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root/OpenMD/trunk/src/io/DumpWriter.cpp

Comparing trunk/src/io/DumpWriter.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1564 by chuckv, Wed May 18 19:28:52 2011 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]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	#include "io/DumpWriter.hpp"
43	>	#include "primitives/Molecule.hpp"
44	>	#include "utils/simError.h"
45	>	#include "io/basic_teebuf.hpp"
46	>	#include "io/gzstream.hpp"
47	>	#include "io/Globals.hpp"
48
4	–	#include <string.h>
5	–	#include <iostream>
6	–	#include <fstream>
7	–	#include <algorithm>
8	–	#include <utility>
49
50		#ifdef IS_MPI
51		#include <mpi.h>
12	–	#include "mpiSimulation.hpp"
13	–
14	–	namespace dWrite{
15	–	void DieDieDie( void );
16	–	}
17	–
18	–	using namespace dWrite;
52		#endif //is_mpi
53
54	<	#include "ReadWrite.hpp"
55	<	#include "simError.h"
54	>	using namespace std;
55	>	namespace OpenMD {
56
57	<	DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
57	>	DumpWriter::DumpWriter(SimInfo* info)
58	>	: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
59
60	<	entry_plug = the_entry_plug;
61	<
60	>	Globals* simParams = info->getSimParams();
61	>	needCompression_ = simParams->getCompressDumpFile();
62	>	needForceVector_ = simParams->getOutputForceVector();
63	>	createDumpFile_ = true;
64	>	#ifdef HAVE_LIBZ
65	>	if (needCompression_) {
66	>	filename_ += ".gz";
67	>	eorFilename_ += ".gz";
68	>	}
69	>	#endif
70	>
71		#ifdef IS_MPI
72	<	if(worldRank == 0 ){
72	>
73	>	if (worldRank == 0) {
74		#endif // is_mpi
75	+
76	+	dumpFile_ = createOStream(filename_);
77
78	<	dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc );
78	>	if (!dumpFile_) {
79	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
80	>	filename_.c_str());
81	>	painCave.isFatal = 1;
82	>	simError();
83	>	}
84
85	<	if( !dumpFile ){
85	>	#ifdef IS_MPI
86
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();
87		}
88
89	<	#ifdef IS_MPI
89	>	#endif // is_mpi
90	>
91		}
92
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	–	}
93
94	<	DumpWriter::~DumpWriter( ){
94	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
95	>	: info_(info), filename_(filename){
96
97	+	Globals* simParams = info->getSimParams();
98	+	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
99	+
100	+	needCompression_ = simParams->getCompressDumpFile();
101	+	needForceVector_ = simParams->getOutputForceVector();
102	+	createDumpFile_ = true;
103	+	#ifdef HAVE_LIBZ
104	+	if (needCompression_) {
105	+	filename_ += ".gz";
106	+	eorFilename_ += ".gz";
107	+	}
108	+	#endif
109	+
110		#ifdef IS_MPI
111	<	if(worldRank == 0 ){
111	>
112	>	if (worldRank == 0) {
113		#endif // is_mpi
114
115	<	dumpFile.close();
115	>
116	>	dumpFile_ = createOStream(filename_);
117
118	<	#ifdef IS_MPI
119	<	}
120	<	#endif // is_mpi
121	<	}
118	>	if (!dumpFile_) {
119	>	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
120	>	filename_.c_str());
121	>	painCave.isFatal = 1;
122	>	simError();
123	>	}
124
125		#ifdef IS_MPI
126
127	<	/**
71	<	* A hook function to load balancing
72	<	*/
127	>	}
128
129	<	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	<	}
129	>	#endif // is_mpi
130
131	<	/**
87	<	* Sorting the local index by global index
88	<	*/
89	<
90	<	void DumpWriter::sortByGlobalIndex(){
91	<	Molecule* mols = entry_plug->molecules;
92	<	indexArray.clear();
131	>	}
132
133	<	for(int i = 0; i < entry_plug->n_mol;i++)
134	<	indexArray.push_back(make_pair(i, mols[i].getGlobalIndex()));
135	<
136	<	sort(indexArray.begin(), indexArray.end(), indexSortingCriterion);
137	<	}
138	<
133	>	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile)
134	>	: info_(info), filename_(filename){
135	>
136	>	Globals* simParams = info->getSimParams();
137	>	eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";
138	>
139	>	needCompression_ = simParams->getCompressDumpFile();
140	>	needForceVector_ = simParams->getOutputForceVector();
141	>
142	>	#ifdef HAVE_LIBZ
143	>	if (needCompression_) {
144	>	filename_ += ".gz";
145	>	eorFilename_ += ".gz";
146	>	}
147		#endif
148	+
149	+	#ifdef IS_MPI
150	+
151	+	if (worldRank == 0) {
152	+	#endif // is_mpi
153	+
154	+	createDumpFile_ = writeDumpFile;
155	+	if (createDumpFile_) {
156	+	dumpFile_ = createOStream(filename_);
157	+
158	+	if (!dumpFile_) {
159	+	sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
160	+	filename_.c_str());
161	+	painCave.isFatal = 1;
162	+	simError();
163	+	}
164	+	}
165	+	#ifdef IS_MPI
166	+
167	+	}
168
169	<	void DumpWriter::writeDump(double currentTime){
169	>
170	>	#endif // is_mpi
171	>
172	>	}
173
174	<	ofstream finalOut;
105	<	vector<ofstream*> fileStreams;
174	>	DumpWriter::~DumpWriter() {
175
176		#ifdef IS_MPI
177	<	if(worldRank == 0 ){
178	<	#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	<	}
177	>
178	>	if (worldRank == 0) {
179		#endif // is_mpi
180	+	if (createDumpFile_){
181	+	writeClosing(*dumpFile_);
182	+	delete dumpFile_;
183	+	}
184	+	#ifdef IS_MPI
185
186	<	fileStreams.push_back(&finalOut);
123	<	fileStreams.push_back(&dumpFile);
186	>	}
187
188	<	writeFrame(fileStreams, currentTime);
188	>	#endif // is_mpi
189
190	<	#ifdef IS_MPI
128	<	finalOut.close();
129	<	#endif
130	<
131	<	}
190	>	}
191
192	<	void DumpWriter::writeFinal(double currentTime){
192	>	void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) {
193
194	<	ofstream finalOut;
136	<	vector<ofstream*> fileStreams;
194	>	char buffer[1024];
195
196	<	#ifdef IS_MPI
139	<	if(worldRank == 0 ){
140	<	#endif // is_mpi
196	>	os << "    <FrameData>\n";
197
198	<	finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc );
198	>	RealType currentTime = s->getTime();
199
200	<	if( !finalOut ){
200	>	if (isinf(currentTime) || isnan(currentTime)) {
201		sprintf( painCave.errMsg,
202	<	"Could not open \"%s\" for final dump output.\n",
147	<	entry_plug->finalName.c_str() );
202	>	"DumpWriter detected a numerical error writing the time");
203		painCave.isFatal = 1;
204		simError();
205		}
206	+
207	+	sprintf(buffer, "        Time: %.10g\n", currentTime);
208	+	os << buffer;
209
210	<	#ifdef IS_MPI
211	<	}
154	<	#endif // is_mpi
155	<
156	<	fileStreams.push_back(&finalOut);
157	<	writeFrame(fileStreams, currentTime);
210	>	Mat3x3d hmat;
211	>	hmat = s->getHmat();
212
213	<	#ifdef IS_MPI
214	<	finalOut.close();
215	<	#endif
216	<
217	<	}
218	<
219	<	void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){
220	<
221	<	const int BUFFERSIZE = 2000;
222	<	const int MINIBUFFERSIZE = 100;
169	<
170	<	char tempBuffer[BUFFERSIZE];
171	<	char writeLine[BUFFERSIZE];
172	<
173	<	int i;
174	<	unsigned int k;
175	<
176	<	#ifdef IS_MPI
177	<
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	<	*********************************************************************/
214	<
215	<	int *potatoes;
216	<	int myPotato;
217	<
218	<	int nProc;
219	<	int j, which_node, done, which_atom, local_index, currentIndex;
220	<	double atomData[13];
221	<	int isDirectional;
222	<	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();
213	>	for (unsigned int i = 0; i < 3; i++) {
214	>	for (unsigned int j = 0; j < 3; j++) {
215	>	if (isinf(hmat(i,j)) || isnan(hmat(i,j))) {
216	>	sprintf( painCave.errMsg,
217	>	"DumpWriter detected a numerical error writing the box");
218	>	painCave.isFatal = 1;
219	>	simError();
220	>	}
221	>	}
222	>	}
223
224	<	for( iter = integrableObjects.begin();iter !=  integrableObjects.end(); ++iter){
225	<	sd = *iter;
226	<	sd->getPos(pos);
227	<	sd->getVel(vel);
224	>	sprintf(buffer, "        Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
225	>	hmat(0, 0), hmat(1, 0), hmat(2, 0),
226	>	hmat(0, 1), hmat(1, 1), hmat(2, 1),
227	>	hmat(0, 2), hmat(1, 2), hmat(2, 2));
228	>	os << buffer;
229
230	<	sprintf( tempBuffer,
231	<	"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
232	<	sd->getType(),
233	<	pos[0],
234	<	pos[1],
235	<	pos[2],
236	<	vel[0],
237	<	vel[1],
238	<	vel[2]);
239	<	strcpy( writeLine, tempBuffer );
230	>	RealType chi = s->getChi();
231	>	RealType integralOfChiDt = s->getIntegralOfChiDt();
232	>	if (isinf(chi) || isnan(chi) ||
233	>	isinf(integralOfChiDt) || isnan(integralOfChiDt)) {
234	>	sprintf( painCave.errMsg,
235	>	"DumpWriter detected a numerical error writing the thermostat");
236	>	painCave.isFatal = 1;
237	>	simError();
238	>	}
239	>	sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
240	>	os << buffer;
241
242	<	if( sd->isDirectional() ){
242	>	Mat3x3d eta;
243	>	eta = s->getEta();
244
245	<	sd->getQ( q );
246	<	sd->getJ( ji );
247	<
248	<	sprintf( tempBuffer,
249	<	"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
250	<	q[0],
251	<	q[1],
252	<	q[2],
290	<	q[3],
291	<	ji[0],
292	<	ji[1],
293	<	ji[2]);
294	<	strcat( writeLine, tempBuffer );
245	>	for (unsigned int i = 0; i < 3; i++) {
246	>	for (unsigned int j = 0; j < 3; j++) {
247	>	if (isinf(eta(i,j)) || isnan(eta(i,j))) {
248	>	sprintf( painCave.errMsg,
249	>	"DumpWriter detected a numerical error writing the barostat");
250	>	painCave.isFatal = 1;
251	>	simError();
252	>	}
253		}
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;
254		}
255
256	<	}
256	>	sprintf(buffer, "    Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n",
257	>	eta(0, 0), eta(1, 0), eta(2, 0),
258	>	eta(0, 1), eta(1, 1), eta(2, 1),
259	>	eta(0, 2), eta(1, 2), eta(2, 2));
260	>	os << buffer;
261
262	<	#else // is_mpi
262	>	os << "    </FrameData>\n";
263	>	}
264
265	<	/* 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	<	}
265	>	void DumpWriter::writeFrame(std::ostream& os) {
266
267	<	int haveError;
267	>	#ifdef IS_MPI
268	>	MPI_Status istatus;
269	>	#endif
270
271	<	MPI_Status istatus;
272	<	int nCurObj;
273	<	int *MolToProcMap = mpiSim->getMolToProcMap();
271	>	Molecule* mol;
272	>	StuntDouble* integrableObject;
273	>	SimInfo::MoleculeIterator mi;
274	>	Molecule::IntegrableObjectIterator ii;
275
276	<	// write out header and node 0's coordinates
276	>	#ifndef IS_MPI
277	>	os << "  <Snapshot>\n";
278	>
279	>	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
280
281	<	if( worldRank == 0 ){
281	>	os << "    <StuntDoubles>\n";
282	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
283
284	<	// Node 0 needs a list of the magic potatoes for each processor;
285	<
286	<	nProc = mpiSim->getNProcessors();
287	<	potatoes = new int[nProc];
288	<
289	<	//write out the comment lines
290	<	for (i = 0; i < nProc; i++)
291	<	potatoes[i] = 0;
284	>
285	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
286	>	integrableObject = mol->nextIntegrableObject(ii)) {
287	>	os << prepareDumpLine(integrableObject);
288	>
289	>	}
290	>	}
291	>	os << "    </StuntDoubles>\n";
292
293	<	for(k = 0; k < outFile.size(); k++){
337	<	*outFile[k] << nTotObjects << "\n";
293	>	os << "  </Snapshot>\n";
294
295	<	*outFile[k] << currentTime << ";\t"
296	<	<< entry_plug->Hmat[0][0] << "\t"
297	<	<< entry_plug->Hmat[1][0] << "\t"
298	<	<< entry_plug->Hmat[2][0] << ";\t"
295	>	os.flush();
296	>	#else
297	>	//every node prepares the dump lines for integrable objects belong to itself
298	>	std::string buffer;
299	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
300
344	–	<< entry_plug->Hmat[0][1] << "\t"
345	–	<< entry_plug->Hmat[1][1] << "\t"
346	–	<< entry_plug->Hmat[2][1] << ";\t"
301
302	<	<< entry_plug->Hmat[0][2] << "\t"
303	<	<< entry_plug->Hmat[1][2] << "\t"
304	<	<< entry_plug->Hmat[2][2] << ";";
305	<
352	<	*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl;
302	>	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
303	>	integrableObject = mol->nextIntegrableObject(ii)) {
304	>	buffer += prepareDumpLine(integrableObject);
305	>	}
306		}
307	+
308	+	const int masterNode = 0;
309	+	int nProc;
310	+	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
311	+	if (worldRank == masterNode) {
312	+	os << "  <Snapshot>\n";
313	+	writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot());
314	+	os << "    <StuntDoubles>\n";
315	+
316	+	os << buffer;
317
318	<	currentIndex = 0;
318	>
319	>	for (int i = 1; i < nProc; ++i) {
320
321	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
322	<
323	<	// Get the Node number which has this atom;
324	<
325	<	which_node = MolToProcMap[i];
326	<
327	<	if (which_node != 0) {
328	<
329	<	if (potatoes[which_node] + 1 >= MAXTAG) {
330	<	// The potato was going to exceed the maximum value,
331	<	// so wrap this processor potato back to 0:
332	<
369	<	potatoes[which_node] = 0;
370	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
371	<
321	>	// receive the length of the string buffer that was
322	>	// prepared by processor i
323	>
324	>	MPI_Bcast(&i, 1, MPI_INT,masterNode,MPI_COMM_WORLD);
325	>	int recvLength;
326	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
327	>	char* recvBuffer = new char[recvLength];
328	>	if (recvBuffer == NULL) {
329	>	} else {
330	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus);
331	>	os << recvBuffer;
332	>	delete [] recvBuffer;
333		}
334	+	}
335	+	os << "    </StuntDoubles>\n";
336	+
337	+	os << "  </Snapshot>\n";
338	+	os.flush();
339	+	} else {
340	+	int sendBufferLength = buffer.size() + 1;
341	+	int myturn = 0;
342	+	for (int i = 1; i < nProc; ++i){
343	+	MPI_Bcast(&myturn,1, MPI_INT,masterNode,MPI_COMM_WORLD);
344	+	if (myturn == worldRank){
345	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
346	+	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
347	+	}
348	+	}
349	+	}
350
351	<	myPotato = potatoes[which_node];
351	>	#endif // is_mpi
352
353	<	//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++){
353	>	}
354
355	<	if (potatoes[which_node] + 2 >= MAXTAG) {
356	<	// The potato was going to exceed the maximum value,
357	<	// so wrap this processor potato back to 0:
355	>	std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
356	>
357	>	int index = integrableObject->getGlobalIntegrableObjectIndex();
358	>	std::string type("pv");
359	>	std::string line;
360	>	char tempBuffer[4096];
361
362	<	potatoes[which_node] = 0;
363	<	MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD);
364	<
390	<	}
362	>	Vector3d pos;
363	>	Vector3d vel;
364	>	pos = integrableObject->getPos();
365
366	<	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node,
367	<	myPotato, MPI_COMM_WORLD, &istatus);
366	>	if (isinf(pos[0]) || isnan(pos[0]) ||
367	>	isinf(pos[1]) || isnan(pos[1]) ||
368	>	isinf(pos[2]) || isnan(pos[2]) ) {
369	>	sprintf( painCave.errMsg,
370	>	"DumpWriter detected a numerical error writing the position"
371	>	" for object %d", index);
372	>	painCave.isFatal = 1;
373	>	simError();
374	>	}
375
376	<	atomTypeString = MPIatomTypeString;
376	>	vel = integrableObject->getVel();
377
378	<	myPotato++;
378	>	if (isinf(vel[0]) || isnan(vel[0]) ||
379	>	isinf(vel[1]) || isnan(vel[1]) ||
380	>	isinf(vel[2]) || isnan(vel[2]) ) {
381	>	sprintf( painCave.errMsg,
382	>	"DumpWriter detected a numerical error writing the velocity"
383	>	" for object %d", index);
384	>	painCave.isFatal = 1;
385	>	simError();
386	>	}
387
388	<	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus);
389	<	myPotato++;
388	>	sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e",
389	>	pos[0], pos[1], pos[2],
390	>	vel[0], vel[1], vel[2]);
391	>	line += tempBuffer;
392
393	<	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
393	>	if (integrableObject->isDirectional()) {
394	>	type += "qj";
395	>	Quat4d q;
396	>	Vector3d ji;
397	>	q = integrableObject->getQ();
398
399	<	if(msgLen  == 13)
400	<	isDirectional = 1;
401	<	else
402	<	isDirectional = 0;
403	<
404	<	// If we've survived to here, format the line:
405	<
406	<	if (!isDirectional) {
407	<
408	<	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;
399	>	if (isinf(q[0]) || isnan(q[0]) ||
400	>	isinf(q[1]) || isnan(q[1]) ||
401	>	isinf(q[2]) || isnan(q[2]) ||
402	>	isinf(q[3]) || isnan(q[3]) ) {
403	>	sprintf( painCave.errMsg,
404	>	"DumpWriter detected a numerical error writing the quaternion"
405	>	" for object %d", index);
406	>	painCave.isFatal = 1;
407	>	simError();
408	>	}
409
410	<	}// end for(int l =0)
451	<	potatoes[which_node] = myPotato;
410	>	ji = integrableObject->getJ();
411
412	+	if (isinf(ji[0]) || isnan(ji[0]) ||
413	+	isinf(ji[1]) || isnan(ji[1]) ||
414	+	isinf(ji[2]) || isnan(ji[2]) ) {
415	+	sprintf( painCave.errMsg,
416	+	"DumpWriter detected a numerical error writing the angular"
417	+	" momentum for object %d", index);
418	+	painCave.isFatal = 1;
419	+	simError();
420		}
421	<	else {
421	>
422	>	sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e",
423	>	q[0], q[1], q[2], q[3],
424	>	ji[0], ji[1], ji[2]);
425	>	line += tempBuffer;
426	>	}
427	>
428	>	if (needForceVector_) {
429	>	type += "f";
430	>	Vector3d frc;
431	>
432	>	frc = integrableObject->getFrc();
433	>
434	>	if (isinf(frc[0]) || isnan(frc[0]) ||
435	>	isinf(frc[1]) || isnan(frc[1]) ||
436	>	isinf(frc[2]) || isnan(frc[2]) ) {
437	>	sprintf( painCave.errMsg,
438	>	"DumpWriter detected a numerical error writing the force"
439	>	" for object %d", index);
440	>	painCave.isFatal = 1;
441	>	simError();
442	>	}
443	>	sprintf(tempBuffer, " %13e %13e %13e",
444	>	frc[0], frc[1], frc[2]);
445	>	line += tempBuffer;
446	>
447	>	if (integrableObject->isDirectional()) {
448	>	type += "t";
449	>	Vector3d trq;
450
451	<	haveError = 0;
451	>	trq = integrableObject->getTrq();
452
453	<	local_index = indexArray[currentIndex].first;
453	>	if (isinf(trq[0]) || isnan(trq[0]) ||
454	>	isinf(trq[1]) || isnan(trq[1]) ||
455	>	isinf(trq[2]) || isnan(trq[2]) ) {
456	>	sprintf( painCave.errMsg,
457	>	"DumpWriter detected a numerical error writing the torque"
458	>	" for object %d", index);
459	>	painCave.isFatal = 1;
460	>	simError();
461	>	}
462	>
463	>	sprintf(tempBuffer, " %13e %13e %13e",
464	>	trq[0], trq[1], trq[2]);
465	>	line += tempBuffer;
466	>	}
467	>	}
468	>
469	>	sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
470	>	return std::string(tempBuffer);
471	>	}
472
473	<	integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects();
473	>	void DumpWriter::writeDump() {
474	>	writeFrame(*dumpFile_);
475	>	}
476
477	<	for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){
478	<	sd = *iter;
479	<	atomTypeString = sd->getType();
480	<
481	<	sd->getPos(pos);
482	<	sd->getVel(vel);
468	<
469	<	atomData[0] = pos[0];
470	<	atomData[1] = pos[1];
471	<	atomData[2] = pos[2];
477	>	void DumpWriter::writeEor() {
478	>	std::ostream* eorStream;
479	>
480	>	#ifdef IS_MPI
481	>	if (worldRank == 0) {
482	>	#endif // is_mpi
483
484	<	atomData[3] = vel[0];
474	<	atomData[4] = vel[1];
475	<	atomData[5] = vel[2];
476	<
477	<	isDirectional = 0;
484	>	eorStream = createOStream(eorFilename_);
485
486	<	if( sd->isDirectional() ){
486	>	#ifdef IS_MPI
487	>	}
488	>	#endif // is_mpi
489
490	<	isDirectional = 1;
482	<
483	<	sd->getQ( q );
484	<	sd->getJ( ji );
490	>	writeFrame(*eorStream);
491
492	<	for (int j = 0; j < 6 ; j++)
493	<	atomData[j] = atomData[j];
494	<
495	<	atomData[6] = q[0];
496	<	atomData[7] = q[1];
497	<	atomData[8] = q[2];
498	<	atomData[9] = q[3];
499	<
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++;
544	<	}
492	>	#ifdef IS_MPI
493	>	if (worldRank == 0) {
494	>	#endif // is_mpi
495	>	writeClosing(*eorStream);
496	>	delete eorStream;
497	>	#ifdef IS_MPI
498	>	}
499	>	#endif // is_mpi
500
501	<	}//end for(i = 0; i < mpiSim->getNmol())
547	<
548	<	for(k = 0; k < outFile.size(); k++)
549	<	outFile[k]->flush();
550	<
551	<	sprintf( checkPointMsg,
552	<	"Sucessfully took a dump.\n");
553	<
554	<	MPIcheckPoint();
555	<
556	<	delete[] potatoes;
557	<
558	<	} else {
501	>	}
502
560	–	// worldRank != 0, so I'm a remote node.
503
504	<	// Set my magic potato to 0:
504	>	void DumpWriter::writeDumpAndEor() {
505	>	std::vector<std::streambuf*> buffers;
506	>	std::ostream* eorStream;
507	>	#ifdef IS_MPI
508	>	if (worldRank == 0) {
509	>	#endif // is_mpi
510
511	<	myPotato = 0;
565	<	currentIndex = 0;
566	<
567	<	for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) {
568	<
569	<	// Am I the node which has this integrableObject?
570	<
571	<	if (MolToProcMap[i] == worldRank) {
511	>	buffers.push_back(dumpFile_->rdbuf());
512
513	+	eorStream = createOStream(eorFilename_);
514
515	<	if (myPotato + 1 >= MAXTAG) {
516	<
517	<	// The potato was going to exceed the maximum value,
577	<	// so wrap this processor potato back to 0 (and block until
578	<	// node 0 says we can go:
579	<
580	<	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus);
581	<
582	<	}
583	<
584	<	local_index = indexArray[currentIndex].first;
585	<	integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects();
586	<
587	<	nCurObj = integrableObjects.size();
588	<
589	<	MPI_Send(&nCurObj, 1, MPI_INT, 0,
590	<	myPotato, MPI_COMM_WORLD);
591	<	myPotato++;
592	<
593	<	for( iter = integrableObjects.begin(); iter  != integrableObjects.end(); iter++){
594	<
595	<	if (myPotato + 2 >= MAXTAG) {
596	<
597	<	// 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();
608	<
609	<	sd->getPos(pos);
610	<	sd->getVel(vel);
611	<
612	<	atomData[0] = pos[0];
613	<	atomData[1] = pos[1];
614	<	atomData[2] = pos[2];
615	<
616	<	atomData[3] = vel[0];
617	<	atomData[4] = vel[1];
618	<	atomData[5] = vel[2];
619	<
620	<	isDirectional = 0;
621	<
622	<	if( sd->isDirectional() ){
623	<
624	<	isDirectional = 1;
625	<
626	<	sd->getQ( q );
627	<	sd->getJ( ji );
628	<
629	<
630	<	atomData[6] = q[0];
631	<	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	<	}
639	<
640	<
641	<	strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
642	<
643	<	// null terminate the string before sending (just in case):
644	<	MPIatomTypeString[MINIBUFFERSIZE-1] = '\0';
645	<
646	<	MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
647	<	myPotato, MPI_COMM_WORLD);
648	<
649	<	myPotato++;
650	<
651	<	if (isDirectional) {
652	<
653	<	MPI_Send(atomData, 13, MPI_DOUBLE, 0,
654	<	myPotato, MPI_COMM_WORLD);
655	<
656	<	} else {
657	<
658	<	MPI_Send(atomData, 6, MPI_DOUBLE, 0,
659	<	myPotato, MPI_COMM_WORLD);
660	<	}
661	<
662	<	myPotato++;
663	<
664	<	}
665	<
666	<	currentIndex++;
667	<
668	<	}
669	<
670	<	}
671	<
672	<	sprintf( checkPointMsg,
673	<	"Sucessfully took a dump.\n");
674	<	MPIcheckPoint();
675	<
515	>	buffers.push_back(eorStream->rdbuf());
516	>
517	>	#ifdef IS_MPI
518		}
519	+	#endif // is_mpi
520
521	+	TeeBuf tbuf(buffers.begin(), buffers.end());
522	+	std::ostream os(&tbuf);
523
524	<
680	<	#endif // is_mpi
681	<	}
524	>	writeFrame(os);
525
526		#ifdef IS_MPI
527	+	if (worldRank == 0) {
528	+	#endif // is_mpi
529	+	writeClosing(*eorStream);
530	+	delete eorStream;
531	+	#ifdef IS_MPI
532	+	}
533	+	#endif // is_mpi
534	+
535	+	}
536
537	<	// a couple of functions to let us escape the write loop
537	>	std::ostream* DumpWriter::createOStream(const std::string& filename) {
538
539	<	void dWrite::DieDieDie( void ){
539	>	std::ostream* newOStream;
540	>	#ifdef HAVE_LIBZ
541	>	if (needCompression_) {
542	>	newOStream = new ogzstream(filename.c_str());
543	>	} else {
544	>	newOStream = new std::ofstream(filename.c_str());
545	>	}
546	>	#else
547	>	newOStream = new std::ofstream(filename.c_str());
548	>	#endif
549	>	//write out MetaData first
550	>	(*newOStream) << "<OpenMD version=1>" << std::endl;
551	>	(*newOStream) << "  <MetaData>" << std::endl;
552	>	(*newOStream) << info_->getRawMetaData();
553	>	(*newOStream) << "  </MetaData>" << std::endl;
554	>	return newOStream;
555	>	}
556
557	<	MPI_Finalize();
690	<	exit (0);
691	<	}
557	>	void DumpWriter::writeClosing(std::ostream& os) {
558
559	<	#endif //is_mpi
559	>	os << "</OpenMD>\n";
560	>	os.flush();
561	>	}
562	>
563	>	}//end namespace OpenMD

Comparing trunk/src/io/DumpWriter.cpp (property svn:keywords):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1564 by chuckv, Wed May 18 19:28:52 2011 UTC

#	Line 0 | Line 1
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