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Renamed trio in trexio

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This commit is contained in:
Anthony Scemama 2021-03-02 13:56:30 +01:00
parent c58231e135
commit 49a73b6d75
13 changed files with 796 additions and 796 deletions
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18
src/Makefile
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@ -6,7 +6,7 @@ ifeq ($(COMPILER),GNU)
CC=gcc -g
CFLAGS=-fPIC -fexceptions -Wall -Werror -Wpedantic -Wextra
LIBS= -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ -lz -lm -lhdf5 -lhdf5_hl #-lgfortran
LIBS= -L/usr/lib/x86_64-linux-gnu/hdf5/serial/ -lz -lm -lhdf5 -lhdf5_hl #-lgfortran
INCLUDE = -I/usr/include/hdf5/serial
endif
@ -17,7 +17,7 @@ CFLAGS=-fPIC -g -O2
FC=ifort -xHost
FFLAGS=-fPIC -g -O2
LIBS= #-lm
LIBS= #-lm
endif
#TODO
@ -32,21 +32,21 @@ LIBS=-lm
endif
OBJECT_FILES= trio.o trio_text.o trio_hdf5.o
HEADER_FILES= trio.h trio_text.h trio_hdf5.h trio_s.h
OBJECT_FILES= trexio.o trexio_text.o trexio_hdf5.o
HEADER_FILES= trexio.h trexio_text.h trexio_hdf5.h trexio_s.h
export CC CFLAGS LIBS
.PHONY: clean
libtrio.so: $(OBJECT_FILES) $(HEADER_FILES)
$(CC) -shared $(OBJECT_FILES) -o libtrio.so
libtrexio.so: $(OBJECT_FILES) $(HEADER_FILES)
$(CC) -shared $(OBJECT_FILES) -o libtrexio.so
test: libtrio.so test.c
$(CC) $(CFLAGS) $(INCLUDE) -Wl,-rpath,$(PWD) -L. test.c -ltrio $(LIBS) -o test
test: libtrexio.so test.c
$(CC) $(CFLAGS) $(INCLUDE) -Wl,-rpath,$(PWD) -L. test.c -ltrexio $(LIBS) -o test
clean:
rm -f *.o libtrio.so test test_write.h5
rm -f *.o libtrexio.so test test_write.h5
%.o: %.c $(HEADER_FILES)
$(CC) $(CFLAGS) $(INCLUDE) -c $*.c -o $*.o

76
src/test.c
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@ -1,4 +1,4 @@
#include "trio.h"
#include "trexio.h"
#include <assert.h>
#include <stdint.h>
#include <stdio.h>
@ -22,10 +22,10 @@ int main() {
int test_h5write() {
const char* file_name = "test_write.h5";
trio_t* file = NULL;
trio_exit_code rc;
trexio_t* file = NULL;
trexio_exit_code rc;
rc = TRIO_SUCCESS;
rc = TREXIO_SUCCESS;
uint64_t num = 12;
@ -44,27 +44,27 @@ int test_h5write() {
0.00000000 , 2.47304151 , 0.00000000 ,
};
file = trio_create(file_name, TRIO_HDF5);
file = trexio_create(file_name, TREXIO_HDF5);
// works: try writing info in an empty file
rc = trio_write_nucleus_num(file,num);
rc = trio_write_nucleus_coord(file,coord);
rc = trexio_write_nucleus_num(file,num);
rc = trexio_write_nucleus_coord(file,coord);
// should not work: try to rewrite the nucleus_num
rc = trio_write_nucleus_num(file,25);
rc = trexio_write_nucleus_num(file,25);
// works: try to rewrite the nucleus_coord
// works: try to rewrite the nucleus_coord
coord[0] = 666.666;
rc = trio_write_nucleus_coord(file,coord);
rc = trexio_write_nucleus_coord(file,coord);
if (rc == TRIO_SUCCESS) {
if (rc == TREXIO_SUCCESS) {
printf("SUCCESS\n");
} else {
printf("FAILURE\n");
}
trio_close(file);
trexio_close(file);
return 0;
}
@ -72,20 +72,20 @@ int test_h5write() {
int test_h5read() {
const char* file_name = "test_write.h5";
trio_t* file = NULL;
trio_exit_code rc;
trexio_t* file = NULL;
trexio_exit_code rc;
uint64_t num;
double* coord;
file = trio_create(file_name, TRIO_HDF5);
file = trexio_create(file_name, TREXIO_HDF5);
rc = trio_read_nucleus_num(file,&num);
rc = trexio_read_nucleus_num(file,&num);
assert (num == 12);
coord = (double*) calloc(3*num, sizeof(double));
rc = trio_read_nucleus_coord(file,coord);
rc = trexio_read_nucleus_coord(file,coord);
/*for (size_t i=0; i<3*num; i++){
printf("%lf \n", coord[i]);
}*/
@ -93,14 +93,14 @@ int test_h5read() {
double x = coord[30] - 2.14171677;
assert( x*x < 1.e-12);
if (rc == TRIO_SUCCESS) {
if (rc == TREXIO_SUCCESS) {
printf("SUCCESS\n");
} else {
printf("FAILURE\n");
}
trio_close(file);
trexio_close(file);
free(coord);
return 0;
@ -108,10 +108,10 @@ int test_h5read() {
int test_write() {
const char* file_name = "trio_test";
const char* file_name = "trexio_test";
trio_t* file = NULL;
trio_exit_code rc;
trexio_t* file = NULL;
trexio_exit_code rc;
uint64_t num = 12;
@ -133,54 +133,54 @@ int test_write() {
0.00000000 , 2.47304151 , 0.00000000 ,
};
file = trio_create(file_name, TRIO_TEXT);
file = trexio_create(file_name, TREXIO_TEXT);
rc = trio_write_nucleus_num(file,num);
rc = trio_write_nucleus_charge(file,charge);
rc = trio_write_nucleus_coord(file,coord);
rc = trexio_write_nucleus_num(file,num);
rc = trexio_write_nucleus_charge(file,charge);
rc = trexio_write_nucleus_coord(file,coord);
if (rc == TRIO_SUCCESS) {
if (rc == TREXIO_SUCCESS) {
printf("SUCCESS\n");
} else {
printf("FAILURE\n");
}
trio_close(file);
trexio_close(file);
return 0;
}
int test_read() {
const char* file_name = "trio_test";
const char* file_name = "trexio_test";
trio_t* file = NULL;
trio_exit_code rc;
trexio_t* file = NULL;
trexio_exit_code rc;
uint64_t num;
double* charge;
double* coord;
file = trio_create(file_name, TRIO_TEXT);
file = trexio_create(file_name, TREXIO_TEXT);
rc = trio_read_nucleus_num(file,&num);
rc = trexio_read_nucleus_num(file,&num);
assert (num == 12);
charge = (double*) calloc(num, sizeof(double));
rc = trio_read_nucleus_charge(file,charge);
rc = trexio_read_nucleus_charge(file,charge);
assert(charge[10] == 1.);
coord = (double*) calloc(3*num, sizeof(double));
rc = trio_read_nucleus_coord(file,coord);
rc = trexio_read_nucleus_coord(file,coord);
double x = coord[30] - 2.14171677;
assert( x*x < 1.e-12);
if (rc == TRIO_SUCCESS) {
if (rc == TREXIO_SUCCESS) {
printf("SUCCESS\n");
} else {
printf("FAILURE\n");
}
trio_close(file);
trexio_close(file);
free(charge);
free(coord);

254
src/trexio.c Normal file
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@ -0,0 +1,254 @@
/* This file was generated from the trexio.org org-mode file.
To generate it, open trexio.org in Emacs and execute
M-x org-babel-tangle
*/
#include <pthread.h>
#include <assert.h>
#include <stdlib.h>
#include <string.h>
#include <pthread.h>
#include "trexio.h"
#include "trexio_s.h"
#include "trexio_text.h"
#include "trexio_hdf5.h"
/*
#include "trexio_json.h"
*/
trexio_t* trexio_create(const char* file_name, back_end_t back_end) {
/* Check that file name is not NULL or empty */
assert (file_name != NULL);
assert (file_name[0] != '\0');
/* Check that back_end is valid */
assert (back_end < TREXIO_INVALID_BACK_END);
trexio_t* result = NULL;
switch (back_end) {
case TREXIO_TEXT:
result = (trexio_t*) malloc (sizeof(trexio_text_t));
break;
case TREXIO_HDF5:
result = (trexio_t*) malloc (sizeof(trexio_hdf5_t));
break;
/*
case TREXIO_JSON:
result = (trexio_t*) malloc (sizeof(trexio_json_t));
break;
*/
default:
assert (1 == 0); /* Impossible case */
}
/* TODO: Error handling */
assert (result != NULL);
result->file_name = (char*) calloc(strlen(file_name)+1,sizeof(char));
strcpy(result->file_name, file_name);
result->back_end = back_end;
result->mode = 'w'; /* Upon creation, mode=write */
int irc = pthread_mutex_init ( &(result->thread_lock), NULL);
assert (irc == 0);
trexio_exit_code rc = TREXIO_FAILURE;
switch (back_end) {
case TREXIO_TEXT:
rc = trexio_text_init(result);
break;
case TREXIO_HDF5:
rc = trexio_hdf5_init(result);
break;
/*
case TREXIO_JSON:
rc = trexio_json_init(result);
break;
*/
default:
assert (1 == 0); /* Impossible case */
}
assert (rc == TREXIO_SUCCESS);
return result;
}
trexio_exit_code trexio_close(trexio_t* file) {
assert (file != NULL);
trexio_exit_code rc;
switch (file->back_end) {
case TREXIO_TEXT:
rc = trexio_text_finalize(file);
break;
case TREXIO_HDF5:
rc = trexio_hdf5_finalize(file);
break;
/*
case TREXIO_JSON:
rc = trexio_json_finalize(file);
break;
*/
default:
assert (1 == 0); /* Impossible case */
}
if (rc != TREXIO_SUCCESS) {
return TREXIO_FAILURE;
}
free(file->file_name);
file->file_name = NULL;
int irc = pthread_mutex_destroy( &(file->thread_lock) );
assert (irc == 0);
free(file);
return TREXIO_SUCCESS;
}
trexio_exit_code trexio_read_nucleus_num(trexio_t* file, uint64_t* num) {
if (file == NULL) return TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_read_nucleus_num(file, num);
break;
case TREXIO_HDF5:
return trexio_hdf5_read_nucleus_num(file, num);
break;
/*
case TREXIO_JSON:
return trexio_json_read_nucleus_num(file, num);
break;
*/
default:
return TREXIO_FAILURE; /* Impossible case */
}
}
trexio_exit_code trexio_write_nucleus_num(trexio_t* file, uint64_t num) {
if (file == NULL) return TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_write_nucleus_num(file, num);
break;
case TREXIO_HDF5:
return trexio_hdf5_write_nucleus_num(file, num);
break;
/*
case TREXIO_JSON:
return trexio_json_write_nucleus_num(file, num);
break;
*/
default:
return TREXIO_FAILURE; /* Impossible case */
}
}
trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
if (file == NULL) return TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_read_nucleus_coord(file, coord);
break;
case TREXIO_HDF5:
return trexio_hdf5_read_nucleus_coord(file, coord);
break;
/*
case TREXIO_JSON:
return trexio_json_read_nucleus_coord(file, coord);
break;
*/
default:
return TREXIO_FAILURE; /* Impossible case */
}
}
trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, double* coord) {
if (file == NULL) return TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_write_nucleus_coord(file, coord);
break;
case TREXIO_HDF5:
return trexio_hdf5_write_nucleus_coord(file, coord);
break;
/*
case TREXIO_JSON:
return trexio_json_write_nucleus_coord(file, coord);
break;
*/
default:
return TREXIO_FAILURE; /* Impossible case */
}
}
trexio_exit_code trexio_read_nucleus_charge(trexio_t* file, double* charge) {
if (file == NULL) return TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_read_nucleus_charge(file, charge);
break;
/*
case TREXIO_HDF5:
return trexio_hdf5_read_nucleus_charge(file, charge);
break;
case TREXIO_JSON:
return trexio_json_read_nucleus_charge(file, charge);
break;
*/
default:
return TREXIO_FAILURE; /* Impossible case */
}
}
trexio_exit_code trexio_write_nucleus_charge(trexio_t* file, double* charge) {
if (file == NULL) return TREXIO_FAILURE;
switch (file->back_end) {
case TREXIO_TEXT:
return trexio_text_write_nucleus_charge(file, charge);
break;
/*
case TREXIO_HDF5:
return trexio_hdf5_write_nucleus_charge(file, charge);
break;
case TREXIO_JSON:
return trexio_json_write_nucleus_charge(file, charge);
break;
*/
default:
return TREXIO_FAILURE; /* Impossible case */
}
}

40
src/trexio.h Normal file
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@ -0,0 +1,40 @@
/* This file was generated from the trexio.org org-mode file.
To generate it, open trexio.org in Emacs and execute
M-x org-babel-tangle
*/
#ifndef _TREXIO_H
#define _TREXIO_H
#include <stdint.h>
typedef int32_t trexio_exit_code;
#define TREXIO_SUCCESS ( (trexio_exit_code) 0 )
#define TREXIO_FAILURE ( (trexio_exit_code) 1 )
typedef uint32_t back_end_t;
#define TREXIO_HDF5 ( (back_end_t) 0 )
#define TREXIO_TEXT ( (back_end_t) 1 )
#define TREXIO_JSON ( (back_end_t) 2 )
#define TREXIO_INVALID_BACK_END ( (back_end_t) 3 )
typedef struct trexio_s trexio_t;
trexio_t* trexio_create(const char* file_name, back_end_t back_end);
trexio_exit_code trexio_close(trexio_t* file);
trexio_exit_code trexio_read_nucleus_num(trexio_t* file, uint64_t* num);
trexio_exit_code trexio_write_nucleus_num(trexio_t* file, uint64_t num);
trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord);
trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, double* coord);
trexio_exit_code trexio_read_nucleus_charge(trexio_t* file, double* charge);
trexio_exit_code trexio_write_nucleus_charge(trexio_t* file, double* charge);
#endif

586
src/trio.org → src/trexio.org
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File diff suppressed because it is too large Load Diff

84
src/trio_hdf5.c → src/trexio_hdf5.c
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@ -1,11 +1,11 @@
/* This file was generated from the trio.org org-mode file.
To generate it, open trio.org in Emacs and execute
/* This file was generated from the trexio.org org-mode file.
To generate it, open trexio.org in Emacs and execute
M-x org-babel-tangle
*/
#include "trio_hdf5.h"
#include "trexio_hdf5.h"
#define NUCLEUS_GROUP_NAME "nucleus"
#define NUCLEUS_NUM_NAME "nucleus_num"
@ -16,7 +16,7 @@
* Currently H5LTread_dataset_ is used instead of this function
* but keep it for later if we decide to get rid of the H5LT API
*/
dset_t* trio_hdf5_read_dset_low(const trio_hdf5_t* file, const char *dset_name, void *buf) {
dset_t* trexio_hdf5_read_dset_low(const trexio_hdf5_t* file, const char *dset_name, void *buf) {
assert (file != NULL);
assert (dset_name != NULL);
@ -63,9 +63,9 @@ dset_t* trio_hdf5_read_dset_low(const trio_hdf5_t* file, const char *dset_name,
}
trio_exit_code trio_hdf5_init(trio_t* file) {
trexio_exit_code trexio_hdf5_init(trexio_t* file) {
trio_hdf5_t* f = (trio_hdf5_t*) file;
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
/* If file doesn't exist, create it */
int f_ishere = 0;
@ -92,12 +92,12 @@ trio_exit_code trio_hdf5_init(trio_t* file) {
assert (f->nucleus_group > 0L);
//assert (f->electron_group > 0L);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
trio_exit_code trio_hdf5_finalize(trio_t* file) {
trexio_exit_code trexio_hdf5_finalize(trexio_t* file) {
trio_hdf5_t* f = (trio_hdf5_t*) file;
trexio_hdf5_t* f = (trexio_hdf5_t*) file;
H5Gclose(f->nucleus_group);
f->nucleus_group = 0;
@ -110,10 +110,10 @@ trio_exit_code trio_hdf5_finalize(trio_t* file) {
H5Fclose(f->file_id);
f->file_id = 0;
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
h5nucleus_t* trio_hdf5_read_nucleus(const trio_hdf5_t* file) {
h5nucleus_t* trexio_hdf5_read_nucleus(const trexio_hdf5_t* file) {
/* Allocate the data structure */
h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
@ -163,7 +163,7 @@ h5nucleus_t* trio_hdf5_read_nucleus(const trio_hdf5_t* file) {
* when not used anymore, see below. Note how this function is similar to H5LTread_dataset_double
*/
/*
nucleus->h5_coord = trio_hdf5_read_dset_low(file, NUCLEUS_COORD_NAME,
nucleus->h5_coord = trexio_hdf5_read_dset_low(file, NUCLEUS_COORD_NAME,
nucleus->coord);
H5Sclose(nucleus->h5_coord->dspace_id);
@ -177,7 +177,7 @@ h5nucleus_t* trio_hdf5_read_nucleus(const trio_hdf5_t* file) {
}
trio_exit_code trio_hdf5_write_nucleus(const trio_hdf5_t* file, h5nucleus_t* nucleus) {
trexio_exit_code trexio_hdf5_write_nucleus(const trexio_hdf5_t* file, h5nucleus_t* nucleus) {
assert (file != NULL);
assert (nucleus != NULL);
@ -287,12 +287,12 @@ trio_exit_code trio_hdf5_write_nucleus(const trio_hdf5_t* file, h5nucleus_t* nuc
}
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
trio_exit_code trio_hdf5_free_nucleus(h5nucleus_t* nucleus) {
trexio_exit_code trexio_hdf5_free_nucleus(h5nucleus_t* nucleus) {
if (nucleus == NULL) return TRIO_FAILURE;
if (nucleus == NULL) return TREXIO_FAILURE;
if (nucleus->coord != NULL) free (nucleus->coord);
nucleus->coord = NULL;
@ -308,33 +308,33 @@ trio_exit_code trio_hdf5_free_nucleus(h5nucleus_t* nucleus) {
free (nucleus);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
trio_exit_code trio_hdf5_read_nucleus_num(const trio_t* file, uint64_t* num) {
trexio_exit_code trexio_hdf5_read_nucleus_num(const trexio_t* file, uint64_t* num) {
assert (file != NULL);
assert (num != NULL);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
if (nucleus == NULL) {
return TRIO_FAILURE;
return TREXIO_FAILURE;
}
/**/ *num = nucleus->num;
trio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
trexio_hdf5_free_nucleus(nucleus);
return TREXIO_SUCCESS;
}
trio_exit_code trio_hdf5_write_nucleus_num(const trio_t* file, const uint64_t num) {
trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint64_t num) {
assert (file != NULL);
assert (num > 0L);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
assert (nucleus != NULL);
@ -343,8 +343,8 @@ trio_exit_code trio_hdf5_write_nucleus_num(const trio_t* file, const uint64_t nu
if (nucleus->num != 0) {
printf("%ld -> %ld %s \n", num, nucleus->num,
"This variable alreasy exists. Overwriting it is not supported");
trio_hdf5_free_nucleus(nucleus);
return TRIO_FAILURE;
trexio_hdf5_free_nucleus(nucleus);
return TREXIO_FAILURE;
}
nucleus->num = num;
@ -365,51 +365,51 @@ trio_exit_code trio_hdf5_write_nucleus_num(const trio_t* file, const uint64_t nu
nucleus->num = num;
}
trio_exit_code rc = trio_hdf5_write_nucleus((trio_hdf5_t*) file, nucleus);
assert (rc == TRIO_SUCCESS);
trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
assert (rc == TREXIO_SUCCESS);
trio_hdf5_free_nucleus(nucleus);
trexio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
trio_exit_code trio_hdf5_read_nucleus_coord(const trio_t* file, double* coord) {
trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord) {
assert (file != NULL);
assert (coord != NULL);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
if (nucleus == NULL) return TRIO_FAILURE;
if (nucleus == NULL) return TREXIO_FAILURE;
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
coord[i] = nucleus->coord[i];
}
trio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
trexio_hdf5_free_nucleus(nucleus);
return TREXIO_SUCCESS;
}
trio_exit_code trio_hdf5_write_nucleus_coord(const trio_t* file, const double* coord) {
trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord) {
assert (file != NULL);
assert (coord != NULL);
h5nucleus_t* nucleus = trio_hdf5_read_nucleus((trio_hdf5_t*) file);
h5nucleus_t* nucleus = trexio_hdf5_read_nucleus((trexio_hdf5_t*) file);
if (nucleus == NULL) return TRIO_FAILURE;
if (nucleus == NULL) return TREXIO_FAILURE;
assert (nucleus->coord != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
nucleus->coord[i] = coord[i];
}
trio_exit_code rc = trio_hdf5_write_nucleus((trio_hdf5_t*) file, nucleus);
assert (rc == TRIO_SUCCESS);
trexio_exit_code rc = trexio_hdf5_write_nucleus((trexio_hdf5_t*) file, nucleus);
assert (rc == TREXIO_SUCCESS);
trio_hdf5_free_nucleus(nucleus);
trexio_hdf5_free_nucleus(nucleus);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}

30
src/trio_hdf5.h → src/trexio_hdf5.h
View File

@ -1,15 +1,15 @@
/* This file was generated from the trio.org org-mode file.
To generate it, open trio.org in Emacs and execute
/* This file was generated from the trexio.org org-mode file.
To generate it, open trexio.org in Emacs and execute
M-x org-babel-tangle
*/
#ifndef _TRIO_HDF5_H
#define _TRIO_HDF5_H
#ifndef _TREXIO_HDF5_H
#define _TREXIO_HDF5_H
#include "trio.h"
#include "trio_s.h"
#include "trexio.h"
#include "trexio_s.h"
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
@ -49,23 +49,23 @@ typedef struct h5electron_s {
uint64_t beta_num;
} h5electron_t;
typedef struct trio_hdf5_s {
trio_t parent ;
typedef struct trexio_hdf5_s {
trexio_t parent ;
hid_t file_id;
hid_t nucleus_group;
hid_t electron_group;
//... other groups' id
const char* file_name;
} trio_hdf5_t;
} trexio_hdf5_t;
trio_exit_code trio_hdf5_init(trio_t* file);
trexio_exit_code trexio_hdf5_init(trexio_t* file);
trio_exit_code trio_hdf5_finalize(trio_t* file);
trexio_exit_code trexio_hdf5_finalize(trexio_t* file);
trio_exit_code trio_hdf5_read_nucleus_num(const trio_t* file, uint64_t* num);
trio_exit_code trio_hdf5_write_nucleus_num(const trio_t* file, const uint64_t num);
trexio_exit_code trexio_hdf5_read_nucleus_num(const trexio_t* file, uint64_t* num);
trexio_exit_code trexio_hdf5_write_nucleus_num(const trexio_t* file, const uint64_t num);
trio_exit_code trio_hdf5_read_nucleus_coord(const trio_t* file, double* coord);
trio_exit_code trio_hdf5_write_nucleus_coord(const trio_t* file, const double* coord);
trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* coord);
trexio_exit_code trexio_hdf5_write_nucleus_coord(const trexio_t* file, const double* coord);
#endif

12
src/trio_s.h → src/trexio_s.h
View File

@ -1,18 +1,18 @@
/* This file was generated from the trio.org org-mode file.
To generate it, open trio.org in Emacs and execute
/* This file was generated from the trexio.org org-mode file.
To generate it, open trexio.org in Emacs and execute
M-x org-babel-tangle
*/
#ifndef _TRIO_S_H
#define _TRIO_S_H
#ifndef _TREXIO_S_H
#define _TREXIO_S_H
#include "trio.h"
#include "trexio.h"
#include <pthread.h>
#include <assert.h>
struct trio_s {
struct trexio_s {
char* file_name;
pthread_mutex_t thread_lock;
back_end_t back_end;

98
src/trio_text.c → src/trexio_text.c
View File

@ -1,15 +1,15 @@
/* This file was generated from the trio.org org-mode file.
To generate it, open trio.org in Emacs and execute
/* This file was generated from the trexio.org org-mode file.
To generate it, open trexio.org in Emacs and execute
M-x org-babel-tangle
*/
#include "trio_text.h"
#include "trexio_text.h"
trio_exit_code trio_text_init(trio_t* file) {
trexio_exit_code trexio_text_init(trexio_t* file) {
trio_text_t* f = (trio_text_t*) file;
trexio_text_t* f = (trexio_text_t*) file;
/* If directory doesn't exist, create it */
struct stat st;
@ -18,7 +18,7 @@ trio_exit_code trio_text_init(trio_t* file) {
/* Do nothing */
} else {
if (mkdir(file->file_name, 0777) != 0) {
return TRIO_FAILURE;
return TREXIO_FAILURE;
}
}
@ -40,12 +40,12 @@ trio_exit_code trio_text_init(trio_t* file) {
strcpy (f->electron_file_name, file->file_name);
strcat (f->electron_file_name, electron_file_name);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
trio_exit_code trio_text_finalize(trio_t* file) {
trexio_exit_code trexio_text_finalize(trexio_t* file) {
trio_text_t* f = (trio_text_t*) file;
trexio_text_t* f = (trexio_text_t*) file;
free (f->nucleus_file_name);
f->nucleus_file_name = NULL;
@ -53,10 +53,10 @@ trio_exit_code trio_text_finalize(trio_t* file) {
free (f->electron_file_name);
f->electron_file_name = NULL;
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
nucleus_t* trio_text_read_nucleus(const trio_text_t* file) {
nucleus_t* trexio_text_read_nucleus(const trexio_text_t* file) {
/* Allocate the data structure */
nucleus_t* nucleus = (nucleus_t*) malloc(sizeof(nucleus_t));
@ -112,7 +112,7 @@ nucleus_t* trio_text_read_nucleus(const trio_text_t* file) {
}
trio_exit_code trio_text_write_nucleus(const trio_text_t* file, nucleus_t* nucleus) {
trexio_exit_code trexio_text_write_nucleus(const trexio_text_t* file, nucleus_t* nucleus) {
assert (nucleus != NULL);
FILE* f = fopen(file->nucleus_file_name,"w");
@ -133,13 +133,13 @@ trio_exit_code trio_text_write_nucleus(const trio_text_t* file, nucleus_t* nucle
}
fclose(f);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
trio_exit_code trio_text_free_nucleus(nucleus_t* nucleus) {
trexio_exit_code trexio_text_free_nucleus(nucleus_t* nucleus) {
if (nucleus == NULL) {
return TRIO_FAILURE;
return TREXIO_FAILURE;
}
if (nucleus->coord != NULL) {
@ -153,33 +153,33 @@ trio_exit_code trio_text_free_nucleus(nucleus_t* nucleus) {
nucleus->charge = NULL;
free (nucleus);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
trio_exit_code trio_text_read_nucleus_num(const trio_t* file, uint64_t* num) {
trexio_exit_code trexio_text_read_nucleus_num(const trexio_t* file, uint64_t* num) {
assert (file != NULL);
assert (num != NULL);
nucleus_t* nucleus = trio_text_read_nucleus((trio_text_t*) file);
nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*) file);
if (nucleus == NULL) {
return TRIO_FAILURE;
return TREXIO_FAILURE;
}
/**/ *num = nucleus->num;
trio_text_free_nucleus(nucleus);
return TRIO_SUCCESS;
trexio_text_free_nucleus(nucleus);
return TREXIO_SUCCESS;
}
trio_exit_code trio_text_write_nucleus_num(const trio_t* file, const uint64_t num) {
trexio_exit_code trexio_text_write_nucleus_num(const trexio_t* file, const uint64_t num) {
assert (num > 0L);
assert (file != NULL);
nucleus_t* nucleus = trio_text_read_nucleus((trio_text_t*) file);
nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*) file);
assert (nucleus != NULL);
@ -203,22 +203,22 @@ trio_exit_code trio_text_write_nucleus_num(const trio_t* file, const uint64_t nu
nucleus->num = num;
}
trio_exit_code rc = trio_text_write_nucleus((trio_text_t*) file, nucleus);
assert (rc == TRIO_SUCCESS);
trexio_exit_code rc = trexio_text_write_nucleus((trexio_text_t*) file, nucleus);
assert (rc == TREXIO_SUCCESS);
trio_text_free_nucleus(nucleus);
trexio_text_free_nucleus(nucleus);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
trio_exit_code trio_text_read_nucleus_coord(const trio_t* file, double* coord) {
trexio_exit_code trexio_text_read_nucleus_coord(const trexio_t* file, double* coord) {
assert (file != NULL);
assert (file != NULL);
nucleus_t* nucleus = trio_text_read_nucleus((trio_text_t*) file);
nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*) file);
if (nucleus == NULL) {
return TRIO_FAILURE;
return TREXIO_FAILURE;
}
assert (coord != NULL);
@ -227,39 +227,39 @@ trio_exit_code trio_text_read_nucleus_coord(const trio_t* file, double* coord) {
coord[i] = nucleus->coord[i];
}
trio_text_free_nucleus(nucleus);
return TRIO_SUCCESS;
trexio_text_free_nucleus(nucleus);
return TREXIO_SUCCESS;
}
trio_exit_code trio_text_write_nucleus_coord(const trio_t* file, const double* coord) {
trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const double* coord) {
assert (coord != NULL);
assert (file != NULL);
nucleus_t* nucleus = trio_text_read_nucleus((trio_text_t*) file);
nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*) file);
assert (nucleus != NULL);
for (size_t i=0 ; i<3*nucleus->num ; i++) {
nucleus->coord[i] = coord[i];
}
trio_exit_code rc = trio_text_write_nucleus((trio_text_t*) file, nucleus);
assert (rc == TRIO_SUCCESS);
trexio_exit_code rc = trexio_text_write_nucleus((trexio_text_t*) file, nucleus);
assert (rc == TREXIO_SUCCESS);
trio_text_free_nucleus(nucleus);
trexio_text_free_nucleus(nucleus);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}
trio_exit_code trio_text_read_nucleus_charge(const trio_t* file, double* charge) {
trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* charge) {
assert (file != NULL);
assert (file != NULL);
nucleus_t* nucleus = trio_text_read_nucleus((trio_text_t*)file);
nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*)file);
if (nucleus == NULL) {
return TRIO_FAILURE;
return TREXIO_FAILURE;
}
assert (charge != NULL);
@ -268,27 +268,27 @@ trio_exit_code trio_text_read_nucleus_charge(const trio_t* file, double* charge)
charge[i] = nucleus->charge[i];
}
trio_text_free_nucleus(nucleus);
return TRIO_SUCCESS;
trexio_text_free_nucleus(nucleus);
return TREXIO_SUCCESS;
}
trio_exit_code trio_text_write_nucleus_charge(const trio_t* file, const double* charge) {
trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* charge) {
assert (charge != NULL);
assert (file != NULL);
nucleus_t* nucleus = trio_text_read_nucleus((trio_text_t*)file);
nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*)file);
assert (nucleus != NULL);
for (size_t i=0 ; i<nucleus->num ; i++) {
nucleus->charge[i] = charge[i];
}
trio_exit_code rc = trio_text_write_nucleus((trio_text_t*) file, nucleus);
assert (rc == TRIO_SUCCESS);
trexio_exit_code rc = trexio_text_write_nucleus((trexio_text_t*) file, nucleus);
assert (rc == TREXIO_SUCCESS);
trio_text_free_nucleus(nucleus);
trexio_text_free_nucleus(nucleus);
return TRIO_SUCCESS;
return TREXIO_SUCCESS;
}

50
src/trexio_text.h Normal file
View File

@ -0,0 +1,50 @@
/* This file was generated from the trexio.org org-mode file.
To generate it, open trexio.org in Emacs and execute
M-x org-babel-tangle
*/
#ifndef _TREXIO_TEXT_H
#define _TREXIO_TEXT_H
#include "trexio.h"
#include "trexio_s.h"
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <sys/stat.h>
typedef struct nucleus_s {
double* coord;
double* charge;
uint64_t num;
} nucleus_t;
typedef struct electron_s {
uint64_t alpha_num;
uint64_t beta_num;
} electron_t;
typedef struct trexio_text_s {
trexio_t parent ;
char* nucleus_file_name;
char* electron_file_name;
} trexio_text_t;
trexio_exit_code trexio_text_init(trexio_t* file);
trexio_exit_code trexio_text_finalize(trexio_t* file);
trexio_exit_code trexio_text_read_nucleus_num(const trexio_t* file, uint64_t* num);
trexio_exit_code trexio_text_write_nucleus_num(const trexio_t* file, const uint64_t num);
trexio_exit_code trexio_text_read_nucleus_coord(const trexio_t* file, double* coord);
trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const double* coord);
trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* coord);
trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* coord);
#endif

254
src/trio.c
View File

@ -1,254 +0,0 @@
/* This file was generated from the trio.org org-mode file.
To generate it, open trio.org in Emacs and execute
M-x org-babel-tangle
*/
#include <pthread.h>
#include <assert.h>
#include <stdlib.h>
#include <string.h>
#include <pthread.h>
#include "trio.h"
#include "trio_s.h"
#include "trio_text.h"
#include "trio_hdf5.h"
/*
#include "trio_json.h"
*/
trio_t* trio_create(const char* file_name, back_end_t back_end) {
/* Check that file name is not NULL or empty */
assert (file_name != NULL);
assert (file_name[0] != '\0');
/* Check that back_end is valid */
assert (back_end < TRIO_INVALID_BACK_END);
trio_t* result = NULL;
switch (back_end) {
case TRIO_TEXT:
result = (trio_t*) malloc (sizeof(trio_text_t));
break;
case TRIO_HDF5:
result = (trio_t*) malloc (sizeof(trio_hdf5_t));
break;
/*
case TRIO_JSON:
result = (trio_t*) malloc (sizeof(trio_json_t));
break;
*/
default:
assert (1 == 0); /* Impossible case */
}
/* TODO: Error handling */
assert (result != NULL);
result->file_name = (char*) calloc(strlen(file_name)+1,sizeof(char));
strcpy(result->file_name, file_name);
result->back_end = back_end;
result->mode = 'w'; /* Upon creation, mode=write */
int irc = pthread_mutex_init ( &(result->thread_lock), NULL);
assert (irc == 0);
trio_exit_code rc = TRIO_FAILURE;
switch (back_end) {
case TRIO_TEXT:
rc = trio_text_init(result);
break;
case TRIO_HDF5:
rc = trio_hdf5_init(result);
break;
/*
case TRIO_JSON:
rc = trio_json_init(result);
break;
*/
default:
assert (1 == 0); /* Impossible case */
}
assert (rc == TRIO_SUCCESS);
return result;
}
trio_exit_code trio_close(trio_t* file) {
assert (file != NULL);
trio_exit_code rc;
switch (file->back_end) {
case TRIO_TEXT:
rc = trio_text_finalize(file);
break;
case TRIO_HDF5:
rc = trio_hdf5_finalize(file);
break;
/*
case TRIO_JSON:
rc = trio_json_finalize(file);
break;
*/
default:
assert (1 == 0); /* Impossible case */
}
if (rc != TRIO_SUCCESS) {
return TRIO_FAILURE;
}
free(file->file_name);
file->file_name = NULL;
int irc = pthread_mutex_destroy( &(file->thread_lock) );
assert (irc == 0);
free(file);
return TRIO_SUCCESS;
}
trio_exit_code trio_read_nucleus_num(trio_t* file, uint64_t* num) {
if (file == NULL) return TRIO_FAILURE;
switch (file->back_end) {
case TRIO_TEXT:
return trio_text_read_nucleus_num(file, num);
break;
case TRIO_HDF5:
return trio_hdf5_read_nucleus_num(file, num);
break;
/*
case TRIO_JSON:
return trio_json_read_nucleus_num(file, num);
break;
*/
default:
return TRIO_FAILURE; /* Impossible case */
}
}
trio_exit_code trio_write_nucleus_num(trio_t* file, uint64_t num) {
if (file == NULL) return TRIO_FAILURE;
switch (file->back_end) {
case TRIO_TEXT:
return trio_text_write_nucleus_num(file, num);
break;
case TRIO_HDF5:
return trio_hdf5_write_nucleus_num(file, num);
break;
/*
case TRIO_JSON:
return trio_json_write_nucleus_num(file, num);
break;
*/
default:
return TRIO_FAILURE; /* Impossible case */
}
}
trio_exit_code trio_read_nucleus_coord(trio_t* file, double* coord) {
if (file == NULL) return TRIO_FAILURE;
switch (file->back_end) {
case TRIO_TEXT:
return trio_text_read_nucleus_coord(file, coord);
break;
case TRIO_HDF5:
return trio_hdf5_read_nucleus_coord(file, coord);
break;
/*
case TRIO_JSON:
return trio_json_read_nucleus_coord(file, coord);
break;
*/
default:
return TRIO_FAILURE; /* Impossible case */
}
}
trio_exit_code trio_write_nucleus_coord(trio_t* file, double* coord) {
if (file == NULL) return TRIO_FAILURE;
switch (file->back_end) {
case TRIO_TEXT:
return trio_text_write_nucleus_coord(file, coord);
break;
case TRIO_HDF5:
return trio_hdf5_write_nucleus_coord(file, coord);
break;
/*
case TRIO_JSON:
return trio_json_write_nucleus_coord(file, coord);
break;
*/
default:
return TRIO_FAILURE; /* Impossible case */
}
}
trio_exit_code trio_read_nucleus_charge(trio_t* file, double* charge) {
if (file == NULL) return TRIO_FAILURE;
switch (file->back_end) {
case TRIO_TEXT:
return trio_text_read_nucleus_charge(file, charge);
break;
/*
case TRIO_HDF5:
return trio_hdf5_read_nucleus_charge(file, charge);
break;
case TRIO_JSON:
return trio_json_read_nucleus_charge(file, charge);
break;
*/
default:
return TRIO_FAILURE; /* Impossible case */
}
}
trio_exit_code trio_write_nucleus_charge(trio_t* file, double* charge) {
if (file == NULL) return TRIO_FAILURE;
switch (file->back_end) {
case TRIO_TEXT:
return trio_text_write_nucleus_charge(file, charge);
break;
/*
case TRIO_HDF5:
return trio_hdf5_write_nucleus_charge(file, charge);
break;
case TRIO_JSON:
return trio_json_write_nucleus_charge(file, charge);
break;
*/
default:
return TRIO_FAILURE; /* Impossible case */
}
}

40
src/trio.h
View File

@ -1,40 +0,0 @@
/* This file was generated from the trio.org org-mode file.
To generate it, open trio.org in Emacs and execute
M-x org-babel-tangle
*/
#ifndef _TRIO_H
#define _TRIO_H
#include <stdint.h>
typedef int32_t trio_exit_code;
#define TRIO_SUCCESS ( (trio_exit_code) 0 )
#define TRIO_FAILURE ( (trio_exit_code) 1 )
typedef uint32_t back_end_t;
#define TRIO_HDF5 ( (back_end_t) 0 )
#define TRIO_TEXT ( (back_end_t) 1 )
#define TRIO_JSON ( (back_end_t) 2 )
#define TRIO_INVALID_BACK_END ( (back_end_t) 3 )
typedef struct trio_s trio_t;
trio_t* trio_create(const char* file_name, back_end_t back_end);
trio_exit_code trio_close(trio_t* file);
trio_exit_code trio_read_nucleus_num(trio_t* file, uint64_t* num);
trio_exit_code trio_write_nucleus_num(trio_t* file, uint64_t num);
trio_exit_code trio_read_nucleus_coord(trio_t* file, double* coord);
trio_exit_code trio_write_nucleus_coord(trio_t* file, double* coord);
trio_exit_code trio_read_nucleus_charge(trio_t* file, double* charge);
trio_exit_code trio_write_nucleus_charge(trio_t* file, double* charge);
#endif

50
src/trio_text.h
View File

@ -1,50 +0,0 @@
/* This file was generated from the trio.org org-mode file.
To generate it, open trio.org in Emacs and execute
M-x org-babel-tangle
*/
#ifndef _TRIO_TEXT_H
#define _TRIO_TEXT_H
#include "trio.h"
#include "trio_s.h"
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <assert.h>
#include <sys/stat.h>
typedef struct nucleus_s {
double* coord;
double* charge;
uint64_t num;
} nucleus_t;
typedef struct electron_s {
uint64_t alpha_num;
uint64_t beta_num;
} electron_t;
typedef struct trio_text_s {
trio_t parent ;
char* nucleus_file_name;
char* electron_file_name;
} trio_text_t;
trio_exit_code trio_text_init(trio_t* file);
trio_exit_code trio_text_finalize(trio_t* file);
trio_exit_code trio_text_read_nucleus_num(const trio_t* file, uint64_t* num);
trio_exit_code trio_text_write_nucleus_num(const trio_t* file, const uint64_t num);
trio_exit_code trio_text_read_nucleus_coord(const trio_t* file, double* coord);
trio_exit_code trio_text_write_nucleus_coord(const trio_t* file, const double* coord);
trio_exit_code trio_text_read_nucleus_charge(const trio_t* file, double* coord);
trio_exit_code trio_text_write_nucleus_charge(const trio_t* file, const double* coord);
#endif