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Merge pull request #26 from TREX-CoE/text

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Improved checks in text back end
This commit is contained in:
Evgeny Posenitskiy 2021-03-13 20:14:55 +01:00 committed by GitHub
commit 8e8b2ba57f
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GPG Key ID: 4AEE18F83AFDEB23
6 changed files with 448 additions and 212 deletions
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2
src/trexio.c
View File

@ -53,7 +53,7 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
/* Data for the parent type */
result->file_name = (char*) calloc(strlen(file_name)+1,sizeof(char));
result->file_name = CALLOC(strlen(file_name)+1,char);
strcpy(result->file_name, file_name);
result->back_end = back_end;
result->mode = mode;

25
src/trexio.h
View File

@ -12,18 +12,19 @@
typedef int32_t trexio_exit_code;
#define TREXIO_FAILURE ( (trexio_exit_code) -1 )
#define TREXIO_SUCCESS ( (trexio_exit_code) 0 )
#define TREXIO_INVALID_ARG_1 ( (trexio_exit_code) 1 )
#define TREXIO_INVALID_ARG_2 ( (trexio_exit_code) 2 )
#define TREXIO_INVALID_ARG_3 ( (trexio_exit_code) 3 )
#define TREXIO_INVALID_ARG_4 ( (trexio_exit_code) 4 )
#define TREXIO_INVALID_ARG_5 ( (trexio_exit_code) 5 )
#define TREXIO_END ( (trexio_exit_code) 10 )
#define TREXIO_READONLY ( (trexio_exit_code) 11 )
#define TREXIO_ERRNO ( (trexio_exit_code) 12 )
#define TREXIO_INVALID_ID ( (trexio_exit_code) 20 )
#define TREXIO_INVALID_NUM ( (trexio_exit_code) 21 )
#define TREXIO_FAILURE ( (trexio_exit_code) -1 )
#define TREXIO_SUCCESS ( (trexio_exit_code) 0 )
#define TREXIO_INVALID_ARG_1 ( (trexio_exit_code) 1 )
#define TREXIO_INVALID_ARG_2 ( (trexio_exit_code) 2 )
#define TREXIO_INVALID_ARG_3 ( (trexio_exit_code) 3 )
#define TREXIO_INVALID_ARG_4 ( (trexio_exit_code) 4 )
#define TREXIO_INVALID_ARG_5 ( (trexio_exit_code) 5 )
#define TREXIO_END ( (trexio_exit_code) 10 )
#define TREXIO_READONLY ( (trexio_exit_code) 11 )
#define TREXIO_ERRNO ( (trexio_exit_code) 12 )
#define TREXIO_INVALID_ID ( (trexio_exit_code) 20 )
#define TREXIO_ALLOCATION_FAILED ( (trexio_exit_code) 21 )
#define TREXIO_INVALID_NUM ( (trexio_exit_code) 22 )
typedef int32_t back_end_t;

27
src/trexio.org
View File

@ -88,18 +88,19 @@
#+begin_src c :tangle trexio.h
typedef int32_t trexio_exit_code;
#define TREXIO_FAILURE ( (trexio_exit_code) -1 )
#define TREXIO_SUCCESS ( (trexio_exit_code) 0 )
#define TREXIO_INVALID_ARG_1 ( (trexio_exit_code) 1 )
#define TREXIO_INVALID_ARG_2 ( (trexio_exit_code) 2 )
#define TREXIO_INVALID_ARG_3 ( (trexio_exit_code) 3 )
#define TREXIO_INVALID_ARG_4 ( (trexio_exit_code) 4 )
#define TREXIO_INVALID_ARG_5 ( (trexio_exit_code) 5 )
#define TREXIO_END ( (trexio_exit_code) 10 )
#define TREXIO_READONLY ( (trexio_exit_code) 11 )
#define TREXIO_ERRNO ( (trexio_exit_code) 12 )
#define TREXIO_INVALID_ID ( (trexio_exit_code) 20 )
#define TREXIO_INVALID_NUM ( (trexio_exit_code) 21 )
#define TREXIO_FAILURE ( (trexio_exit_code) -1 )
#define TREXIO_SUCCESS ( (trexio_exit_code) 0 )
#define TREXIO_INVALID_ARG_1 ( (trexio_exit_code) 1 )
#define TREXIO_INVALID_ARG_2 ( (trexio_exit_code) 2 )
#define TREXIO_INVALID_ARG_3 ( (trexio_exit_code) 3 )
#define TREXIO_INVALID_ARG_4 ( (trexio_exit_code) 4 )
#define TREXIO_INVALID_ARG_5 ( (trexio_exit_code) 5 )
#define TREXIO_END ( (trexio_exit_code) 10 )
#define TREXIO_READONLY ( (trexio_exit_code) 11 )
#define TREXIO_ERRNO ( (trexio_exit_code) 12 )
#define TREXIO_INVALID_ID ( (trexio_exit_code) 20 )
#define TREXIO_ALLOCATION_FAILED ( (trexio_exit_code) 21 )
#define TREXIO_INVALID_NUM ( (trexio_exit_code) 22 )
#+end_src
** Back ends
@ -212,7 +213,7 @@ trexio_t* trexio_open(const char* file_name, const char mode, const back_end_t b
/* Data for the parent type */
result->file_name = (char*) calloc(strlen(file_name)+1,sizeof(char));
result->file_name = CALLOC(strlen(file_name)+1,char);
strcpy(result->file_name, file_name);
result->back_end = back_end;
result->mode = mode;

284
src/trexio_text.c
View File

@ -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;
@ -27,21 +30,23 @@ 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);
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 = MALLOC(nucleus_t);
assert (nucleus != NULL);
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 = 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);
if (rc != 1) {
FREE(buffer);
FREE(file_name);
FREE(nucleus);
DEBUG
return NULL;
}
nucleus->dims_charge = (uint64_t*) calloc(nucleus->rank_charge, sizeof(uint64_t));
assert (nucleus->dims_charge != 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);
assert(!(rc != 1));
if (rc != 1) {
FREE(buffer);
FREE(file_name);
FREE(nucleus);
DEBUG
return NULL;
}
nucleus->dims_coord = (uint64_t*) calloc(nucleus->rank_coord, sizeof(uint64_t));
assert (nucleus->dims_coord != 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);
rc = fscanf(f, "%s", buffer);
assert (rc == 1);
assert (strcmp(buffer, "charge") == 0);
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, "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));
if (rc != 1) {
FREE(buffer);
FREE(file_name);
FREE(nucleus->charge);
FREE(nucleus);
DEBUG
return NULL;
}
}
rc = fscanf(f, "%s", buffer);
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);
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);
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];
}
@ -292,18 +423,10 @@ trexio_exit_code trexio_text_free_nucleus(trexio_text_t* file) {
nucleus->file = NULL;
}
if (nucleus->dims_coord != NULL) {
FREE (nucleus->dims_coord);
}
if (nucleus->coord != NULL) {
FREE (nucleus->coord);
}
if (nucleus->dims_charge != NULL) {
FREE (nucleus->dims_charge);
}
if (nucleus->charge != NULL) {
FREE (nucleus->charge);
}
@ -352,7 +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];
}
@ -378,15 +501,10 @@ trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const dou
FREE(nucleus->coord);
}
if (nucleus->dims_coord != NULL) {
FREE(nucleus->dims_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];
}
@ -412,7 +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];
}
@ -438,16 +556,10 @@ trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const do
FREE(nucleus->charge);
}
if (nucleus->dims_charge != NULL) {
FREE(nucleus->dims_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];
}

4
src/trexio_text.h
View File

@ -26,8 +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;

318
src/trexio_text.org
View File

@ -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.
@ -34,7 +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
@ -59,8 +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;
@ -81,13 +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
@ -114,6 +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;
@ -129,24 +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);
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
@ -172,7 +188,6 @@ trexio_exit_code trexio_text_lock(trexio_t* file) {
return TREXIO_SUCCESS;
}
#+end_src
@ -229,29 +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 = MALLOC(nucleus_t);
assert (nucleus != NULL);
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);
@ -263,98 +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 = 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);
if (rc != 1) {
FREE(buffer);
FREE(file_name);
FREE(nucleus);
DEBUG
return NULL;
}
nucleus->dims_charge = (uint64_t*) calloc(nucleus->rank_charge, sizeof(uint64_t));
assert (nucleus->dims_charge != 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);
assert(!(rc != 1));
if (rc != 1) {
FREE(buffer);
FREE(file_name);
FREE(nucleus);
DEBUG
return NULL;
}
nucleus->dims_coord = (uint64_t*) calloc(nucleus->rank_coord, sizeof(uint64_t));
assert (nucleus->dims_coord != 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);
rc = fscanf(f, "%s", buffer);
assert (rc == 1);
assert (strcmp(buffer, "charge") == 0);
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, "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));
if (rc != 1) {
FREE(buffer);
FREE(file_name);
FREE(nucleus->charge);
FREE(nucleus);
DEBUG
return NULL;
}
}
rc = fscanf(f, "%s", buffer);
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);
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);
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;
}
@ -386,16 +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];
}
@ -443,18 +584,10 @@ trexio_exit_code trexio_text_free_nucleus(trexio_text_t* file) {
nucleus->file = NULL;
}
if (nucleus->dims_coord != NULL) {
FREE (nucleus->dims_coord);
}
if (nucleus->coord != NULL) {
FREE (nucleus->coord);
}
if (nucleus->dims_charge != NULL) {
FREE (nucleus->dims_charge);
}
if (nucleus->charge != NULL) {
FREE (nucleus->charge);
}
@ -523,7 +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];
}
@ -549,15 +682,10 @@ trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const dou
FREE(nucleus->coord);
}
if (nucleus->dims_coord != NULL) {
FREE(nucleus->dims_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];
}
@ -593,7 +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];
}
@ -619,16 +747,10 @@ trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const do
FREE(nucleus->charge);
}
if (nucleus->dims_charge != NULL) {
FREE(nucleus->dims_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];
}