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
    int nproc = MPI::COMM_WORLD.Get_size();
    const int masterNode = 0;
    int myNode = worldRank;
    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::COMM_WORLD.Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], 
                              nproc, MPI::INT, MPI::SUM);

    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::COMM_WORLD.Recv(&zmolIndex, 1, MPI::INT, i, 0, ierr);
            MPI::COMM_WORLD.Recv(data, 3, MPI::REALTYPE, i, 0, 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::COMM_WORLD.Send(&zmolIndex, 1, MPI::INT, masterNode, 0);
        MPI::COMM_WORLD.Send(data, 3, MPI::REALTYPE, masterNode, 0);
            
      }
    }
#endif
  }

}
Revision:	1938
Committed:	Thu Oct 31 15:32:17 2013 UTC (11 years, 6 months ago) by gezelter
File size:	5886 byte(s)
Log Message:	Some MPI include re-ordering to work with the Intel MPI implementation.
#	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/ZConsWriter.hpp"
52	#include "utils/simError.h"
53
54	namespace OpenMD {
55	ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
56	//use master - slave mode, only master node writes to disk
57	#ifdef IS_MPI
58	if(worldRank == 0){
59	#endif
60
61	output_.open(filename.c_str());
62
63	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
70	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
74	#ifdef IS_MPI
75	}
76	#endif
77
78	}
79
80	ZConsWriter::~ZConsWriter()
81	{
82
83	#ifdef IS_MPI
84	if(worldRank == 0 ){
85	#endif
86	output_.close();
87	#ifdef IS_MPI
88	}
89	#endif
90	}
91
92	void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
93	#ifndef IS_MPI
94	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
95	output_ << fixedZmols.size() << std::endl;
96
97	std::list<ZconstraintMol>::const_iterator i;
98	for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
99	output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
100	}
101	#else
102	int nproc = MPI::COMM_WORLD.Get_size();
103	const int masterNode = 0;
104	int myNode = worldRank;
105	std::vector<int> tmpNFixedZmols(nproc, 0);
106	std::vector<int> nFixedZmolsInProc(nproc, 0);
107	tmpNFixedZmols[myNode] = fixedZmols.size();
108
109	//do MPI_ALLREDUCE to exchange the total number of atoms,
110	//rigidbodies and cutoff groups
111	MPI::COMM_WORLD.Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0],
112	nproc, MPI::INT, MPI::SUM);
113
114	MPI::Status ierr;
115	int zmolIndex;
116	RealType data[3];
117
118	if (masterNode == 0) {
119
120	std::vector<ZconsData> zconsData;
121	ZconsData tmpData;
122	for(int i =0 ; i < nproc; ++i) {
123	if (i == masterNode) {
124	std::list<ZconstraintMol>::const_iterator j;
125	for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
126	tmpData.zmolIndex = j->mol->getGlobalIndex() ;
127	tmpData.zforce= j->fz;
128	tmpData.zpos = j->zpos;
129	tmpData.zconsPos = j->param.zTargetPos;
130	zconsData.push_back(tmpData);
131	}
132
133	} else {
134	for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
135	MPI::COMM_WORLD.Recv(&zmolIndex, 1, MPI::INT, i, 0, ierr);
136	MPI::COMM_WORLD.Recv(data, 3, MPI::REALTYPE, i, 0, ierr);
137	tmpData.zmolIndex = zmolIndex;
138	tmpData.zforce= data[0];
139	tmpData.zpos = data[1];
140	tmpData.zconsPos = data[2];
141	zconsData.push_back(tmpData);
142	}
143	}
144
145	}
146
147
148	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
149	output_ << zconsData.size() << std::endl;
150
151	std::vector<ZconsData>::iterator l;
152	for (l = zconsData.begin(); l != zconsData.end(); ++l) {
153	output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" << l->zconsPos << std::endl;
154	}
155
156	} else {
157
158	std::list<ZconstraintMol>::const_iterator j;
159	for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
160	zmolIndex = j->mol->getGlobalIndex();
161	data[0] = j->fz;
162	data[1] = j->zpos;
163	data[2] = j->param.zTargetPos;
164	MPI::COMM_WORLD.Send(&zmolIndex, 1, MPI::INT, masterNode, 0);
165	MPI::COMM_WORLD.Send(data, 3, MPI::REALTYPE, masterNode, 0);
166
167	}
168	}
169	#endif
170	}
171
172	}