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 <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){

    //use master - slave mode, only master node writes to disk
#ifdef IS_MPI
    if(worldRank == 0){
#endif
      
      output_.open(filename.c_str());
      
      if(!output_){
        sprintf( painCave.errMsg,
                 "Could not open %s for restraint output.\n", 
                 filename.c_str());
        painCave.isFatal = 1;
        simError();
      }

      output_ << "#time\t";
      
      // TODO:  get Restraint info from slave nodes:
      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";
#ifdef IS_MPI
    }
#endif      
  }
  
  RestWriter::~RestWriter() {
#ifdef IS_MPI
    if(worldRank == 0 ){
#endif  
      output_.close();  
#ifdef IS_MPI  
    }
#endif
  }
  
  void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
      
    
    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;
    }
  }
  
}// end namespace OpenMD
  
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/io/RestWriter.cpp*
File size:	4605 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	chrisfen	417	*/
41
42	cli2	1360
43			#include <iostream>
44
45	chrisfen	993	#include "io/RestWriter.hpp"
46	chrisfen	417	#include "utils/simError.h"
47	cli2	1360	#include "brains/SnapshotManager.hpp"
48	chrisfen	993	#ifdef IS_MPI
49			#include <mpi.h>
50	cli2	1360	#endif
51	chrisfen	417
52	gezelter	1390	namespace OpenMD {
53	cli2	1360	RestWriter::RestWriter(SimInfo* info, const std::string& filename,
54			std::vector<Restraint*> restraints ) :
55			info_(info){
56
57			//use master - slave mode, only master node writes to disk
58	chrisfen	990	#ifdef IS_MPI
59	cli2	1360	if(worldRank == 0){
60			#endif
61	chrisfen	993
62	cli2	1360	output_.open(filename.c_str());
63	chrisfen	993
64	cli2	1360	if(!output_){
65			sprintf( painCave.errMsg,
66			"Could not open %s for restraint output.\n",
67			filename.c_str());
68			painCave.isFatal = 1;
69			simError();
70			}
71
72			output_ << "#time\t";
73
74			// TODO: get Restraint info from slave nodes:
75			std::vector<Restraint*>::const_iterator resti;
76			for(resti=restraints.begin(); resti != restraints.end(); ++resti){
77	cli2	1364
78			if ((*resti)->getPrintRestraint()) {
79			std::string myName = (*resti)->getRestraintName();
80			int myType = (*resti)->getRestraintType();
81
82			output_ << myName << ":";
83
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			}
97	cli2	1360	}
98			output_ << "\n";
99	chrisfen	990	#ifdef IS_MPI
100	gezelter	507	}
101	cli2	1360	#endif
102			}
103
104			RestWriter::~RestWriter() {
105	chrisfen	993	#ifdef IS_MPI
106	cli2	1360	if(worldRank == 0 ){
107			#endif
108			output_.close();
109			#ifdef IS_MPI
110	chrisfen	993	}
111	cli2	1360	#endif
112	chrisfen	990	}
113	cli2	1360
114			void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
115	chrisfen	417
116
117	cli2	1360	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
118	chrisfen	990
119	cli2	1360	// output some information about the molecules
120			std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
121			std::map<int, Restraint::RealPair>::const_iterator j;
122			for( i = restInfo.begin(); i != restInfo.end(); ++i){
123			for(j = (i).begin(); j != (i).end(); ++j){
124			output_ << "\t" << (j->second).first << "\t" << (j->second).second;
125	chrisfen	417	}
126	cli2	1360	output_ << std::endl;
127	chrisfen	417	}
128			}
129
130	gezelter	1390	}// end namespace OpenMD
131	cli2	1360