ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/io/RestWriter.cpp (file contents):
Revision 1364 by cli2, Wed Oct 7 20:49:50 2009 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 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, 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
44	+	#include <string>
45	+	#include <sstream>
46		#include <iostream>
47
48		#include "io/RestWriter.hpp"
#	Line 49 | Line 52
52		#include <mpi.h>
53		#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:
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 = MPI::COMM_WORLD.Get_size();
152	>	for (int i = 1; i < nProc; ++i) {
153	>
154	>	// receive the length of the string buffer that was
155	>	// prepared by processor i
156	>
157	>	int recvLength;
158	>	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, 0, istatus);
159	>	char* recvBuffer = new char[recvLength];
160	>	if (recvBuffer == NULL) {
161	>	} else {
162	>	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i, 0,
163	>	istatus);
164	>	(*output_) << recvBuffer;
165	>	delete [] recvBuffer;
166	>	}
167	>	}
168	>	(*output_).flush();
169	>	} else {
170	>	int sendBufferLength = buffer.size() + 1;
171	>	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
172	>	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength, MPI::CHAR,
173	>	masterNode, 0);
174	>	}
175	>
176	>	#endif // is_mpi
177	>
178	>	}
179
180	<	RestWriter::~RestWriter() {
180	>	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
181	>
182		#ifdef IS_MPI
183	<	if(worldRank == 0 ){
107	<	#endif
108	<	output_.close();
109	<	#ifdef IS_MPI
110	<	}
183	>	MPI::Status istatus;
184		#endif
112	–	}
113	–
114	–	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
115	–
185
186	<	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
187	<
186	>	#ifndef IS_MPI
187	>	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
188	>
189		// output some information about the molecules
190		std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
191		std::map<int, Restraint::RealPair>::const_iterator j;
192	+
193		for( i = restInfo.begin(); i != restInfo.end(); ++i){
194		for(j = (*i).begin(); j != (*i).end(); ++j){
195	<	output_ << "\t" << (j->second).first << "\t" << (j->second).second;
195	>	(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
196		}
197	<	output_ << std::endl;
197	>	(*output_) << std::endl;
198		}
199	+	(*output_).flush();
200	+	#else
201	+	std::string buffer, first, second;
202	+	std::stringstream ss;
203	+
204	+	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
205	+	std::map<int, Restraint::RealPair>::const_iterator j;
206	+
207	+	for( i = restInfo.begin(); i != restInfo.end(); ++i){
208	+	for(j = (*i).begin(); j != (*i).end(); ++j){
209	+	ss.clear();
210	+	ss << (j->second).first;
211	+	ss >> first;
212	+	ss.clear();
213	+	ss << (j->second).second;
214	+	ss >> second;
215	+	buffer += ("\t" + first + "\t" + second);
216	+	}
217	+	buffer += "\n";
218	+	}
219	+
220	+	const int masterNode = 0;
221	+
222	+	if (worldRank == masterNode) {
223	+	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
224	+	(*output_) << buffer;
225	+
226	+	int nProc;
227	+	nProc = MPI::COMM_WORLD.Get_size();
228	+	for (int i = 1; i < nProc; ++i) {
229	+
230	+	// receive the length of the string buffer that was
231	+	// prepared by processor i
232	+
233	+	int recvLength;
234	+	MPI::COMM_WORLD.Recv(&recvLength, 1, MPI::INT, i, 0, istatus);
235	+	char* recvBuffer = new char[recvLength];
236	+	if (recvBuffer == NULL) {
237	+	} else {
238	+	MPI::COMM_WORLD.Recv(recvBuffer, recvLength, MPI::CHAR, i, 0,
239	+	istatus);
240	+	(*output_) << recvBuffer;
241	+
242	+	delete [] recvBuffer;
243	+	}
244	+	}
245	+	(*output_).flush();
246	+	} else {
247	+	int sendBufferLength = buffer.size() + 1;
248	+	MPI::COMM_WORLD.Send(&sendBufferLength, 1, MPI::INT, masterNode, 0);
249	+	MPI::COMM_WORLD.Send((void *)buffer.c_str(), sendBufferLength,
250	+	MPI::CHAR, masterNode, 0);
251	+	}
252	+	#endif // is_mpi
253		}
254
130	–	}// end oopse
255
256	+	RestWriter::~RestWriter() {
257	+
258	+	#ifdef IS_MPI
259	+
260	+	if (worldRank == 0) {
261	+	#endif // is_mpi
262	+	if (createRestFile_){
263	+	writeClosing(*output_);
264	+	delete output_;
265	+	}
266	+	#ifdef IS_MPI
267	+	}
268	+	#endif // is_mpi
269	+	}
270	+
271	+	void RestWriter::writeClosing(std::ostream& os) {
272	+	os.flush();
273	+	}
274	+
275	+	}// end namespace OpenMD
276	+

Comparing trunk/src/io/RestWriter.cpp (property svn:keywords):
Revision 1364 by cli2, Wed Oct 7 20:49:50 2009 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines