1 |
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#include <cstring> |
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#define _FILE_OFFSET_BITS 64 |
2 |
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|
3 |
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#include <string.h> |
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#include <iostream> |
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#include <fstream> |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
7 |
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#include <mpi++.h> |
9 |
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#include "mpiSimulation.hpp" |
10 |
< |
#define TAKE_THIS_TAG 0 |
10 |
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|
11 |
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namespace dWrite{ |
12 |
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void DieDieDie( void ); |
13 |
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} |
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|
15 |
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using namespace dWrite; |
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#endif //is_mpi |
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|
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#include "ReadWrite.hpp" |
25 |
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#ifdef IS_MPI |
26 |
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if(worldRank == 0 ){ |
27 |
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#endif // is_mpi |
28 |
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|
23 |
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|
24 |
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|
28 |
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|
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strcpy( outName, entry_plug->sampleName ); |
30 |
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|
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|
31 |
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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, |
36 |
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"Could not open \"%s\" for dump output.\n", |
37 |
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outName); |
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painCave.isFatal = 1; |
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simError(); |
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} |
41 |
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|
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|
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//outFile.setf( ios::scientific ); |
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|
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#ifdef IS_MPI |
64 |
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} |
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66 |
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void DumpWriter::writeDump( double currentTime ){ |
67 |
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|
67 |
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|
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const int BUFFERSIZE = 2000; |
69 |
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const int MINIBUFFERSIZE = 10; |
70 |
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|
71 |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
74 |
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int i, j, which_node, done, game_over, which_atom, local_index; |
74 |
> |
int i; |
75 |
> |
#ifdef IS_MPI |
76 |
> |
int j, which_node, done, which_atom, local_index; |
77 |
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double atomTransData[6]; |
78 |
> |
double atomOrientData[7]; |
79 |
> |
int isDirectional; |
80 |
> |
char* atomTypeString; |
81 |
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char MPIatomTypeString[MINIBUFFERSIZE]; |
82 |
> |
int me; |
83 |
> |
int atomTypeTag; |
84 |
> |
int atomIsDirectionalTag; |
85 |
> |
int atomTransDataTag; |
86 |
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int atomOrientDataTag; |
87 |
> |
#else //is_mpi |
88 |
> |
int nAtoms = entry_plug->n_atoms; |
89 |
> |
#endif //is_mpi |
90 |
> |
|
91 |
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double q[4]; |
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DirectionalAtom* dAtom; |
71 |
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int nAtoms = entry_plug->n_atoms; |
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Atom** atoms = entry_plug->atoms; |
94 |
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|
94 |
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double pos[3], vel[3]; |
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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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|
101 |
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|
102 |
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outFile << nAtoms << "\n"; |
103 |
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|
104 |
< |
outFile << currentTime << "\t" |
105 |
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<< entry_plug->box_x << "\t" |
106 |
< |
<< entry_plug->box_y << "\t" |
107 |
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<< entry_plug->box_z << "\n"; |
108 |
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|
103 |
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|
104 |
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outFile << currentTime << ";\t" |
105 |
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<< entry_plug->Hmat[0][0] << "\t" |
106 |
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<< entry_plug->Hmat[1][0] << "\t" |
107 |
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<< entry_plug->Hmat[2][0] << ";\t" |
108 |
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|
109 |
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
111 |
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<< entry_plug->Hmat[2][1] << ";\t" |
112 |
> |
|
113 |
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<< entry_plug->Hmat[0][2] << "\t" |
114 |
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<< entry_plug->Hmat[1][2] << "\t" |
115 |
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<< entry_plug->Hmat[2][2] << ";"; |
116 |
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//write out additional parameters, such as chi and eta |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
118 |
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outFile << endl; |
119 |
> |
|
120 |
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for( i=0; i<nAtoms; i++ ){ |
85 |
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|
121 |
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|
122 |
+ |
atoms[i]->getPos(pos); |
123 |
+ |
atoms[i]->getVel(vel); |
124 |
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|
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sprintf( tempBuffer, |
126 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
127 |
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atoms[i]->getType(), |
128 |
< |
atoms[i]->getX(), |
129 |
< |
atoms[i]->getY(), |
130 |
< |
atoms[i]->getZ(), |
131 |
< |
atoms[i]->get_vx(), |
132 |
< |
atoms[i]->get_vy(), |
133 |
< |
atoms[i]->get_vz()); |
128 |
> |
pos[0], |
129 |
> |
pos[1], |
130 |
> |
pos[2], |
131 |
> |
vel[0], |
132 |
> |
vel[1], |
133 |
> |
vel[2]); |
134 |
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strcpy( writeLine, tempBuffer ); |
135 |
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|
136 |
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if( atoms[i]->isDirectional() ){ |
137 |
< |
|
137 |
> |
|
138 |
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dAtom = (DirectionalAtom *)atoms[i]; |
139 |
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dAtom->getQ( q ); |
140 |
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|
140 |
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|
141 |
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sprintf( tempBuffer, |
142 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
143 |
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q[0], |
151 |
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} |
152 |
|
else |
153 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
154 |
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|
154 |
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|
155 |
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outFile << writeLine; |
156 |
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} |
157 |
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outFile.flush(); |
158 |
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|
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#else // is_mpi |
160 |
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|
161 |
< |
MPI::Status istatus; |
161 |
> |
// first thing first, suspend fatalities. |
162 |
> |
painCave.isEventLoop = 1; |
163 |
> |
|
164 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
165 |
> |
int haveError; |
166 |
> |
|
167 |
> |
MPI_Status istatus; |
168 |
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
169 |
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|
169 |
> |
|
170 |
|
// write out header and node 0's coordinates |
171 |
< |
|
171 |
> |
|
172 |
|
if( worldRank == 0 ){ |
173 |
|
outFile << mpiSim->getTotAtoms() << "\n"; |
174 |
< |
|
175 |
< |
outFile << currentTime << "\t" |
176 |
< |
<< entry_plug->box_x << "\t" |
177 |
< |
<< entry_plug->box_y << "\t" |
178 |
< |
<< entry_plug->box_z << "\n"; |
179 |
< |
|
174 |
> |
|
175 |
> |
outFile << currentTime << ";\t" |
176 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
177 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
178 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
179 |
> |
|
180 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
181 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
182 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
183 |
> |
|
184 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
185 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
186 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
187 |
> |
|
188 |
> |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
189 |
> |
outFile << endl; |
190 |
> |
outFile.flush(); |
191 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
192 |
|
// Get the Node number which has this atom; |
193 |
< |
|
194 |
< |
which_node = AtomToProcMap[i]; |
195 |
< |
|
196 |
< |
if (which_node == mpiSim->getMyNode()) { |
193 |
> |
|
194 |
> |
which_node = AtomToProcMap[i]; |
195 |
> |
|
196 |
> |
if (which_node != 0) { |
197 |
|
|
198 |
+ |
atomTypeTag = 4*i; |
199 |
+ |
atomIsDirectionalTag = 4*i + 1; |
200 |
+ |
atomTransDataTag = 4*i + 2; |
201 |
+ |
atomOrientDataTag = 4*i + 3; |
202 |
+ |
|
203 |
+ |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
204 |
+ |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
205 |
+ |
|
206 |
+ |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
207 |
+ |
|
208 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
209 |
+ |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
210 |
+ |
|
211 |
+ |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
212 |
+ |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
213 |
+ |
|
214 |
+ |
if (isDirectional) { |
215 |
+ |
|
216 |
+ |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
217 |
+ |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
218 |
+ |
|
219 |
+ |
} |
220 |
+ |
|
221 |
+ |
} else { |
222 |
+ |
|
223 |
+ |
haveError = 0; |
224 |
+ |
which_atom = i; |
225 |
+ |
local_index=-1; |
226 |
+ |
|
227 |
+ |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
228 |
+ |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
229 |
+ |
} |
230 |
+ |
|
231 |
+ |
if (local_index != -1) { |
232 |
+ |
|
233 |
+ |
atomTypeString = atoms[local_index]->getType(); |
234 |
+ |
|
235 |
+ |
atoms[local_index]->getPos(pos); |
236 |
+ |
atoms[local_index]->getVel(vel); |
237 |
+ |
|
238 |
+ |
atomTransData[0] = pos[0]; |
239 |
+ |
atomTransData[1] = pos[1]; |
240 |
+ |
atomTransData[2] = pos[2]; |
241 |
+ |
|
242 |
+ |
atomTransData[3] = vel[0]; |
243 |
+ |
atomTransData[4] = vel[1]; |
244 |
+ |
atomTransData[5] = vel[2]; |
245 |
+ |
|
246 |
+ |
isDirectional = 0; |
247 |
+ |
|
248 |
+ |
if( atoms[local_index]->isDirectional() ){ |
249 |
+ |
|
250 |
+ |
isDirectional = 1; |
251 |
+ |
|
252 |
+ |
dAtom = (DirectionalAtom *)atoms[local_index]; |
253 |
+ |
dAtom->getQ( q ); |
254 |
+ |
|
255 |
+ |
atomOrientData[0] = q[0]; |
256 |
+ |
atomOrientData[1] = q[1]; |
257 |
+ |
atomOrientData[2] = q[2]; |
258 |
+ |
atomOrientData[3] = q[3]; |
259 |
+ |
|
260 |
+ |
atomOrientData[4] = dAtom->getJx(); |
261 |
+ |
atomOrientData[5] = dAtom->getJy(); |
262 |
+ |
atomOrientData[6] = dAtom->getJz(); |
263 |
+ |
} |
264 |
+ |
|
265 |
+ |
} else { |
266 |
+ |
sprintf(painCave.errMsg, |
267 |
+ |
"Atom %d not found on processor %d\n", |
268 |
+ |
i, worldRank ); |
269 |
+ |
haveError= 1; |
270 |
+ |
simError(); |
271 |
+ |
} |
272 |
+ |
|
273 |
+ |
if(haveError) DieDieDie(); |
274 |
+ |
|
275 |
+ |
// If we've survived to here, format the line: |
276 |
+ |
|
277 |
|
sprintf( tempBuffer, |
278 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
279 |
< |
atoms[i]->getType(), |
280 |
< |
atoms[i]->getX(), |
281 |
< |
atoms[i]->getY(), |
282 |
< |
atoms[i]->getZ(), |
283 |
< |
atoms[i]->get_vx(), |
284 |
< |
atoms[i]->get_vy(), |
285 |
< |
atoms[i]->get_vz()); |
279 |
> |
atomTypeString, |
280 |
> |
atomTransData[0], |
281 |
> |
atomTransData[1], |
282 |
> |
atomTransData[2], |
283 |
> |
atomTransData[3], |
284 |
> |
atomTransData[4], |
285 |
> |
atomTransData[5]); |
286 |
> |
|
287 |
|
strcpy( writeLine, tempBuffer ); |
288 |
< |
|
289 |
< |
if( atoms[i]->isDirectional() ){ |
290 |
< |
|
156 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
157 |
< |
dAtom->getQ( q ); |
158 |
< |
|
288 |
> |
|
289 |
> |
if (isDirectional) { |
290 |
> |
|
291 |
|
sprintf( tempBuffer, |
292 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
293 |
< |
q[0], |
294 |
< |
q[1], |
295 |
< |
q[2], |
296 |
< |
q[3], |
297 |
< |
dAtom->getJx(), |
298 |
< |
dAtom->getJy(), |
299 |
< |
dAtom->getJz()); |
293 |
> |
atomOrientData[0], |
294 |
> |
atomOrientData[1], |
295 |
> |
atomOrientData[2], |
296 |
> |
atomOrientData[3], |
297 |
> |
atomOrientData[4], |
298 |
> |
atomOrientData[5], |
299 |
> |
atomOrientData[6]); |
300 |
|
strcat( writeLine, tempBuffer ); |
301 |
+ |
|
302 |
+ |
} else { |
303 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
304 |
|
} |
305 |
< |
else |
306 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
307 |
< |
|
173 |
< |
} else { |
174 |
< |
|
175 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
176 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
177 |
< |
TAKE_THIS_TAG, istatus); |
305 |
> |
|
306 |
> |
outFile << writeLine; |
307 |
> |
outFile.flush(); |
308 |
|
} |
179 |
– |
|
180 |
– |
outFile << writeLine; |
309 |
|
} |
182 |
– |
|
183 |
– |
// kill everyone off: |
184 |
– |
game_over = -1; |
185 |
– |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
186 |
– |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
187 |
– |
} |
310 |
|
|
311 |
+ |
outFile.flush(); |
312 |
+ |
sprintf( checkPointMsg, |
313 |
+ |
"Sucessfully took a dump.\n"); |
314 |
+ |
MPIcheckPoint(); |
315 |
+ |
|
316 |
|
} else { |
317 |
+ |
|
318 |
+ |
// worldRank != 0, so I'm a remote node. |
319 |
|
|
320 |
< |
done = 0; |
192 |
< |
while (!done) { |
193 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
194 |
< |
TAKE_THIS_TAG, istatus); |
320 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
321 |
|
|
322 |
< |
if (which_atom == -1) { |
323 |
< |
done=1; |
324 |
< |
continue; |
325 |
< |
} else { |
326 |
< |
local_index=-1; |
327 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
322 |
> |
// Am I the node which has this atom? |
323 |
> |
|
324 |
> |
if (AtomToProcMap[i] == worldRank) { |
325 |
> |
|
326 |
> |
local_index=-1; |
327 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
328 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
329 |
|
} |
330 |
|
if (local_index != -1) { |
331 |
< |
//format the line |
332 |
< |
sprintf( tempBuffer, |
333 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
334 |
< |
atoms[local_index]->getType(), |
335 |
< |
atoms[local_index]->getX(), |
336 |
< |
atoms[local_index]->getY(), |
337 |
< |
atoms[local_index]->getZ(), |
338 |
< |
atoms[local_index]->get_vx(), |
339 |
< |
atoms[local_index]->get_vy(), |
340 |
< |
atoms[local_index]->get_vz()); // check here. |
341 |
< |
strcpy( writeLine, tempBuffer ); |
342 |
< |
|
331 |
> |
|
332 |
> |
atomTypeString = atoms[local_index]->getType(); |
333 |
> |
|
334 |
> |
atoms[local_index]->getPos(pos); |
335 |
> |
atoms[local_index]->getVel(vel); |
336 |
> |
|
337 |
> |
atomTransData[0] = pos[0]; |
338 |
> |
atomTransData[1] = pos[1]; |
339 |
> |
atomTransData[2] = pos[2]; |
340 |
> |
|
341 |
> |
atomTransData[3] = vel[0]; |
342 |
> |
atomTransData[4] = vel[1]; |
343 |
> |
atomTransData[5] = vel[2]; |
344 |
> |
|
345 |
> |
isDirectional = 0; |
346 |
> |
|
347 |
|
if( atoms[local_index]->isDirectional() ){ |
348 |
+ |
|
349 |
+ |
isDirectional = 1; |
350 |
|
|
351 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
352 |
|
dAtom->getQ( q ); |
353 |
|
|
354 |
< |
sprintf( tempBuffer, |
355 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
356 |
< |
q[0], |
357 |
< |
q[1], |
358 |
< |
q[2], |
359 |
< |
q[3], |
360 |
< |
dAtom->getJx(), |
361 |
< |
dAtom->getJy(), |
230 |
< |
dAtom->getJz()); |
231 |
< |
strcat( writeLine, tempBuffer ); |
354 |
> |
atomOrientData[0] = q[0]; |
355 |
> |
atomOrientData[1] = q[1]; |
356 |
> |
atomOrientData[2] = q[2]; |
357 |
> |
atomOrientData[3] = q[3]; |
358 |
> |
|
359 |
> |
atomOrientData[4] = dAtom->getJx(); |
360 |
> |
atomOrientData[5] = dAtom->getJy(); |
361 |
> |
atomOrientData[6] = dAtom->getJz(); |
362 |
|
} |
363 |
< |
else |
234 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
235 |
< |
|
236 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
237 |
< |
TAKE_THIS_TAG); |
363 |
> |
|
364 |
|
} else { |
365 |
< |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
366 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
367 |
< |
TAKE_THIS_TAG); |
365 |
> |
sprintf(painCave.errMsg, |
366 |
> |
"Atom %d not found on processor %d\n", |
367 |
> |
i, worldRank ); |
368 |
> |
haveError= 1; |
369 |
> |
simError(); |
370 |
> |
} |
371 |
> |
|
372 |
> |
// I've survived this far, so send off the data! |
373 |
> |
|
374 |
> |
atomTypeTag = 4*i; |
375 |
> |
atomIsDirectionalTag = 4*i + 1; |
376 |
> |
atomTransDataTag = 4*i + 2; |
377 |
> |
atomOrientDataTag = 4*i + 3; |
378 |
> |
|
379 |
> |
|
380 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
381 |
> |
|
382 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
383 |
> |
atomTypeTag, MPI_COMM_WORLD); |
384 |
> |
|
385 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
386 |
> |
atomIsDirectionalTag, MPI_COMM_WORLD); |
387 |
> |
|
388 |
> |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
389 |
> |
atomTransDataTag, MPI_COMM_WORLD); |
390 |
> |
|
391 |
> |
if (isDirectional) { |
392 |
> |
|
393 |
> |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
394 |
> |
atomOrientDataTag, MPI_COMM_WORLD); |
395 |
> |
|
396 |
|
} |
397 |
+ |
|
398 |
|
} |
399 |
|
} |
400 |
< |
} |
401 |
< |
outFile.flush(); |
402 |
< |
sprintf( checkPointMsg, |
403 |
< |
"Sucessfully took a dump.\n"); |
404 |
< |
MPIcheckPoint(); |
400 |
> |
|
401 |
> |
sprintf( checkPointMsg, |
402 |
> |
"Sucessfully took a dump.\n"); |
403 |
> |
MPIcheckPoint(); |
404 |
> |
|
405 |
> |
} |
406 |
> |
|
407 |
> |
painCave.isEventLoop = 0; |
408 |
> |
|
409 |
|
#endif // is_mpi |
410 |
|
} |
411 |
|
|
412 |
< |
void DumpWriter::writeFinal(){ |
412 |
> |
void DumpWriter::writeFinal(double finalTime){ |
413 |
|
|
414 |
|
char finalName[500]; |
415 |
|
ofstream finalOut; |
416 |
|
|
417 |
|
const int BUFFERSIZE = 2000; |
418 |
+ |
const int MINIBUFFERSIZE = 10; |
419 |
|
char tempBuffer[BUFFERSIZE]; |
420 |
< |
char writeLine[BUFFERSIZE]; |
420 |
> |
char writeLine[BUFFERSIZE]; |
421 |
|
|
422 |
|
double q[4]; |
423 |
|
DirectionalAtom* dAtom; |
264 |
– |
int nAtoms = entry_plug->n_atoms; |
424 |
|
Atom** atoms = entry_plug->atoms; |
425 |
< |
int i, j, which_node, done, game_over, which_atom, local_index; |
426 |
< |
|
427 |
< |
|
425 |
> |
int i; |
426 |
> |
#ifdef IS_MPI |
427 |
> |
int j, which_node, done, which_atom, local_index; |
428 |
> |
double atomTransData[6]; |
429 |
> |
double atomOrientData[7]; |
430 |
> |
int isDirectional; |
431 |
> |
char* atomTypeString; |
432 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
433 |
> |
int atomTypeTag; |
434 |
> |
int atomIsDirectionalTag; |
435 |
> |
int atomTransDataTag; |
436 |
> |
int atomOrientDataTag; |
437 |
> |
#else //is_mpi |
438 |
> |
int nAtoms = entry_plug->n_atoms; |
439 |
> |
#endif //is_mpi |
440 |
> |
|
441 |
> |
double pos[3], vel[3]; |
442 |
> |
|
443 |
|
#ifdef IS_MPI |
444 |
|
if(worldRank == 0 ){ |
445 |
|
#endif // is_mpi |
446 |
< |
|
446 |
> |
|
447 |
|
strcpy( finalName, entry_plug->finalName ); |
448 |
< |
|
448 |
> |
|
449 |
|
finalOut.open( finalName, ios::out | ios::trunc ); |
450 |
|
if( !finalOut ){ |
451 |
|
sprintf( painCave.errMsg, |
454 |
|
painCave.isFatal = 1; |
455 |
|
simError(); |
456 |
|
} |
457 |
< |
|
457 |
> |
|
458 |
|
// finalOut.setf( ios::scientific ); |
459 |
< |
|
459 |
> |
|
460 |
|
#ifdef IS_MPI |
461 |
|
} |
462 |
< |
|
462 |
> |
|
463 |
|
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
464 |
< |
MPIcheckPoint(); |
465 |
< |
|
464 |
> |
MPIcheckPoint(); |
465 |
> |
|
466 |
|
#endif //is_mpi |
467 |
|
|
468 |
< |
|
468 |
> |
|
469 |
|
#ifndef IS_MPI |
470 |
< |
|
470 |
> |
|
471 |
|
finalOut << nAtoms << "\n"; |
472 |
< |
|
473 |
< |
finalOut << entry_plug->box_x << "\t" |
474 |
< |
<< entry_plug->box_y << "\t" |
475 |
< |
<< entry_plug->box_z << "\n"; |
476 |
< |
|
472 |
> |
|
473 |
> |
finalOut << finalTime << ";\t" |
474 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
475 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
476 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
477 |
> |
|
478 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
479 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
480 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
481 |
> |
|
482 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
483 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
484 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
485 |
> |
|
486 |
> |
//write out additional parameters, such as chi and eta |
487 |
> |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
488 |
> |
finalOut << endl; |
489 |
> |
|
490 |
|
for( i=0; i<nAtoms; i++ ){ |
491 |
< |
|
491 |
> |
|
492 |
> |
atoms[i]->getPos(pos); |
493 |
> |
atoms[i]->getVel(vel); |
494 |
> |
|
495 |
|
sprintf( tempBuffer, |
496 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
497 |
|
atoms[i]->getType(), |
498 |
< |
atoms[i]->getX(), |
499 |
< |
atoms[i]->getY(), |
500 |
< |
atoms[i]->getZ(), |
501 |
< |
atoms[i]->get_vx(), |
502 |
< |
atoms[i]->get_vy(), |
503 |
< |
atoms[i]->get_vz()); |
498 |
> |
pos[0], |
499 |
> |
pos[1], |
500 |
> |
pos[2], |
501 |
> |
vel[0], |
502 |
> |
vel[1], |
503 |
> |
vel[2]); |
504 |
|
strcpy( writeLine, tempBuffer ); |
505 |
|
|
506 |
|
if( atoms[i]->isDirectional() ){ |
507 |
< |
|
507 |
> |
|
508 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
509 |
|
dAtom->getQ( q ); |
510 |
< |
|
510 |
> |
|
511 |
|
sprintf( tempBuffer, |
512 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
513 |
|
q[0], |
521 |
|
} |
522 |
|
else |
523 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
524 |
< |
|
524 |
> |
|
525 |
|
finalOut << writeLine; |
526 |
|
} |
527 |
|
finalOut.flush(); |
528 |
|
finalOut.close(); |
529 |
|
|
530 |
|
#else // is_mpi |
531 |
< |
|
532 |
< |
MPI::Status istatus; |
531 |
> |
|
532 |
> |
// first thing first, suspend fatalities. |
533 |
> |
painCave.isEventLoop = 1; |
534 |
> |
|
535 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
536 |
> |
int haveError; |
537 |
> |
|
538 |
> |
MPI_Status istatus; |
539 |
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
540 |
|
|
541 |
|
// write out header and node 0's coordinates |
542 |
< |
|
542 |
> |
|
543 |
|
if( worldRank == 0 ){ |
544 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
545 |
< |
|
546 |
< |
finalOut << entry_plug->box_x << "\t" |
547 |
< |
<< entry_plug->box_y << "\t" |
548 |
< |
<< entry_plug->box_z << "\n"; |
549 |
< |
|
545 |
> |
|
546 |
> |
finalOut << finalTime << ";\t" |
547 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
548 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
549 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
550 |
> |
|
551 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
552 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
553 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
554 |
> |
|
555 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
556 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
557 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
558 |
> |
|
559 |
> |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
560 |
> |
finalOut << endl; |
561 |
> |
finalOut.flush(); |
562 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
563 |
< |
// Get the Node number which has this molecule: |
564 |
< |
|
565 |
< |
which_node = AtomToProcMap[i]; |
566 |
< |
|
567 |
< |
if (which_node == mpiSim->getMyNode()) { |
563 |
> |
// Get the Node number which has this atom; |
564 |
> |
|
565 |
> |
which_node = AtomToProcMap[i]; |
566 |
> |
|
567 |
> |
if (which_node != 0) { |
568 |
|
|
569 |
+ |
atomTypeTag = 4*i; |
570 |
+ |
atomIsDirectionalTag = 4*i + 1; |
571 |
+ |
atomTransDataTag = 4*i + 2; |
572 |
+ |
atomOrientDataTag = 4*i + 3; |
573 |
+ |
|
574 |
+ |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
575 |
+ |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
576 |
+ |
|
577 |
+ |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
578 |
+ |
|
579 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
580 |
+ |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
581 |
+ |
|
582 |
+ |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
583 |
+ |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
584 |
+ |
|
585 |
+ |
if (isDirectional) { |
586 |
+ |
|
587 |
+ |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
588 |
+ |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
589 |
+ |
|
590 |
+ |
} |
591 |
+ |
|
592 |
+ |
} else { |
593 |
+ |
|
594 |
+ |
haveError = 0; |
595 |
+ |
which_atom = i; |
596 |
+ |
local_index=-1; |
597 |
+ |
|
598 |
+ |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
599 |
+ |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
600 |
+ |
} |
601 |
+ |
|
602 |
+ |
if (local_index != -1) { |
603 |
+ |
|
604 |
+ |
atomTypeString = atoms[local_index]->getType(); |
605 |
+ |
|
606 |
+ |
atoms[local_index]->getPos(pos); |
607 |
+ |
atoms[local_index]->getVel(vel); |
608 |
+ |
|
609 |
+ |
atomTransData[0] = pos[0]; |
610 |
+ |
atomTransData[1] = pos[1]; |
611 |
+ |
atomTransData[2] = pos[2]; |
612 |
+ |
|
613 |
+ |
atomTransData[3] = vel[0]; |
614 |
+ |
atomTransData[4] = vel[1]; |
615 |
+ |
atomTransData[5] = vel[2]; |
616 |
+ |
|
617 |
+ |
isDirectional = 0; |
618 |
+ |
|
619 |
+ |
if( atoms[local_index]->isDirectional() ){ |
620 |
+ |
|
621 |
+ |
isDirectional = 1; |
622 |
+ |
|
623 |
+ |
dAtom = (DirectionalAtom *)atoms[local_index]; |
624 |
+ |
dAtom->getQ( q ); |
625 |
+ |
|
626 |
+ |
atomOrientData[0] = q[0]; |
627 |
+ |
atomOrientData[1] = q[1]; |
628 |
+ |
atomOrientData[2] = q[2]; |
629 |
+ |
atomOrientData[3] = q[3]; |
630 |
+ |
|
631 |
+ |
atomOrientData[4] = dAtom->getJx(); |
632 |
+ |
atomOrientData[5] = dAtom->getJy(); |
633 |
+ |
atomOrientData[6] = dAtom->getJz(); |
634 |
+ |
} |
635 |
+ |
|
636 |
+ |
} else { |
637 |
+ |
sprintf(painCave.errMsg, |
638 |
+ |
"Atom %d not found on processor %d\n", |
639 |
+ |
i, worldRank ); |
640 |
+ |
haveError= 1; |
641 |
+ |
simError(); |
642 |
+ |
} |
643 |
+ |
|
644 |
+ |
if(haveError) DieDieDie(); |
645 |
+ |
|
646 |
+ |
// If we've survived to here, format the line: |
647 |
+ |
|
648 |
|
sprintf( tempBuffer, |
649 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
650 |
< |
atoms[i]->getType(), |
651 |
< |
atoms[i]->getX(), |
652 |
< |
atoms[i]->getY(), |
653 |
< |
atoms[i]->getZ(), |
654 |
< |
atoms[i]->get_vx(), |
655 |
< |
atoms[i]->get_vy(), |
656 |
< |
atoms[i]->get_vz()); |
650 |
> |
atomTypeString, |
651 |
> |
atomTransData[0], |
652 |
> |
atomTransData[1], |
653 |
> |
atomTransData[2], |
654 |
> |
atomTransData[3], |
655 |
> |
atomTransData[4], |
656 |
> |
atomTransData[5]); |
657 |
> |
|
658 |
|
strcpy( writeLine, tempBuffer ); |
659 |
< |
|
660 |
< |
if( atoms[i]->isDirectional() ){ |
661 |
< |
|
374 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
375 |
< |
dAtom->getQ( q ); |
376 |
< |
|
659 |
> |
|
660 |
> |
if (isDirectional) { |
661 |
> |
|
662 |
|
sprintf( tempBuffer, |
663 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
664 |
< |
q[0], |
665 |
< |
q[1], |
666 |
< |
q[2], |
667 |
< |
q[3], |
668 |
< |
dAtom->getJx(), |
669 |
< |
dAtom->getJy(), |
670 |
< |
dAtom->getJz()); |
664 |
> |
atomOrientData[0], |
665 |
> |
atomOrientData[1], |
666 |
> |
atomOrientData[2], |
667 |
> |
atomOrientData[3], |
668 |
> |
atomOrientData[4], |
669 |
> |
atomOrientData[5], |
670 |
> |
atomOrientData[6]); |
671 |
|
strcat( writeLine, tempBuffer ); |
672 |
+ |
|
673 |
+ |
} else { |
674 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
675 |
|
} |
676 |
< |
else |
677 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
678 |
< |
|
391 |
< |
} else { |
392 |
< |
|
393 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
394 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
395 |
< |
TAKE_THIS_TAG, istatus); |
676 |
> |
|
677 |
> |
finalOut << writeLine; |
678 |
> |
finalOut.flush(); |
679 |
|
} |
397 |
– |
|
398 |
– |
finalOut << writeLine; |
680 |
|
} |
400 |
– |
|
401 |
– |
// kill everyone off: |
402 |
– |
game_over = -1; |
403 |
– |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
404 |
– |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
405 |
– |
} |
681 |
|
|
682 |
+ |
finalOut.flush(); |
683 |
+ |
sprintf( checkPointMsg, |
684 |
+ |
"Sucessfully took a dump.\n"); |
685 |
+ |
MPIcheckPoint(); |
686 |
+ |
|
687 |
|
} else { |
688 |
+ |
|
689 |
+ |
// worldRank != 0, so I'm a remote node. |
690 |
|
|
691 |
< |
done = 0; |
692 |
< |
while (!done) { |
693 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
694 |
< |
TAKE_THIS_TAG, istatus); |
691 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
692 |
> |
|
693 |
> |
// Am I the node which has this atom? |
694 |
> |
|
695 |
> |
if (AtomToProcMap[i] == worldRank) { |
696 |
|
|
697 |
< |
if (which_atom == -1) { |
698 |
< |
done=1; |
416 |
< |
continue; |
417 |
< |
} else { |
418 |
< |
|
419 |
< |
local_index=-1; |
420 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
697 |
> |
local_index=-1; |
698 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
699 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
700 |
|
} |
701 |
|
if (local_index != -1) { |
702 |
+ |
|
703 |
+ |
atomTypeString = atoms[local_index]->getType(); |
704 |
|
|
705 |
< |
//format the line |
706 |
< |
sprintf( tempBuffer, |
707 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
708 |
< |
atoms[local_index]->getType(), |
709 |
< |
atoms[local_index]->getX(), |
710 |
< |
atoms[local_index]->getY(), |
711 |
< |
atoms[local_index]->getZ(), |
712 |
< |
atoms[local_index]->get_vx(), |
713 |
< |
atoms[local_index]->get_vy(), |
714 |
< |
atoms[local_index]->get_vz()); // check here. |
715 |
< |
strcpy( writeLine, tempBuffer ); |
716 |
< |
|
705 |
> |
atoms[local_index]->getPos(pos); |
706 |
> |
atoms[local_index]->getVel(vel); |
707 |
> |
|
708 |
> |
atomTransData[0] = pos[0]; |
709 |
> |
atomTransData[1] = pos[1]; |
710 |
> |
atomTransData[2] = pos[2]; |
711 |
> |
|
712 |
> |
atomTransData[3] = vel[0]; |
713 |
> |
atomTransData[4] = vel[1]; |
714 |
> |
atomTransData[5] = vel[2]; |
715 |
> |
|
716 |
> |
isDirectional = 0; |
717 |
> |
|
718 |
|
if( atoms[local_index]->isDirectional() ){ |
719 |
+ |
|
720 |
+ |
isDirectional = 1; |
721 |
|
|
722 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
723 |
|
dAtom->getQ( q ); |
724 |
< |
|
725 |
< |
sprintf( tempBuffer, |
726 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
727 |
< |
q[0], |
728 |
< |
q[1], |
729 |
< |
q[2], |
730 |
< |
q[3], |
731 |
< |
dAtom->getJx(), |
732 |
< |
dAtom->getJy(), |
450 |
< |
dAtom->getJz()); |
451 |
< |
strcat( writeLine, tempBuffer ); |
724 |
> |
|
725 |
> |
atomOrientData[0] = q[0]; |
726 |
> |
atomOrientData[1] = q[1]; |
727 |
> |
atomOrientData[2] = q[2]; |
728 |
> |
atomOrientData[3] = q[3]; |
729 |
> |
|
730 |
> |
atomOrientData[4] = dAtom->getJx(); |
731 |
> |
atomOrientData[5] = dAtom->getJy(); |
732 |
> |
atomOrientData[6] = dAtom->getJz(); |
733 |
|
} |
734 |
< |
else |
454 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
455 |
< |
|
456 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
457 |
< |
TAKE_THIS_TAG); |
734 |
> |
|
735 |
|
} else { |
736 |
< |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
737 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
738 |
< |
TAKE_THIS_TAG); |
736 |
> |
sprintf(painCave.errMsg, |
737 |
> |
"Atom %d not found on processor %d\n", |
738 |
> |
i, worldRank ); |
739 |
> |
haveError= 1; |
740 |
> |
simError(); |
741 |
> |
} |
742 |
> |
|
743 |
> |
// I've survived this far, so send off the data! |
744 |
> |
|
745 |
> |
atomTypeTag = 4*i; |
746 |
> |
atomIsDirectionalTag = 4*i + 1; |
747 |
> |
atomTransDataTag = 4*i + 2; |
748 |
> |
atomOrientDataTag = 4*i + 3; |
749 |
> |
|
750 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
751 |
> |
|
752 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
753 |
> |
atomTypeTag, MPI_COMM_WORLD); |
754 |
> |
|
755 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
756 |
> |
atomIsDirectionalTag, MPI_COMM_WORLD); |
757 |
> |
|
758 |
> |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
759 |
> |
atomTransDataTag, MPI_COMM_WORLD); |
760 |
> |
|
761 |
> |
if (isDirectional) { |
762 |
> |
|
763 |
> |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
764 |
> |
atomOrientDataTag, MPI_COMM_WORLD); |
765 |
> |
|
766 |
|
} |
767 |
+ |
|
768 |
|
} |
769 |
|
} |
770 |
+ |
|
771 |
+ |
sprintf( checkPointMsg, |
772 |
+ |
"Sucessfully wrote final file.\n"); |
773 |
+ |
MPIcheckPoint(); |
774 |
+ |
|
775 |
|
} |
776 |
< |
finalOut.flush(); |
777 |
< |
sprintf( checkPointMsg, |
468 |
< |
"Sucessfully took a dump.\n"); |
469 |
< |
MPIcheckPoint(); |
776 |
> |
|
777 |
> |
painCave.isEventLoop = 0; |
778 |
|
|
779 |
< |
if( worldRank == 0 ) finalOut.close(); |
779 |
> |
if( worldRank == 0 ) finalOut.close(); |
780 |
|
#endif // is_mpi |
781 |
|
} |
782 |
+ |
|
783 |
+ |
|
784 |
+ |
|
785 |
+ |
#ifdef IS_MPI |
786 |
+ |
|
787 |
+ |
// a couple of functions to let us escape the write loop |
788 |
+ |
|
789 |
+ |
void dWrite::DieDieDie( void ){ |
790 |
+ |
|
791 |
+ |
MPI_Finalize(); |
792 |
+ |
exit (0); |
793 |
+ |
} |
794 |
+ |
|
795 |
+ |
#endif //is_mpi |