19 |
|
#include "mpiSimulation.hpp" |
20 |
|
#define TAKE_THIS_TAG_CHAR 0 |
21 |
|
#define TAKE_THIS_TAG_INT 1 |
22 |
+ |
#endif // is_mpi |
23 |
|
|
24 |
|
namespace dumpRead{ |
25 |
+ |
|
26 |
+ |
#ifdef IS_MPI |
27 |
|
void nodeZeroError( void ); |
28 |
|
void anonymousNodeDie( void ); |
29 |
< |
|
29 |
> |
#endif // is_mpi |
30 |
|
|
31 |
|
class FilePos{ |
29 |
– |
public: |
32 |
|
|
33 |
+ |
public: |
34 |
+ |
FilePos(){ myPos = NULL; } |
35 |
+ |
FilePos( fpos_t* thePos ) { myPos = thePos; } |
36 |
+ |
~FilePos(){ if( myPos != NULL ) delete myPos; } |
37 |
|
|
38 |
+ |
FilePos &operator=(fpos_t *thePos){ myPos = thePos; return *this; } |
39 |
+ |
|
40 |
+ |
void setPos( fpos_t *thePos ){ myPos = thePos; } |
41 |
+ |
fpos_t *getPos( void ){ return myPos; } |
42 |
+ |
|
43 |
|
private: |
44 |
|
|
45 |
+ |
fpos_t *myPos |
46 |
|
|
47 |
|
}; |
48 |
|
|
49 |
+ |
bool operator<(FilePos a, FilePos b){ |
50 |
+ |
return (a.getPos())->__pos < (b.getPos())->__pos; } |
51 |
+ |
|
52 |
+ |
bool operator==(FilePos a, FilePos b){ |
53 |
+ |
return (a.getPos())->__pos == (b.getPos())->__pos; } |
54 |
+ |
|
55 |
|
vector<FilePos> frameStart; |
56 |
|
} |
57 |
|
|
58 |
|
using namespace dumpRead; |
59 |
|
|
42 |
– |
#endif // is_mpi |
60 |
|
|
61 |
|
DumpReader :: DumpReader( char *in_name ){ |
62 |
+ |
|
63 |
+ |
isScanned = false; |
64 |
+ |
|
65 |
|
#ifdef IS_MPI |
66 |
|
if (worldRank == 0) { |
67 |
|
#endif |
68 |
|
|
69 |
< |
c_in_file = fopen(in_name, "r"); |
70 |
< |
if(c_in_file == NULL){ |
69 |
> |
inFile = fopen(in_name, "r"); |
70 |
> |
if(inFile == NULL){ |
71 |
|
sprintf(painCave.errMsg, |
72 |
|
"Cannot open file: %s\n", in_name); |
73 |
|
painCave.isFatal = 1; |
74 |
|
simError(); |
75 |
|
} |
76 |
|
|
77 |
< |
strcpy( c_in_name, in_name); |
77 |
> |
strcpy( inName, in_name); |
78 |
|
#ifdef IS_MPI |
79 |
|
} |
80 |
|
strcpy( checkPointMsg, "Dump file opened for reading successfully." ); |
88 |
|
if (worldRank == 0) { |
89 |
|
#endif |
90 |
|
int error; |
91 |
< |
error = fclose( c_in_file ); |
91 |
> |
error = fclose( inFile ); |
92 |
|
if( error ){ |
93 |
|
sprintf( painCave.errMsg, |
94 |
< |
"Error closing %s\n", c_in_name ); |
94 |
> |
"Error closing %s\n", inName ); |
95 |
|
simError(); |
96 |
|
} |
97 |
|
#ifdef IS_MPI |
103 |
|
return; |
104 |
|
} |
105 |
|
|
106 |
+ |
int DumpReader::getNframes( void ){ |
107 |
|
|
108 |
+ |
if( !isScanned ) scanFile(); |
109 |
+ |
return nFrames; |
110 |
+ |
} |
111 |
|
|
112 |
< |
void DumpReader :: getFrame( SimInfo* the_simnfo, int whichFrame){ |
112 |
> |
void DumpReader::scanFile( void ){ |
113 |
|
|
114 |
+ |
int vectorSize; |
115 |
+ |
int i, j, k; |
116 |
+ |
int lineNum = 0; |
117 |
+ |
char readBuffer[2000]; |
118 |
+ |
char* foo; |
119 |
+ |
fpos_t *currPos; |
120 |
+ |
|
121 |
+ |
#ifdef IS_MPI |
122 |
+ |
if( worldRank == 0 ){ |
123 |
+ |
#endif // is_mpi |
124 |
+ |
|
125 |
+ |
rewind( inFile ); |
126 |
+ |
|
127 |
+ |
currPos = new fpos_t; |
128 |
+ |
fgetpos( inFile, currPos ); |
129 |
+ |
fgets( readBuffer, sizeof( readBuffer ), in_file ); |
130 |
+ |
lineNum++; |
131 |
+ |
if( feof( in_file ) ){ |
132 |
+ |
sprintf( painCave.errMsg, |
133 |
+ |
"File \"%s\" ended unexpectedly at line %d\n", |
134 |
+ |
inName, |
135 |
+ |
lineNum ); |
136 |
+ |
painCave.isFatal = 1; |
137 |
+ |
simError(); |
138 |
+ |
} |
139 |
+ |
|
140 |
+ |
while( !feof( in_file ) ){ |
141 |
+ |
|
142 |
+ |
frameStart.push_back( FilePos( currPos ) ); |
143 |
+ |
i = atoi(readBuffer); |
144 |
+ |
|
145 |
+ |
fgets( readBuffer, sizeof( readBuffer ), in_file ); |
146 |
+ |
lineNum++; |
147 |
+ |
if( feof( in_file ) ){ |
148 |
+ |
sprintf( painCave.errMsg, |
149 |
+ |
"File \"%s\" ended unexpectedly at line %d\n", |
150 |
+ |
inName, |
151 |
+ |
lineNum ); |
152 |
+ |
painCave.isFatal = 1; |
153 |
+ |
simError(); |
154 |
+ |
} |
155 |
+ |
|
156 |
+ |
if(outTime){ |
157 |
+ |
foo = strtok( readBuffer, " ,;\t" ); |
158 |
+ |
time = atof( foo ); |
159 |
+ |
} |
160 |
+ |
|
161 |
+ |
for(j=0; j<i; j++){ |
162 |
+ |
|
163 |
+ |
fgets( readBuffer, sizeof( readBuffer ), in_file ); |
164 |
+ |
lineNum++; |
165 |
+ |
if( feof( in_file ) ){ |
166 |
+ |
sprintf( painCave.errMsg, |
167 |
+ |
"File \"%s\" ended unexpectedly at line %d," |
168 |
+ |
" with atom %d\n", |
169 |
+ |
inName, |
170 |
+ |
lineNum, |
171 |
+ |
j ); |
172 |
+ |
painCave.isFatal = 1; |
173 |
+ |
simError(); |
174 |
+ |
} |
175 |
+ |
|
176 |
+ |
} |
177 |
+ |
|
178 |
+ |
currPos = new fpos_t; |
179 |
+ |
fgetpos( inFile, currPos ); |
180 |
+ |
fgets( readBuffer, sizeof( readBuffer ), in_file ); |
181 |
+ |
lineNum++; |
182 |
+ |
} |
183 |
+ |
|
184 |
+ |
delete currPos; |
185 |
+ |
vectorSize = frameStart.size(); |
186 |
+ |
rewind( inFile ); |
187 |
+ |
|
188 |
+ |
#ifdef IS_MPI |
189 |
+ |
} |
190 |
+ |
strcpy( checkPointMsg, "Successfully scanned DumpFile\n" ); |
191 |
+ |
MPIcheckPoint(); |
192 |
+ |
#endif // is_mpi |
193 |
+ |
|
194 |
+ |
nFrames = vectorSize; |
195 |
+ |
isScanned = true; |
196 |
+ |
} |
197 |
+ |
|
198 |
+ |
void DumpReader :: readFrame( SimInfo* the_simnfo, int whichFrame){ |
199 |
+ |
|
200 |
+ |
simnfo = the_simnfo; |
201 |
+ |
|
202 |
+ |
this->readSet( whichFrame ); |
203 |
+ |
} |
204 |
+ |
|
205 |
+ |
|
206 |
+ |
|
207 |
+ |
void DumpReader :: readSet( int whichFrame ){ |
208 |
+ |
|
209 |
|
int i, j, done, which_node, which_atom; // loop counter |
210 |
|
|
211 |
|
const int BUFFERSIZE = 2000; // size of the read buffer |
220 |
|
int procIndex; |
221 |
|
double boxMat[9]; |
222 |
|
double theBoxMat3[3][3]; |
223 |
+ |
|
224 |
+ |
fpos_t *framePos; |
225 |
+ |
|
226 |
+ |
#ifndef IS_MPI |
227 |
+ |
|
228 |
+ |
framePos = startFrame[whichFrame].getPos(); |
229 |
|
|
230 |
< |
simnfo = the_simnfo; |
230 |
> |
|
231 |
|
|
232 |
< |
#ifndef IS_MPI |
233 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
232 |
> |
|
233 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
234 |
|
if( eof_test == NULL ){ |
235 |
|
sprintf( painCave.errMsg, |
236 |
|
"DumpReader error: error reading 1st line of \"%s\"\n", |
237 |
< |
c_in_name ); |
237 |
> |
inName ); |
238 |
|
painCave.isFatal = 1; |
239 |
|
simError(); |
240 |
|
} |
248 |
|
sprintf( painCave.errMsg, |
249 |
|
"DumpReader error. %s n_atoms, %d, " |
250 |
|
"does not match the BASS file's n_atoms, %d.\n", |
251 |
< |
c_in_name, n_atoms, simnfo->n_atoms ); |
251 |
> |
inName, n_atoms, simnfo->n_atoms ); |
252 |
|
painCave.isFatal = 1; |
253 |
|
simError(); |
254 |
|
} |
255 |
|
|
256 |
|
//read the box mat from the comment line |
257 |
|
|
258 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
258 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
259 |
|
if(eof_test == NULL){ |
260 |
|
sprintf( painCave.errMsg, |
261 |
< |
"error in reading commment in %s\n", c_in_name); |
261 |
> |
"error in reading commment in %s\n", inName); |
262 |
|
painCave.isFatal = 1; |
263 |
|
simError(); |
264 |
|
} |
281 |
|
|
282 |
|
for( i=0; i < n_atoms; i++){ |
283 |
|
|
284 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
284 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
285 |
|
if(eof_test == NULL){ |
286 |
|
sprintf(painCave.errMsg, |
287 |
|
"error in reading file %s\n" |
288 |
|
"natoms = %d; index = %d\n" |
289 |
|
"error reading the line from the file.\n", |
290 |
< |
c_in_name, n_atoms, i ); |
290 |
> |
inName, n_atoms, i ); |
291 |
|
painCave.isFatal = 1; |
292 |
|
simError(); |
293 |
|
} |
318 |
|
haveError = 0; |
319 |
|
if (worldRank == 0) { |
320 |
|
|
321 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
321 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
322 |
|
if( eof_test == NULL ){ |
323 |
|
sprintf( painCave.errMsg, |
324 |
< |
"Error reading 1st line of %d \n ",c_in_name); |
324 |
> |
"Error reading 1st line of %d \n ",inName); |
325 |
|
haveError = 1; |
326 |
|
simError(); |
327 |
|
} |
338 |
|
sprintf( painCave.errMsg, |
339 |
|
"Initialize from File error. %s n_atoms, %d, " |
340 |
|
"does not match the BASS file's n_atoms, %d.\n", |
341 |
< |
c_in_name, n_atoms, simnfo->n_atoms ); |
341 |
> |
inName, n_atoms, simnfo->n_atoms ); |
342 |
|
haveError= 1; |
343 |
|
simError(); |
344 |
|
} |
345 |
|
|
346 |
|
//read the time and boxMat from the comment line |
347 |
|
|
348 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
348 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
349 |
|
if(eof_test == NULL){ |
350 |
|
sprintf( painCave.errMsg, |
351 |
< |
"error in reading commment in %s\n", c_in_name); |
351 |
> |
"error in reading commment in %s\n", inName); |
352 |
|
haveError = 1; |
353 |
|
simError(); |
354 |
|
} |
368 |
|
|
369 |
|
for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
370 |
|
|
371 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
371 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
372 |
|
if(eof_test == NULL){ |
373 |
|
sprintf(painCave.errMsg, |
374 |
|
"error in reading file %s\n" |
375 |
|
"natoms = %d; index = %d\n" |
376 |
|
"error reading the line from the file.\n", |
377 |
< |
c_in_name, n_atoms, i ); |
377 |
> |
inName, n_atoms, i ); |
378 |
|
haveError= 1; |
379 |
|
simError(); |
380 |
|
} |
487 |
|
sprintf( painCave.errMsg, |
488 |
|
"Initialize from file error. Atom at index %d " |
489 |
|
"in file %s does not exist on processor %d .\n", |
490 |
< |
globalIndex, c_in_name, mpiSim->getMyNode() ); |
490 |
> |
globalIndex, inName, mpiSim->getMyNode() ); |
491 |
|
return strdup( painCave.errMsg ); |
492 |
|
} |
493 |
|
#else |
506 |
|
"Initialize from file error. Atom %s at index %d " |
507 |
|
"in file %s does not" |
508 |
|
" match the BASS atom %s.\n", |
509 |
< |
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
509 |
> |
foo, atomIndex, inName, atoms[atomIndex]->getType() ); |
510 |
|
return strdup( painCave.errMsg ); |
511 |
|
} |
512 |
|
|
517 |
|
sprintf( painCave.errMsg, |
518 |
|
"error in reading postition x from %s\n" |
519 |
|
"natoms = %d, index = %d\n", |
520 |
< |
c_in_name, n_atoms, atomIndex ); |
520 |
> |
inName, n_atoms, atomIndex ); |
521 |
|
return strdup( painCave.errMsg ); |
522 |
|
} |
523 |
|
rx = atof( foo ); |
527 |
|
sprintf( painCave.errMsg, |
528 |
|
"error in reading postition y from %s\n" |
529 |
|
"natoms = %d, index = %d\n", |
530 |
< |
c_in_name, n_atoms, atomIndex ); |
530 |
> |
inName, n_atoms, atomIndex ); |
531 |
|
return strdup( painCave.errMsg ); |
532 |
|
} |
533 |
|
ry = atof( foo ); |
537 |
|
sprintf( painCave.errMsg, |
538 |
|
"error in reading postition z from %s\n" |
539 |
|
"natoms = %d, index = %d\n", |
540 |
< |
c_in_name, n_atoms, atomIndex ); |
540 |
> |
inName, n_atoms, atomIndex ); |
541 |
|
return strdup( painCave.errMsg ); |
542 |
|
} |
543 |
|
rz = atof( foo ); |
550 |
|
sprintf( painCave.errMsg, |
551 |
|
"error in reading velocity x from %s\n" |
552 |
|
"natoms = %d, index = %d\n", |
553 |
< |
c_in_name, n_atoms, atomIndex ); |
553 |
> |
inName, n_atoms, atomIndex ); |
554 |
|
return strdup( painCave.errMsg ); |
555 |
|
} |
556 |
|
vx = atof( foo ); |
560 |
|
sprintf( painCave.errMsg, |
561 |
|
"error in reading velocity y from %s\n" |
562 |
|
"natoms = %d, index = %d\n", |
563 |
< |
c_in_name, n_atoms, atomIndex ); |
563 |
> |
inName, n_atoms, atomIndex ); |
564 |
|
return strdup( painCave.errMsg ); |
565 |
|
} |
566 |
|
vy = atof( foo ); |
570 |
|
sprintf( painCave.errMsg, |
571 |
|
"error in reading velocity z from %s\n" |
572 |
|
"natoms = %d, index = %d\n", |
573 |
< |
c_in_name, n_atoms, atomIndex ); |
573 |
> |
inName, n_atoms, atomIndex ); |
574 |
|
return strdup( painCave.errMsg ); |
575 |
|
} |
576 |
|
vz = atof( foo ); |
585 |
|
sprintf(painCave.errMsg, |
586 |
|
"error in reading quaternion 0 from %s\n" |
587 |
|
"natoms = %d, index = %d\n", |
588 |
< |
c_in_name, n_atoms, atomIndex ); |
588 |
> |
inName, n_atoms, atomIndex ); |
589 |
|
return strdup( painCave.errMsg ); |
590 |
|
} |
591 |
|
q[0] = atof( foo ); |
595 |
|
sprintf( painCave.errMsg, |
596 |
|
"error in reading quaternion 1 from %s\n" |
597 |
|
"natoms = %d, index = %d\n", |
598 |
< |
c_in_name, n_atoms, atomIndex ); |
598 |
> |
inName, n_atoms, atomIndex ); |
599 |
|
return strdup( painCave.errMsg ); |
600 |
|
} |
601 |
|
q[1] = atof( foo ); |
605 |
|
sprintf( painCave.errMsg, |
606 |
|
"error in reading quaternion 2 from %s\n" |
607 |
|
"natoms = %d, index = %d\n", |
608 |
< |
c_in_name, n_atoms, atomIndex ); |
608 |
> |
inName, n_atoms, atomIndex ); |
609 |
|
return strdup( painCave.errMsg ); |
610 |
|
} |
611 |
|
q[2] = atof( foo ); |
615 |
|
sprintf( painCave.errMsg, |
616 |
|
"error in reading quaternion 3 from %s\n" |
617 |
|
"natoms = %d, index = %d\n", |
618 |
< |
c_in_name, n_atoms, atomIndex ); |
618 |
> |
inName, n_atoms, atomIndex ); |
619 |
|
return strdup( painCave.errMsg ); |
620 |
|
} |
621 |
|
q[3] = atof( foo ); |
627 |
|
sprintf( painCave.errMsg, |
628 |
|
"error in reading angular momentum jx from %s\n" |
629 |
|
"natoms = %d, index = %d\n", |
630 |
< |
c_in_name, n_atoms, atomIndex ); |
630 |
> |
inName, n_atoms, atomIndex ); |
631 |
|
return strdup( painCave.errMsg ); |
632 |
|
} |
633 |
|
jx = atof( foo ); |
637 |
|
sprintf( painCave.errMsg, |
638 |
|
"error in reading angular momentum jy from %s\n" |
639 |
|
"natoms = %d, index = %d\n", |
640 |
< |
c_in_name, n_atoms, atomIndex ); |
640 |
> |
inName, n_atoms, atomIndex ); |
641 |
|
return strdup( painCave.errMsg ); |
642 |
|
} |
643 |
|
jy = atof(foo ); |
647 |
|
sprintf( painCave.errMsg, |
648 |
|
"error in reading angular momentum jz from %s\n" |
649 |
|
"natoms = %d, index = %d\n", |
650 |
< |
c_in_name, n_atoms, atomIndex ); |
650 |
> |
inName, n_atoms, atomIndex ); |
651 |
|
return strdup( painCave.errMsg ); |
652 |
|
} |
653 |
|
jz = atof( foo ); |
699 |
|
if(foo == NULL){ |
700 |
|
sprintf( painCave.errMsg, |
701 |
|
"error in reading time from %s\n", |
702 |
< |
c_in_name ); |
702 |
> |
inName ); |
703 |
|
return strdup( painCave.errMsg ); |
704 |
|
} |
705 |
|
time = atof( foo ); |
710 |
|
if(foo == NULL){ |
711 |
|
sprintf( painCave.errMsg, |
712 |
|
"error in reading Hx[0] from %s\n", |
713 |
< |
c_in_name ); |
713 |
> |
inName ); |
714 |
|
return strdup( painCave.errMsg ); |
715 |
|
} |
716 |
|
boxMat[0] = atof( foo ); |
719 |
|
if(foo == NULL){ |
720 |
|
sprintf( painCave.errMsg, |
721 |
|
"error in reading Hx[1] from %s\n", |
722 |
< |
c_in_name ); |
722 |
> |
inName ); |
723 |
|
return strdup( painCave.errMsg ); |
724 |
|
} |
725 |
|
boxMat[1] = atof( foo ); |
728 |
|
if(foo == NULL){ |
729 |
|
sprintf( painCave.errMsg, |
730 |
|
"error in reading Hx[2] from %s\n", |
731 |
< |
c_in_name ); |
731 |
> |
inName ); |
732 |
|
return strdup( painCave.errMsg ); |
733 |
|
} |
734 |
|
boxMat[2] = atof( foo ); |
739 |
|
if(foo == NULL){ |
740 |
|
sprintf( painCave.errMsg, |
741 |
|
"error in reading Hy[0] from %s\n", |
742 |
< |
c_in_name ); |
742 |
> |
inName ); |
743 |
|
return strdup( painCave.errMsg ); |
744 |
|
} |
745 |
|
boxMat[3] = atof( foo ); |
748 |
|
if(foo == NULL){ |
749 |
|
sprintf( painCave.errMsg, |
750 |
|
"error in reading Hy[1] from %s\n", |
751 |
< |
c_in_name ); |
751 |
> |
inName ); |
752 |
|
return strdup( painCave.errMsg ); |
753 |
|
} |
754 |
|
boxMat[4] = atof( foo ); |
757 |
|
if(foo == NULL){ |
758 |
|
sprintf( painCave.errMsg, |
759 |
|
"error in reading Hy[2] from %s\n", |
760 |
< |
c_in_name ); |
760 |
> |
inName ); |
761 |
|
return strdup( painCave.errMsg ); |
762 |
|
} |
763 |
|
boxMat[5] = atof( foo ); |
768 |
|
if(foo == NULL){ |
769 |
|
sprintf( painCave.errMsg, |
770 |
|
"error in reading Hz[0] from %s\n", |
771 |
< |
c_in_name ); |
771 |
> |
inName ); |
772 |
|
return strdup( painCave.errMsg ); |
773 |
|
} |
774 |
|
boxMat[6] = atof( foo ); |
777 |
|
if(foo == NULL){ |
778 |
|
sprintf( painCave.errMsg, |
779 |
|
"error in reading Hz[1] from %s\n", |
780 |
< |
c_in_name ); |
780 |
> |
inName ); |
781 |
|
return strdup( painCave.errMsg ); |
782 |
|
} |
783 |
|
boxMat[7] = atof( foo ); |
786 |
|
if(foo == NULL){ |
787 |
|
sprintf( painCave.errMsg, |
788 |
|
"error in reading Hz[2] from %s\n", |
789 |
< |
c_in_name ); |
789 |
> |
inName ); |
790 |
|
return strdup( painCave.errMsg ); |
791 |
|
} |
792 |
|
boxMat[8] = atof( foo ); |