src/io/RestWriter.cpp

/*
 * Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */


#include <string>
#include <sstream>
#include <iostream>

#include "io/RestWriter.hpp"
#include "utils/simError.h"
#include "brains/SnapshotManager.hpp"
#ifdef IS_MPI
#include <mpi.h>
#endif

namespace OpenMD {
  RestWriter::RestWriter(SimInfo* info, const std::string& filename, 
                         std::vector<Restraint*> restraints ) : 
    info_(info){
    createRestFile_ = true;
    
#ifdef IS_MPI
    if(worldRank == 0){
#endif
  
      output_ = new std::ofstream(filename.c_str());
 
      if(!output_){
        sprintf( painCave.errMsg,
                 "Could not open %s for restraint output.\n", 
                 filename.c_str());
        painCave.isFatal = 1;
        simError();
      }

#ifdef IS_MPI
    }
#endif // is_mpi


#ifdef IS_MPI
    MPI_Status istatus;
#endif
    
#ifndef IS_MPI
         
    (*output_) << "#time\t";

    std::vector<Restraint*>::const_iterator resti;

    for(resti=restraints.begin(); resti != restraints.end(); ++resti){
      if ((*resti)->getPrintRestraint()) {
        
        std::string myName = (*resti)->getRestraintName();
        int myType = (*resti)->getRestraintType();
        
        (*output_) << myName << ":";
        
        if (myType & Restraint::rtDisplacement)
          (*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
        
        if (myType & Restraint::rtTwist)
          (*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
        
        if (myType & Restraint::rtSwingX)
          (*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
          
        if (myType & Restraint::rtSwingY)
          (*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
      }
    }

    (*output_) << "\n";
    (*output_).flush();
    
#else
    
    std::string buffer;

    std::vector<Restraint*>::const_iterator resti;

    for(resti=restraints.begin(); resti != restraints.end(); ++resti){
      if ((*resti)->getPrintRestraint()) {
        
        std::string myName = (*resti)->getRestraintName();
        int myType = (*resti)->getRestraintType();

        buffer += (myName + ":");
        
        if (myType & Restraint::rtDisplacement)
          buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)";
        
        if (myType & Restraint::rtTwist)
          buffer += "\tTwistAngle(radians)\tEnergy(kcal/mol)";
        
        if (myType & Restraint::rtSwingX)
          buffer += "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
        
        if (myType & Restraint::rtSwingY)
          buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
        
        buffer += "\n";
      }
    }
    
    const int masterNode = 0;
    
    if (worldRank == masterNode) {
      (*output_) << "#time\t";
      (*output_) << buffer;
      
      int nProc;
      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
      for (int i = 1; i < nProc; ++i) {
        
        // receive the length of the string buffer that was
        // prepared by processor i
        
        int recvLength;
        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
        char* recvBuffer = new char[recvLength];
        if (recvBuffer == NULL) {
        } else {
          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, 
                   &istatus);
          (*output_) << recvBuffer;
          delete [] recvBuffer;
        }
      } 
      (*output_).flush();
    } else {
      int sendBufferLength = buffer.size() + 1;
      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
               0, MPI_COMM_WORLD);
    }
    
#endif // is_mpi    
    
  }    
  
  void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
    
#ifdef IS_MPI
    MPI_Status istatus;
#endif
    
#ifndef IS_MPI
    (*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
    
    // output some information about the molecules
    std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
    std::map<int, Restraint::RealPair>::const_iterator j;
    
    for( i = restInfo.begin(); i != restInfo.end(); ++i){
      for(j = (*i).begin(); j != (*i).end(); ++j){                
        (*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
      }
      (*output_) << std::endl;
    }
    (*output_).flush();
#else
    std::string buffer, first, second;
    std::stringstream ss;
    
    std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
    std::map<int, Restraint::RealPair>::const_iterator j;
    
    for( i = restInfo.begin(); i != restInfo.end(); ++i){
      for(j = (*i).begin(); j != (*i).end(); ++j){
        ss.clear(); 
        ss << (j->second).first;
        ss >> first;
        ss.clear();
        ss << (j->second).second;
        ss >> second;
        buffer += ("\t" + first + "\t" + second);       
      }
      buffer += "\n";     
    }
    
    const int masterNode = 0;
    
    if (worldRank == masterNode) {
      (*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
      (*output_) << buffer;
      
      int nProc;
      MPI_Comm_size(MPI_COMM_WORLD, &nProc);
      for (int i = 1; i < nProc; ++i) {
        
        // receive the length of the string buffer that was
        // prepared by processor i
        
        int recvLength;
        MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
        char* recvBuffer = new char[recvLength];
        if (recvBuffer == NULL) {
        } else {
          MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, 
                   &istatus);
          (*output_) << recvBuffer;
          
          delete [] recvBuffer;
        }
      } 
      (*output_).flush();
    } else {
      int sendBufferLength = buffer.size() + 1;
      MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
      MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
               0, MPI_COMM_WORLD);
    }
#endif // is_mpi
  }
  
  
  RestWriter::~RestWriter() {
    
#ifdef IS_MPI
    
    if (worldRank == 0) {
#endif // is_mpi
      if (createRestFile_){
        writeClosing(*output_);
        delete output_;
      }
#ifdef IS_MPI 
    }
#endif // is_mpi
  }
  
  void RestWriter::writeClosing(std::ostream& os) {
    os.flush();
  }
  
}// end namespace OpenMD

Revision:	1407
Committed:	Wed Jan 20 16:04:40 2010 UTC (15 years, 3 months ago) by cli2
File size:	8523 byte(s)
Log Message:	Fixed bugs in Restraint, refactored RestReader and RestWriter
#	Content
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
43	#include <string>
44	#include <sstream>
45	#include <iostream>
46
47	#include "io/RestWriter.hpp"
48	#include "utils/simError.h"
49	#include "brains/SnapshotManager.hpp"
50	#ifdef IS_MPI
51	#include <mpi.h>
52	#endif
53
54	namespace OpenMD {
55	RestWriter::RestWriter(SimInfo* info, const std::string& filename,
56	std::vector<Restraint*> restraints ) :
57	info_(info){
58	createRestFile_ = true;
59
60	#ifdef IS_MPI
61	if(worldRank == 0){
62	#endif
63
64	output_ = new std::ofstream(filename.c_str());
65
66	if(!output_){
67	sprintf( painCave.errMsg,
68	"Could not open %s for restraint output.\n",
69	filename.c_str());
70	painCave.isFatal = 1;
71	simError();
72	}
73
74	#ifdef IS_MPI
75	}
76	#endif // is_mpi
77
78
79	#ifdef IS_MPI
80	MPI_Status istatus;
81	#endif
82
83	#ifndef IS_MPI
84
85	(*output_) << "#time\t";
86
87	std::vector<Restraint*>::const_iterator resti;
88
89	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
90	if ((*resti)->getPrintRestraint()) {
91
92	std::string myName = (*resti)->getRestraintName();
93	int myType = (*resti)->getRestraintType();
94
95	(*output_) << myName << ":";
96
97	if (myType & Restraint::rtDisplacement)
98	(*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
99
100	if (myType & Restraint::rtTwist)
101	(*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
102
103	if (myType & Restraint::rtSwingX)
104	(*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
105
106	if (myType & Restraint::rtSwingY)
107	(*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
108	}
109	}
110
111	(*output_) << "\n";
112	(*output_).flush();
113
114	#else
115
116	std::string buffer;
117
118	std::vector<Restraint*>::const_iterator resti;
119
120	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
121	if ((*resti)->getPrintRestraint()) {
122
123	std::string myName = (*resti)->getRestraintName();
124	int myType = (*resti)->getRestraintType();
125
126	buffer += (myName + ":");
127
128	if (myType & Restraint::rtDisplacement)
129	buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)";
130
131	if (myType & Restraint::rtTwist)
132	buffer += "\tTwistAngle(radians)\tEnergy(kcal/mol)";
133
134	if (myType & Restraint::rtSwingX)
135	buffer += "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
136
137	if (myType & Restraint::rtSwingY)
138	buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
139
140	buffer += "\n";
141	}
142	}
143
144	const int masterNode = 0;
145
146	if (worldRank == masterNode) {
147	(*output_) << "#time\t";
148	(*output_) << buffer;
149
150	int nProc;
151	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
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_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
159	char* recvBuffer = new char[recvLength];
160	if (recvBuffer == NULL) {
161	} else {
162	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
163	&istatus);
164	(*output_) << recvBuffer;
165	delete [] recvBuffer;
166	}
167	}
168	(*output_).flush();
169	} else {
170	int sendBufferLength = buffer.size() + 1;
171	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
172	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
173	0, MPI_COMM_WORLD);
174	}
175
176	#endif // is_mpi
177
178	}
179
180	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
181
182	#ifdef IS_MPI
183	MPI_Status istatus;
184	#endif
185
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;
196	}
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	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
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_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus);
235	char* recvBuffer = new char[recvLength];
236	if (recvBuffer == NULL) {
237	} else {
238	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
239	&istatus);
240	(*output_) << recvBuffer;
241
242	delete [] recvBuffer;
243	}
244	}
245	(*output_).flush();
246	} else {
247	int sendBufferLength = buffer.size() + 1;
248	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
249	MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode,
250	0, MPI_COMM_WORLD);
251	}
252	#endif // is_mpi
253	}
254
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