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. 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 <algorithm>
#include <iostream>
#include <vector>


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


namespace oopse {
  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_size(MPI_COMM_WORLD, &nproc);
    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_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT,
                  MPI_SUM, MPI_COMM_WORLD);

    MPI_Status ierr;
    int zmolIndex;
    double 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_DOUBLE, 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_DOUBLE, masterNode, 0, MPI_COMM_WORLD);
            
      }
    }
#endif
  }

}
Revision:	2204
Committed:	Fri Apr 15 22:04:00 2005 UTC (19 years, 2 months ago) by gezelter
File size:	5714 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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. 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	gezelter	1490	#include <algorithm>
43			#include <iostream>
44			#include <vector>
45	gezelter	1930
46
47	tim	1492	#include "io/ZConsWriter.hpp"
48			#include "utils/simError.h"
49	gezelter	1490
50
51	gezelter	1930	namespace oopse {
52	gezelter	2204	ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) {
53			//use master - slave mode, only master node writes to disk
54	gezelter	1490	#ifdef IS_MPI
55	gezelter	1930	if(worldRank == 0){
56	gezelter	1490	#endif
57
58	gezelter	2204	output_.open(filename.c_str());
59	gezelter	1490
60	gezelter	2204	if(!output_){
61			sprintf( painCave.errMsg,
62			"Could not open %s for z constrain output_ \n", filename.c_str());
63			painCave.isFatal = 1;
64			simError();
65			}
66	gezelter	1490
67	gezelter	2204	output_ << "//time(fs)" << std::endl;
68			output_ << "//number of fixed z-constrain molecules" << std::endl;
69			output_ << "//global Index of molecule\tzconstrain force\tcurrentZPos" << std::endl;
70	gezelter	1930
71	gezelter	1490	#ifdef IS_MPI
72	gezelter	1930	}
73	gezelter	1490	#endif
74
75	gezelter	2204	}
76	gezelter	1490
77	gezelter	2204	ZConsWriter::~ZConsWriter()
78			{
79	gezelter	1490
80			#ifdef IS_MPI
81	gezelter	2204	if(worldRank == 0 ){
82	gezelter	1490	#endif
83	gezelter	2204	output_.close();
84	gezelter	1490	#ifdef IS_MPI
85	gezelter	2204	}
86			#endif
87	gezelter	1490	}
88
89	gezelter	2204	void ZConsWriter::writeFZ(const std::list<ZconstraintMol>& fixedZmols){
90	gezelter	1490	#ifndef IS_MPI
91	gezelter	1930	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
92			output_ << fixedZmols.size() << std::endl;
93	gezelter	1490
94	gezelter	1930	std::list<ZconstraintMol>::const_iterator i;
95			for ( i = fixedZmols.begin(); i != fixedZmols.end(); ++i) {
96	gezelter	2204	output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl;
97	gezelter	1930	}
98	gezelter	1490	#else
99	gezelter	1930	int nproc;
100			MPI_Comm_size(MPI_COMM_WORLD, &nproc);
101			const int masterNode = 0;
102			int myNode = worldRank;
103			std::vector<int> tmpNFixedZmols(nproc, 0);
104			std::vector<int> nFixedZmolsInProc(nproc, 0);
105			tmpNFixedZmols[myNode] = fixedZmols.size();
106	gezelter	1490
107	gezelter	1930	//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
108			MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT,
109			MPI_SUM, MPI_COMM_WORLD);
110	gezelter	1490
111	gezelter	1930	MPI_Status ierr;
112			int zmolIndex;
113			double data[3];
114	gezelter	1490
115	gezelter	1930	if (masterNode == 0) {
116	gezelter	1490
117	gezelter	2204	std::vector<ZconsData> zconsData;
118			ZconsData tmpData;
119			for(int i =0 ; i < nproc; ++i) {
120			if (i == masterNode) {
121			std::list<ZconstraintMol>::const_iterator j;
122			for ( j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
123			tmpData.zmolIndex = j->mol->getGlobalIndex() ;
124			tmpData.zforce= j->fz;
125			tmpData.zpos = j->zpos;
126			tmpData.zconsPos = j->param.zTargetPos;
127			zconsData.push_back(tmpData);
128			}
129	gezelter	1490
130	gezelter	2204	} else {
131			for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) {
132			MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
133			MPI_Recv(data, 3, MPI_DOUBLE, i, 0, MPI_COMM_WORLD,&ierr);
134			tmpData.zmolIndex = zmolIndex;
135			tmpData.zforce= data[0];
136			tmpData.zpos = data[1];
137			tmpData.zconsPos = data[2];
138			zconsData.push_back(tmpData);
139			}
140			}
141	gezelter	1930
142	gezelter	2204	}
143	gezelter	1490
144
145	gezelter	2204	output_ << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() << std::endl;
146			output_ << zconsData.size() << std::endl;
147	gezelter	1490
148	gezelter	2204	std::vector<ZconsData>::iterator l;
149			for (l = zconsData.begin(); l != zconsData.end(); ++l) {
150			output_ << l->zmolIndex << "\t" << l->zforce << "\t" << l->zpos << "\t" << l->zconsPos << std::endl;
151			}
152	gezelter	1930
153			} else {
154	gezelter	1490
155	gezelter	2204	std::list<ZconstraintMol>::const_iterator j;
156			for (j = fixedZmols.begin(); j != fixedZmols.end(); ++j) {
157			zmolIndex = j->mol->getGlobalIndex();
158			data[0] = j->fz;
159			data[1] = j->zpos;
160			data[2] = j->param.zTargetPos;
161			MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
162			MPI_Send(data, 3, MPI_DOUBLE, masterNode, 0, MPI_COMM_WORLD);
163	gezelter	1930
164	gezelter	2204	}
165	gezelter	1930	}
166	gezelter	1490	#endif
167	gezelter	2204	}
168	gezelter	1930
169			}