mirror of
https://github.com/TREX-CoE/trexio.git
synced 2024-11-03 20:54:07 +01:00
Merge branch 'master' of github.com:TREX-CoE/trexio into generator-1
This commit is contained in:
commit
6a2533be3b
19
src/trexio.c
19
src/trexio.c
@ -53,7 +53,7 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
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/* Data for the parent type */
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result->file_name = (char*) calloc(strlen(file_name)+1,sizeof(char));
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result->file_name = CALLOC(strlen(file_name)+1,char);
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strcpy(result->file_name, file_name);
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result->back_end = back_end;
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result->mode = mode;
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@ -83,8 +83,8 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
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}
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if (rc != TREXIO_SUCCESS) {
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free(result->file_name);
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free(result);
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FREE(result->file_name);
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FREE(result);
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return NULL;
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}
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@ -109,8 +109,8 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
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}
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if (rc != TREXIO_SUCCESS) {
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free(result->file_name);
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free(result);
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FREE(result->file_name);
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FREE(result);
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return NULL;
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}
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@ -143,8 +143,8 @@ trexio_exit_code trexio_close(trexio_t* file) {
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}
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if (rc != TREXIO_SUCCESS) {
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free(file->file_name);
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free(file);
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FREE(file->file_name);
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FREE(file);
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return TREXIO_FAILURE;
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}
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@ -170,12 +170,11 @@ trexio_exit_code trexio_close(trexio_t* file) {
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/* Terminate front end */
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free(file->file_name);
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file->file_name = NULL;
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FREE(file->file_name);
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int irc = pthread_mutex_destroy( &(file->thread_lock) );
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free(file);
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FREE(file);
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if (irc != 0) return TREXIO_ERRNO;
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if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
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@ -23,7 +23,8 @@ typedef int32_t trexio_exit_code;
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#define TREXIO_READONLY ( (trexio_exit_code) 11 )
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#define TREXIO_ERRNO ( (trexio_exit_code) 12 )
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#define TREXIO_INVALID_ID ( (trexio_exit_code) 20 )
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#define TREXIO_INVALID_NUM ( (trexio_exit_code) 21 )
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#define TREXIO_ALLOCATION_FAILED ( (trexio_exit_code) 21 )
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#define TREXIO_INVALID_NUM ( (trexio_exit_code) 22 )
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typedef int32_t back_end_t;
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@ -46,6 +46,7 @@
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#define _TREXIO_S_H
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#include "trexio.h"
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#include "trexio_private.h"
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#include <pthread.h>
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#include <assert.h>
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#+end_src
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@ -61,6 +62,24 @@
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- structs are suffixed by ~_s~
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- types are suffixed by ~_t~
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** Memory allocation
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Memory allocation of structures can be facilitated by using the
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following macro, which ensures that the size of the allocated
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object is the same as the size of the data type pointed by the pointer.
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#+begin_src c :tangle trexio_private.h
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#define MALLOC(T) (T*) malloc (sizeof(T));
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#define CALLOC(N,T) (T*) calloc ((N),sizeof(T));
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#+end_src
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When a pointer is freed, it should be set to ~NULL~.
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This can be facilitated by the use of the following macro:
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#+begin_src c :tangle trexio_private.h
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#define FREE(X) { free(X) ; (X)=NULL; }
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#+end_src
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* Front end
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All calls to TREXIO are thread-safe.
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@ -80,7 +99,8 @@ typedef int32_t trexio_exit_code;
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#define TREXIO_READONLY ( (trexio_exit_code) 11 )
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#define TREXIO_ERRNO ( (trexio_exit_code) 12 )
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#define TREXIO_INVALID_ID ( (trexio_exit_code) 20 )
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#define TREXIO_INVALID_NUM ( (trexio_exit_code) 21 )
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#define TREXIO_ALLOCATION_FAILED ( (trexio_exit_code) 21 )
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#define TREXIO_INVALID_NUM ( (trexio_exit_code) 22 )
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#+end_src
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** Back ends
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@ -193,7 +213,7 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
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/* Data for the parent type */
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||||
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result->file_name = (char*) calloc(strlen(file_name)+1,sizeof(char));
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result->file_name = CALLOC(strlen(file_name)+1,char);
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strcpy(result->file_name, file_name);
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result->back_end = back_end;
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result->mode = mode;
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@ -223,8 +243,8 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
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}
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if (rc != TREXIO_SUCCESS) {
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free(result->file_name);
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free(result);
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FREE(result->file_name);
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FREE(result);
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return NULL;
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}
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@ -249,8 +269,8 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
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}
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if (rc != TREXIO_SUCCESS) {
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free(result->file_name);
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free(result);
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FREE(result->file_name);
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FREE(result);
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return NULL;
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}
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@ -291,8 +311,8 @@ trexio_exit_code trexio_close(trexio_t* file) {
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}
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if (rc != TREXIO_SUCCESS) {
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free(file->file_name);
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free(file);
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FREE(file->file_name);
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FREE(file);
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return TREXIO_FAILURE;
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}
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@ -318,12 +338,11 @@ trexio_exit_code trexio_close(trexio_t* file) {
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/* Terminate front end */
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free(file->file_name);
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file->file_name = NULL;
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FREE(file->file_name);
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int irc = pthread_mutex_destroy( &(file->thread_lock) );
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free(file);
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FREE(file);
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if (irc != 0) return TREXIO_ERRNO;
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if (rc != TREXIO_SUCCESS) return TREXIO_FAILURE;
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@ -7,10 +7,10 @@
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#include "trexio_hdf5.h"
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#define NUCLEUS_GROUP_NAME "nucleus"
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#define NUCLEUS_NUM_NAME "nucleus_num"
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#define NUCLEUS_CHARGE_NAME "nucleus_charge"
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#define NUCLEUS_COORD_NAME "nucleus_coord"
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#define NUCLEUS_GROUP_NAME "nucleus"
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#define NUCLEUS_NUM_NAME "nucleus_num"
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#define NUCLEUS_CHARGE_NAME "nucleus_charge"
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#define NUCLEUS_COORD_NAME "nucleus_coord"
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/*
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* Currently H5LTread_dataset_ is used instead of this function
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@ -24,7 +24,7 @@ dset_t* trexio_hdf5_read_dset_low(const trexio_hdf5_t* file, const char *dset_na
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/*
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* Low-level implementation. Involves dealing with all HDF5 handles and dimensions
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*/
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dset_t* dset = (dset_t*) malloc(sizeof(dset_t));
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dset_t* dset = MALLOC(dset_t);
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assert (dset != NULL);
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dset->dset_id = H5Dopen(file->nucleus_group,
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@ -145,7 +145,7 @@ trexio_exit_code trexio_hdf5_finalize(trexio_t* file) {
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h5nucleus_t* trexio_hdf5_read_nucleus(const trexio_hdf5_t* file) {
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/* Allocate the data structure */
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h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
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h5nucleus_t* nucleus = MALLOC(h5nucleus_t);
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assert (nucleus != NULL);
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nucleus->num = 0;
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@ -323,19 +323,19 @@ trexio_exit_code trexio_hdf5_free_nucleus(h5nucleus_t* nucleus) {
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if (nucleus == NULL) return TREXIO_FAILURE;
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if (nucleus->coord != NULL) free (nucleus->coord);
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nucleus->coord = NULL;
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if (nucleus->coord != NULL)
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FREE (nucleus->coord);
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if (nucleus->charge != NULL) free (nucleus->charge);
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nucleus->charge = NULL;
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if (nucleus->charge != NULL)
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FREE (nucleus->charge);
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if (nucleus->h5_coord != NULL) free (nucleus->h5_coord);
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nucleus->h5_coord = NULL;
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if (nucleus->h5_coord != NULL)
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FREE (nucleus->h5_coord);
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if (nucleus->h5_charge != NULL) free (nucleus->h5_charge);
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nucleus->h5_charge = NULL;
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if (nucleus->h5_charge != NULL)
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FREE (nucleus->h5_charge);
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free (nucleus);
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FREE (nucleus);
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return TREXIO_SUCCESS;
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}
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@ -446,17 +446,17 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
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H5Dclose(dset_id);
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if (status < 0) {
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free(ddims);
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FREE(ddims);
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return TREXIO_FAILURE;
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}
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for (uint32_t i=0; i<rank; i++){
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if (ddims[i] != dims[i]) {
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free(ddims);
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FREE(ddims);
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return TREXIO_INVALID_ARG_4;
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}
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}
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free(ddims);
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FREE(ddims);
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/* High-level H5LT API. No need to deal with dataspaces and datatypes */
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status = H5LTread_dataset_double(f->nucleus_group,
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@ -9,6 +9,7 @@
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#define _TREXIO_HDF5_H
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#include "trexio.h"
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#include "trexio_private.h"
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#include "trexio_s.h"
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#include <stdint.h>
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#include <stdio.h>
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@ -19,6 +19,7 @@
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#define _TREXIO_HDF5_H
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#include "trexio.h"
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#include "trexio_private.h"
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#include "trexio_s.h"
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#include <stdint.h>
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#include <stdio.h>
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@ -115,7 +116,7 @@ dset_t* trexio_hdf5_read_dset_low(const trexio_hdf5_t* file, const char *dset_na
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/*
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* Low-level implementation. Involves dealing with all HDF5 handles and dimensions
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*/
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dset_t* dset = (dset_t*) malloc(sizeof(dset_t));
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dset_t* dset = MALLOC(dset_t);
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assert (dset != NULL);
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dset->dset_id = H5Dopen(file->nucleus_group,
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@ -280,7 +281,7 @@ typedef struct four_index_s {
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h5nucleus_t* trexio_hdf5_read_nucleus(const trexio_hdf5_t* file) {
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/* Allocate the data structure */
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h5nucleus_t* nucleus = (h5nucleus_t*) malloc(sizeof(h5nucleus_t));
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h5nucleus_t* nucleus = MALLOC(h5nucleus_t);
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assert (nucleus != NULL);
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nucleus->num = 0;
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@ -465,19 +466,19 @@ trexio_exit_code trexio_hdf5_free_nucleus(h5nucleus_t* nucleus) {
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if (nucleus == NULL) return TREXIO_FAILURE;
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if (nucleus->coord != NULL) free (nucleus->coord);
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nucleus->coord = NULL;
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if (nucleus->coord != NULL)
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FREE (nucleus->coord);
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if (nucleus->charge != NULL) free (nucleus->charge);
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nucleus->charge = NULL;
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if (nucleus->charge != NULL)
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FREE (nucleus->charge);
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if (nucleus->h5_coord != NULL) free (nucleus->h5_coord);
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nucleus->h5_coord = NULL;
|
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if (nucleus->h5_coord != NULL)
|
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FREE (nucleus->h5_coord);
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|
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if (nucleus->h5_charge != NULL) free (nucleus->h5_charge);
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nucleus->h5_charge = NULL;
|
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if (nucleus->h5_charge != NULL)
|
||||
FREE (nucleus->h5_charge);
|
||||
|
||||
free (nucleus);
|
||||
FREE (nucleus);
|
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|
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return TREXIO_SUCCESS;
|
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}
|
||||
@ -607,17 +608,17 @@ trexio_exit_code trexio_hdf5_read_nucleus_coord(const trexio_t* file, double* co
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|
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H5Dclose(dset_id);
|
||||
if (status < 0) {
|
||||
free(ddims);
|
||||
FREE(ddims);
|
||||
return TREXIO_FAILURE;
|
||||
}
|
||||
|
||||
for (uint32_t i=0; i<rank; i++){
|
||||
if (ddims[i] != dims[i]) {
|
||||
free(ddims);
|
||||
FREE(ddims);
|
||||
return TREXIO_INVALID_ARG_4;
|
||||
}
|
||||
}
|
||||
free(ddims);
|
||||
FREE(ddims);
|
||||
|
||||
/* High-level H5LT API. No need to deal with dataspaces and datatypes */
|
||||
status = H5LTread_dataset_double(f->nucleus_group,
|
||||
|
||||
@ -9,6 +9,7 @@
|
||||
#define _TREXIO_S_H
|
||||
|
||||
#include "trexio.h"
|
||||
#include "trexio_private.h"
|
||||
#include <pthread.h>
|
||||
#include <assert.h>
|
||||
|
||||
|
||||
@ -12,6 +12,9 @@ trexio_exit_code trexio_text_init(trexio_t* file) {
|
||||
|
||||
trexio_text_t* f = (trexio_text_t*) file;
|
||||
|
||||
/* Put all pointers to NULL but leave parent untouched */
|
||||
memset(&(f->parent)+1,0,sizeof(trexio_text_t)-sizeof(trexio_t));
|
||||
|
||||
/* If directory doesn't exist, create it in write mode */
|
||||
struct stat st;
|
||||
|
||||
@ -27,20 +30,22 @@ trexio_exit_code trexio_text_init(trexio_t* file) {
|
||||
|
||||
/* Create the lock file in the directory */
|
||||
const char* lock_file_name = "/.lock";
|
||||
char* file_name = (char*)
|
||||
calloc( strlen(file->file_name) + strlen(lock_file_name) + 1,
|
||||
sizeof(char));
|
||||
assert (file_name != NULL);
|
||||
char* file_name =
|
||||
CALLOC(strlen(file->file_name) + strlen(lock_file_name) + 1, char);
|
||||
|
||||
if (file_name == NULL) {
|
||||
return TREXIO_ALLOCATION_FAILED;
|
||||
}
|
||||
|
||||
strcpy (file_name, file->file_name);
|
||||
strcat (file_name, lock_file_name);
|
||||
|
||||
f->lock_file = open(file_name,O_WRONLY|O_CREAT|O_TRUNC, 0644);
|
||||
assert (f->lock_file > 0);
|
||||
free(file_name);
|
||||
FREE(file_name);
|
||||
|
||||
f->nucleus = NULL;
|
||||
f->electron= NULL;
|
||||
f->rdm = NULL;
|
||||
if (f->lock_file <= 0) {
|
||||
return TREXIO_FAILURE;
|
||||
}
|
||||
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
@ -96,29 +101,34 @@ trexio_exit_code trexio_text_unlock(trexio_t* file) {
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
|
||||
#define DEBUG printf("%s : line %d\n", __FILE__, __LINE__);
|
||||
|
||||
nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
|
||||
if (file == NULL) return NULL;
|
||||
|
||||
if (file->nucleus != NULL) return file->nucleus;
|
||||
/* If the data structure exists, return it */
|
||||
if (file->nucleus != NULL) {
|
||||
return file->nucleus;
|
||||
}
|
||||
|
||||
/* Allocate the data structure */
|
||||
nucleus_t* nucleus = (nucleus_t*) malloc(sizeof(nucleus_t));
|
||||
assert (nucleus != NULL);
|
||||
nucleus_t* nucleus = MALLOC(nucleus_t);
|
||||
if (nucleus == NULL) return NULL;
|
||||
|
||||
nucleus->file = NULL;
|
||||
nucleus->num = 0;
|
||||
nucleus->coord = NULL;
|
||||
nucleus->dims_coord = NULL;
|
||||
nucleus->charge = NULL;
|
||||
nucleus->dims_charge = NULL;
|
||||
nucleus->to_flush = 0;
|
||||
memset(nucleus,0,sizeof(nucleus_t));
|
||||
|
||||
/* Try to open the file. If the file does not exist, return */
|
||||
/* Build the file name */
|
||||
const char* nucleus_file_name = "/nucleus.txt";
|
||||
char * file_name = (char*)
|
||||
calloc( strlen(file->parent.file_name) + strlen(nucleus_file_name) + 1,
|
||||
sizeof(char));
|
||||
assert (file_name != NULL);
|
||||
|
||||
if (file_name == NULL) {
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
strcpy (file_name, file->parent.file_name);
|
||||
strcat (file_name, nucleus_file_name);
|
||||
|
||||
@ -130,98 +140,219 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
|
||||
fseek(f, 0L, SEEK_END);
|
||||
size_t sz = ftell(f);
|
||||
fseek(f, 0L, SEEK_SET);
|
||||
char* buffer = (char*) malloc(sz*sizeof(char));
|
||||
|
||||
char* buffer = CALLOC(sz,char);
|
||||
if (buffer == NULL) {
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* Read the dimensioning variables */
|
||||
int rc;
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "rank_charge") == 0);
|
||||
if ((rc != 1) || (strcmp(buffer, "rank_charge") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%u", &(nucleus->rank_charge));
|
||||
assert (rc == 1);
|
||||
|
||||
nucleus->dims_charge = (uint64_t*) calloc(nucleus->rank_charge, sizeof(uint64_t));
|
||||
assert (nucleus->dims_charge != NULL);
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
uint64_t size_charge = 1;
|
||||
for (uint i=0; i<nucleus->rank_charge; i++){
|
||||
for (unsigned int i=0; i<nucleus->rank_charge; i++){
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
//assert (strcmp(buffer, "dims_charge") == 0);
|
||||
unsigned int j=-1;
|
||||
rc = fscanf(f, "%s %u", buffer, &j);
|
||||
if ((rc != 2) || (strcmp(buffer, "dims_charge") != 0) || (j!=i)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%lu", &(nucleus->dims_charge[i]));
|
||||
assert (rc == 1);
|
||||
rc = fscanf(f, "%lu\n", &(nucleus->dims_charge[i]));
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
size_charge *= nucleus->dims_charge[i];
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "rank_coord") == 0);
|
||||
if ((rc != 1) || (strcmp(buffer, "rank_coord") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%u", &(nucleus->rank_coord));
|
||||
assert (rc == 1);
|
||||
|
||||
nucleus->dims_coord = (uint64_t*) calloc(nucleus->rank_coord, sizeof(uint64_t));
|
||||
assert (nucleus->dims_coord != NULL);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
uint64_t size_coord = 1;
|
||||
for (uint i=0; i<nucleus->rank_coord; i++){
|
||||
for (unsigned int i=0; i<nucleus->rank_coord; i++){
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
//assert (strcmp(buffer, "dims_coord") == 0);
|
||||
unsigned int j=-1;
|
||||
rc = fscanf(f, "%s %u", buffer, &j);
|
||||
if ((rc != 2) || (strcmp(buffer, "dims_coord") != 0) || (j!=i)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%lu", &(nucleus->dims_coord[i]));
|
||||
assert (rc == 1);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
size_coord *= nucleus->dims_coord[i];
|
||||
}
|
||||
|
||||
/* Allocate arrays */
|
||||
nucleus->charge = (double*) calloc(size_charge, sizeof(double));
|
||||
assert (nucleus->charge != NULL);
|
||||
assert (!(nucleus->charge == NULL));
|
||||
if (nucleus->charge == NULL) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
nucleus->coord = (double*) calloc(size_coord, sizeof(double));
|
||||
assert (nucleus->coord != NULL);
|
||||
assert (!(nucleus->coord == NULL));
|
||||
if (nucleus->coord == NULL) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* Read data */
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "num") == 0);
|
||||
assert(!((rc != 1) || (strcmp(buffer, "num") != 0)));
|
||||
if ((rc != 1) || (strcmp(buffer, "num") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%lu", &(nucleus->num));
|
||||
assert (rc == 1);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "charge") == 0);
|
||||
assert(!((rc != 1) || (strcmp(buffer, "charge") != 0)));
|
||||
if ((rc != 1) || (strcmp(buffer, "charge") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
for (uint64_t i=0 ; i<size_charge ; i++) {
|
||||
rc = fscanf(f, "%lf", &(nucleus->charge[i]));
|
||||
assert (rc == 1);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "coord") == 0);
|
||||
assert(!((rc != 1) || (strcmp(buffer, "coord") != 0)));
|
||||
if ((rc != 1) || (strcmp(buffer, "coord") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
for (uint64_t i=0 ; i<size_coord ; i++) {
|
||||
rc = fscanf(f, "%lf", &(nucleus->coord[i]));
|
||||
assert (rc == 1);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
free(buffer);
|
||||
}
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
f = NULL;
|
||||
}
|
||||
|
||||
if (file->parent.mode == 'w') {
|
||||
nucleus->file = fopen(file_name,"a");
|
||||
} else {
|
||||
nucleus->file = fopen(file_name,"r");
|
||||
}
|
||||
free(file_name);
|
||||
FREE(file_name);
|
||||
assert (!(nucleus->file == NULL));
|
||||
if (nucleus->file == NULL) {
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
fseek(nucleus->file, 0L, SEEK_SET);
|
||||
file->nucleus = nucleus;
|
||||
return nucleus;
|
||||
}
|
||||
@ -245,16 +376,16 @@ trexio_exit_code trexio_text_flush_nucleus(const trexio_text_t* file) {
|
||||
fprintf(f, "rank_charge %d\n", nucleus->rank_charge);
|
||||
|
||||
uint64_t size_charge = 1;
|
||||
for (uint i=0; i<nucleus->rank_charge; i++){
|
||||
fprintf(f, "dims_charge[%d] %ld\n", i, nucleus->dims_charge[i]);
|
||||
for (unsigned int i=0; i<nucleus->rank_charge; i++){
|
||||
fprintf(f, "dims_charge %d %ld\n", i, nucleus->dims_charge[i]);
|
||||
size_charge *= nucleus->dims_charge[i];
|
||||
}
|
||||
|
||||
fprintf(f, "rank_coord %d\n", nucleus->rank_coord);
|
||||
|
||||
uint64_t size_coord = 1;
|
||||
for (uint i=0; i<nucleus->rank_coord; i++){
|
||||
fprintf(f, "dims_coord[%d] %ld\n", i, nucleus->dims_coord[i]);
|
||||
for (unsigned int i=0; i<nucleus->rank_coord; i++){
|
||||
fprintf(f, "dims_coord %d %ld\n", i, nucleus->dims_coord[i]);
|
||||
size_coord *= nucleus->dims_coord[i];
|
||||
}
|
||||
|
||||
@ -292,28 +423,15 @@ trexio_exit_code trexio_text_free_nucleus(trexio_text_t* file) {
|
||||
nucleus->file = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->dims_coord != NULL) {
|
||||
free (nucleus->dims_coord);
|
||||
nucleus->dims_coord = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->coord != NULL) {
|
||||
free (nucleus->coord);
|
||||
nucleus->coord = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->dims_charge != NULL) {
|
||||
free (nucleus->dims_charge);
|
||||
nucleus->dims_charge = NULL;
|
||||
FREE (nucleus->coord);
|
||||
}
|
||||
|
||||
if (nucleus->charge != NULL) {
|
||||
free (nucleus->charge);
|
||||
nucleus->charge = NULL;
|
||||
FREE (nucleus->charge);
|
||||
}
|
||||
|
||||
free (nucleus);
|
||||
file->nucleus = NULL;
|
||||
FREE (nucleus);
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
|
||||
@ -357,7 +475,7 @@ trexio_exit_code trexio_text_read_nucleus_coord(const trexio_t* file, double* co
|
||||
if (rank != nucleus->rank_coord) return TREXIO_INVALID_ARG_3;
|
||||
|
||||
uint64_t dim_size = 1;
|
||||
for (uint i=0; i<rank; i++){
|
||||
for (unsigned int i=0; i<rank; i++){
|
||||
if (dims[i] != nucleus->dims_coord[i]) return TREXIO_INVALID_ARG_4;
|
||||
dim_size *= dims[i];
|
||||
}
|
||||
@ -380,20 +498,13 @@ trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const dou
|
||||
if (nucleus == NULL) return TREXIO_FAILURE;
|
||||
|
||||
if (nucleus->coord != NULL) {
|
||||
free(nucleus->coord);
|
||||
nucleus->coord = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->dims_coord != NULL) {
|
||||
free(nucleus->dims_coord);
|
||||
nucleus->dims_coord = NULL;
|
||||
FREE(nucleus->coord);
|
||||
}
|
||||
|
||||
nucleus->rank_coord = rank;
|
||||
nucleus->dims_coord = (uint64_t*) calloc(rank, sizeof(uint64_t));
|
||||
|
||||
uint64_t dim_size = 1;
|
||||
for (uint i=0; i<nucleus->rank_coord; i++){
|
||||
for (unsigned int i=0; i<nucleus->rank_coord; i++){
|
||||
nucleus->dims_coord[i] = dims[i];
|
||||
dim_size *= dims[i];
|
||||
}
|
||||
@ -419,7 +530,7 @@ trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* c
|
||||
if (rank != nucleus->rank_charge) return TREXIO_INVALID_ARG_3;
|
||||
|
||||
uint64_t dim_size = 1;
|
||||
for (uint i=0; i<rank; i++){
|
||||
for (unsigned int i=0; i<rank; i++){
|
||||
if (dims[i] != nucleus->dims_charge[i]) return TREXIO_INVALID_ARG_4;
|
||||
dim_size *= dims[i];
|
||||
}
|
||||
@ -442,21 +553,13 @@ trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const do
|
||||
if (nucleus == NULL) return TREXIO_FAILURE;
|
||||
|
||||
if (nucleus->charge != NULL) {
|
||||
free(nucleus->charge);
|
||||
nucleus->charge = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->dims_charge != NULL) {
|
||||
free(nucleus->dims_charge);
|
||||
nucleus->dims_charge = NULL;
|
||||
FREE(nucleus->charge);
|
||||
}
|
||||
|
||||
nucleus->rank_charge = rank;
|
||||
|
||||
nucleus->dims_charge = (uint64_t*) calloc(rank, sizeof(uint64_t));
|
||||
|
||||
uint64_t dim_size = 1;
|
||||
for (uint i=0; i<nucleus->rank_charge; i++){
|
||||
for (unsigned int i=0; i<nucleus->rank_charge; i++){
|
||||
nucleus->dims_charge[i] = dims[i];
|
||||
dim_size *= dims[i];
|
||||
}
|
||||
@ -477,7 +580,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
|
||||
if (file->rdm != NULL) return file->rdm;
|
||||
|
||||
/* Allocate the data structure */
|
||||
rdm_t* rdm = (rdm_t*) malloc(sizeof(rdm_t));
|
||||
rdm_t* rdm = MALLOC(rdm_t);
|
||||
assert (rdm != NULL);
|
||||
|
||||
rdm->one_e = NULL;
|
||||
@ -502,7 +605,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
|
||||
fseek(f, 0L, SEEK_END);
|
||||
size_t sz = ftell(f);
|
||||
fseek(f, 0L, SEEK_SET);
|
||||
char* buffer = (char*) malloc(sz*sizeof(char));
|
||||
char* buffer = CALLOC(sz,char);
|
||||
|
||||
/* Read the dimensioning variables */
|
||||
int rc;
|
||||
@ -534,10 +637,10 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
rdm->two_e_file_name = (char*) malloc (strlen(buffer)*sizeof(char));
|
||||
rdm->two_e_file_name = CALLOC (strlen(buffer),char);
|
||||
strcpy(rdm->two_e_file_name, buffer);
|
||||
|
||||
free(buffer);
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
f = NULL;
|
||||
}
|
||||
@ -546,7 +649,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
|
||||
} else {
|
||||
rdm->file = fopen(file_name,"r");
|
||||
}
|
||||
free(file_name);
|
||||
FREE(file_name);
|
||||
file->rdm = rdm ;
|
||||
return rdm;
|
||||
}
|
||||
@ -600,13 +703,11 @@ trexio_exit_code trexio_text_free_rdm(trexio_text_t* file) {
|
||||
}
|
||||
|
||||
if (rdm->one_e != NULL) {
|
||||
free (rdm->one_e);
|
||||
rdm->one_e = NULL;
|
||||
FREE (rdm->one_e);
|
||||
}
|
||||
|
||||
if (rdm->two_e_file_name != NULL) {
|
||||
free (rdm->two_e_file_name);
|
||||
rdm->two_e_file_name = NULL;
|
||||
FREE (rdm->two_e_file_name);
|
||||
}
|
||||
|
||||
free (rdm);
|
||||
|
||||
@ -9,6 +9,7 @@
|
||||
#define _TREXIO_TEXT_H
|
||||
|
||||
#include "trexio.h"
|
||||
#include "trexio_private.h"
|
||||
#include "trexio_s.h"
|
||||
#include <errno.h>
|
||||
#include <stdint.h>
|
||||
@ -25,8 +26,8 @@ typedef struct nucleus_s {
|
||||
double* coord;
|
||||
double* charge;
|
||||
uint64_t num;
|
||||
uint64_t* dims_charge;
|
||||
uint64_t* dims_coord;
|
||||
uint64_t dims_charge[16];
|
||||
uint64_t dims_coord[16];
|
||||
uint32_t rank_charge;
|
||||
uint32_t rank_coord;
|
||||
int to_flush;
|
||||
|
||||
@ -2,6 +2,19 @@
|
||||
|
||||
* File prefixes :noxport:
|
||||
|
||||
#+begin_src emacs-lisp
|
||||
(setq-local org-babel-default-header-args:c '((:comments . "both")))
|
||||
org-babel-default-header-args:c
|
||||
#+end_src
|
||||
|
||||
#+RESULTS:
|
||||
: ((:comments . both))
|
||||
|
||||
# Local Variables:
|
||||
# eval: (setq-local org-babel-default-header-args:Python '((:session . "foo")))
|
||||
# End:
|
||||
|
||||
|
||||
#+NAME:header
|
||||
#+begin_src c
|
||||
/* This file was generated from the trexio.org org-mode file.
|
||||
@ -19,6 +32,7 @@
|
||||
#define _TREXIO_TEXT_H
|
||||
|
||||
#include "trexio.h"
|
||||
#include "trexio_private.h"
|
||||
#include "trexio_s.h"
|
||||
#include <errno.h>
|
||||
#include <stdint.h>
|
||||
@ -33,7 +47,13 @@
|
||||
#+end_src
|
||||
|
||||
#+begin_src c :tangle trexio_text.c :noweb yes
|
||||
<<header>>
|
||||
/* 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 "trexio_text.h"
|
||||
#+end_src
|
||||
|
||||
@ -58,8 +78,8 @@ typedef struct nucleus_s {
|
||||
double* coord;
|
||||
double* charge;
|
||||
uint64_t num;
|
||||
uint64_t* dims_charge;
|
||||
uint64_t* dims_coord;
|
||||
uint64_t dims_charge[16];
|
||||
uint64_t dims_coord[16];
|
||||
uint32_t rank_charge;
|
||||
uint32_t rank_coord;
|
||||
int to_flush;
|
||||
@ -80,13 +100,6 @@ typedef struct rdm_s {
|
||||
int to_flush;
|
||||
} rdm_t;
|
||||
#+end_src
|
||||
|
||||
|
||||
*** TO DO
|
||||
- to_flush = 1 in write
|
||||
- to_flush = 0 when flushed
|
||||
- name
|
||||
|
||||
*** Structs for the text back end
|
||||
|
||||
#+begin_src c :tangle trexio_text.h
|
||||
@ -113,6 +126,9 @@ trexio_exit_code trexio_text_init(trexio_t* file) {
|
||||
|
||||
trexio_text_t* f = (trexio_text_t*) file;
|
||||
|
||||
/* Put all pointers to NULL but leave parent untouched */
|
||||
memset(&(f->parent)+1,0,sizeof(trexio_text_t)-sizeof(trexio_t));
|
||||
|
||||
/* If directory doesn't exist, create it in write mode */
|
||||
struct stat st;
|
||||
|
||||
@ -128,24 +144,25 @@ trexio_exit_code trexio_text_init(trexio_t* file) {
|
||||
|
||||
/* Create the lock file in the directory */
|
||||
const char* lock_file_name = "/.lock";
|
||||
char* file_name = (char*)
|
||||
calloc( strlen(file->file_name) + strlen(lock_file_name) + 1,
|
||||
sizeof(char));
|
||||
assert (file_name != NULL);
|
||||
char* file_name =
|
||||
CALLOC(strlen(file->file_name) + strlen(lock_file_name) + 1, char);
|
||||
|
||||
if (file_name == NULL) {
|
||||
return TREXIO_ALLOCATION_FAILED;
|
||||
}
|
||||
|
||||
strcpy (file_name, file->file_name);
|
||||
strcat (file_name, lock_file_name);
|
||||
|
||||
f->lock_file = open(file_name,O_WRONLY|O_CREAT|O_TRUNC, 0644);
|
||||
assert (f->lock_file > 0);
|
||||
free(file_name);
|
||||
FREE(file_name);
|
||||
|
||||
f->nucleus = NULL;
|
||||
f->electron= NULL;
|
||||
f->rdm = NULL;
|
||||
if (f->lock_file <= 0) {
|
||||
return TREXIO_FAILURE;
|
||||
}
|
||||
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
|
||||
#+end_src
|
||||
|
||||
#+begin_src c :tangle trexio_text.h
|
||||
@ -171,7 +188,6 @@ trexio_exit_code trexio_text_lock(trexio_t* file) {
|
||||
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
|
||||
#+end_src
|
||||
|
||||
|
||||
@ -228,29 +244,34 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file);
|
||||
#+end_src
|
||||
|
||||
#+begin_src c :tangle trexio_text.c
|
||||
#define DEBUG printf("%s : line %d\n", __FILE__, __LINE__);
|
||||
|
||||
nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
|
||||
if (file == NULL) return NULL;
|
||||
|
||||
if (file->nucleus != NULL) return file->nucleus;
|
||||
/* If the data structure exists, return it */
|
||||
if (file->nucleus != NULL) {
|
||||
return file->nucleus;
|
||||
}
|
||||
|
||||
/* Allocate the data structure */
|
||||
nucleus_t* nucleus = (nucleus_t*) malloc(sizeof(nucleus_t));
|
||||
assert (nucleus != NULL);
|
||||
nucleus_t* nucleus = MALLOC(nucleus_t);
|
||||
if (nucleus == NULL) return NULL;
|
||||
|
||||
nucleus->file = NULL;
|
||||
nucleus->num = 0;
|
||||
nucleus->coord = NULL;
|
||||
nucleus->dims_coord = NULL;
|
||||
nucleus->charge = NULL;
|
||||
nucleus->dims_charge = NULL;
|
||||
nucleus->to_flush = 0;
|
||||
memset(nucleus,0,sizeof(nucleus_t));
|
||||
|
||||
/* Try to open the file. If the file does not exist, return */
|
||||
/* Build the file name */
|
||||
const char* nucleus_file_name = "/nucleus.txt";
|
||||
char * file_name = (char*)
|
||||
calloc( strlen(file->parent.file_name) + strlen(nucleus_file_name) + 1,
|
||||
sizeof(char));
|
||||
assert (file_name != NULL);
|
||||
|
||||
if (file_name == NULL) {
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
strcpy (file_name, file->parent.file_name);
|
||||
strcat (file_name, nucleus_file_name);
|
||||
|
||||
@ -262,98 +283,219 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
|
||||
fseek(f, 0L, SEEK_END);
|
||||
size_t sz = ftell(f);
|
||||
fseek(f, 0L, SEEK_SET);
|
||||
char* buffer = (char*) malloc(sz*sizeof(char));
|
||||
|
||||
char* buffer = CALLOC(sz,char);
|
||||
if (buffer == NULL) {
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* Read the dimensioning variables */
|
||||
int rc;
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "rank_charge") == 0);
|
||||
if ((rc != 1) || (strcmp(buffer, "rank_charge") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%u", &(nucleus->rank_charge));
|
||||
assert (rc == 1);
|
||||
|
||||
nucleus->dims_charge = (uint64_t*) calloc(nucleus->rank_charge, sizeof(uint64_t));
|
||||
assert (nucleus->dims_charge != NULL);
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
uint64_t size_charge = 1;
|
||||
for (uint i=0; i<nucleus->rank_charge; i++){
|
||||
for (unsigned int i=0; i<nucleus->rank_charge; i++){
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
//assert (strcmp(buffer, "dims_charge") == 0);
|
||||
unsigned int j=-1;
|
||||
rc = fscanf(f, "%s %u", buffer, &j);
|
||||
if ((rc != 2) || (strcmp(buffer, "dims_charge") != 0) || (j!=i)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%lu", &(nucleus->dims_charge[i]));
|
||||
assert (rc == 1);
|
||||
rc = fscanf(f, "%lu\n", &(nucleus->dims_charge[i]));
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
size_charge *= nucleus->dims_charge[i];
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "rank_coord") == 0);
|
||||
if ((rc != 1) || (strcmp(buffer, "rank_coord") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%u", &(nucleus->rank_coord));
|
||||
assert (rc == 1);
|
||||
|
||||
nucleus->dims_coord = (uint64_t*) calloc(nucleus->rank_coord, sizeof(uint64_t));
|
||||
assert (nucleus->dims_coord != NULL);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
uint64_t size_coord = 1;
|
||||
for (uint i=0; i<nucleus->rank_coord; i++){
|
||||
for (unsigned int i=0; i<nucleus->rank_coord; i++){
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
//assert (strcmp(buffer, "dims_coord") == 0);
|
||||
unsigned int j=-1;
|
||||
rc = fscanf(f, "%s %u", buffer, &j);
|
||||
if ((rc != 2) || (strcmp(buffer, "dims_coord") != 0) || (j!=i)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%lu", &(nucleus->dims_coord[i]));
|
||||
assert (rc == 1);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
size_coord *= nucleus->dims_coord[i];
|
||||
}
|
||||
|
||||
/* Allocate arrays */
|
||||
nucleus->charge = (double*) calloc(size_charge, sizeof(double));
|
||||
assert (nucleus->charge != NULL);
|
||||
assert (!(nucleus->charge == NULL));
|
||||
if (nucleus->charge == NULL) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
nucleus->coord = (double*) calloc(size_coord, sizeof(double));
|
||||
assert (nucleus->coord != NULL);
|
||||
assert (!(nucleus->coord == NULL));
|
||||
if (nucleus->coord == NULL) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
/* Read data */
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "num") == 0);
|
||||
assert(!((rc != 1) || (strcmp(buffer, "num") != 0)));
|
||||
if ((rc != 1) || (strcmp(buffer, "num") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%lu", &(nucleus->num));
|
||||
assert (rc == 1);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "charge") == 0);
|
||||
assert(!((rc != 1) || (strcmp(buffer, "charge") != 0)));
|
||||
if ((rc != 1) || (strcmp(buffer, "charge") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
for (uint64_t i=0 ; i<size_charge ; i++) {
|
||||
rc = fscanf(f, "%lf", &(nucleus->charge[i]));
|
||||
assert (rc == 1);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
}
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
assert (strcmp(buffer, "coord") == 0);
|
||||
assert(!((rc != 1) || (strcmp(buffer, "coord") != 0)));
|
||||
if ((rc != 1) || (strcmp(buffer, "coord") != 0)) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
for (uint64_t i=0 ; i<size_coord ; i++) {
|
||||
rc = fscanf(f, "%lf", &(nucleus->coord[i]));
|
||||
assert (rc == 1);
|
||||
assert(!(rc != 1));
|
||||
if (rc != 1) {
|
||||
FREE(buffer);
|
||||
FREE(file_name);
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
free(buffer);
|
||||
}
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
f = NULL;
|
||||
}
|
||||
|
||||
if (file->parent.mode == 'w') {
|
||||
nucleus->file = fopen(file_name,"a");
|
||||
} else {
|
||||
nucleus->file = fopen(file_name,"r");
|
||||
}
|
||||
free(file_name);
|
||||
FREE(file_name);
|
||||
assert (!(nucleus->file == NULL));
|
||||
if (nucleus->file == NULL) {
|
||||
FREE(nucleus->charge);
|
||||
FREE(nucleus);
|
||||
DEBUG
|
||||
return NULL;
|
||||
}
|
||||
|
||||
fseek(nucleus->file, 0L, SEEK_SET);
|
||||
file->nucleus = nucleus;
|
||||
return nucleus;
|
||||
}
|
||||
@ -385,16 +527,16 @@ trexio_exit_code trexio_text_flush_nucleus(const trexio_text_t* file) {
|
||||
fprintf(f, "rank_charge %d\n", nucleus->rank_charge);
|
||||
|
||||
uint64_t size_charge = 1;
|
||||
for (uint i=0; i<nucleus->rank_charge; i++){
|
||||
fprintf(f, "dims_charge[%d] %ld\n", i, nucleus->dims_charge[i]);
|
||||
for (unsigned int i=0; i<nucleus->rank_charge; i++){
|
||||
fprintf(f, "dims_charge %d %ld\n", i, nucleus->dims_charge[i]);
|
||||
size_charge *= nucleus->dims_charge[i];
|
||||
}
|
||||
|
||||
fprintf(f, "rank_coord %d\n", nucleus->rank_coord);
|
||||
|
||||
uint64_t size_coord = 1;
|
||||
for (uint i=0; i<nucleus->rank_coord; i++){
|
||||
fprintf(f, "dims_coord[%d] %ld\n", i, nucleus->dims_coord[i]);
|
||||
for (unsigned int i=0; i<nucleus->rank_coord; i++){
|
||||
fprintf(f, "dims_coord %d %ld\n", i, nucleus->dims_coord[i]);
|
||||
size_coord *= nucleus->dims_coord[i];
|
||||
}
|
||||
|
||||
@ -442,28 +584,15 @@ trexio_exit_code trexio_text_free_nucleus(trexio_text_t* file) {
|
||||
nucleus->file = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->dims_coord != NULL) {
|
||||
free (nucleus->dims_coord);
|
||||
nucleus->dims_coord = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->coord != NULL) {
|
||||
free (nucleus->coord);
|
||||
nucleus->coord = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->dims_charge != NULL) {
|
||||
free (nucleus->dims_charge);
|
||||
nucleus->dims_charge = NULL;
|
||||
FREE (nucleus->coord);
|
||||
}
|
||||
|
||||
if (nucleus->charge != NULL) {
|
||||
free (nucleus->charge);
|
||||
nucleus->charge = NULL;
|
||||
FREE (nucleus->charge);
|
||||
}
|
||||
|
||||
free (nucleus);
|
||||
file->nucleus = NULL;
|
||||
FREE (nucleus);
|
||||
return TREXIO_SUCCESS;
|
||||
}
|
||||
#+end_src
|
||||
@ -527,7 +656,7 @@ trexio_exit_code trexio_text_read_nucleus_coord(const trexio_t* file, double* co
|
||||
if (rank != nucleus->rank_coord) return TREXIO_INVALID_ARG_3;
|
||||
|
||||
uint64_t dim_size = 1;
|
||||
for (uint i=0; i<rank; i++){
|
||||
for (unsigned int i=0; i<rank; i++){
|
||||
if (dims[i] != nucleus->dims_coord[i]) return TREXIO_INVALID_ARG_4;
|
||||
dim_size *= dims[i];
|
||||
}
|
||||
@ -550,20 +679,13 @@ trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const dou
|
||||
if (nucleus == NULL) return TREXIO_FAILURE;
|
||||
|
||||
if (nucleus->coord != NULL) {
|
||||
free(nucleus->coord);
|
||||
nucleus->coord = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->dims_coord != NULL) {
|
||||
free(nucleus->dims_coord);
|
||||
nucleus->dims_coord = NULL;
|
||||
FREE(nucleus->coord);
|
||||
}
|
||||
|
||||
nucleus->rank_coord = rank;
|
||||
nucleus->dims_coord = (uint64_t*) calloc(rank, sizeof(uint64_t));
|
||||
|
||||
uint64_t dim_size = 1;
|
||||
for (uint i=0; i<nucleus->rank_coord; i++){
|
||||
for (unsigned int i=0; i<nucleus->rank_coord; i++){
|
||||
nucleus->dims_coord[i] = dims[i];
|
||||
dim_size *= dims[i];
|
||||
}
|
||||
@ -599,7 +721,7 @@ trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* c
|
||||
if (rank != nucleus->rank_charge) return TREXIO_INVALID_ARG_3;
|
||||
|
||||
uint64_t dim_size = 1;
|
||||
for (uint i=0; i<rank; i++){
|
||||
for (unsigned int i=0; i<rank; i++){
|
||||
if (dims[i] != nucleus->dims_charge[i]) return TREXIO_INVALID_ARG_4;
|
||||
dim_size *= dims[i];
|
||||
}
|
||||
@ -622,21 +744,13 @@ trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const do
|
||||
if (nucleus == NULL) return TREXIO_FAILURE;
|
||||
|
||||
if (nucleus->charge != NULL) {
|
||||
free(nucleus->charge);
|
||||
nucleus->charge = NULL;
|
||||
}
|
||||
|
||||
if (nucleus->dims_charge != NULL) {
|
||||
free(nucleus->dims_charge);
|
||||
nucleus->dims_charge = NULL;
|
||||
FREE(nucleus->charge);
|
||||
}
|
||||
|
||||
nucleus->rank_charge = rank;
|
||||
|
||||
nucleus->dims_charge = (uint64_t*) calloc(rank, sizeof(uint64_t));
|
||||
|
||||
uint64_t dim_size = 1;
|
||||
for (uint i=0; i<nucleus->rank_charge; i++){
|
||||
for (unsigned int i=0; i<nucleus->rank_charge; i++){
|
||||
nucleus->dims_charge[i] = dims[i];
|
||||
dim_size *= dims[i];
|
||||
}
|
||||
@ -666,7 +780,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
|
||||
if (file->rdm != NULL) return file->rdm;
|
||||
|
||||
/* Allocate the data structure */
|
||||
rdm_t* rdm = (rdm_t*) malloc(sizeof(rdm_t));
|
||||
rdm_t* rdm = MALLOC(rdm_t);
|
||||
assert (rdm != NULL);
|
||||
|
||||
rdm->one_e = NULL;
|
||||
@ -691,7 +805,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
|
||||
fseek(f, 0L, SEEK_END);
|
||||
size_t sz = ftell(f);
|
||||
fseek(f, 0L, SEEK_SET);
|
||||
char* buffer = (char*) malloc(sz*sizeof(char));
|
||||
char* buffer = CALLOC(sz,char);
|
||||
|
||||
/* Read the dimensioning variables */
|
||||
int rc;
|
||||
@ -723,10 +837,10 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
|
||||
|
||||
rc = fscanf(f, "%s", buffer);
|
||||
assert (rc == 1);
|
||||
rdm->two_e_file_name = (char*) malloc (strlen(buffer)*sizeof(char));
|
||||
rdm->two_e_file_name = CALLOC (strlen(buffer),char);
|
||||
strcpy(rdm->two_e_file_name, buffer);
|
||||
|
||||
free(buffer);
|
||||
FREE(buffer);
|
||||
fclose(f);
|
||||
f = NULL;
|
||||
}
|
||||
@ -735,7 +849,7 @@ rdm_t* trexio_text_read_rdm(trexio_text_t* file) {
|
||||
} else {
|
||||
rdm->file = fopen(file_name,"r");
|
||||
}
|
||||
free(file_name);
|
||||
FREE(file_name);
|
||||
file->rdm = rdm ;
|
||||
return rdm;
|
||||
}
|
||||
@ -807,13 +921,11 @@ trexio_exit_code trexio_text_free_rdm(trexio_text_t* file) {
|
||||
}
|
||||
|
||||
if (rdm->one_e != NULL) {
|
||||
free (rdm->one_e);
|
||||
rdm->one_e = NULL;
|
||||
FREE (rdm->one_e);
|
||||
}
|
||||
|
||||
if (rdm->two_e_file_name != NULL) {
|
||||
free (rdm->two_e_file_name);
|
||||
rdm->two_e_file_name = NULL;
|
||||
FREE (rdm->two_e_file_name);
|
||||
}
|
||||
|
||||
free (rdm);
|
||||
|
||||
Loading…
Reference in New Issue
Block a user