = grid[ii][jj][kk] _MOMY;
pz = grid[ii][jj][kk] _MOMZ;
et = grid[ii][jj][kk] _ENER;
bx = grid[ii][jj][kk] _B_X;
by = grid[ii][jj][kk] _B_Y;
bz = grid[ii][jj][kk] _B_Z;
ri = 1.0 / rl;
ul = px * ri;
vl = py * ri;
wl = pz * ri;
ke = 0.5 * rl * (ul * ul + vl * vl + wl * wl);
bsquared = bx * bx + by * by + bz * bz;
pressure = et - ke - 0.5 * bsquared;
pressure = pressure * gammam1;
al = sqrt (gammag * pressure * ri);
#ifdef DEBUG_BC
if (ii == 2 && jj == 2 && px != 0)
{
cout << px << endl;
cout << ul << endl;
cout << "wtf?" << endl;
}
#endif /* DEBUG_BC */
fout
<< setiosflags (ios::scientific)
<< " " << (rl)
<< " " << ul
<< " " << vl
<< " " << wl
<< " " << et
<< " " << bx
<< " " << by
<< " " << bz
<< " " << (pressure)
<< " " << (al)
<< " " << divb[ii][jj]
<< endl;
}
#ifdef TWODIM
fout << endl;
#endif /* TWODIM */
}
fout.close ();
gout.open ("gm.general");
gout << "file = /home/gmurphy/mhdvanleer-0.0.1/" << str_input_filename <<
endl;
gout << "grid = " << nx << " x " << ny << endl;
gout << "format = ascii" << endl;
gout << "interleaving = field" << endl;
gout << "majority = row" << endl;
gout << "field = V_sound, E_tot, Rho, Vel_X, Vel_Y, Pressure" << endl;
gout << "structure = scalar, scalar, scalar, scalar, scalar, scalar" <<
endl;
gout << "type = double, double, double, double, double, double" << endl;
gout <<
"dependency = positions, positions, positions, positions, positions, positions"
<< endl;
gout << "positions = regular, regular, 0, 1, 0, 1" << endl;
gout << "" << endl;
gout << "end" << endl;
gout.close ();
return 0;
}
