69 |
|
} |
70 |
|
|
71 |
|
|
72 |
< |
void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){ |
72 |
> |
void InitializeFromFile :: readInit( SimInfo* the_simnfo ){ |
73 |
|
|
74 |
|
int i, j, done, which_node, which_atom; // loop counter |
75 |
|
|
83 |
|
char *eof_test; // ptr to see when we reach the end of the file |
84 |
|
char *parseErr; |
85 |
|
int procIndex; |
86 |
+ |
double currTime; |
87 |
+ |
double boxMat[9]; |
88 |
+ |
double theBoxMat3[3][3]; |
89 |
|
|
90 |
< |
entry_plug = the_entry_plug; |
90 |
> |
simnfo = the_simnfo; |
91 |
|
|
92 |
|
|
93 |
|
#ifndef IS_MPI |
102 |
|
|
103 |
|
n_atoms = atoi( read_buffer ); |
104 |
|
|
105 |
< |
Atom **atoms = entry_plug->atoms; |
105 |
> |
Atom **atoms = simnfo->atoms; |
106 |
|
DirectionalAtom* dAtom; |
107 |
|
|
108 |
< |
if( n_atoms != entry_plug->n_atoms ){ |
108 |
> |
if( n_atoms != simnfo->n_atoms ){ |
109 |
|
sprintf( painCave.errMsg, |
110 |
|
"Initialize from File error. %s n_atoms, %d, " |
111 |
|
"does not match the BASS file's n_atoms, %d.\n", |
112 |
< |
c_in_name, n_atoms, entry_plug->n_atoms ); |
112 |
> |
c_in_name, n_atoms, simnfo->n_atoms ); |
113 |
|
painCave.isFatal = 1; |
114 |
|
simError(); |
115 |
|
} |
116 |
|
|
117 |
< |
//read and toss the comment line |
117 |
> |
//read the box mat from the comment line |
118 |
|
|
119 |
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
120 |
|
if(eof_test == NULL){ |
124 |
|
simError(); |
125 |
|
} |
126 |
|
|
127 |
+ |
parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
128 |
+ |
if( parseErr != NULL ){ |
129 |
+ |
strcpy( painCave.errMsg, parseErr ); |
130 |
+ |
painCave.isFatal = 1; |
131 |
+ |
simError(); |
132 |
+ |
} |
133 |
+ |
|
134 |
+ |
for(i=0;i<3;i++) |
135 |
+ |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
136 |
+ |
|
137 |
+ |
simnfo->setBoxM( theBoxMat3 ); |
138 |
+ |
simnfo->setTime( currTime ); |
139 |
+ |
|
140 |
+ |
|
141 |
|
for( i=0; i < n_atoms; i++){ |
142 |
|
|
143 |
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
157 |
|
strcpy( painCave.errMsg, parseErr ); |
158 |
|
painCave.isFatal = 1; |
159 |
|
simError(); |
160 |
< |
} |
160 |
> |
} |
161 |
|
} |
162 |
|
|
163 |
|
|
187 |
|
|
188 |
|
n_atoms = atoi( read_buffer ); |
189 |
|
|
190 |
< |
Atom **atoms = entry_plug->atoms; |
190 |
> |
Atom **atoms = simnfo->atoms; |
191 |
|
DirectionalAtom* dAtom; |
192 |
|
|
193 |
|
// Check to see that the number of atoms in the intial configuration file is the |
197 |
|
sprintf( painCave.errMsg, |
198 |
|
"Initialize from File error. %s n_atoms, %d, " |
199 |
|
"does not match the BASS file's n_atoms, %d.\n", |
200 |
< |
c_in_name, n_atoms, entry_plug->n_atoms ); |
200 |
> |
c_in_name, n_atoms, simnfo->n_atoms ); |
201 |
|
haveError= 1; |
202 |
|
simError(); |
203 |
|
} |
204 |
|
|
205 |
< |
//read and toss the comment line |
205 |
> |
//read the boxMat from the comment line |
206 |
|
|
207 |
|
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
208 |
|
if(eof_test == NULL){ |
209 |
|
sprintf( painCave.errMsg, |
210 |
|
"error in reading commment in %s\n", c_in_name); |
211 |
< |
haveError= 1; |
211 |
> |
haveError = 1; |
212 |
> |
simError(); |
213 |
> |
} |
214 |
> |
|
215 |
> |
parseErr = parseBoxLine( read_buffer, boxMat, currTime ); |
216 |
> |
if( parseErr != NULL ){ |
217 |
> |
strcpy( painCave.errMsg, parseErr ); |
218 |
> |
haveError = 1; |
219 |
|
simError(); |
220 |
|
} |
221 |
+ |
|
222 |
+ |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
223 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD ); |
224 |
|
|
225 |
|
if(haveError) nodeZeroError(); |
226 |
|
|
274 |
|
|
275 |
|
} else { |
276 |
|
|
277 |
+ |
MPI_Bcast(boxMat, 9, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
278 |
+ |
MPI_Bcast(&currTime, 1, MPI_DOUBLE, 0, MPI_COMM_WORLD); |
279 |
+ |
|
280 |
|
done = 0; |
281 |
|
while (!done) { |
282 |
|
|
308 |
|
|
309 |
|
// last thing last, enable fatalities. |
310 |
|
painCave.isEventLoop = 0; |
311 |
+ |
|
312 |
+ |
for(i=0;i<3;i++) |
313 |
+ |
for(j=0;j<3;j++) theBoxMat3[i][j] = boxMat[3*j+i]; |
314 |
+ |
|
315 |
+ |
simnfo->setBoxM( theBoxMat3 ); |
316 |
+ |
simnfo->setTime( currTime ); |
317 |
+ |
|
318 |
|
|
319 |
|
#endif |
320 |
|
} |
329 |
|
double jx, jy, jz; // angular velocity placeholders; |
330 |
|
double qSqr, qLength; // needed to normalize the quaternion vector. |
331 |
|
|
332 |
< |
Atom **atoms = entry_plug->atoms; |
332 |
> |
Atom **atoms = simnfo->atoms; |
333 |
|
DirectionalAtom* dAtom; |
334 |
|
|
335 |
|
int j, n_atoms, atomIndex; |
348 |
|
return strdup( painCave.errMsg ); |
349 |
|
} |
350 |
|
#else |
351 |
< |
n_atoms = entry_plug->n_atoms; |
351 |
> |
n_atoms = simnfo->n_atoms; |
352 |
|
atomIndex = globalIndex; |
353 |
|
#endif // is_mpi |
354 |
|
|
542 |
|
|
543 |
|
return NULL; |
544 |
|
} |
545 |
+ |
|
546 |
+ |
|
547 |
+ |
char* InitializeFromFile::parseBoxLine(char* readLine, double boxMat[9], |
548 |
+ |
double &time ){ |
549 |
|
|
550 |
+ |
char *foo; // the pointer to the current string token |
551 |
+ |
int j; |
552 |
|
|
553 |
+ |
// set the string tokenizer |
554 |
+ |
|
555 |
+ |
foo = strtok(readLine, " ,;\t"); |
556 |
+ |
// set the timeToken. |
557 |
+ |
|
558 |
+ |
if(foo == NULL){ |
559 |
+ |
sprintf( painCave.errMsg, |
560 |
+ |
"error in reading Time from %s\n", |
561 |
+ |
c_in_name ); |
562 |
+ |
return strdup( painCave.errMsg ); |
563 |
+ |
} |
564 |
+ |
time = atof( foo ); |
565 |
+ |
|
566 |
+ |
// get the Hx vector |
567 |
+ |
|
568 |
+ |
foo = strtok(NULL, " ,;\t"); |
569 |
+ |
if(foo == NULL){ |
570 |
+ |
sprintf( painCave.errMsg, |
571 |
+ |
"error in reading Hx[0] from %s\n", |
572 |
+ |
c_in_name ); |
573 |
+ |
return strdup( painCave.errMsg ); |
574 |
+ |
} |
575 |
+ |
boxMat[0] = atof( foo ); |
576 |
+ |
|
577 |
+ |
foo = strtok(NULL, " ,;\t"); |
578 |
+ |
if(foo == NULL){ |
579 |
+ |
sprintf( painCave.errMsg, |
580 |
+ |
"error in reading Hx[1] from %s\n", |
581 |
+ |
c_in_name ); |
582 |
+ |
return strdup( painCave.errMsg ); |
583 |
+ |
} |
584 |
+ |
boxMat[1] = atof( foo ); |
585 |
+ |
|
586 |
+ |
foo = strtok(NULL, " ,;\t"); |
587 |
+ |
if(foo == NULL){ |
588 |
+ |
sprintf( painCave.errMsg, |
589 |
+ |
"error in reading Hx[2] from %s\n", |
590 |
+ |
c_in_name ); |
591 |
+ |
return strdup( painCave.errMsg ); |
592 |
+ |
} |
593 |
+ |
boxMat[2] = atof( foo ); |
594 |
+ |
|
595 |
+ |
// get the Hy vector |
596 |
+ |
|
597 |
+ |
foo = strtok(NULL, " ,;\t"); |
598 |
+ |
if(foo == NULL){ |
599 |
+ |
sprintf( painCave.errMsg, |
600 |
+ |
"error in reading Hy[0] from %s\n", |
601 |
+ |
c_in_name ); |
602 |
+ |
return strdup( painCave.errMsg ); |
603 |
+ |
} |
604 |
+ |
boxMat[3] = atof( foo ); |
605 |
+ |
|
606 |
+ |
foo = strtok(NULL, " ,;\t"); |
607 |
+ |
if(foo == NULL){ |
608 |
+ |
sprintf( painCave.errMsg, |
609 |
+ |
"error in reading Hy[1] from %s\n", |
610 |
+ |
c_in_name ); |
611 |
+ |
return strdup( painCave.errMsg ); |
612 |
+ |
} |
613 |
+ |
boxMat[4] = atof( foo ); |
614 |
+ |
|
615 |
+ |
foo = strtok(NULL, " ,;\t"); |
616 |
+ |
if(foo == NULL){ |
617 |
+ |
sprintf( painCave.errMsg, |
618 |
+ |
"error in reading Hy[2] from %s\n", |
619 |
+ |
c_in_name ); |
620 |
+ |
return strdup( painCave.errMsg ); |
621 |
+ |
} |
622 |
+ |
boxMat[5] = atof( foo ); |
623 |
+ |
|
624 |
+ |
// get the Hz vector |
625 |
+ |
|
626 |
+ |
foo = strtok(NULL, " ,;\t"); |
627 |
+ |
if(foo == NULL){ |
628 |
+ |
sprintf( painCave.errMsg, |
629 |
+ |
"error in reading Hz[0] from %s\n", |
630 |
+ |
c_in_name ); |
631 |
+ |
return strdup( painCave.errMsg ); |
632 |
+ |
} |
633 |
+ |
boxMat[6] = atof( foo ); |
634 |
+ |
|
635 |
+ |
foo = strtok(NULL, " ,;\t"); |
636 |
+ |
if(foo == NULL){ |
637 |
+ |
sprintf( painCave.errMsg, |
638 |
+ |
"error in reading Hz[1] from %s\n", |
639 |
+ |
c_in_name ); |
640 |
+ |
return strdup( painCave.errMsg ); |
641 |
+ |
} |
642 |
+ |
boxMat[7] = atof( foo ); |
643 |
+ |
|
644 |
+ |
foo = strtok(NULL, " ,;\t"); |
645 |
+ |
if(foo == NULL){ |
646 |
+ |
sprintf( painCave.errMsg, |
647 |
+ |
"error in reading Hz[2] from %s\n", |
648 |
+ |
c_in_name ); |
649 |
+ |
return strdup( painCave.errMsg ); |
650 |
+ |
} |
651 |
+ |
boxMat[8] = atof( foo ); |
652 |
+ |
|
653 |
+ |
return NULL; |
654 |
+ |
} |
655 |
+ |
|
656 |
+ |
|
657 |
|
#ifdef IS_MPI |
658 |
|
|
659 |
|
// a couple of functions to let us escape the read loop |