TREX/trexio
1
0
Fork 0
mirror of https://github.com/TREX-CoE/trexio.git synced 2024-11-03 20:54:07 +01:00
Code Issues Projects Releases Wiki Activity

works for charges

Browse Source
This commit is contained in:
q-posev 2021-03-12 14:05:31 +01:00
parent cbddfa6010
commit 798c1a1d99
5 changed files with 168 additions and 80 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

18
src/trexio.c
View File

@ -245,9 +245,6 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num); trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num);
if (rc != TREXIO_SUCCESS) return rc; if (rc != TREXIO_SUCCESS) return rc;
int64_t dim_coord = nucleus_num*3;
if (dim_coord < 0) return TREXIO_FAILURE;
uint32_t rank = 2; uint32_t rank = 2;
uint64_t dims[2] = {nucleus_num, 3}; uint64_t dims[2] = {nucleus_num, 3};
@ -278,9 +275,6 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num); trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num);
if (rc != TREXIO_SUCCESS) return rc; if (rc != TREXIO_SUCCESS) return rc;
int64_t dim_coord = nucleus_num*3;
if (dim_coord < 0) return TREXIO_FAILURE;
uint32_t rank = 2; uint32_t rank = 2;
uint64_t dims[2] = {nucleus_num, 3}; uint64_t dims[2] = {nucleus_num, 3};
@ -311,13 +305,13 @@ trexio_exit_code trexio_read_nucleus_charge(trexio_t* file, double* charge) {
trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num); trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num);
if (rc != TREXIO_SUCCESS) return rc; if (rc != TREXIO_SUCCESS) return rc;
int64_t dim_charge = nucleus_num; uint32_t rank = 1;
if (dim_charge < 0) return TREXIO_FAILURE; uint64_t dims[1] = {nucleus_num};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
return trexio_text_read_nucleus_charge(file, charge, (uint64_t) dim_charge); return trexio_text_read_nucleus_charge(file, charge, rank, dims);
break; break;
/* /*
case TREXIO_HDF5: case TREXIO_HDF5:
@ -341,13 +335,13 @@ trexio_exit_code trexio_write_nucleus_charge(trexio_t* file, const double* charg
trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num); trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num);
if (rc != TREXIO_SUCCESS) return rc; if (rc != TREXIO_SUCCESS) return rc;
int64_t dim_charge = nucleus_num; uint32_t rank = 1;
if (dim_charge < 0) return TREXIO_FAILURE; uint64_t dims[1] = {nucleus_num};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
return trexio_text_write_nucleus_charge(file, charge, (uint64_t) dim_charge); return trexio_text_write_nucleus_charge(file, charge, rank, dims);
break; break;
/* /*
case TREXIO_HDF5: case TREXIO_HDF5:

18
src/trexio.org
View File

@ -410,9 +410,6 @@ trexio_exit_code trexio_read_nucleus_coord(trexio_t* file, double* coord) {
trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num); trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num);
if (rc != TREXIO_SUCCESS) return rc; if (rc != TREXIO_SUCCESS) return rc;
int64_t dim_coord = nucleus_num*3;
if (dim_coord < 0) return TREXIO_FAILURE;
uint32_t rank = 2; uint32_t rank = 2;
uint64_t dims[2] = {nucleus_num, 3}; uint64_t dims[2] = {nucleus_num, 3};
@ -443,9 +440,6 @@ trexio_exit_code trexio_write_nucleus_coord(trexio_t* file, const double* coord)
trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num); trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num);
if (rc != TREXIO_SUCCESS) return rc; if (rc != TREXIO_SUCCESS) return rc;
int64_t dim_coord = nucleus_num*3;
if (dim_coord < 0) return TREXIO_FAILURE;
uint32_t rank = 2; uint32_t rank = 2;
uint64_t dims[2] = {nucleus_num, 3}; uint64_t dims[2] = {nucleus_num, 3};
@ -484,13 +478,13 @@ trexio_exit_code trexio_read_nucleus_charge(trexio_t* file, double* charge) {
trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num); trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num);
if (rc != TREXIO_SUCCESS) return rc; if (rc != TREXIO_SUCCESS) return rc;
int64_t dim_charge = nucleus_num; uint32_t rank = 1;
if (dim_charge < 0) return TREXIO_FAILURE; uint64_t dims[1] = {nucleus_num};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
return trexio_text_read_nucleus_charge(file, charge, (uint64_t) dim_charge); return trexio_text_read_nucleus_charge(file, charge, rank, dims);
break; break;
/* /*
case TREXIO_HDF5: case TREXIO_HDF5:
@ -514,13 +508,13 @@ trexio_exit_code trexio_write_nucleus_charge(trexio_t* file, const double* charg
trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num); trexio_exit_code rc = trexio_read_nucleus_num(file, &nucleus_num);
if (rc != TREXIO_SUCCESS) return rc; if (rc != TREXIO_SUCCESS) return rc;
int64_t dim_charge = nucleus_num; uint32_t rank = 1;
if (dim_charge < 0) return TREXIO_FAILURE; uint64_t dims[1] = {nucleus_num};
switch (file->back_end) { switch (file->back_end) {
case TREXIO_TEXT: case TREXIO_TEXT:
return trexio_text_write_nucleus_charge(file, charge, (uint64_t) dim_charge); return trexio_text_write_nucleus_charge(file, charge, rank, dims);
break; break;
/* /*
case TREXIO_HDF5: case TREXIO_HDF5:

99
src/trexio_text.c
View File

@ -110,6 +110,7 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
nucleus->coord = NULL; nucleus->coord = NULL;
nucleus->dims_coord = NULL; nucleus->dims_coord = NULL;
nucleus->charge = NULL; nucleus->charge = NULL;
nucleus->dims_charge = NULL;
nucleus->to_flush = 0; nucleus->to_flush = 0;
/* Try to open the file. If the file does not exist, return */ /* Try to open the file. If the file does not exist, return */
@ -135,10 +136,26 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
int rc; int rc;
rc = fscanf(f, "%s", buffer); rc = fscanf(f, "%s", buffer);
assert (rc == 1); assert (rc == 1);
assert (strcmp(buffer, "dim_charge") == 0); assert (strcmp(buffer, "rank_charge") == 0);
rc = fscanf(f, "%lu", &(nucleus->dim_charge)); rc = fscanf(f, "%u", &(nucleus->rank_charge));
assert (rc == 1); assert (rc == 1);
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++){
rc = fscanf(f, "%s", buffer);
assert (rc == 1);
//assert (strcmp(buffer, "dims_charge") == 0);
rc = fscanf(f, "%lu", &(nucleus->dims_charge[i]));
assert (rc == 1);
size_charge *= nucleus->dims_charge[i];
}
rc = fscanf(f, "%s", buffer); rc = fscanf(f, "%s", buffer);
assert (rc == 1); assert (rc == 1);
@ -150,7 +167,7 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
nucleus->dims_coord = (uint64_t*) calloc(nucleus->rank_coord, sizeof(uint64_t)); nucleus->dims_coord = (uint64_t*) calloc(nucleus->rank_coord, sizeof(uint64_t));
assert (nucleus->dims_coord != NULL); assert (nucleus->dims_coord != NULL);
uint64_t dim_coord = 1; uint64_t size_coord = 1;
for (uint i=0; i<nucleus->rank_coord; i++){ for (uint i=0; i<nucleus->rank_coord; i++){
rc = fscanf(f, "%s", buffer); rc = fscanf(f, "%s", buffer);
@ -160,14 +177,14 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
rc = fscanf(f, "%lu", &(nucleus->dims_coord[i])); rc = fscanf(f, "%lu", &(nucleus->dims_coord[i]));
assert (rc == 1); assert (rc == 1);
dim_coord *= nucleus->dims_coord[i]; size_coord *= nucleus->dims_coord[i];
} }
/* Allocate arrays */ /* Allocate arrays */
nucleus->charge = (double*) calloc(nucleus->dim_charge, sizeof(double)); nucleus->charge = (double*) calloc(size_charge, sizeof(double));
assert (nucleus->charge != NULL); assert (nucleus->charge != NULL);
nucleus->coord = (double*) calloc(dim_coord, sizeof(double)); nucleus->coord = (double*) calloc(size_coord, sizeof(double));
assert (nucleus->coord != NULL); assert (nucleus->coord != NULL);
/* Read data */ /* Read data */
@ -182,7 +199,7 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
assert (rc == 1); assert (rc == 1);
assert (strcmp(buffer, "charge") == 0); assert (strcmp(buffer, "charge") == 0);
for (uint64_t i=0 ; i<nucleus->dim_charge ; i++) { for (uint64_t i=0 ; i<size_charge ; i++) {
rc = fscanf(f, "%lf", &(nucleus->charge[i])); rc = fscanf(f, "%lf", &(nucleus->charge[i]));
assert (rc == 1); assert (rc == 1);
} }
@ -191,7 +208,7 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
assert (rc == 1); assert (rc == 1);
assert (strcmp(buffer, "coord") == 0); assert (strcmp(buffer, "coord") == 0);
for (uint64_t i=0 ; i<dim_coord ; i++) { for (uint64_t i=0 ; i<size_coord ; i++) {
rc = fscanf(f, "%lf", &(nucleus->coord[i])); rc = fscanf(f, "%lf", &(nucleus->coord[i]));
assert (rc == 1); assert (rc == 1);
} }
@ -225,24 +242,31 @@ trexio_exit_code trexio_text_flush_nucleus(const trexio_text_t* file) {
rewind(f); rewind(f);
/* Write the dimensioning variables */ /* Write the dimensioning variables */
fprintf(f, "dim_charge %ld\n", nucleus->dim_charge ); 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]);
size_charge *= nucleus->dims_charge[i];
}
fprintf(f, "rank_coord %d\n", nucleus->rank_coord); fprintf(f, "rank_coord %d\n", nucleus->rank_coord);
uint64_t dim_coord = (nucleus->dims_coord[0])*(nucleus->dims_coord[1]); uint64_t size_coord = 1;
for (uint i=0; i<nucleus->rank_coord; i++){ for (uint i=0; i<nucleus->rank_coord; i++){
fprintf(f, "dims_coord[%d] %ld\n", i, nucleus->dims_coord[i]); fprintf(f, "dims_coord[%d] %ld\n", i, nucleus->dims_coord[i]);
//dim_coord *= nucleus->dims_coord[i]; size_coord *= nucleus->dims_coord[i];
} }
/* Write arrays */ /* Write arrays */
fprintf(f, "num %ld\n", nucleus->num); fprintf(f, "num %ld\n", nucleus->num);
fprintf(f, "charge\n"); fprintf(f, "charge\n");
for (uint64_t i=0 ; i<nucleus->dim_charge ; i++) { for (uint64_t i=0 ; i<size_charge ; i++) {
fprintf(f, "%lf\n", nucleus->charge[i]); fprintf(f, "%lf\n", nucleus->charge[i]);
} }
fprintf(f, "coord\n"); fprintf(f, "coord\n");
for (uint64_t i=0 ; i<dim_coord ; i++) { for (uint64_t i=0 ; i<size_coord ; i++) {
fprintf(f, "%lf\n", nucleus->coord[i]); fprintf(f, "%lf\n", nucleus->coord[i]);
} }
fflush(f); fflush(f);
@ -277,7 +301,12 @@ trexio_exit_code trexio_text_free_nucleus(trexio_text_t* file) {
free (nucleus->coord); free (nucleus->coord);
nucleus->coord = NULL; nucleus->coord = NULL;
} }
if (nucleus->dims_charge != NULL) {
free (nucleus->dims_charge);
nucleus->dims_charge = NULL;
}
if (nucleus->charge != NULL) { if (nucleus->charge != NULL) {
free (nucleus->charge); free (nucleus->charge);
nucleus->charge = NULL; nucleus->charge = NULL;
@ -327,11 +356,11 @@ trexio_exit_code trexio_text_read_nucleus_coord(const trexio_t* file, double* co
if (rank != nucleus->rank_coord) return TREXIO_INVALID_ARG_3; if (rank != nucleus->rank_coord) return TREXIO_INVALID_ARG_3;
uint64_t dim_size = 1;
for (uint i=0; i<rank; i++){ for (uint i=0; i<rank; i++){
if (dims[i] != nucleus->dims_coord[i]) return TREXIO_INVALID_ARG_4; if (dims[i] != nucleus->dims_coord[i]) return TREXIO_INVALID_ARG_4;
dim_size *= dims[i];
} }
//if (dim_coord != nucleus->dim_coord) return TREXIO_INVALID_ARG_3;
uint64_t dim_size = dims[0]*dims[1];
for (uint64_t i=0 ; i<dim_size ; i++) { for (uint64_t i=0 ; i<dim_size ; i++) {
coord[i] = nucleus->coord[i]; coord[i] = nucleus->coord[i];
@ -361,14 +390,14 @@ trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const dou
} }
nucleus->rank_coord = rank; nucleus->rank_coord = rank;
nucleus->dims_coord = (uint64_t*) calloc(rank, sizeof(uint64_t)); 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 (uint i=0; i<nucleus->rank_coord; i++){
nucleus->dims_coord[i] = dims[i]; nucleus->dims_coord[i] = dims[i];
dim_size *= dims[i];
} }
uint64_t dim_size = dims[0]*dims[1];
nucleus->coord = (double*) calloc(dim_size, sizeof(double)); nucleus->coord = (double*) calloc(dim_size, sizeof(double));
for (uint64_t i=0 ; i<dim_size ; i++) { for (uint64_t i=0 ; i<dim_size ; i++) {
@ -379,7 +408,7 @@ trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const dou
return TREXIO_SUCCESS; return TREXIO_SUCCESS;
} }
trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* charge, const uint64_t dim_charge) { trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* charge, const uint32_t rank, const uint64_t* dims) {
if (file == NULL) return TREXIO_INVALID_ARG_1; if (file == NULL) return TREXIO_INVALID_ARG_1;
if (charge == NULL) return TREXIO_INVALID_ARG_2; if (charge == NULL) return TREXIO_INVALID_ARG_2;
@ -387,9 +416,15 @@ trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* c
nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*) file); nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*) file);
if (nucleus == NULL) return TREXIO_FAILURE; if (nucleus == NULL) return TREXIO_FAILURE;
if (dim_charge != nucleus->dim_charge) return TREXIO_INVALID_ARG_3; if (rank != nucleus->rank_charge) return TREXIO_INVALID_ARG_3;
for (uint64_t i=0 ; i<dim_charge ; i++) { uint64_t dim_size = 1;
for (uint i=0; i<rank; i++){
if (dims[i] != nucleus->dims_charge[i]) return TREXIO_INVALID_ARG_4;
dim_size *= dims[i];
}
for (uint64_t i=0 ; i<dim_size ; i++) {
charge[i] = nucleus->charge[i]; charge[i] = nucleus->charge[i];
} }
@ -397,7 +432,7 @@ trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* c
} }
trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* charge, const uint64_t dim_charge) { trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* charge, const uint32_t rank, const uint64_t* dims) {
if (file == NULL) return TREXIO_INVALID_ARG_1; if (file == NULL) return TREXIO_INVALID_ARG_1;
if (charge == NULL) return TREXIO_INVALID_ARG_2; if (charge == NULL) return TREXIO_INVALID_ARG_2;
@ -411,10 +446,24 @@ trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const do
nucleus->charge = NULL; nucleus->charge = NULL;
} }
nucleus->dim_charge = dim_charge; if (nucleus->dims_charge != NULL) {
nucleus->charge = (double*) calloc(dim_charge, sizeof(double)); free(nucleus->dims_charge);
nucleus->dims_charge = NULL;
}
for (uint64_t i=0 ; i<dim_charge ; i++) { 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++){
nucleus->dims_charge[i] = dims[i];
dim_size *= dims[i];
}
nucleus->charge = (double*) calloc(dim_size, sizeof(double));
for (uint64_t i=0 ; i<dim_size ; i++) {
nucleus->charge[i] = charge[i]; nucleus->charge[i] = charge[i];
} }

7
src/trexio_text.h
View File

@ -25,8 +25,9 @@ typedef struct nucleus_s {
double* coord; double* coord;
double* charge; double* charge;
uint64_t num; uint64_t num;
uint64_t dim_charge; uint64_t* dims_charge;
uint64_t* dims_coord; uint64_t* dims_coord;
uint32_t rank_charge;
uint32_t rank_coord; uint32_t rank_coord;
int to_flush; int to_flush;
} nucleus_t; } nucleus_t;
@ -75,8 +76,8 @@ trexio_exit_code trexio_text_write_nucleus_num(const trexio_t* file, const uint6
trexio_exit_code trexio_text_read_nucleus_coord(const trexio_t* file, double* coord, const uint32_t rank, const uint64_t* dims); trexio_exit_code trexio_text_read_nucleus_coord(const trexio_t* file, double* coord, const uint32_t rank, const uint64_t* dims);
trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const double* coord, const uint32_t rank, const uint64_t* dims); trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const double* coord, const uint32_t rank, const uint64_t* dims);
trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* charge, const uint64_t dim_charge); trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* charge, const uint32_t rank, const uint64_t* dims);
trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* charge, const uint64_t dim_charge); trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* charge, const uint32_t rank, const uint64_t* dims);
rdm_t* trexio_text_read_rdm(trexio_text_t* file); rdm_t* trexio_text_read_rdm(trexio_text_t* file);

106
src/trexio_text.org
View File

@ -58,8 +58,9 @@ typedef struct nucleus_s {
double* coord; double* coord;
double* charge; double* charge;
uint64_t num; uint64_t num;
uint64_t dim_charge; uint64_t* dims_charge;
uint64_t* dims_coord; uint64_t* dims_coord;
uint32_t rank_charge;
uint32_t rank_coord; uint32_t rank_coord;
int to_flush; int to_flush;
} nucleus_t; } nucleus_t;
@ -241,6 +242,7 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
nucleus->coord = NULL; nucleus->coord = NULL;
nucleus->dims_coord = NULL; nucleus->dims_coord = NULL;
nucleus->charge = NULL; nucleus->charge = NULL;
nucleus->dims_charge = NULL;
nucleus->to_flush = 0; nucleus->to_flush = 0;
/* Try to open the file. If the file does not exist, return */ /* Try to open the file. If the file does not exist, return */
@ -266,10 +268,26 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
int rc; int rc;
rc = fscanf(f, "%s", buffer); rc = fscanf(f, "%s", buffer);
assert (rc == 1); assert (rc == 1);
assert (strcmp(buffer, "dim_charge") == 0); assert (strcmp(buffer, "rank_charge") == 0);
rc = fscanf(f, "%lu", &(nucleus->dim_charge)); rc = fscanf(f, "%u", &(nucleus->rank_charge));
assert (rc == 1); assert (rc == 1);
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++){
rc = fscanf(f, "%s", buffer);
assert (rc == 1);
//assert (strcmp(buffer, "dims_charge") == 0);
rc = fscanf(f, "%lu", &(nucleus->dims_charge[i]));
assert (rc == 1);
size_charge *= nucleus->dims_charge[i];
}
rc = fscanf(f, "%s", buffer); rc = fscanf(f, "%s", buffer);
assert (rc == 1); assert (rc == 1);
@ -281,7 +299,7 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
nucleus->dims_coord = (uint64_t*) calloc(nucleus->rank_coord, sizeof(uint64_t)); nucleus->dims_coord = (uint64_t*) calloc(nucleus->rank_coord, sizeof(uint64_t));
assert (nucleus->dims_coord != NULL); assert (nucleus->dims_coord != NULL);
uint64_t dim_coord = 1; uint64_t size_coord = 1;
for (uint i=0; i<nucleus->rank_coord; i++){ for (uint i=0; i<nucleus->rank_coord; i++){
rc = fscanf(f, "%s", buffer); rc = fscanf(f, "%s", buffer);
@ -291,14 +309,14 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
rc = fscanf(f, "%lu", &(nucleus->dims_coord[i])); rc = fscanf(f, "%lu", &(nucleus->dims_coord[i]));
assert (rc == 1); assert (rc == 1);
dim_coord *= nucleus->dims_coord[i]; size_coord *= nucleus->dims_coord[i];
} }
/* Allocate arrays */ /* Allocate arrays */
nucleus->charge = (double*) calloc(nucleus->dim_charge, sizeof(double)); nucleus->charge = (double*) calloc(size_charge, sizeof(double));
assert (nucleus->charge != NULL); assert (nucleus->charge != NULL);
nucleus->coord = (double*) calloc(dim_coord, sizeof(double)); nucleus->coord = (double*) calloc(size_coord, sizeof(double));
assert (nucleus->coord != NULL); assert (nucleus->coord != NULL);
/* Read data */ /* Read data */
@ -313,7 +331,7 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
assert (rc == 1); assert (rc == 1);
assert (strcmp(buffer, "charge") == 0); assert (strcmp(buffer, "charge") == 0);
for (uint64_t i=0 ; i<nucleus->dim_charge ; i++) { for (uint64_t i=0 ; i<size_charge ; i++) {
rc = fscanf(f, "%lf", &(nucleus->charge[i])); rc = fscanf(f, "%lf", &(nucleus->charge[i]));
assert (rc == 1); assert (rc == 1);
} }
@ -322,7 +340,7 @@ nucleus_t* trexio_text_read_nucleus(trexio_text_t* file) {
assert (rc == 1); assert (rc == 1);
assert (strcmp(buffer, "coord") == 0); assert (strcmp(buffer, "coord") == 0);
for (uint64_t i=0 ; i<dim_coord ; i++) { for (uint64_t i=0 ; i<size_coord ; i++) {
rc = fscanf(f, "%lf", &(nucleus->coord[i])); rc = fscanf(f, "%lf", &(nucleus->coord[i]));
assert (rc == 1); assert (rc == 1);
} }
@ -364,24 +382,31 @@ trexio_exit_code trexio_text_flush_nucleus(const trexio_text_t* file) {
rewind(f); rewind(f);
/* Write the dimensioning variables */ /* Write the dimensioning variables */
fprintf(f, "dim_charge %ld\n", nucleus->dim_charge ); 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]);
size_charge *= nucleus->dims_charge[i];
}
fprintf(f, "rank_coord %d\n", nucleus->rank_coord); fprintf(f, "rank_coord %d\n", nucleus->rank_coord);
uint64_t dim_coord = (nucleus->dims_coord[0])*(nucleus->dims_coord[1]); uint64_t size_coord = 1;
for (uint i=0; i<nucleus->rank_coord; i++){ for (uint i=0; i<nucleus->rank_coord; i++){
fprintf(f, "dims_coord[%d] %ld\n", i, nucleus->dims_coord[i]); fprintf(f, "dims_coord[%d] %ld\n", i, nucleus->dims_coord[i]);
//dim_coord *= nucleus->dims_coord[i]; size_coord *= nucleus->dims_coord[i];
} }
/* Write arrays */ /* Write arrays */
fprintf(f, "num %ld\n", nucleus->num); fprintf(f, "num %ld\n", nucleus->num);
fprintf(f, "charge\n"); fprintf(f, "charge\n");
for (uint64_t i=0 ; i<nucleus->dim_charge ; i++) { for (uint64_t i=0 ; i<size_charge ; i++) {
fprintf(f, "%lf\n", nucleus->charge[i]); fprintf(f, "%lf\n", nucleus->charge[i]);
} }
fprintf(f, "coord\n"); fprintf(f, "coord\n");
for (uint64_t i=0 ; i<dim_coord ; i++) { for (uint64_t i=0 ; i<size_coord ; i++) {
fprintf(f, "%lf\n", nucleus->coord[i]); fprintf(f, "%lf\n", nucleus->coord[i]);
} }
fflush(f); fflush(f);
@ -426,7 +451,12 @@ trexio_exit_code trexio_text_free_nucleus(trexio_text_t* file) {
free (nucleus->coord); free (nucleus->coord);
nucleus->coord = NULL; nucleus->coord = NULL;
} }
if (nucleus->dims_charge != NULL) {
free (nucleus->dims_charge);
nucleus->dims_charge = NULL;
}
if (nucleus->charge != NULL) { if (nucleus->charge != NULL) {
free (nucleus->charge); free (nucleus->charge);
nucleus->charge = NULL; nucleus->charge = NULL;
@ -496,11 +526,11 @@ trexio_exit_code trexio_text_read_nucleus_coord(const trexio_t* file, double* co
if (rank != nucleus->rank_coord) return TREXIO_INVALID_ARG_3; if (rank != nucleus->rank_coord) return TREXIO_INVALID_ARG_3;
uint64_t dim_size = 1;
for (uint i=0; i<rank; i++){ for (uint i=0; i<rank; i++){
if (dims[i] != nucleus->dims_coord[i]) return TREXIO_INVALID_ARG_4; if (dims[i] != nucleus->dims_coord[i]) return TREXIO_INVALID_ARG_4;
dim_size *= dims[i];
} }
//if (dim_coord != nucleus->dim_coord) return TREXIO_INVALID_ARG_3;
uint64_t dim_size = dims[0]*dims[1];
for (uint64_t i=0 ; i<dim_size ; i++) { for (uint64_t i=0 ; i<dim_size ; i++) {
coord[i] = nucleus->coord[i]; coord[i] = nucleus->coord[i];
@ -530,14 +560,14 @@ trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const dou
} }
nucleus->rank_coord = rank; nucleus->rank_coord = rank;
nucleus->dims_coord = (uint64_t*) calloc(rank, sizeof(uint64_t)); 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 (uint i=0; i<nucleus->rank_coord; i++){
nucleus->dims_coord[i] = dims[i]; nucleus->dims_coord[i] = dims[i];
dim_size *= dims[i];
} }
uint64_t dim_size = dims[0]*dims[1];
nucleus->coord = (double*) calloc(dim_size, sizeof(double)); nucleus->coord = (double*) calloc(dim_size, sizeof(double));
for (uint64_t i=0 ; i<dim_size ; i++) { for (uint64_t i=0 ; i<dim_size ; i++) {
@ -553,12 +583,12 @@ trexio_exit_code trexio_text_write_nucleus_coord(const trexio_t* file, const dou
The ~charge~ array is assumed allocated with the appropriate size. The ~charge~ array is assumed allocated with the appropriate size.
#+begin_src c :tangle trexio_text.h #+begin_src c :tangle trexio_text.h
trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* charge, const uint64_t dim_charge); trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* charge, const uint32_t rank, const uint64_t* dims);
trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* charge, const uint64_t dim_charge); trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* charge, const uint32_t rank, const uint64_t* dims);
#+end_src #+end_src
#+begin_src c :tangle trexio_text.c #+begin_src c :tangle trexio_text.c
trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* charge, const uint64_t dim_charge) { trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* charge, const uint32_t rank, const uint64_t* dims) {
if (file == NULL) return TREXIO_INVALID_ARG_1; if (file == NULL) return TREXIO_INVALID_ARG_1;
if (charge == NULL) return TREXIO_INVALID_ARG_2; if (charge == NULL) return TREXIO_INVALID_ARG_2;
@ -566,9 +596,15 @@ trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* c
nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*) file); nucleus_t* nucleus = trexio_text_read_nucleus((trexio_text_t*) file);
if (nucleus == NULL) return TREXIO_FAILURE; if (nucleus == NULL) return TREXIO_FAILURE;
if (dim_charge != nucleus->dim_charge) return TREXIO_INVALID_ARG_3; if (rank != nucleus->rank_charge) return TREXIO_INVALID_ARG_3;
for (uint64_t i=0 ; i<dim_charge ; i++) { uint64_t dim_size = 1;
for (uint i=0; i<rank; i++){
if (dims[i] != nucleus->dims_charge[i]) return TREXIO_INVALID_ARG_4;
dim_size *= dims[i];
}
for (uint64_t i=0 ; i<dim_size ; i++) {
charge[i] = nucleus->charge[i]; charge[i] = nucleus->charge[i];
} }
@ -576,7 +612,7 @@ trexio_exit_code trexio_text_read_nucleus_charge(const trexio_t* file, double* c
} }
trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* charge, const uint64_t dim_charge) { trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const double* charge, const uint32_t rank, const uint64_t* dims) {
if (file == NULL) return TREXIO_INVALID_ARG_1; if (file == NULL) return TREXIO_INVALID_ARG_1;
if (charge == NULL) return TREXIO_INVALID_ARG_2; if (charge == NULL) return TREXIO_INVALID_ARG_2;
@ -590,10 +626,24 @@ trexio_exit_code trexio_text_write_nucleus_charge(const trexio_t* file, const do
nucleus->charge = NULL; nucleus->charge = NULL;
} }
nucleus->dim_charge = dim_charge; if (nucleus->dims_charge != NULL) {
nucleus->charge = (double*) calloc(dim_charge, sizeof(double)); free(nucleus->dims_charge);
nucleus->dims_charge = NULL;
}
for (uint64_t i=0 ; i<dim_charge ; i++) { 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++){
nucleus->dims_charge[i] = dims[i];
dim_size *= dims[i];
}
nucleus->charge = (double*) calloc(dim_size, sizeof(double));
for (uint64_t i=0 ; i<dim_size ; i++) {
nucleus->charge[i] = charge[i]; nucleus->charge[i] = charge[i];
} }