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root/OpenMD/branches/development/src/io/DumpWriter.cpp

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trunk/src/io/DumpWriter.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/io/DumpWriter.cpp (file contents), Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

#	Line 1 | Line 1
1	<	#define _LARGEFILE_SOURCE64
2	<	#define _FILE_OFFSET_BITS 64
1	>	/*
2	>	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42	>
43	>	#include "io/DumpWriter.hpp"
44	>	#include "primitives/Molecule.hpp"
45	>	#include "utils/simError.h"
46	>	#include "io/basic_teebuf.hpp"
47	>	#include "io/gzstream.hpp"
48	>	#include "io/Globals.hpp"
49
4	–	#include <string.h>
5	–	#include <iostream>
6	–	#include <fstream>
7	–	#include <algorithm>
8	–	#include <utility>
50
51		#ifdef IS_MPI
52		#include <mpi.h>
12	–	#include "brains/mpiSimulation.hpp"
13	–
14	–	namespace dWrite{
15	–	void DieDieDie( void );
16	–	}
17	–
18	–	using namespace dWrite;
53		#endif //is_mpi
54
55	<	#include "io/ReadWrite.hpp"
56	<	#include "utils/simError.h"
55	>	using namespace std;
56	>	namespace OpenMD {
57
58	<	DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
58	>	DumpWriter::DumpWriter(SimInfo* info)
59	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
60
61	<	entry_plug = the_entry_plug;
61	>	Globals* simParams = info->getSimParams();
62	>	needCompression_   = simParams->getCompressDumpFile();
63	>	needForceVector_   = simParams->getOutputForceVector();
64	>	needParticlePot_   = simParams->getOutputParticlePotential();
65	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
66	>	needElectricField_ = simParams->getOutputElectricField();
67
68	+	createDumpFile_ = true;
69	+	#ifdef HAVE_LIBZ
70	+	if (needCompression_) {
71	+	filename_ += ".gz";
72	+	eorFilename_ += ".gz";
73	+	}
74	+	#endif
75	+
76		#ifdef IS_MPI
77	<	if(worldRank == 0 ){
77	>
78	>	if (worldRank == 0) {
79		#endif // is_mpi
80	+
81	+	dumpFile_ = createOStream(filename_);
82
83	<	dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
83	>	if (!dumpFile_) {
84	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
85	>	filename_.c_str());
86	>	painCave.isFatal = 1;
87	>	simError();
88	>	}
89
90	<	if( !dumpFile ){
90	>	#ifdef IS_MPI
91
36	–	sprintf( painCave.errMsg,
37	–	"Could not open \"%s\" for dump output.\n",
38	–	entry_plug->sampleName.c_str());
39	–	painCave.isFatal = 1;
40	–	simError();
92		}
93
94	<	#ifdef IS_MPI
94	>	#endif // is_mpi
95	>
96		}
97
46	–	//sort the local atoms by global index
47	–	sortByGlobalIndex();
48	–
49	–	sprintf( checkPointMsg,
50	–	"Sucessfully opened output file for dumping.\n");
51	–	MPIcheckPoint();
52	–	#endif // is_mpi
53	–	}
98
99	<	DumpWriter::~DumpWriter( ){
99	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
100	>	: info_(info), filename_(filename){
101
102	<	#ifdef IS_MPI
103	<	if(worldRank == 0 ){
59	<	#endif // is_mpi
102	>	Globals* simParams = info->getSimParams();
103	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
104
105	<	dumpFile.close();
105	>	needCompression_   = simParams->getCompressDumpFile();
106	>	needForceVector_   = simParams->getOutputForceVector();
107	>	needParticlePot_   = simParams->getOutputParticlePotential();
108	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
109	>	needElectricField_ = simParams->getOutputElectricField();
110
111	+	createDumpFile_ = true;
112	+	#ifdef HAVE_LIBZ
113	+	if (needCompression_) {
114	+	filename_ += ".gz";
115	+	eorFilename_ += ".gz";
116	+	}
117	+	#endif
118	+
119		#ifdef IS_MPI
120	<	}
120	>
121	>	if (worldRank == 0) {
122		#endif // is_mpi
66	–	}
123
124	+
125	+	dumpFile_ = createOStream(filename_);
126	+
127	+	if (!dumpFile_) {
128	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
129	+	filename_.c_str());
130	+	painCave.isFatal = 1;
131	+	simError();
132	+	}
133	+
134		#ifdef IS_MPI
135
136	<	/**
71	<	* A hook function to load balancing
72	<	*/
136	>	}
137
138	<	void DumpWriter::update(){
75	<	sortByGlobalIndex();
76	<	}
77	<
78	<	/**
79	<	* Auxiliary sorting function
80	<	*/
81	<
82	<	bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){
83	<	return p1.second < p2.second;
84	<	}
138	>	#endif // is_mpi
139
140	<	/**
87	<	* Sorting the local index by global index
88	<	*/
89	<
90	<	void DumpWriter::sortByGlobalIndex(){
91	<	Molecule* mols = entry_plug->molecules;
92	<	indexArray.clear();
140	>	}
141
142	<	for(int i = 0; i < entry_plug->n_mol;i++)
143	<	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
144	<
145	<	sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
146	<	}
142	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
143	>	: info_(info), filename_(filename){
144	>
145	>	Globals* simParams = info->getSimParams();
146	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
147	>
148	>	needCompression_   = simParams->getCompressDumpFile();
149	>	needForceVector_   = simParams->getOutputForceVector();
150	>	needParticlePot_   = simParams->getOutputParticlePotential();
151	>	needFlucQ_         = simParams->getOutputFluctuatingCharges();
152	>	needElectricField_ = simParams->getOutputElectricField();
153
154	+	#ifdef HAVE_LIBZ
155	+	if (needCompression_) {
156	+	filename_ += ".gz";
157	+	eorFilename_ += ".gz";
158	+	}
159		#endif
160	+
161	+	#ifdef IS_MPI
162	+
163	+	if (worldRank == 0) {
164	+	#endif // is_mpi
165	+
166	+	createDumpFile_ = writeDumpFile;
167	+	if (createDumpFile_) {
168	+	dumpFile_ = createOStream(filename_);
169	+
170	+	if (!dumpFile_) {
171	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
172	+	filename_.c_str());
173	+	painCave.isFatal = 1;
174	+	simError();
175	+	}
176	+	}
177	+	#ifdef IS_MPI
178	+
179	+	}
180
181	<	void DumpWriter::writeDump(double currentTime){
181	>
182	>	#endif // is_mpi
183	>
184	>	}
185
186	<	ofstream finalOut;
105	<	vector<ofstream*> fileStreams;
186	>	DumpWriter::~DumpWriter() {
187
188		#ifdef IS_MPI
189	<	if(worldRank == 0 ){
190	<	#endif
110	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
111	<	if( !finalOut ){
112	<	sprintf( painCave.errMsg,
113	<	"Could not open \"%s\" for final dump output.\n",
114	<	entry_plug->finalName.c_str() );
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
118	<	#ifdef IS_MPI
119	<	}
189	>
190	>	if (worldRank == 0) {
191		#endif // is_mpi
192	+	if (createDumpFile_){
193	+	writeClosing(*dumpFile_);
194	+	delete dumpFile_;
195	+	}
196	+	#ifdef IS_MPI
197
198	<	fileStreams.push_back(&finalOut);
123	<	fileStreams.push_back(&dumpFile);
198	>	}
199
200	<	writeFrame(fileStreams, currentTime);
200	>	#endif // is_mpi
201
202	<	#ifdef IS_MPI
128	<	finalOut.close();
129	<	#endif
130	<
131	<	}
202	>	}
203
204	<	void DumpWriter::writeFinal(double currentTime){
204	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
205
206	<	ofstream finalOut;
136	<	vector<ofstream*> fileStreams;
206	>	char buffer[1024];
207
208	<	#ifdef IS_MPI
139	<	if(worldRank == 0 ){
140	<	#endif // is_mpi
208	>	os << "    <FrameData>\n";
209
210	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
210	>	RealType currentTime = s->getTime();
211
212	<	if( !finalOut ){
212	>	if (isinf(currentTime) || isnan(currentTime)) {
213		sprintf( painCave.errMsg,
214	<	"Could not open \"%s\" for final dump output.\n",
147	<	entry_plug->finalName.c_str() );
214	>	"DumpWriter detected a numerical error writing the time");
215		painCave.isFatal = 1;
216		simError();
217		}
218	+
219	+	sprintf(buffer, "        Time: %.10g\n", currentTime);
220	+	os << buffer;
221
222	<	#ifdef IS_MPI
223	<	}
154	<	#endif // is_mpi
155	<
156	<	fileStreams.push_back(&finalOut);
157	<	writeFrame(fileStreams, currentTime);
222	>	Mat3x3d hmat;
223	>	hmat = s->getHmat();
224
225	<	#ifdef IS_MPI
226	<	finalOut.close();
227	<	#endif
228	<
229	<	}
225	>	for (unsigned int i = 0; i < 3; i++) {
226	>	for (unsigned int j = 0; j < 3; j++) {
227	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
228	>	sprintf( painCave.errMsg,
229	>	"DumpWriter detected a numerical error writing the box");
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
233	>	}
234	>	}
235	>
236	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
237	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
238	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
239	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
240	>	os << buffer;
241
242	<	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
243	<
244	<	const int BUFFERSIZE = 2000;
245	<	const int MINIBUFFERSIZE = 100;
246	<
247	<	char tempBuffer[BUFFERSIZE];
248	<	char writeLine[BUFFERSIZE];
249	<
250	<	int i;
251	<	unsigned int k;
242	>	RealType chi = s->getChi();
243	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
244	>	if (isinf(chi) || isnan(chi) ||
245	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
246	>	sprintf( painCave.errMsg,
247	>	"DumpWriter detected a numerical error writing the thermostat");
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
252	>	os << buffer;
253
254	<	#ifdef IS_MPI
255	<
178	<	/*********************************************************************
179	<	* Documentation?  You want DOCUMENTATION?
180	<	*
181	<	* Why all the potatoes below?
182	<	*
183	<	* To make a long story short, the original version of DumpWriter
184	<	* worked in the most inefficient way possible.  Node 0 would
185	<	* poke each of the node for an individual atom's formatted data
186	<	* as node 0 worked its way down the global index. This was particularly
187	<	* inefficient since the method blocked all processors at every atom
188	<	* (and did it twice!).
189	<	*
190	<	* An intermediate version of DumpWriter could be described from Node
191	<	* zero's perspective as follows:
192	<	*
193	<	*  1) Have 100 of your friends stand in a circle.
194	<	*  2) When you say go, have all of them start tossing potatoes at
195	<	*     you (one at a time).
196	<	*  3) Catch the potatoes.
197	<	*
198	<	* It was an improvement, but MPI has buffers and caches that could
199	<	* best be described in this analogy as "potato nets", so there's no
200	<	* need to block the processors atom-by-atom.
201	<	*
202	<	* This new and improved DumpWriter works in an even more efficient
203	<	* way:
204	<	*
205	<	*  1) Have 100 of your friend stand in a circle.
206	<	*  2) When you say go, have them start tossing 5-pound bags of
207	<	*     potatoes at you.
208	<	*  3) Once you've caught a friend's bag of potatoes,
209	<	*     toss them a spud to let them know they can toss another bag.
210	<	*
211	<	* How's THAT for documentation?
212	<	*
213	<	*********************************************************************/
254	>	Mat3x3d eta;
255	>	eta = s->getEta();
256
257	<	int *potatoes;
258	<	int myPotato;
259	<
260	<	int nProc;
261	<	int j, which_node, done, which_atom, local_index, currentIndex;
262	<	double atomData[13];
263	<	int isDirectional;
264	<	char* atomTypeString;
223	<	char MPIatomTypeString[MINIBUFFERSIZE];
224	<	int nObjects;
225	<	int msgLen; // the length of message actually recieved at master nodes
226	<	#endif //is_mpi
227	<
228	<	double q[4], ji[3];
229	<	DirectionalAtom* dAtom;
230	<	double pos[3], vel[3];
231	<	int nTotObjects;
232	<	StuntDouble* sd;
233	<	char* molName;
234	<	vector<StuntDouble*> integrableObjects;
235	<	vector<StuntDouble*>::iterator iter;
236	<	nTotObjects = entry_plug->getTotIntegrableObjects();
237	<	#ifndef IS_MPI
238	<
239	<	for(k = 0; k < outFile.size(); k++){
240	<	*outFile[k] << nTotObjects << "\n";
241	<
242	<	*outFile[k] << currentTime << ";\t"
243	<	<< entry_plug->Hmat[0][0] << "\t"
244	<	<< entry_plug->Hmat[1][0] << "\t"
245	<	<< entry_plug->Hmat[2][0] << ";\t"
246	<
247	<	<< entry_plug->Hmat[0][1] << "\t"
248	<	<< entry_plug->Hmat[1][1] << "\t"
249	<	<< entry_plug->Hmat[2][1] << ";\t"
250	<
251	<	<< entry_plug->Hmat[0][2] << "\t"
252	<	<< entry_plug->Hmat[1][2] << "\t"
253	<	<< entry_plug->Hmat[2][2] << ";";
254	<
255	<	//write out additional parameters, such as chi and eta
256	<	*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
257	<	}
258	<
259	<	for( i=0; i< entry_plug->n_mol; i++ ){
260	<
261	<	integrableObjects = entry_plug->molecules[i].getIntegrableObjects();
262	<	molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID();
263	<
264	<	for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
265	<	sd = *iter;
266	<	sd->getPos(pos);
267	<	sd->getVel(vel);
268	<
269	<	sprintf( tempBuffer,
270	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
271	<	sd->getType(),
272	<	pos[0],
273	<	pos[1],
274	<	pos[2],
275	<	vel[0],
276	<	vel[1],
277	<	vel[2]);
278	<	strcpy( writeLine, tempBuffer );
279	<
280	<	if( sd->isDirectional() ){
281	<
282	<	sd->getQ( q );
283	<	sd->getJ( ji );
284	<
285	<	sprintf( tempBuffer,
286	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
287	<	q[0],
288	<	q[1],
289	<	q[2],
290	<	q[3],
291	<	ji[0],
292	<	ji[1],
293	<	ji[2]);
294	<	strcat( writeLine, tempBuffer );
257	>	for (unsigned int i = 0; i < 3; i++) {
258	>	for (unsigned int j = 0; j < 3; j++) {
259	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
260	>	sprintf( painCave.errMsg,
261	>	"DumpWriter detected a numerical error writing the barostat");
262	>	painCave.isFatal = 1;
263	>	simError();
264	>	}
265		}
296	–	else
297	–	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
298	–
299	–	for(k = 0; k < outFile.size(); k++)
300	–	*outFile[k] << writeLine;
266		}
267
268	<	}
268	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
269	>	eta(0, 0), eta(1, 0), eta(2, 0),
270	>	eta(0, 1), eta(1, 1), eta(2, 1),
271	>	eta(0, 2), eta(1, 2), eta(2, 2));
272	>	os << buffer;
273
274	<	#else // is_mpi
274	>	os << "    </FrameData>\n";
275	>	}
276
277	<	/* code to find maximum tag value */
308	<
309	<	int *tagub, flag, MAXTAG;
310	<	MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
311	<	if (flag) {
312	<	MAXTAG = *tagub;
313	<	} else {
314	<	MAXTAG = 32767;
315	<	}
277	>	void DumpWriter::writeFrame(std::ostream& os) {
278
279	<	int haveError;
279	>	#ifdef IS_MPI
280	>	MPI_Status istatus;
281	>	#endif
282
283	<	MPI_Status istatus;
284	<	int nCurObj;
285	<	int *MolToProcMap = mpiSim->getMolToProcMap();
283	>	Molecule* mol;
284	>	StuntDouble* integrableObject;
285	>	SimInfo::MoleculeIterator mi;
286	>	Molecule::IntegrableObjectIterator ii;
287
288	<	// write out header and node 0's coordinates
288	>	#ifndef IS_MPI
289	>	os << "  <Snapshot>\n";
290	>
291	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
292
293	<	if( worldRank == 0 ){
293	>	os << "    <StuntDoubles>\n";
294	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
295
296	<	// Node 0 needs a list of the magic potatoes for each processor;
297	<
298	<	nProc = mpiSim->getNProcessors();
299	<	potatoes = new int[nProc];
300	<
301	<	//write out the comment lines
302	<	for (i = 0; i < nProc; i++)
303	<	potatoes[i] = 0;
296	>
297	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
298	>	integrableObject = mol->nextIntegrableObject(ii)) {
299	>	os << prepareDumpLine(integrableObject);
300	>
301	>	}
302	>	}
303	>	os << "    </StuntDoubles>\n";
304
305	<	for(k = 0; k < outFile.size(); k++){
337	<	*outFile[k] << nTotObjects << "\n";
305	>	os << "  </Snapshot>\n";
306
307	<	*outFile[k] << currentTime << ";\t"
308	<	<< entry_plug->Hmat[0][0] << "\t"
309	<	<< entry_plug->Hmat[1][0] << "\t"
310	<	<< entry_plug->Hmat[2][0] << ";\t"
307	>	os.flush();
308	>	#else
309	>	//every node prepares the dump lines for integrable objects belong to itself
310	>	std::string buffer;
311	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
312
344	–	<< entry_plug->Hmat[0][1] << "\t"
345	–	<< entry_plug->Hmat[1][1] << "\t"
346	–	<< entry_plug->Hmat[2][1] << ";\t"
313
314	<	<< entry_plug->Hmat[0][2] << "\t"
315	<	<< entry_plug->Hmat[1][2] << "\t"
316	<	<< entry_plug->Hmat[2][2] << ";";
317	<
352	<	*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
314	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
315	>	integrableObject = mol->nextIntegrableObject(ii)) {
316	>	buffer += prepareDumpLine(integrableObject);
317	>	}
318		}
319	+
320	+	const int masterNode = 0;
321	+	int nProc;
322	+	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
323	+	if (worldRank == masterNode) {
324	+	os << "  <Snapshot>\n";
325	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
326	+	os << "    <StuntDoubles>\n";
327	+
328	+	os << buffer;
329
330	<	currentIndex = 0;
330	>	for (int i = 1; i < nProc; ++i) {
331
332	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
333	<
359	<	// Get the Node number which has this atom;
360	<
361	<	which_node = MolToProcMap[i];
362	<
363	<	if (which_node != 0) {
364	<
365	<	if (potatoes[which_node] + 1 >= MAXTAG) {
366	<	// The potato was going to exceed the maximum value,
367	<	// so wrap this processor potato back to 0:
332	>	// receive the length of the string buffer that was
333	>	// prepared by processor i
334
335	<	potatoes[which_node] = 0;
336	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
337	<
335	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
336	>	int recvLength;
337	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
338	>	char* recvBuffer = new char[recvLength];
339	>	if (recvBuffer == NULL) {
340	>	} else {
341	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
342	>	os << recvBuffer;
343	>	delete [] recvBuffer;
344		}
345	+	}
346	+	os << "    </StuntDoubles>\n";
347	+
348	+	os << "  </Snapshot>\n";
349	+	os.flush();
350	+	} else {
351	+	int sendBufferLength = buffer.size() + 1;
352	+	int myturn = 0;
353	+	for (int i = 1; i < nProc; ++i){
354	+	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
355	+	if (myturn == worldRank){
356	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
357	+	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
358	+	}
359	+	}
360	+	}
361
362	<	myPotato = potatoes[which_node];
362	>	#endif // is_mpi
363
364	<	//recieve the number of integrableObject in current molecule
377	<	MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
378	<	myPotato, MPI_COMM_WORLD, &istatus);
379	<	myPotato++;
380	<
381	<	for(int l = 0; l < nCurObj; l++){
364	>	}
365
366	<	if (potatoes[which_node] + 2 >= MAXTAG) {
367	<	// The potato was going to exceed the maximum value,
368	<	// so wrap this processor potato back to 0:
366	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
367	>
368	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
369	>	std::string type("pv");
370	>	std::string line;
371	>	char tempBuffer[4096];
372
373	<	potatoes[which_node] = 0;
374	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
375	<
390	<	}
373	>	Vector3d pos;
374	>	Vector3d vel;
375	>	pos = integrableObject->getPos();
376
377	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
378	<	myPotato, MPI_COMM_WORLD, &istatus);
377	>	if (isinf(pos[0]) || isnan(pos[0]) ||
378	>	isinf(pos[1]) || isnan(pos[1]) ||
379	>	isinf(pos[2]) || isnan(pos[2]) ) {
380	>	sprintf( painCave.errMsg,
381	>	"DumpWriter detected a numerical error writing the position"
382	>	" for object %d", index);
383	>	painCave.isFatal = 1;
384	>	simError();
385	>	}
386
387	<	atomTypeString = MPIatomTypeString;
387	>	vel = integrableObject->getVel();
388
389	<	myPotato++;
389	>	if (isinf(vel[0]) || isnan(vel[0]) ||
390	>	isinf(vel[1]) || isnan(vel[1]) ||
391	>	isinf(vel[2]) || isnan(vel[2]) ) {
392	>	sprintf( painCave.errMsg,
393	>	"DumpWriter detected a numerical error writing the velocity"
394	>	" for object %d", index);
395	>	painCave.isFatal = 1;
396	>	simError();
397	>	}
398
399	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
400	<	myPotato++;
399	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
400	>	pos[0], pos[1], pos[2],
401	>	vel[0], vel[1], vel[2]);
402	>	line += tempBuffer;
403
404	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
404	>	if (integrableObject->isDirectional()) {
405	>	type += "qj";
406	>	Quat4d q;
407	>	Vector3d ji;
408	>	q = integrableObject->getQ();
409
410	<	if(msgLen  == 13)
411	<	isDirectional = 1;
412	<	else
413	<	isDirectional = 0;
414	<
415	<	// If we've survived to here, format the line:
416	<
417	<	if (!isDirectional) {
418	<
413	<	sprintf( writeLine,
414	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
415	<	atomTypeString,
416	<	atomData[0],
417	<	atomData[1],
418	<	atomData[2],
419	<	atomData[3],
420	<	atomData[4],
421	<	atomData[5]);
422	<
423	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
424	<
425	<	}
426	<	else {
427	<
428	<	sprintf( writeLine,
429	<	"%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",
430	<	atomTypeString,
431	<	atomData[0],
432	<	atomData[1],
433	<	atomData[2],
434	<	atomData[3],
435	<	atomData[4],
436	<	atomData[5],
437	<	atomData[6],
438	<	atomData[7],
439	<	atomData[8],
440	<	atomData[9],
441	<	atomData[10],
442	<	atomData[11],
443	<	atomData[12]);
444	<
445	<	}
446	<
447	<	for(k = 0; k < outFile.size(); k++)
448	<	*outFile[k] << writeLine;
449	<
450	<	}// end for(int l =0)
451	<	potatoes[which_node] = myPotato;
452	<
410	>	if (isinf(q[0]) || isnan(q[0]) ||
411	>	isinf(q[1]) || isnan(q[1]) ||
412	>	isinf(q[2]) || isnan(q[2]) ||
413	>	isinf(q[3]) || isnan(q[3]) ) {
414	>	sprintf( painCave.errMsg,
415	>	"DumpWriter detected a numerical error writing the quaternion"
416	>	" for object %d", index);
417	>	painCave.isFatal = 1;
418	>	simError();
419		}
454	–	else {
455	–
456	–	haveError = 0;
457	–
458	–	local_index = indexArray[currentIndex].first;
420
421	<	integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
421	>	ji = integrableObject->getJ();
422
423	<	for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
424	<	sd = *iter;
425	<	atomTypeString = sd->getType();
426	<
427	<	sd->getPos(pos);
428	<	sd->getVel(vel);
429	<
430	<	atomData[0] = pos[0];
470	<	atomData[1] = pos[1];
471	<	atomData[2] = pos[2];
472	<
473	<	atomData[3] = vel[0];
474	<	atomData[4] = vel[1];
475	<	atomData[5] = vel[2];
476	<
477	<	isDirectional = 0;
478	<
479	<	if( sd->isDirectional() ){
480	<
481	<	isDirectional = 1;
482	<
483	<	sd->getQ( q );
484	<	sd->getJ( ji );
485	<
486	<	for (int j = 0; j < 6 ; j++)
487	<	atomData[j] = atomData[j];
488	<
489	<	atomData[6] = q[0];
490	<	atomData[7] = q[1];
491	<	atomData[8] = q[2];
492	<	atomData[9] = q[3];
493	<
494	<	atomData[10] = ji[0];
495	<	atomData[11] = ji[1];
496	<	atomData[12] = ji[2];
497	<	}
498	<
499	<	// If we've survived to here, format the line:
500	<
501	<	if (!isDirectional) {
502	<
503	<	sprintf( writeLine,
504	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
505	<	atomTypeString,
506	<	atomData[0],
507	<	atomData[1],
508	<	atomData[2],
509	<	atomData[3],
510	<	atomData[4],
511	<	atomData[5]);
512	<
513	<	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
514	<
515	<	}
516	<	else {
517	<
518	<	sprintf( writeLine,
519	<	"%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",
520	<	atomTypeString,
521	<	atomData[0],
522	<	atomData[1],
523	<	atomData[2],
524	<	atomData[3],
525	<	atomData[4],
526	<	atomData[5],
527	<	atomData[6],
528	<	atomData[7],
529	<	atomData[8],
530	<	atomData[9],
531	<	atomData[10],
532	<	atomData[11],
533	<	atomData[12]);
534	<
535	<	}
536	<
537	<	for(k = 0; k < outFile.size(); k++)
538	<	*outFile[k] << writeLine;
539	<
540	<
541	<	}//end for(iter = integrableObject.begin())
542	<
543	<	currentIndex++;
423	>	if (isinf(ji[0]) || isnan(ji[0]) ||
424	>	isinf(ji[1]) || isnan(ji[1]) ||
425	>	isinf(ji[2]) || isnan(ji[2]) ) {
426	>	sprintf( painCave.errMsg,
427	>	"DumpWriter detected a numerical error writing the angular"
428	>	" momentum for object %d", index);
429	>	painCave.isFatal = 1;
430	>	simError();
431		}
432
433	<	}//end for(i = 0; i < mpiSim->getNmol())
434	<
435	<	for(k = 0; k < outFile.size(); k++)
436	<	outFile[k]->flush();
437	<
551	<	sprintf( checkPointMsg,
552	<	"Sucessfully took a dump.\n");
553	<
554	<	MPIcheckPoint();
555	<
556	<	delete[] potatoes;
557	<
558	<	} else {
433	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
434	>	q[0], q[1], q[2], q[3],
435	>	ji[0], ji[1], ji[2]);
436	>	line += tempBuffer;
437	>	}
438
439	<	// worldRank != 0, so I'm a remote node.
440	<
441	<	// Set my magic potato to 0:
442	<
443	<	myPotato = 0;
444	<	currentIndex = 0;
445	<
446	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
439	>	if (needForceVector_) {
440	>	type += "f";
441	>	Vector3d frc = integrableObject->getFrc();
442	>	if (isinf(frc[0]) || isnan(frc[0]) ||
443	>	isinf(frc[1]) || isnan(frc[1]) ||
444	>	isinf(frc[2]) || isnan(frc[2]) ) {
445	>	sprintf( painCave.errMsg,
446	>	"DumpWriter detected a numerical error writing the force"
447	>	" for object %d", index);
448	>	painCave.isFatal = 1;
449	>	simError();
450	>	}
451	>	sprintf(tempBuffer, " %13e %13e %13e",
452	>	frc[0], frc[1], frc[2]);
453	>	line += tempBuffer;
454
455	<	// Am I the node which has this integrableObject?
456	<
457	<	if (MolToProcMap[i] == worldRank) {
455	>	if (integrableObject->isDirectional()) {
456	>	type += "t";
457	>	Vector3d trq = integrableObject->getTrq();
458	>	if (isinf(trq[0]) || isnan(trq[0]) ||
459	>	isinf(trq[1]) || isnan(trq[1]) ||
460	>	isinf(trq[2]) || isnan(trq[2]) ) {
461	>	sprintf( painCave.errMsg,
462	>	"DumpWriter detected a numerical error writing the torque"
463	>	" for object %d", index);
464	>	painCave.isFatal = 1;
465	>	simError();
466	>	}
467	>	sprintf(tempBuffer, " %13e %13e %13e",
468	>	trq[0], trq[1], trq[2]);
469	>	line += tempBuffer;
470	>	}
471	>	}
472
473	+	if (needParticlePot_) {
474	+	type += "u";
475	+	RealType particlePot = integrableObject->getParticlePot();
476	+	if (isinf(particlePot) || isnan(particlePot)) {
477	+	sprintf( painCave.errMsg,
478	+	"DumpWriter detected a numerical error writing the particle "
479	+	" potential for object %d", index);
480	+	painCave.isFatal = 1;
481	+	simError();
482	+	}
483	+	sprintf(tempBuffer, " %13e", particlePot);
484	+	line += tempBuffer;
485	+	}
486	+
487	+	if (needFlucQ_) {
488	+	type += "cw";
489	+	RealType fqPos = integrableObject->getFlucQPos();
490	+	if (isinf(fqPos) || isnan(fqPos) ) {
491	+	sprintf( painCave.errMsg,
492	+	"DumpWriter detected a numerical error writing the"
493	+	" fluctuating charge for object %d", index);
494	+	painCave.isFatal = 1;
495	+	simError();
496	+	}
497	+	sprintf(tempBuffer, " %13e ", fqPos);
498	+	line += tempBuffer;
499	+
500	+	RealType fqVel = integrableObject->getFlucQVel();
501	+	if (isinf(fqVel) || isnan(fqVel) ) {
502	+	sprintf( painCave.errMsg,
503	+	"DumpWriter detected a numerical error writing the"
504	+	" fluctuating charge velocity for object %d", index);
505	+	painCave.isFatal = 1;
506	+	simError();
507	+	}
508	+	sprintf(tempBuffer, " %13e ", fqVel);
509	+	line += tempBuffer;
510
511	<	if (myPotato + 1 >= MAXTAG) {
512	<
513	<	// The potato was going to exceed the maximum value,
514	<	// so wrap this processor potato back to 0 (and block until
515	<	// node 0 says we can go:
516	<
517	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
518	<
511	>	if (needForceVector_) {
512	>	type += "g";
513	>	RealType fqFrc = integrableObject->getFlucQFrc();
514	>	if (isinf(fqFrc) || isnan(fqFrc) ) {
515	>	sprintf( painCave.errMsg,
516	>	"DumpWriter detected a numerical error writing the"
517	>	" fluctuating charge force for object %d", index);
518	>	painCave.isFatal = 1;
519	>	simError();
520		}
521	+	sprintf(tempBuffer, " %13e ", fqFrc);
522	+	line += tempBuffer;
523	+	}
524	+	}
525
526	<	local_index = indexArray[currentIndex].first;
527	<	integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
528	<
529	<	nCurObj = integrableObjects.size();
530	<
531	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
532	<	myPotato, MPI_COMM_WORLD);
533	<	myPotato++;
526	>	if (needElectricField_) {
527	>	type += "e";
528	>	Vector3d eField= integrableObject->getElectricField();
529	>	if (isinf(eField[0]) || isnan(eField[0]) ||
530	>	isinf(eField[1]) || isnan(eField[1]) ||
531	>	isinf(eField[2]) || isnan(eField[2]) ) {
532	>	sprintf( painCave.errMsg,
533	>	"DumpWriter detected a numerical error writing the electric"
534	>	" field for object %d", index);
535	>	painCave.isFatal = 1;
536	>	simError();
537	>	}
538	>	sprintf(tempBuffer, " %13e %13e %13e",
539	>	eField[0], eField[1], eField[2]);
540	>	line += tempBuffer;
541	>	}
542
543	<	for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
543	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
544	>	return std::string(tempBuffer);
545	>	}
546
547	<	if (myPotato + 2 >= MAXTAG) {
548	<
549	<	// The potato was going to exceed the maximum value,
598	<	// so wrap this processor potato back to 0 (and block until
599	<	// node 0 says we can go:
600	<
601	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
602	<
603	<	}
604	<
605	<	sd = *iter;
606	<
607	<	atomTypeString = sd->getType();
547	>	void DumpWriter::writeDump() {
548	>	writeFrame(*dumpFile_);
549	>	}
550
551	<	sd->getPos(pos);
552	<	sd->getVel(vel);
551	>	void DumpWriter::writeEor() {
552	>	std::ostream* eorStream;
553	>
554	>	#ifdef IS_MPI
555	>	if (worldRank == 0) {
556	>	#endif // is_mpi
557
558	<	atomData[0] = pos[0];
613	<	atomData[1] = pos[1];
614	<	atomData[2] = pos[2];
558	>	eorStream = createOStream(eorFilename_);
559
560	<	atomData[3] = vel[0];
561	<	atomData[4] = vel[1];
562	<	atomData[5] = vel[2];
619	<
620	<	isDirectional = 0;
560	>	#ifdef IS_MPI
561	>	}
562	>	#endif // is_mpi
563
564	<	if( sd->isDirectional() ){
564	>	writeFrame(*eorStream);
565
566	<	isDirectional = 1;
567	<
568	<	sd->getQ( q );
569	<	sd->getJ( ji );
570	<
571	<
572	<	atomData[6] = q[0];
573	<	atomData[7] = q[1];
632	<	atomData[8] = q[2];
633	<	atomData[9] = q[3];
634	<
635	<	atomData[10] = ji[0];
636	<	atomData[11] = ji[1];
637	<	atomData[12] = ji[2];
638	<	}
566	>	#ifdef IS_MPI
567	>	if (worldRank == 0) {
568	>	#endif // is_mpi
569	>	writeClosing(*eorStream);
570	>	delete eorStream;
571	>	#ifdef IS_MPI
572	>	}
573	>	#endif // is_mpi
574
575	<
641	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
575	>	}
576
643	–	// null terminate the string before sending (just in case):
644	–	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
577
578	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
579	<	myPotato, MPI_COMM_WORLD);
580	<
581	<	myPotato++;
582	<
583	<	if (isDirectional) {
578	>	void DumpWriter::writeDumpAndEor() {
579	>	std::vector<std::streambuf*> buffers;
580	>	std::ostream* eorStream;
581	>	#ifdef IS_MPI
582	>	if (worldRank == 0) {
583	>	#endif // is_mpi
584
585	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0,
654	<	myPotato, MPI_COMM_WORLD);
655	<
656	<	} else {
585	>	buffers.push_back(dumpFile_->rdbuf());
586
587	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0,
659	<	myPotato, MPI_COMM_WORLD);
660	<	}
587	>	eorStream = createOStream(eorFilename_);
588
589	<	myPotato++;
590	<
591	<	}
665	<
666	<	currentIndex++;
667	<
668	<	}
669	<
670	<	}
671	<
672	<	sprintf( checkPointMsg,
673	<	"Sucessfully took a dump.\n");
674	<	MPIcheckPoint();
675	<
589	>	buffers.push_back(eorStream->rdbuf());
590	>
591	>	#ifdef IS_MPI
592		}
593	+	#endif // is_mpi
594
595	+	TeeBuf tbuf(buffers.begin(), buffers.end());
596	+	std::ostream os(&tbuf);
597
598	<
680	<	#endif // is_mpi
681	<	}
598	>	writeFrame(os);
599
600		#ifdef IS_MPI
601	+	if (worldRank == 0) {
602	+	#endif // is_mpi
603	+	writeClosing(*eorStream);
604	+	delete eorStream;
605	+	#ifdef IS_MPI
606	+	}
607	+	#endif // is_mpi
608	+
609	+	}
610
611	<	// a couple of functions to let us escape the write loop
611	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
612
613	<	void dWrite::DieDieDie( void ){
613	>	std::ostream* newOStream;
614	>	#ifdef HAVE_LIBZ
615	>	if (needCompression_) {
616	>	newOStream = new ogzstream(filename.c_str());
617	>	} else {
618	>	newOStream = new std::ofstream(filename.c_str());
619	>	}
620	>	#else
621	>	newOStream = new std::ofstream(filename.c_str());
622	>	#endif
623	>	//write out MetaData first
624	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
625	>	(*newOStream) << "  <MetaData>" << std::endl;
626	>	(*newOStream) << info_->getRawMetaData();
627	>	(*newOStream) << "  </MetaData>" << std::endl;
628	>	return newOStream;
629	>	}
630
631	<	MPI_Finalize();
690	<	exit (0);
691	<	}
631	>	void DumpWriter::writeClosing(std::ostream& os) {
632
633	<	#endif //is_mpi
633	>	os << "</OpenMD>\n";
634	>	os.flush();
635	>	}
636	>
637	>	}//end namespace OpenMD

Comparing:
trunk/src/io/DumpWriter.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/io/DumpWriter.cpp (property svn:keywords), Revision 1714 by gezelter, Sat May 19 18:12:46 2012 UTC

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