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){

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

    createRestFile_ = false;  

#ifdef IS_MPI    
    MPI_Status* istatus;
#endif
    
    int printAny = 0;
    for(resti=restraints.begin(); resti != restraints.end(); ++resti){
      if ((*resti)->getPrintRestraint()) {
        printAny = 1;
      }
    }
    
#ifdef IS_MPI
    MPI_Allreduce(MPI_IN_PLACE, &printAny, 1, MPI_INT, MPI_SUM, 
                  MPI_COMM_WORLD);
#endif

    if (printAny) createRestFile_ = true;

#ifdef IS_MPI
    if(worldRank == 0){
#endif
  
      if (createRestFile_) {
        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


#ifndef IS_MPI
         
    if (createRestFile_) (*output_) << "#time\t";

    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)";
      }
    }

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

    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) {
      if (createRestFile_) (*output_) << "#time\t";
      if (createRestFile_) (*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);
          if (createRestFile_) (*output_) << recvBuffer;
          delete [] recvBuffer;
        }
      } 
       if (createRestFile_) (*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
     if (createRestFile_)  (*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;
    
    cerr << "risize = " << restInfo.size() << "\n";

    if ( createRestFile_ ) {
      
      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;
    
    if ( createRestFile_ ) {
      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 (createRestFile_) {
      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);
            if (createRestFile_) (*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:	2020
Committed:	Mon Sep 22 19:18:35 2014 UTC (10 years, 7 months ago) by gezelter
File size:	9417 byte(s)
Log Message:	Fixes for restraints, renaming of UniformField
#	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	gezelter	2020
60			std::vector<Restraint*>::const_iterator resti;
61
62			createRestFile_ = false;
63
64			#ifdef IS_MPI
65			MPI_Status* istatus;
66			#endif
67	cli2	1407
68	gezelter	2020	int printAny = 0;
69			for(resti=restraints.begin(); resti != restraints.end(); ++resti){
70			if ((*resti)->getPrintRestraint()) {
71			printAny = 1;
72			}
73			}
74
75	chrisfen	990	#ifdef IS_MPI
76	gezelter	2020	MPI_Allreduce(MPI_IN_PLACE, &printAny, 1, MPI_INT, MPI_SUM,
77			MPI_COMM_WORLD);
78			#endif
79
80			if (printAny) createRestFile_ = true;
81
82			#ifdef IS_MPI
83	cli2	1360	if(worldRank == 0){
84			#endif
85	cli2	1407
86	gezelter	2020	if (createRestFile_) {
87			output_ = new std::ofstream(filename.c_str());
88
89			if(!output_){
90			sprintf( painCave.errMsg,
91			"Could not open %s for restraint output.\n",
92			filename.c_str());
93			painCave.isFatal = 1;
94			simError();
95			}
96	cli2	1360	}
97	gezelter	2020
98	cli2	1407	#ifdef IS_MPI
99			}
100			#endif // is_mpi
101	cli2	1364
102	cli2	1407
103			#ifndef IS_MPI
104
105	gezelter	2020	if (createRestFile_) (*output_) << "#time\t";
106	cli2	1407
107			for(resti=restraints.begin(); resti != restraints.end(); ++resti){
108			if ((*resti)->getPrintRestraint()) {
109			std::string myName = (*resti)->getRestraintName();
110			int myType = (*resti)->getRestraintType();
111
112			(*output_) << myName << ":";
113
114			if (myType & Restraint::rtDisplacement)
115			(*output_) << "\tPosition(angstroms)\tEnergy(kcal/mol)";
116
117			if (myType & Restraint::rtTwist)
118			(*output_) << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
119
120			if (myType & Restraint::rtSwingX)
121			(*output_) << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
122	cli2	1364
123	cli2	1407	if (myType & Restraint::rtSwingY)
124			(*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
125	cli2	1360	}
126	gezelter	507	}
127	cli2	1407
128	gezelter	2020	if (createRestFile_) (*output_) << "\n";
129			if (createRestFile_) (*output_).flush();
130	cli2	1407
131			#else
132
133			std::string buffer;
134
135			for(resti=restraints.begin(); resti != restraints.end(); ++resti){
136			if ((*resti)->getPrintRestraint()) {
137			std::string myName = (*resti)->getRestraintName();
138			int myType = (*resti)->getRestraintType();
139
140			buffer += (myName + ":");
141
142			if (myType & Restraint::rtDisplacement)
143			buffer += "\tPosition(angstroms)\tEnergy(kcal/mol)";
144
145			if (myType & Restraint::rtTwist)
146			buffer += "\tTwistAngle(radians)\tEnergy(kcal/mol)";
147
148			if (myType & Restraint::rtSwingX)
149			buffer += "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
150
151			if (myType & Restraint::rtSwingY)
152			buffer += "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
153
154			buffer += "\n";
155			}
156			}
157
158			const int masterNode = 0;
159
160			if (worldRank == masterNode) {
161	gezelter	2020	if (createRestFile_) (*output_) << "#time\t";
162			if (createRestFile_) (*output_) << buffer;
163	cli2	1407
164	gezelter	1969	int nProc;
165			MPI_Comm_size( MPI_COMM_WORLD, &nProc);
166
167	cli2	1407	for (int i = 1; i < nProc; ++i) {
168
169			// receive the length of the string buffer that was
170			// prepared by processor i
171
172			int recvLength;
173	gezelter	1969	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
174	cli2	1407	char* recvBuffer = new char[recvLength];
175			if (recvBuffer == NULL) {
176			} else {
177	gezelter	1969	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
178			istatus);
179	gezelter	2020	if (createRestFile_) (*output_) << recvBuffer;
180	cli2	1407	delete [] recvBuffer;
181			}
182			}
183	gezelter	2020	if (createRestFile_) (*output_).flush();
184	cli2	1407	} else {
185			int sendBufferLength = buffer.size() + 1;
186	gezelter	1969	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
187			MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR,
188			masterNode, 0, MPI_COMM_WORLD);
189	cli2	1407	}
190
191			#endif // is_mpi
192
193			}
194	cli2	1360
195	cli2	1407	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
196
197	chrisfen	993	#ifdef IS_MPI
198	gezelter	1969	MPI_Status* istatus;
199	cli2	1360	#endif
200	chrisfen	417
201	cli2	1407	#ifndef IS_MPI
202	gezelter	2020	if (createRestFile_) (*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
203	cli2	1407
204	cli2	1360	// output some information about the molecules
205			std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
206			std::map<int, Restraint::RealPair>::const_iterator j;
207	cli2	1407
208	gezelter	2020	cerr << "risize = " << restInfo.size() << "\n";
209
210			if ( createRestFile_ ) {
211
212			for( i = restInfo.begin(); i != restInfo.end(); ++i){
213			for(j = (i).begin(); j != (i).end(); ++j){
214			(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
215			}
216			(*output_) << std::endl;
217			}
218			(*output_).flush();
219	chrisfen	417	}
220	cli2	1407	#else
221			std::string buffer, first, second;
222			std::stringstream ss;
223
224			std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
225			std::map<int, Restraint::RealPair>::const_iterator j;
226
227	gezelter	2020	if ( createRestFile_ ) {
228			for( i = restInfo.begin(); i != restInfo.end(); ++i){
229
230			for(j = (i).begin(); j != (i).end(); ++j){
231			ss.clear();
232			ss << (j->second).first;
233			ss >> first;
234			ss.clear();
235			ss << (j->second).second;
236			ss >> second;
237			buffer += ("\t" + first + "\t" + second);
238			}
239			buffer += "\n";
240	cli2	1407	}
241			}
242
243			const int masterNode = 0;
244
245	gezelter	2020	if (createRestFile_) {
246			if (worldRank == masterNode) {
247
248			(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
249			(*output_) << buffer;
250	cli2	1407
251	gezelter	2020	int nProc;
252			MPI_Comm_size( MPI_COMM_WORLD, &nProc);
253			for (int i = 1; i < nProc; ++i) {
254	cli2	1407
255	gezelter	2020	// receive the length of the string buffer that was
256			// prepared by processor i
257
258			int recvLength;
259			MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
260			char* recvBuffer = new char[recvLength];
261			if (recvBuffer == NULL) {
262			} else {
263			MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
264			istatus);
265			if (createRestFile_) (*output_) << recvBuffer;
266
267			delete [] recvBuffer;
268			}
269			}
270			(*output_).flush();
271			} else {
272			int sendBufferLength = buffer.size() + 1;
273			MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
274			MPI_Send((void *)buffer.c_str(), sendBufferLength,
275			MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
276			}
277	cli2	1407	}
278			#endif // is_mpi
279	chrisfen	417	}
280
281	cli2	1407
282			RestWriter::~RestWriter() {
283
284			#ifdef IS_MPI
285
286			if (worldRank == 0) {
287			#endif // is_mpi
288			if (createRestFile_){
289			writeClosing(*output_);
290			delete output_;
291			}
292			#ifdef IS_MPI
293			}
294			#endif // is_mpi
295			}
296
297			void RestWriter::writeClosing(std::ostream& os) {
298			os.flush();
299			}
300
301	gezelter	1390	}// end namespace OpenMD
302	cli2	1407