src/io/ZConsWriter.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/ZConsWriter.hpp"
#include "utils/simError.h"

namespace OpenMD {
  ZConsWriter::ZConsWriter(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 z constrain output_ \n", filename.c_str());
        painCave.isFatal = 1;
        simError();
      }

      output_ << "//time(fs)" << std::endl;
      output_ << "//number of fixed z-constrain molecules" << std::endl;
      output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl;

#ifdef IS_MPI
    }
#endif  

  }

  ZConsWriter::~ZConsWriter()
  {

#ifdef IS_MPI
    if(worldRank == 0 ){
#endif  
      output_.close();  
#ifdef IS_MPI  
    }
#endif
  }

  void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
#ifndef IS_MPI
    output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
    output_ << fixedZmols.size() << std::endl;

    std::list<ZconstraintMol>::const_iterator i;
    for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
      output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<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> tmpNFixedZmols(nproc, 0);
    std::vector<int> nFixedZmolsInProc(nproc, 0);
    tmpNFixedZmols[myNode] = fixedZmols.size();
    
    //do MPI_ALLREDUCE to exchange the total number of atoms,
    //rigidbodies and cutoff groups
    MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], 
                  nproc, MPI_INT, MPI_SUM, MPI_COMM_WORLD);

    MPI_Status* ierr;
    int zmolIndex;
    RealType data[3];
    
    if (masterNode == 0) {

      std::vector<ZconsData> zconsData;
      ZconsData tmpData;       
      for(int i =0 ; i < nproc; ++i) {
        if (i == masterNode) {
          std::list<ZconstraintMol>::const_iterator j;
          for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
            tmpData.zmolIndex = j->mol->getGlobalIndex() ;
            tmpData.zforce= j->fz;
            tmpData.zpos = j->zpos;
            tmpData.zconsPos = j->param.zTargetPos;
            zconsData.push_back(tmpData);
          }                

        } else {
          for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
            MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD, ierr);
            MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD, ierr);
            tmpData.zmolIndex = zmolIndex;
            tmpData.zforce= data[0];
            tmpData.zpos = data[1];
            tmpData.zconsPos = data[2];
            zconsData.push_back(tmpData);                                        
          }
        }
            
      }


      output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
      output_ << zconsData.size() << std::endl;

      std::vector<ZconsData>::iterator l;
      for (l = zconsData.begin(); l != zconsData.end(); ++l) {
        output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" <<  l->zconsPos << std::endl;
      }
        
    } else {

      std::list<ZconstraintMol>::const_iterator j;
      for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
        zmolIndex = j->mol->getGlobalIndex();            
        data[0] = j->fz;
        data[1] = j->zpos;
        data[2] = j->param.zTargetPos;
        MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
        MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
            
      }
    }
#endif
  }

}
Revision:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 8 months ago) by gezelter
File size:	5947 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	1938	#ifdef IS_MPI
44			#include <mpi.h>
45			#endif
46
47	gezelter	2	#include <algorithm>
48			#include <iostream>
49			#include <vector>
50	gezelter	246
51	tim	3	#include "io/ZConsWriter.hpp"
52			#include "utils/simError.h"
53	gezelter	2
54	gezelter	1390	namespace OpenMD {
55	gezelter	507	ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
56			//use master - slave mode, only master node writes to disk
57	gezelter	2	#ifdef IS_MPI
58	gezelter	246	if(worldRank == 0){
59	gezelter	2	#endif
60
61	gezelter	507	output_.open(filename.c_str());
62	gezelter	2
63	gezelter	507	if(!output_){
64			sprintf( painCave.errMsg,
65			"Could not open %s for z constrain output_ \n", filename.c_str());
66			painCave.isFatal = 1;
67			simError();
68			}
69	gezelter	2
70	gezelter	507	output_ << "//time(fs)" << std::endl;
71			output_ << "//number of fixed z-constrain molecules" << std::endl;
72			output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl;
73	gezelter	246
74	gezelter	2	#ifdef IS_MPI
75	gezelter	246	}
76	gezelter	2	#endif
77
78	gezelter	507	}
79	gezelter	2
80	gezelter	507	ZConsWriter::~ZConsWriter()
81			{
82	gezelter	2
83			#ifdef IS_MPI
84	gezelter	507	if(worldRank == 0 ){
85	gezelter	2	#endif
86	gezelter	507	output_.close();
87	gezelter	2	#ifdef IS_MPI
88	gezelter	507	}
89			#endif
90	gezelter	2	}
91
92	gezelter	507	void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
93	gezelter	2	#ifndef IS_MPI
94	gezelter	246	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
95			output_ << fixedZmols.size() << std::endl;
96	gezelter	2
97	gezelter	246	std::list<ZconstraintMol>::const_iterator i;
98			for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
99	gezelter	507	output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
100	gezelter	246	}
101	gezelter	2	#else
102	gezelter	1969
103	gezelter	246	const int masterNode = 0;
104	gezelter	1969	int nproc;
105			int myNode;
106			MPI_Comm_size( MPI_COMM_WORLD, &nproc);
107			MPI_Comm_rank( MPI_COMM_WORLD, &myNode);
108
109	gezelter	246	std::vector<int> tmpNFixedZmols(nproc, 0);
110			std::vector<int> nFixedZmolsInProc(nproc, 0);
111			tmpNFixedZmols[myNode] = fixedZmols.size();
112	gezelter	2
113	gezelter	1796	//do MPI_ALLREDUCE to exchange the total number of atoms,
114			//rigidbodies and cutoff groups
115	gezelter	1969	MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0],
116			nproc, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
117	gezelter	2
118	gezelter	1969	MPI_Status* ierr;
119	gezelter	246	int zmolIndex;
120	tim	963	RealType data[3];
121	gezelter	2
122	gezelter	246	if (masterNode == 0) {
123	gezelter	2
124	gezelter	507	std::vector<ZconsData> zconsData;
125			ZconsData tmpData;
126			for(int i =0 ; i < nproc; ++i) {
127			if (i == masterNode) {
128			std::list<ZconstraintMol>::const_iterator j;
129			for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
130			tmpData.zmolIndex = j->mol->getGlobalIndex() ;
131			tmpData.zforce= j->fz;
132			tmpData.zpos = j->zpos;
133			tmpData.zconsPos = j->param.zTargetPos;
134			zconsData.push_back(tmpData);
135			}
136	gezelter	2
137	gezelter	507	} else {
138			for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
139	gezelter	1969	MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD, ierr);
140			MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD, ierr);
141	gezelter	507	tmpData.zmolIndex = zmolIndex;
142			tmpData.zforce= data[0];
143			tmpData.zpos = data[1];
144			tmpData.zconsPos = data[2];
145			zconsData.push_back(tmpData);
146			}
147			}
148	gezelter	246
149	gezelter	507	}
150	gezelter	2
151
152	gezelter	507	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
153			output_ << zconsData.size() << std::endl;
154	gezelter	2
155	gezelter	507	std::vector<ZconsData>::iterator l;
156			for (l = zconsData.begin(); l != zconsData.end(); ++l) {
157			output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" << l->zconsPos << std::endl;
158			}
159	gezelter	246
160			} else {
161	gezelter	2
162	gezelter	507	std::list<ZconstraintMol>::const_iterator j;
163			for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
164			zmolIndex = j->mol->getGlobalIndex();
165			data[0] = j->fz;
166			data[1] = j->zpos;
167			data[2] = j->param.zTargetPos;
168	gezelter	1969	MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
169			MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
170	gezelter	246
171	gezelter	507	}
172	gezelter	246	}
173	gezelter	2	#endif
174	gezelter	507	}
175	gezelter	246
176			}