diff --git a/src/Makefile.am b/src/Makefile.am
index 93b0843a20405cd133752d0adc5dbdc82e5fe5e0..b0615db01c467f243ba3eb0b961370c31a26fe22 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -45,7 +45,7 @@ include_HEADERS = space.h runner.h queue.h task.h lock.h cell.h part.h const.h \
physical_constants.h physical_constants_cgs.h potential.h version.h \
hydro_properties.h riemann.h threadpool.h cooling.h cooling_struct.h sourceterms.h \
sourceterms_struct.h statistics.h memswap.h cache.h runner_doiact_vec.h profiler.h \
- dump.h logger.h active.h timeline.h
+ dump.h logger.h active.h timeline.h xmf.h
# Common source files
AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
@@ -54,7 +54,8 @@ AM_SOURCES = space.c runner.c queue.c task.c cell.c engine.c \
kernel_hydro.c tools.c part.c partition.c clocks.c parser.c \
physical_constants.c potential.c hydro_properties.c \
runner_doiact_fft.c threadpool.c cooling.c sourceterms.c \
- statistics.c runner_doiact_vec.c profiler.c dump.c logger.c
+ statistics.c runner_doiact_vec.c profiler.c dump.c logger.c \
+ part_type.c xmf.c
# Include files for distribution, not installation.
nobase_noinst_HEADERS = align.h approx_math.h atomic.h cycle.h error.h inline.h kernel_hydro.h kernel_gravity.h \
diff --git a/src/common_io.c b/src/common_io.c
index 20fa622c4023b159cd8071409e33f0754173cbf7..567ae7249dba788e6b379f8c05eb1139bff6bb94 100644
--- a/src/common_io.c
+++ b/src/common_io.c
@@ -47,9 +47,6 @@
#include "units.h"
#include "version.h"
-const char* particle_type_names[NUM_PARTICLE_TYPES] = {
- "Gas", "DM", "Boundary", "Dummy", "Star", "BH"};
-
/**
* @brief Converts a C data type to the HDF5 equivalent.
*
@@ -57,7 +54,7 @@ const char* particle_type_names[NUM_PARTICLE_TYPES] = {
* to change the exact storage types matching the code types in a transparent
*way.
*/
-hid_t hdf5Type(enum DATA_TYPE type) {
+hid_t io_hdf5_type(enum IO_DATA_TYPE type) {
switch (type) {
case INT:
@@ -87,7 +84,7 @@ hid_t hdf5Type(enum DATA_TYPE type) {
/**
* @brief Returns the memory size of the data type
*/
-size_t sizeOfType(enum DATA_TYPE type) {
+size_t io_sizeof_type(enum IO_DATA_TYPE type) {
switch (type) {
case INT:
@@ -119,7 +116,7 @@ size_t sizeOfType(enum DATA_TYPE type) {
*
* Returns an error if the type is not FLOAT or DOUBLE
*/
-int isDoublePrecision(enum DATA_TYPE type) {
+int io_is_double_precision(enum IO_DATA_TYPE type) {
switch (type) {
case FLOAT:
@@ -142,7 +139,8 @@ int isDoublePrecision(enum DATA_TYPE type) {
*
* Calls #error() if an error occurs.
*/
-void readAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data) {
+void io_read_attribute(hid_t grp, char* name, enum IO_DATA_TYPE type,
+ void* data) {
hid_t h_attr = 0, h_err = 0;
h_attr = H5Aopen(grp, name, H5P_DEFAULT);
@@ -150,7 +148,7 @@ void readAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data) {
error("Error while opening attribute '%s'", name);
}
- h_err = H5Aread(h_attr, hdf5Type(type), data);
+ h_err = H5Aread(h_attr, io_hdf5_type(type), data);
if (h_err < 0) {
error("Error while reading attribute '%s'", name);
}
@@ -169,8 +167,8 @@ void readAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data) {
*
* Calls #error() if an error occurs.
*/
-void writeAttribute(hid_t grp, const char* name, enum DATA_TYPE type,
- void* data, int num) {
+void io_write_attribute(hid_t grp, const char* name, enum IO_DATA_TYPE type,
+ void* data, int num) {
hid_t h_space = 0, h_attr = 0, h_err = 0;
hsize_t dim[1] = {num};
@@ -184,12 +182,12 @@ void writeAttribute(hid_t grp, const char* name, enum DATA_TYPE type,
error("Error while changing dataspace shape for attribute '%s'.", name);
}
- h_attr = H5Acreate1(grp, name, hdf5Type(type), h_space, H5P_DEFAULT);
+ h_attr = H5Acreate1(grp, name, io_hdf5_type(type), h_space, H5P_DEFAULT);
if (h_attr < 0) {
error("Error while creating attribute '%s'.", name);
}
- h_err = H5Awrite(h_attr, hdf5Type(type), data);
+ h_err = H5Awrite(h_attr, io_hdf5_type(type), data);
if (h_err < 0) {
error("Error while reading attribute '%s'.", name);
}
@@ -208,8 +206,8 @@ void writeAttribute(hid_t grp, const char* name, enum DATA_TYPE type,
*
* Calls #error() if an error occurs.
*/
-void writeStringAttribute(hid_t grp, const char* name, const char* str,
- int length) {
+void io_writeStringAttribute(hid_t grp, const char* name, const char* str,
+ int length) {
hid_t h_space = 0, h_attr = 0, h_err = 0, h_type = 0;
h_space = H5Screate(H5S_SCALAR);
@@ -248,8 +246,8 @@ void writeStringAttribute(hid_t grp, const char* name, const char* str,
* @param name The name of the attribute
* @param data The value to write
*/
-void writeAttribute_d(hid_t grp, const char* name, double data) {
- writeAttribute(grp, name, DOUBLE, &data, 1);
+void io_write_attribute_d(hid_t grp, const char* name, double data) {
+ io_write_attribute(grp, name, DOUBLE, &data, 1);
}
/**
@@ -258,8 +256,8 @@ void writeAttribute_d(hid_t grp, const char* name, double data) {
* @param name The name of the attribute
* @param data The value to write
*/
-void writeAttribute_f(hid_t grp, const char* name, float data) {
- writeAttribute(grp, name, FLOAT, &data, 1);
+void io_write_attribute_f(hid_t grp, const char* name, float data) {
+ io_write_attribute(grp, name, FLOAT, &data, 1);
}
/**
@@ -269,8 +267,8 @@ void writeAttribute_f(hid_t grp, const char* name, float data) {
* @param data The value to write
*/
-void writeAttribute_i(hid_t grp, const char* name, int data) {
- writeAttribute(grp, name, INT, &data, 1);
+void io_write_attribute_i(hid_t grp, const char* name, int data) {
+ io_write_attribute(grp, name, INT, &data, 1);
}
/**
@@ -279,8 +277,8 @@ void writeAttribute_i(hid_t grp, const char* name, int data) {
* @param name The name of the attribute
* @param data The value to write
*/
-void writeAttribute_l(hid_t grp, const char* name, long data) {
- writeAttribute(grp, name, LONG, &data, 1);
+void io_write_attribute_l(hid_t grp, const char* name, long data) {
+ io_write_attribute(grp, name, LONG, &data, 1);
}
/**
@@ -289,8 +287,8 @@ void writeAttribute_l(hid_t grp, const char* name, long data) {
* @param name The name of the attribute
* @param str The string to write
*/
-void writeAttribute_s(hid_t grp, const char* name, const char* str) {
- writeStringAttribute(grp, name, str, strlen(str));
+void io_write_attribute_s(hid_t grp, const char* name, const char* str) {
+ io_writeStringAttribute(grp, name, str, strlen(str));
}
/**
@@ -300,7 +298,7 @@ void writeAttribute_s(hid_t grp, const char* name, const char* str) {
*
* If the 'Units' group does not exist in the ICs, cgs units will be assumed
*/
-void readUnitSystem(hid_t h_file, struct UnitSystem* us) {
+void io_read_UnitSystem(hid_t h_file, struct UnitSystem* us) {
hid_t h_grp = H5Gopen(h_file, "/Units", H5P_DEFAULT);
@@ -318,14 +316,16 @@ void readUnitSystem(hid_t h_file, struct UnitSystem* us) {
}
/* Ok, Read the damn thing */
- readAttribute(h_grp, "Unit length in cgs (U_L)", DOUBLE,
- &us->UnitLength_in_cgs);
- readAttribute(h_grp, "Unit mass in cgs (U_M)", DOUBLE, &us->UnitMass_in_cgs);
- readAttribute(h_grp, "Unit time in cgs (U_t)", DOUBLE, &us->UnitTime_in_cgs);
- readAttribute(h_grp, "Unit current in cgs (U_I)", DOUBLE,
- &us->UnitCurrent_in_cgs);
- readAttribute(h_grp, "Unit temperature in cgs (U_T)", DOUBLE,
- &us->UnitTemperature_in_cgs);
+ io_read_attribute(h_grp, "Unit length in cgs (U_L)", DOUBLE,
+ &us->UnitLength_in_cgs);
+ io_read_attribute(h_grp, "Unit mass in cgs (U_M)", DOUBLE,
+ &us->UnitMass_in_cgs);
+ io_read_attribute(h_grp, "Unit time in cgs (U_t)", DOUBLE,
+ &us->UnitTime_in_cgs);
+ io_read_attribute(h_grp, "Unit current in cgs (U_I)", DOUBLE,
+ &us->UnitCurrent_in_cgs);
+ io_read_attribute(h_grp, "Unit temperature in cgs (U_T)", DOUBLE,
+ &us->UnitTemperature_in_cgs);
/* Clean up */
H5Gclose(h_grp);
@@ -337,23 +337,23 @@ void readUnitSystem(hid_t h_file, struct UnitSystem* us) {
* @param us The UnitSystem to dump
* @param groupName The name of the HDF5 group to write to
*/
-void writeUnitSystem(hid_t h_file, const struct UnitSystem* us,
- const char* groupName) {
+void io_write_UnitSystem(hid_t h_file, const struct UnitSystem* us,
+ const char* groupName) {
hid_t h_grpunit = 0;
h_grpunit = H5Gcreate1(h_file, groupName, 0);
if (h_grpunit < 0) error("Error while creating Unit System group");
- writeAttribute_d(h_grpunit, "Unit mass in cgs (U_M)",
- units_get_base_unit(us, UNIT_MASS));
- writeAttribute_d(h_grpunit, "Unit length in cgs (U_L)",
- units_get_base_unit(us, UNIT_LENGTH));
- writeAttribute_d(h_grpunit, "Unit time in cgs (U_t)",
- units_get_base_unit(us, UNIT_TIME));
- writeAttribute_d(h_grpunit, "Unit current in cgs (U_I)",
- units_get_base_unit(us, UNIT_CURRENT));
- writeAttribute_d(h_grpunit, "Unit temperature in cgs (U_T)",
- units_get_base_unit(us, UNIT_TEMPERATURE));
+ io_write_attribute_d(h_grpunit, "Unit mass in cgs (U_M)",
+ units_get_base_unit(us, UNIT_MASS));
+ io_write_attribute_d(h_grpunit, "Unit length in cgs (U_L)",
+ units_get_base_unit(us, UNIT_LENGTH));
+ io_write_attribute_d(h_grpunit, "Unit time in cgs (U_t)",
+ units_get_base_unit(us, UNIT_TIME));
+ io_write_attribute_d(h_grpunit, "Unit current in cgs (U_I)",
+ units_get_base_unit(us, UNIT_CURRENT));
+ io_write_attribute_d(h_grpunit, "Unit temperature in cgs (U_T)",
+ units_get_base_unit(us, UNIT_TEMPERATURE));
H5Gclose(h_grpunit);
}
@@ -362,31 +362,32 @@ void writeUnitSystem(hid_t h_file, const struct UnitSystem* us,
* @brief Writes the code version to the file
* @param h_file The (opened) HDF5 file in which to write
*/
-void writeCodeDescription(hid_t h_file) {
+void io_write_code_description(hid_t h_file) {
hid_t h_grpcode = 0;
h_grpcode = H5Gcreate1(h_file, "/Code", 0);
if (h_grpcode < 0) error("Error while creating code group");
- writeAttribute_s(h_grpcode, "Code Version", package_version());
- writeAttribute_s(h_grpcode, "Compiler Name", compiler_name());
- writeAttribute_s(h_grpcode, "Compiler Version", compiler_version());
- writeAttribute_s(h_grpcode, "Git Branch", git_branch());
- writeAttribute_s(h_grpcode, "Git Revision", git_revision());
- writeAttribute_s(h_grpcode, "Git Date", git_date());
- writeAttribute_s(h_grpcode, "Configuration options", configuration_options());
- writeAttribute_s(h_grpcode, "CFLAGS", compilation_cflags());
- writeAttribute_s(h_grpcode, "HDF5 library version", hdf5_version());
+ io_write_attribute_s(h_grpcode, "Code Version", package_version());
+ io_write_attribute_s(h_grpcode, "Compiler Name", compiler_name());
+ io_write_attribute_s(h_grpcode, "Compiler Version", compiler_version());
+ io_write_attribute_s(h_grpcode, "Git Branch", git_branch());
+ io_write_attribute_s(h_grpcode, "Git Revision", git_revision());
+ io_write_attribute_s(h_grpcode, "Git Date", git_date());
+ io_write_attribute_s(h_grpcode, "Configuration options",
+ configuration_options());
+ io_write_attribute_s(h_grpcode, "CFLAGS", compilation_cflags());
+ io_write_attribute_s(h_grpcode, "HDF5 library version", hdf5_version());
#ifdef HAVE_FFTW
- writeAttribute_s(h_grpcode, "FFTW library version", fftw3_version());
+ io_write_attribute_s(h_grpcode, "FFTW library version", fftw3_version());
#endif
#ifdef WITH_MPI
- writeAttribute_s(h_grpcode, "MPI library", mpi_version());
+ io_write_attribute_s(h_grpcode, "MPI library", mpi_version());
#ifdef HAVE_METIS
- writeAttribute_s(h_grpcode, "METIS library version", metis_version());
+ io_write_attribute_s(h_grpcode, "METIS library version", metis_version());
#endif
#else
- writeAttribute_s(h_grpcode, "MPI library", "Non-MPI version of SWIFT");
+ io_write_attribute_s(h_grpcode, "MPI library", "Non-MPI version of SWIFT");
#endif
H5Gclose(h_grpcode);
}
@@ -406,170 +407,6 @@ void writeCodeDescription(hid_t h_file) {
*
* @todo Use a proper XML library to avoid stupid copies.
*/
-FILE* prepareXMFfile(const char* baseName) {
- char buffer[1024];
-
- char fileName[FILENAME_BUFFER_SIZE];
- char tempFileName[FILENAME_BUFFER_SIZE];
- snprintf(fileName, FILENAME_BUFFER_SIZE, "%s.xmf", baseName);
- snprintf(tempFileName, FILENAME_BUFFER_SIZE, "%s_temp.xmf", baseName);
- FILE* xmfFile = fopen(fileName, "r");
- FILE* tempFile = fopen(tempFileName, "w");
-
- if (xmfFile == NULL) error("Unable to open current XMF file.");
-
- if (tempFile == NULL) error("Unable to open temporary file.");
-
- /* First we make a temporary copy of the XMF file and count the lines */
- int counter = 0;
- while (fgets(buffer, 1024, xmfFile) != NULL) {
- counter++;
- fprintf(tempFile, "%s", buffer);
- }
- fclose(tempFile);
- fclose(xmfFile);
-
- /* We then copy the XMF file back up to the closing lines */
- xmfFile = fopen(fileName, "w");
- tempFile = fopen(tempFileName, "r");
-
- if (xmfFile == NULL) error("Unable to open current XMF file.");
-
- if (tempFile == NULL) error("Unable to open temporary file.");
-
- int i = 0;
- while (fgets(buffer, 1024, tempFile) != NULL && i < counter - 3) {
- i++;
- fprintf(xmfFile, "%s", buffer);
- }
- fprintf(xmfFile, "\n");
- fclose(tempFile);
- remove(tempFileName);
-
- return xmfFile;
-}
-
-/**
- * @brief Writes the begin of the XMF file
- *
- * @todo Exploit the XML nature of the XMF format to write a proper XML writer
- *and simplify all the XMF-related stuff.
- */
-void createXMFfile(const char* baseName) {
-
- char fileName[FILENAME_BUFFER_SIZE];
- snprintf(fileName, FILENAME_BUFFER_SIZE, "%s.xmf", baseName);
- FILE* xmfFile = fopen(fileName, "w");
-
- 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 Name=\"TimeSeries\" GridType=\"Collection\" "
- "CollectionType=\"Temporal\">\n\n");
-
- fprintf(xmfFile, "</Grid>\n");
- fprintf(xmfFile, "</Domain>\n");
- fprintf(xmfFile, "</Xdmf>\n");
-
- fclose(xmfFile);
-}
-
-/**
- * @brief Writes the part of the XMF entry presenting the geometry of the
- *snapshot
- *
- * @param xmfFile The file to write in.
- * @param hdfFileName The name of the HDF5 file corresponding to this output.
- * @param time The current simulation time.
- */
-void writeXMFoutputheader(FILE* xmfFile, char* hdfFileName, float time) {
- /* Write end of file */
-
- fprintf(xmfFile, "<!-- XMF description for file: %s -->\n", hdfFileName);
- fprintf(xmfFile,
- "<Grid GridType=\"Collection\" CollectionType=\"Spatial\">\n");
- fprintf(xmfFile, "<Time Type=\"Single\" Value=\"%f\"/>\n", time);
-}
-
-/**
- * @brief Writes the end of the XMF file (closes all open markups)
- *
- * @param xmfFile The file to write in.
- * @param output The number of this output.
- * @param time The current simulation time.
- */
-void writeXMFoutputfooter(FILE* xmfFile, int output, float time) {
- /* Write end of the section of this time step */
-
- fprintf(xmfFile,
- "\n</Grid> <!-- End of meta-data for output=%03i, time=%f -->\n",
- output, time);
- fprintf(xmfFile, "\n</Grid> <!-- timeSeries -->\n");
- fprintf(xmfFile, "</Domain>\n");
- fprintf(xmfFile, "</Xdmf>\n");
-
- fclose(xmfFile);
-}
-
-void writeXMFgroupheader(FILE* xmfFile, char* hdfFileName, size_t N,
- enum PARTICLE_TYPE ptype) {
- fprintf(xmfFile, "\n<Grid Name=\"%s\" GridType=\"Uniform\">\n",
- particle_type_names[ptype]);
- fprintf(xmfFile,
- "<Topology TopologyType=\"Polyvertex\" Dimensions=\"%zu\"/>\n", N);
- fprintf(xmfFile, "<Geometry GeometryType=\"XYZ\">\n");
- fprintf(xmfFile,
- "<DataItem Dimensions=\"%zu 3\" NumberType=\"Double\" "
- "Precision=\"8\" "
- "Format=\"HDF\">%s:/PartType%d/Coordinates</DataItem>\n",
- N, hdfFileName, (int)ptype);
- fprintf(xmfFile,
- "</Geometry>\n <!-- Done geometry for %s, start of particle fields "
- "list -->\n",
- particle_type_names[ptype]);
-}
-
-void writeXMFgroupfooter(FILE* xmfFile, enum PARTICLE_TYPE ptype) {
- fprintf(xmfFile, "</Grid> <!-- End of meta-data for parttype=%s -->\n",
- particle_type_names[ptype]);
-}
-
-/**
- * @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 partTypeGroupName The name of the group containing the particles in
- *the HDF5 file.
- * @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, const char* fileName,
- const char* partTypeGroupName, const char* name, size_t 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=\"%zu\" NumberType=\"Double\" "
- "Precision=\"%d\" Format=\"HDF\">%s:%s/%s</DataItem>\n",
- N, type == FLOAT ? 4 : 8, fileName, partTypeGroupName, name);
- else
- fprintf(xmfFile,
- "<DataItem Dimensions=\"%zu %d\" NumberType=\"Double\" "
- "Precision=\"%d\" Format=\"HDF\">%s:%s/%s</DataItem>\n",
- N, dim, type == FLOAT ? 4 : 8, fileName, partTypeGroupName, name);
- fprintf(xmfFile, "</Attribute>\n");
-}
/**
* @brief Prepare the DM particles (in gparts) read in for the addition of the
@@ -581,7 +418,7 @@ void writeXMFline(FILE* xmfFile, const char* fileName,
* @param gparts The array of #gpart freshly read in.
* @param Ndm The number of DM particles read in.
*/
-void prepare_dm_gparts(struct gpart* const gparts, size_t Ndm) {
+void io_prepare_dm_gparts(struct gpart* const gparts, size_t Ndm) {
/* Let's give all these gparts a negative id */
for (size_t i = 0; i < Ndm; ++i) {
@@ -607,9 +444,9 @@ void prepare_dm_gparts(struct gpart* const gparts, size_t Ndm) {
* @param Ngas The number of gas particles read in.
* @param Ndm The number of DM particles read in.
*/
-void duplicate_hydro_gparts(struct part* const parts,
- struct gpart* const gparts, size_t Ngas,
- size_t Ndm) {
+void io_duplicate_hydro_gparts(struct part* const parts,
+ struct gpart* const gparts, size_t Ngas,
+ size_t Ndm) {
for (size_t i = 0; i < Ngas; ++i) {
@@ -645,9 +482,9 @@ void duplicate_hydro_gparts(struct part* const parts,
* @param Nstars The number of stars particles read in.
* @param Ndm The number of DM and gas particles read in.
*/
-void duplicate_star_gparts(struct spart* const sparts,
- struct gpart* const gparts, size_t Nstars,
- size_t Ndm) {
+void io_duplicate_star_gparts(struct spart* const sparts,
+ struct gpart* const gparts, size_t Nstars,
+ size_t Ndm) {
for (size_t i = 0; i < Nstars; ++i) {
@@ -679,8 +516,8 @@ void duplicate_star_gparts(struct spart* const sparts,
* @param dmparts The array of #gpart containg DM particles to be filled.
* @param Ndm The number of DM particles.
*/
-void collect_dm_gparts(const struct gpart* const gparts, size_t Ntot,
- struct gpart* const dmparts, size_t Ndm) {
+void io_collect_dm_gparts(const struct gpart* const gparts, size_t Ntot,
+ struct gpart* const dmparts, size_t Ndm) {
size_t count = 0;
diff --git a/src/common_io.h b/src/common_io.h
index bf1840d497c46f58568d1bed7cb3409f60e047ee..2ebfbbadcfd81ac09275da51a58235fa7e283ee3 100644
--- a/src/common_io.h
+++ b/src/common_io.h
@@ -23,17 +23,22 @@
/* Config parameters. */
#include "../config.h"
-#if defined(HAVE_HDF5)
-
+/* Local includes. */
#include "part.h"
#include "units.h"
+#define FIELD_BUFFER_SIZE 200
+#define PARTICLE_GROUP_BUFFER_SIZE 50
+#define FILENAME_BUFFER_SIZE 150
+
+#if defined(HAVE_HDF5)
+
/**
* @brief The different types of data used in the GADGET IC files.
*
* (This is admittedly a poor substitute to C++ templates...)
*/
-enum DATA_TYPE {
+enum IO_DATA_TYPE {
INT,
LONG,
LONGLONG,
@@ -45,68 +50,38 @@ enum DATA_TYPE {
CHAR
};
-/**
- * @brief The different particle types present in a GADGET IC file
- *
- */
-enum PARTICLE_TYPE {
- GAS = 0,
- DM = 1,
- BOUNDARY = 2,
- DUMMY = 3,
- STAR = 4,
- BH = 5,
- NUM_PARTICLE_TYPES
-};
-
-extern const char* particle_type_names[];
-
-#define FILENAME_BUFFER_SIZE 150
-#define FIELD_BUFFER_SIZE 200
-#define PARTICLE_GROUP_BUFFER_SIZE 50
-
-hid_t hdf5Type(enum DATA_TYPE type);
-size_t sizeOfType(enum DATA_TYPE type);
-int isDoublePrecision(enum DATA_TYPE type);
-
-void collect_dm_gparts(const struct gpart* const gparts, size_t Ntot,
- struct gpart* const dmparts, size_t Ndm);
-void prepare_dm_gparts(struct gpart* const gparts, size_t Ndm);
-void duplicate_hydro_gparts(struct part* const parts,
- struct gpart* const gparts, size_t Ngas,
- size_t Ndm);
-void duplicate_star_gparts(struct spart* const sparts,
- struct gpart* const gparts, size_t Nstars,
- size_t Ndm);
+hid_t io_hdf5_type(enum IO_DATA_TYPE type);
+size_t io_sizeof_type(enum IO_DATA_TYPE type);
+int io_is_double_precision(enum IO_DATA_TYPE type);
-void readAttribute(hid_t grp, char* name, enum DATA_TYPE type, void* data);
+void io_read_attribute(hid_t grp, char* name, enum IO_DATA_TYPE type,
+ void* data);
-void writeAttribute(hid_t grp, const char* name, enum DATA_TYPE type,
- void* data, int num);
+void io_write_attribute(hid_t grp, const char* name, enum IO_DATA_TYPE type,
+ void* data, int num);
-void writeAttribute_d(hid_t grp, const char* name, double data);
-void writeAttribute_f(hid_t grp, const char* name, float data);
-void writeAttribute_i(hid_t grp, const char* name, int data);
-void writeAttribute_l(hid_t grp, const char* name, long data);
-void writeAttribute_s(hid_t grp, const char* name, const char* str);
+void io_write_attribute_d(hid_t grp, const char* name, double data);
+void io_write_attribute_f(hid_t grp, const char* name, float data);
+void io_write_attribute_i(hid_t grp, const char* name, int data);
+void io_write_attribute_l(hid_t grp, const char* name, long data);
+void io_write_attribute_s(hid_t grp, const char* name, const char* str);
-void createXMFfile(const char* baseName);
-FILE* prepareXMFfile(const char* baseName);
-void writeXMFoutputheader(FILE* xmfFile, char* hdfFileName, float time);
-void writeXMFoutputfooter(FILE* xmfFile, int outputCount, float time);
-void writeXMFgroupheader(FILE* xmfFile, char* hdfFileName, size_t N,
- enum PARTICLE_TYPE ptype);
-void writeXMFgroupfooter(FILE* xmfFile, enum PARTICLE_TYPE ptype);
-void writeXMFline(FILE* xmfFile, const char* fileName,
- const char* partTypeGroupName, const char* name, size_t N,
- int dim, enum DATA_TYPE type);
+void io_write_code_description(hid_t h_file);
-void writeCodeDescription(hid_t h_file);
-
-void readUnitSystem(hid_t h_file, struct UnitSystem* us);
-void writeUnitSystem(hid_t h_grp, const struct UnitSystem* us,
- const char* groupName);
+void io_read_UnitSystem(hid_t h_file, struct UnitSystem* us);
+void io_write_UnitSystem(hid_t h_grp, const struct UnitSystem* us,
+ const char* groupName);
#endif /* defined HDF5 */
+void io_collect_dm_gparts(const struct gpart* const gparts, size_t Ntot,
+ struct gpart* const dmparts, size_t Ndm);
+void io_prepare_dm_gparts(struct gpart* const gparts, size_t Ndm);
+void io_duplicate_hydro_gparts(struct part* const parts,
+ struct gpart* const gparts, size_t Ngas,
+ size_t Ndm);
+void io_duplicate_star_gparts(struct spart* const sparts,
+ struct gpart* const gparts, size_t Nstars,
+ size_t Ndm);
+
#endif /* SWIFT_COMMON_IO_H */
diff --git a/src/hydro/Default/hydro_io.h b/src/hydro/Default/hydro_io.h
index bb35c914bcab8787f609b4dd49acd0cc883b4263..62e94b05ffea259aac99d4b3714e0eea7e7c955f 100644
--- a/src/hydro/Default/hydro_io.h
+++ b/src/hydro/Default/hydro_io.h
@@ -91,21 +91,25 @@ void hydro_write_particles(struct part* parts, struct io_props* list,
void writeSPHflavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
- writeAttribute_s(h_grpsph, "Thermal Conductivity Model",
- "Price (2008) without switch");
- writeAttribute_f(h_grpsph, "Thermal Conductivity alpha",
- const_conductivity_alpha);
- writeAttribute_s(h_grpsph, "Viscosity Model",
- "Morris & Monaghan (1997), Rosswog, Davies, Thielemann & "
- "Piran (2000) with additional Balsara (1995) switch");
- writeAttribute_f(h_grpsph, "Viscosity alpha_min", const_viscosity_alpha_min);
- writeAttribute_f(h_grpsph, "Viscosity alpha_max", const_viscosity_alpha_max);
- writeAttribute_f(h_grpsph, "Viscosity beta", 2.f);
- writeAttribute_f(h_grpsph, "Viscosity decay length", const_viscosity_length);
+ io_write_attribute_s(h_grpsph, "Thermal Conductivity Model",
+ "Price (2008) without switch");
+ io_write_attribute_f(h_grpsph, "Thermal Conductivity alpha",
+ const_conductivity_alpha);
+ io_write_attribute_s(
+ h_grpsph, "Viscosity Model",
+ "Morris & Monaghan (1997), Rosswog, Davies, Thielemann & "
+ "Piran (2000) with additional Balsara (1995) switch");
+ io_write_attribute_f(h_grpsph, "Viscosity alpha_min",
+ const_viscosity_alpha_min);
+ io_write_attribute_f(h_grpsph, "Viscosity alpha_max",
+ const_viscosity_alpha_max);
+ io_write_attribute_f(h_grpsph, "Viscosity beta", 2.f);
+ io_write_attribute_f(h_grpsph, "Viscosity decay length",
+ const_viscosity_length);
/* Time integration properties */
- writeAttribute_f(h_grpsph, "Maximal Delta u change over dt",
- const_max_u_change);
+ io_write_attribute_f(h_grpsph, "Maximal Delta u change over dt",
+ const_max_u_change);
}
/**
diff --git a/src/hydro/Gadget2/hydro_io.h b/src/hydro/Gadget2/hydro_io.h
index 162d368dd073be2fd0f06f4ecbc1431fb34e7798..3e46b2351eb6a3871946dd9c69c8d108b10da0df 100644
--- a/src/hydro/Gadget2/hydro_io.h
+++ b/src/hydro/Gadget2/hydro_io.h
@@ -108,13 +108,13 @@ void hydro_write_particles(struct part* parts, struct io_props* list,
void writeSPHflavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
- writeAttribute_s(h_grpsph, "Thermal Conductivity Model",
- "(No treatment) as in Springel (2005)");
- writeAttribute_s(
+ io_write_attribute_s(h_grpsph, "Thermal Conductivity Model",
+ "(No treatment) as in Springel (2005)");
+ io_write_attribute_s(
h_grpsph, "Viscosity Model",
"as in Springel (2005), i.e. Monaghan (1992) with Balsara (1995) switch");
- writeAttribute_f(h_grpsph, "Viscosity alpha", const_viscosity_alpha);
- writeAttribute_f(h_grpsph, "Viscosity beta", 3.f);
+ io_write_attribute_f(h_grpsph, "Viscosity alpha", const_viscosity_alpha);
+ io_write_attribute_f(h_grpsph, "Viscosity beta", 3.f);
}
/**
diff --git a/src/hydro/Gizmo/hydro_io.h b/src/hydro/Gizmo/hydro_io.h
index e5f221ae4345dc519a50d332131ecf296f318338..dcf8cd8fd6cf37c0d7f4ba718746ec7dc3e79b01 100644
--- a/src/hydro/Gizmo/hydro_io.h
+++ b/src/hydro/Gizmo/hydro_io.h
@@ -143,18 +143,18 @@ void hydro_write_particles(struct part* parts, struct io_props* list,
*/
void writeSPHflavour(hid_t h_grpsph) {
/* Gradient information */
- writeAttribute_s(h_grpsph, "Gradient reconstruction model",
- HYDRO_GRADIENT_IMPLEMENTATION);
+ io_write_attribute_s(h_grpsph, "Gradient reconstruction model",
+ HYDRO_GRADIENT_IMPLEMENTATION);
/* Slope limiter information */
- writeAttribute_s(h_grpsph, "Cell wide slope limiter model",
- HYDRO_SLOPE_LIMITER_CELL_IMPLEMENTATION);
- writeAttribute_s(h_grpsph, "Piecewise slope limiter model",
- HYDRO_SLOPE_LIMITER_FACE_IMPLEMENTATION);
+ io_write_attribute_s(h_grpsph, "Cell wide slope limiter model",
+ HYDRO_SLOPE_LIMITER_CELL_IMPLEMENTATION);
+ io_write_attribute_s(h_grpsph, "Piecewise slope limiter model",
+ HYDRO_SLOPE_LIMITER_FACE_IMPLEMENTATION);
/* Riemann solver information */
- writeAttribute_s(h_grpsph, "Riemann solver type",
- RIEMANN_SOLVER_IMPLEMENTATION);
+ io_write_attribute_s(h_grpsph, "Riemann solver type",
+ RIEMANN_SOLVER_IMPLEMENTATION);
}
/**
diff --git a/src/hydro/Minimal/hydro_io.h b/src/hydro/Minimal/hydro_io.h
index 8c83349a3e17d6b3375663698af7beeeab0636bc..2ec0cb11d1e3ccaaa09d9822c75b396364912df8 100644
--- a/src/hydro/Minimal/hydro_io.h
+++ b/src/hydro/Minimal/hydro_io.h
@@ -123,13 +123,13 @@ void writeSPHflavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
/* Nothing in this minimal model... */
- writeAttribute_s(h_grpsph, "Thermal Conductivity Model", "No treatment");
- writeAttribute_s(h_grpsph, "Viscosity Model",
- "Minimal treatment as in Monaghan (1992)");
+ io_write_attribute_s(h_grpsph, "Thermal Conductivity Model", "No treatment");
+ io_write_attribute_s(h_grpsph, "Viscosity Model",
+ "Minimal treatment as in Monaghan (1992)");
/* Time integration properties */
- writeAttribute_f(h_grpsph, "Maximal Delta u change over dt",
- const_max_u_change);
+ io_write_attribute_f(h_grpsph, "Maximal Delta u change over dt",
+ const_max_u_change);
}
/**
diff --git a/src/hydro/PressureEntropy/hydro_io.h b/src/hydro/PressureEntropy/hydro_io.h
index fcc8439f64d299b7dcb59e819f8dd273112ce25a..10243750c01d6bc64664f9834bc4cc245c786f49 100644
--- a/src/hydro/PressureEntropy/hydro_io.h
+++ b/src/hydro/PressureEntropy/hydro_io.h
@@ -123,16 +123,16 @@ void writeSPHflavour(hid_t h_grpsph) {
/* Viscosity and thermal conduction */
/* Nothing in this minimal model... */
- writeAttribute_s(h_grpsph, "Thermal Conductivity Model", "No treatment");
- writeAttribute_s(
+ io_write_attribute_s(h_grpsph, "Thermal Conductivity Model", "No treatment");
+ io_write_attribute_s(
h_grpsph, "Viscosity Model",
"as in Springel (2005), i.e. Monaghan (1992) with Balsara (1995) switch");
- writeAttribute_f(h_grpsph, "Viscosity alpha", const_viscosity_alpha);
- writeAttribute_f(h_grpsph, "Viscosity beta", 3.f);
+ io_write_attribute_f(h_grpsph, "Viscosity alpha", const_viscosity_alpha);
+ io_write_attribute_f(h_grpsph, "Viscosity beta", 3.f);
/* Time integration properties */
- writeAttribute_f(h_grpsph, "Maximal Delta u change over dt",
- const_max_u_change);
+ io_write_attribute_f(h_grpsph, "Maximal Delta u change over dt",
+ const_max_u_change);
}
/**
diff --git a/src/hydro_properties.c b/src/hydro_properties.c
index 815969975b4f5e6b39099e71bbbec4e43c875ddc..8db23a3de0123400fe691b0d60f076929e1b0b48 100644
--- a/src/hydro_properties.c
+++ b/src/hydro_properties.c
@@ -89,18 +89,19 @@ void hydro_props_print(const struct hydro_props *p) {
#if defined(HAVE_HDF5)
void hydro_props_print_snapshot(hid_t h_grpsph, const struct hydro_props *p) {
- writeAttribute_f(h_grpsph, "Adiabatic index", hydro_gamma);
- writeAttribute_i(h_grpsph, "Dimension", (int)hydro_dimension);
- writeAttribute_s(h_grpsph, "Scheme", SPH_IMPLEMENTATION);
- writeAttribute_s(h_grpsph, "Kernel function", kernel_name);
- writeAttribute_f(h_grpsph, "Kernel target N_ngb", p->target_neighbours);
- writeAttribute_f(h_grpsph, "Kernel delta N_ngb", p->delta_neighbours);
- writeAttribute_f(h_grpsph, "Kernel eta", p->eta_neighbours);
- writeAttribute_f(h_grpsph, "CFL parameter", p->CFL_condition);
- writeAttribute_f(h_grpsph, "Volume log(max(delta h))", p->log_max_h_change);
- writeAttribute_f(h_grpsph, "Volume max change time-step",
- pow_dimension(expf(p->log_max_h_change)));
- writeAttribute_i(h_grpsph, "Max ghost iterations",
- p->max_smoothing_iterations);
+ io_write_attribute_f(h_grpsph, "Adiabatic index", hydro_gamma);
+ io_write_attribute_i(h_grpsph, "Dimension", (int)hydro_dimension);
+ io_write_attribute_s(h_grpsph, "Scheme", SPH_IMPLEMENTATION);
+ io_write_attribute_s(h_grpsph, "Kernel function", kernel_name);
+ io_write_attribute_f(h_grpsph, "Kernel target N_ngb", p->target_neighbours);
+ io_write_attribute_f(h_grpsph, "Kernel delta N_ngb", p->delta_neighbours);
+ io_write_attribute_f(h_grpsph, "Kernel eta", p->eta_neighbours);
+ io_write_attribute_f(h_grpsph, "CFL parameter", p->CFL_condition);
+ io_write_attribute_f(h_grpsph, "Volume log(max(delta h))",
+ p->log_max_h_change);
+ io_write_attribute_f(h_grpsph, "Volume max change time-step",
+ pow_dimension(expf(p->log_max_h_change)));
+ io_write_attribute_i(h_grpsph, "Max ghost iterations",
+ p->max_smoothing_iterations);
}
#endif
diff --git a/src/io_properties.h b/src/io_properties.h
index af0d81aec8cf4901d2bfcce8cd023a2e04b804bf..4c972ea90c3353c80559a2ee82b9ded571a39d41 100644
--- a/src/io_properties.h
+++ b/src/io_properties.h
@@ -38,7 +38,7 @@ struct io_props {
char name[FIELD_BUFFER_SIZE];
/* Type of the field */
- enum DATA_TYPE type;
+ enum IO_DATA_TYPE type;
/* Dimension (1D, 3D, ...) */
int dimension;
@@ -87,7 +87,7 @@ struct io_props {
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_input_field_(char name[FIELD_BUFFER_SIZE],
- enum DATA_TYPE type, int dimension,
+ enum IO_DATA_TYPE type, int dimension,
enum DATA_IMPORTANCE importance,
enum UnitConversionFactor units,
char* field, size_t partSize) {
@@ -127,7 +127,7 @@ struct io_props io_make_input_field_(char name[FIELD_BUFFER_SIZE],
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE],
- enum DATA_TYPE type, int dimension,
+ enum IO_DATA_TYPE type, int dimension,
enum UnitConversionFactor units,
char* field, size_t partSize) {
struct io_props r;
@@ -170,7 +170,7 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE],
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_output_field_convert_part_(
- char name[FIELD_BUFFER_SIZE], enum DATA_TYPE type, int dimension,
+ char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum UnitConversionFactor units, char* field, size_t partSize,
struct part* parts, float (*functionPtr)(struct engine*, struct part*)) {
@@ -214,7 +214,7 @@ struct io_props io_make_output_field_convert_part_(
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_output_field_convert_gpart_(
- char name[FIELD_BUFFER_SIZE], enum DATA_TYPE type, int dimension,
+ char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum UnitConversionFactor units, char* field, size_t partSize,
struct gpart* gparts, float (*functionPtr)(struct engine*, struct gpart*)) {
diff --git a/src/parallel_io.c b/src/parallel_io.c
index e429ff641961da342187f0c297eba8041cfcc51a..d210ad05cefd659934e795bfbf9812fef4f82bd7 100644
--- a/src/parallel_io.c
+++ b/src/parallel_io.c
@@ -48,6 +48,7 @@
#include "part.h"
#include "stars_io.h"
#include "units.h"
+#include "xmf.h"
/**
* @brief Reads a data array from a given HDF5 group.
@@ -73,7 +74,7 @@ void readArray(hid_t grp, const struct io_props prop, size_t N,
const struct UnitSystem* internal_units,
const struct UnitSystem* ic_units) {
- const size_t typeSize = sizeOfType(prop.type);
+ const size_t typeSize = io_sizeof_type(prop.type);
const size_t copySize = typeSize * prop.dimension;
const size_t num_elements = N * prop.dimension;
@@ -102,7 +103,7 @@ void readArray(hid_t grp, const struct io_props prop, size_t N,
/* Check data type */
const hid_t h_type = H5Dget_type(h_data);
if (h_type < 0) error("Unable to retrieve data type from the file");
- /* if (!H5Tequal(h_type, hdf5Type(type))) */
+ /* if (!H5Tequal(h_type, hdf5_type(type))) */
/* error("Non-matching types between the code and the file"); */
/* Allocate temporary buffer */
@@ -140,7 +141,7 @@ void readArray(hid_t grp, const struct io_props prop, size_t N,
/* Read HDF5 dataspace in temporary buffer */
/* Dirty version that happens to work for vectors but should be improved */
/* Using HDF5 dataspaces would be better */
- const hid_t h_err = H5Dread(h_data, hdf5Type(prop.type), h_memspace,
+ const hid_t h_err = H5Dread(h_data, io_hdf5_type(prop.type), h_memspace,
h_filespace, h_plist_id, temp);
if (h_err < 0) {
error("Error while reading data array '%s'.", prop.name);
@@ -153,7 +154,7 @@ void readArray(hid_t grp, const struct io_props prop, size_t N,
/* message("Converting ! factor=%e", factor); */
- if (isDoublePrecision(prop.type)) {
+ if (io_is_double_precision(prop.type)) {
double* temp_d = temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
@@ -203,14 +204,14 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
const struct UnitSystem* internal_units,
const struct UnitSystem* snapshot_units) {
- const size_t typeSize = sizeOfType(props.type);
+ const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
/* message("Writing '%s' array...", props.name); */
/* Allocate temporary buffer */
- void* temp = malloc(num_elements * sizeOfType(props.type));
+ void* temp = malloc(num_elements * io_sizeof_type(props.type));
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Copy particle data to temporary buffer */
@@ -241,7 +242,7 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* message("Converting ! factor=%e", factor); */
- if (isDoublePrecision(props.type)) {
+ if (io_is_double_precision(props.type)) {
double* temp_d = temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
@@ -300,8 +301,8 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* Create dataset */
const hid_t h_data =
- H5Dcreate(grp, props.name, hdf5Type(props.type), h_filespace, H5P_DEFAULT,
- H5P_DEFAULT, H5P_DEFAULT);
+ H5Dcreate(grp, props.name, io_hdf5_type(props.type), h_filespace,
+ H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
if (h_data < 0) {
error("Error while creating dataset '%s'.", props.name);
}
@@ -315,7 +316,7 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
H5Pset_dxpl_mpio(h_plist_id, H5FD_MPIO_COLLECTIVE);
/* Write temporary buffer to HDF5 dataspace */
- h_err = H5Dwrite(h_data, hdf5Type(props.type), h_memspace, h_filespace,
+ h_err = H5Dwrite(h_data, io_hdf5_type(props.type), h_memspace, h_filespace,
h_plist_id, temp);
if (h_err < 0) {
error("Error while writing data array '%s'.", props.name);
@@ -323,19 +324,20 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* Write XMF description for this data set */
if (mpi_rank == 0)
- writeXMFline(xmfFile, fileName, partTypeGroupName, props.name, N_total,
- props.dimension, props.type);
+ xmf_write_line(xmfFile, fileName, partTypeGroupName, props.name, N_total,
+ props.dimension, props.type);
/* Write unit conversion factors for this data set */
char buffer[FIELD_BUFFER_SIZE];
units_cgs_conversion_string(buffer, snapshot_units, props.units);
- writeAttribute_d(h_data, "CGS conversion factor",
- units_cgs_conversion_factor(snapshot_units, props.units));
- writeAttribute_f(h_data, "h-scale exponent",
- units_h_factor(snapshot_units, props.units));
- writeAttribute_f(h_data, "a-scale exponent",
- units_a_factor(snapshot_units, props.units));
- writeAttribute_s(h_data, "Conversion factor", buffer);
+ io_write_attribute_d(
+ h_data, "CGS conversion factor",
+ units_cgs_conversion_factor(snapshot_units, props.units));
+ io_write_attribute_f(h_data, "h-scale exponent",
+ units_h_factor(snapshot_units, props.units));
+ io_write_attribute_f(h_data, "a-scale exponent",
+ units_a_factor(snapshot_units, props.units));
+ io_write_attribute_s(h_data, "Conversion factor", buffer);
/* Free and close everything */
free(temp);
@@ -383,11 +385,11 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
hid_t h_file = 0, h_grp = 0;
/* GADGET has only cubic boxes (in cosmological mode) */
double boxSize[3] = {0.0, -1.0, -1.0};
- long long numParticles[NUM_PARTICLE_TYPES] = {0};
- long long numParticles_highWord[NUM_PARTICLE_TYPES] = {0};
- size_t N[NUM_PARTICLE_TYPES] = {0};
- long long N_total[NUM_PARTICLE_TYPES] = {0};
- long long offset[NUM_PARTICLE_TYPES] = {0};
+ long long numParticles[swift_type_count] = {0};
+ long long numParticles_highWord[swift_type_count] = {0};
+ size_t N[swift_type_count] = {0};
+ long long N_total[swift_type_count] = {0};
+ long long offset[swift_type_count] = {0};
int dimension = 3; /* Assume 3D if nothing is specified */
size_t Ndm = 0;
@@ -406,7 +408,7 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
if (h_grp < 0) error("Error while opening runtime parameters\n");
/* Read the relevant information */
- readAttribute(h_grp, "PeriodicBoundariesOn", INT, periodic);
+ io_read_attribute(h_grp, "PeriodicBoundariesOn", INT, periodic);
/* Close runtime parameters */
H5Gclose(h_grp);
@@ -420,21 +422,21 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
const hid_t hid_dim = H5Aexists(h_grp, "Dimension");
if (hid_dim < 0)
error("Error while testing existance of 'Dimension' attribute");
- if (hid_dim > 0) readAttribute(h_grp, "Dimension", INT, &dimension);
+ if (hid_dim > 0) io_read_attribute(h_grp, "Dimension", INT, &dimension);
if (dimension != hydro_dimension)
error("ICs dimensionality (%dD) does not match code dimensionality (%dD)",
dimension, (int)hydro_dimension);
/* Read the relevant information and print status */
int flag_entropy_temp[6];
- readAttribute(h_grp, "Flag_Entropy_ICs", INT, flag_entropy_temp);
+ io_read_attribute(h_grp, "Flag_Entropy_ICs", INT, flag_entropy_temp);
*flag_entropy = flag_entropy_temp[0];
- readAttribute(h_grp, "BoxSize", DOUBLE, boxSize);
- readAttribute(h_grp, "NumPart_Total", LONGLONG, numParticles);
- readAttribute(h_grp, "NumPart_Total_HighWord", LONGLONG,
- numParticles_highWord);
+ io_read_attribute(h_grp, "BoxSize", DOUBLE, boxSize);
+ io_read_attribute(h_grp, "NumPart_Total", LONGLONG, numParticles);
+ io_read_attribute(h_grp, "NumPart_Total_HighWord", LONGLONG,
+ numParticles_highWord);
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ for (int ptype = 0; ptype < swift_type_count; ++ptype)
N_total[ptype] =
(numParticles[ptype]) + (numParticles_highWord[ptype] << 32);
@@ -447,7 +449,7 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
/* dim[1], dim[2]); */
/* Divide the particles among the tasks. */
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ for (int ptype = 0; ptype < swift_type_count; ++ptype) {
offset[ptype] = mpi_rank * N_total[ptype] / mpi_size;
N[ptype] = (mpi_rank + 1) * N_total[ptype] / mpi_size - offset[ptype];
}
@@ -458,7 +460,7 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
/* Read the unit system used in the ICs */
struct UnitSystem* ic_units = malloc(sizeof(struct UnitSystem));
if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
- readUnitSystem(h_file, ic_units);
+ io_read_UnitSystem(h_file, ic_units);
/* Tell the user if a conversion will be needed */
if (mpi_rank == 0) {
@@ -507,7 +509,7 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
/* Allocate memory to store star particles */
if (with_stars) {
- *Nstars = N[STAR];
+ *Nstars = N[swift_type_star];
if (posix_memalign((void*)sparts, spart_align,
*Nstars * sizeof(struct spart)) != 0)
error("Error while allocating memory for star particles");
@@ -517,7 +519,9 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
/* Allocate memory to store gravity particles */
if (with_gravity) {
Ndm = N[1];
- *Ngparts = (with_hydro ? N[GAS] : 0) + N[DM] + (with_stars ? N[STAR] : 0);
+ *Ngparts = (with_hydro ? N[swift_type_gas] : 0) +
+ N[swift_type_dark_matter] +
+ (with_stars ? N[swift_type_star] : 0);
if (posix_memalign((void*)gparts, gpart_align,
*Ngparts * sizeof(struct gpart)) != 0)
error("Error while allocating memory for gravity particles");
@@ -531,7 +535,7 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
/* message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm, *Ngparts); */
/* Loop over all particle types */
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
+ for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (N_total[ptype] == 0) continue;
@@ -552,21 +556,21 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
/* Read particle fields into the particle structure */
switch (ptype) {
- case GAS:
+ case swift_type_gas:
if (with_hydro) {
Nparticles = *Ngas;
hydro_read_particles(*parts, list, &num_fields);
}
break;
- case DM:
+ case swift_type_dark_matter:
if (with_gravity) {
Nparticles = Ndm;
darkmatter_read_particles(*gparts, list, &num_fields);
}
break;
- case STAR:
+ case swift_type_star:
if (with_stars) {
Nparticles = *Nstars;
star_read_particles(*sparts, list, &num_fields);
@@ -588,15 +592,15 @@ void read_ic_parallel(char* fileName, const struct UnitSystem* internal_units,
}
/* Prepare the DM particles */
- if (!dry_run && with_gravity) prepare_dm_gparts(*gparts, Ndm);
+ if (!dry_run && with_gravity) io_prepare_dm_gparts(*gparts, Ndm);
/* Duplicate the hydro particles into gparts */
if (!dry_run && with_gravity && with_hydro)
- duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
+ io_duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
/* Duplicate the star particles into gparts */
if (!dry_run && with_gravity && with_stars)
- duplicate_star_gparts(*sparts, *gparts, *Nstars, Ndm + *Ngas);
+ io_duplicate_star_gparts(*sparts, *gparts, *Nstars, Ndm + *Ngas);
/* message("Done Reading particles..."); */
@@ -659,10 +663,10 @@ void write_output_parallel(struct engine* e, const char* baseName,
outputCount);
/* First time, we need to create the XMF file */
- if (outputCount == 0 && mpi_rank == 0) createXMFfile(baseName);
+ if (outputCount == 0 && mpi_rank == 0) xmf_create_file(baseName);
/* Prepare the XMF file for the new entry */
- if (mpi_rank == 0) xmfFile = prepareXMFfile(baseName);
+ if (mpi_rank == 0) xmfFile = xmf_prepare_file(baseName);
/* Open HDF5 file */
hid_t plist_id = H5Pcreate(H5P_FILE_ACCESS);
@@ -674,11 +678,11 @@ void write_output_parallel(struct engine* e, const char* baseName,
/* Compute offset in the file and total number of
* particles */
- size_t N[NUM_PARTICLE_TYPES] = {Ngas, Ndm, 0, 0, Nstars, 0};
- long long N_total[NUM_PARTICLE_TYPES] = {0};
- long long offset[NUM_PARTICLE_TYPES] = {0};
- MPI_Exscan(&N, &offset, NUM_PARTICLE_TYPES, MPI_LONG_LONG_INT, MPI_SUM, comm);
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ size_t N[swift_type_count] = {Ngas, Ndm, 0, 0, Nstars, 0};
+ long long N_total[swift_type_count] = {0};
+ long long offset[swift_type_count] = {0};
+ MPI_Exscan(&N, &offset, swift_type_count, MPI_LONG_LONG_INT, MPI_SUM, comm);
+ for (int ptype = 0; ptype < swift_type_count; ++ptype)
N_total[ptype] = offset[ptype] + N[ptype];
/* The last rank now has the correct N_total. Let's
@@ -691,7 +695,7 @@ void write_output_parallel(struct engine* e, const char* baseName,
/* Write the part of the XMF file corresponding to this
* specific output */
- if (mpi_rank == 0) writeXMFoutputheader(xmfFile, fileName, e->time);
+ if (mpi_rank == 0) xmf_write_outputheader(xmfFile, fileName, e->time);
/* Open header to write simulation properties */
/* message("Writing runtime parameters..."); */
@@ -700,7 +704,7 @@ void write_output_parallel(struct engine* e, const char* baseName,
if (h_grp < 0) error("Error while creating runtime parameters group\n");
/* Write the relevant information */
- writeAttribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1);
+ io_write_attribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1);
/* Close runtime parameters */
H5Gclose(h_grp);
@@ -711,39 +715,39 @@ void write_output_parallel(struct engine* e, const char* baseName,
if (h_grp < 0) error("Error while creating file header\n");
/* Print the relevant information and print status */
- writeAttribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
+ io_write_attribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
double dblTime = e->time;
- writeAttribute(h_grp, "Time", DOUBLE, &dblTime, 1);
+ io_write_attribute(h_grp, "Time", DOUBLE, &dblTime, 1);
int dimension = (int)hydro_dimension;
- writeAttribute(h_grp, "Dimension", INT, &dimension, 1);
+ io_write_attribute(h_grp, "Dimension", INT, &dimension, 1);
/* GADGET-2 legacy values */
/* Number of particles of each type */
- unsigned int numParticles[NUM_PARTICLE_TYPES] = {0};
- unsigned int numParticlesHighWord[NUM_PARTICLE_TYPES] = {0};
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ unsigned int numParticles[swift_type_count] = {0};
+ unsigned int numParticlesHighWord[swift_type_count] = {0};
+ for (int ptype = 0; ptype < swift_type_count; ++ptype) {
numParticles[ptype] = (unsigned int)N_total[ptype];
numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
}
- writeAttribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
- NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "NumPart_Total", UINT, numParticles,
- NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord,
- NUM_PARTICLE_TYPES);
+ io_write_attribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
+ swift_type_count);
+ io_write_attribute(h_grp, "NumPart_Total", UINT, numParticles,
+ swift_type_count);
+ io_write_attribute(h_grp, "NumPart_Total_HighWord", UINT,
+ numParticlesHighWord, swift_type_count);
double MassTable[6] = {0., 0., 0., 0., 0., 0.};
- writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, NUM_PARTICLE_TYPES);
- unsigned int flagEntropy[NUM_PARTICLE_TYPES] = {0};
+ io_write_attribute(h_grp, "MassTable", DOUBLE, MassTable, swift_type_count);
+ unsigned int flagEntropy[swift_type_count] = {0};
flagEntropy[0] = writeEntropyFlag();
- writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
- NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
+ io_write_attribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
+ swift_type_count);
+ io_write_attribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
/* Close header */
H5Gclose(h_grp);
/* Print the code version */
- writeCodeDescription(h_file);
+ io_write_code_description(h_file);
/* Print the SPH parameters */
h_grp =
@@ -761,10 +765,10 @@ void write_output_parallel(struct engine* e, const char* baseName,
H5Gclose(h_grp);
/* Print the system of Units used in the spashot */
- writeUnitSystem(h_file, snapshot_units, "Units");
+ io_write_UnitSystem(h_file, snapshot_units, "Units");
/* Print the system of Units used internally */
- writeUnitSystem(h_file, internal_units, "InternalCodeUnits");
+ io_write_UnitSystem(h_file, internal_units, "InternalCodeUnits");
/* Tell the user if a conversion will be needed */
if (e->verbose && mpi_rank == 0) {
@@ -800,7 +804,7 @@ void write_output_parallel(struct engine* e, const char* baseName,
}
/* Loop over all particle types */
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
+ for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (N_total[ptype] == 0) continue;
@@ -808,8 +812,8 @@ void write_output_parallel(struct engine* e, const char* baseName,
/* Add the global information for that particle type to
* the XMF meta-file */
if (mpi_rank == 0)
- writeXMFgroupheader(xmfFile, fileName, N_total[ptype],
- (enum PARTICLE_TYPE)ptype);
+ xmf_write_groupheader(xmfFile, fileName, N_total[ptype],
+ (enum part_type)ptype);
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
@@ -828,12 +832,12 @@ void write_output_parallel(struct engine* e, const char* baseName,
/* Write particle fields from the particle structure */
switch (ptype) {
- case GAS:
+ case swift_type_gas:
Nparticles = Ngas;
hydro_write_particles(parts, list, &num_fields);
break;
- case DM:
+ case swift_type_dark_matter:
/* Allocate temporary array */
if (posix_memalign((void*)&dmparts, gpart_align,
Ndm * sizeof(struct gpart)) != 0)
@@ -843,14 +847,14 @@ void write_output_parallel(struct engine* e, const char* baseName,
bzero(dmparts, Ndm * sizeof(struct gpart));
/* Collect the DM particles from gpart */
- collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
+ io_collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
/* Write DM particles */
Nparticles = Ndm;
darkmatter_write_particles(dmparts, list, &num_fields);
break;
- case STAR:
+ case swift_type_star:
Nparticles = Nstars;
star_write_particles(sparts, list, &num_fields);
break;
@@ -875,11 +879,11 @@ void write_output_parallel(struct engine* e, const char* baseName,
H5Gclose(h_grp);
/* Close this particle group in the XMF file as well */
- if (mpi_rank == 0) writeXMFgroupfooter(xmfFile, (enum PARTICLE_TYPE)ptype);
+ if (mpi_rank == 0) xmf_write_groupfooter(xmfFile, (enum part_type)ptype);
}
/* Write LXMF file descriptor */
- if (mpi_rank == 0) writeXMFoutputfooter(xmfFile, outputCount, e->time);
+ if (mpi_rank == 0) xmf_write_outputfooter(xmfFile, outputCount, e->time);
/* message("Done writing particles..."); */
diff --git a/src/parser.c b/src/parser.c
index 879605760bedb5e4bb282788c2392edf0d3a64df..41a3e8637630eceb3beb9383acb3344028d38659 100644
--- a/src/parser.c
+++ b/src/parser.c
@@ -722,6 +722,6 @@ void parser_write_params_to_file(const struct swift_params *params,
void parser_write_params_to_hdf5(const struct swift_params *params, hid_t grp) {
for (int i = 0; i < params->paramCount; i++)
- writeAttribute_s(grp, params->data[i].name, params->data[i].value);
+ io_write_attribute_s(grp, params->data[i].name, params->data[i].value);
}
#endif
diff --git a/src/part_type.c b/src/part_type.c
new file mode 100644
index 0000000000000000000000000000000000000000..af97bd34aaace93a9faa953c0c9345d83ca3bc34
--- /dev/null
+++ b/src/part_type.c
@@ -0,0 +1,24 @@
+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2016 Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 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 Lesser General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+/* This object's header. */
+#include "part_type.h"
+
+const char* part_type_names[swift_type_count] = {"Gas", "DM", "Dummy",
+ "Dummy", "Star", "BH"};
diff --git a/src/part_type.h b/src/part_type.h
index 2c564d6908c8887e8fa8a5197a0a92ed85cbe5bb..fbe2b2aeaea37503635372b0f09f8edde4578721 100644
--- a/src/part_type.h
+++ b/src/part_type.h
@@ -28,7 +28,10 @@ enum part_type {
swift_type_gas = 0,
swift_type_dark_matter = 1,
swift_type_star = 4,
- swift_type_black_hole = 5
+ swift_type_black_hole = 5,
+ swift_type_count
} __attribute__((packed));
+extern const char* part_type_names[];
+
#endif /* SWIFT_PART_TYPES_H */
diff --git a/src/serial_io.c b/src/serial_io.c
index eaf5541992981463213db9685290fa9f624a4130..03f7df82c549b49c76799470bab733e0a6820759 100644
--- a/src/serial_io.c
+++ b/src/serial_io.c
@@ -48,6 +48,7 @@
#include "part.h"
#include "stars_io.h"
#include "units.h"
+#include "xmf.h"
/*-----------------------------------------------------------------------------
* Routines reading an IC file
@@ -76,7 +77,7 @@ void readArray(hid_t grp, const struct io_props props, size_t N,
const struct UnitSystem* internal_units,
const struct UnitSystem* ic_units) {
- const size_t typeSize = sizeOfType(props.type);
+ const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
@@ -105,7 +106,7 @@ void readArray(hid_t grp, const struct io_props props, size_t N,
/* Check data type */
const hid_t h_type = H5Dget_type(h_data);
if (h_type < 0) error("Unable to retrieve data type from the file");
- /* if (!H5Tequal(h_type, hdf5Type(type))) */
+ /* if (!H5Tequal(h_type, hdf5_type(type))) */
/* error("Non-matching types between the code and the file"); */
/* Allocate temporary buffer */
@@ -139,7 +140,7 @@ void readArray(hid_t grp, const struct io_props props, size_t N,
/* Read HDF5 dataspace in temporary buffer */
/* Dirty version that happens to work for vectors but should be improved */
/* Using HDF5 dataspaces would be better */
- const hid_t h_err = H5Dread(h_data, hdf5Type(props.type), h_memspace,
+ const hid_t h_err = H5Dread(h_data, io_hdf5_type(props.type), h_memspace,
h_filespace, H5P_DEFAULT, temp);
if (h_err < 0) {
error("Error while reading data array '%s'.", props.name);
@@ -152,7 +153,7 @@ void readArray(hid_t grp, const struct io_props props, size_t N,
/* message("Converting ! factor=%e", factor); */
- if (isDoublePrecision(props.type)) {
+ if (io_is_double_precision(props.type)) {
double* temp_d = temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
@@ -236,26 +237,27 @@ void prepareArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
}
/* Create dataset */
- const hid_t h_data = H5Dcreate(grp, props.name, hdf5Type(props.type), h_space,
- H5P_DEFAULT, h_prop, H5P_DEFAULT);
+ const hid_t h_data = H5Dcreate(grp, props.name, io_hdf5_type(props.type),
+ h_space, H5P_DEFAULT, h_prop, H5P_DEFAULT);
if (h_data < 0) {
error("Error while creating dataspace '%s'.", props.name);
}
/* Write XMF description for this data set */
- writeXMFline(xmfFile, fileName, partTypeGroupName, props.name, N_total,
- props.dimension, props.type);
+ xmf_write_line(xmfFile, fileName, partTypeGroupName, props.name, N_total,
+ props.dimension, props.type);
/* Write unit conversion factors for this data set */
char buffer[FIELD_BUFFER_SIZE];
units_cgs_conversion_string(buffer, snapshot_units, props.units);
- writeAttribute_d(h_data, "CGS conversion factor",
- units_cgs_conversion_factor(snapshot_units, props.units));
- writeAttribute_f(h_data, "h-scale exponent",
- units_h_factor(snapshot_units, props.units));
- writeAttribute_f(h_data, "a-scale exponent",
- units_a_factor(snapshot_units, props.units));
- writeAttribute_s(h_data, "Conversion factor", buffer);
+ io_write_attribute_d(
+ h_data, "CGS conversion factor",
+ units_cgs_conversion_factor(snapshot_units, props.units));
+ io_write_attribute_f(h_data, "h-scale exponent",
+ units_h_factor(snapshot_units, props.units));
+ io_write_attribute_f(h_data, "a-scale exponent",
+ units_a_factor(snapshot_units, props.units));
+ io_write_attribute_s(h_data, "Conversion factor", buffer);
/* Close everything */
H5Pclose(h_prop);
@@ -288,7 +290,7 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
const struct UnitSystem* internal_units,
const struct UnitSystem* snapshot_units) {
- const size_t typeSize = sizeOfType(props.type);
+ const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
@@ -300,7 +302,7 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
internal_units, snapshot_units);
/* Allocate temporary buffer */
- void* temp = malloc(num_elements * sizeOfType(props.type));
+ void* temp = malloc(num_elements * io_sizeof_type(props.type));
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Copy particle data to temporary buffer */
@@ -331,7 +333,7 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* message("Converting ! factor=%e", factor); */
- if (isDoublePrecision(props.type)) {
+ if (io_is_double_precision(props.type)) {
double* temp_d = temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
@@ -379,7 +381,7 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
H5Sselect_hyperslab(h_filespace, H5S_SELECT_SET, offsets, NULL, shape, NULL);
/* Write temporary buffer to HDF5 dataspace */
- h_err = H5Dwrite(h_data, hdf5Type(props.type), h_memspace, h_filespace,
+ h_err = H5Dwrite(h_data, io_hdf5_type(props.type), h_memspace, h_filespace,
H5P_DEFAULT, temp);
if (h_err < 0) error("Error while writing data array '%s'.", props.name);
@@ -434,11 +436,11 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
/* GADGET has only cubic boxes (in cosmological mode) */
double boxSize[3] = {0.0, -1.0, -1.0};
/* GADGET has 6 particle types. We only keep the type 0 & 1 for now*/
- long long numParticles[NUM_PARTICLE_TYPES] = {0};
- long long numParticles_highWord[NUM_PARTICLE_TYPES] = {0};
- size_t N[NUM_PARTICLE_TYPES] = {0};
- long long N_total[NUM_PARTICLE_TYPES] = {0};
- long long offset[NUM_PARTICLE_TYPES] = {0};
+ long long numParticles[swift_type_count] = {0};
+ long long numParticles_highWord[swift_type_count] = {0};
+ size_t N[swift_type_count] = {0};
+ long long N_total[swift_type_count] = {0};
+ long long offset[swift_type_count] = {0};
int dimension = 3; /* Assume 3D if nothing is specified */
size_t Ndm = 0;
struct UnitSystem* ic_units = malloc(sizeof(struct UnitSystem));
@@ -458,7 +460,7 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
if (h_grp < 0) error("Error while opening runtime parameters\n");
/* Read the relevant information */
- readAttribute(h_grp, "PeriodicBoundariesOn", INT, periodic);
+ io_read_attribute(h_grp, "PeriodicBoundariesOn", INT, periodic);
/* Close runtime parameters */
H5Gclose(h_grp);
@@ -472,21 +474,21 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
const hid_t hid_dim = H5Aexists(h_grp, "Dimension");
if (hid_dim < 0)
error("Error while testing existance of 'Dimension' attribute");
- if (hid_dim > 0) readAttribute(h_grp, "Dimension", INT, &dimension);
+ if (hid_dim > 0) io_read_attribute(h_grp, "Dimension", INT, &dimension);
if (dimension != hydro_dimension)
error("ICs dimensionality (%dD) does not match code dimensionality (%dD)",
dimension, (int)hydro_dimension);
/* Read the relevant information and print status */
int flag_entropy_temp[6];
- readAttribute(h_grp, "Flag_Entropy_ICs", INT, flag_entropy_temp);
+ io_read_attribute(h_grp, "Flag_Entropy_ICs", INT, flag_entropy_temp);
*flag_entropy = flag_entropy_temp[0];
- readAttribute(h_grp, "BoxSize", DOUBLE, boxSize);
- readAttribute(h_grp, "NumPart_Total", LONGLONG, numParticles);
- readAttribute(h_grp, "NumPart_Total_HighWord", LONGLONG,
- numParticles_highWord);
+ io_read_attribute(h_grp, "BoxSize", DOUBLE, boxSize);
+ io_read_attribute(h_grp, "NumPart_Total", LONGLONG, numParticles);
+ io_read_attribute(h_grp, "NumPart_Total_HighWord", LONGLONG,
+ numParticles_highWord);
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ for (int ptype = 0; ptype < swift_type_count; ++ptype)
N_total[ptype] =
(numParticles[ptype]) + (numParticles_highWord[ptype] << 32);
@@ -505,7 +507,7 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
/* Read the unit system used in the ICs */
if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
- readUnitSystem(h_file, ic_units);
+ io_read_UnitSystem(h_file, ic_units);
if (units_are_equal(ic_units, internal_units)) {
@@ -547,12 +549,12 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
/* Now need to broadcast that information to all ranks. */
MPI_Bcast(flag_entropy, 1, MPI_INT, 0, comm);
MPI_Bcast(periodic, 1, MPI_INT, 0, comm);
- MPI_Bcast(&N_total, NUM_PARTICLE_TYPES, MPI_LONG_LONG_INT, 0, comm);
+ MPI_Bcast(&N_total, swift_type_count, MPI_LONG_LONG_INT, 0, comm);
MPI_Bcast(dim, 3, MPI_DOUBLE, 0, comm);
MPI_Bcast(ic_units, sizeof(struct UnitSystem), MPI_BYTE, 0, comm);
/* Divide the particles among the tasks. */
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ for (int ptype = 0; ptype < swift_type_count; ++ptype) {
offset[ptype] = mpi_rank * N_total[ptype] / mpi_size;
N[ptype] = (mpi_rank + 1) * N_total[ptype] / mpi_size - offset[ptype];
}
@@ -568,7 +570,7 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
/* Allocate memory to store star particles */
if (with_stars) {
- *Nstars = N[STAR];
+ *Nstars = N[swift_type_star];
if (posix_memalign((void*)sparts, spart_align,
*Nstars * sizeof(struct spart)) != 0)
error("Error while allocating memory for star particles");
@@ -578,7 +580,9 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
/* Allocate memory to store all gravity particles */
if (with_gravity) {
Ndm = N[1];
- *Ngparts = (with_hydro ? N[GAS] : 0) + N[DM] + (with_stars ? N[STAR] : 0);
+ *Ngparts = (with_hydro ? N[swift_type_gas] : 0) +
+ N[swift_type_dark_matter] +
+ (with_stars ? N[swift_type_star] : 0);
if (posix_memalign((void*)gparts, gpart_align,
*Ngparts * sizeof(struct gpart)) != 0)
error("Error while allocating memory for gravity particles");
@@ -604,7 +608,7 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
/* Loop over all particle types */
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
+ for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (N[ptype] == 0) continue;
@@ -625,21 +629,21 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
/* Read particle fields into the particle structure */
switch (ptype) {
- case GAS:
+ case swift_type_gas:
if (with_hydro) {
Nparticles = *Ngas;
hydro_read_particles(*parts, list, &num_fields);
}
break;
- case DM:
+ case swift_type_dark_matter:
if (with_gravity) {
Nparticles = Ndm;
darkmatter_read_particles(*gparts, list, &num_fields);
}
break;
- case STAR:
+ case swift_type_star:
if (with_stars) {
Nparticles = *Nstars;
star_read_particles(*sparts, list, &num_fields);
@@ -670,15 +674,15 @@ void read_ic_serial(char* fileName, const struct UnitSystem* internal_units,
}
/* Prepare the DM particles */
- if (!dry_run && with_gravity) prepare_dm_gparts(*gparts, Ndm);
+ if (!dry_run && with_gravity) io_prepare_dm_gparts(*gparts, Ndm);
/* Duplicate the hydro particles into gparts */
if (!dry_run && with_gravity && with_hydro)
- duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
+ io_duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
/* Duplicate the star particles into gparts */
if (!dry_run && with_gravity && with_stars)
- duplicate_star_gparts(*sparts, *gparts, *Nstars, Ndm + *Ngas);
+ io_duplicate_star_gparts(*sparts, *gparts, *Nstars, Ndm + *Ngas);
/* message("Done Reading particles..."); */
@@ -733,11 +737,11 @@ void write_output_serial(struct engine* e, const char* baseName,
outputCount);
/* Compute offset in the file and total number of particles */
- size_t N[NUM_PARTICLE_TYPES] = {Ngas, Ndm, 0, 0, Nstars, 0};
- long long N_total[NUM_PARTICLE_TYPES] = {0};
- long long offset[NUM_PARTICLE_TYPES] = {0};
- MPI_Exscan(&N, &offset, NUM_PARTICLE_TYPES, MPI_LONG_LONG_INT, MPI_SUM, comm);
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ size_t N[swift_type_count] = {Ngas, Ndm, 0, 0, Nstars, 0};
+ long long N_total[swift_type_count] = {0};
+ long long offset[swift_type_count] = {0};
+ MPI_Exscan(&N, &offset, swift_type_count, MPI_LONG_LONG_INT, MPI_SUM, comm);
+ for (int ptype = 0; ptype < swift_type_count; ++ptype)
N_total[ptype] = offset[ptype] + N[ptype];
/* The last rank now has the correct N_total. Let's broadcast from there */
@@ -750,13 +754,13 @@ void write_output_serial(struct engine* e, const char* baseName,
if (mpi_rank == 0) {
/* First time, we need to create the XMF file */
- if (outputCount == 0) createXMFfile(baseName);
+ if (outputCount == 0) xmf_create_file(baseName);
/* Prepare the XMF file for the new entry */
- xmfFile = prepareXMFfile(baseName);
+ xmfFile = xmf_prepare_file(baseName);
/* Write the part corresponding to this specific output */
- writeXMFoutputheader(xmfFile, fileName, e->time);
+ xmf_write_outputheader(xmfFile, fileName, e->time);
/* Open file */
/* message("Opening file '%s'.", fileName); */
@@ -772,7 +776,7 @@ void write_output_serial(struct engine* e, const char* baseName,
if (h_grp < 0) error("Error while creating runtime parameters group\n");
/* Write the relevant information */
- writeAttribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1);
+ io_write_attribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1);
/* Close runtime parameters */
H5Gclose(h_grp);
@@ -783,39 +787,39 @@ void write_output_serial(struct engine* e, const char* baseName,
if (h_grp < 0) error("Error while creating file header\n");
/* Print the relevant information and print status */
- writeAttribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
+ io_write_attribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
double dblTime = e->time;
- writeAttribute(h_grp, "Time", DOUBLE, &dblTime, 1);
+ io_write_attribute(h_grp, "Time", DOUBLE, &dblTime, 1);
int dimension = (int)hydro_dimension;
- writeAttribute(h_grp, "Dimension", INT, &dimension, 1);
+ io_write_attribute(h_grp, "Dimension", INT, &dimension, 1);
/* GADGET-2 legacy values */
/* Number of particles of each type */
- unsigned int numParticles[NUM_PARTICLE_TYPES] = {0};
- unsigned int numParticlesHighWord[NUM_PARTICLE_TYPES] = {0};
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ unsigned int numParticles[swift_type_count] = {0};
+ unsigned int numParticlesHighWord[swift_type_count] = {0};
+ for (int ptype = 0; ptype < swift_type_count; ++ptype) {
numParticles[ptype] = (unsigned int)N_total[ptype];
numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
}
- writeAttribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
- NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "NumPart_Total", UINT, numParticles,
- NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord,
- NUM_PARTICLE_TYPES);
+ io_write_attribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
+ swift_type_count);
+ io_write_attribute(h_grp, "NumPart_Total", UINT, numParticles,
+ swift_type_count);
+ io_write_attribute(h_grp, "NumPart_Total_HighWord", UINT,
+ numParticlesHighWord, swift_type_count);
double MassTable[6] = {0., 0., 0., 0., 0., 0.};
- writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, NUM_PARTICLE_TYPES);
- unsigned int flagEntropy[NUM_PARTICLE_TYPES] = {0};
+ io_write_attribute(h_grp, "MassTable", DOUBLE, MassTable, swift_type_count);
+ unsigned int flagEntropy[swift_type_count] = {0};
flagEntropy[0] = writeEntropyFlag();
- writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
- NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
+ io_write_attribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
+ swift_type_count);
+ io_write_attribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
/* Close header */
H5Gclose(h_grp);
/* Print the code version */
- writeCodeDescription(h_file);
+ io_write_code_description(h_file);
/* Print the SPH parameters */
h_grp = H5Gcreate(h_file, "/HydroScheme", H5P_DEFAULT, H5P_DEFAULT,
@@ -833,10 +837,10 @@ void write_output_serial(struct engine* e, const char* baseName,
H5Gclose(h_grp);
/* Print the system of Units used in the spashot */
- writeUnitSystem(h_file, snapshot_units, "Units");
+ io_write_UnitSystem(h_file, snapshot_units, "Units");
/* Print the system of Units used internally */
- writeUnitSystem(h_file, internal_units, "InternalCodeUnits");
+ io_write_UnitSystem(h_file, internal_units, "InternalCodeUnits");
/* Tell the user if a conversion will be needed */
if (e->verbose) {
@@ -872,7 +876,7 @@ void write_output_serial(struct engine* e, const char* baseName,
}
/* Loop over all particle types */
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
+ for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (N_total[ptype] == 0) continue;
@@ -906,7 +910,7 @@ void write_output_serial(struct engine* e, const char* baseName,
error("Error while opening file '%s' on rank %d.", fileName, mpi_rank);
/* Loop over all particle types */
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
+ for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (N_total[ptype] == 0) continue;
@@ -914,8 +918,8 @@ void write_output_serial(struct engine* e, const char* baseName,
/* Add the global information for that particle type to the XMF
* meta-file */
if (mpi_rank == 0)
- writeXMFgroupheader(xmfFile, fileName, N_total[ptype],
- (enum PARTICLE_TYPE)ptype);
+ xmf_write_groupheader(xmfFile, fileName, N_total[ptype],
+ (enum part_type)ptype);
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
@@ -933,12 +937,12 @@ void write_output_serial(struct engine* e, const char* baseName,
/* Write particle fields from the particle structure */
switch (ptype) {
- case GAS:
+ case swift_type_gas:
Nparticles = Ngas;
hydro_write_particles(parts, list, &num_fields);
break;
- case DM:
+ case swift_type_dark_matter:
/* Allocate temporary array */
if (posix_memalign((void*)&dmparts, gpart_align,
Ndm * sizeof(struct gpart)) != 0)
@@ -946,14 +950,14 @@ void write_output_serial(struct engine* e, const char* baseName,
bzero(dmparts, Ndm * sizeof(struct gpart));
/* Collect the DM particles from gpart */
- collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
+ io_collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
/* Write DM particles */
Nparticles = Ndm;
darkmatter_write_particles(dmparts, list, &num_fields);
break;
- case STAR:
+ case swift_type_star:
Nparticles = Nstars;
star_write_particles(sparts, list, &num_fields);
break;
@@ -979,7 +983,7 @@ void write_output_serial(struct engine* e, const char* baseName,
/* Close this particle group in the XMF file as well */
if (mpi_rank == 0)
- writeXMFgroupfooter(xmfFile, (enum PARTICLE_TYPE)ptype);
+ xmf_write_groupfooter(xmfFile, (enum part_type)ptype);
}
/* Close file */
@@ -991,7 +995,7 @@ void write_output_serial(struct engine* e, const char* baseName,
}
/* Write footer of LXMF file descriptor */
- if (mpi_rank == 0) writeXMFoutputfooter(xmfFile, outputCount, e->time);
+ if (mpi_rank == 0) xmf_write_outputfooter(xmfFile, outputCount, e->time);
/* message("Done writing particles..."); */
++outputCount;
diff --git a/src/single_io.c b/src/single_io.c
index b279f22086833bc689919f41a8904232e234a394..f8696e96a15078a83069368094cfca198d3bb32a 100644
--- a/src/single_io.c
+++ b/src/single_io.c
@@ -47,6 +47,7 @@
#include "part.h"
#include "stars_io.h"
#include "units.h"
+#include "xmf.h"
/*-----------------------------------------------------------------------------
* Routines reading an IC file
@@ -69,7 +70,7 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
const struct UnitSystem* internal_units,
const struct UnitSystem* ic_units) {
- const size_t typeSize = sizeOfType(prop.type);
+ const size_t typeSize = io_sizeof_type(prop.type);
const size_t copySize = typeSize * prop.dimension;
const size_t num_elements = N * prop.dimension;
@@ -104,7 +105,7 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
/* Check data type */
const hid_t h_type = H5Dget_type(h_data);
if (h_type < 0) error("Unable to retrieve data type from the file");
- // if (!H5Tequal(h_type, hdf5Type(type)))
+ // if (!H5Tequal(h_type, hdf5_type(type)))
// error("Non-matching types between the code and the file");
/* Allocate temporary buffer */
@@ -114,8 +115,8 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
/* Read HDF5 dataspace in temporary buffer */
/* Dirty version that happens to work for vectors but should be improved */
/* Using HDF5 dataspaces would be better */
- const hid_t h_err =
- H5Dread(h_data, hdf5Type(prop.type), H5S_ALL, H5S_ALL, H5P_DEFAULT, temp);
+ const hid_t h_err = H5Dread(h_data, io_hdf5_type(prop.type), H5S_ALL, H5S_ALL,
+ H5P_DEFAULT, temp);
if (h_err < 0) {
error("Error while reading data array '%s'.", prop.name);
}
@@ -127,7 +128,7 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
/* message("Converting ! factor=%e", factor); */
- if (isDoublePrecision(prop.type)) {
+ if (io_is_double_precision(prop.type)) {
double* temp_d = temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
@@ -173,14 +174,14 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
const struct UnitSystem* internal_units,
const struct UnitSystem* snapshot_units) {
- const size_t typeSize = sizeOfType(props.type);
+ const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
/* message("Writing '%s' array...", props.name); */
/* Allocate temporary buffer */
- void* temp = malloc(num_elements * sizeOfType(props.type));
+ void* temp = malloc(num_elements * io_sizeof_type(props.type));
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
/* Copy particle data to temporary buffer */
@@ -211,7 +212,7 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* message("Converting ! factor=%e", factor); */
- if (isDoublePrecision(props.type)) {
+ if (io_is_double_precision(props.type)) {
double* temp_d = temp;
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
@@ -272,33 +273,34 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
}
/* Create dataset */
- const hid_t h_data = H5Dcreate(grp, props.name, hdf5Type(props.type), h_space,
- H5P_DEFAULT, h_prop, H5P_DEFAULT);
+ const hid_t h_data = H5Dcreate(grp, props.name, io_hdf5_type(props.type),
+ h_space, H5P_DEFAULT, h_prop, H5P_DEFAULT);
if (h_data < 0) {
error("Error while creating dataspace '%s'.", props.name);
}
/* Write temporary buffer to HDF5 dataspace */
- h_err = H5Dwrite(h_data, hdf5Type(props.type), h_space, H5S_ALL, H5P_DEFAULT,
- temp);
+ h_err = H5Dwrite(h_data, io_hdf5_type(props.type), h_space, H5S_ALL,
+ H5P_DEFAULT, temp);
if (h_err < 0) {
error("Error while writing data array '%s'.", props.name);
}
/* Write XMF description for this data set */
- writeXMFline(xmfFile, fileName, partTypeGroupName, props.name, N,
- props.dimension, props.type);
+ xmf_write_line(xmfFile, fileName, partTypeGroupName, props.name, N,
+ props.dimension, props.type);
/* Write unit conversion factors for this data set */
char buffer[FIELD_BUFFER_SIZE];
units_cgs_conversion_string(buffer, snapshot_units, props.units);
- writeAttribute_d(h_data, "CGS conversion factor",
- units_cgs_conversion_factor(snapshot_units, props.units));
- writeAttribute_f(h_data, "h-scale exponent",
- units_h_factor(snapshot_units, props.units));
- writeAttribute_f(h_data, "a-scale exponent",
- units_a_factor(snapshot_units, props.units));
- writeAttribute_s(h_data, "Conversion factor", buffer);
+ io_write_attribute_d(
+ h_data, "CGS conversion factor",
+ units_cgs_conversion_factor(snapshot_units, props.units));
+ io_write_attribute_f(h_data, "h-scale exponent",
+ units_h_factor(snapshot_units, props.units));
+ io_write_attribute_f(h_data, "a-scale exponent",
+ units_a_factor(snapshot_units, props.units));
+ io_write_attribute_s(h_data, "Conversion factor", buffer);
/* Free and close everything */
free(temp);
@@ -346,9 +348,9 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
/* GADGET has only cubic boxes (in cosmological mode) */
double boxSize[3] = {0.0, -1.0, -1.0};
/* GADGET has 6 particle types. We only keep the type 0 & 1 for now...*/
- int numParticles[NUM_PARTICLE_TYPES] = {0};
- int numParticles_highWord[NUM_PARTICLE_TYPES] = {0};
- size_t N[NUM_PARTICLE_TYPES] = {0};
+ int numParticles[swift_type_count] = {0};
+ int numParticles_highWord[swift_type_count] = {0};
+ size_t N[swift_type_count] = {0};
int dimension = 3; /* Assume 3D if nothing is specified */
size_t Ndm = 0;
@@ -365,7 +367,7 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
if (h_grp < 0) error("Error while opening runtime parameters\n");
/* Read the relevant information */
- readAttribute(h_grp, "PeriodicBoundariesOn", INT, periodic);
+ io_read_attribute(h_grp, "PeriodicBoundariesOn", INT, periodic);
/* Close runtime parameters */
H5Gclose(h_grp);
@@ -379,20 +381,21 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
const hid_t hid_dim = H5Aexists(h_grp, "Dimension");
if (hid_dim < 0)
error("Error while testing existance of 'Dimension' attribute");
- if (hid_dim > 0) readAttribute(h_grp, "Dimension", INT, &dimension);
+ if (hid_dim > 0) io_read_attribute(h_grp, "Dimension", INT, &dimension);
if (dimension != hydro_dimension)
error("ICs dimensionality (%dD) does not match code dimensionality (%dD)",
dimension, (int)hydro_dimension);
/* Read the relevant information and print status */
int flag_entropy_temp[6];
- readAttribute(h_grp, "Flag_Entropy_ICs", INT, flag_entropy_temp);
+ io_read_attribute(h_grp, "Flag_Entropy_ICs", INT, flag_entropy_temp);
*flag_entropy = flag_entropy_temp[0];
- readAttribute(h_grp, "BoxSize", DOUBLE, boxSize);
- readAttribute(h_grp, "NumPart_Total", UINT, numParticles);
- readAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticles_highWord);
+ io_read_attribute(h_grp, "BoxSize", DOUBLE, boxSize);
+ io_read_attribute(h_grp, "NumPart_Total", UINT, numParticles);
+ io_read_attribute(h_grp, "NumPart_Total_HighWord", UINT,
+ numParticles_highWord);
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype)
+ for (int ptype = 0; ptype < swift_type_count; ++ptype)
N[ptype] = ((long long)numParticles[ptype]) +
((long long)numParticles_highWord[ptype] << 32);
@@ -409,7 +412,7 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
/* Read the unit system used in the ICs */
struct UnitSystem* ic_units = malloc(sizeof(struct UnitSystem));
if (ic_units == NULL) error("Unable to allocate memory for IC unit system");
- readUnitSystem(h_file, ic_units);
+ io_read_UnitSystem(h_file, ic_units);
/* Tell the user if a conversion will be needed */
if (units_are_equal(ic_units, internal_units)) {
@@ -447,7 +450,7 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
/* Allocate memory to store SPH particles */
if (with_hydro) {
- *Ngas = N[GAS];
+ *Ngas = N[swift_type_gas];
if (posix_memalign((void*)parts, part_align, *Ngas * sizeof(struct part)) !=
0)
error("Error while allocating memory for SPH particles");
@@ -456,7 +459,7 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
/* Allocate memory to store star particles */
if (with_stars) {
- *Nstars = N[STAR];
+ *Nstars = N[swift_type_star];
if (posix_memalign((void*)sparts, spart_align,
*Nstars * sizeof(struct spart)) != 0)
error("Error while allocating memory for star particles");
@@ -465,8 +468,10 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
/* Allocate memory to store all gravity particles */
if (with_gravity) {
- Ndm = N[DM];
- *Ngparts = (with_hydro ? N[GAS] : 0) + N[DM] + (with_stars ? N[STAR] : 0);
+ Ndm = N[swift_type_dark_matter];
+ *Ngparts = (with_hydro ? N[swift_type_gas] : 0) +
+ N[swift_type_dark_matter] +
+ (with_stars ? N[swift_type_star] : 0);
if (posix_memalign((void*)gparts, gpart_align,
*Ngparts * sizeof(struct gpart)) != 0)
error("Error while allocating memory for gravity particles");
@@ -480,7 +485,7 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
/* message("NumPart = [%zd, %zd] Total = %zd", *Ngas, Ndm, *Ngparts); */
/* Loop over all particle types */
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
+ for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (N[ptype] == 0) continue;
@@ -501,21 +506,21 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
/* Read particle fields into the structure */
switch (ptype) {
- case GAS:
+ case swift_type_gas:
if (with_hydro) {
Nparticles = *Ngas;
hydro_read_particles(*parts, list, &num_fields);
}
break;
- case DM:
+ case swift_type_dark_matter:
if (with_gravity) {
Nparticles = Ndm;
darkmatter_read_particles(*gparts, list, &num_fields);
}
break;
- case STAR:
+ case swift_type_star:
if (with_stars) {
Nparticles = *Nstars;
star_read_particles(*sparts, list, &num_fields);
@@ -536,15 +541,15 @@ void read_ic_single(char* fileName, const struct UnitSystem* internal_units,
}
/* Prepare the DM particles */
- if (!dry_run && with_gravity) prepare_dm_gparts(*gparts, Ndm);
+ if (!dry_run && with_gravity) io_prepare_dm_gparts(*gparts, Ndm);
/* Duplicate the hydro particles into gparts */
if (!dry_run && with_gravity && with_hydro)
- duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
+ io_duplicate_hydro_gparts(*parts, *gparts, *Ngas, Ndm);
/* Duplicate the star particles into gparts */
if (!dry_run && with_gravity && with_stars)
- duplicate_star_gparts(*sparts, *gparts, *Nstars, Ndm + *Ngas);
+ io_duplicate_star_gparts(*sparts, *gparts, *Nstars, Ndm + *Ngas);
/* message("Done Reading particles..."); */
@@ -590,7 +595,7 @@ void write_output_single(struct engine* e, const char* baseName,
/* Number of unassociated gparts */
const size_t Ndm = Ntot > 0 ? Ntot - (Ngas + Nstars) : 0;
- long long N_total[NUM_PARTICLE_TYPES] = {Ngas, Ndm, 0, 0, Nstars, 0};
+ long long N_total[swift_type_count] = {Ngas, Ndm, 0, 0, Nstars, 0};
/* File name */
char fileName[FILENAME_BUFFER_SIZE];
@@ -598,14 +603,14 @@ void write_output_single(struct engine* e, const char* baseName,
outputCount);
/* First time, we need to create the XMF file */
- if (outputCount == 0) createXMFfile(baseName);
+ if (outputCount == 0) xmf_create_file(baseName);
/* Prepare the XMF file for the new entry */
FILE* xmfFile = 0;
- xmfFile = prepareXMFfile(baseName);
+ xmfFile = xmf_prepare_file(baseName);
/* Write the part corresponding to this specific output */
- writeXMFoutputheader(xmfFile, fileName, e->time);
+ xmf_write_outputheader(xmfFile, fileName, e->time);
/* Open file */
/* message("Opening file '%s'.", fileName); */
@@ -621,7 +626,7 @@ void write_output_single(struct engine* e, const char* baseName,
if (h_grp < 0) error("Error while creating runtime parameters group\n");
/* Write the relevant information */
- writeAttribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1);
+ io_write_attribute(h_grp, "PeriodicBoundariesOn", INT, &periodic, 1);
/* Close runtime parameters */
H5Gclose(h_grp);
@@ -632,39 +637,39 @@ void write_output_single(struct engine* e, const char* baseName,
if (h_grp < 0) error("Error while creating file header\n");
/* Print the relevant information and print status */
- writeAttribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
+ io_write_attribute(h_grp, "BoxSize", DOUBLE, e->s->dim, 3);
double dblTime = e->time;
- writeAttribute(h_grp, "Time", DOUBLE, &dblTime, 1);
+ io_write_attribute(h_grp, "Time", DOUBLE, &dblTime, 1);
int dimension = (int)hydro_dimension;
- writeAttribute(h_grp, "Dimension", INT, &dimension, 1);
+ io_write_attribute(h_grp, "Dimension", INT, &dimension, 1);
/* GADGET-2 legacy values */
/* Number of particles of each type */
- unsigned int numParticles[NUM_PARTICLE_TYPES] = {0};
- unsigned int numParticlesHighWord[NUM_PARTICLE_TYPES] = {0};
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ++ptype) {
+ unsigned int numParticles[swift_type_count] = {0};
+ unsigned int numParticlesHighWord[swift_type_count] = {0};
+ for (int ptype = 0; ptype < swift_type_count; ++ptype) {
numParticles[ptype] = (unsigned int)N_total[ptype];
numParticlesHighWord[ptype] = (unsigned int)(N_total[ptype] >> 32);
}
- writeAttribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
- NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "NumPart_Total", UINT, numParticles,
- NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "NumPart_Total_HighWord", UINT, numParticlesHighWord,
- NUM_PARTICLE_TYPES);
- double MassTable[NUM_PARTICLE_TYPES] = {0};
- writeAttribute(h_grp, "MassTable", DOUBLE, MassTable, NUM_PARTICLE_TYPES);
- unsigned int flagEntropy[NUM_PARTICLE_TYPES] = {0};
+ io_write_attribute(h_grp, "NumPart_ThisFile", LONGLONG, N_total,
+ swift_type_count);
+ io_write_attribute(h_grp, "NumPart_Total", UINT, numParticles,
+ swift_type_count);
+ io_write_attribute(h_grp, "NumPart_Total_HighWord", UINT,
+ numParticlesHighWord, swift_type_count);
+ double MassTable[swift_type_count] = {0};
+ io_write_attribute(h_grp, "MassTable", DOUBLE, MassTable, swift_type_count);
+ unsigned int flagEntropy[swift_type_count] = {0};
flagEntropy[0] = writeEntropyFlag();
- writeAttribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
- NUM_PARTICLE_TYPES);
- writeAttribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
+ io_write_attribute(h_grp, "Flag_Entropy_ICs", UINT, flagEntropy,
+ swift_type_count);
+ io_write_attribute(h_grp, "NumFilesPerSnapshot", INT, &numFiles, 1);
/* Close header */
H5Gclose(h_grp);
/* Print the code version */
- writeCodeDescription(h_file);
+ io_write_code_description(h_file);
/* Print the SPH parameters */
h_grp =
@@ -682,10 +687,10 @@ void write_output_single(struct engine* e, const char* baseName,
H5Gclose(h_grp);
/* Print the system of Units used in the spashot */
- writeUnitSystem(h_file, snapshot_units, "Units");
+ io_write_UnitSystem(h_file, snapshot_units, "Units");
/* Print the system of Units used internally */
- writeUnitSystem(h_file, internal_units, "InternalCodeUnits");
+ io_write_UnitSystem(h_file, internal_units, "InternalCodeUnits");
/* Tell the user if a conversion will be needed */
if (e->verbose) {
@@ -721,14 +726,14 @@ void write_output_single(struct engine* e, const char* baseName,
}
/* Loop over all particle types */
- for (int ptype = 0; ptype < NUM_PARTICLE_TYPES; ptype++) {
+ for (int ptype = 0; ptype < swift_type_count; ptype++) {
/* Don't do anything if no particle of this kind */
if (numParticles[ptype] == 0) continue;
/* Add the global information for that particle type to the XMF meta-file */
- writeXMFgroupheader(xmfFile, fileName, numParticles[ptype],
- (enum PARTICLE_TYPE)ptype);
+ xmf_write_groupheader(xmfFile, fileName, numParticles[ptype],
+ (enum part_type)ptype);
/* Open the particle group in the file */
char partTypeGroupName[PARTICLE_GROUP_BUFFER_SIZE];
@@ -747,12 +752,12 @@ void write_output_single(struct engine* e, const char* baseName,
/* Write particle fields from the particle structure */
switch (ptype) {
- case GAS:
+ case swift_type_gas:
N = Ngas;
hydro_write_particles(parts, list, &num_fields);
break;
- case DM:
+ case swift_type_dark_matter:
/* Allocate temporary array */
if (posix_memalign((void*)&dmparts, gpart_align,
Ndm * sizeof(struct gpart)) != 0)
@@ -760,14 +765,14 @@ void write_output_single(struct engine* e, const char* baseName,
bzero(dmparts, Ndm * sizeof(struct gpart));
/* Collect the DM particles from gpart */
- collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
+ io_collect_dm_gparts(gparts, Ntot, dmparts, Ndm);
/* Write DM particles */
N = Ndm;
darkmatter_write_particles(dmparts, list, &num_fields);
break;
- case STAR:
+ case swift_type_star:
N = Nstars;
star_write_particles(sparts, list, &num_fields);
break;
@@ -791,11 +796,11 @@ void write_output_single(struct engine* e, const char* baseName,
H5Gclose(h_grp);
/* Close this particle group in the XMF file as well */
- writeXMFgroupfooter(xmfFile, (enum PARTICLE_TYPE)ptype);
+ xmf_write_groupfooter(xmfFile, (enum part_type)ptype);
}
/* Write LXMF file descriptor */
- writeXMFoutputfooter(xmfFile, outputCount, e->time);
+ xmf_write_outputfooter(xmfFile, outputCount, e->time);
/* message("Done writing particles..."); */
diff --git a/src/xmf.c b/src/xmf.c
new file mode 100644
index 0000000000000000000000000000000000000000..7292606c9f013601db1e9e9b35ee843dea63f785
--- /dev/null
+++ b/src/xmf.c
@@ -0,0 +1,215 @@
+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2017 Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 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 Lesser General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+/* Config parameters. */
+#include "../config.h"
+
+/* Some standard headers. */
+#include <stdio.h>
+
+/* This object's header. */
+#include "xmf.h"
+
+/* Local headers. */
+#include "common_io.h"
+#include "error.h"
+
+/**
+ * @brief Prepare the XMF file corresponding to a snapshot.
+ *
+ * @param baseName The common part of the file name.
+ */
+FILE* xmf_prepare_file(const char* baseName) {
+ char buffer[1024];
+
+ char fileName[FILENAME_BUFFER_SIZE];
+ char tempFileName[FILENAME_BUFFER_SIZE];
+ snprintf(fileName, FILENAME_BUFFER_SIZE, "%s.xmf", baseName);
+ snprintf(tempFileName, FILENAME_BUFFER_SIZE, "%s_temp.xmf", baseName);
+ FILE* xmfFile = fopen(fileName, "r");
+ FILE* tempFile = fopen(tempFileName, "w");
+
+ if (xmfFile == NULL) error("Unable to open current XMF file.");
+
+ if (tempFile == NULL) error("Unable to open temporary file.");
+
+ /* First we make a temporary copy of the XMF file and count the lines */
+ int counter = 0;
+ while (fgets(buffer, 1024, xmfFile) != NULL) {
+ counter++;
+ fprintf(tempFile, "%s", buffer);
+ }
+ fclose(tempFile);
+ fclose(xmfFile);
+
+ /* We then copy the XMF file back up to the closing lines */
+ xmfFile = fopen(fileName, "w");
+ tempFile = fopen(tempFileName, "r");
+
+ if (xmfFile == NULL) error("Unable to open current XMF file.");
+
+ if (tempFile == NULL) error("Unable to open temporary file.");
+
+ int i = 0;
+ while (fgets(buffer, 1024, tempFile) != NULL && i < counter - 3) {
+ i++;
+ fprintf(xmfFile, "%s", buffer);
+ }
+ fprintf(xmfFile, "\n");
+ fclose(tempFile);
+ remove(tempFileName);
+
+ return xmfFile;
+}
+
+/**
+ * @brief Writes the begin of the XMF file
+ *
+ * @todo Exploit the XML nature of the XMF format to write a proper XML writer
+ * and simplify all the XMF-related stuff.
+ */
+void xmf_create_file(const char* baseName) {
+
+ char fileName[FILENAME_BUFFER_SIZE];
+ snprintf(fileName, FILENAME_BUFFER_SIZE, "%s.xmf", baseName);
+ FILE* xmfFile = fopen(fileName, "w");
+
+ 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 Name=\"TimeSeries\" GridType=\"Collection\" "
+ "CollectionType=\"Temporal\">\n\n");
+
+ fprintf(xmfFile, "</Grid>\n");
+ fprintf(xmfFile, "</Domain>\n");
+ fprintf(xmfFile, "</Xdmf>\n");
+
+ fclose(xmfFile);
+}
+
+/**
+ * @brief Writes the part of the XMF entry presenting the geometry of the
+ * snapshot
+ *
+ * @param xmfFile The file to write in.
+ * @param hdfFileName The name of the HDF5 file corresponding to this output.
+ * @param time The current simulation time.
+ */
+void xmf_write_outputheader(FILE* xmfFile, char* hdfFileName, float time) {
+ /* Write end of file */
+
+ fprintf(xmfFile, "<!-- XMF description for file: %s -->\n", hdfFileName);
+ fprintf(xmfFile,
+ "<Grid GridType=\"Collection\" CollectionType=\"Spatial\">\n");
+ fprintf(xmfFile, "<Time Type=\"Single\" Value=\"%f\"/>\n", time);
+}
+
+/**
+ * @brief Writes the end of the XMF file (closes all open markups)
+ *
+ * @param xmfFile The file to write in.
+ * @param output The number of this output.
+ * @param time The current simulation time.
+ */
+void xmf_write_outputfooter(FILE* xmfFile, int output, float time) {
+ /* Write end of the section of this time step */
+
+ fprintf(xmfFile,
+ "\n</Grid> <!-- End of meta-data for output=%03i, time=%f -->\n",
+ output, time);
+ fprintf(xmfFile, "\n</Grid> <!-- timeSeries -->\n");
+ fprintf(xmfFile, "</Domain>\n");
+ fprintf(xmfFile, "</Xdmf>\n");
+
+ fclose(xmfFile);
+}
+
+/**
+ * @brief Writes the header of an XMF group for a given particle type.
+ *
+ * @param xmfFile The file to write to.
+ * @param hdfFileName The name of the corresponding HDF5 file.
+ * @param N The number of particles to write.
+ * @param ptype The particle type we are writing.
+ */
+void xmf_write_groupheader(FILE* xmfFile, char* hdfFileName, size_t N,
+ enum part_type ptype) {
+ fprintf(xmfFile, "\n<Grid Name=\"%s\" GridType=\"Uniform\">\n",
+ part_type_names[ptype]);
+ fprintf(xmfFile,
+ "<Topology TopologyType=\"Polyvertex\" Dimensions=\"%zu\"/>\n", N);
+ fprintf(xmfFile, "<Geometry GeometryType=\"XYZ\">\n");
+ fprintf(xmfFile,
+ "<DataItem Dimensions=\"%zu 3\" NumberType=\"Double\" "
+ "Precision=\"8\" "
+ "Format=\"HDF\">%s:/PartType%d/Coordinates</DataItem>\n",
+ N, hdfFileName, (int)ptype);
+ fprintf(xmfFile,
+ "</Geometry>\n <!-- Done geometry for %s, start of particle fields "
+ "list -->\n",
+ part_type_names[ptype]);
+}
+
+/**
+ * @brief Writes the footer of an XMF group for a given particle type.
+ *
+ * @param xmfFile The file to write to.
+ * @param ptype The particle type we are writing.
+ */
+void xmf_write_groupfooter(FILE* xmfFile, enum part_type ptype) {
+ fprintf(xmfFile, "</Grid> <!-- End of meta-data for parttype=%s -->\n",
+ part_type_names[ptype]);
+}
+
+/**
+ * @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 partTypeGroupName The name of the group containing the particles in
+ * the HDF5 file.
+ * @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 xmf_write_line(FILE* xmfFile, const char* fileName,
+ const char* partTypeGroupName, const char* name, size_t N,
+ int dim, enum IO_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=\"%zu\" NumberType=\"Double\" "
+ "Precision=\"%d\" Format=\"HDF\">%s:%s/%s</DataItem>\n",
+ N, type == FLOAT ? 4 : 8, fileName, partTypeGroupName, name);
+ else
+ fprintf(xmfFile,
+ "<DataItem Dimensions=\"%zu %d\" NumberType=\"Double\" "
+ "Precision=\"%d\" Format=\"HDF\">%s:%s/%s</DataItem>\n",
+ N, dim, type == FLOAT ? 4 : 8, fileName, partTypeGroupName, name);
+ fprintf(xmfFile, "</Attribute>\n");
+}
diff --git a/src/xmf.h b/src/xmf.h
new file mode 100644
index 0000000000000000000000000000000000000000..bd2781685f8d1f96daf6e5bfeb45a2bf645fca6e
--- /dev/null
+++ b/src/xmf.h
@@ -0,0 +1,40 @@
+/*******************************************************************************
+ * This file is part of SWIFT.
+ * Copyright (c) 2017 Matthieu Schaller (matthieu.schaller@durham.ac.uk).
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published
+ * by the Free Software Foundation, either version 3 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 Lesser General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+#ifndef SWIFT_XMF_H
+#define SWIFT_XMF_H
+
+/* Config parameters. */
+#include "../config.h"
+
+/* Local headers. */
+#include "common_io.h"
+#include "part_type.h"
+
+void xmf_create_file(const char* baseName);
+FILE* xmf_prepare_file(const char* baseName);
+void xmf_write_outputheader(FILE* xmfFile, char* hdfFileName, float time);
+void xmf_write_outputfooter(FILE* xmfFile, int outputCount, float time);
+void xmf_write_groupheader(FILE* xmfFile, char* hdfFileName, size_t N,
+ enum part_type ptype);
+void xmf_write_groupfooter(FILE* xmfFile, enum part_type ptype);
+void xmf_write_line(FILE* xmfFile, const char* fileName,
+ const char* partTypeGroupName, const char* name, size_t N,
+ int dim, enum IO_DATA_TYPE type);
+
+#endif /* SWIFT_XMF_H */