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#include <cstring> |
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#define _FILE_OFFSET_BITS 64 |
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|
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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 0 |
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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" |
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#include "simError.h" |
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|
14 |
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#define GAME_OVER -1 |
15 |
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|
21 |
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
22 |
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|
23 |
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entry_plug = the_entry_plug; |
25 |
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#ifdef IS_MPI |
26 |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
28 |
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|
24 |
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|
25 |
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|
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|
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strcpy( outName, entry_plug->sampleName ); |
30 |
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|
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|
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outFile.open(outName, ios::out | ios::trunc ); |
32 |
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|
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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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painCave.isFatal = 1; |
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simError(); |
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} |
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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 |
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} |
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void DumpWriter::writeDump( double currentTime ){ |
67 |
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|
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|
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const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
70 |
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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]; |
78 |
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double atomOrientData[7]; |
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int isDirectional; |
80 |
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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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|
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double q[4]; |
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DirectionalAtom* dAtom; |
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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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|
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outFile << nAtoms << "\n"; |
103 |
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|
104 |
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outFile << currentTime << "\t" |
105 |
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<< entry_plug->box_x << "\t" |
106 |
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<< 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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|
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outFile << currentTime << ";\t" |
105 |
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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][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\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] << ";"; |
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//write out additional parameters, such as chi and eta |
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outFile << entry_plug->the_integrator->getAdditionalParameters(); |
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outFile << endl; |
119 |
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|
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for( i=0; i<nAtoms; i++ ){ |
86 |
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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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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
128 |
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atoms[i]->getX(), |
129 |
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atoms[i]->getY(), |
130 |
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atoms[i]->getZ(), |
131 |
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atoms[i]->get_vx(), |
132 |
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atoms[i]->get_vy(), |
133 |
< |
atoms[i]->get_vz()); |
128 |
> |
pos[0], |
129 |
> |
pos[1], |
130 |
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pos[2], |
131 |
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vel[0], |
132 |
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vel[1], |
133 |
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vel[2]); |
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strcpy( writeLine, tempBuffer ); |
135 |
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|
136 |
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if( atoms[i]->isDirectional() ){ |
137 |
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|
137 |
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|
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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|
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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 |
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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" ); |
154 |
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|
154 |
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|
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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 |
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MPI_Status istatus[MPI_STATUS_SIZE]; |
162 |
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|
160 |
> |
|
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 |
> |
|
170 |
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// write out header and node 0's coordinates |
171 |
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|
171 |
> |
|
172 |
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if( worldRank == 0 ){ |
173 |
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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 |
< |
|
180 |
< |
for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) { |
181 |
< |
// Get the Node number which has this molecule: |
182 |
< |
|
183 |
< |
which_node = AtomToProcMap[i]; |
184 |
< |
|
185 |
< |
if (which_node == mpiPlug->myNode) { |
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 != 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 |
+ |
// Null terminate the atomTypeString just in case: |
209 |
+ |
|
210 |
+ |
atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
211 |
+ |
|
212 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
213 |
+ |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
214 |
+ |
|
215 |
+ |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
216 |
+ |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
217 |
+ |
|
218 |
+ |
if (isDirectional) { |
219 |
+ |
|
220 |
+ |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
221 |
+ |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
222 |
+ |
|
223 |
+ |
} |
224 |
+ |
|
225 |
+ |
} else { |
226 |
+ |
|
227 |
+ |
haveError = 0; |
228 |
+ |
which_atom = i; |
229 |
+ |
local_index=-1; |
230 |
+ |
|
231 |
+ |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
232 |
+ |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
233 |
+ |
} |
234 |
+ |
|
235 |
+ |
if (local_index != -1) { |
236 |
+ |
|
237 |
+ |
atomTypeString = atoms[local_index]->getType(); |
238 |
+ |
|
239 |
+ |
atoms[local_index]->getPos(pos); |
240 |
+ |
atoms[local_index]->getVel(vel); |
241 |
+ |
|
242 |
+ |
atomTransData[0] = pos[0]; |
243 |
+ |
atomTransData[1] = pos[1]; |
244 |
+ |
atomTransData[2] = pos[2]; |
245 |
+ |
|
246 |
+ |
atomTransData[3] = vel[0]; |
247 |
+ |
atomTransData[4] = vel[1]; |
248 |
+ |
atomTransData[5] = vel[2]; |
249 |
+ |
|
250 |
+ |
isDirectional = 0; |
251 |
+ |
|
252 |
+ |
if( atoms[local_index]->isDirectional() ){ |
253 |
+ |
|
254 |
+ |
isDirectional = 1; |
255 |
+ |
|
256 |
+ |
dAtom = (DirectionalAtom *)atoms[local_index]; |
257 |
+ |
dAtom->getQ( q ); |
258 |
+ |
|
259 |
+ |
atomOrientData[0] = q[0]; |
260 |
+ |
atomOrientData[1] = q[1]; |
261 |
+ |
atomOrientData[2] = q[2]; |
262 |
+ |
atomOrientData[3] = q[3]; |
263 |
+ |
|
264 |
+ |
atomOrientData[4] = dAtom->getJx(); |
265 |
+ |
atomOrientData[5] = dAtom->getJy(); |
266 |
+ |
atomOrientData[6] = dAtom->getJz(); |
267 |
+ |
} |
268 |
+ |
|
269 |
+ |
} else { |
270 |
+ |
sprintf(painCave.errMsg, |
271 |
+ |
"Atom %d not found on processor %d\n", |
272 |
+ |
i, worldRank ); |
273 |
+ |
haveError= 1; |
274 |
+ |
simError(); |
275 |
+ |
} |
276 |
+ |
|
277 |
+ |
if(haveError) DieDieDie(); |
278 |
+ |
|
279 |
+ |
// If we've survived to here, format the line: |
280 |
+ |
|
281 |
|
sprintf( tempBuffer, |
282 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
283 |
< |
atoms[i]->getType(), |
284 |
< |
atoms[i]->getX(), |
285 |
< |
atoms[i]->getY(), |
286 |
< |
atoms[i]->getZ(), |
287 |
< |
atoms[i]->get_vx(), |
288 |
< |
atoms[i]->get_vy(), |
289 |
< |
atoms[i]->get_vz()); |
283 |
> |
atomTypeString, |
284 |
> |
atomTransData[0], |
285 |
> |
atomTransData[1], |
286 |
> |
atomTransData[2], |
287 |
> |
atomTransData[3], |
288 |
> |
atomTransData[4], |
289 |
> |
atomTransData[5]); |
290 |
> |
|
291 |
|
strcpy( writeLine, tempBuffer ); |
292 |
< |
|
293 |
< |
if( atoms[i]->isDirectional() ){ |
294 |
< |
|
156 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
157 |
< |
dAtom->getQ( q ); |
158 |
< |
|
292 |
> |
|
293 |
> |
if (isDirectional) { |
294 |
> |
|
295 |
|
sprintf( tempBuffer, |
296 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
297 |
< |
q[0], |
298 |
< |
q[1], |
299 |
< |
q[2], |
300 |
< |
q[3], |
301 |
< |
dAtom->getJx(), |
302 |
< |
dAtom->getJy(), |
303 |
< |
dAtom->getJz()); |
297 |
> |
atomOrientData[0], |
298 |
> |
atomOrientData[1], |
299 |
> |
atomOrientData[2], |
300 |
> |
atomOrientData[3], |
301 |
> |
atomOrientData[4], |
302 |
> |
atomOrientData[5], |
303 |
> |
atomOrientData[6]); |
304 |
|
strcat( writeLine, tempBuffer ); |
305 |
+ |
|
306 |
+ |
} else { |
307 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
308 |
|
} |
309 |
< |
else |
310 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
311 |
< |
|
173 |
< |
} else { |
174 |
< |
|
175 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
176 |
< |
MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
177 |
< |
TAKE_THIS_TAG, istatus); |
309 |
> |
|
310 |
> |
outFile << writeLine; |
311 |
> |
outFile.flush(); |
312 |
|
} |
179 |
– |
|
180 |
– |
outFile << writeLine; |
313 |
|
} |
182 |
– |
|
183 |
– |
// kill everyone off: |
184 |
– |
for (j = 0; j < mpiPlug->numberProcessors; j++) { |
185 |
– |
MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG); |
186 |
– |
} |
314 |
|
|
315 |
+ |
outFile.flush(); |
316 |
+ |
sprintf( checkPointMsg, |
317 |
+ |
"Sucessfully took a dump.\n"); |
318 |
+ |
MPIcheckPoint(); |
319 |
+ |
|
320 |
|
} else { |
321 |
+ |
|
322 |
+ |
// worldRank != 0, so I'm a remote node. |
323 |
|
|
324 |
< |
done = 0; |
325 |
< |
while (!done) { |
326 |
< |
MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, |
327 |
< |
TAKE_THIS_TAG, istatus); |
324 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
325 |
> |
|
326 |
> |
// Am I the node which has this atom? |
327 |
> |
|
328 |
> |
if (AtomToProcMap[i] == worldRank) { |
329 |
|
|
330 |
< |
if (which_atom == GAME_OVER) { |
331 |
< |
done=1; |
332 |
< |
continue; |
333 |
< |
} else { |
330 |
> |
local_index=-1; |
331 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
332 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
333 |
> |
} |
334 |
> |
if (local_index != -1) { |
335 |
> |
|
336 |
> |
atomTypeString = atoms[local_index]->getType(); |
337 |
|
|
338 |
< |
//format the line |
339 |
< |
sprintf( tempBuffer, |
340 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
341 |
< |
atoms[which_atom]->getType(), |
342 |
< |
atoms[which_atom]->getX(), |
343 |
< |
atoms[which_atom]->getY(), |
344 |
< |
atoms[which_atom]->getZ(), |
345 |
< |
atoms[which_atom]->get_vx(), |
346 |
< |
atoms[which_atom]->get_vy(), |
347 |
< |
atoms[which_atom]->get_vz()); // check here. |
348 |
< |
strcpy( writeLine, tempBuffer ); |
349 |
< |
|
350 |
< |
if( atoms[which_atom]->isDirectional() ){ |
351 |
< |
|
352 |
< |
dAtom = (DirectionalAtom *)atoms[which_atom]; |
353 |
< |
dAtom->getQ( q ); |
354 |
< |
|
355 |
< |
sprintf( tempBuffer, |
356 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
357 |
< |
q[0], |
358 |
< |
q[1], |
359 |
< |
q[2], |
360 |
< |
q[3], |
361 |
< |
dAtom->getJx(), |
362 |
< |
dAtom->getJy(), |
363 |
< |
dAtom->getJz()); |
364 |
< |
strcat( writeLine, tempBuffer ); |
338 |
> |
atoms[local_index]->getPos(pos); |
339 |
> |
atoms[local_index]->getVel(vel); |
340 |
> |
|
341 |
> |
atomTransData[0] = pos[0]; |
342 |
> |
atomTransData[1] = pos[1]; |
343 |
> |
atomTransData[2] = pos[2]; |
344 |
> |
|
345 |
> |
atomTransData[3] = vel[0]; |
346 |
> |
atomTransData[4] = vel[1]; |
347 |
> |
atomTransData[5] = vel[2]; |
348 |
> |
|
349 |
> |
isDirectional = 0; |
350 |
> |
|
351 |
> |
if( atoms[local_index]->isDirectional() ){ |
352 |
> |
|
353 |
> |
isDirectional = 1; |
354 |
> |
|
355 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
356 |
> |
dAtom->getQ( q ); |
357 |
> |
|
358 |
> |
atomOrientData[0] = q[0]; |
359 |
> |
atomOrientData[1] = q[1]; |
360 |
> |
atomOrientData[2] = q[2]; |
361 |
> |
atomOrientData[3] = q[3]; |
362 |
> |
|
363 |
> |
atomOrientData[4] = dAtom->getJx(); |
364 |
> |
atomOrientData[5] = dAtom->getJy(); |
365 |
> |
atomOrientData[6] = dAtom->getJz(); |
366 |
> |
} |
367 |
> |
|
368 |
> |
} else { |
369 |
> |
sprintf(painCave.errMsg, |
370 |
> |
"Atom %d not found on processor %d\n", |
371 |
> |
i, worldRank ); |
372 |
> |
haveError= 1; |
373 |
> |
simError(); |
374 |
|
} |
375 |
< |
else |
376 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
375 |
> |
|
376 |
> |
// I've survived this far, so send off the data! |
377 |
> |
|
378 |
> |
atomTypeTag = 4*i; |
379 |
> |
atomIsDirectionalTag = 4*i + 1; |
380 |
> |
atomTransDataTag = 4*i + 2; |
381 |
> |
atomOrientDataTag = 4*i + 3; |
382 |
> |
|
383 |
> |
|
384 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
385 |
> |
|
386 |
> |
// null terminate the string before sending (just in case): |
387 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
388 |
> |
|
389 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
390 |
> |
atomTypeTag, MPI_COMM_WORLD); |
391 |
|
|
392 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
393 |
< |
TAKE_THIS_TAG); |
392 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
393 |
> |
atomIsDirectionalTag, MPI_COMM_WORLD); |
394 |
> |
|
395 |
> |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
396 |
> |
atomTransDataTag, MPI_COMM_WORLD); |
397 |
> |
|
398 |
> |
if (isDirectional) { |
399 |
> |
|
400 |
> |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
401 |
> |
atomOrientDataTag, MPI_COMM_WORLD); |
402 |
> |
|
403 |
> |
} |
404 |
> |
|
405 |
|
} |
406 |
|
} |
407 |
< |
} |
408 |
< |
outFile.flush(); |
409 |
< |
sprintf( checkPointMsg, |
410 |
< |
"Sucessfully took a dump.\n"); |
411 |
< |
MPIcheckPoint(); |
407 |
> |
|
408 |
> |
sprintf( checkPointMsg, |
409 |
> |
"Sucessfully took a dump.\n"); |
410 |
> |
MPIcheckPoint(); |
411 |
> |
|
412 |
> |
} |
413 |
> |
|
414 |
> |
painCave.isEventLoop = 0; |
415 |
> |
|
416 |
|
#endif // is_mpi |
417 |
|
} |
418 |
|
|
419 |
< |
void DumpWriter::writeFinal(){ |
420 |
< |
|
419 |
> |
void DumpWriter::writeFinal(double finalTime){ |
420 |
> |
|
421 |
|
char finalName[500]; |
422 |
|
ofstream finalOut; |
423 |
< |
|
423 |
> |
|
424 |
> |
const int BUFFERSIZE = 2000; |
425 |
> |
const int MINIBUFFERSIZE = 100; |
426 |
> |
char tempBuffer[BUFFERSIZE]; |
427 |
> |
char writeLine[BUFFERSIZE]; |
428 |
> |
|
429 |
> |
double q[4]; |
430 |
> |
DirectionalAtom* dAtom; |
431 |
> |
Atom** atoms = entry_plug->atoms; |
432 |
> |
int i; |
433 |
|
#ifdef IS_MPI |
434 |
+ |
int j, which_node, done, which_atom, local_index; |
435 |
+ |
double atomTransData[6]; |
436 |
+ |
double atomOrientData[7]; |
437 |
+ |
int isDirectional; |
438 |
+ |
char* atomTypeString; |
439 |
+ |
char MPIatomTypeString[MINIBUFFERSIZE]; |
440 |
+ |
int atomTypeTag; |
441 |
+ |
int atomIsDirectionalTag; |
442 |
+ |
int atomTransDataTag; |
443 |
+ |
int atomOrientDataTag; |
444 |
+ |
#else //is_mpi |
445 |
+ |
int nAtoms = entry_plug->n_atoms; |
446 |
+ |
#endif //is_mpi |
447 |
+ |
|
448 |
+ |
double pos[3], vel[3]; |
449 |
+ |
|
450 |
+ |
#ifdef IS_MPI |
451 |
|
if(worldRank == 0 ){ |
452 |
|
#endif // is_mpi |
453 |
< |
|
453 |
> |
|
454 |
|
strcpy( finalName, entry_plug->finalName ); |
455 |
< |
|
455 |
> |
|
456 |
|
finalOut.open( finalName, ios::out | ios::trunc ); |
457 |
|
if( !finalOut ){ |
458 |
|
sprintf( painCave.errMsg, |
461 |
|
painCave.isFatal = 1; |
462 |
|
simError(); |
463 |
|
} |
464 |
< |
|
464 |
> |
|
465 |
|
// finalOut.setf( ios::scientific ); |
466 |
< |
|
466 |
> |
|
467 |
|
#ifdef IS_MPI |
468 |
|
} |
469 |
< |
|
469 |
> |
|
470 |
|
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
471 |
< |
MPIcheckPoint(); |
472 |
< |
|
471 |
> |
MPIcheckPoint(); |
472 |
> |
|
473 |
|
#endif //is_mpi |
474 |
|
|
475 |
< |
|
475 |
> |
|
476 |
|
#ifndef IS_MPI |
477 |
< |
|
477 |
> |
|
478 |
|
finalOut << nAtoms << "\n"; |
479 |
< |
|
480 |
< |
finalOut << entry_plug->box_x << "\t" |
481 |
< |
<< entry_plug->box_y << "\t" |
482 |
< |
<< entry_plug->box_z << "\n"; |
483 |
< |
|
479 |
> |
|
480 |
> |
finalOut << finalTime << ";\t" |
481 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
482 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
483 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
484 |
> |
|
485 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
486 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
487 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
488 |
> |
|
489 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
490 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
491 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
492 |
> |
|
493 |
> |
//write out additional parameters, such as chi and eta |
494 |
> |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
495 |
> |
finalOut << endl; |
496 |
> |
|
497 |
|
for( i=0; i<nAtoms; i++ ){ |
498 |
< |
|
498 |
> |
|
499 |
> |
atoms[i]->getPos(pos); |
500 |
> |
atoms[i]->getVel(vel); |
501 |
> |
|
502 |
|
sprintf( tempBuffer, |
503 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
504 |
|
atoms[i]->getType(), |
505 |
< |
atoms[i]->getX(), |
506 |
< |
atoms[i]->getY(), |
507 |
< |
atoms[i]->getZ(), |
508 |
< |
atoms[i]->get_vx(), |
509 |
< |
atoms[i]->get_vy(), |
510 |
< |
atoms[i]->get_vz()); |
505 |
> |
pos[0], |
506 |
> |
pos[1], |
507 |
> |
pos[2], |
508 |
> |
vel[0], |
509 |
> |
vel[1], |
510 |
> |
vel[2]); |
511 |
|
strcpy( writeLine, tempBuffer ); |
512 |
|
|
513 |
|
if( atoms[i]->isDirectional() ){ |
514 |
< |
|
514 |
> |
|
515 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
516 |
|
dAtom->getQ( q ); |
517 |
< |
|
517 |
> |
|
518 |
|
sprintf( tempBuffer, |
519 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
520 |
|
q[0], |
528 |
|
} |
529 |
|
else |
530 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
531 |
< |
|
531 |
> |
|
532 |
|
finalOut << writeLine; |
533 |
|
} |
534 |
|
finalOut.flush(); |
535 |
|
finalOut.close(); |
536 |
|
|
537 |
|
#else // is_mpi |
538 |
< |
|
539 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
540 |
< |
|
538 |
> |
|
539 |
> |
// first thing first, suspend fatalities. |
540 |
> |
painCave.isEventLoop = 1; |
541 |
> |
|
542 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
543 |
> |
int haveError; |
544 |
> |
|
545 |
> |
MPI_Status istatus; |
546 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
547 |
> |
|
548 |
|
// write out header and node 0's coordinates |
549 |
< |
|
549 |
> |
|
550 |
|
if( worldRank == 0 ){ |
551 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
552 |
< |
|
553 |
< |
finalOut << entry_plug->box_x << "\t" |
554 |
< |
<< entry_plug->box_y << "\t" |
555 |
< |
<< entry_plug->box_z << "\n"; |
556 |
< |
|
557 |
< |
for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) { |
558 |
< |
// Get the Node number which has this molecule: |
559 |
< |
|
560 |
< |
which_node = AtomToProcMap[i]; |
561 |
< |
|
562 |
< |
if (which_node == mpiPlug->myNode) { |
552 |
> |
|
553 |
> |
finalOut << finalTime << ";\t" |
554 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
555 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
556 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
557 |
> |
|
558 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
559 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
560 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
561 |
> |
|
562 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
563 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
564 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
565 |
> |
|
566 |
> |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
567 |
> |
finalOut << endl; |
568 |
> |
finalOut.flush(); |
569 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
570 |
> |
// Get the Node number which has this atom; |
571 |
> |
|
572 |
> |
which_node = AtomToProcMap[i]; |
573 |
> |
|
574 |
> |
if (which_node != 0) { |
575 |
|
|
576 |
+ |
atomTypeTag = 4*i; |
577 |
+ |
atomIsDirectionalTag = 4*i + 1; |
578 |
+ |
atomTransDataTag = 4*i + 2; |
579 |
+ |
atomOrientDataTag = 4*i + 3; |
580 |
+ |
|
581 |
+ |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
582 |
+ |
atomTypeTag, MPI_COMM_WORLD, &istatus); |
583 |
+ |
|
584 |
+ |
strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
585 |
+ |
|
586 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
587 |
+ |
atomIsDirectionalTag, MPI_COMM_WORLD, &istatus); |
588 |
+ |
|
589 |
+ |
MPI_Recv(atomTransData, 6, MPI_DOUBLE, which_node, |
590 |
+ |
atomTransDataTag, MPI_COMM_WORLD, &istatus); |
591 |
+ |
|
592 |
+ |
if (isDirectional) { |
593 |
+ |
|
594 |
+ |
MPI_Recv(atomOrientData, 7, MPI_DOUBLE, which_node, |
595 |
+ |
atomOrientDataTag, MPI_COMM_WORLD, &istatus); |
596 |
+ |
|
597 |
+ |
} |
598 |
+ |
|
599 |
+ |
} else { |
600 |
+ |
|
601 |
+ |
haveError = 0; |
602 |
+ |
which_atom = i; |
603 |
+ |
local_index=-1; |
604 |
+ |
|
605 |
+ |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
606 |
+ |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
607 |
+ |
} |
608 |
+ |
|
609 |
+ |
if (local_index != -1) { |
610 |
+ |
|
611 |
+ |
atomTypeString = atoms[local_index]->getType(); |
612 |
+ |
|
613 |
+ |
atoms[local_index]->getPos(pos); |
614 |
+ |
atoms[local_index]->getVel(vel); |
615 |
+ |
|
616 |
+ |
atomTransData[0] = pos[0]; |
617 |
+ |
atomTransData[1] = pos[1]; |
618 |
+ |
atomTransData[2] = pos[2]; |
619 |
+ |
|
620 |
+ |
atomTransData[3] = vel[0]; |
621 |
+ |
atomTransData[4] = vel[1]; |
622 |
+ |
atomTransData[5] = vel[2]; |
623 |
+ |
|
624 |
+ |
isDirectional = 0; |
625 |
+ |
|
626 |
+ |
if( atoms[local_index]->isDirectional() ){ |
627 |
+ |
|
628 |
+ |
isDirectional = 1; |
629 |
+ |
|
630 |
+ |
dAtom = (DirectionalAtom *)atoms[local_index]; |
631 |
+ |
dAtom->getQ( q ); |
632 |
+ |
|
633 |
+ |
atomOrientData[0] = q[0]; |
634 |
+ |
atomOrientData[1] = q[1]; |
635 |
+ |
atomOrientData[2] = q[2]; |
636 |
+ |
atomOrientData[3] = q[3]; |
637 |
+ |
|
638 |
+ |
atomOrientData[4] = dAtom->getJx(); |
639 |
+ |
atomOrientData[5] = dAtom->getJy(); |
640 |
+ |
atomOrientData[6] = dAtom->getJz(); |
641 |
+ |
} |
642 |
+ |
|
643 |
+ |
} else { |
644 |
+ |
sprintf(painCave.errMsg, |
645 |
+ |
"Atom %d not found on processor %d\n", |
646 |
+ |
i, worldRank ); |
647 |
+ |
haveError= 1; |
648 |
+ |
simError(); |
649 |
+ |
} |
650 |
+ |
|
651 |
+ |
if(haveError) DieDieDie(); |
652 |
+ |
|
653 |
+ |
// If we've survived to here, format the line: |
654 |
+ |
|
655 |
|
sprintf( tempBuffer, |
656 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
657 |
< |
atoms[i]->getType(), |
658 |
< |
atoms[i]->getX(), |
659 |
< |
atoms[i]->getY(), |
660 |
< |
atoms[i]->getZ(), |
661 |
< |
atoms[i]->get_vx(), |
662 |
< |
atoms[i]->get_vy(), |
663 |
< |
atoms[i]->get_vz()); |
657 |
> |
atomTypeString, |
658 |
> |
atomTransData[0], |
659 |
> |
atomTransData[1], |
660 |
> |
atomTransData[2], |
661 |
> |
atomTransData[3], |
662 |
> |
atomTransData[4], |
663 |
> |
atomTransData[5]); |
664 |
> |
|
665 |
|
strcpy( writeLine, tempBuffer ); |
666 |
< |
|
667 |
< |
if( atoms[i]->isDirectional() ){ |
668 |
< |
|
352 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
353 |
< |
dAtom->getQ( q ); |
354 |
< |
|
666 |
> |
|
667 |
> |
if (isDirectional) { |
668 |
> |
|
669 |
|
sprintf( tempBuffer, |
670 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
671 |
< |
q[0], |
672 |
< |
q[1], |
673 |
< |
q[2], |
674 |
< |
q[3], |
675 |
< |
dAtom->getJx(), |
676 |
< |
dAtom->getJy(), |
677 |
< |
dAtom->getJz()); |
671 |
> |
atomOrientData[0], |
672 |
> |
atomOrientData[1], |
673 |
> |
atomOrientData[2], |
674 |
> |
atomOrientData[3], |
675 |
> |
atomOrientData[4], |
676 |
> |
atomOrientData[5], |
677 |
> |
atomOrientData[6]); |
678 |
|
strcat( writeLine, tempBuffer ); |
679 |
+ |
|
680 |
+ |
} else { |
681 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
682 |
|
} |
683 |
< |
else |
684 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
685 |
< |
|
369 |
< |
} else { |
370 |
< |
|
371 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
372 |
< |
MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
373 |
< |
TAKE_THIS_TAG, istatus); |
683 |
> |
|
684 |
> |
finalOut << writeLine; |
685 |
> |
finalOut.flush(); |
686 |
|
} |
375 |
– |
|
376 |
– |
finalOut << writeLine; |
687 |
|
} |
378 |
– |
|
379 |
– |
// kill everyone off: |
380 |
– |
for (j = 0; j < mpiPlug->numberProcessors; j++) { |
381 |
– |
MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG); |
382 |
– |
} |
688 |
|
|
689 |
+ |
finalOut.flush(); |
690 |
+ |
sprintf( checkPointMsg, |
691 |
+ |
"Sucessfully took a dump.\n"); |
692 |
+ |
MPIcheckPoint(); |
693 |
+ |
|
694 |
|
} else { |
695 |
+ |
|
696 |
+ |
// worldRank != 0, so I'm a remote node. |
697 |
|
|
698 |
< |
done = 0; |
699 |
< |
while (!done) { |
700 |
< |
MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, |
701 |
< |
TAKE_THIS_TAG, istatus); |
698 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
699 |
> |
|
700 |
> |
// Am I the node which has this atom? |
701 |
> |
|
702 |
> |
if (AtomToProcMap[i] == worldRank) { |
703 |
|
|
704 |
< |
if (which_atom == GAME_OVER) { |
705 |
< |
done=1; |
706 |
< |
continue; |
707 |
< |
} else { |
704 |
> |
local_index=-1; |
705 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
706 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
707 |
> |
} |
708 |
> |
if (local_index != -1) { |
709 |
> |
|
710 |
> |
atomTypeString = atoms[local_index]->getType(); |
711 |
|
|
712 |
< |
//format the line |
713 |
< |
sprintf( tempBuffer, |
714 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
715 |
< |
atoms[which_atom]->getType(), |
716 |
< |
atoms[which_atom]->getX(), |
717 |
< |
atoms[which_atom]->getY(), |
718 |
< |
atoms[which_atom]->getZ(), |
719 |
< |
atoms[which_atom]->get_vx(), |
720 |
< |
atoms[which_atom]->get_vy(), |
721 |
< |
atoms[which_atom]->get_vz()); // check here. |
722 |
< |
strcpy( writeLine, tempBuffer ); |
723 |
< |
|
724 |
< |
if( atoms[which_atom]->isDirectional() ){ |
725 |
< |
|
726 |
< |
dAtom = (DirectionalAtom *)atoms[which_atom]; |
727 |
< |
dAtom->getQ( q ); |
728 |
< |
|
729 |
< |
sprintf( tempBuffer, |
730 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
731 |
< |
q[0], |
732 |
< |
q[1], |
733 |
< |
q[2], |
734 |
< |
q[3], |
735 |
< |
dAtom->getJx(), |
736 |
< |
dAtom->getJy(), |
737 |
< |
dAtom->getJz()); |
738 |
< |
strcat( writeLine, tempBuffer ); |
712 |
> |
atoms[local_index]->getPos(pos); |
713 |
> |
atoms[local_index]->getVel(vel); |
714 |
> |
|
715 |
> |
atomTransData[0] = pos[0]; |
716 |
> |
atomTransData[1] = pos[1]; |
717 |
> |
atomTransData[2] = pos[2]; |
718 |
> |
|
719 |
> |
atomTransData[3] = vel[0]; |
720 |
> |
atomTransData[4] = vel[1]; |
721 |
> |
atomTransData[5] = vel[2]; |
722 |
> |
|
723 |
> |
isDirectional = 0; |
724 |
> |
|
725 |
> |
if( atoms[local_index]->isDirectional() ){ |
726 |
> |
|
727 |
> |
isDirectional = 1; |
728 |
> |
|
729 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
730 |
> |
dAtom->getQ( q ); |
731 |
> |
|
732 |
> |
atomOrientData[0] = q[0]; |
733 |
> |
atomOrientData[1] = q[1]; |
734 |
> |
atomOrientData[2] = q[2]; |
735 |
> |
atomOrientData[3] = q[3]; |
736 |
> |
|
737 |
> |
atomOrientData[4] = dAtom->getJx(); |
738 |
> |
atomOrientData[5] = dAtom->getJy(); |
739 |
> |
atomOrientData[6] = dAtom->getJz(); |
740 |
> |
} |
741 |
> |
|
742 |
> |
} else { |
743 |
> |
sprintf(painCave.errMsg, |
744 |
> |
"Atom %d not found on processor %d\n", |
745 |
> |
i, worldRank ); |
746 |
> |
haveError= 1; |
747 |
> |
simError(); |
748 |
|
} |
749 |
< |
else |
750 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
749 |
> |
|
750 |
> |
// I've survived this far, so send off the data! |
751 |
> |
|
752 |
> |
atomTypeTag = 4*i; |
753 |
> |
atomIsDirectionalTag = 4*i + 1; |
754 |
> |
atomTransDataTag = 4*i + 2; |
755 |
> |
atomOrientDataTag = 4*i + 3; |
756 |
> |
|
757 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
758 |
> |
|
759 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
760 |
> |
atomTypeTag, MPI_COMM_WORLD); |
761 |
|
|
762 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
763 |
< |
TAKE_THIS_TAG); |
762 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
763 |
> |
atomIsDirectionalTag, MPI_COMM_WORLD); |
764 |
> |
|
765 |
> |
MPI_Send(atomTransData, 6, MPI_DOUBLE, 0, |
766 |
> |
atomTransDataTag, MPI_COMM_WORLD); |
767 |
> |
|
768 |
> |
if (isDirectional) { |
769 |
> |
|
770 |
> |
MPI_Send(atomOrientData, 7, MPI_DOUBLE, 0, |
771 |
> |
atomOrientDataTag, MPI_COMM_WORLD); |
772 |
> |
|
773 |
> |
} |
774 |
> |
|
775 |
|
} |
776 |
|
} |
431 |
– |
} |
432 |
– |
finalOut.flush(); |
433 |
– |
sprintf( checkPointMsg, |
434 |
– |
"Sucessfully took a dump.\n"); |
435 |
– |
MPIcheckPoint(); |
777 |
|
|
778 |
< |
if( worldRank == 0 ) finalOut.close(); |
778 |
> |
sprintf( checkPointMsg, |
779 |
> |
"Sucessfully wrote final file.\n"); |
780 |
> |
MPIcheckPoint(); |
781 |
> |
|
782 |
> |
} |
783 |
> |
|
784 |
> |
painCave.isEventLoop = 0; |
785 |
> |
|
786 |
> |
if( worldRank == 0 ) finalOut.close(); |
787 |
|
#endif // is_mpi |
788 |
|
} |
789 |
+ |
|
790 |
+ |
|
791 |
+ |
|
792 |
+ |
#ifdef IS_MPI |
793 |
+ |
|
794 |
+ |
// a couple of functions to let us escape the write loop |
795 |
+ |
|
796 |
+ |
void dWrite::DieDieDie( void ){ |
797 |
+ |
|
798 |
+ |
MPI_Finalize(); |
799 |
+ |
exit (0); |
800 |
+ |
} |
801 |
+ |
|
802 |
+ |
#endif //is_mpi |