Revision 0461d2e117ce88704a56dd8bcbf6bf7787991b15 authored by Eh Tan on 08 November 2007, 23:28:46 UTC, committed by Eh Tan on 08 November 2007, 23:28:46 UTC
svn+ssh://svn@geodynamics.org/cig/mc/3D/CitcomS/trunk ........ r8194 | tan2 | 2007-10-30 14:49:58 -0700 (Tue, 30 Oct 2007) | 1 line Compute d(rho)/dr/rho from rho(r) ........ r8195 | tan2 | 2007-10-30 14:50:52 -0700 (Tue, 30 Oct 2007) | 1 line Fixed a bug in dimensionalizing density. Provided the formula of geoid calculation in the comments. Rearranged the order of functions. ........ r8196 | tan2 | 2007-10-30 14:53:50 -0700 (Tue, 30 Oct 2007) | 1 line A post-processing program to project geoid coefficents onto a regular (longitude, latitude) mesh ........ r8197 | tan2 | 2007-10-30 14:54:14 -0700 (Tue, 30 Oct 2007) | 1 line Added the C program project_geoid to the makefile ........ r8199 | tan2 | 2007-10-30 15:29:44 -0700 (Tue, 30 Oct 2007) | 1 line Minor modification ........ r8201 | tan2 | 2007-11-01 16:33:30 -0700 (Thu, 01 Nov 2007) | 1 line Print dv/v=dp/p=1.0 for the 1st Uzawa iteraion ........ r8202 | tan2 | 2007-11-01 16:33:50 -0700 (Thu, 01 Nov 2007) | 1 line Fixed an error in comment ........ r8204 | tan2 | 2007-11-05 17:03:35 -0800 (Mon, 05 Nov 2007) | 1 line Scaled topo with variable gravity. Fixed an error in comment. Rearranged computation. ........ r8205 | tan2 | 2007-11-05 17:03:55 -0800 (Mon, 05 Nov 2007) | 1 line Removed functions related sph. harm in lib/Regional_obsolete.c ........ r8206 | tan2 | 2007-11-05 17:04:20 -0800 (Mon, 05 Nov 2007) | 1 line Shrank the size of sph. harm arrays ........ r8207 | tan2 | 2007-11-05 17:04:43 -0800 (Mon, 05 Nov 2007) | 1 line Init'd some variables about vtk_io, which might be accessed with uninit'd values in output_finalize() ........ r8212 | tan2 | 2007-11-06 15:17:54 -0800 (Tue, 06 Nov 2007) | 1 line Fixed a few memory errors ........ r8213 | tan2 | 2007-11-06 15:18:12 -0800 (Tue, 06 Nov 2007) | 1 line Increase vlowstep to match the default value in pyre ........ r8214 | tan2 | 2007-11-06 15:18:35 -0800 (Tue, 06 Nov 2007) | 1 line Removed unused multigrid parameters ........ r8215 | tan2 | 2007-11-06 15:18:54 -0800 (Tue, 06 Nov 2007) | 1 line Added cgrad solver convergence parameters, increased buoyancy_ratio and lower the # of steps ........ r8226 | tan2 | 2007-11-07 11:51:56 -0800 (Wed, 07 Nov 2007) | 1 line Print a warning when matrix eqn solver not converging ........ r8227 | tan2 | 2007-11-07 11:52:17 -0800 (Wed, 07 Nov 2007) | 1 line Removed comp_el from default output, since it is not required for restart anymore. ........ r8228 | tan2 | 2007-11-07 11:52:39 -0800 (Wed, 07 Nov 2007) | 1 line Decreased the # of processors. This is the only way I can reproduce single-cell convection as in the manual. ........ r8235 | tan2 | 2007-11-08 11:18:26 -0800 (Thu, 08 Nov 2007) | 1 line Dereased the timestep size to reduce artifacts in advection ........ r8236 | tan2 | 2007-11-08 11:18:52 -0800 (Thu, 08 Nov 2007) | 1 line Update NEWS ........ r8237 | tan2 | 2007-11-08 11:19:12 -0800 (Thu, 08 Nov 2007) | 1 line Update the version number ........ r8241 | tan2 | 2007-11-08 13:17:14 -0800 (Thu, 08 Nov 2007) | 1 line Updated file ChangeLog to r8240 ........ r8242 | tan2 | 2007-11-08 13:36:55 -0800 (Thu, 08 Nov 2007) | 1 line Removed binary checkpoint files from makefile, as the file size is too big for distribution. ........ r8243 | tan2 | 2007-11-08 13:38:09 -0800 (Thu, 08 Nov 2007) | 1 line Updated file ChangeLog to r8242 ........ r8244 | tan2 | 2007-11-08 14:31:21 -0800 (Thu, 08 Nov 2007) | 1 line Replaced a system call by std C library remove() and disabled another system call (backup input file). Partially fixed issue130. All remaining system calls are in lib/Output_gzdir.c. ........ r8245 | tan2 | 2007-11-08 14:41:31 -0800 (Thu, 08 Nov 2007) | 1 line Updated file ChangeLog to r8244 ........
1 parent a828fa9
h5tocap.c
/*
* h5tocap.c by Luis Armendariz and Eh Tan.
* Copyright (C) 2006, California Institute of Technology.
*
* This program 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 2 of the License, or
* (at your option) any later version.
*
* This program 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 this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
#include <stdio.h>
#include <stdlib.h>
#include "hdf5.h"
#include "h5util.h"
static const char usage[] =
"Convert the CitcomS HDF5 output files to ASCII files,\n"
"with the format of the combined cap files\n"
"\n"
"Usage: h5tocap modelname step1 [step2 [...] ]\n";
static int convert(field_t **all_coord, int ncaps, char *prefix, int step);
static void output(const char *filename, field_t *coord, field_t *velocity,
field_t *temperature, field_t *viscosity);
int main(int argc, char *argv[])
{
char filename[100];
char prefix[100];
hid_t h5file;
hid_t input;
herr_t status;
int ncaps;
int cap;
int *steps;
int n, nsteps;
field_t *all_coord[12];
/************************************************************************
* Parse command-line parameters. *
************************************************************************/
/*
* Check number of arguments
*/
if (argc < 3)
{
fputs(usage, stderr);
return EXIT_FAILURE;
}
/*
* Recognize help arguments.
*/
if (strcmp(argv[1], "-h") == 0 || strcmp(argv[1], "--help") == 0)
{
fputs(usage, stderr);
return EXIT_FAILURE;
}
/*
* Read modelname
*/
sscanf(argv[1], "%s", prefix);
/*
* Read step(s) from argv[2:]
*/
/* Allocate at least one step (we know argc > 2) */
nsteps = argc - 2;
steps = (int *) malloc(nsteps * sizeof(int));
/* Convert argv[2:] into int array */
for(n = 2; n < argc; n++)
{
char *endptr;
steps[n-2] = (int)strtol(argv[n], &endptr, 10);
if (!(argv[n][0] != '\0' && *endptr == '\0'))
{
fprintf(stderr, "Error: Invalid step \"%s\"\n", argv[n]);
return EXIT_FAILURE;
}
}
/*
* Open HDF5 file (read-only). Complain if invalid.
*/
snprintf(filename, 99, "%s.h5", prefix);
h5file = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
if (h5file < 0)
{
fprintf(stderr, "Could not open HDF5 file \"%s\"\n", filename);
return EXIT_FAILURE;
}
/*
* Read model parameters from file
*/
input = H5Gopen(h5file, "input");
if (input < 0)
{
fprintf(stderr, "Could not open /input group in \"%s\"\n", filename);
status = H5Fclose(h5file);
return EXIT_FAILURE;
}
status = get_attribute_int(input, "nproc_surf", &ncaps);
status = H5Gclose(input);
/*
* Read coordinate of all caps
*/
for(cap = 0; cap < ncaps; cap++)
{
all_coord[cap] = open_field(h5file, "coord");
read_field(h5file, all_coord[cap], cap);
}
status = H5Fclose(h5file);
/*
* Convert files for each step
*/
for(n = 0; n < nsteps; n++)
convert(all_coord, ncaps, prefix, steps[n]);
/* Release resources. */
for(cap = 0; cap < ncaps; cap++)
status = close_field(all_coord[cap]);
free(steps);
return EXIT_SUCCESS;
}
static int convert(field_t **all_coord, int ncaps, char *prefix, int step)
{
char filename[100];
hid_t h5file;
herr_t status;
field_t *velocity;
field_t *temperature;
field_t *viscosity;
int cap;
/*
* Open HDF5 file (read-only). Complain if invalid.
*/
snprintf(filename, 99, "%s.%d.h5", prefix, step);
h5file = H5Fopen(filename, H5F_ACC_RDONLY, H5P_DEFAULT);
if (h5file < 0)
{
fprintf(stderr, "Could not open HDF5 file \"%s\"\n", filename);
return EXIT_FAILURE;
}
/*
* Read data from file
*/
velocity = open_field(h5file, "velocity");
temperature = open_field(h5file, "temperature");
viscosity = open_field(h5file, "viscosity");
for(cap = 0; cap < ncaps; cap++)
{
char outfile[100];
read_field(h5file, velocity, cap);
read_field(h5file, temperature, cap);
read_field(h5file, viscosity, cap);
snprintf(outfile, 99, "%s.cap%02d.%d", prefix, cap, step);
output(outfile, all_coord[cap], velocity, temperature, viscosity);
}
/* Release resources. */
status = close_field(velocity);
status = close_field(temperature);
status = close_field(viscosity);
status = H5Fclose(h5file);
return 0;
}
static void output(const char *filename, field_t *coord, field_t *velocity,
field_t *temperature, field_t *viscosity)
{
int i, j, k;
int nodex = coord->dims[1];
int nodey = coord->dims[2];
int nodez = coord->dims[3];
FILE *file = fopen(filename, "w");
fprintf(stderr, "Writing %s\n", filename);
fprintf(file, "%d x %d x %d\n", nodex, nodey, nodez);
/* Traverse data in Citcom order */
for(j = 0; j < nodey; j++)
for(i = 0; i < nodex; i++)
for(k = 0; k < nodez; k++)
{
int n = k + j*nodez + i*nodez*nodey;
fprintf(file, "%.6e %.6e %.6e %.6e %.6e %.6e %.6e %.6e\n",
coord->data[3*n+0],
coord->data[3*n+1],
coord->data[3*n+2],
velocity->data[3*n+0],
velocity->data[3*n+1],
velocity->data[3*n+2],
temperature->data[n],
viscosity->data[n]);
}
fclose(file);
}
/* vim:noet:ts=8 sw=8
*/
Computing file changes ...