1 |
< |
#define _LARGEFILE_SOURCE64 |
2 |
< |
#define _FILE_OFFSET_BITS 64 |
1 |
> |
#include "io/DumpWriter.hpp" |
2 |
> |
#include "primitives/Molecule.hpp" |
3 |
> |
#include "utils/simError.h" |
4 |
|
|
4 |
– |
#include <string.h> |
5 |
– |
#include <iostream> |
6 |
– |
#include <fstream> |
7 |
– |
#include <algorithm> |
8 |
– |
#include <utility> |
9 |
– |
|
5 |
|
#ifdef IS_MPI |
11 |
– |
|
6 |
|
#include <mpi.h> |
13 |
– |
#include "brains/mpiSimulation.hpp" |
14 |
– |
|
15 |
– |
namespace dWrite { |
16 |
– |
void DieDieDie(void); |
17 |
– |
|
18 |
– |
} |
19 |
– |
|
20 |
– |
using namespace dWrite; |
21 |
– |
|
7 |
|
#endif //is_mpi |
8 |
|
|
9 |
< |
#include "io/ReadWrite.hpp" |
25 |
< |
#include "utils/simError.h" |
9 |
> |
namespace oopse { |
10 |
|
|
11 |
< |
DumpWriter::DumpWriter(SimInfo *the_entry_plug) { |
12 |
< |
entry_plug = the_entry_plug; |
29 |
< |
|
11 |
> |
DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
12 |
> |
: info_(info), filename_(filename){ |
13 |
|
#ifdef IS_MPI |
14 |
|
|
15 |
|
if (worldRank == 0) { |
16 |
|
#endif // is_mpi |
17 |
|
|
18 |
< |
dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc); |
18 |
> |
dumpFile_.open(filename_.c_str(), ios::out | ios::trunc); |
19 |
|
|
20 |
< |
if (!dumpFile) { |
20 |
> |
if (!dumpFile_) { |
21 |
|
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
22 |
< |
entry_plug->sampleName.c_str()); |
22 |
> |
filename_.c_str()); |
23 |
|
painCave.isFatal = 1; |
24 |
|
simError(); |
25 |
|
} |
28 |
|
|
29 |
|
} |
30 |
|
|
48 |
– |
//sort the local atoms by global index |
49 |
– |
sortByGlobalIndex(); |
50 |
– |
|
31 |
|
sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
32 |
|
MPIcheckPoint(); |
33 |
|
|
42 |
|
if (worldRank == 0) { |
43 |
|
#endif // is_mpi |
44 |
|
|
45 |
< |
dumpFile.close(); |
45 |
> |
dumpFile_.close(); |
46 |
|
|
47 |
|
#ifdef IS_MPI |
48 |
|
|
52 |
|
|
53 |
|
} |
54 |
|
|
55 |
< |
#ifdef IS_MPI |
55 |
> |
void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) { |
56 |
|
|
57 |
< |
/** |
58 |
< |
* A hook function to load balancing |
59 |
< |
*/ |
57 |
> |
double currentTime; |
58 |
> |
Mat3x3d hmat; |
59 |
> |
double chi; |
60 |
> |
double integralOfChiDt; |
61 |
> |
Mat3x3d eta; |
62 |
> |
|
63 |
> |
currentTime = s->getTime(); |
64 |
> |
hmat = s->getHmat(); |
65 |
> |
chi = s->getChi(); |
66 |
> |
integralOfChiDt = s->getIntegralOfChiDt(); |
67 |
> |
eta = s->getEta(); |
68 |
> |
|
69 |
> |
os << currentTime << ";\t" |
70 |
> |
<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" |
71 |
> |
<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t" |
72 |
> |
<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";"; |
73 |
|
|
74 |
< |
void DumpWriter::update() { |
82 |
< |
sortByGlobalIndex(); |
83 |
< |
} |
74 |
> |
//write out additional parameters, such as chi and eta |
75 |
|
|
76 |
< |
/** |
86 |
< |
* Auxiliary sorting function |
87 |
< |
*/ |
76 |
> |
os << chi << "\t" << integralOfChiDt << "\t;"; |
77 |
|
|
78 |
< |
bool indexSortingCriterion(const pair < int, int > &p1, const pair < int, |
79 |
< |
int > &p2) { |
80 |
< |
return p1.second < p2.second; |
78 |
> |
os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" |
79 |
> |
<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t" |
80 |
> |
<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";"; |
81 |
> |
|
82 |
> |
os << endl; |
83 |
|
} |
84 |
|
|
85 |
< |
/** |
86 |
< |
* Sorting the local index by global index |
87 |
< |
*/ |
85 |
> |
void DumpWriter::writeFrame(std::ostream& os) { |
86 |
> |
const int BUFFERSIZE = 2000; |
87 |
> |
const int MINIBUFFERSIZE = 100; |
88 |
|
|
89 |
< |
void DumpWriter::sortByGlobalIndex() { |
90 |
< |
Molecule * mols = entry_plug->molecules; |
100 |
< |
indexArray.clear(); |
89 |
> |
char tempBuffer[BUFFERSIZE]; |
90 |
> |
char writeLine[BUFFERSIZE]; |
91 |
|
|
92 |
< |
for(int i = 0; i < entry_plug->n_mol; i++) { |
93 |
< |
indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); |
94 |
< |
} |
92 |
> |
Quat4d q; |
93 |
> |
Vector3d ji; |
94 |
> |
Vector3d pos; |
95 |
> |
Vector3d vel; |
96 |
|
|
97 |
< |
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
98 |
< |
} |
97 |
> |
Molecule* mol; |
98 |
> |
StuntDouble* integrableObject; |
99 |
> |
SimInfo::MoleculeIterator mi; |
100 |
> |
Molecule::IntegrableObjectIterator ii; |
101 |
> |
|
102 |
> |
int nTotObjects; |
103 |
> |
nTotObjects = info_->getNGlobalIntegrableObjects(); |
104 |
|
|
105 |
< |
#endif |
105 |
> |
#ifndef IS_MPI |
106 |
|
|
111 |
– |
void DumpWriter::writeDump(double currentTime) { |
112 |
– |
ofstream finalOut; |
113 |
– |
vector<ofstream *>fileStreams; |
107 |
|
|
108 |
< |
#ifdef IS_MPI |
108 |
> |
os << nTotObjects << "\n"; |
109 |
> |
|
110 |
> |
writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
111 |
|
|
112 |
< |
if (worldRank == 0) { |
118 |
< |
#endif |
112 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
113 |
|
|
114 |
< |
finalOut.open(entry_plug->finalName.c_str(), ios::out | ios::trunc); |
114 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
115 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
116 |
> |
|
117 |
|
|
118 |
< |
if (!finalOut) { |
119 |
< |
sprintf(painCave.errMsg, |
124 |
< |
"Could not open \"%s\" for final dump output.\n", |
125 |
< |
entry_plug->finalName.c_str()); |
126 |
< |
painCave.isFatal = 1; |
127 |
< |
simError(); |
128 |
< |
} |
118 |
> |
pos = integrableObject->getPos(); |
119 |
> |
vel = integrableObject->getVel(); |
120 |
|
|
121 |
< |
#ifdef IS_MPI |
121 |
> |
sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
122 |
> |
integrableObject->getType().c_str(), |
123 |
> |
pos[0], pos[1], pos[2], |
124 |
> |
vel[0], vel[1], vel[2]); |
125 |
|
|
126 |
< |
} |
126 |
> |
strcpy(writeLine, tempBuffer); |
127 |
|
|
128 |
< |
#endif // is_mpi |
128 |
> |
if (integrableObject->isDirectional()) { |
129 |
> |
q = integrableObject->getQ(); |
130 |
> |
ji = integrableObject->getJ(); |
131 |
|
|
132 |
< |
fileStreams.push_back(&finalOut); |
133 |
< |
fileStreams.push_back(&dumpFile); |
132 |
> |
sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
133 |
> |
q[0], q[1], q[2], q[3], |
134 |
> |
ji[0], ji[1], ji[2]); |
135 |
> |
strcat(writeLine, tempBuffer); |
136 |
> |
} else { |
137 |
> |
strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
138 |
> |
} |
139 |
|
|
140 |
< |
writeFrame(fileStreams, currentTime); |
140 |
> |
os << writeLine; |
141 |
|
|
141 |
– |
#ifdef IS_MPI |
142 |
– |
|
143 |
– |
finalOut.close(); |
144 |
– |
|
145 |
– |
#endif |
146 |
– |
|
147 |
– |
} |
148 |
– |
|
149 |
– |
void DumpWriter::writeFinal(double currentTime) { |
150 |
– |
ofstream finalOut; |
151 |
– |
vector<ofstream *>fileStreams; |
152 |
– |
|
153 |
– |
#ifdef IS_MPI |
154 |
– |
|
155 |
– |
if (worldRank == 0) { |
156 |
– |
#endif // is_mpi |
157 |
– |
|
158 |
– |
finalOut.open(entry_plug->finalName.c_str(), ios::out | ios::trunc); |
159 |
– |
|
160 |
– |
if (!finalOut) { |
161 |
– |
sprintf(painCave.errMsg, |
162 |
– |
"Could not open \"%s\" for final dump output.\n", |
163 |
– |
entry_plug->finalName.c_str()); |
164 |
– |
painCave.isFatal = 1; |
165 |
– |
simError(); |
142 |
|
} |
167 |
– |
|
168 |
– |
#ifdef IS_MPI |
169 |
– |
|
143 |
|
} |
144 |
|
|
145 |
< |
#endif // is_mpi |
173 |
< |
|
174 |
< |
fileStreams.push_back(&finalOut); |
175 |
< |
writeFrame(fileStreams, currentTime); |
176 |
< |
|
177 |
< |
#ifdef IS_MPI |
178 |
< |
|
179 |
< |
finalOut.close(); |
180 |
< |
|
181 |
< |
#endif |
182 |
< |
|
183 |
< |
} |
184 |
< |
|
185 |
< |
void DumpWriter::writeFrame(vector<ofstream *>&outFile, double currentTime) { |
186 |
< |
const int BUFFERSIZE = 2000; |
187 |
< |
const int MINIBUFFERSIZE = 100; |
188 |
< |
|
189 |
< |
char tempBuffer[BUFFERSIZE]; |
190 |
< |
char writeLine[BUFFERSIZE]; |
191 |
< |
|
192 |
< |
int i; |
193 |
< |
unsigned int k; |
194 |
< |
|
195 |
< |
#ifdef IS_MPI |
196 |
< |
|
145 |
> |
#else // is_mpi |
146 |
|
/********************************************************************* |
147 |
|
* Documentation? You want DOCUMENTATION? |
148 |
|
* |
179 |
|
* How's THAT for documentation? |
180 |
|
* |
181 |
|
*********************************************************************/ |
182 |
+ |
const int masterNode = 0; |
183 |
|
|
184 |
|
int * potatoes; |
185 |
|
int myPotato; |
236 |
– |
|
186 |
|
int nProc; |
238 |
– |
int j; |
187 |
|
int which_node; |
240 |
– |
int done; |
241 |
– |
int which_atom; |
242 |
– |
int local_index; |
243 |
– |
int currentIndex; |
188 |
|
double atomData[13]; |
189 |
|
int isDirectional; |
190 |
< |
char * atomTypeString; |
190 |
> |
const char * atomTypeString; |
191 |
|
char MPIatomTypeString[MINIBUFFERSIZE]; |
248 |
– |
int nObjects; |
192 |
|
int msgLen; // the length of message actually recieved at master nodes |
193 |
< |
|
194 |
< |
#endif //is_mpi |
195 |
< |
|
196 |
< |
Quat4d q; |
197 |
< |
Vector3d ji; |
198 |
< |
DirectionalAtom * dAtom; |
199 |
< |
Vector3d pos; |
200 |
< |
Vector3d vel; |
258 |
< |
|
259 |
< |
int nTotObjects; |
260 |
< |
StuntDouble * sd; |
261 |
< |
char * molName; |
262 |
< |
vector<StuntDouble *>integrableObjects; |
263 |
< |
vector<StuntDouble *>::iterator iter; |
264 |
< |
nTotObjects = entry_plug->getTotIntegrableObjects(); |
265 |
< |
|
266 |
< |
#ifndef IS_MPI |
267 |
< |
|
268 |
< |
for(k = 0; k < outFile.size(); k++) { |
269 |
< |
*outFile[k] << nTotObjects << "\n"; |
270 |
< |
|
271 |
< |
*outFile[k] << currentTime << ";\t" << entry_plug->Hmat[0][0] << "\t" |
272 |
< |
<< entry_plug->Hmat[1][0] << "\t" << entry_plug->Hmat[2][0] |
273 |
< |
<< ";\t" << entry_plug->Hmat[0][1] << "\t" |
274 |
< |
<< entry_plug->Hmat[1][1] << "\t" << entry_plug->Hmat[2][1] |
275 |
< |
<< ";\t" << entry_plug->Hmat[0][2] << "\t" |
276 |
< |
<< entry_plug->Hmat[1][2] << "\t" << entry_plug->Hmat[2][2] << ";"; |
277 |
< |
|
278 |
< |
//write out additional parameters, such as chi and eta |
279 |
< |
//another circular reference nightmare |
280 |
< |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() |
281 |
< |
<< endl; |
282 |
< |
} |
283 |
< |
|
284 |
< |
for(i = 0; i < entry_plug->n_mol; i++) { |
285 |
< |
integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
286 |
< |
molName |
287 |
< |
= (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
288 |
< |
|
289 |
< |
for(iter = integrableObjects.begin(); |
290 |
< |
iter != integrableObjects.end(); ++iter) { |
291 |
< |
sd = *iter; |
292 |
< |
pos = sd->getPos(); |
293 |
< |
vel = sd->getVel(); |
294 |
< |
|
295 |
< |
sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
296 |
< |
sd->getType(), pos[0], |
297 |
< |
pos[1], pos[2], |
298 |
< |
vel[0], vel[1], |
299 |
< |
vel[2]); |
300 |
< |
|
301 |
< |
strcpy(writeLine, tempBuffer); |
302 |
< |
|
303 |
< |
if (sd->isDirectional()) { |
304 |
< |
q = sd->getQ(); |
305 |
< |
ji = sd->getJ(); |
306 |
< |
|
307 |
< |
sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], |
308 |
< |
q[1], q[2], q[3], |
309 |
< |
ji[0], ji[1], ji[2]); |
310 |
< |
strcat(writeLine, tempBuffer); |
311 |
< |
} else { |
312 |
< |
strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
313 |
< |
} |
314 |
< |
|
315 |
< |
for(k = 0; k < outFile.size(); k++) { |
316 |
< |
*outFile[k] << writeLine; |
317 |
< |
} |
318 |
< |
} |
319 |
< |
} |
320 |
< |
|
321 |
< |
#else // is_mpi |
322 |
< |
|
323 |
< |
/* code to find maximum tag value */ |
324 |
< |
|
325 |
< |
int * tagub, flag, MAXTAG; |
193 |
> |
int haveError; |
194 |
> |
MPI_Status istatus; |
195 |
> |
int nCurObj; |
196 |
> |
|
197 |
> |
// code to find maximum tag value |
198 |
> |
int * tagub; |
199 |
> |
int flag; |
200 |
> |
int MAXTAG; |
201 |
|
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
202 |
|
|
203 |
|
if (flag) { |
206 |
|
MAXTAG = 32767; |
207 |
|
} |
208 |
|
|
209 |
< |
int haveError; |
209 |
> |
if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file |
210 |
|
|
336 |
– |
MPI_Status istatus; |
337 |
– |
int nCurObj; |
338 |
– |
int * MolToProcMap = mpiSim->getMolToProcMap(); |
339 |
– |
|
340 |
– |
// write out header and node 0's coordinates |
341 |
– |
|
342 |
– |
if (worldRank == 0) { |
343 |
– |
|
211 |
|
// Node 0 needs a list of the magic potatoes for each processor; |
212 |
|
|
213 |
< |
nProc = mpiSim->getNProcessors(); |
213 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
214 |
|
potatoes = new int[nProc]; |
215 |
|
|
216 |
|
//write out the comment lines |
218 |
|
potatoes[i] = 0; |
219 |
|
} |
220 |
|
|
354 |
– |
for(k = 0; k < outFile.size(); k++) { |
355 |
– |
*outFile[k] << nTotObjects << "\n"; |
221 |
|
|
222 |
< |
*outFile[k] << currentTime << ";\t" << entry_plug->Hmat[0][0] |
223 |
< |
<< "\t" << entry_plug->Hmat[1][0] << "\t" |
359 |
< |
<< entry_plug->Hmat[2][0] << ";\t" << entry_plug->Hmat[0][1] |
360 |
< |
<< "\t" << entry_plug->Hmat[1][1] << "\t" |
361 |
< |
<< entry_plug->Hmat[2][1] << ";\t" << entry_plug->Hmat[0][2] |
362 |
< |
<< "\t" << entry_plug->Hmat[1][2] << "\t" |
363 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
222 |
> |
os << nTotObjects << "\n"; |
223 |
> |
writeCommentLine(info_->getSnapshotManager()->getCurrentSnapshot()); |
224 |
|
|
225 |
< |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() |
366 |
< |
<< endl; |
367 |
< |
} |
225 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
226 |
|
|
369 |
– |
currentIndex = 0; |
370 |
– |
|
371 |
– |
for(i = 0; i < mpiSim->getNMolGlobal(); i++) { |
372 |
– |
|
227 |
|
// Get the Node number which has this atom; |
228 |
|
|
229 |
< |
which_node = MolToProcMap[i]; |
229 |
> |
which_node = info_->getMolToProc(i); |
230 |
|
|
231 |
< |
if (which_node != 0) { |
231 |
> |
if (which_node != masterNode) { //current molecule is in slave node |
232 |
|
if (potatoes[which_node] + 1 >= MAXTAG) { |
233 |
|
// The potato was going to exceed the maximum value, |
234 |
|
// so wrap this processor potato back to 0: |
304 |
|
atomData[12]); |
305 |
|
} |
306 |
|
|
307 |
< |
for(k = 0; k < outFile.size(); k++) { |
308 |
< |
*outFile[k] << writeLine; |
455 |
< |
} |
307 |
> |
os << writeLine; |
308 |
> |
|
309 |
|
} // end for(int l =0) |
310 |
|
|
311 |
|
potatoes[which_node] = myPotato; |
312 |
< |
} else { |
460 |
< |
haveError = 0; |
312 |
> |
} else { //master node has current molecule |
313 |
|
|
314 |
< |
local_index = indexArray[currentIndex].first; |
314 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
315 |
|
|
316 |
< |
integrableObjects |
317 |
< |
= (entry_plug->molecules[local_index]).getIntegrableObjects(); |
316 |
> |
if (mol == NULL) { |
317 |
> |
strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
318 |
> |
painCave.isFatal = 1; |
319 |
> |
simError(); |
320 |
> |
} |
321 |
> |
|
322 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
323 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
324 |
> |
|
325 |
> |
atomTypeString = integrableObject->getType().c_str(); |
326 |
|
|
327 |
< |
for(iter = integrableObjects.begin(); |
328 |
< |
iter != integrableObjects.end(); ++iter) { |
469 |
< |
sd = *iter; |
470 |
< |
atomTypeString = sd->getType(); |
327 |
> |
pos = integrableObject->getPos(); |
328 |
> |
vel = integrableObject->getVel(); |
329 |
|
|
472 |
– |
pos = sd->getPos(); |
473 |
– |
vel = sd->getVel(); |
474 |
– |
|
330 |
|
atomData[0] = pos[0]; |
331 |
|
atomData[1] = pos[1]; |
332 |
|
atomData[2] = pos[2]; |
337 |
|
|
338 |
|
isDirectional = 0; |
339 |
|
|
340 |
< |
if (sd->isDirectional()) { |
340 |
> |
if (integrableObject->isDirectional()) { |
341 |
|
isDirectional = 1; |
342 |
|
|
343 |
< |
q = sd->getQ(); |
344 |
< |
ji = sd->getJ(); |
343 |
> |
q = integrableObject->getQ(); |
344 |
> |
ji = integrableObject->getJ(); |
345 |
|
|
346 |
|
for(int j = 0; j < 6; j++) { |
347 |
|
atomData[j] = atomData[j]; |
387 |
|
atomData[12]); |
388 |
|
} |
389 |
|
|
535 |
– |
for(k = 0; k < outFile.size(); k++) { |
536 |
– |
*outFile[k] << writeLine; |
537 |
– |
} |
538 |
– |
} //end for(iter = integrableObject.begin()) |
390 |
|
|
391 |
< |
currentIndex++; |
391 |
> |
os << writeLine; |
392 |
> |
|
393 |
> |
} //end for(iter = integrableObject.begin()) |
394 |
|
} |
395 |
|
} //end for(i = 0; i < mpiSim->getNmol()) |
396 |
|
|
397 |
< |
for(k = 0; k < outFile.size(); k++) { |
545 |
< |
outFile[k]->flush(); |
546 |
< |
} |
397 |
> |
os.flush(); |
398 |
|
|
399 |
|
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
400 |
|
|
408 |
|
// Set my magic potato to 0: |
409 |
|
|
410 |
|
myPotato = 0; |
560 |
– |
currentIndex = 0; |
411 |
|
|
412 |
< |
for(i = 0; i < mpiSim->getNMolGlobal(); i++) { |
412 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
413 |
|
|
414 |
|
// Am I the node which has this integrableObject? |
415 |
< |
|
416 |
< |
if (MolToProcMap[i] == worldRank) { |
415 |
> |
whichNode = info_->getMolToProc(i); |
416 |
> |
if (whichNode == worldRank) { |
417 |
|
if (myPotato + 1 >= MAXTAG) { |
418 |
|
|
419 |
|
// The potato was going to exceed the maximum value, |
424 |
|
&istatus); |
425 |
|
} |
426 |
|
|
427 |
< |
local_index = indexArray[currentIndex].first; |
578 |
< |
integrableObjects = |
579 |
< |
entry_plug->molecules[local_index].getIntegrableObjects(); |
427 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
428 |
|
|
429 |
< |
nCurObj = integrableObjects.size(); |
429 |
> |
|
430 |
> |
nCurObj = mol->getNIntegrableObjects(); |
431 |
|
|
432 |
|
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
433 |
|
myPotato++; |
434 |
|
|
435 |
< |
for(iter = integrableObjects.begin(); |
436 |
< |
iter != integrableObjects.end(); iter++) { |
435 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
436 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
437 |
> |
|
438 |
|
if (myPotato + 2 >= MAXTAG) { |
439 |
|
|
440 |
|
// The potato was going to exceed the maximum value, |
445 |
|
&istatus); |
446 |
|
} |
447 |
|
|
448 |
< |
sd = *iter; |
448 |
> |
atomTypeString = integrableObject->getType().c_str(); |
449 |
|
|
450 |
< |
atomTypeString = sd->getType(); |
450 |
> |
pos = integrableObject->getPos(); |
451 |
> |
vel = integrableObject->getVel(); |
452 |
|
|
602 |
– |
pos = sd->getPos(); |
603 |
– |
vel = sd->getVel(); |
604 |
– |
|
453 |
|
atomData[0] = pos[0]; |
454 |
|
atomData[1] = pos[1]; |
455 |
|
atomData[2] = pos[2]; |
460 |
|
|
461 |
|
isDirectional = 0; |
462 |
|
|
463 |
< |
if (sd->isDirectional()) { |
463 |
> |
if (integrableObject->isDirectional()) { |
464 |
|
isDirectional = 1; |
465 |
|
|
466 |
< |
q = sd->getQ(); |
467 |
< |
ji = sd->getJ(); |
466 |
> |
q = integrableObject->getQ(); |
467 |
> |
ji = integrableObject->getJ(); |
468 |
|
|
469 |
|
atomData[6] = q[0]; |
470 |
|
atomData[7] = q[1]; |
496 |
|
|
497 |
|
myPotato++; |
498 |
|
} |
499 |
< |
|
652 |
< |
currentIndex++; |
499 |
> |
|
500 |
|
} |
501 |
+ |
|
502 |
|
} |
503 |
|
|
504 |
|
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
509 |
|
|
510 |
|
} |
511 |
|
|
512 |
< |
#ifdef IS_MPI |
665 |
< |
|
666 |
< |
// a couple of functions to let us escape the write loop |
667 |
< |
|
668 |
< |
void dWrite::DieDieDie(void) { |
669 |
< |
MPI_Finalize(); |
670 |
< |
exit(0); |
671 |
< |
} |
672 |
< |
|
673 |
< |
#endif //is_mpi |
512 |
> |
}//end namespace oopse |