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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#ifdef IS_MPI
#include <mpi.h>
#endif

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

#include "io/RestWriter.hpp"
#include "utils/simError.h"
#include "brains/SnapshotManager.hpp"

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:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 2 months ago) by gezelter
File size:	8590 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	User	Rev	Content
1	gezelter	507	/*
2	cli2	1360	* Copyright (c) 2009 The University of Notre Dame. All Rights Reserved.
3	chrisfen	417	*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	chrisfen	417	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	chrisfen	417	* 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	gezelter	1390	*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	chrisfen	417	*/
42
43	gezelter	1938	#ifdef IS_MPI
44			#include <mpi.h>
45			#endif
46	cli2	1360
47	cli2	1407	#include <string>
48			#include <sstream>
49	cli2	1360	#include <iostream>
50
51	chrisfen	993	#include "io/RestWriter.hpp"
52	chrisfen	417	#include "utils/simError.h"
53	cli2	1360	#include "brains/SnapshotManager.hpp"
54	chrisfen	417
55	gezelter	1390	namespace OpenMD {
56	cli2	1360	RestWriter::RestWriter(SimInfo* info, const std::string& filename,
57			std::vector<Restraint*> restraints ) :
58			info_(info){
59	cli2	1407	createRestFile_ = true;
60
61	chrisfen	990	#ifdef IS_MPI
62	cli2	1360	if(worldRank == 0){
63			#endif
64	cli2	1407
65			output_ = new std::ofstream(filename.c_str());
66
67	cli2	1360	if(!output_){
68			sprintf( painCave.errMsg,
69			"Could not open %s for restraint output.\n",
70			filename.c_str());
71			painCave.isFatal = 1;
72			simError();
73			}
74
75	cli2	1407	#ifdef IS_MPI
76			}
77			#endif // is_mpi
78	cli2	1364
79	cli2	1407
80			#ifdef IS_MPI
81	gezelter	1969	MPI_Status* istatus;
82	cli2	1407	#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	cli2	1364
107	cli2	1407	if (myType & Restraint::rtSwingY)
108			(*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
109	cli2	1360	}
110	gezelter	507	}
111	cli2	1407
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	gezelter	1969	int nProc;
152			MPI_Comm_size( MPI_COMM_WORLD, &nProc);
153
154	cli2	1407	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	gezelter	1969	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
161	cli2	1407	char* recvBuffer = new char[recvLength];
162			if (recvBuffer == NULL) {
163			} else {
164	gezelter	1969	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
165			istatus);
166	cli2	1407	(*output_) << recvBuffer;
167			delete [] recvBuffer;
168			}
169			}
170			(*output_).flush();
171			} else {
172			int sendBufferLength = buffer.size() + 1;
173	gezelter	1969	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	cli2	1407	}
177
178			#endif // is_mpi
179
180			}
181	cli2	1360
182	cli2	1407	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
183
184	chrisfen	993	#ifdef IS_MPI
185	gezelter	1969	MPI_Status* istatus;
186	cli2	1360	#endif
187	chrisfen	417
188	cli2	1407	#ifndef IS_MPI
189			(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
190
191	cli2	1360	// 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	cli2	1407
195	cli2	1360	for( i = restInfo.begin(); i != restInfo.end(); ++i){
196			for(j = (i).begin(); j != (i).end(); ++j){
197	cli2	1407	(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
198	chrisfen	417	}
199	cli2	1407	(*output_) << std::endl;
200	chrisfen	417	}
201	cli2	1407	(*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	gezelter	1969	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
230	cli2	1407	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	gezelter	1969	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
237	cli2	1407	char* recvBuffer = new char[recvLength];
238			if (recvBuffer == NULL) {
239			} else {
240	gezelter	1969	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
241			istatus);
242	cli2	1407	(*output_) << recvBuffer;
243
244			delete [] recvBuffer;
245			}
246			}
247			(*output_).flush();
248			} else {
249			int sendBufferLength = buffer.size() + 1;
250	gezelter	1969	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	cli2	1407	}
254			#endif // is_mpi
255	chrisfen	417	}
256
257	cli2	1407
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	gezelter	1390	}// end namespace OpenMD
278	cli2	1407