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

Comparing trunk/src/io/RestWriter.cpp (file contents):
Revision 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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, 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 oopse {
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 oopse {
72		simError();
73		}
74
75	<	output_ << "#time\t";
76	<
77	<	// TODO:  get Restraint info from slave nodes:
78	<	std::vector<Restraint*>::const_iterator resti;
79	<	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
75	>	#ifdef IS_MPI
76	>	}
77	>	#endif // is_mpi
78	>
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 << ":";
96	>	(*output_) << myName << ":";
97
98		if (myType & Restraint::rtDisplacement)
99	<	output_ << "\tPosition(angstroms)\tEnergy(kcal/mol)";
99	>	(*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
100
101		if (myType & Restraint::rtTwist)
102	<	output_ << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
102	>	(*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
103
104		if (myType & Restraint::rtSwingX)
105	<	output_ << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
105	>	(*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
106	>
107	>	if (myType & Restraint::rtSwingY)
108	>	(*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
109	>	}
110	>	}
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	<	output_ << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
139	>	buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
140
141	+	buffer += "\n";
142		}
95	–	output_ << "\n";
96	–	#ifdef IS_MPI
143		}
144	<	#endif
145	<	}
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 ){
104	<	#endif
105	<	output_.close();
106	<	#ifdef IS_MPI
107	<	}
185	>	MPI_Status* istatus;
186		#endif
109	–	}
110	–
111	–	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
112	–
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
127	–	}// end oopse
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 1360 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 1969 by gezelter, Wed Feb 26 14:14:50 2014 UTC

#	Line 0 | Line 1
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