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;
    
    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:	2021
Committed:	Tue Sep 23 15:25:08 2014 UTC (10 years, 7 months ago) by gezelter
File size:	9364 byte(s)
Log Message:	Took out a spurious debugging line
#	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, 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"
54
55	namespace OpenMD {
56	RestWriter::RestWriter(SimInfo* info, const std::string& filename,
57	std::vector<Restraint*> restraints ) :
58	info_(info){
59
60	std::vector<Restraint*>::const_iterator resti;
61
62	createRestFile_ = false;
63
64	#ifdef IS_MPI
65	MPI_Status* istatus;
66	#endif
67
68	int printAny = 0;
69	for(resti=restraints.begin(); resti != restraints.end(); ++resti){
70	if ((*resti)->getPrintRestraint()) {
71	printAny = 1;
72	}
73	}
74
75	#ifdef IS_MPI
76	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	if(worldRank == 0){
84	#endif
85
86	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	}
97
98	#ifdef IS_MPI
99	}
100	#endif // is_mpi
101
102
103	#ifndef IS_MPI
104
105	if (createRestFile_) (*output_) << "#time\t";
106
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
123	if (myType & Restraint::rtSwingY)
124	(*output_) << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
125	}
126	}
127
128	if (createRestFile_) (*output_) << "\n";
129	if (createRestFile_) (*output_).flush();
130
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	if (createRestFile_) (*output_) << "#time\t";
162	if (createRestFile_) (*output_) << buffer;
163
164	int nProc;
165	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
166
167	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	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
174	char* recvBuffer = new char[recvLength];
175	if (recvBuffer == NULL) {
176	} else {
177	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
178	istatus);
179	if (createRestFile_) (*output_) << recvBuffer;
180	delete [] recvBuffer;
181	}
182	}
183	if (createRestFile_) (*output_).flush();
184	} else {
185	int sendBufferLength = buffer.size() + 1;
186	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	}
190
191	#endif // is_mpi
192
193	}
194
195	void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo) {
196
197	#ifdef IS_MPI
198	MPI_Status* istatus;
199	#endif
200
201	#ifndef IS_MPI
202	if (createRestFile_) (*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
203
204	// 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
208	if ( createRestFile_ ) {
209
210	for( i = restInfo.begin(); i != restInfo.end(); ++i){
211	for(j = (i).begin(); j != (i).end(); ++j){
212	(*output_) << "\t" << (j->second).first << "\t" << (j->second).second;
213	}
214	(*output_) << std::endl;
215	}
216	(*output_).flush();
217	}
218	#else
219	std::string buffer, first, second;
220	std::stringstream ss;
221
222	std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
223	std::map<int, Restraint::RealPair>::const_iterator j;
224
225	if ( createRestFile_ ) {
226	for( i = restInfo.begin(); i != restInfo.end(); ++i){
227
228	for(j = (i).begin(); j != (i).end(); ++j){
229	ss.clear();
230	ss << (j->second).first;
231	ss >> first;
232	ss.clear();
233	ss << (j->second).second;
234	ss >> second;
235	buffer += ("\t" + first + "\t" + second);
236	}
237	buffer += "\n";
238	}
239	}
240
241	const int masterNode = 0;
242
243	if (createRestFile_) {
244	if (worldRank == masterNode) {
245
246	(*output_) << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
247	(*output_) << buffer;
248
249	int nProc;
250	MPI_Comm_size( MPI_COMM_WORLD, &nProc);
251	for (int i = 1; i < nProc; ++i) {
252
253	// receive the length of the string buffer that was
254	// prepared by processor i
255
256	int recvLength;
257	MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, istatus);
258	char* recvBuffer = new char[recvLength];
259	if (recvBuffer == NULL) {
260	} else {
261	MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD,
262	istatus);
263	if (createRestFile_) (*output_) << recvBuffer;
264
265	delete [] recvBuffer;
266	}
267	}
268	(*output_).flush();
269	} else {
270	int sendBufferLength = buffer.size() + 1;
271	MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
272	MPI_Send((void *)buffer.c_str(), sendBufferLength,
273	MPI_CHAR, masterNode, 0, MPI_COMM_WORLD);
274	}
275	}
276	#endif // is_mpi
277	}
278
279
280	RestWriter::~RestWriter() {
281
282	#ifdef IS_MPI
283
284	if (worldRank == 0) {
285	#endif // is_mpi
286	if (createRestFile_){
287	writeClosing(*output_);
288	delete output_;
289	}
290	#ifdef IS_MPI
291	}
292	#endif // is_mpi
293	}
294
295	void RestWriter::writeClosing(std::ostream& os) {
296	os.flush();
297	}
298
299	}// end namespace OpenMD
300