src/io/ConstraintWriter.cpp

/*
 * Copyright (c) 2005 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 <algorithm>
#include <iostream>
#include <vector>

#include "io/ConstraintWriter.hpp"
#include "utils/simError.h"

namespace OpenMD {
  ConstraintWriter::ConstraintWriter(SimInfo* info, 
                                     const std::string& filename): 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 Constraint output\n", 
                 filename.c_str());
        painCave.isFatal = 1;
        simError();
      }
      
      output_ << "#time(fs)\t"
              << "Index of atom 1\t"
              << "Index of atom 2\tconstraint force" << std::endl; 
      
#ifdef IS_MPI
    }
#endif      
  }
  
  ConstraintWriter::~ConstraintWriter() {    
#ifdef IS_MPI
    if(worldRank == 0 ){
#endif  
      output_.close();  
#ifdef IS_MPI  
    }
#endif
  }
  
  void ConstraintWriter::writeConstraintForces(const std::list<ConstraintPair*>& constraints){
#ifndef IS_MPI
    std::list<ConstraintPair*>::const_iterator i;
    for ( i = constraints.begin(); i != constraints.end(); ++i) {

      if ((*i)->getPrintForce()) {
        output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()  << "\t"
                << (*i)->getConsElem1()->getGlobalIndex() <<"\t" 
                << (*i)->getConsElem2()->getGlobalIndex() <<"\t" 
                << (*i)->getConstraintForce() <<std::endl;
      }
    }
#else
    
    const int masterNode = 0;
    int nproc;
    int myNode;      
    MPI_Comm_size( MPI_COMM_WORLD, &nproc);
    MPI_Comm_rank( MPI_COMM_WORLD, &myNode);

    std::vector<int> nConstraints(nproc, 0);
    nConstraints[myNode] = constraints.size();
    
    //do MPI_ALLREDUCE to exchange the total number of constraints:
    MPI_Allreduce(MPI_IN_PLACE, &nConstraints[0], nproc, MPI_INT, MPI_SUM, 
                  MPI_COMM_WORLD);

    MPI_Status ierr;
    int atom1, atom2, doPrint;
    RealType force;
    
    if (myNode == masterNode) {
      std::vector<ConstraintData> constraintData;
      ConstraintData tmpData;       
      for(int i = 0 ; i < nproc; ++i) {
        if (i == masterNode) {
          std::list<ConstraintPair*>::const_iterator j;
          for ( j = constraints.begin(); j != constraints.end(); ++j) {
            tmpData.atom1 = (*j)->getConsElem1()->getGlobalIndex();
            tmpData.atom2 = (*j)->getConsElem2()->getGlobalIndex();         
            tmpData.constraintForce= (*j)->getConstraintForce();
            tmpData.printForce = (*j)->getPrintForce();
            constraintData.push_back(tmpData);
          }                
          
        } else {
          for(int k = 0; k < nConstraints[i]; ++k) {
            MPI_Recv(&atom1, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &ierr);
            MPI_Recv(&atom2, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &ierr);
            MPI_Recv(&force, 1, MPI_REALTYPE, i, 0, MPI_COMM_WORLD, &ierr);
            MPI_Recv(&doPrint, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &ierr);
            
            tmpData.atom1 = atom1;
            tmpData.atom2 = atom2;
            tmpData.constraintForce = force;
            tmpData.printForce = (doPrint == 0) ? false : true;
            constraintData.push_back(tmpData);                                        
          }
        }            
      }
            
      std::vector<ConstraintData>::iterator l;
      for (l = constraintData.begin(); l != constraintData.end(); ++l) {
        if (l->printForce) {
          output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << "\t"
                  << l->atom1 <<"\t" 
                  << l->atom2 <<"\t" 
                  << l->constraintForce << std::endl;
        }
      }     
    } else {

      std::list<ConstraintPair*>::const_iterator j;
      for (j = constraints.begin(); j != constraints.end(); ++j) {
        int atom1 = (*j)->getConsElem1()->getGlobalIndex();
        int atom2 = (*j)->getConsElem2()->getGlobalIndex();         
        RealType constraintForce= (*j)->getConstraintForce();
        int printForce = (int) (*j)->getPrintForce();
        
        MPI_Send(&atom1, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
        MPI_Send(&atom2, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
        MPI_Send(&constraintForce, 1, MPI_REALTYPE, masterNode, 0, 
                 MPI_COMM_WORLD);
        MPI_Send(&printForce, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);            
      }
    }
#endif
  }
}
Revision:	1984
Committed:	Tue Apr 15 21:15:35 2014 UTC (11 years, 6 months ago) by gezelter
File size:	6686 byte(s)
Log Message:	Some small compilation fixes for MSVC
#	User	Rev	Content
1	gezelter	1981	/*
2			* Copyright (c) 2005 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 <algorithm>
48			#include <iostream>
49			#include <vector>
50
51			#include "io/ConstraintWriter.hpp"
52			#include "utils/simError.h"
53
54			namespace OpenMD {
55	gezelter	1983	ConstraintWriter::ConstraintWriter(SimInfo* info,
56			const std::string& filename): info_(info) {
57	gezelter	1981	//use master - slave mode, only master node writes to disk
58			#ifdef IS_MPI
59			if(worldRank == 0){
60			#endif
61			output_.open(filename.c_str());
62	gezelter	1983
63	gezelter	1981	if(!output_){
64			sprintf( painCave.errMsg,
65	gezelter	1983	"Could not open %s for Constraint output\n",
66			filename.c_str());
67	gezelter	1981	painCave.isFatal = 1;
68			simError();
69			}
70
71			output_ << "#time(fs)\t"
72			<< "Index of atom 1\t"
73			<< "Index of atom 2\tconstraint force" << std::endl;
74	gezelter	1983
75	gezelter	1981	#ifdef IS_MPI
76			}
77	gezelter	1983	#endif
78	gezelter	1981	}
79	gezelter	1983
80			ConstraintWriter::~ConstraintWriter() {
81	gezelter	1981	#ifdef IS_MPI
82			if(worldRank == 0 ){
83			#endif
84			output_.close();
85			#ifdef IS_MPI
86			}
87			#endif
88			}
89	gezelter	1983
90	gezelter	1981	void ConstraintWriter::writeConstraintForces(const std::list<ConstraintPair*>& constraints){
91			#ifndef IS_MPI
92			std::list<ConstraintPair*>::const_iterator i;
93			for ( i = constraints.begin(); i != constraints.end(); ++i) {
94
95			if ((*i)->getPrintForce()) {
96			output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << "\t"
97			<< (*i)->getConsElem1()->getGlobalIndex() <<"\t"
98			<< (*i)->getConsElem2()->getGlobalIndex() <<"\t"
99			<< (*i)->getConstraintForce() <<std::endl;
100			}
101			}
102			#else
103	gezelter	1983
104	gezelter	1981	const int masterNode = 0;
105			int nproc;
106			int myNode;
107			MPI_Comm_size( MPI_COMM_WORLD, &nproc);
108			MPI_Comm_rank( MPI_COMM_WORLD, &myNode);
109
110			std::vector<int> nConstraints(nproc, 0);
111			nConstraints[myNode] = constraints.size();
112
113			//do MPI_ALLREDUCE to exchange the total number of constraints:
114	gezelter	1983	MPI_Allreduce(MPI_IN_PLACE, &nConstraints[0], nproc, MPI_INT, MPI_SUM,
115			MPI_COMM_WORLD);
116	gezelter	1981
117			MPI_Status ierr;
118			int atom1, atom2, doPrint;
119			RealType force;
120
121			if (myNode == masterNode) {
122			std::vector<ConstraintData> constraintData;
123			ConstraintData tmpData;
124			for(int i = 0 ; i < nproc; ++i) {
125			if (i == masterNode) {
126			std::list<ConstraintPair*>::const_iterator j;
127			for ( j = constraints.begin(); j != constraints.end(); ++j) {
128			tmpData.atom1 = (*j)->getConsElem1()->getGlobalIndex();
129			tmpData.atom2 = (*j)->getConsElem2()->getGlobalIndex();
130			tmpData.constraintForce= (*j)->getConstraintForce();
131			tmpData.printForce = (*j)->getPrintForce();
132			constraintData.push_back(tmpData);
133			}
134
135			} else {
136			for(int k = 0; k < nConstraints[i]; ++k) {
137			MPI_Recv(&atom1, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &ierr);
138			MPI_Recv(&atom2, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &ierr);
139			MPI_Recv(&force, 1, MPI_REALTYPE, i, 0, MPI_COMM_WORLD, &ierr);
140			MPI_Recv(&doPrint, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &ierr);
141
142			tmpData.atom1 = atom1;
143			tmpData.atom2 = atom2;
144			tmpData.constraintForce = force;
145			tmpData.printForce = (doPrint == 0) ? false : true;
146			constraintData.push_back(tmpData);
147			}
148			}
149			}
150	gezelter	1983
151	gezelter	1981	std::vector<ConstraintData>::iterator l;
152			for (l = constraintData.begin(); l != constraintData.end(); ++l) {
153			if (l->printForce) {
154			output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << "\t"
155			<< l->atom1 <<"\t"
156			<< l->atom2 <<"\t"
157			<< l->constraintForce << std::endl;
158			}
159			}
160			} else {
161
162			std::list<ConstraintPair*>::const_iterator j;
163			for (j = constraints.begin(); j != constraints.end(); ++j) {
164			int atom1 = (*j)->getConsElem1()->getGlobalIndex();
165			int atom2 = (*j)->getConsElem2()->getGlobalIndex();
166			RealType constraintForce= (*j)->getConstraintForce();
167			int printForce = (int) (*j)->getPrintForce();
168
169			MPI_Send(&atom1, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
170			MPI_Send(&atom2, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
171	gezelter	1983	MPI_Send(&constraintForce, 1, MPI_REALTYPE, masterNode, 0,
172			MPI_COMM_WORLD);
173	gezelter	1981	MPI_Send(&printForce, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
174			}
175			}
176			#endif
177			}
178			}