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

Comparing trunk/src/io/RestWriter.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 36 | Line 36
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).
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
44	+	#include <string>
45	+	#include <sstream>
46		#include <iostream>
47
48		#include "io/RestWriter.hpp"
#	Line 53 | Line 56 | namespace OpenMD {
56		RestWriter::RestWriter(SimInfo* info, const std::string& filename,
57		std::vector<Restraint*> restraints ) :
58		info_(info){
59	<
60	<	//use master - slave mode, only master node writes to disk
59	>	createRestFile_ = true;
60	>
61		#ifdef IS_MPI
62		if(worldRank == 0){
63		#endif
64	<
65	<	output_.open(filename.c_str());
66	<
64	>
65	>	output_ = new std::ofstream(filename.c_str());
66	>
67		if(!output_){
68		sprintf( painCave.errMsg,
69		"Could not open %s for restraint output.\n",
#	Line 69 | Line 72 | namespace OpenMD {
72		simError();
73		}
74
75	<	output_ << "#time\t";
76	<
77	<	// TODO:  get Restraint info from slave nodes:
75	<	std::vector<Restraint*>::const_iterator resti;
76	<	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
75	>	#ifdef IS_MPI
76	>	}
77	>	#endif // is_mpi
78
79	<	if ((*resti)->getPrintRestraint()) {
80	<	std::string myName = (*resti)->getRestraintName();
81	<	int myType = (*resti)->getRestraintType();
79	>
80	>	#ifdef IS_MPI
81	>	MPI_Status istatus;
82	>	#endif
83	>
84	>	#ifndef IS_MPI
85	>
86	>	(*output_) << "#time\t";
87	>
88	>	std::vector<Restraint*>::const_iterator resti;
89	>
90	>	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
91	>	if ((*resti)->getPrintRestraint()) {
92	>
93	>	std::string myName = (*resti)->getRestraintName();
94	>	int myType = (*resti)->getRestraintType();
95	>
96	>	(*output_) << myName << ":";
97	>
98	>	if (myType & Restraint::rtDisplacement)
99	>	(*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
100	>
101	>	if (myType & Restraint::rtTwist)
102	>	(*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
103	>
104	>	if (myType & Restraint::rtSwingX)
105	>	(*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
106
107	<	output_ << myName << ":";
108	<
84	<	if (myType & Restraint::rtDisplacement)
85	<	output_ << "\tPosition(angstroms)\tEnergy(kcal/mol)";
86	<
87	<	if (myType & Restraint::rtTwist)
88	<	output_ << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
89	<
90	<	if (myType & Restraint::rtSwingX)
91	<	output_ << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
92	<
93	<	if (myType & Restraint::rtSwingY)
94	<	output_ << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
95	<
96	<	}
107	>	if (myType & Restraint::rtSwingY)
108	>	(*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
109		}
98	–	output_ << "\n";
99	–	#ifdef IS_MPI
110		}
111	<	#endif
112	<	}
111	>
112	>	(*output_) << "\n";
113	>	(*output_).flush();
114	>
115	>	#else
116	>
117	>	std::string buffer;
118	>
119	>	std::vector<Restraint*>::const_iterator resti;
120	>
121	>	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
122	>	if ((*resti)->getPrintRestraint()) {
123	>
124	>	std::string myName = (*resti)->getRestraintName();
125	>	int myType = (*resti)->getRestraintType();
126	>
127	>	buffer += (myName + ":");
128	>
129	>	if (myType & Restraint::rtDisplacement)
130	>	buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)";
131	>
132	>	if (myType & Restraint::rtTwist)
133	>	buffer += "\tTwistAngle(radians)\tEnergy(kcal/mol)";
134	>
135	>	if (myType & Restraint::rtSwingX)
136	>	buffer += "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
137	>
138	>	if (myType & Restraint::rtSwingY)
139	>	buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
140	>
141	>	buffer += "\n";
142	>	}
143	>	}
144	>
145	>	const int masterNode = 0;
146	>
147	>	if (worldRank == masterNode) {
148	>	(*output_) << "#time\t";
149	>	(*output_) << buffer;
150	>
151	>	int nProc;
152	>	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
153	>	for (int i = 1; i < nProc; ++i) {
154	>
155	>	// receive the length of the string buffer that was
156	>	// prepared by processor i
157	>
158	>	int recvLength;
159	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
160	>	char* recvBuffer = new char[recvLength];
161	>	if (recvBuffer == NULL) {
162	>	} else {
163	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
164	>	&istatus);
165	>	(*output_) << recvBuffer;
166	>	delete [] recvBuffer;
167	>	}
168	>	}
169	>	(*output_).flush();
170	>	} else {
171	>	int sendBufferLength = buffer.size() + 1;
172	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
173	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
174	>	0, MPI_COMM_WORLD);
175	>	}
176	>
177	>	#endif // is_mpi
178	>
179	>	}
180
181	<	RestWriter::~RestWriter() {
181	>	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
182	>
183		#ifdef IS_MPI
184	<	if(worldRank == 0 ){
107	<	#endif
108	<	output_.close();
109	<	#ifdef IS_MPI
110	<	}
184	>	MPI_Status istatus;
185		#endif
112	–	}
113	–
114	–	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
115	–
186
187	<	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
188	<
187	>	#ifndef IS_MPI
188	>	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
189	>
190		// output some information about the molecules
191		std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
192		std::map<int, Restraint::RealPair>::const_iterator j;
193	+
194		for( i = restInfo.begin(); i != restInfo.end(); ++i){
195		for(j = (*i).begin(); j != (*i).end(); ++j){
196	<	output_ << "\t" << (j->second).first << "\t" << (j->second).second;
196	>	(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
197		}
198	<	output_ << std::endl;
198	>	(*output_) << std::endl;
199		}
200	+	(*output_).flush();
201	+	#else
202	+	std::string buffer, first, second;
203	+	std::stringstream ss;
204	+
205	+	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
206	+	std::map<int, Restraint::RealPair>::const_iterator j;
207	+
208	+	for( i = restInfo.begin(); i != restInfo.end(); ++i){
209	+	for(j = (*i).begin(); j != (*i).end(); ++j){
210	+	ss.clear();
211	+	ss << (j->second).first;
212	+	ss >> first;
213	+	ss.clear();
214	+	ss << (j->second).second;
215	+	ss >> second;
216	+	buffer += ("\t" + first + "\t" + second);
217	+	}
218	+	buffer += "\n";
219	+	}
220	+
221	+	const int masterNode = 0;
222	+
223	+	if (worldRank == masterNode) {
224	+	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
225	+	(*output_) << buffer;
226	+
227	+	int nProc;
228	+	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
229	+	for (int i = 1; i < nProc; ++i) {
230	+
231	+	// receive the length of the string buffer that was
232	+	// prepared by processor i
233	+
234	+	int recvLength;
235	+	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
236	+	char* recvBuffer = new char[recvLength];
237	+	if (recvBuffer == NULL) {
238	+	} else {
239	+	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
240	+	&istatus);
241	+	(*output_) << recvBuffer;
242	+
243	+	delete [] recvBuffer;
244	+	}
245	+	}
246	+	(*output_).flush();
247	+	} else {
248	+	int sendBufferLength = buffer.size() + 1;
249	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
250	+	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
251	+	0, MPI_COMM_WORLD);
252	+	}
253	+	#endif // is_mpi
254		}
255
130	–	}// end namespace OpenMD
256
257	+	RestWriter::~RestWriter() {
258	+
259	+	#ifdef IS_MPI
260	+
261	+	if (worldRank == 0) {
262	+	#endif // is_mpi
263	+	if (createRestFile_){
264	+	writeClosing(*output_);
265	+	delete output_;
266	+	}
267	+	#ifdef IS_MPI
268	+	}
269	+	#endif // is_mpi
270	+	}
271	+
272	+	void RestWriter::writeClosing(std::ostream& os) {
273	+	os.flush();
274	+	}
275	+
276	+	}// end namespace OpenMD
277	+

Comparing trunk/src/io/RestWriter.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
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