3 |
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#include <string.h> |
4 |
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#include <iostream> |
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#include <fstream> |
6 |
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#include <algorithm> |
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#include <utility> |
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|
9 |
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#ifdef IS_MPI |
10 |
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#include <mpi.h> |
11 |
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#include "mpiSimulation.hpp" |
10 |
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#define TAKE_THIS_TAG_CHAR 15 |
11 |
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#define TAKE_THIS_TAG_INT 20 |
12 |
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|
13 |
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namespace dWrite{ |
14 |
< |
void nodeZeroError( void ); |
15 |
< |
void anonymousNodeDie( void ); |
14 |
> |
void DieDieDie( void ); |
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} |
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|
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using namespace dWrite; |
28 |
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if(worldRank == 0 ){ |
29 |
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#endif // is_mpi |
30 |
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|
32 |
– |
strcpy( outName, entry_plug->sampleName ); |
31 |
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|
32 |
< |
outFile.open(outName, ios::out | ios::trunc ); |
32 |
> |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
33 |
|
|
34 |
< |
if( !outFile ){ |
34 |
> |
if( !dumpFile ){ |
35 |
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|
36 |
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sprintf( painCave.errMsg, |
37 |
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"Could not open \"%s\" for dump output.\n", |
38 |
< |
outName); |
38 |
> |
entry_plug->sampleName); |
39 |
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painCave.isFatal = 1; |
40 |
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simError(); |
41 |
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} |
45 |
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#ifdef IS_MPI |
46 |
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} |
47 |
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|
48 |
+ |
//sort the local atoms by global index |
49 |
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sortByGlobalIndex(); |
50 |
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|
51 |
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sprintf( checkPointMsg, |
52 |
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"Sucessfully opened output file for dumping.\n"); |
53 |
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MPIcheckPoint(); |
60 |
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if(worldRank == 0 ){ |
61 |
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#endif // is_mpi |
62 |
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|
63 |
< |
outFile.close(); |
63 |
> |
dumpFile.close(); |
64 |
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|
65 |
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#ifdef IS_MPI |
66 |
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} |
67 |
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#endif // is_mpi |
68 |
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} |
69 |
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|
70 |
< |
void DumpWriter::writeDump( double currentTime ){ |
70 |
> |
#ifdef IS_MPI |
71 |
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|
72 |
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/** |
73 |
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* A hook function to load balancing |
74 |
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*/ |
75 |
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|
76 |
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void DumpWriter::update(){ |
77 |
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sortByGlobalIndex(); |
78 |
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} |
79 |
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|
80 |
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/** |
81 |
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* Auxiliary sorting function |
82 |
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*/ |
83 |
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|
84 |
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
85 |
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return p1.second < p2.second; |
86 |
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} |
87 |
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|
88 |
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/** |
89 |
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* Sorting the local index by global index |
90 |
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*/ |
91 |
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|
92 |
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void DumpWriter::sortByGlobalIndex(){ |
93 |
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Atom** atoms = entry_plug->atoms; |
94 |
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|
95 |
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indexArray.clear(); |
96 |
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|
97 |
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for(int i = 0; i < mpiSim->getMyNlocal();i++) |
98 |
+ |
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
99 |
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|
100 |
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
101 |
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} |
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#endif |
103 |
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|
104 |
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void DumpWriter::writeDump(double currentTime){ |
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|
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// write to eor file |
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writeFinal(currentTime); |
108 |
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|
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//write to dump file |
110 |
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writeFrame(dumpFile, currentTime); |
111 |
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|
112 |
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} |
113 |
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|
114 |
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void DumpWriter::writeFinal(double currentTime){ |
115 |
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|
116 |
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ofstream finalOut; |
117 |
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|
118 |
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//Open eor file |
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#ifdef IS_MPI |
120 |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
122 |
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|
123 |
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finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
124 |
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if( !finalOut ){ |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for final dump output.\n", |
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entry_plug->finalName ); |
128 |
+ |
painCave.isFatal = 1; |
129 |
+ |
simError(); |
130 |
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} |
131 |
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|
132 |
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#ifdef IS_MPI |
133 |
+ |
} |
134 |
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#endif |
135 |
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|
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//write to eor file |
137 |
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writeFrame(finalOut, currentTime); |
138 |
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|
139 |
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//close eor file |
140 |
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#ifdef IS_MPI |
141 |
+ |
if(worldRank == 0 ){ |
142 |
+ |
finalOut.close(); |
143 |
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} |
144 |
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#endif // is_mpi |
145 |
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|
146 |
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} |
147 |
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|
148 |
+ |
void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){ |
149 |
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|
150 |
|
const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
152 |
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|
153 |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
156 |
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int i; |
157 |
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|
158 |
|
#ifdef IS_MPI |
159 |
< |
int j, which_node, done, which_atom, local_index; |
159 |
> |
|
160 |
> |
int *potatoes; |
161 |
> |
int myPotato; |
162 |
> |
|
163 |
> |
int nProc; |
164 |
> |
int j, which_node, done, which_atom, local_index, currentIndex; |
165 |
> |
double atomData6[6]; |
166 |
> |
double atomData13[13]; |
167 |
> |
int isDirectional; |
168 |
> |
char* atomTypeString; |
169 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
170 |
> |
|
171 |
|
#else //is_mpi |
172 |
|
int nAtoms = entry_plug->n_atoms; |
173 |
|
#endif //is_mpi |
177 |
|
Atom** atoms = entry_plug->atoms; |
178 |
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double pos[3], vel[3]; |
179 |
|
|
87 |
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|
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// write current frame to the eor file |
89 |
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|
90 |
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this->writeFinal( currentTime ); |
91 |
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|
180 |
|
#ifndef IS_MPI |
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|
|
182 |
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outFile << nAtoms << "\n"; |
234 |
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|
235 |
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outFile << writeLine; |
236 |
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} |
149 |
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outFile.flush(); |
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|
238 |
|
#else // is_mpi |
239 |
|
|
240 |
< |
// first thing first, suspend fatalities. |
241 |
< |
painCave.isEventLoop = 1; |
240 |
> |
/* code to find maximum tag value */ |
241 |
> |
|
242 |
> |
int *tagub, flag, MAXTAG; |
243 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
244 |
> |
if (flag) { |
245 |
> |
MAXTAG = *tagub; |
246 |
> |
} else { |
247 |
> |
MAXTAG = 32767; |
248 |
> |
} |
249 |
|
|
156 |
– |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
250 |
|
int haveError; |
251 |
|
|
252 |
|
MPI_Status istatus; |
255 |
|
// write out header and node 0's coordinates |
256 |
|
|
257 |
|
if( worldRank == 0 ){ |
258 |
+ |
|
259 |
+ |
// Node 0 needs a list of the magic potatoes for each processor; |
260 |
+ |
|
261 |
+ |
nProc = mpiSim->getNumberProcessors(); |
262 |
+ |
potatoes = new int[nProc]; |
263 |
+ |
|
264 |
+ |
for (i = 0; i < nProc; i++) |
265 |
+ |
potatoes[i] = 0; |
266 |
+ |
|
267 |
|
outFile << mpiSim->getTotAtoms() << "\n"; |
268 |
|
|
269 |
|
outFile << currentTime << ";\t" |
282 |
|
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
283 |
|
outFile << endl; |
284 |
|
outFile.flush(); |
285 |
+ |
|
286 |
+ |
currentIndex = 0; |
287 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
288 |
+ |
|
289 |
|
// Get the Node number which has this atom; |
290 |
< |
|
290 |
> |
|
291 |
|
which_node = AtomToProcMap[i]; |
292 |
+ |
|
293 |
+ |
if (which_node != 0) { |
294 |
|
|
295 |
< |
if (which_node == 0 ) { |
295 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
296 |
> |
// The potato was going to exceed the maximum value, |
297 |
> |
// so wrap this processor potato back to 0: |
298 |
|
|
299 |
+ |
potatoes[which_node] = 0; |
300 |
+ |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
301 |
+ |
|
302 |
+ |
} |
303 |
+ |
|
304 |
+ |
myPotato = potatoes[which_node]; |
305 |
+ |
|
306 |
+ |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
307 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
308 |
+ |
|
309 |
+ |
atomTypeString = MPIatomTypeString; |
310 |
+ |
|
311 |
+ |
myPotato++; |
312 |
+ |
|
313 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
314 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
315 |
+ |
|
316 |
+ |
myPotato++; |
317 |
+ |
|
318 |
+ |
if (isDirectional) { |
319 |
+ |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
320 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
321 |
+ |
} else { |
322 |
+ |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
323 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
324 |
+ |
} |
325 |
+ |
|
326 |
+ |
myPotato++; |
327 |
+ |
potatoes[which_node] = myPotato; |
328 |
+ |
|
329 |
+ |
} else { |
330 |
+ |
|
331 |
|
haveError = 0; |
332 |
|
which_atom = i; |
333 |
< |
local_index=-1; |
334 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
335 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
336 |
< |
} |
337 |
< |
if (local_index != -1) { |
338 |
< |
//format the line |
333 |
> |
|
334 |
> |
local_index = indexArray[currentIndex].first; |
335 |
> |
|
336 |
> |
if (which_atom == indexArray[currentIndex].second) { |
337 |
> |
|
338 |
> |
atomTypeString = atoms[local_index]->getType(); |
339 |
|
|
340 |
|
atoms[local_index]->getPos(pos); |
341 |
< |
atoms[local_index]->getVel(vel); |
341 |
> |
atoms[local_index]->getVel(vel); |
342 |
|
|
343 |
< |
sprintf( tempBuffer, |
344 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
345 |
< |
atoms[local_index]->getType(), |
205 |
< |
pos[0], |
206 |
< |
pos[1], |
207 |
< |
pos[2], |
208 |
< |
vel[0], |
209 |
< |
vel[1], |
210 |
< |
vel[2]); // check here. |
211 |
< |
strcpy( writeLine, tempBuffer ); |
343 |
> |
atomData6[0] = pos[0]; |
344 |
> |
atomData6[1] = pos[1]; |
345 |
> |
atomData6[2] = pos[2]; |
346 |
|
|
347 |
+ |
atomData6[3] = vel[0]; |
348 |
+ |
atomData6[4] = vel[1]; |
349 |
+ |
atomData6[5] = vel[2]; |
350 |
+ |
|
351 |
+ |
isDirectional = 0; |
352 |
+ |
|
353 |
|
if( atoms[local_index]->isDirectional() ){ |
354 |
|
|
355 |
+ |
isDirectional = 1; |
356 |
+ |
|
357 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
358 |
|
dAtom->getQ( q ); |
359 |
|
|
360 |
< |
sprintf( tempBuffer, |
361 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
362 |
< |
q[0], |
363 |
< |
q[1], |
364 |
< |
q[2], |
365 |
< |
q[3], |
366 |
< |
dAtom->getJx(), |
367 |
< |
dAtom->getJy(), |
368 |
< |
dAtom->getJz()); |
369 |
< |
strcat( writeLine, tempBuffer ); |
370 |
< |
|
371 |
< |
} |
372 |
< |
else |
373 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
232 |
< |
} |
233 |
< |
else { |
360 |
> |
for (int j = 0; j < 6 ; j++) |
361 |
> |
atomData13[j] = atomData6[j]; |
362 |
> |
|
363 |
> |
atomData13[6] = q[0]; |
364 |
> |
atomData13[7] = q[1]; |
365 |
> |
atomData13[8] = q[2]; |
366 |
> |
atomData13[9] = q[3]; |
367 |
> |
|
368 |
> |
atomData13[10] = dAtom->getJx(); |
369 |
> |
atomData13[11] = dAtom->getJy(); |
370 |
> |
atomData13[12] = dAtom->getJz(); |
371 |
> |
} |
372 |
> |
|
373 |
> |
} else { |
374 |
|
sprintf(painCave.errMsg, |
375 |
|
"Atom %d not found on processor %d\n", |
376 |
|
i, worldRank ); |
377 |
|
haveError= 1; |
378 |
|
simError(); |
379 |
|
} |
380 |
< |
|
381 |
< |
if(haveError) nodeZeroError(); |
382 |
< |
|
380 |
> |
|
381 |
> |
if(haveError) DieDieDie(); |
382 |
> |
|
383 |
> |
currentIndex ++; |
384 |
|
} |
385 |
< |
else { |
386 |
< |
myStatus = 1; |
387 |
< |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
388 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
389 |
< |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
390 |
< |
MPI_COMM_WORLD); |
391 |
< |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
392 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
393 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
394 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
385 |
> |
// If we've survived to here, format the line: |
386 |
> |
|
387 |
> |
if (!isDirectional) { |
388 |
> |
|
389 |
> |
sprintf( writeLine, |
390 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
391 |
> |
atomTypeString, |
392 |
> |
atomData6[0], |
393 |
> |
atomData6[1], |
394 |
> |
atomData6[2], |
395 |
> |
atomData6[3], |
396 |
> |
atomData6[4], |
397 |
> |
atomData6[5]); |
398 |
|
|
399 |
< |
if(!myStatus) nodeZeroError(); |
400 |
< |
|
399 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
400 |
> |
|
401 |
> |
} else { |
402 |
> |
|
403 |
> |
sprintf( writeLine, |
404 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
405 |
> |
atomTypeString, |
406 |
> |
atomData13[0], |
407 |
> |
atomData13[1], |
408 |
> |
atomData13[2], |
409 |
> |
atomData13[3], |
410 |
> |
atomData13[4], |
411 |
> |
atomData13[5], |
412 |
> |
atomData13[6], |
413 |
> |
atomData13[7], |
414 |
> |
atomData13[8], |
415 |
> |
atomData13[9], |
416 |
> |
atomData13[10], |
417 |
> |
atomData13[11], |
418 |
> |
atomData13[12]); |
419 |
> |
|
420 |
|
} |
421 |
< |
|
421 |
> |
|
422 |
|
outFile << writeLine; |
260 |
– |
outFile.flush(); |
423 |
|
} |
424 |
+ |
|
425 |
|
|
426 |
< |
// kill everyone off: |
427 |
< |
myStatus = -1; |
428 |
< |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
429 |
< |
MPI_Send(&myStatus, 1, MPI_INT, j, |
430 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
268 |
< |
} |
269 |
< |
|
426 |
> |
outFile.flush(); |
427 |
> |
sprintf( checkPointMsg, |
428 |
> |
"Sucessfully took a dump.\n"); |
429 |
> |
MPIcheckPoint(); |
430 |
> |
delete[] potatoes; |
431 |
|
} else { |
432 |
|
|
433 |
< |
done = 0; |
273 |
< |
while (!done) { |
433 |
> |
// worldRank != 0, so I'm a remote node. |
434 |
|
|
435 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
276 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
435 |
> |
// Set my magic potato to 0: |
436 |
|
|
437 |
< |
if(!myStatus) anonymousNodeDie(); |
437 |
> |
myPotato = 0; |
438 |
> |
currentIndex = 0; |
439 |
> |
|
440 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
441 |
> |
|
442 |
> |
// Am I the node which has this atom? |
443 |
> |
|
444 |
> |
if (AtomToProcMap[i] == worldRank) { |
445 |
|
|
446 |
< |
if(myStatus < 0) break; |
446 |
> |
if (myPotato + 3 >= MAXTAG) { |
447 |
|
|
448 |
< |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
449 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
448 |
> |
// The potato was going to exceed the maximum value, |
449 |
> |
// so wrap this processor potato back to 0 (and block until |
450 |
> |
// node 0 says we can go: |
451 |
|
|
452 |
< |
myStatus = 1; |
453 |
< |
local_index=-1; |
454 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
455 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
456 |
< |
} |
457 |
< |
if (local_index != -1) { |
458 |
< |
//format the line |
452 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
453 |
> |
|
454 |
> |
} |
455 |
> |
which_atom = i; |
456 |
> |
local_index = indexArray[currentIndex].first; |
457 |
> |
|
458 |
> |
if (which_atom == indexArray[currentIndex].second) { |
459 |
> |
|
460 |
> |
atomTypeString = atoms[local_index]->getType(); |
461 |
|
|
462 |
< |
atoms[local_index]->getPos(pos); |
463 |
< |
atoms[local_index]->getVel(vel); |
462 |
> |
atoms[local_index]->getPos(pos); |
463 |
> |
atoms[local_index]->getVel(vel); |
464 |
|
|
465 |
< |
sprintf( tempBuffer, |
466 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
467 |
< |
atoms[local_index]->getType(), |
299 |
< |
pos[0], |
300 |
< |
pos[1], |
301 |
< |
pos[2], |
302 |
< |
vel[0], |
303 |
< |
vel[1], |
304 |
< |
vel[2]); // check here. |
305 |
< |
strcpy( writeLine, tempBuffer ); |
465 |
> |
atomData6[0] = pos[0]; |
466 |
> |
atomData6[1] = pos[1]; |
467 |
> |
atomData6[2] = pos[2]; |
468 |
|
|
469 |
< |
if( atoms[local_index]->isDirectional() ){ |
469 |
> |
atomData6[3] = vel[0]; |
470 |
> |
atomData6[4] = vel[1]; |
471 |
> |
atomData6[5] = vel[2]; |
472 |
> |
|
473 |
> |
isDirectional = 0; |
474 |
|
|
475 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
310 |
< |
dAtom->getQ( q ); |
475 |
> |
if( atoms[local_index]->isDirectional() ){ |
476 |
|
|
477 |
< |
sprintf( tempBuffer, |
478 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
479 |
< |
q[0], |
480 |
< |
q[1], |
481 |
< |
q[2], |
482 |
< |
q[3], |
483 |
< |
dAtom->getJx(), |
484 |
< |
dAtom->getJy(), |
485 |
< |
dAtom->getJz()); |
486 |
< |
strcat( writeLine, tempBuffer ); |
487 |
< |
} |
488 |
< |
else{ |
324 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
325 |
< |
} |
326 |
< |
} |
327 |
< |
else { |
328 |
< |
sprintf(painCave.errMsg, |
329 |
< |
"Atom %d not found on processor %d\n", |
330 |
< |
which_atom, worldRank ); |
331 |
< |
myStatus = 0; |
332 |
< |
simError(); |
477 |
> |
isDirectional = 1; |
478 |
> |
|
479 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
480 |
> |
dAtom->getQ( q ); |
481 |
> |
|
482 |
> |
for (int j = 0; j < 6 ; j++) |
483 |
> |
atomData13[j] = atomData6[j]; |
484 |
> |
|
485 |
> |
atomData13[6] = q[0]; |
486 |
> |
atomData13[7] = q[1]; |
487 |
> |
atomData13[8] = q[2]; |
488 |
> |
atomData13[9] = q[3]; |
489 |
|
|
490 |
< |
strcpy( writeLine, "Hello, I'm an error.\n"); |
491 |
< |
} |
490 |
> |
atomData13[10] = dAtom->getJx(); |
491 |
> |
atomData13[11] = dAtom->getJy(); |
492 |
> |
atomData13[12] = dAtom->getJz(); |
493 |
> |
} |
494 |
|
|
495 |
< |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
338 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
339 |
< |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
340 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
341 |
< |
} |
342 |
< |
} |
343 |
< |
outFile.flush(); |
344 |
< |
sprintf( checkPointMsg, |
345 |
< |
"Sucessfully took a dump.\n"); |
346 |
< |
MPIcheckPoint(); |
347 |
< |
|
348 |
< |
// last thing last, enable fatalities. |
349 |
< |
painCave.isEventLoop = 0; |
350 |
< |
|
351 |
< |
#endif // is_mpi |
352 |
< |
} |
353 |
< |
|
354 |
< |
void DumpWriter::writeFinal(double finalTime){ |
355 |
< |
|
356 |
< |
char finalName[500]; |
357 |
< |
ofstream finalOut; |
358 |
< |
|
359 |
< |
const int BUFFERSIZE = 2000; |
360 |
< |
char tempBuffer[BUFFERSIZE]; |
361 |
< |
char writeLine[BUFFERSIZE]; |
362 |
< |
|
363 |
< |
double q[4]; |
364 |
< |
DirectionalAtom* dAtom; |
365 |
< |
Atom** atoms = entry_plug->atoms; |
366 |
< |
int i; |
367 |
< |
#ifdef IS_MPI |
368 |
< |
int j, which_node, done, which_atom, local_index; |
369 |
< |
#else //is_mpi |
370 |
< |
int nAtoms = entry_plug->n_atoms; |
371 |
< |
#endif //is_mpi |
372 |
< |
|
373 |
< |
double pos[3], vel[3]; |
374 |
< |
|
375 |
< |
#ifdef IS_MPI |
376 |
< |
if(worldRank == 0 ){ |
377 |
< |
#endif // is_mpi |
378 |
< |
|
379 |
< |
strcpy( finalName, entry_plug->finalName ); |
380 |
< |
|
381 |
< |
finalOut.open( finalName, ios::out | ios::trunc ); |
382 |
< |
if( !finalOut ){ |
383 |
< |
sprintf( painCave.errMsg, |
384 |
< |
"Could not open \"%s\" for final dump output.\n", |
385 |
< |
finalName ); |
386 |
< |
painCave.isFatal = 1; |
387 |
< |
simError(); |
388 |
< |
} |
389 |
< |
|
390 |
< |
// finalOut.setf( ios::scientific ); |
391 |
< |
|
392 |
< |
#ifdef IS_MPI |
393 |
< |
} |
394 |
< |
|
395 |
< |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
396 |
< |
MPIcheckPoint(); |
397 |
< |
|
398 |
< |
#endif //is_mpi |
399 |
< |
|
400 |
< |
|
401 |
< |
#ifndef IS_MPI |
402 |
< |
|
403 |
< |
finalOut << nAtoms << "\n"; |
404 |
< |
|
405 |
< |
finalOut << finalTime << ";\t" |
406 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
407 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
408 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
409 |
< |
|
410 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
411 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
412 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
413 |
< |
|
414 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
415 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
416 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
417 |
< |
|
418 |
< |
//write out additional parameters, such as chi and eta |
419 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
420 |
< |
finalOut << endl; |
421 |
< |
|
422 |
< |
for( i=0; i<nAtoms; i++ ){ |
423 |
< |
|
424 |
< |
atoms[i]->getPos(pos); |
425 |
< |
atoms[i]->getVel(vel); |
426 |
< |
|
427 |
< |
sprintf( tempBuffer, |
428 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
429 |
< |
atoms[i]->getType(), |
430 |
< |
pos[0], |
431 |
< |
pos[1], |
432 |
< |
pos[2], |
433 |
< |
vel[0], |
434 |
< |
vel[1], |
435 |
< |
vel[2]); |
436 |
< |
strcpy( writeLine, tempBuffer ); |
437 |
< |
|
438 |
< |
if( atoms[i]->isDirectional() ){ |
439 |
< |
|
440 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
441 |
< |
dAtom->getQ( q ); |
442 |
< |
|
443 |
< |
sprintf( tempBuffer, |
444 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
445 |
< |
q[0], |
446 |
< |
q[1], |
447 |
< |
q[2], |
448 |
< |
q[3], |
449 |
< |
dAtom->getJx(), |
450 |
< |
dAtom->getJy(), |
451 |
< |
dAtom->getJz()); |
452 |
< |
strcat( writeLine, tempBuffer ); |
453 |
< |
} |
454 |
< |
else |
455 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
456 |
< |
|
457 |
< |
finalOut << writeLine; |
458 |
< |
} |
459 |
< |
finalOut.flush(); |
460 |
< |
finalOut.close(); |
461 |
< |
|
462 |
< |
#else // is_mpi |
463 |
< |
|
464 |
< |
// first thing first, suspend fatalities. |
465 |
< |
painCave.isEventLoop = 1; |
466 |
< |
|
467 |
< |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
468 |
< |
int haveError; |
469 |
< |
|
470 |
< |
MPI_Status istatus; |
471 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
472 |
< |
|
473 |
< |
// write out header and node 0's coordinates |
474 |
< |
|
475 |
< |
haveError = 0; |
476 |
< |
if( worldRank == 0 ){ |
477 |
< |
finalOut << mpiSim->getTotAtoms() << "\n"; |
478 |
< |
|
479 |
< |
finalOut << finalTime << ";\t" |
480 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
481 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
482 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
483 |
< |
|
484 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
485 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
486 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
487 |
< |
|
488 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
489 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
490 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
491 |
< |
|
492 |
< |
//write out additional parameters, such as chi and eta |
493 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
494 |
< |
finalOut << endl; |
495 |
< |
|
496 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
497 |
< |
// Get the Node number which has this molecule: |
498 |
< |
|
499 |
< |
which_node = AtomToProcMap[i]; |
500 |
< |
|
501 |
< |
if (which_node == mpiSim->getMyNode()) { |
502 |
< |
|
503 |
< |
which_atom = i; |
504 |
< |
local_index=-1; |
505 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
506 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
507 |
< |
} |
508 |
< |
if (local_index != -1) { |
509 |
< |
|
510 |
< |
atoms[local_index]->getPos(pos); |
511 |
< |
atoms[local_index]->getVel(vel); |
512 |
< |
|
513 |
< |
sprintf( tempBuffer, |
514 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
515 |
< |
atoms[local_index]->getType(), |
516 |
< |
pos[0], |
517 |
< |
pos[1], |
518 |
< |
pos[2], |
519 |
< |
vel[0], |
520 |
< |
vel[1], |
521 |
< |
vel[2]); |
522 |
< |
strcpy( writeLine, tempBuffer ); |
523 |
< |
|
524 |
< |
if( atoms[local_index]->isDirectional() ){ |
525 |
< |
|
526 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
527 |
< |
dAtom->getQ( q ); |
528 |
< |
|
529 |
< |
sprintf( tempBuffer, |
530 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
531 |
< |
q[0], |
532 |
< |
q[1], |
533 |
< |
q[2], |
534 |
< |
q[3], |
535 |
< |
dAtom->getJx(), |
536 |
< |
dAtom->getJy(), |
537 |
< |
dAtom->getJz()); |
538 |
< |
strcat( writeLine, tempBuffer ); |
539 |
< |
} |
540 |
< |
else |
541 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
542 |
< |
} |
543 |
< |
else { |
495 |
> |
} else { |
496 |
|
sprintf(painCave.errMsg, |
497 |
|
"Atom %d not found on processor %d\n", |
498 |
|
i, worldRank ); |
500 |
|
simError(); |
501 |
|
} |
502 |
|
|
503 |
< |
if(haveError) nodeZeroError(); |
503 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
504 |
|
|
505 |
< |
} |
506 |
< |
else { |
505 |
> |
// null terminate the string before sending (just in case): |
506 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
507 |
|
|
508 |
< |
myStatus = 1; |
509 |
< |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
510 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
511 |
< |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
560 |
< |
MPI_COMM_WORLD); |
561 |
< |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
562 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
563 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
564 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
508 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
509 |
> |
myPotato, MPI_COMM_WORLD); |
510 |
> |
|
511 |
> |
myPotato++; |
512 |
|
|
513 |
< |
if(!myStatus) nodeZeroError(); |
514 |
< |
} |
513 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
514 |
> |
myPotato, MPI_COMM_WORLD); |
515 |
> |
|
516 |
> |
myPotato++; |
517 |
> |
|
518 |
> |
if (isDirectional) { |
519 |
|
|
520 |
< |
finalOut << writeLine; |
521 |
< |
} |
520 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
521 |
> |
myPotato, MPI_COMM_WORLD); |
522 |
> |
|
523 |
> |
} else { |
524 |
|
|
525 |
< |
// kill everyone off: |
526 |
< |
myStatus = -1; |
527 |
< |
for (j = 1; j < mpiSim->getNumberProcessors(); j++) { |
575 |
< |
MPI_Send(&myStatus, 1, MPI_INT, j, |
576 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
577 |
< |
} |
525 |
> |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
526 |
> |
myPotato, MPI_COMM_WORLD); |
527 |
> |
} |
528 |
|
|
529 |
< |
} else { |
530 |
< |
|
581 |
< |
done = 0; |
582 |
< |
while (!done) { |
583 |
< |
|
584 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
585 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
586 |
< |
|
587 |
< |
if(!myStatus) anonymousNodeDie(); |
588 |
< |
|
589 |
< |
if(myStatus < 0) break; |
590 |
< |
|
591 |
< |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
592 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
593 |
< |
|
594 |
< |
myStatus = 1; |
595 |
< |
local_index=-1; |
596 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
597 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
529 |
> |
myPotato++; |
530 |
> |
currentIndex++; |
531 |
|
} |
599 |
– |
if (local_index != -1) { |
600 |
– |
|
601 |
– |
atoms[local_index]->getPos(pos); |
602 |
– |
atoms[local_index]->getVel(vel); |
603 |
– |
|
604 |
– |
//format the line |
605 |
– |
sprintf( tempBuffer, |
606 |
– |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
607 |
– |
atoms[local_index]->getType(), |
608 |
– |
pos[0], |
609 |
– |
pos[1], |
610 |
– |
pos[2], |
611 |
– |
vel[0], |
612 |
– |
vel[1], |
613 |
– |
vel[2]); // check here. |
614 |
– |
strcpy( writeLine, tempBuffer ); |
615 |
– |
|
616 |
– |
if( atoms[local_index]->isDirectional() ){ |
617 |
– |
|
618 |
– |
dAtom = (DirectionalAtom *)atoms[local_index]; |
619 |
– |
dAtom->getQ( q ); |
620 |
– |
|
621 |
– |
sprintf( tempBuffer, |
622 |
– |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
623 |
– |
q[0], |
624 |
– |
q[1], |
625 |
– |
q[2], |
626 |
– |
q[3], |
627 |
– |
dAtom->getJx(), |
628 |
– |
dAtom->getJy(), |
629 |
– |
dAtom->getJz()); |
630 |
– |
strcat( writeLine, tempBuffer ); |
631 |
– |
} |
632 |
– |
else{ |
633 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
634 |
– |
} |
635 |
– |
} |
636 |
– |
else { |
637 |
– |
sprintf(painCave.errMsg, |
638 |
– |
"Atom %d not found on processor %d\n", |
639 |
– |
which_atom, worldRank ); |
640 |
– |
myStatus = 0; |
641 |
– |
simError(); |
642 |
– |
|
643 |
– |
strcpy( writeLine, "Hello, I'm an error.\n"); |
644 |
– |
} |
645 |
– |
|
646 |
– |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
647 |
– |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
648 |
– |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
649 |
– |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
532 |
|
} |
651 |
– |
} |
652 |
– |
finalOut.flush(); |
653 |
– |
sprintf( checkPointMsg, |
654 |
– |
"Sucessfully took a dump.\n"); |
655 |
– |
MPIcheckPoint(); |
533 |
|
|
534 |
< |
if( worldRank == 0 ) finalOut.close(); |
534 |
> |
sprintf( checkPointMsg, |
535 |
> |
"Sucessfully took a dump.\n"); |
536 |
> |
MPIcheckPoint(); |
537 |
> |
|
538 |
> |
} |
539 |
> |
|
540 |
|
#endif // is_mpi |
541 |
|
} |
542 |
|
|
661 |
– |
|
662 |
– |
|
543 |
|
#ifdef IS_MPI |
544 |
|
|
545 |
|
// a couple of functions to let us escape the write loop |
546 |
|
|
547 |
< |
void dWrite::nodeZeroError( void ){ |
668 |
< |
int j, myStatus; |
547 |
> |
void dWrite::DieDieDie( void ){ |
548 |
|
|
670 |
– |
myStatus = 0; |
671 |
– |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
672 |
– |
MPI_Send( &myStatus, 1, MPI_INT, j, |
673 |
– |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
674 |
– |
} |
675 |
– |
|
676 |
– |
|
549 |
|
MPI_Finalize(); |
550 |
|
exit (0); |
679 |
– |
|
551 |
|
} |
552 |
|
|
682 |
– |
void dWrite::anonymousNodeDie( void ){ |
683 |
– |
|
684 |
– |
MPI_Finalize(); |
685 |
– |
exit (0); |
686 |
– |
} |
687 |
– |
|
553 |
|
#endif //is_mpi |