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#define _FILE_OFFSET_BITS 64 |
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< |
#include <cstring> |
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#include <string.h> |
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#include <iostream> |
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#include <fstream> |
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|
7 |
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#ifdef IS_MPI |
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#include <mpi.h> |
9 |
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#include "mpiSimulation.hpp" |
10 |
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#define TAKE_THIS_TAG_CHAR 1 |
11 |
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#define TAKE_THIS_TAG_INT 2 |
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|
11 |
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namespace dWrite{ |
12 |
< |
void nodeZeroError( void ); |
15 |
< |
void anonymousNodeDie( void ); |
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> |
void DieDieDie( void ); |
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} |
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|
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using namespace dWrite; |
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#ifdef IS_MPI |
26 |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
28 |
< |
|
28 |
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|
29 |
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strcpy( outName, entry_plug->sampleName ); |
30 |
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|
30 |
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|
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outFile.open(outName, ios::out | ios::trunc ); |
32 |
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|
32 |
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|
33 |
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if( !outFile ){ |
34 |
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|
34 |
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|
35 |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for dump output.\n", |
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outName); |
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} |
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void DumpWriter::writeDump( double currentTime ){ |
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|
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|
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const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
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|
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
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int i; |
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#ifdef IS_MPI |
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int j, which_node, done, which_atom, local_index; |
77 |
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double atomTransData[6]; |
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double atomOrientData[7]; |
79 |
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int isDirectional; |
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char* atomTypeString; |
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char MPIatomTypeString[MINIBUFFERSIZE]; |
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int me; |
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int atomTypeTag; |
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int atomIsDirectionalTag; |
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int atomTransDataTag; |
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int atomOrientDataTag; |
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#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
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#endif //is_mpi |
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DirectionalAtom* dAtom; |
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Atom** atoms = entry_plug->atoms; |
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double pos[3], vel[3]; |
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|
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|
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// write current frame to the eor file |
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|
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this->writeFinal( currentTime ); |
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|
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#ifndef IS_MPI |
101 |
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|
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outFile << nAtoms << "\n"; |
103 |
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|
104 |
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outFile << currentTime << ";\t" |
103 |
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|
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outFile << currentTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";\n"; |
116 |
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|
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<< entry_plug->Hmat[2][2] << ";"; |
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//write out additional parameters, such as chi and eta |
117 |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
118 |
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outFile << endl; |
119 |
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|
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for( i=0; i<nAtoms; i++ ){ |
121 |
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|
121 |
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|
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atoms[i]->getPos(pos); |
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atoms[i]->getVel(vel); |
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|
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[i]->isDirectional() ){ |
137 |
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|
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|
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dAtom = (DirectionalAtom *)atoms[i]; |
139 |
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dAtom->getQ( q ); |
140 |
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|
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|
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sprintf( tempBuffer, |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], |
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} |
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else |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
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|
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outFile << writeLine; |
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} |
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outFile.flush(); |
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|
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#else // is_mpi |
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|
161 |
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// first thing first, suspend fatalities. |
162 |
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painCave.isEventLoop = 1; |
161 |
> |
/* code to find maximum tag value */ |
162 |
> |
int *tagub, flag, MAXTAG; |
163 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
164 |
> |
if (flag) { |
165 |
> |
MAXTAG = *tagub; |
166 |
> |
} else { |
167 |
> |
MAXTAG = 32767; |
168 |
> |
} |
169 |
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|
149 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
170 |
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int haveError; |
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|
172 |
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MPI_Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
174 |
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|
174 |
> |
|
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// write out header and node 0's coordinates |
176 |
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|
176 |
> |
|
177 |
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if( worldRank == 0 ){ |
178 |
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outFile << mpiSim->getTotAtoms() << "\n"; |
179 |
< |
|
180 |
< |
outFile << currentTime << ";\t" |
179 |
> |
|
180 |
> |
outFile << currentTime << ";\t" |
181 |
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<< entry_plug->Hmat[0][0] << "\t" |
182 |
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<< entry_plug->Hmat[1][0] << "\t" |
183 |
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<< entry_plug->Hmat[2][0] << ";\t" |
184 |
< |
|
184 |
> |
|
185 |
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<< entry_plug->Hmat[0][1] << "\t" |
186 |
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<< entry_plug->Hmat[1][1] << "\t" |
187 |
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<< entry_plug->Hmat[2][1] << ";\t" |
188 |
< |
|
188 |
> |
|
189 |
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<< entry_plug->Hmat[0][2] << "\t" |
190 |
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<< entry_plug->Hmat[1][2] << "\t" |
191 |
< |
<< entry_plug->Hmat[2][2] << ";\n"; |
192 |
< |
|
191 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
192 |
> |
|
193 |
> |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
194 |
> |
outFile << endl; |
195 |
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outFile.flush(); |
196 |
+ |
|
197 |
+ |
tag = 0; |
198 |
+ |
|
199 |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
200 |
+ |
|
201 |
+ |
if (tag + 2 >= MAXTAG) { |
202 |
+ |
// The tag was going to exceed the maximum value, so wrap around to 0: |
203 |
+ |
tag = 0; |
204 |
+ |
// Send the newly zeroed tag on to the other nodes: |
205 |
+ |
MPI_Bcast(&tag, 1, MPI_INT, 0, MPI_COMM_WORLD); |
206 |
+ |
} |
207 |
+ |
|
208 |
|
// Get the Node number which has this atom; |
209 |
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|
210 |
< |
which_node = AtomToProcMap[i]; |
210 |
> |
which_node = AtomToProcMap[i]; |
211 |
|
|
212 |
< |
if (which_node == 0 ) { |
213 |
< |
|
212 |
> |
if (which_node != 0) { |
213 |
> |
|
214 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
215 |
> |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
216 |
> |
|
217 |
> |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
218 |
> |
|
219 |
> |
// Null terminate the atomTypeString just in case: |
220 |
> |
|
221 |
> |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
222 |
> |
|
223 |
> |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
224 |
> |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
225 |
> |
|
226 |
> |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
227 |
> |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
228 |
> |
|
229 |
> |
if (isDirectional) { |
230 |
> |
|
231 |
> |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
232 |
> |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
233 |
> |
|
234 |
> |
} |
235 |
> |
|
236 |
> |
} else { |
237 |
> |
|
238 |
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haveError = 0; |
239 |
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which_atom = i; |
240 |
< |
local_index=-1; |
240 |
> |
local_index=-1; |
241 |
> |
|
242 |
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
243 |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
244 |
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} |
245 |
+ |
|
246 |
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if (local_index != -1) { |
247 |
< |
//format the line |
248 |
< |
|
247 |
> |
|
248 |
> |
atomTypeString = atoms[local_index]->getType(); |
249 |
> |
|
250 |
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atoms[local_index]->getPos(pos); |
251 |
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atoms[local_index]->getVel(vel); |
252 |
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|
253 |
< |
sprintf( tempBuffer, |
254 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
255 |
< |
atoms[local_index]->getType(), |
256 |
< |
pos[0], |
257 |
< |
pos[1], |
258 |
< |
pos[2], |
259 |
< |
vel[0], |
260 |
< |
vel[1], |
261 |
< |
vel[2]); // check here. |
262 |
< |
strcpy( writeLine, tempBuffer ); |
203 |
< |
|
253 |
> |
atomTransData[0] = pos[0]; |
254 |
> |
atomTransData[1] = pos[1]; |
255 |
> |
atomTransData[2] = pos[2]; |
256 |
> |
|
257 |
> |
atomTransData[3] = vel[0]; |
258 |
> |
atomTransData[4] = vel[1]; |
259 |
> |
atomTransData[5] = vel[2]; |
260 |
> |
|
261 |
> |
isDirectional = 0; |
262 |
> |
|
263 |
|
if( atoms[local_index]->isDirectional() ){ |
264 |
+ |
|
265 |
+ |
isDirectional = 1; |
266 |
|
|
267 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
268 |
|
dAtom->getQ( q ); |
269 |
|
|
270 |
< |
sprintf( tempBuffer, |
271 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
272 |
< |
q[0], |
273 |
< |
q[1], |
274 |
< |
q[2], |
275 |
< |
q[3], |
276 |
< |
dAtom->getJx(), |
277 |
< |
dAtom->getJy(), |
278 |
< |
dAtom->getJz()); |
279 |
< |
strcat( writeLine, tempBuffer ); |
280 |
< |
|
220 |
< |
} |
221 |
< |
else |
222 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
223 |
< |
} |
224 |
< |
else { |
270 |
> |
atomOrientData[0] = q[0]; |
271 |
> |
atomOrientData[1] = q[1]; |
272 |
> |
atomOrientData[2] = q[2]; |
273 |
> |
atomOrientData[3] = q[3]; |
274 |
> |
|
275 |
> |
atomOrientData[4] = dAtom->getJx(); |
276 |
> |
atomOrientData[5] = dAtom->getJy(); |
277 |
> |
atomOrientData[6] = dAtom->getJz(); |
278 |
> |
} |
279 |
> |
|
280 |
> |
} else { |
281 |
|
sprintf(painCave.errMsg, |
282 |
|
"Atom %d not found on processor %d\n", |
283 |
|
i, worldRank ); |
284 |
|
haveError= 1; |
285 |
|
simError(); |
286 |
< |
} |
231 |
< |
|
232 |
< |
if(haveError) nodeZeroError(); |
286 |
> |
} |
287 |
|
|
288 |
< |
} |
289 |
< |
else { |
290 |
< |
myStatus = 1; |
291 |
< |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
292 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
293 |
< |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
294 |
< |
MPI_COMM_WORLD); |
295 |
< |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
296 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
297 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
298 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
299 |
< |
|
300 |
< |
if(!myStatus) nodeZeroError(); |
288 |
> |
if(haveError) DieDieDie(); |
289 |
> |
|
290 |
> |
// If we've survived to here, format the line: |
291 |
> |
|
292 |
> |
sprintf( tempBuffer, |
293 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
294 |
> |
atomTypeString, |
295 |
> |
atomTransData[0], |
296 |
> |
atomTransData[1], |
297 |
> |
atomTransData[2], |
298 |
> |
atomTransData[3], |
299 |
> |
atomTransData[4], |
300 |
> |
atomTransData[5]); |
301 |
|
|
302 |
+ |
strcpy( writeLine, tempBuffer ); |
303 |
+ |
|
304 |
+ |
if (isDirectional) { |
305 |
+ |
|
306 |
+ |
sprintf( tempBuffer, |
307 |
+ |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
308 |
+ |
atomOrientData[0], |
309 |
+ |
atomOrientData[1], |
310 |
+ |
atomOrientData[2], |
311 |
+ |
atomOrientData[3], |
312 |
+ |
atomOrientData[4], |
313 |
+ |
atomOrientData[5], |
314 |
+ |
atomOrientData[6]); |
315 |
+ |
strcat( writeLine, tempBuffer ); |
316 |
+ |
|
317 |
+ |
} else { |
318 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
319 |
+ |
} |
320 |
+ |
|
321 |
+ |
outFile << writeLine; |
322 |
+ |
outFile.flush(); |
323 |
|
} |
249 |
– |
|
250 |
– |
outFile << writeLine; |
251 |
– |
outFile.flush(); |
324 |
|
} |
253 |
– |
|
254 |
– |
// kill everyone off: |
255 |
– |
myStatus = -1; |
256 |
– |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
257 |
– |
MPI_Send(&myStatus, 1, MPI_INT, j, |
258 |
– |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
259 |
– |
} |
325 |
|
|
326 |
+ |
outFile.flush(); |
327 |
+ |
sprintf( checkPointMsg, |
328 |
+ |
"Sucessfully took a dump.\n"); |
329 |
+ |
MPIcheckPoint(); |
330 |
+ |
|
331 |
|
} else { |
332 |
+ |
|
333 |
+ |
// worldRank != 0, so I'm a remote node. |
334 |
|
|
335 |
< |
done = 0; |
264 |
< |
while (!done) { |
335 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
336 |
|
|
337 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
267 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
268 |
< |
|
269 |
< |
if(!myStatus) anonymousNodeDie(); |
337 |
> |
// Am I the node which has this atom? |
338 |
|
|
339 |
< |
if(myStatus < 0) break; |
339 |
> |
if (AtomToProcMap[i] == worldRank) { |
340 |
|
|
341 |
< |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
342 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
343 |
< |
|
344 |
< |
myStatus = 1; |
345 |
< |
local_index=-1; |
346 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
347 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
280 |
< |
} |
281 |
< |
if (local_index != -1) { |
282 |
< |
//format the line |
341 |
> |
local_index=-1; |
342 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
343 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
344 |
> |
} |
345 |
> |
if (local_index != -1) { |
346 |
> |
|
347 |
> |
atomTypeString = atoms[local_index]->getType(); |
348 |
|
|
349 |
< |
atoms[local_index]->getPos(pos); |
350 |
< |
atoms[local_index]->getVel(vel); |
349 |
> |
atoms[local_index]->getPos(pos); |
350 |
> |
atoms[local_index]->getVel(vel); |
351 |
|
|
352 |
< |
sprintf( tempBuffer, |
353 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
354 |
< |
atoms[local_index]->getType(), |
355 |
< |
pos[0], |
356 |
< |
pos[1], |
357 |
< |
pos[2], |
358 |
< |
vel[0], |
359 |
< |
vel[1], |
360 |
< |
vel[2]); // check here. |
361 |
< |
strcpy( writeLine, tempBuffer ); |
362 |
< |
|
363 |
< |
if( atoms[local_index]->isDirectional() ){ |
364 |
< |
|
365 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
366 |
< |
dAtom->getQ( q ); |
367 |
< |
|
368 |
< |
sprintf( tempBuffer, |
369 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
370 |
< |
q[0], |
371 |
< |
q[1], |
372 |
< |
q[2], |
373 |
< |
q[3], |
374 |
< |
dAtom->getJx(), |
375 |
< |
dAtom->getJy(), |
376 |
< |
dAtom->getJz()); |
377 |
< |
strcat( writeLine, tempBuffer ); |
352 |
> |
atomTransData[0] = pos[0]; |
353 |
> |
atomTransData[1] = pos[1]; |
354 |
> |
atomTransData[2] = pos[2]; |
355 |
> |
|
356 |
> |
atomTransData[3] = vel[0]; |
357 |
> |
atomTransData[4] = vel[1]; |
358 |
> |
atomTransData[5] = vel[2]; |
359 |
> |
|
360 |
> |
isDirectional = 0; |
361 |
> |
|
362 |
> |
if( atoms[local_index]->isDirectional() ){ |
363 |
> |
|
364 |
> |
isDirectional = 1; |
365 |
> |
|
366 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
367 |
> |
dAtom->getQ( q ); |
368 |
> |
|
369 |
> |
atomOrientData[0] = q[0]; |
370 |
> |
atomOrientData[1] = q[1]; |
371 |
> |
atomOrientData[2] = q[2]; |
372 |
> |
atomOrientData[3] = q[3]; |
373 |
> |
|
374 |
> |
atomOrientData[4] = dAtom->getJx(); |
375 |
> |
atomOrientData[5] = dAtom->getJy(); |
376 |
> |
atomOrientData[6] = dAtom->getJz(); |
377 |
> |
} |
378 |
> |
|
379 |
> |
} else { |
380 |
> |
sprintf(painCave.errMsg, |
381 |
> |
"Atom %d not found on processor %d\n", |
382 |
> |
i, worldRank ); |
383 |
> |
haveError= 1; |
384 |
> |
simError(); |
385 |
|
} |
314 |
– |
else{ |
315 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
316 |
– |
} |
317 |
– |
} |
318 |
– |
else { |
319 |
– |
sprintf(painCave.errMsg, |
320 |
– |
"Atom %d not found on processor %d\n", |
321 |
– |
which_atom, worldRank ); |
322 |
– |
myStatus = 0; |
323 |
– |
simError(); |
386 |
|
|
387 |
< |
strcpy( writeLine, "Hello, I'm an error.\n"); |
326 |
< |
} |
387 |
> |
// I've survived this far, so send off the data! |
388 |
|
|
389 |
< |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
390 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
391 |
< |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
392 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
389 |
> |
atomTypeTag = 4*i; |
390 |
> |
atomIsDirectionalTag = 4*i + 1; |
391 |
> |
atomTransDataTag = 4*i + 2; |
392 |
> |
atomOrientDataTag = 4*i + 3; |
393 |
> |
|
394 |
> |
|
395 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
396 |
> |
|
397 |
> |
// null terminate the string before sending (just in case): |
398 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
399 |
> |
|
400 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
401 |
> |
atomTypeTag, MPI_COMM_WORLD); |
402 |
> |
|
403 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
404 |
> |
atomIsDirectionalTag, MPI_COMM_WORLD); |
405 |
> |
|
406 |
> |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
407 |
> |
atomTransDataTag, MPI_COMM_WORLD); |
408 |
> |
|
409 |
> |
if (isDirectional) { |
410 |
> |
|
411 |
> |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
412 |
> |
atomOrientDataTag, MPI_COMM_WORLD); |
413 |
> |
|
414 |
> |
} |
415 |
> |
|
416 |
> |
} |
417 |
|
} |
333 |
– |
} |
334 |
– |
outFile.flush(); |
335 |
– |
sprintf( checkPointMsg, |
336 |
– |
"Sucessfully took a dump.\n"); |
337 |
– |
MPIcheckPoint(); |
418 |
|
|
419 |
< |
// last thing last, enable fatalities. |
419 |
> |
sprintf( checkPointMsg, |
420 |
> |
"Sucessfully took a dump.\n"); |
421 |
> |
MPIcheckPoint(); |
422 |
> |
|
423 |
> |
} |
424 |
> |
|
425 |
|
painCave.isEventLoop = 0; |
426 |
|
|
427 |
|
#endif // is_mpi |
433 |
|
ofstream finalOut; |
434 |
|
|
435 |
|
const int BUFFERSIZE = 2000; |
436 |
+ |
const int MINIBUFFERSIZE = 100; |
437 |
|
char tempBuffer[BUFFERSIZE]; |
438 |
< |
char writeLine[BUFFERSIZE]; |
438 |
> |
char writeLine[BUFFERSIZE]; |
439 |
|
|
440 |
|
double q[4]; |
441 |
|
DirectionalAtom* dAtom; |
443 |
|
int i; |
444 |
|
#ifdef IS_MPI |
445 |
|
int j, which_node, done, which_atom, local_index; |
446 |
+ |
double atomTransData[6]; |
447 |
+ |
double atomOrientData[7]; |
448 |
+ |
int isDirectional; |
449 |
+ |
char* atomTypeString; |
450 |
+ |
char MPIatomTypeString[MINIBUFFERSIZE]; |
451 |
+ |
int atomTypeTag; |
452 |
+ |
int atomIsDirectionalTag; |
453 |
+ |
int atomTransDataTag; |
454 |
+ |
int atomOrientDataTag; |
455 |
|
#else //is_mpi |
456 |
|
int nAtoms = entry_plug->n_atoms; |
457 |
|
#endif //is_mpi |
458 |
< |
|
458 |
> |
|
459 |
|
double pos[3], vel[3]; |
460 |
< |
|
460 |
> |
|
461 |
|
#ifdef IS_MPI |
462 |
|
if(worldRank == 0 ){ |
463 |
|
#endif // is_mpi |
464 |
< |
|
464 |
> |
|
465 |
|
strcpy( finalName, entry_plug->finalName ); |
466 |
< |
|
466 |
> |
|
467 |
|
finalOut.open( finalName, ios::out | ios::trunc ); |
468 |
|
if( !finalOut ){ |
469 |
|
sprintf( painCave.errMsg, |
472 |
|
painCave.isFatal = 1; |
473 |
|
simError(); |
474 |
|
} |
475 |
< |
|
475 |
> |
|
476 |
|
// finalOut.setf( ios::scientific ); |
477 |
< |
|
477 |
> |
|
478 |
|
#ifdef IS_MPI |
479 |
|
} |
480 |
< |
|
480 |
> |
|
481 |
|
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
482 |
< |
MPIcheckPoint(); |
483 |
< |
|
482 |
> |
MPIcheckPoint(); |
483 |
> |
|
484 |
|
#endif //is_mpi |
485 |
|
|
486 |
< |
|
486 |
> |
|
487 |
|
#ifndef IS_MPI |
488 |
< |
|
488 |
> |
|
489 |
|
finalOut << nAtoms << "\n"; |
490 |
< |
|
490 |
> |
|
491 |
|
finalOut << finalTime << ";\t" |
492 |
|
<< entry_plug->Hmat[0][0] << "\t" |
493 |
|
<< entry_plug->Hmat[1][0] << "\t" |
494 |
|
<< entry_plug->Hmat[2][0] << ";\t" |
495 |
< |
|
495 |
> |
|
496 |
|
<< entry_plug->Hmat[0][1] << "\t" |
497 |
|
<< entry_plug->Hmat[1][1] << "\t" |
498 |
|
<< entry_plug->Hmat[2][1] << ";\t" |
499 |
< |
|
499 |
> |
|
500 |
|
<< entry_plug->Hmat[0][2] << "\t" |
501 |
|
<< entry_plug->Hmat[1][2] << "\t" |
502 |
< |
<< entry_plug->Hmat[2][2] << ";\n"; |
503 |
< |
|
502 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
503 |
> |
|
504 |
> |
//write out additional parameters, such as chi and eta |
505 |
> |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
506 |
> |
finalOut << endl; |
507 |
> |
|
508 |
|
for( i=0; i<nAtoms; i++ ){ |
509 |
< |
|
509 |
> |
|
510 |
|
atoms[i]->getPos(pos); |
511 |
|
atoms[i]->getVel(vel); |
512 |
< |
|
512 |
> |
|
513 |
|
sprintf( tempBuffer, |
514 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
515 |
|
atoms[i]->getType(), |
522 |
|
strcpy( writeLine, tempBuffer ); |
523 |
|
|
524 |
|
if( atoms[i]->isDirectional() ){ |
525 |
< |
|
525 |
> |
|
526 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
527 |
|
dAtom->getQ( q ); |
528 |
< |
|
528 |
> |
|
529 |
|
sprintf( tempBuffer, |
530 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
531 |
|
q[0], |
539 |
|
} |
540 |
|
else |
541 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
542 |
< |
|
542 |
> |
|
543 |
|
finalOut << writeLine; |
544 |
|
} |
545 |
|
finalOut.flush(); |
546 |
|
finalOut.close(); |
547 |
|
|
548 |
|
#else // is_mpi |
549 |
< |
|
549 |
> |
|
550 |
|
// first thing first, suspend fatalities. |
551 |
|
painCave.isEventLoop = 1; |
552 |
|
|
557 |
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
558 |
|
|
559 |
|
// write out header and node 0's coordinates |
560 |
< |
|
462 |
< |
haveError = 0; |
560 |
> |
|
561 |
|
if( worldRank == 0 ){ |
562 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
563 |
< |
|
563 |
> |
|
564 |
|
finalOut << finalTime << ";\t" |
565 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
566 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
567 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
568 |
< |
|
569 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
570 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
571 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
572 |
< |
|
573 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
574 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
575 |
< |
<< entry_plug->Hmat[2][2] << ";\n"; |
576 |
< |
|
565 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
566 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
567 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
568 |
> |
|
569 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
570 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
571 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
572 |
> |
|
573 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
574 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
575 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
576 |
> |
|
577 |
> |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
578 |
> |
finalOut << endl; |
579 |
> |
finalOut.flush(); |
580 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
581 |
< |
// Get the Node number which has this molecule: |
481 |
< |
|
482 |
< |
which_node = AtomToProcMap[i]; |
483 |
< |
|
484 |
< |
if (which_node == mpiSim->getMyNode()) { |
581 |
> |
// Get the Node number which has this atom; |
582 |
|
|
583 |
+ |
which_node = AtomToProcMap[i]; |
584 |
+ |
|
585 |
+ |
if (which_node != 0) { |
586 |
+ |
|
587 |
+ |
atomTypeTag = 4*i; |
588 |
+ |
atomIsDirectionalTag = 4*i + 1; |
589 |
+ |
atomTransDataTag = 4*i + 2; |
590 |
+ |
atomOrientDataTag = 4*i + 3; |
591 |
+ |
|
592 |
+ |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
593 |
+ |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
594 |
+ |
|
595 |
+ |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
596 |
+ |
|
597 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
598 |
+ |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
599 |
+ |
|
600 |
+ |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
601 |
+ |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
602 |
+ |
|
603 |
+ |
if (isDirectional) { |
604 |
+ |
|
605 |
+ |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
606 |
+ |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
607 |
+ |
|
608 |
+ |
} |
609 |
+ |
|
610 |
+ |
} else { |
611 |
+ |
|
612 |
+ |
haveError = 0; |
613 |
|
which_atom = i; |
614 |
< |
local_index=-1; |
614 |
> |
local_index=-1; |
615 |
> |
|
616 |
|
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
617 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
618 |
|
} |
491 |
– |
if (local_index != -1) { |
619 |
|
|
620 |
+ |
if (local_index != -1) { |
621 |
+ |
|
622 |
+ |
atomTypeString = atoms[local_index]->getType(); |
623 |
+ |
|
624 |
|
atoms[local_index]->getPos(pos); |
625 |
|
atoms[local_index]->getVel(vel); |
626 |
< |
|
627 |
< |
sprintf( tempBuffer, |
628 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
629 |
< |
atoms[local_index]->getType(), |
630 |
< |
pos[0], |
631 |
< |
pos[1], |
632 |
< |
pos[2], |
633 |
< |
vel[0], |
634 |
< |
vel[1], |
635 |
< |
vel[2]); |
636 |
< |
strcpy( writeLine, tempBuffer ); |
637 |
< |
|
638 |
< |
if( atoms[local_index]->isDirectional() ){ |
639 |
< |
|
640 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
641 |
< |
dAtom->getQ( q ); |
642 |
< |
|
643 |
< |
sprintf( tempBuffer, |
644 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
645 |
< |
q[0], |
646 |
< |
q[1], |
647 |
< |
q[2], |
648 |
< |
q[3], |
649 |
< |
dAtom->getJx(), |
650 |
< |
dAtom->getJy(), |
651 |
< |
dAtom->getJz()); |
652 |
< |
strcat( writeLine, tempBuffer ); |
653 |
< |
} |
654 |
< |
else |
524 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
525 |
< |
} |
526 |
< |
else { |
626 |
> |
|
627 |
> |
atomTransData[0] = pos[0]; |
628 |
> |
atomTransData[1] = pos[1]; |
629 |
> |
atomTransData[2] = pos[2]; |
630 |
> |
|
631 |
> |
atomTransData[3] = vel[0]; |
632 |
> |
atomTransData[4] = vel[1]; |
633 |
> |
atomTransData[5] = vel[2]; |
634 |
> |
|
635 |
> |
isDirectional = 0; |
636 |
> |
|
637 |
> |
if( atoms[local_index]->isDirectional() ){ |
638 |
> |
|
639 |
> |
isDirectional = 1; |
640 |
> |
|
641 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
642 |
> |
dAtom->getQ( q ); |
643 |
> |
|
644 |
> |
atomOrientData[0] = q[0]; |
645 |
> |
atomOrientData[1] = q[1]; |
646 |
> |
atomOrientData[2] = q[2]; |
647 |
> |
atomOrientData[3] = q[3]; |
648 |
> |
|
649 |
> |
atomOrientData[4] = dAtom->getJx(); |
650 |
> |
atomOrientData[5] = dAtom->getJy(); |
651 |
> |
atomOrientData[6] = dAtom->getJz(); |
652 |
> |
} |
653 |
> |
|
654 |
> |
} else { |
655 |
|
sprintf(painCave.errMsg, |
656 |
|
"Atom %d not found on processor %d\n", |
657 |
|
i, worldRank ); |
658 |
|
haveError= 1; |
659 |
|
simError(); |
660 |
< |
} |
660 |
> |
} |
661 |
|
|
662 |
< |
if(haveError) nodeZeroError(); |
663 |
< |
|
664 |
< |
} |
537 |
< |
else { |
662 |
> |
if(haveError) DieDieDie(); |
663 |
> |
|
664 |
> |
// If we've survived to here, format the line: |
665 |
|
|
666 |
< |
myStatus = 1; |
667 |
< |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
668 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
669 |
< |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
670 |
< |
MPI_COMM_WORLD); |
671 |
< |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
672 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
673 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
674 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
675 |
< |
|
676 |
< |
if(!myStatus) nodeZeroError(); |
666 |
> |
sprintf( tempBuffer, |
667 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
668 |
> |
atomTypeString, |
669 |
> |
atomTransData[0], |
670 |
> |
atomTransData[1], |
671 |
> |
atomTransData[2], |
672 |
> |
atomTransData[3], |
673 |
> |
atomTransData[4], |
674 |
> |
atomTransData[5]); |
675 |
> |
|
676 |
> |
strcpy( writeLine, tempBuffer ); |
677 |
> |
|
678 |
> |
if (isDirectional) { |
679 |
> |
|
680 |
> |
sprintf( tempBuffer, |
681 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
682 |
> |
atomOrientData[0], |
683 |
> |
atomOrientData[1], |
684 |
> |
atomOrientData[2], |
685 |
> |
atomOrientData[3], |
686 |
> |
atomOrientData[4], |
687 |
> |
atomOrientData[5], |
688 |
> |
atomOrientData[6]); |
689 |
> |
strcat( writeLine, tempBuffer ); |
690 |
> |
|
691 |
> |
} else { |
692 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
693 |
> |
} |
694 |
> |
|
695 |
> |
finalOut << writeLine; |
696 |
> |
finalOut.flush(); |
697 |
|
} |
551 |
– |
|
552 |
– |
finalOut << writeLine; |
698 |
|
} |
554 |
– |
|
555 |
– |
// kill everyone off: |
556 |
– |
myStatus = -1; |
557 |
– |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
558 |
– |
MPI_Send(&myStatus, 1, MPI_INT, j, |
559 |
– |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
560 |
– |
} |
699 |
|
|
700 |
< |
} else { |
700 |
> |
finalOut.flush(); |
701 |
> |
sprintf( checkPointMsg, |
702 |
> |
"Sucessfully took a dump.\n"); |
703 |
> |
MPIcheckPoint(); |
704 |
|
|
705 |
< |
done = 0; |
565 |
< |
while (!done) { |
705 |
> |
} else { |
706 |
|
|
707 |
< |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
708 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
707 |
> |
// worldRank != 0, so I'm a remote node. |
708 |
> |
|
709 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
710 |
|
|
711 |
< |
if(!myStatus) anonymousNodeDie(); |
711 |
> |
// Am I the node which has this atom? |
712 |
|
|
713 |
< |
if(myStatus < 0) break; |
573 |
< |
|
574 |
< |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
575 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
576 |
< |
|
577 |
< |
myStatus = 1; |
578 |
< |
local_index=-1; |
579 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
580 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
581 |
< |
} |
582 |
< |
if (local_index != -1) { |
713 |
> |
if (AtomToProcMap[i] == worldRank) { |
714 |
|
|
715 |
< |
atoms[local_index]->getPos(pos); |
716 |
< |
atoms[local_index]->getVel(vel); |
715 |
> |
local_index=-1; |
716 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
717 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
718 |
> |
} |
719 |
> |
if (local_index != -1) { |
720 |
> |
|
721 |
> |
atomTypeString = atoms[local_index]->getType(); |
722 |
|
|
723 |
< |
//format the line |
724 |
< |
sprintf( tempBuffer, |
725 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
726 |
< |
atoms[local_index]->getType(), |
727 |
< |
pos[0], |
728 |
< |
pos[1], |
729 |
< |
pos[2], |
730 |
< |
vel[0], |
731 |
< |
vel[1], |
732 |
< |
vel[2]); // check here. |
733 |
< |
strcpy( writeLine, tempBuffer ); |
734 |
< |
|
735 |
< |
if( atoms[local_index]->isDirectional() ){ |
736 |
< |
|
737 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
738 |
< |
dAtom->getQ( q ); |
739 |
< |
|
740 |
< |
sprintf( tempBuffer, |
741 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
742 |
< |
q[0], |
743 |
< |
q[1], |
744 |
< |
q[2], |
745 |
< |
q[3], |
746 |
< |
dAtom->getJx(), |
747 |
< |
dAtom->getJy(), |
748 |
< |
dAtom->getJz()); |
749 |
< |
strcat( writeLine, tempBuffer ); |
723 |
> |
atoms[local_index]->getPos(pos); |
724 |
> |
atoms[local_index]->getVel(vel); |
725 |
> |
|
726 |
> |
atomTransData[0] = pos[0]; |
727 |
> |
atomTransData[1] = pos[1]; |
728 |
> |
atomTransData[2] = pos[2]; |
729 |
> |
|
730 |
> |
atomTransData[3] = vel[0]; |
731 |
> |
atomTransData[4] = vel[1]; |
732 |
> |
atomTransData[5] = vel[2]; |
733 |
> |
|
734 |
> |
isDirectional = 0; |
735 |
> |
|
736 |
> |
if( atoms[local_index]->isDirectional() ){ |
737 |
> |
|
738 |
> |
isDirectional = 1; |
739 |
> |
|
740 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
741 |
> |
dAtom->getQ( q ); |
742 |
> |
|
743 |
> |
atomOrientData[0] = q[0]; |
744 |
> |
atomOrientData[1] = q[1]; |
745 |
> |
atomOrientData[2] = q[2]; |
746 |
> |
atomOrientData[3] = q[3]; |
747 |
> |
|
748 |
> |
atomOrientData[4] = dAtom->getJx(); |
749 |
> |
atomOrientData[5] = dAtom->getJy(); |
750 |
> |
atomOrientData[6] = dAtom->getJz(); |
751 |
> |
} |
752 |
> |
|
753 |
> |
} else { |
754 |
> |
sprintf(painCave.errMsg, |
755 |
> |
"Atom %d not found on processor %d\n", |
756 |
> |
i, worldRank ); |
757 |
> |
haveError= 1; |
758 |
> |
simError(); |
759 |
|
} |
615 |
– |
else{ |
616 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
617 |
– |
} |
618 |
– |
} |
619 |
– |
else { |
620 |
– |
sprintf(painCave.errMsg, |
621 |
– |
"Atom %d not found on processor %d\n", |
622 |
– |
which_atom, worldRank ); |
623 |
– |
myStatus = 0; |
624 |
– |
simError(); |
625 |
– |
|
626 |
– |
strcpy( writeLine, "Hello, I'm an error.\n"); |
627 |
– |
} |
760 |
|
|
761 |
< |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
762 |
< |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
763 |
< |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
764 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
761 |
> |
// I've survived this far, so send off the data! |
762 |
> |
|
763 |
> |
atomTypeTag = 4*i; |
764 |
> |
atomIsDirectionalTag = 4*i + 1; |
765 |
> |
atomTransDataTag = 4*i + 2; |
766 |
> |
atomOrientDataTag = 4*i + 3; |
767 |
> |
|
768 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
769 |
> |
|
770 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
771 |
> |
atomTypeTag, MPI_COMM_WORLD); |
772 |
> |
|
773 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
774 |
> |
atomIsDirectionalTag, MPI_COMM_WORLD); |
775 |
> |
|
776 |
> |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
777 |
> |
atomTransDataTag, MPI_COMM_WORLD); |
778 |
> |
|
779 |
> |
if (isDirectional) { |
780 |
> |
|
781 |
> |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
782 |
> |
atomOrientDataTag, MPI_COMM_WORLD); |
783 |
> |
|
784 |
> |
} |
785 |
> |
|
786 |
> |
} |
787 |
|
} |
788 |
+ |
|
789 |
+ |
sprintf( checkPointMsg, |
790 |
+ |
"Sucessfully wrote final file.\n"); |
791 |
+ |
MPIcheckPoint(); |
792 |
+ |
|
793 |
|
} |
635 |
– |
finalOut.flush(); |
636 |
– |
sprintf( checkPointMsg, |
637 |
– |
"Sucessfully took a dump.\n"); |
638 |
– |
MPIcheckPoint(); |
794 |
|
|
795 |
< |
if( worldRank == 0 ) finalOut.close(); |
795 |
> |
painCave.isEventLoop = 0; |
796 |
> |
|
797 |
> |
if( worldRank == 0 ) finalOut.close(); |
798 |
|
#endif // is_mpi |
799 |
|
} |
800 |
|
|
804 |
|
|
805 |
|
// a couple of functions to let us escape the write loop |
806 |
|
|
807 |
< |
void dWrite::nodeZeroError( void ){ |
651 |
< |
int j, myStatus; |
652 |
< |
|
653 |
< |
myStatus = 0; |
654 |
< |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
655 |
< |
MPI_Send( &myStatus, 1, MPI_INT, j, |
656 |
< |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
657 |
< |
} |
658 |
< |
|
807 |
> |
void dWrite::DieDieDie( void ){ |
808 |
|
|
809 |
|
MPI_Finalize(); |
810 |
|
exit (0); |
662 |
– |
|
811 |
|
} |
812 |
|
|
665 |
– |
void dWrite::anonymousNodeDie( void ){ |
666 |
– |
|
667 |
– |
MPI_Finalize(); |
668 |
– |
exit (0); |
669 |
– |
} |
670 |
– |
|
813 |
|
#endif //is_mpi |