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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 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

#	Line 35 | Line 35
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).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	+	#ifdef IS_MPI
44	+	#include <mpi.h>
45	+	#endif
46
47	+	#include <string>
48	+	#include <sstream>
49		#include <iostream>
50
51		#include "io/RestWriter.hpp"
52		#include "utils/simError.h"
53		#include "brains/SnapshotManager.hpp"
48	–	#ifdef IS_MPI
49	–	#include <mpi.h>
50	–	#endif
54
55		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	>
154	>	for (int i = 1; i < nProc; ++i) {
155	>
156	>	// receive the length of the string buffer that was
157	>	// prepared by processor i
158	>
159	>	int recvLength;
160	>	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
161	>	char* recvBuffer = new char[recvLength];
162	>	if (recvBuffer == NULL) {
163	>	} else {
164	>	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
165	>	istatus);
166	>	(*output_) << recvBuffer;
167	>	delete [] recvBuffer;
168	>	}
169	>	}
170	>	(*output_).flush();
171	>	} else {
172	>	int sendBufferLength = buffer.size() + 1;
173	>	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
174	>	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR,
175	>	masterNode, 0, MPI_COMM_WORLD);
176	>	}
177	>
178	>	#endif // is_mpi
179	>
180	>	}
181
182	<	RestWriter::~RestWriter() {
182	>	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
183	>
184		#ifdef IS_MPI
185	<	if(worldRank == 0 ){
107	<	#endif
108	<	output_.close();
109	<	#ifdef IS_MPI
110	<	}
185	>	MPI_Status* istatus;
186		#endif
112	–	}
113	–
114	–	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
115	–
187
188	<	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
189	<
188	>	#ifndef IS_MPI
189	>	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
190	>
191		// output some information about the molecules
192		std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
193		std::map<int, Restraint::RealPair>::const_iterator j;
194	+
195		for( i = restInfo.begin(); i != restInfo.end(); ++i){
196		for(j = (*i).begin(); j != (*i).end(); ++j){
197	<	output_ << "\t" << (j->second).first << "\t" << (j->second).second;
197	>	(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
198		}
199	<	output_ << std::endl;
199	>	(*output_) << std::endl;
200		}
201	+	(*output_).flush();
202	+	#else
203	+	std::string buffer, first, second;
204	+	std::stringstream ss;
205	+
206	+	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
207	+	std::map<int, Restraint::RealPair>::const_iterator j;
208	+
209	+	for( i = restInfo.begin(); i != restInfo.end(); ++i){
210	+	for(j = (*i).begin(); j != (*i).end(); ++j){
211	+	ss.clear();
212	+	ss << (j->second).first;
213	+	ss >> first;
214	+	ss.clear();
215	+	ss << (j->second).second;
216	+	ss >> second;
217	+	buffer += ("\t" + first + "\t" + second);
218	+	}
219	+	buffer += "\n";
220	+	}
221	+
222	+	const int masterNode = 0;
223	+
224	+	if (worldRank == masterNode) {
225	+	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
226	+	(*output_) << buffer;
227	+
228	+	int nProc;
229	+	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
230	+	for (int i = 1; i < nProc; ++i) {
231	+
232	+	// receive the length of the string buffer that was
233	+	// prepared by processor i
234	+
235	+	int recvLength;
236	+	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
237	+	char* recvBuffer = new char[recvLength];
238	+	if (recvBuffer == NULL) {
239	+	} else {
240	+	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
241	+	istatus);
242	+	(*output_) << recvBuffer;
243	+
244	+	delete [] recvBuffer;
245	+	}
246	+	}
247	+	(*output_).flush();
248	+	} else {
249	+	int sendBufferLength = buffer.size() + 1;
250	+	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
251	+	MPI_Send((void *)buffer.c_str(), sendBufferLength,
252	+	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
253	+	}
254	+	#endif // is_mpi
255		}
256
130	–	}// end namespace OpenMD
257
258	+	RestWriter::~RestWriter() {
259	+
260	+	#ifdef IS_MPI
261	+
262	+	if (worldRank == 0) {
263	+	#endif // is_mpi
264	+	if (createRestFile_){
265	+	writeClosing(*output_);
266	+	delete output_;
267	+	}
268	+	#ifdef IS_MPI
269	+	}
270	+	#endif // is_mpi
271	+	}
272	+
273	+	void RestWriter::writeClosing(std::ostream& os) {
274	+	os.flush();
275	+	}
276	+
277	+	}// end namespace OpenMD
278	+

Comparing trunk/src/io/RestWriter.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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