Commit 95d9c22a authored by Matthieu Schaller's avatar Matthieu Schaller
Browse files

The write_output() routine now writes an addition XMF file descriptor which...

The write_output() routine now writes an addition XMF file descriptor which can be used with ParaView to visualize the data in the HDF5 file.


Former-commit-id: fb33b6044b0c55c06bbf44df35c2f74ff0cafbca
parent c8a2b6f3
......@@ -39,6 +39,12 @@
#include "io_types.h"
/* File descriptor output routine */
void writeXMFheader(FILE** xmfFile, char* hdf5fileName, int N);
void writeXMFfooter(FILE* xmfFile);
void writeXMFline(FILE* xmfFile, char* fileName, char* name, int N, int dim, enum DATA_TYPE type);
/**
* @brief Write an attribute to a given HDF5 group.
*
......@@ -97,6 +103,8 @@ void writeAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data, int
* @brief Writes a data array in given HDF5 group.
*
* @param grp The group in which to write.
* @param fileName The name of the file in which the data is written
* @param xmfFile The FILE used to write the XMF description
* @param name The name of the array to write.
* @param type The #DATA_TYPE of the array.
* @param N The number of particles to write.
......@@ -108,7 +116,7 @@ void writeAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data, int
*
* Calls #error() if an error occurs.
*/
void writeArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N, int dim, char* part_c)
void writeArrayBackEnd(hid_t grp, char* fileName, FILE* xmfFile, char* name, enum DATA_TYPE type, int N, int dim, char* part_c)
{
hid_t h_data=0, h_err=0, h_space=0;
void* temp = 0;
......@@ -177,6 +185,10 @@ void writeArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N, int di
sprintf(buf, "Error while reading data array '%s'\n", name);
error(buf);
}
/* Write XMF description for this data set */
writeXMFline(xmfFile, fileName, name, N, dim, type);
/* Free and close everything */
free(temp);
......@@ -188,6 +200,8 @@ void writeArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N, int di
* @brief A helper macro to call the readArrayBackEnd function more easily.
*
* @param grp The group in which to write.
* @param fileName The name of the file in which the data is written
* @param xmfFile The FILE used to write the XMF description
* @param name The name of the array to write.
* @param type The #DATA_TYPE of the array.
* @param N The number of particles to write.
......@@ -195,10 +209,10 @@ void writeArrayBackEnd(hid_t grp, char* name, enum DATA_TYPE type, int N, int di
* @param part_c A (char*) pointer on the first occurence of the field of interest in the parts array
*
*/
#define writeArray(grp, name, type, N, dim, part, field) writeArrayBackEnd(grp, name, type, N, dim, (char*)(&(part[0]).field))
#define writeArray(grp, fileName, xmfFile, name, type, N, dim, part, field) writeArrayBackEnd(grp, fileName, xmfFile, name, type, N, dim, (char*)(&(part[0]).field))
/**
* @brief Writes an HDF5 output file (GADGET-3 type)
* @brief Writes an HDF5 output file (GADGET-3 type) with its XMF descriptor
*
* @param fileName The file to write.
* @param dim The dimension of the volume written to the file.
......@@ -218,6 +232,9 @@ void write_output ( char* fileName, double dim[3], struct part *parts, int N, i
{
hid_t h_file=0, h_grp=0;
int numParticles[6]={N,0};
FILE* xmfFile;
writeXMFheader(&xmfFile, fileName, N);
/* Open file */
printf("write_output: Opening file '%s'.\n", fileName);
......@@ -263,25 +280,106 @@ void write_output ( char* fileName, double dim[3], struct part *parts, int N, i
error( "Error while creating particle group.\n");
/* Write arrays */
writeArray(h_grp, "Coordinates", DOUBLE, N, 3, parts, x);
writeArray(h_grp, "Velocity", FLOAT, N, 3, parts, v);
writeArray(h_grp, "Mass", FLOAT, N, 1, parts, mass);
writeArray(h_grp, "SmoothingLength", FLOAT, N, 1, parts, h);
writeArray(h_grp, "InternalEnergy", FLOAT, N, 1, parts, u);
writeArray(h_grp, "ParticleIDs", ULONGLONG, N, 1, parts, id);
writeArray(h_grp, "TimeStep", FLOAT, N, 1, parts, dt);
writeArray(h_grp, "Acceleration", FLOAT, N, 3, parts, a);
writeArray(h_grp, "Density", FLOAT, N, 1, parts, rho);
writeArray(h_grp, fileName, xmfFile, "Coordinates", DOUBLE, N, 3, parts, x);
writeArray(h_grp, fileName, xmfFile, "Velocity", FLOAT, N, 3, parts, v);
writeArray(h_grp, fileName, xmfFile, "Mass", FLOAT, N, 1, parts, mass);
writeArray(h_grp, fileName, xmfFile, "SmoothingLength", FLOAT, N, 1, parts, h);
writeArray(h_grp, fileName, xmfFile, "InternalEnergy", FLOAT, N, 1, parts, u);
writeArray(h_grp, fileName, xmfFile, "ParticleIDs", ULONGLONG, N, 1, parts, id);
writeArray(h_grp, fileName, xmfFile, "TimeStep", FLOAT, N, 1, parts, dt);
writeArray(h_grp, fileName, xmfFile, "Acceleration", FLOAT, N, 3, parts, a);
writeArray(h_grp, fileName, xmfFile, "Density", FLOAT, N, 1, parts, rho);
/* Close particle group */
H5Gclose(h_grp);
/* Write LXMF file descriptor */
writeXMFfooter(xmfFile);
printf("write_output: Done writing particles...\n");
/* Close file */
H5Fclose(h_file);
}
/* ------------------------------------------------------------------------------------------------
* This part writes the XMF file descriptor enabling a visualisation through ParaView
* ------------------------------------------------------------------------------------------------ */
/**
* @brief Writes the lines corresponding to an array of the HDF5 output
*
* @param xmfFile The file in which to write
* @param fileName The name of the HDF5 file associated to this XMF descriptor.
* @param name The name of the array in the HDF5 file.
* @param N The number of particles.
* @param dim The dimension of the quantity (1 for scalars, 3 for vectors).
* @param type The type of the data to write.
*
* @todo Treat the types in a better way.
*/
void writeXMFline(FILE* xmfFile, char* fileName, char* name, int N, int dim, enum DATA_TYPE type )
{
fprintf(xmfFile, "<Attribute Name=\"%s\" AttributeType=\"%s\" Center=\"Node\">\n", name, dim == 1 ? "Scalar": "Vector");
if(dim == 1)
fprintf(xmfFile, "<DataItem Dimensions=\"%d\" NumberType=\"Double\" Precision=\"%d\" Format=\"HDF\">%s:/PartType0/%s</DataItem>\n", N, type==FLOAT ? 4:8, fileName, name);
else
fprintf(xmfFile, "<DataItem Dimensions=\"%d %d\" NumberType=\"Double\" Precision=\"%d\" Format=\"HDF\">%s:/PartType0/%s</DataItem>\n", N, dim, type==FLOAT ? 4:8, fileName, name);
fprintf(xmfFile, "</Attribute>\n");
}
/**
* @brief Writes the begin of the XMF file
*
* @param xmfFile The file to write in.
* @param hdf5FileName The name of the HDF5 file associated to this XMF descriptor.
* @param N The number of particles to write.
*
* @todo Exploit the XML nature of the XMF format to write a proper XML writer and simplify all the XMF-related stuff.
*/
void writeXMFheader(FILE** xmfFile, char* hdf5FileName, int N)
{
char buf[500];
sprintf(buf, "%s.xmf", hdf5FileName);
*xmfFile = fopen(buf, "w");
/* Write header */
fprintf(*xmfFile, "<?xml version=\"1.0\" ?> \n");
fprintf(*xmfFile, "<!DOCTYPE Xdmf SYSTEM \"Xdmf.dtd\" []> \n");
fprintf(*xmfFile, "<Xdmf xmlns:xi=\"http://www.w3.org/2003/XInclude\" Version=\"2.1\">\n");
fprintf(*xmfFile, "<Domain>\n");
fprintf(*xmfFile, "<Grid GridType=\"Collection\" CollectionType=\"Spatial\">\n");
fprintf(*xmfFile, "<Time Type=\"Single\" Value=\"%f\"/>\n", 0.);
fprintf(*xmfFile, "<Grid Name=\"Gas\" GridType=\"Uniform\">\n");
fprintf(*xmfFile, "<Topology TopologyType=\"Polyvertex\" Dimensions=\"%d\"/>\n", N);
/* Write coordinates info */
fprintf(*xmfFile, "<Geometry GeometryType=\"XYZ\">\n");
fprintf(*xmfFile, "<DataItem Dimensions=\"%d 3\" NumberType=\"Double\" Precision=\"8\" Format=\"HDF\">%s:/PartType0/Coordinates</DataItem>\n", N, hdf5FileName);
fprintf(*xmfFile, "</Geometry>\n");
}
/**
* @brief Writes the end of the XMF file (closes all open markups)
*
* @param xmfFile The file to write in.
*/
void writeXMFfooter(FILE* xmfFile)
{
/* Write end of file */
fprintf(xmfFile, "</Grid>\n");
fprintf(xmfFile, "</Grid>\n");
fprintf(xmfFile, "</Domain>\n");
fprintf(xmfFile, "</Xdmf>\n");
fclose(xmfFile);
}
#endif /* HAVE_HDF5 */
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