Skip to content

GitLab

gitlab is upgraded to version 13, please report any issues and enjoy

Commit 1d64aa96 authored by Matthieu Schaller's avatar Matthieu Schaller
Browse files

Implement more general conversion functions for i/o. Can now add one that does... 

Implement more general conversion functions for i/o. Can now add one that does box-wrapping  of particles.
parent bee23d1c
Hide whitespace changes
Inline Side-by-side
Showing with 282 additions and 84 deletions
src/gravity/Default/gravity_io.h
View file @ 1d64aa96
......@@ -21,6 +21,20 @@
#include "io_properties.h"
void convert_gpart_pos(const struct engine* e, const struct gpart* gp,
double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(gp->x[0], 0.0, e->s->dim[0]);
ret[1] = box_wrap(gp->x[1], 0.0, e->s->dim[1]);
ret[2] = box_wrap(gp->x[2], 0.0, e->s->dim[2]);
} else {
ret[0] = gp->x[0];
ret[1] = gp->x[1];
ret[2] = gp->x[2];
}
}
/**
* @brief Specifies which g-particle fields to read from a dataset
*
......@@ -52,15 +66,15 @@ void darkmatter_read_particles(struct gpart* gparts, struct io_props* list,
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
void darkmatter_write_particles(struct gpart* gparts, struct io_props* list,
int* num_fields) {
void darkmatter_write_particles(const struct gpart* gparts,
struct io_props* list, int* num_fields) {
/* Say how much we want to read */
*num_fields = 5;
/* List what we want to read */
list[0] = io_make_output_field("Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH,
gparts, x);
list[0] = io_make_output_field_convert_gpart(
"Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH, gparts, convert_gpart_pos);
list[1] = io_make_output_field("Velocities", FLOAT, 3, UNIT_CONV_SPEED,
gparts, v_full);
list[2] =
......
src/hydro/Gadget2/hydro_io.h
View file @ 1d64aa96
......@@ -55,14 +55,28 @@ void hydro_read_particles(struct part* parts, struct io_props* list,
UNIT_CONV_DENSITY, parts, rho);
}
float convert_u(struct engine* e, struct part* p) {
void convert_u(const struct engine* e, const struct part* p, float* ret) {
return hydro_get_internal_energy(p);
ret[0] = hydro_get_internal_energy(p);
}
float convert_P(struct engine* e, struct part* p) {
void convert_P(const struct engine* e, const struct part* p, float* ret) {
return hydro_get_pressure(p);
ret[0] = hydro_get_pressure(p);
}
void convert_part_pos(const struct engine* e, const struct part* p,
double* ret) {
if (e->s->periodic) {
ret[0] = box_wrap(p->x[0], 0.0, e->s->dim[0]);
ret[1] = box_wrap(p->x[1], 0.0, e->s->dim[1]);
ret[2] = box_wrap(p->x[2], 0.0, e->s->dim[2]);
} else {
ret[0] = p->x[0];
ret[1] = p->x[1];
ret[2] = p->x[2];
}
}
/**
......@@ -72,14 +86,14 @@ float convert_P(struct engine* e, struct part* p) {
* @param list The list of i/o properties to write.
* @param num_fields The number of i/o fields to write.
*/
void hydro_write_particles(struct part* parts, struct io_props* list,
void hydro_write_particles(const struct part* parts, struct io_props* list,
int* num_fields) {
*num_fields = 10;
/* List what we want to write */
list[0] = io_make_output_field("Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH,
parts, x);
list[0] = io_make_output_field_convert_part(
"Coordinates", DOUBLE, 3, UNIT_CONV_LENGTH, parts, convert_part_pos);
list[1] =
io_make_output_field("Velocities", FLOAT, 3, UNIT_CONV_SPEED, parts, v);
list[2] =
......@@ -96,9 +110,9 @@ void hydro_write_particles(struct part* parts, struct io_props* list,
io_make_output_field("Density", FLOAT, 1, UNIT_CONV_DENSITY, parts, rho);
list[8] = io_make_output_field_convert_part("InternalEnergy", FLOAT, 1,
UNIT_CONV_ENERGY_PER_UNIT_MASS,
parts, rho, convert_u);
parts, convert_u);
list[9] = io_make_output_field_convert_part(
"Pressure", FLOAT, 1, UNIT_CONV_PRESSURE, parts, rho, convert_P);
"Pressure", FLOAT, 1, UNIT_CONV_PRESSURE, parts, convert_P);
}
/**
......
src/io_properties.h
View file @ 1d64aa96
......@@ -16,7 +16,6 @@
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
#ifndef SWIFT_IO_PROPERTIES_H
#define SWIFT_IO_PROPERTIES_H
......@@ -29,6 +28,16 @@
*/
enum DATA_IMPORTANCE { COMPULSORY = 1, OPTIONAL = 0, UNUSED = -1 };
/* Helper typedefs */
typedef void (*conversion_func_part_float)(const struct engine*,
const struct part*, float*);
typedef void (*conversion_func_part_double)(const struct engine*,
const struct part*, double*);
typedef void (*conversion_func_gpart_float)(const struct engine*,
const struct gpart*, float*);
typedef void (*conversion_func_gpart_double)(const struct engine*,
const struct gpart*, double*);
/**
* @brief The properties of a given dataset for i/o
*/
......@@ -56,14 +65,19 @@ struct io_props {
size_t partSize;
/* The particle arrays */
struct part* parts;
struct gpart* gparts;
const struct part* parts;
const struct gpart* gparts;
/* Are we converting? */
int conversion;
/* Conversion function for part */
float (*convert_part)(struct engine*, struct part*);
conversion_func_part_float convert_part_f;
conversion_func_part_double convert_part_d;
/* Conversion function for gpart */
float (*convert_gpart)(struct engine*, struct gpart*);
conversion_func_gpart_float convert_gpart_f;
conversion_func_gpart_double convert_gpart_d;
};
/**
......@@ -101,8 +115,11 @@ struct io_props io_make_input_field_(char name[FIELD_BUFFER_SIZE],
r.partSize = partSize;
r.parts = NULL;
r.gparts = NULL;
r.convert_part = NULL;
r.convert_gpart = NULL;
r.conversion = 0;
r.convert_part_f = NULL;
r.convert_part_d = NULL;
r.convert_gpart_f = NULL;
r.convert_gpart_d = NULL;
return r;
}
......@@ -140,8 +157,11 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE],
r.partSize = partSize;
r.parts = NULL;
r.gparts = NULL;
r.convert_part = NULL;
r.convert_gpart = NULL;
r.conversion = 0;
r.convert_part_f = NULL;
r.convert_part_d = NULL;
r.convert_gpart_f = NULL;
r.convert_gpart_d = NULL;
return r;
}
......@@ -149,11 +169,10 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE],
/**
* @brief Constructs an #io_props (with conversion) from its parameters
*/
#define io_make_output_field_convert_part(name, type, dim, units, part, field, \
convert) \
io_make_output_field_convert_part_(name, type, dim, units, \
(char*)(&(part[0]).field), \
sizeof(part[0]), part, convert)
#define io_make_output_field_convert_part(name, type, dim, units, part, \
convert) \
io_make_output_field_convert_part_##type(name, type, dim, units, \
sizeof(part[0]), part, convert)
/**
* @brief Construct an #io_props from its parameters
......@@ -162,17 +181,16 @@ struct io_props io_make_output_field_(char name[FIELD_BUFFER_SIZE],
* @param type The type of the data
* @param dimension Dataset dimension (1D, 3D, ...)
* @param units The units of the dataset
* @param field Pointer to the field of the first particle
* @param partSize The size in byte of the particle
* @param parts The particle array
* @param functionPtr The function used to convert a particle to a float
*
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_output_field_convert_part_(
struct io_props io_make_output_field_convert_part_FLOAT(
char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum unit_conversion_factor units, char* field, size_t partSize,
struct part* parts, float (*functionPtr)(struct engine*, struct part*)) {
enum unit_conversion_factor units, size_t partSize,
const struct part* parts, conversion_func_part_float functionPtr) {
struct io_props r;
strcpy(r.name, name);
......@@ -180,12 +198,52 @@ struct io_props io_make_output_field_convert_part_(
r.dimension = dimension;
r.importance = UNUSED;
r.units = units;
r.field = field;
r.field = NULL;
r.partSize = partSize;
r.parts = parts;
r.gparts = NULL;
r.convert_part = functionPtr;
r.convert_gpart = NULL;
r.conversion = 1;
r.convert_part_f = functionPtr;
r.convert_part_d = NULL;
r.convert_gpart_f = NULL;
r.convert_gpart_d = NULL;
return r;
}
/**
* @brief Construct an #io_props from its parameters
*
* @param name Name of the field to read
* @param type The type of the data
* @param dimension Dataset dimension (1D, 3D, ...)
* @param units The units of the dataset
* @param partSize The size in byte of the particle
* @param parts The particle array
* @param functionPtr The function used to convert a particle to a float
*
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_output_field_convert_part_DOUBLE(
char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum unit_conversion_factor units, size_t partSize,
const struct part* parts, conversion_func_part_double functionPtr) {
struct io_props r;
strcpy(r.name, name);
r.type = type;
r.dimension = dimension;
r.importance = UNUSED;
r.units = units;
r.field = NULL;
r.partSize = partSize;
r.parts = parts;
r.gparts = NULL;
r.conversion = 1;
r.convert_part_f = NULL;
r.convert_part_d = functionPtr;
r.convert_gpart_f = NULL;
r.convert_gpart_d = NULL;
return r;
}
......@@ -193,11 +251,10 @@ struct io_props io_make_output_field_convert_part_(
/**
* @brief Constructs an #io_props (with conversion) from its parameters
*/
#define io_make_output_field_convert_gpart(name, type, dim, units, part, \
field, convert) \
io_make_output_field_convert_gpart_(name, type, dim, units, \
(char*)(&(part[0]).field), \
sizeof(part[0]), gpart, convert)
#define io_make_output_field_convert_gpart(name, type, dim, units, gpart, \
convert) \
io_make_output_field_convert_gpart_##type(name, type, dim, units, \
sizeof(gpart[0]), gpart, convert)
/**
* @brief Construct an #io_props from its parameters
......@@ -206,17 +263,16 @@ struct io_props io_make_output_field_convert_part_(
* @param type The type of the data
* @param dimension Dataset dimension (1D, 3D, ...)
* @param units The units of the dataset
* @param field Pointer to the field of the first particle
* @param partSize The size in byte of the particle
* @param gpartSize The size in byte of the particle
* @param gparts The particle array
* @param functionPtr The function used to convert a g-particle to a float
*
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_output_field_convert_gpart_(
struct io_props io_make_output_field_convert_gpart_FLOAT(
char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum unit_conversion_factor units, char* field, size_t partSize,
struct gpart* gparts, float (*functionPtr)(struct engine*, struct gpart*)) {
enum unit_conversion_factor units, size_t gpartSize,
const struct gpart* gparts, conversion_func_gpart_float functionPtr) {
struct io_props r;
strcpy(r.name, name);
......@@ -224,12 +280,52 @@ struct io_props io_make_output_field_convert_gpart_(
r.dimension = dimension;
r.importance = UNUSED;
r.units = units;
r.field = field;
r.partSize = partSize;
r.field = NULL;
r.partSize = gpartSize;
r.parts = NULL;
r.gparts = gparts;
r.conversion = 1;
r.convert_part_f = NULL;
r.convert_part_d = NULL;
r.convert_gpart_f = functionPtr;
r.convert_gpart_d = NULL;
return r;
}
/**
* @brief Construct an #io_props from its parameters
*
* @param name Name of the field to read
* @param type The type of the data
* @param dimension Dataset dimension (1D, 3D, ...)
* @param units The units of the dataset
* @param gpartSize The size in byte of the particle
* @param gparts The particle array
* @param functionPtr The function used to convert a g-particle to a float
*
* Do not call this function directly. Use the macro defined above.
*/
struct io_props io_make_output_field_convert_gpart_DOUBLE(
char name[FIELD_BUFFER_SIZE], enum IO_DATA_TYPE type, int dimension,
enum unit_conversion_factor units, size_t gpartSize,
const struct gpart* gparts, conversion_func_gpart_double functionPtr) {
struct io_props r;
strcpy(r.name, name);
r.type = type;
r.dimension = dimension;
r.importance = UNUSED;
r.units = units;
r.field = NULL;
r.partSize = gpartSize;
r.parts = NULL;
r.gparts = gparts;
r.convert_part = NULL;
r.convert_gpart = functionPtr;
r.conversion = 1;
r.convert_part_f = NULL;
r.convert_part_d = NULL;
r.convert_gpart_f = NULL;
r.convert_gpart_d = functionPtr;
return r;
}
......
src/serial_io.c
View file @ 1d64aa96
......@@ -176,9 +176,9 @@ void readArray(hid_t grp, const struct io_props props, size_t N,
* Routines writing an output file
*-----------------------------------------------------------------------------*/
void prepareArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
char* partTypeGroupName, const struct io_props props,
unsigned long long N_total,
void prepareArray(const struct engine* e, hid_t grp, char* fileName,
FILE* xmfFile, char* partTypeGroupName,
const struct io_props props, unsigned long long N_total,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units) {
......@@ -282,15 +282,17 @@ void prepareArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
* @todo A better version using HDF5 hyper-slabs to write the file directly from
* the part array will be written once the structures have been stabilized.
*/
void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
char* partTypeGroupName, const struct io_props props, size_t N,
long long N_total, int mpi_rank, long long offset,
void writeArray(const struct engine* e, hid_t grp, char* fileName,
FILE* xmfFile, char* partTypeGroupName,
const struct io_props props, size_t N, long long N_total,
int mpi_rank, long long offset,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units) {
const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
const size_t dim = props.dimension;
/* message("Writing '%s' array...", props.name); */
......@@ -300,28 +302,63 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
internal_units, snapshot_units);
/* Allocate temporary buffer */
void* temp = malloc(num_elements * io_sizeof_type(props.type));
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
void* temp = NULL;
if (posix_memalign((void**)&temp, SWIFT_CACHE_ALIGNMENT,
num_elements * io_sizeof_type(props.type)) != 0)
error("Unable to allocate temporary i/o buffer");
/* Copy particle data to temporary buffer */
if (props.convert_part == NULL &&
props.convert_gpart == NULL) { /* No conversion */
if (props.conversion == 0) { /* No conversion */
char* temp_c = temp;
for (size_t i = 0; i < N; ++i)
memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize);
} else if (props.convert_part != NULL) { /* conversion (for parts)*/
} else { /* Converting particle to data */
float* temp_f = temp;
for (size_t i = 0; i < N; ++i)
temp_f[i] = props.convert_part(e, &props.parts[i]);
if (props.convert_part_f != NULL) {
} else if (props.convert_gpart != NULL) { /* conversion (for gparts)*/
swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct part, parts, props.parts,
SWIFT_STRUCT_ALIGNMENT);
float* temp_f = temp;
for (size_t i = 0; i < N; ++i)
temp_f[i] = props.convert_gpart(e, &props.gparts[i]);
/* float conversion for parts */
for (size_t i = 0; i < N; i++)
props.convert_part_f(e, &parts[i], &temp_f[i * dim]);
} else if (props.convert_part_d != NULL) {
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct part, parts, props.parts,
SWIFT_STRUCT_ALIGNMENT);
/* double conversion for parts */
for (size_t i = 0; i < N; i++)
props.convert_part_d(e, &parts[i], &temp_d[i * dim]);
} else if (props.convert_gpart_f != NULL) {
swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct gpart, gparts, props.gparts,
SWIFT_STRUCT_ALIGNMENT);
/* float conversion for gparts */
for (size_t i = 0; i < N; i++)
props.convert_gpart_f(e, &gparts[i], &temp_f[i * dim]);
} else if (props.convert_gpart_d != NULL) {
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct gpart, gparts, props.gparts,
SWIFT_STRUCT_ALIGNMENT);
/* double conversion for gparts */
for (size_t i = 0; i < N; i++)
props.convert_gpart_d(e, &gparts[i], &temp_d[i * dim]);
} else {
error("Missing conversion function");
}
}
/* Unit conversion if necessary */
......@@ -332,10 +369,10 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* message("Converting ! factor=%e", factor); */
if (io_is_double_precision(props.type)) {
double* temp_d = temp;
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
float* temp_f = temp;
swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
}
}
......
src/single_io.c
View file @ 1d64aa96
......@@ -169,40 +169,77 @@ void readArray(hid_t h_grp, const struct io_props prop, size_t N,
* @todo A better version using HDF5 hyper-slabs to write the file directly from
* the part array will be written once the structures have been stabilized.
*/
void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
char* partTypeGroupName, const struct io_props props, size_t N,
void writeArray(const struct engine* e, hid_t grp, char* fileName,
FILE* xmfFile, char* partTypeGroupName,
const struct io_props props, size_t N,
const struct unit_system* internal_units,
const struct unit_system* snapshot_units) {
const size_t typeSize = io_sizeof_type(props.type);
const size_t copySize = typeSize * props.dimension;
const size_t num_elements = N * props.dimension;
const size_t dim = props.dimension;
/* message("Writing '%s' array...", props.name); */
/* Allocate temporary buffer */
void* temp = malloc(num_elements * io_sizeof_type(props.type));
if (temp == NULL) error("Unable to allocate memory for temporary buffer");
void* temp = NULL;
if (posix_memalign((void**)&temp, SWIFT_CACHE_ALIGNMENT,
num_elements * io_sizeof_type(props.type)) != 0)
error("Unable to allocate temporary i/o buffer");
/* Copy particle data to temporary buffer */
if (props.convert_part == NULL &&
props.convert_gpart == NULL) { /* No conversion */
if (props.conversion == 0) { /* No conversion */
char* temp_c = temp;
for (size_t i = 0; i < N; ++i)
memcpy(&temp_c[i * copySize], props.field + i * props.partSize, copySize);
} else if (props.convert_part != NULL) { /* conversion (for parts)*/
} else { /* Converting particle to data */
float* temp_f = temp;
for (size_t i = 0; i < N; ++i)
temp_f[i] = props.convert_part(e, &props.parts[i]);
if (props.convert_part_f != NULL) {
} else if (props.convert_gpart != NULL) { /* conversion (for gparts)*/
swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct part, parts, props.parts,
SWIFT_STRUCT_ALIGNMENT);
float* temp_f = temp;
for (size_t i = 0; i < N; ++i)
temp_f[i] = props.convert_gpart(e, &props.gparts[i]);
/* float conversion for parts */
for (size_t i = 0; i < N; i++)
props.convert_part_f(e, &parts[i], &temp_f[i * dim]);
} else if (props.convert_part_d != NULL) {
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct part, parts, props.parts,
SWIFT_STRUCT_ALIGNMENT);
/* double conversion for parts */
for (size_t i = 0; i < N; i++)
props.convert_part_d(e, &parts[i], &temp_d[i * dim]);
} else if (props.convert_gpart_f != NULL) {
swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct gpart, gparts, props.gparts,
SWIFT_STRUCT_ALIGNMENT);
/* float conversion for gparts */
for (size_t i = 0; i < N; i++)
props.convert_gpart_f(e, &gparts[i], &temp_f[i * dim]);
} else if (props.convert_gpart_d != NULL) {
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
swift_declare_aligned_ptr(const struct gpart, gparts, props.gparts,
SWIFT_STRUCT_ALIGNMENT);
/* double conversion for gparts */
for (size_t i = 0; i < N; i++)
props.convert_gpart_d(e, &gparts[i], &temp_d[i * dim]);
} else {
error("Missing conversion function");
}
}
/* Unit conversion if necessary */
......@@ -213,10 +250,10 @@ void writeArray(struct engine* e, hid_t grp, char* fileName, FILE* xmfFile,
/* message("Converting ! factor=%e", factor); */
if (io_is_double_precision(props.type)) {
double* temp_d = temp;
swift_declare_aligned_ptr(double, temp_d, temp, SWIFT_CACHE_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_d[i] *= factor;
} else {
float* temp_f = temp;
swift_declare_aligned_ptr(float, temp_f, temp, SWIFT_CACHE_ALIGNMENT);
for (size_t i = 0; i < num_elements; ++i) temp_f[i] *= factor;
}
}
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment