Hash*
Hash_deserialize(Hash *self, InStream *instream) {
uint32_t size = InStream_Read_C32(instream);
uint32_t num_charbufs = InStream_Read_C32(instream);
uint32_t num_other = size - num_charbufs;
CharBuf *key = num_charbufs ? CB_new(0) : NULL;
Hash_init(self, size);
// Read key-value pairs with CharBuf keys.
while (num_charbufs--) {
uint32_t len = InStream_Read_C32(instream);
char *key_buf = CB_Grow(key, len);
InStream_Read_Bytes(instream, key_buf, len);
key_buf[len] = '\0';
CB_Set_Size(key, len);
Hash_Store(self, (Obj*)key, THAW(instream));
}
DECREF(key);
// Read remaining key/value pairs.
while (num_other--) {
Obj *k = THAW(instream);
Hash_Store(self, k, THAW(instream));
DECREF(k);
}
return self;
}
void Hash_copy(struct Hash *dst, struct Hash *src)
{
Hash_delete(dst);
Hash_init(dst, src->elemsSize);
dst->elemsSize = src->elemsSize;
dst->numElems = src->numElems;
memcpy(dst->elems, src->elems, src->numElems * sizeof(struct HashElem));
}
Hash*
Freezer_deserialize_hash(Hash *hash, InStream *instream) {
uint32_t size = InStream_Read_C32(instream);
Hash_init(hash, size);
while (size--) {
uint32_t len = InStream_Read_C32(instream);
char *key_buf = (char*)MALLOCATE(len + 1);
InStream_Read_Bytes(instream, key_buf, len);
key_buf[len] = '\0';
String *key = Str_new_steal_utf8(key_buf, len);
Hash_Store(hash, key, THAW(instream));
DECREF(key);
}
return hash;
}
void *thread_synchronizer(void *attr){
int ret;
/* Инициализируем кэш */
ret = Cache_init(DEFAULT_CACHE_PATH"server_cache.sqlite3", &server_pool.cache);
if(ret == LC_CODE_BADF_ERR)
syslog(LOG_ERR, "Sync: произошла ошибка создания / открытия файла.");
if(ret == LC_CODE_TABLE_ERR)
syslog(LOG_ERR, "Sync: невозможно создать стандартную таблицу");
/* Инициализируем хэш */
Hash_init(&server_pool.hash, -1);
ret = sync_cache_and_db(&server_pool.cache);
if(ret != 0){
syslog(LOG_ERR, "Sync with db failed.");
}
ret = sync_cache_and_hash(&server_pool.cache, &server_pool.hash);
/* TODO Wait conditions cycle here... */
pthread_exit(NULL);
}
Hash*
Hash_new(uint32_t capacity) {
Hash *self = (Hash*)VTable_Make_Obj(HASH);
return Hash_init(self, capacity);
}
NoCloneHash*
NoCloneHash_init(NoCloneHash *self, uint32_t capacity) {
return (NoCloneHash*)Hash_init((Hash*)self, capacity);
}
int main(int argc, char *argv[])
{
const char *desc[] = { "Do statistics on pair distance",
"from an existing molecular dynamics trajectory." };
gmx_bool bGREC = FALSE;
gmx_bool bTraj = FALSE;
int i, j;
rvec *x = NULL, *x_ref = NULL;
matrix box;
char buf[256];
t_topology top;
output_env_t oenv;
int ePBC;
t_trxstatus *status;
int natoms_trx;
real t;
t_filenm fnm[] =
{
{ efTPS, NULL, NULL, ffREAD },
{ efLOG, "-n", NULL, ffREAD },
{ efTRX, "-f", NULL, ffOPTRD },
{ efLOG, "-o", NULL, ffWRITE },
};
t_pargs pa[] =
{
{ "-grec", FALSE, etBOOL, {&bGREC},
"Using GREC"}
};
#define NFILE asize(fnm)
#define NPA asize(pa)
CopyRight(stderr, argv[0]);
parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW
| PCA_BE_NICE, NFILE, fnm, NPA, pa, asize(desc),
desc, 0, NULL, &oenv);
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), buf, &top, &ePBC, &x_ref,
NULL, box, TRUE);
bTraj = opt2bSet("-f", NFILE, fnm);
/* obtain GREC_FA */
int *GREC_ind;
if (bGREC)
{
FILE *fgrec;
fgrec = fopen("GREC", "r");
int grec_size;
fscanf(fgrec, "%d", &grec_size);
snew(GREC_ind, grec_size);
for(i=0; i<grec_size; i++)
fscanf(fgrec, "%d", GREC_ind + i);
fclose(fgrec);
}
#define myIndex(i) (bGREC ? GREC_ind[i] : i)
/* read index file */
FILE *findex;
findex = fopen(opt2fn("-n", NFILE, fnm), "r");
int ind1, ind2;
hashTable *h = Hash_init(113);
while (fscanf(findex, "%d", &ind1) != EOF)
{
fscanf(findex, "%d", &ind2);
Hash_insertKey(h, "dd", ind1, ind2);
}
fclose(findex);
int size;
void ***vectorKeyList;
Hash_getSize(h, &size);
snew(vectorKeyList, size);
Hash_dump(h, NULL, NULL, NULL, NULL, vectorKeyList);
printf("size=%d\n", size);
/* set reference value from the topology file */
double diff;
for(i=0; i< size; i++)
{
ind1 = *(int *)(vectorKeyList[i][0]);
ind2 = *(int *)(vectorKeyList[i][1]);
/* indicating coordinate data is missing in the topology file */
if(fabs(x_ref[myIndex(ind1)][0]) < 5e-6 &&
fabs(x_ref[myIndex(ind1)][1]) < 5e-6 &&
fabs(x_ref[myIndex(ind1)][2]) < 5e-6 )
continue;
if(fabs(x_ref[myIndex(ind2)][0]) < 5e-6 &&
fabs(x_ref[myIndex(ind2)][1]) < 5e-6 &&
fabs(x_ref[myIndex(ind2)][2]) < 5e-6 )
continue;
diff = 0;
diff += (x_ref[myIndex(ind1)][0] - x_ref[myIndex(ind2)][0]) *
(x_ref[myIndex(ind1)][0] - x_ref[myIndex(ind2)][0]);
diff += (x_ref[myIndex(ind1)][1] - x_ref[myIndex(ind2)][1]) *
(x_ref[myIndex(ind1)][1] - x_ref[myIndex(ind2)][1]);
diff += (x_ref[myIndex(ind1)][2] - x_ref[myIndex(ind2)][2]) *
(x_ref[myIndex(ind1)][2] - x_ref[myIndex(ind2)][2]);
diff = sqrt(diff);
Hash_setReferenceValue(h, diff, "dd", ind1, ind2);
}
if(bTraj)
{
/* read first frame */
natoms_trx = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t,
&x, box);
if (natoms_trx != top.atoms.nr)
fprintf(stderr,
"\nWARNING: topology has %d atoms, whereas trajectory has %d\n",
top.atoms.nr, natoms_trx);
/* start looping over frames: */
do
{
for(i=0; i< size; i++)
{
ind1 = *(int *)(vectorKeyList[i][0]);
ind2 = *(int *)(vectorKeyList[i][1]);
diff = 0;
diff += (x[myIndex(ind1)][0] - x[myIndex(ind2)][0]) *
(x[myIndex(ind1)][0] - x[myIndex(ind2)][0]);
diff += (x[myIndex(ind1)][1] - x[myIndex(ind2)][1]) *
(x[myIndex(ind1)][1] - x[myIndex(ind2)][1]);
diff += (x[myIndex(ind1)][2] - x[myIndex(ind2)][2]) *
(x[myIndex(ind1)][2] - x[myIndex(ind2)][2]);
diff = sqrt(diff);
Hash_addData(h, diff, "dd", ind1, ind2);
}
}
while (read_next_x(oenv, status, &t, natoms_trx, x, box));
close_trj(status);
}
/* output the statistics */
FILE *fopt;
fopt = fopen(opt2fn("-o", NFILE, fnm), "w");
double **a;
snew(a, size);
for(i=0; i<size; i++)
snew(a[i], 3);
Hash_dump(h, a, NULL, NULL, NULL, NULL);
for(i=0; i<size; i++)
{
ind1 = *(int *)(vectorKeyList[i][0]);
ind2 = *(int *)(vectorKeyList[i][1]);
/* using standard deviation */
fprintf(fopt, "%4d %4d %13.6f %13.6f %13.6f\n",
ind1, ind2, a[i][0], sqrt(a[i][1]), a[i][2]);
}
fclose(fopt);
Hash_del(h);
sfree(x_ref);
sfree(x);
sfree(GREC_ind);
sfree(vectorKeyList);
for(i=0; i<size; i++)
sfree(a[i]);
sfree(a);
}
