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#include <cstring> |
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#define _FILE_OFFSET_BITS 64 |
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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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#include <algorithm> |
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#include <utility> |
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|
9 |
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#ifdef IS_MPI |
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#include <mpi.h> |
7 |
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#include <mpi++.h> |
11 |
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#include "mpiSimulation.hpp" |
12 |
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#define TAKE_THIS_TAG 0 |
12 |
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|
13 |
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namespace dWrite{ |
14 |
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void DieDieDie( void ); |
15 |
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} |
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|
17 |
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using namespace dWrite; |
18 |
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#endif //is_mpi |
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|
20 |
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#include "ReadWrite.hpp" |
27 |
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#ifdef IS_MPI |
28 |
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if(worldRank == 0 ){ |
29 |
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#endif // is_mpi |
30 |
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|
31 |
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|
32 |
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|
33 |
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strcpy( outName, entry_plug->sampleName ); |
34 |
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|
35 |
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outFile.open(outName, ios::out | ios::trunc ); |
28 |
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|
29 |
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if( !outFile ){ |
30 |
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|
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|
31 |
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|
32 |
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dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
33 |
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|
34 |
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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 |
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outName); |
38 |
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entry_plug->sampleName); |
39 |
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painCave.isFatal = 1; |
40 |
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simError(); |
41 |
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} |
42 |
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|
42 |
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|
43 |
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//outFile.setf( ios::scientific ); |
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|
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#ifdef IS_MPI |
46 |
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} |
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|
48 |
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//sort the local atoms by global index |
49 |
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sortByGlobalIndex(); |
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|
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sprintf( checkPointMsg, |
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"Sucessfully opened output file for dumping.\n"); |
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MPIcheckPoint(); |
60 |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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outFile.close(); |
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dumpFile.close(); |
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|
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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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} |
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|
70 |
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void DumpWriter::writeDump( double currentTime ){ |
70 |
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#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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*/ |
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|
76 |
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void DumpWriter::update(){ |
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sortByGlobalIndex(); |
78 |
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} |
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|
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/** |
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* Auxiliary sorting function |
82 |
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*/ |
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|
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
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return p1.second < p2.second; |
86 |
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} |
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|
88 |
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/** |
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* Sorting the local index by global index |
90 |
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*/ |
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|
92 |
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void DumpWriter::sortByGlobalIndex(){ |
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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 |
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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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} |
102 |
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#endif |
103 |
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|
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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); |
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|
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//write to dump file |
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writeFrame(dumpFile, currentTime); |
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|
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} |
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|
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void DumpWriter::writeFinal(double currentTime){ |
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|
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ofstream finalOut; |
117 |
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|
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//Open eor file |
119 |
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#ifdef IS_MPI |
120 |
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if(worldRank == 0 ){ |
121 |
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#endif // is_mpi |
122 |
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|
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finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
124 |
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if( !finalOut ){ |
125 |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for final dump output.\n", |
127 |
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entry_plug->finalName ); |
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painCave.isFatal = 1; |
129 |
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simError(); |
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} |
131 |
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|
132 |
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#ifdef IS_MPI |
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} |
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 |
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if(worldRank == 0 ){ |
142 |
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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 |
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void DumpWriter::writeFrame( ofstream& outFile, double currentTime ){ |
149 |
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|
150 |
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const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
152 |
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|
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char tempBuffer[BUFFERSIZE]; |
154 |
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char writeLine[BUFFERSIZE]; |
155 |
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|
156 |
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int i, j, which_node, done, game_over, which_atom, local_index; |
156 |
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int i; |
157 |
> |
|
158 |
> |
#ifdef IS_MPI |
159 |
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|
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 |
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#else //is_mpi |
172 |
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int nAtoms = entry_plug->n_atoms; |
173 |
> |
#endif //is_mpi |
174 |
> |
|
175 |
|
double q[4]; |
176 |
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DirectionalAtom* dAtom; |
71 |
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int nAtoms = entry_plug->n_atoms; |
177 |
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Atom** atoms = entry_plug->atoms; |
178 |
< |
|
178 |
> |
double pos[3], vel[3]; |
179 |
|
|
180 |
|
#ifndef IS_MPI |
181 |
< |
|
181 |
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|
182 |
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outFile << nAtoms << "\n"; |
183 |
< |
|
184 |
< |
outFile << currentTime << "\t" |
185 |
< |
<< entry_plug->box_x << "\t" |
186 |
< |
<< entry_plug->box_y << "\t" |
187 |
< |
<< entry_plug->box_z << "\n"; |
188 |
< |
|
183 |
> |
|
184 |
> |
outFile << currentTime << ";\t" |
185 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
186 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
187 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
188 |
> |
|
189 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
190 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
191 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
192 |
> |
|
193 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
194 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
195 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
196 |
> |
//write out additional parameters, such as chi and eta |
197 |
> |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
198 |
> |
outFile << endl; |
199 |
> |
|
200 |
|
for( i=0; i<nAtoms; i++ ){ |
85 |
– |
|
201 |
|
|
202 |
+ |
atoms[i]->getPos(pos); |
203 |
+ |
atoms[i]->getVel(vel); |
204 |
+ |
|
205 |
|
sprintf( tempBuffer, |
206 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
207 |
|
atoms[i]->getType(), |
208 |
< |
atoms[i]->getX(), |
209 |
< |
atoms[i]->getY(), |
210 |
< |
atoms[i]->getZ(), |
211 |
< |
atoms[i]->get_vx(), |
212 |
< |
atoms[i]->get_vy(), |
213 |
< |
atoms[i]->get_vz()); |
208 |
> |
pos[0], |
209 |
> |
pos[1], |
210 |
> |
pos[2], |
211 |
> |
vel[0], |
212 |
> |
vel[1], |
213 |
> |
vel[2]); |
214 |
|
strcpy( writeLine, tempBuffer ); |
215 |
|
|
216 |
|
if( atoms[i]->isDirectional() ){ |
217 |
< |
|
217 |
> |
|
218 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
219 |
|
dAtom->getQ( q ); |
220 |
< |
|
220 |
> |
|
221 |
|
sprintf( tempBuffer, |
222 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
223 |
|
q[0], |
231 |
|
} |
232 |
|
else |
233 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
234 |
< |
|
234 |
> |
|
235 |
|
outFile << writeLine; |
236 |
|
} |
119 |
– |
outFile.flush(); |
237 |
|
|
238 |
|
#else // is_mpi |
239 |
|
|
240 |
< |
MPI::Status istatus; |
124 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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 |
+ |
|
250 |
+ |
int haveError; |
251 |
+ |
|
252 |
+ |
MPI_Status istatus; |
253 |
+ |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
254 |
+ |
|
255 |
|
// write out header and node 0's coordinates |
256 |
< |
|
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" |
270 |
+ |
<< entry_plug->Hmat[0][0] << "\t" |
271 |
+ |
<< entry_plug->Hmat[1][0] << "\t" |
272 |
+ |
<< entry_plug->Hmat[2][0] << ";\t" |
273 |
+ |
|
274 |
+ |
<< entry_plug->Hmat[0][1] << "\t" |
275 |
+ |
<< entry_plug->Hmat[1][1] << "\t" |
276 |
+ |
<< entry_plug->Hmat[2][1] << ";\t" |
277 |
+ |
|
278 |
+ |
<< entry_plug->Hmat[0][2] << "\t" |
279 |
+ |
<< entry_plug->Hmat[1][2] << "\t" |
280 |
+ |
<< entry_plug->Hmat[2][2] << ";"; |
281 |
+ |
|
282 |
+ |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
283 |
+ |
outFile << endl; |
284 |
+ |
outFile.flush(); |
285 |
|
|
286 |
< |
outFile << currentTime << "\t" |
132 |
< |
<< entry_plug->box_x << "\t" |
133 |
< |
<< entry_plug->box_y << "\t" |
134 |
< |
<< entry_plug->box_z << "\n"; |
135 |
< |
|
286 |
> |
currentIndex = 0; |
287 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
288 |
+ |
|
289 |
|
// Get the Node number which has this atom; |
290 |
|
|
291 |
< |
which_node = AtomToProcMap[i]; |
291 |
> |
which_node = AtomToProcMap[i]; |
292 |
|
|
293 |
< |
if (which_node == mpiSim->getMyNode()) { |
293 |
> |
if (which_node != 0) { |
294 |
> |
|
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 |
< |
sprintf( tempBuffer, |
307 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
308 |
< |
atoms[i]->getType(), |
309 |
< |
atoms[i]->getX(), |
147 |
< |
atoms[i]->getY(), |
148 |
< |
atoms[i]->getZ(), |
149 |
< |
atoms[i]->get_vx(), |
150 |
< |
atoms[i]->get_vy(), |
151 |
< |
atoms[i]->get_vz()); |
152 |
< |
strcpy( writeLine, tempBuffer ); |
306 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
307 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
308 |
> |
|
309 |
> |
atomTypeString = MPIatomTypeString; |
310 |
|
|
311 |
< |
if( atoms[i]->isDirectional() ){ |
312 |
< |
|
313 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
314 |
< |
dAtom->getQ( q ); |
315 |
< |
|
316 |
< |
sprintf( tempBuffer, |
317 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
318 |
< |
q[0], |
319 |
< |
q[1], |
320 |
< |
q[2], |
321 |
< |
q[3], |
322 |
< |
dAtom->getJx(), |
323 |
< |
dAtom->getJy(), |
167 |
< |
dAtom->getJz()); |
168 |
< |
strcat( writeLine, tempBuffer ); |
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 |
|
} |
170 |
– |
else |
171 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
325 |
|
|
326 |
+ |
myPotato++; |
327 |
+ |
potatoes[which_node] = myPotato; |
328 |
+ |
|
329 |
|
} else { |
330 |
|
|
331 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
332 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
333 |
< |
TAKE_THIS_TAG, istatus); |
334 |
< |
} |
335 |
< |
|
336 |
< |
outFile << writeLine; |
337 |
< |
} |
338 |
< |
|
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 |
< |
} |
331 |
> |
haveError = 0; |
332 |
> |
which_atom = i; |
333 |
> |
|
334 |
> |
local_index = indexArray[currentIndex].first; |
335 |
> |
|
336 |
> |
if (which_atom == indexArray[currentIndex].second) { |
337 |
> |
|
338 |
> |
atomTypeString = atoms[local_index]->getType(); |
339 |
|
|
340 |
< |
} else { |
341 |
< |
|
342 |
< |
done = 0; |
343 |
< |
while (!done) { |
344 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
345 |
< |
TAKE_THIS_TAG, istatus); |
346 |
< |
|
347 |
< |
if (which_atom == -1) { |
348 |
< |
done=1; |
349 |
< |
continue; |
350 |
< |
} else { |
351 |
< |
local_index=-1; |
352 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
202 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
203 |
< |
} |
204 |
< |
if (local_index != -1) { |
205 |
< |
//format the line |
206 |
< |
sprintf( tempBuffer, |
207 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
208 |
< |
atoms[local_index]->getType(), |
209 |
< |
atoms[local_index]->getX(), |
210 |
< |
atoms[local_index]->getY(), |
211 |
< |
atoms[local_index]->getZ(), |
212 |
< |
atoms[local_index]->get_vx(), |
213 |
< |
atoms[local_index]->get_vy(), |
214 |
< |
atoms[local_index]->get_vz()); // check here. |
215 |
< |
strcpy( writeLine, tempBuffer ); |
216 |
< |
|
340 |
> |
atoms[local_index]->getPos(pos); |
341 |
> |
atoms[local_index]->getVel(vel); |
342 |
> |
|
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 |
+ |
for (int j = 0; j < 6 ; j++) |
361 |
+ |
atomData13[j] = atomData6[j]; |
362 |
|
|
363 |
< |
sprintf( tempBuffer, |
364 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
365 |
< |
q[0], |
366 |
< |
q[1], |
367 |
< |
q[2], |
368 |
< |
q[3], |
369 |
< |
dAtom->getJx(), |
370 |
< |
dAtom->getJy(), |
230 |
< |
dAtom->getJz()); |
231 |
< |
strcat( writeLine, tempBuffer ); |
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 |
|
} |
233 |
– |
else |
234 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
372 |
|
|
373 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
374 |
< |
TAKE_THIS_TAG); |
375 |
< |
} else { |
376 |
< |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
377 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
378 |
< |
TAKE_THIS_TAG); |
379 |
< |
} |
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) DieDieDie(); |
382 |
> |
|
383 |
> |
currentIndex ++; |
384 |
|
} |
385 |
< |
} |
245 |
< |
} |
246 |
< |
outFile.flush(); |
247 |
< |
sprintf( checkPointMsg, |
248 |
< |
"Sucessfully took a dump.\n"); |
249 |
< |
MPIcheckPoint(); |
250 |
< |
#endif // is_mpi |
251 |
< |
} |
252 |
< |
|
253 |
< |
void DumpWriter::writeFinal(){ |
254 |
< |
|
255 |
< |
char finalName[500]; |
256 |
< |
ofstream finalOut; |
257 |
< |
|
258 |
< |
const int BUFFERSIZE = 2000; |
259 |
< |
char tempBuffer[BUFFERSIZE]; |
260 |
< |
char writeLine[BUFFERSIZE]; |
261 |
< |
|
262 |
< |
double q[4]; |
263 |
< |
DirectionalAtom* dAtom; |
264 |
< |
int nAtoms = entry_plug->n_atoms; |
265 |
< |
Atom** atoms = entry_plug->atoms; |
266 |
< |
int i, j, which_node, done, game_over, which_atom, local_index; |
267 |
< |
|
268 |
< |
|
269 |
< |
#ifdef IS_MPI |
270 |
< |
if(worldRank == 0 ){ |
271 |
< |
#endif // is_mpi |
272 |
< |
|
273 |
< |
strcpy( finalName, entry_plug->finalName ); |
274 |
< |
|
275 |
< |
finalOut.open( finalName, ios::out | ios::trunc ); |
276 |
< |
if( !finalOut ){ |
277 |
< |
sprintf( painCave.errMsg, |
278 |
< |
"Could not open \"%s\" for final dump output.\n", |
279 |
< |
finalName ); |
280 |
< |
painCave.isFatal = 1; |
281 |
< |
simError(); |
282 |
< |
} |
283 |
< |
|
284 |
< |
// finalOut.setf( ios::scientific ); |
285 |
< |
|
286 |
< |
#ifdef IS_MPI |
287 |
< |
} |
288 |
< |
|
289 |
< |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
290 |
< |
MPIcheckPoint(); |
291 |
< |
|
292 |
< |
#endif //is_mpi |
293 |
< |
|
294 |
< |
|
295 |
< |
#ifndef IS_MPI |
296 |
< |
|
297 |
< |
finalOut << nAtoms << "\n"; |
298 |
< |
|
299 |
< |
finalOut << entry_plug->box_x << "\t" |
300 |
< |
<< entry_plug->box_y << "\t" |
301 |
< |
<< entry_plug->box_z << "\n"; |
302 |
< |
|
303 |
< |
for( i=0; i<nAtoms; i++ ){ |
385 |
> |
// If we've survived to here, format the line: |
386 |
|
|
387 |
< |
sprintf( tempBuffer, |
306 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
307 |
< |
atoms[i]->getType(), |
308 |
< |
atoms[i]->getX(), |
309 |
< |
atoms[i]->getY(), |
310 |
< |
atoms[i]->getZ(), |
311 |
< |
atoms[i]->get_vx(), |
312 |
< |
atoms[i]->get_vy(), |
313 |
< |
atoms[i]->get_vz()); |
314 |
< |
strcpy( writeLine, tempBuffer ); |
315 |
< |
|
316 |
< |
if( atoms[i]->isDirectional() ){ |
387 |
> |
if (!isDirectional) { |
388 |
|
|
389 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
390 |
< |
dAtom->getQ( q ); |
391 |
< |
|
392 |
< |
sprintf( tempBuffer, |
393 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
394 |
< |
q[0], |
395 |
< |
q[1], |
396 |
< |
q[2], |
397 |
< |
q[3], |
327 |
< |
dAtom->getJx(), |
328 |
< |
dAtom->getJy(), |
329 |
< |
dAtom->getJz()); |
330 |
< |
strcat( writeLine, tempBuffer ); |
331 |
< |
} |
332 |
< |
else |
333 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
334 |
< |
|
335 |
< |
finalOut << writeLine; |
336 |
< |
} |
337 |
< |
finalOut.flush(); |
338 |
< |
finalOut.close(); |
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 |
< |
#else // is_mpi |
341 |
< |
|
342 |
< |
MPI::Status istatus; |
343 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
344 |
< |
|
345 |
< |
// write out header and node 0's coordinates |
346 |
< |
|
347 |
< |
if( worldRank == 0 ){ |
348 |
< |
finalOut << mpiSim->getTotAtoms() << "\n"; |
349 |
< |
|
350 |
< |
finalOut << entry_plug->box_x << "\t" |
351 |
< |
<< entry_plug->box_y << "\t" |
352 |
< |
<< entry_plug->box_z << "\n"; |
353 |
< |
|
354 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
355 |
< |
// Get the Node number which has this molecule: |
356 |
< |
|
357 |
< |
which_node = AtomToProcMap[i]; |
358 |
< |
|
359 |
< |
if (which_node == mpiSim->getMyNode()) { |
360 |
< |
|
361 |
< |
sprintf( tempBuffer, |
362 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
363 |
< |
atoms[i]->getType(), |
364 |
< |
atoms[i]->getX(), |
365 |
< |
atoms[i]->getY(), |
366 |
< |
atoms[i]->getZ(), |
367 |
< |
atoms[i]->get_vx(), |
368 |
< |
atoms[i]->get_vy(), |
369 |
< |
atoms[i]->get_vz()); |
370 |
< |
strcpy( writeLine, tempBuffer ); |
399 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
400 |
|
|
372 |
– |
if( atoms[i]->isDirectional() ){ |
373 |
– |
|
374 |
– |
dAtom = (DirectionalAtom *)atoms[i]; |
375 |
– |
dAtom->getQ( q ); |
376 |
– |
|
377 |
– |
sprintf( tempBuffer, |
378 |
– |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
379 |
– |
q[0], |
380 |
– |
q[1], |
381 |
– |
q[2], |
382 |
– |
q[3], |
383 |
– |
dAtom->getJx(), |
384 |
– |
dAtom->getJy(), |
385 |
– |
dAtom->getJz()); |
386 |
– |
strcat( writeLine, tempBuffer ); |
387 |
– |
} |
388 |
– |
else |
389 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
390 |
– |
|
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 |
|
|
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); |
420 |
|
} |
421 |
|
|
422 |
< |
finalOut << writeLine; |
422 |
> |
outFile << writeLine; |
423 |
|
} |
424 |
|
|
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 |
– |
} |
425 |
|
|
426 |
+ |
outFile.flush(); |
427 |
+ |
sprintf( checkPointMsg, |
428 |
+ |
"Sucessfully took a dump.\n"); |
429 |
+ |
MPIcheckPoint(); |
430 |
+ |
delete[] potatoes; |
431 |
|
} else { |
432 |
+ |
|
433 |
+ |
// worldRank != 0, so I'm a remote node. |
434 |
+ |
|
435 |
+ |
// Set my magic potato to 0: |
436 |
+ |
|
437 |
+ |
myPotato = 0; |
438 |
+ |
currentIndex = 0; |
439 |
|
|
440 |
< |
done = 0; |
441 |
< |
while (!done) { |
442 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
443 |
< |
TAKE_THIS_TAG, istatus); |
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 (which_atom == -1) { |
415 |
< |
done=1; |
416 |
< |
continue; |
417 |
< |
} else { |
446 |
> |
if (myPotato + 3 >= MAXTAG) { |
447 |
|
|
448 |
< |
local_index=-1; |
449 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
450 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
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 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
453 |
> |
|
454 |
|
} |
455 |
< |
if (local_index != -1) { |
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 |
< |
//format the line |
463 |
< |
sprintf( tempBuffer, |
464 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
465 |
< |
atoms[local_index]->getType(), |
466 |
< |
atoms[local_index]->getX(), |
467 |
< |
atoms[local_index]->getY(), |
468 |
< |
atoms[local_index]->getZ(), |
469 |
< |
atoms[local_index]->get_vx(), |
470 |
< |
atoms[local_index]->get_vy(), |
471 |
< |
atoms[local_index]->get_vz()); // check here. |
472 |
< |
strcpy( writeLine, tempBuffer ); |
473 |
< |
|
462 |
> |
atoms[local_index]->getPos(pos); |
463 |
> |
atoms[local_index]->getVel(vel); |
464 |
> |
|
465 |
> |
atomData6[0] = pos[0]; |
466 |
> |
atomData6[1] = pos[1]; |
467 |
> |
atomData6[2] = pos[2]; |
468 |
> |
|
469 |
> |
atomData6[3] = vel[0]; |
470 |
> |
atomData6[4] = vel[1]; |
471 |
> |
atomData6[5] = vel[2]; |
472 |
> |
|
473 |
> |
isDirectional = 0; |
474 |
> |
|
475 |
|
if( atoms[local_index]->isDirectional() ){ |
476 |
+ |
|
477 |
+ |
isDirectional = 1; |
478 |
|
|
479 |
|
dAtom = (DirectionalAtom *)atoms[local_index]; |
480 |
|
dAtom->getQ( q ); |
481 |
< |
|
482 |
< |
sprintf( tempBuffer, |
483 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
484 |
< |
q[0], |
485 |
< |
q[1], |
486 |
< |
q[2], |
487 |
< |
q[3], |
488 |
< |
dAtom->getJx(), |
489 |
< |
dAtom->getJy(), |
490 |
< |
dAtom->getJz()); |
491 |
< |
strcat( writeLine, tempBuffer ); |
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 |
> |
atomData13[10] = dAtom->getJx(); |
491 |
> |
atomData13[11] = dAtom->getJy(); |
492 |
> |
atomData13[12] = dAtom->getJz(); |
493 |
|
} |
494 |
< |
else |
495 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
494 |
> |
|
495 |
> |
} else { |
496 |
> |
sprintf(painCave.errMsg, |
497 |
> |
"Atom %d not found on processor %d\n", |
498 |
> |
i, worldRank ); |
499 |
> |
haveError= 1; |
500 |
> |
simError(); |
501 |
> |
} |
502 |
> |
|
503 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
504 |
> |
|
505 |
> |
// null terminate the string before sending (just in case): |
506 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
507 |
> |
|
508 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
509 |
> |
myPotato, MPI_COMM_WORLD); |
510 |
> |
|
511 |
> |
myPotato++; |
512 |
> |
|
513 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
514 |
> |
myPotato, MPI_COMM_WORLD); |
515 |
> |
|
516 |
> |
myPotato++; |
517 |
> |
|
518 |
> |
if (isDirectional) { |
519 |
> |
|
520 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
521 |
> |
myPotato, MPI_COMM_WORLD); |
522 |
|
|
456 |
– |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
457 |
– |
TAKE_THIS_TAG); |
523 |
|
} else { |
524 |
< |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
525 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
526 |
< |
TAKE_THIS_TAG); |
524 |
> |
|
525 |
> |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
526 |
> |
myPotato, MPI_COMM_WORLD); |
527 |
|
} |
528 |
+ |
|
529 |
+ |
myPotato++; |
530 |
+ |
currentIndex++; |
531 |
|
} |
532 |
|
} |
465 |
– |
} |
466 |
– |
finalOut.flush(); |
467 |
– |
sprintf( checkPointMsg, |
468 |
– |
"Sucessfully took a dump.\n"); |
469 |
– |
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 |
+ |
|
543 |
+ |
#ifdef IS_MPI |
544 |
+ |
|
545 |
+ |
// a couple of functions to let us escape the write loop |
546 |
+ |
|
547 |
+ |
void dWrite::DieDieDie( void ){ |
548 |
+ |
|
549 |
+ |
MPI_Finalize(); |
550 |
+ |
exit (0); |
551 |
+ |
} |
552 |
+ |
|
553 |
+ |
#endif //is_mpi |