1 |
+ |
#define _FILE_OFFSET_BITS 64 |
2 |
+ |
|
3 |
|
#include <iostream> |
4 |
|
#include <cmath> |
5 |
+ |
#include <vector> |
6 |
|
|
7 |
|
#include <stdio.h> |
8 |
|
#include <stdlib.h> |
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 |
+ |
#endif // is_mpi |
30 |
+ |
|
31 |
+ |
class FilePos{ |
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 |
|
|
27 |
– |
#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 |
101 |
|
#endif |
102 |
|
|
103 |
|
return; |
104 |
+ |
} |
105 |
+ |
|
106 |
+ |
int DumpReader::getNframes( void ){ |
107 |
+ |
|
108 |
+ |
if( !isScanned ) scanFile(); |
109 |
+ |
return nFrames; |
110 |
+ |
} |
111 |
+ |
|
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 |
|
|
199 |
+ |
|
200 |
|
void DumpReader :: getFrame( SimInfo* the_simnfo, int whichFrame){ |
201 |
|
|
202 |
|
int i, j, done, which_node, which_atom; // loop counter |
217 |
|
simnfo = the_simnfo; |
218 |
|
|
219 |
|
#ifndef IS_MPI |
220 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
220 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
221 |
|
if( eof_test == NULL ){ |
222 |
|
sprintf( painCave.errMsg, |
223 |
|
"DumpReader error: error reading 1st line of \"%s\"\n", |
224 |
< |
c_in_name ); |
224 |
> |
inName ); |
225 |
|
painCave.isFatal = 1; |
226 |
|
simError(); |
227 |
|
} |
235 |
|
sprintf( painCave.errMsg, |
236 |
|
"DumpReader error. %s n_atoms, %d, " |
237 |
|
"does not match the BASS file's n_atoms, %d.\n", |
238 |
< |
c_in_name, n_atoms, simnfo->n_atoms ); |
238 |
> |
inName, n_atoms, simnfo->n_atoms ); |
239 |
|
painCave.isFatal = 1; |
240 |
|
simError(); |
241 |
|
} |
242 |
|
|
243 |
|
//read the box mat from the comment line |
244 |
|
|
245 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
245 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
246 |
|
if(eof_test == NULL){ |
247 |
|
sprintf( painCave.errMsg, |
248 |
< |
"error in reading commment in %s\n", c_in_name); |
248 |
> |
"error in reading commment in %s\n", inName); |
249 |
|
painCave.isFatal = 1; |
250 |
|
simError(); |
251 |
|
} |
268 |
|
|
269 |
|
for( i=0; i < n_atoms; i++){ |
270 |
|
|
271 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
271 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
272 |
|
if(eof_test == NULL){ |
273 |
|
sprintf(painCave.errMsg, |
274 |
|
"error in reading file %s\n" |
275 |
|
"natoms = %d; index = %d\n" |
276 |
|
"error reading the line from the file.\n", |
277 |
< |
c_in_name, n_atoms, i ); |
277 |
> |
inName, n_atoms, i ); |
278 |
|
painCave.isFatal = 1; |
279 |
|
simError(); |
280 |
|
} |
305 |
|
haveError = 0; |
306 |
|
if (worldRank == 0) { |
307 |
|
|
308 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
308 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
309 |
|
if( eof_test == NULL ){ |
310 |
|
sprintf( painCave.errMsg, |
311 |
< |
"Error reading 1st line of %d \n ",c_in_name); |
311 |
> |
"Error reading 1st line of %d \n ",inName); |
312 |
|
haveError = 1; |
313 |
|
simError(); |
314 |
|
} |
325 |
|
sprintf( painCave.errMsg, |
326 |
|
"Initialize from File error. %s n_atoms, %d, " |
327 |
|
"does not match the BASS file's n_atoms, %d.\n", |
328 |
< |
c_in_name, n_atoms, simnfo->n_atoms ); |
328 |
> |
inName, n_atoms, simnfo->n_atoms ); |
329 |
|
haveError= 1; |
330 |
|
simError(); |
331 |
|
} |
332 |
|
|
333 |
|
//read the time and boxMat from the comment line |
334 |
|
|
335 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
335 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
336 |
|
if(eof_test == NULL){ |
337 |
|
sprintf( painCave.errMsg, |
338 |
< |
"error in reading commment in %s\n", c_in_name); |
338 |
> |
"error in reading commment in %s\n", inName); |
339 |
|
haveError = 1; |
340 |
|
simError(); |
341 |
|
} |
355 |
|
|
356 |
|
for (i=0 ; i < mpiSim->getTotAtoms(); i++) { |
357 |
|
|
358 |
< |
eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file); |
358 |
> |
eof_test = fgets(read_buffer, sizeof(read_buffer), inFile); |
359 |
|
if(eof_test == NULL){ |
360 |
|
sprintf(painCave.errMsg, |
361 |
|
"error in reading file %s\n" |
362 |
|
"natoms = %d; index = %d\n" |
363 |
|
"error reading the line from the file.\n", |
364 |
< |
c_in_name, n_atoms, i ); |
364 |
> |
inName, n_atoms, i ); |
365 |
|
haveError= 1; |
366 |
|
simError(); |
367 |
|
} |
474 |
|
sprintf( painCave.errMsg, |
475 |
|
"Initialize from file error. Atom at index %d " |
476 |
|
"in file %s does not exist on processor %d .\n", |
477 |
< |
globalIndex, c_in_name, mpiSim->getMyNode() ); |
477 |
> |
globalIndex, inName, mpiSim->getMyNode() ); |
478 |
|
return strdup( painCave.errMsg ); |
479 |
|
} |
480 |
|
#else |
493 |
|
"Initialize from file error. Atom %s at index %d " |
494 |
|
"in file %s does not" |
495 |
|
" match the BASS atom %s.\n", |
496 |
< |
foo, atomIndex, c_in_name, atoms[atomIndex]->getType() ); |
496 |
> |
foo, atomIndex, inName, atoms[atomIndex]->getType() ); |
497 |
|
return strdup( painCave.errMsg ); |
498 |
|
} |
499 |
|
|
504 |
|
sprintf( painCave.errMsg, |
505 |
|
"error in reading postition x from %s\n" |
506 |
|
"natoms = %d, index = %d\n", |
507 |
< |
c_in_name, n_atoms, atomIndex ); |
507 |
> |
inName, n_atoms, atomIndex ); |
508 |
|
return strdup( painCave.errMsg ); |
509 |
|
} |
510 |
|
rx = atof( foo ); |
514 |
|
sprintf( painCave.errMsg, |
515 |
|
"error in reading postition y from %s\n" |
516 |
|
"natoms = %d, index = %d\n", |
517 |
< |
c_in_name, n_atoms, atomIndex ); |
517 |
> |
inName, n_atoms, atomIndex ); |
518 |
|
return strdup( painCave.errMsg ); |
519 |
|
} |
520 |
|
ry = atof( foo ); |
524 |
|
sprintf( painCave.errMsg, |
525 |
|
"error in reading postition z from %s\n" |
526 |
|
"natoms = %d, index = %d\n", |
527 |
< |
c_in_name, n_atoms, atomIndex ); |
527 |
> |
inName, n_atoms, atomIndex ); |
528 |
|
return strdup( painCave.errMsg ); |
529 |
|
} |
530 |
|
rz = atof( foo ); |
537 |
|
sprintf( painCave.errMsg, |
538 |
|
"error in reading velocity x 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 |
|
vx = atof( foo ); |
547 |
|
sprintf( painCave.errMsg, |
548 |
|
"error in reading velocity y from %s\n" |
549 |
|
"natoms = %d, index = %d\n", |
550 |
< |
c_in_name, n_atoms, atomIndex ); |
550 |
> |
inName, n_atoms, atomIndex ); |
551 |
|
return strdup( painCave.errMsg ); |
552 |
|
} |
553 |
|
vy = atof( foo ); |
557 |
|
sprintf( painCave.errMsg, |
558 |
|
"error in reading velocity z from %s\n" |
559 |
|
"natoms = %d, index = %d\n", |
560 |
< |
c_in_name, n_atoms, atomIndex ); |
560 |
> |
inName, n_atoms, atomIndex ); |
561 |
|
return strdup( painCave.errMsg ); |
562 |
|
} |
563 |
|
vz = atof( foo ); |
572 |
|
sprintf(painCave.errMsg, |
573 |
|
"error in reading quaternion 0 from %s\n" |
574 |
|
"natoms = %d, index = %d\n", |
575 |
< |
c_in_name, n_atoms, atomIndex ); |
575 |
> |
inName, n_atoms, atomIndex ); |
576 |
|
return strdup( painCave.errMsg ); |
577 |
|
} |
578 |
|
q[0] = atof( foo ); |
582 |
|
sprintf( painCave.errMsg, |
583 |
|
"error in reading quaternion 1 from %s\n" |
584 |
|
"natoms = %d, index = %d\n", |
585 |
< |
c_in_name, n_atoms, atomIndex ); |
585 |
> |
inName, n_atoms, atomIndex ); |
586 |
|
return strdup( painCave.errMsg ); |
587 |
|
} |
588 |
|
q[1] = atof( foo ); |
592 |
|
sprintf( painCave.errMsg, |
593 |
|
"error in reading quaternion 2 from %s\n" |
594 |
|
"natoms = %d, index = %d\n", |
595 |
< |
c_in_name, n_atoms, atomIndex ); |
595 |
> |
inName, n_atoms, atomIndex ); |
596 |
|
return strdup( painCave.errMsg ); |
597 |
|
} |
598 |
|
q[2] = atof( foo ); |
602 |
|
sprintf( painCave.errMsg, |
603 |
|
"error in reading quaternion 3 from %s\n" |
604 |
|
"natoms = %d, index = %d\n", |
605 |
< |
c_in_name, n_atoms, atomIndex ); |
605 |
> |
inName, n_atoms, atomIndex ); |
606 |
|
return strdup( painCave.errMsg ); |
607 |
|
} |
608 |
|
q[3] = atof( foo ); |
614 |
|
sprintf( painCave.errMsg, |
615 |
|
"error in reading angular momentum jx from %s\n" |
616 |
|
"natoms = %d, index = %d\n", |
617 |
< |
c_in_name, n_atoms, atomIndex ); |
617 |
> |
inName, n_atoms, atomIndex ); |
618 |
|
return strdup( painCave.errMsg ); |
619 |
|
} |
620 |
|
jx = atof( foo ); |
624 |
|
sprintf( painCave.errMsg, |
625 |
|
"error in reading angular momentum jy from %s\n" |
626 |
|
"natoms = %d, index = %d\n", |
627 |
< |
c_in_name, n_atoms, atomIndex ); |
627 |
> |
inName, n_atoms, atomIndex ); |
628 |
|
return strdup( painCave.errMsg ); |
629 |
|
} |
630 |
|
jy = atof(foo ); |
634 |
|
sprintf( painCave.errMsg, |
635 |
|
"error in reading angular momentum jz from %s\n" |
636 |
|
"natoms = %d, index = %d\n", |
637 |
< |
c_in_name, n_atoms, atomIndex ); |
637 |
> |
inName, n_atoms, atomIndex ); |
638 |
|
return strdup( painCave.errMsg ); |
639 |
|
} |
640 |
|
jz = atof( foo ); |
686 |
|
if(foo == NULL){ |
687 |
|
sprintf( painCave.errMsg, |
688 |
|
"error in reading time from %s\n", |
689 |
< |
c_in_name ); |
689 |
> |
inName ); |
690 |
|
return strdup( painCave.errMsg ); |
691 |
|
} |
692 |
|
time = atof( foo ); |
697 |
|
if(foo == NULL){ |
698 |
|
sprintf( painCave.errMsg, |
699 |
|
"error in reading Hx[0] from %s\n", |
700 |
< |
c_in_name ); |
700 |
> |
inName ); |
701 |
|
return strdup( painCave.errMsg ); |
702 |
|
} |
703 |
|
boxMat[0] = atof( foo ); |
706 |
|
if(foo == NULL){ |
707 |
|
sprintf( painCave.errMsg, |
708 |
|
"error in reading Hx[1] from %s\n", |
709 |
< |
c_in_name ); |
709 |
> |
inName ); |
710 |
|
return strdup( painCave.errMsg ); |
711 |
|
} |
712 |
|
boxMat[1] = atof( foo ); |
715 |
|
if(foo == NULL){ |
716 |
|
sprintf( painCave.errMsg, |
717 |
|
"error in reading Hx[2] from %s\n", |
718 |
< |
c_in_name ); |
718 |
> |
inName ); |
719 |
|
return strdup( painCave.errMsg ); |
720 |
|
} |
721 |
|
boxMat[2] = atof( foo ); |
726 |
|
if(foo == NULL){ |
727 |
|
sprintf( painCave.errMsg, |
728 |
|
"error in reading Hy[0] from %s\n", |
729 |
< |
c_in_name ); |
729 |
> |
inName ); |
730 |
|
return strdup( painCave.errMsg ); |
731 |
|
} |
732 |
|
boxMat[3] = atof( foo ); |
735 |
|
if(foo == NULL){ |
736 |
|
sprintf( painCave.errMsg, |
737 |
|
"error in reading Hy[1] from %s\n", |
738 |
< |
c_in_name ); |
738 |
> |
inName ); |
739 |
|
return strdup( painCave.errMsg ); |
740 |
|
} |
741 |
|
boxMat[4] = atof( foo ); |
744 |
|
if(foo == NULL){ |
745 |
|
sprintf( painCave.errMsg, |
746 |
|
"error in reading Hy[2] from %s\n", |
747 |
< |
c_in_name ); |
747 |
> |
inName ); |
748 |
|
return strdup( painCave.errMsg ); |
749 |
|
} |
750 |
|
boxMat[5] = atof( foo ); |
755 |
|
if(foo == NULL){ |
756 |
|
sprintf( painCave.errMsg, |
757 |
|
"error in reading Hz[0] from %s\n", |
758 |
< |
c_in_name ); |
758 |
> |
inName ); |
759 |
|
return strdup( painCave.errMsg ); |
760 |
|
} |
761 |
|
boxMat[6] = atof( foo ); |
764 |
|
if(foo == NULL){ |
765 |
|
sprintf( painCave.errMsg, |
766 |
|
"error in reading Hz[1] from %s\n", |
767 |
< |
c_in_name ); |
767 |
> |
inName ); |
768 |
|
return strdup( painCave.errMsg ); |
769 |
|
} |
770 |
|
boxMat[7] = atof( foo ); |
773 |
|
if(foo == NULL){ |
774 |
|
sprintf( painCave.errMsg, |
775 |
|
"error in reading Hz[2] from %s\n", |
776 |
< |
c_in_name ); |
776 |
> |
inName ); |
777 |
|
return strdup( painCave.errMsg ); |
778 |
|
} |
779 |
|
boxMat[8] = atof( foo ); |