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"

//   debugging:
#include <unistd.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:	1983
Committed:	Tue Apr 15 20:36:19 2014 UTC (11 years ago) by gezelter
File size:	6723 byte(s)
Log Message:	Fixes for ConstraintWriter in parallel, some cppcheck cleanup starting preparation for 2.2 release
#	Content
1	/*
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	// debugging:
55	#include <unistd.h>
56
57	namespace OpenMD {
58	ConstraintWriter::ConstraintWriter(SimInfo* info,
59	const std::string& filename): info_(info) {
60	//use master - slave mode, only master node writes to disk
61	#ifdef IS_MPI
62	if(worldRank == 0){
63	#endif
64	output_.open(filename.c_str());
65
66	if(!output_){
67	sprintf( painCave.errMsg,
68	"Could not open %s for Constraint output\n",
69	filename.c_str());
70	painCave.isFatal = 1;
71	simError();
72	}
73
74	output_ << "#time(fs)\t"
75	<< "Index of atom 1\t"
76	<< "Index of atom 2\tconstraint force" << std::endl;
77
78	#ifdef IS_MPI
79	}
80	#endif
81	}
82
83	ConstraintWriter::~ConstraintWriter() {
84	#ifdef IS_MPI
85	if(worldRank == 0 ){
86	#endif
87	output_.close();
88	#ifdef IS_MPI
89	}
90	#endif
91	}
92
93	void ConstraintWriter::writeConstraintForces(const std::list<ConstraintPair*>& constraints){
94	#ifndef IS_MPI
95	std::list<ConstraintPair*>::const_iterator i;
96	for ( i = constraints.begin(); i != constraints.end(); ++i) {
97
98	if ((*i)->getPrintForce()) {
99	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << "\t"
100	<< (*i)->getConsElem1()->getGlobalIndex() <<"\t"
101	<< (*i)->getConsElem2()->getGlobalIndex() <<"\t"
102	<< (*i)->getConstraintForce() <<std::endl;
103	}
104	}
105	#else
106
107	const int masterNode = 0;
108	int nproc;
109	int myNode;
110	MPI_Comm_size( MPI_COMM_WORLD, &nproc);
111	MPI_Comm_rank( MPI_COMM_WORLD, &myNode);
112
113	std::vector<int> nConstraints(nproc, 0);
114	nConstraints[myNode] = constraints.size();
115
116	//do MPI_ALLREDUCE to exchange the total number of constraints:
117	MPI_Allreduce(MPI_IN_PLACE, &nConstraints[0], nproc, MPI_INT, MPI_SUM,
118	MPI_COMM_WORLD);
119
120	MPI_Status ierr;
121	int atom1, atom2, doPrint;
122	RealType force;
123
124	if (myNode == masterNode) {
125	std::vector<ConstraintData> constraintData;
126	ConstraintData tmpData;
127	for(int i = 0 ; i < nproc; ++i) {
128	if (i == masterNode) {
129	std::list<ConstraintPair*>::const_iterator j;
130	for ( j = constraints.begin(); j != constraints.end(); ++j) {
131	tmpData.atom1 = (*j)->getConsElem1()->getGlobalIndex();
132	tmpData.atom2 = (*j)->getConsElem2()->getGlobalIndex();
133	tmpData.constraintForce= (*j)->getConstraintForce();
134	tmpData.printForce = (*j)->getPrintForce();
135	constraintData.push_back(tmpData);
136	}
137
138	} else {
139	for(int k = 0; k < nConstraints[i]; ++k) {
140	MPI_Recv(&atom1, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &ierr);
141	MPI_Recv(&atom2, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &ierr);
142	MPI_Recv(&force, 1, MPI_REALTYPE, i, 0, MPI_COMM_WORLD, &ierr);
143	MPI_Recv(&doPrint, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &ierr);
144
145	tmpData.atom1 = atom1;
146	tmpData.atom2 = atom2;
147	tmpData.constraintForce = force;
148	tmpData.printForce = (doPrint == 0) ? false : true;
149	constraintData.push_back(tmpData);
150	}
151	}
152	}
153
154	std::vector<ConstraintData>::iterator l;
155	for (l = constraintData.begin(); l != constraintData.end(); ++l) {
156	if (l->printForce) {
157	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << "\t"
158	<< l->atom1 <<"\t"
159	<< l->atom2 <<"\t"
160	<< l->constraintForce << std::endl;
161	}
162	}
163	} else {
164
165	std::list<ConstraintPair*>::const_iterator j;
166	for (j = constraints.begin(); j != constraints.end(); ++j) {
167	int atom1 = (*j)->getConsElem1()->getGlobalIndex();
168	int atom2 = (*j)->getConsElem2()->getGlobalIndex();
169	RealType constraintForce= (*j)->getConstraintForce();
170	int printForce = (int) (*j)->getPrintForce();
171
172	MPI_Send(&atom1, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
173	MPI_Send(&atom2, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
174	MPI_Send(&constraintForce, 1, MPI_REALTYPE, masterNode, 0,
175	MPI_COMM_WORLD);
176	MPI_Send(&printForce, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
177	}
178	}
179	#endif
180	}
181	}