int Traj_GmxTrX::ReadTrxHeader() {
int version = 0;
// Read past magic byte
if (file_.Read(&version, 4) != 4) return 1;
// Read version for TRR
if (format_ != TRJ)
read_int( version );
//mprintf("DEBUG: TRX Version= %i\n", version);
// Read in title string
SetTitle( read_string() );
// Read in size data
if ( read_int( ir_size_ ) ) return 1;
if ( read_int( e_size_ ) ) return 1;
if ( read_int( box_size_ ) ) return 1;
if ( read_int( vir_size_ ) ) return 1;
if ( read_int( pres_size_ ) ) return 1;
if ( read_int( top_size_ ) ) return 1;
if ( read_int( sym_size_ ) ) return 1;
if ( read_int( x_size_ ) ) return 1;
if ( read_int( v_size_ ) ) return 1;
if ( read_int( f_size_ ) ) return 1;
if ( read_int( natoms_ ) ) return 1;
if (natoms_ < 1) {
mprinterr("Error: No atoms detected in TRX trajectory.\n");
return 1;
}
natom3_ = natoms_ * 3;
if ( read_int( step_ ) ) return 1;
if ( read_int( nre_ ) ) return 1;
// Determine precision
if (x_size_ > 0)
precision_ = x_size_ / natom3_;
else if (v_size_ > 0)
precision_ = v_size_ / natom3_;
else if (f_size_ > 0)
precision_ = f_size_ / natom3_;
else {
mprinterr("Error: X/V/F sizes are 0 in TRX trajectory.\n");
return 1;
}
if ( precision_ != sizeof(float) &&
precision_ != sizeof(double) )
{
mprinterr("Error: TRX precision %i not recognized.\n", precision_);
return 1;
}
// Read timestep and lambda
if ( read_real( dt_ ) ) return 1;
if ( read_real( lambda_ ) ) return 1;
return 0;
}
Chunk *read_chunk(FILE *fp) {
Chunk *chunk = malloc(sizeof *chunk);
if (!chunk) {
fatal("Out of memory.");
}
chunk->numtemps = read_int(fp);
chunk->numconstants = read_int(fp);
chunk->numinstructions = read_int(fp);
chunk->numchildren = read_int(fp);
chunk->numlocals = read_int(fp);
chunk->numupvars = read_int(fp);
chunk->numparams = read_int(fp);
Constant **constants = malloc(chunk->numconstants * sizeof **constants);
int *instructions = malloc(chunk->numinstructions * sizeof *instructions);
Chunk **children = malloc(chunk->numchildren * sizeof **children);
if (!constants || !instructions || !children) {
fatal("Out of memory.");
}
chunk->constants = constants;
chunk->instructions = instructions;
chunk->children = children;
int i;
for (i = 0; i < chunk->numinstructions; i++) {
chunk->instructions[i] = read_int(fp);
}
for (i = 0; i < chunk->numconstants; i++) {
int type = read_int(fp);
Constant *c = malloc(sizeof *c);
if (!c) {
fatal("Out of memory.");
}
c->type = type;
switch (type) {
case CONST_INT:
case CONST_BOOL:
c->value.i = read_int(fp);
break;
case CONST_REAL:
c->value.d = read_real(fp);
break;
case CONST_NULL:
break;
case CONST_STRING:
{
c->value.s = read_string(fp);
} break;
}
chunk->constants[i] = c;
}
for (i = 0; i < chunk->numchildren; i++) {
chunk->children[i] = read_chunk(fp);
}
return chunk;
}
void input_schema(Pschema s, char *attr_name, int spaces, int pretty, FILE *in_file){ // reads a schema and puts it on the top op tstack
if(attr_name!=NULL && pretty){
print_spaces(spaces, stdout);
fprintf(stdout, "Input record attribute \"%s\"\n",attr_name);
}
if(pretty){
print_spaces(spaces, stdout);
}
if(s->type == TY_RECORD || s->type == TY_ARRAY || s->type == TY_ATTR){
int size = get_schema_size(s);
int nfields = 0;
switch(s->type){
case TY_RECORD:{
if(pretty){
fprintf(stdout,"Input for a record\n");
}
Pschema temp = s->child;
while(temp){
input_schema(temp->child, temp->id, spaces+1, pretty, in_file);
nfields++;
temp = temp->brother;
}
break;
}
case TY_ARRAY:{
int i;
if(pretty){
fprintf(stdout, "Input for an array\n");
}
nfields = s->size;
for(i=0; i<nfields; i++){
input_schema(s->child, NULL, spaces+1, pretty, in_file);
}
break;
}
default: print_schema(s,0); machine_error("TY_ATTR cannot be used in input_schema()."); break;
}
exec_cat(nfields,size);
} else{
switch(s->type){
case TY_INT: {
int in = read_int(stdout, in_file, "Insert an integer: ", pretty);
push_int(in);
break;
}
case TY_CHAR: {
char in = read_char(stdout, in_file, "Insert a char: ", pretty);
push_char(in);
break;
}
case TY_REAL: {
float in = read_real(stdout, in_file, "Insert a number of type real: ", pretty);
push_real(in);
break;
}
case TY_STRING: {
char *in = read_string(stdout, in_file, "Insert a string: ", pretty);
char *strig_to_store = stringtable_store(in, stringtable);
freemem(in, strlen(in) + 1);
push_string(strig_to_store);
break;
}
case TY_BOOL: {
char in = read_char(stdout, in_file, "Insert a boolean (0 or 1): ", pretty);
push_bool(in == '1');
break;
}
default: {machine_error("Unknown type of schema in input_schema()."); break;}
}
}
}
void
read_basis (const char *filename, wfa_t *wfa)
/*
* Read WFA initial basis 'filename' and fill 'wfa' struct.
*
* No return value.
*
* Side effects:
* wfa->into, wfa->weights, wfa->final_distribution, wfa->basis_states
* wfa->domain_type wfa->wfainfo->basis_name, are filled with the
* values of the WFA basis.
*/
{
FILE *input; /* ASCII WFA initial basis file */
assert (filename && wfa);
if (!wfa->wfainfo->basis_name ||
!streq (wfa->wfainfo->basis_name, filename))
{
if (wfa->wfainfo->basis_name)
Free (wfa->wfainfo->basis_name);
wfa->wfainfo->basis_name = strdup (filename);
}
if (get_linked_basis (filename, wfa))
return; /* basis is linked with excecutable */
/*
* Check whether 'wfa_name' is a regular ASCII WFA initial basis file
*/
{
char magic [MAXSTRLEN]; /* WFA magic number */
if (!(input = open_file (filename, "FIASCO_DATA", READ_ACCESS)))
file_error(filename);
if (fscanf (input, MAXSTRLEN_SCANF, magic) != 1)
error ("Format error: ASCII FIASCO initial basis file %s", filename);
else if (strneq (FIASCO_BASIS_MAGIC, magic))
error ("Input file %s is not an ASCII FIASCO initial basis!",
filename);
}
/*
* WFA ASCII format:
*
* Note: State 0 is assumed to be the constant function f(x, y) = 128.
* Don't define any transitions of state 0 in an initial basis.
*
* Header:
* type |description
* ----------------+-----------
* string |MAGIC Number "Wfa"
* int |Number of basis states 'N'
* bool_t-array[N] |use vector in linear combinations,
* |0: don't use vector (auxilliary state)
* |1: use vector in linear combinations
* float-array[N] |final distribution of every state
*
* Transitions:
*
* <state 1> current state
* <label> <into> <weight> transition 1 of current state
* <label> <into> <weight> transition 2 of current state
* ...
* <-1> last transition marker
* <state 2>
* ...
* <-1> last transition marker
* <state N>
* ...
*
* <-1> last transition marker
* <-1> last state marker
*/
{
unsigned state;
if (fscanf (input ,"%u", &wfa->basis_states) != 1)
error ("Format error: ASCII FIASCO initial basis file %s", filename);
/*
* State 0 is assumed to be the constant function f(x, y) = 128.
*/
wfa->domain_type [0] = USE_DOMAIN_MASK;
wfa->final_distribution [0] = 128;
wfa->states = wfa->basis_states;
wfa->basis_states++;
append_edge (0, 0, 1.0, 0, wfa);
append_edge (0, 0, 1.0, 1, wfa);
for (state = 1; state < wfa->basis_states; state++)
wfa->domain_type [state]
= read_int (input) ? USE_DOMAIN_MASK : AUXILIARY_MASK;
for (state = 1; state < wfa->basis_states; state++)
wfa->final_distribution[state] = read_real (input);
/*
* Read transitions
*/
for (state = 1; state < wfa->basis_states; state++)
{
unsigned domain;
int label;
real_t weight;
if (read_int (input) != (int) state)
error ("Format error: ASCII FIASCO initial basis file %s",
filename);
while((label = read_int (input)) != -1)
{
domain = read_int (input);
weight = read_real (input);
append_edge (state, domain, weight, label, wfa);
}
}
}
fclose (input);
}