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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */


#include <iostream>

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

namespace oopse {
  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){
        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 oopse
  
Revision:	1360
Committed:	Mon Sep 7 16:31:51 2009 UTC (16 years, 1 month ago) by cli2
File size:	4462 byte(s)
Log Message:	Added new restraint infrastructure Added MolecularRestraints Added ObjectRestraints Added RestraintStamp Updated thermodynamic integration to use ObjectRestraints Added Quaternion mathematics for twist swing decompositions Significantly updated RestWriter and RestReader to use dump-like files Added selections for x, y, and z coordinates of atoms Removed monolithic Restraints class Fixed a few bugs in gradients of Euler angles in DirectionalAtom and RigidBody Added some rotational capabilities to prinicpalAxisCalculator
#	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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
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			namespace oopse {
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			std::string myName = (*resti)->getRestraintName();
78			int myType = (*resti)->getRestraintType();
79
80			output_ << myName << ":";
81
82			if (myType & Restraint::rtDisplacement)
83			output_ << "\tPosition(angstroms)\tEnergy(kcal/mol)";
84
85			if (myType & Restraint::rtTwist)
86			output_ << "\tTwistAngle(radians)\tEnergy(kcal/mol)";
87
88			if (myType & Restraint::rtSwingX)
89			output_ << "\tSwingXAngle(radians)\tEnergy(kcal/mol)";
90
91			if (myType & Restraint::rtSwingY)
92			output_ << "\tSwingYAngle(radians)\tEnergy(kcal/mol)";
93
94			}
95			output_ << "\n";
96	chrisfen	990	#ifdef IS_MPI
97	gezelter	507	}
98	cli2	1360	#endif
99			}
100
101			RestWriter::~RestWriter() {
102	chrisfen	993	#ifdef IS_MPI
103	cli2	1360	if(worldRank == 0 ){
104			#endif
105			output_.close();
106			#ifdef IS_MPI
107	chrisfen	993	}
108	cli2	1360	#endif
109	chrisfen	990	}
110	cli2	1360
111			void RestWriter::writeRest(std::vector<std::map<int, Restraint::RealPair> > restInfo){
112	chrisfen	417
113
114	cli2	1360	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime();
115	chrisfen	990
116	cli2	1360	// output some information about the molecules
117			std::vector<std::map<int, Restraint::RealPair> >::const_iterator i;
118			std::map<int, Restraint::RealPair>::const_iterator j;
119			for( i = restInfo.begin(); i != restInfo.end(); ++i){
120			for(j = (i).begin(); j != (i).end(); ++j){
121			output_ << "\t" << (j->second).first << "\t" << (j->second).second;
122	chrisfen	417	}
123	cli2	1360	output_ << std::endl;
124	chrisfen	417	}
125			}
126
127	cli2	1360	}// end oopse
128