src/parallel/ForceDecomposition.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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
#include "parallel/ForceDecomposition.hpp"
#include "math/Vector3.hpp"
#ifdef IS_MPI
#include <mpi.h>
#endif

using namespace std;
namespace OpenMD {

  ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan) {
    sman_ = info_->getSnapshotManager();
    storageLayout_ = sman_->getStorageLayout();
    ff_ = info_->getForceField();
    userChoseCutoff_ = false;

    Globals* simParams_ = info_->getSimParams();    
  
    if (simParams_->haveSkinThickness()) {
      skinThickness_ = simParams_->getSkinThickness();
    } else {      
      skinThickness_ = 1.0;
      sprintf(painCave.errMsg,
              "ForceDecomposition: No value was set for the skinThickness.\n"
              "\tOpenMD will use a default value of %f Angstroms\n"
              "\tfor this simulation\n", skinThickness_);
      painCave.severity = OPENMD_INFO;
      painCave.isFatal = 0;
      simError();
    }             

    // cellOffsets are the partial space for the cell lists used in
    // constructing the neighbor lists
    cellOffsets_.clear();
    cellOffsets_.push_back( Vector3i(0, 0, 0) );
    cellOffsets_.push_back( Vector3i(1, 0, 0) );
    cellOffsets_.push_back( Vector3i(1, 1, 0) );
    cellOffsets_.push_back( Vector3i(0, 1, 0) );
    cellOffsets_.push_back( Vector3i(-1,1, 0) );
    cellOffsets_.push_back( Vector3i(0, 0, 1) );
    cellOffsets_.push_back( Vector3i(1, 0, 1) );
    cellOffsets_.push_back( Vector3i(1, 1, 1) );
    cellOffsets_.push_back( Vector3i(0, 1, 1) );
    cellOffsets_.push_back( Vector3i(-1,1, 1) );
    cellOffsets_.push_back( Vector3i(-1,0, 1) );
    cellOffsets_.push_back( Vector3i(-1,-1,1) );
    cellOffsets_.push_back( Vector3i(0, -1,1) );
    cellOffsets_.push_back( Vector3i(1, -1,1) );
  }

  void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {

    sdat.atype = ff_->getAtomType(idents[atom1]);
        
    // Still Missing skippedCharge
    if (storageLayout_ & DataStorage::dslElectroFrame) {
      sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
    }
    
    if (storageLayout_ & DataStorage::dslTorque) {
      sdat.t = &(snap_->atomData.torque[atom1]);
    }
    
    if (storageLayout_ & DataStorage::dslDensity) {
      sdat.rho = &(snap_->atomData.density[atom1]);
    }
    
    if (storageLayout_ & DataStorage::dslFunctional) {
      sdat.frho = &(snap_->atomData.functional[atom1]);
    }
    
    if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
      sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
    }

    if (storageLayout_ & DataStorage::dslParticlePot) {
      sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
    }
  }

  bool ForceDecomposition::checkNeighborList() {

    int nGroups = snap_->cgData.position.size();

    // if we have changed the group identities or haven't set up the
    // saved positions we automatically will need a neighbor list update:

    if ( saved_CG_positions_.size() != nGroups ) {
      cerr << "build because size\n";
      return true;
    }

    RealType dispmax = 0.0;
    Vector3d disp;    

    for (int i = 0; i < nGroups; i++) {
      disp = snap_->cgData.position[i]  - saved_CG_positions_[i];
      for (int j = 0; j < 3; j++)
        dispmax = max( abs(disp[j]), dispmax);
    }

#ifdef IS_MPI
    MPI::COMM_WORLD.Allreduce(&dispmax, &dispmax, 1, MPI::REALTYPE, MPI::MAX);
#endif

    // a conservative test of list skin crossings
    dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);


    if (dispmax > skinThickness_) {
      cerr << "build because movement\n";
      return (dispmax > skinThickness_);   
    } else {
      cerr << "not rebuilding\n";
    }
    return false;
  }
}
Revision:	1583
Committed:	Thu Jun 16 22:00:08 2011 UTC (13 years, 10 months ago) by gezelter
Original Path:	*branches/development/src/parallel/ForceDecomposition.cpp*
File size:	5829 byte(s)
Log Message:	Bug squashing
#	User	Rev	Content
1	gezelter	1572	/*
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, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40			*/
41			#include "parallel/ForceDecomposition.hpp"
42			#include "math/Vector3.hpp"
43			#ifdef IS_MPI
44			#include <mpi.h>
45			#endif
46
47			using namespace std;
48			namespace OpenMD {
49
50	gezelter	1579	ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan) {
51	gezelter	1572	sman_ = info_->getSnapshotManager();
52			storageLayout_ = sman_->getStorageLayout();
53			ff_ = info_->getForceField();
54	gezelter	1576	userChoseCutoff_ = false;
55	gezelter	1572
56			Globals* simParams_ = info_->getSimParams();
57
58			if (simParams_->haveSkinThickness()) {
59			skinThickness_ = simParams_->getSkinThickness();
60			} else {
61			skinThickness_ = 1.0;
62			sprintf(painCave.errMsg,
63			"ForceDecomposition: No value was set for the skinThickness.\n"
64			"\tOpenMD will use a default value of %f Angstroms\n"
65			"\tfor this simulation\n", skinThickness_);
66			painCave.severity = OPENMD_INFO;
67			painCave.isFatal = 0;
68			simError();
69			}
70
71			// cellOffsets are the partial space for the cell lists used in
72			// constructing the neighbor lists
73			cellOffsets_.clear();
74			cellOffsets_.push_back( Vector3i(0, 0, 0) );
75			cellOffsets_.push_back( Vector3i(1, 0, 0) );
76			cellOffsets_.push_back( Vector3i(1, 1, 0) );
77			cellOffsets_.push_back( Vector3i(0, 1, 0) );
78			cellOffsets_.push_back( Vector3i(-1,1, 0) );
79			cellOffsets_.push_back( Vector3i(0, 0, 1) );
80			cellOffsets_.push_back( Vector3i(1, 0, 1) );
81			cellOffsets_.push_back( Vector3i(1, 1, 1) );
82			cellOffsets_.push_back( Vector3i(0, 1, 1) );
83			cellOffsets_.push_back( Vector3i(-1,1, 1) );
84			cellOffsets_.push_back( Vector3i(-1,0, 1) );
85			cellOffsets_.push_back( Vector3i(-1,-1,1) );
86			cellOffsets_.push_back( Vector3i(0, -1,1) );
87			cellOffsets_.push_back( Vector3i(1, -1,1) );
88			}
89
90	gezelter	1582	void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
91	gezelter	1583
92			sdat.atype = ff_->getAtomType(idents[atom1]);
93
94			// Still Missing skippedCharge
95	gezelter	1572	if (storageLayout_ & DataStorage::dslElectroFrame) {
96			sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
97			}
98
99			if (storageLayout_ & DataStorage::dslTorque) {
100			sdat.t = &(snap_->atomData.torque[atom1]);
101			}
102
103			if (storageLayout_ & DataStorage::dslDensity) {
104			sdat.rho = &(snap_->atomData.density[atom1]);
105			}
106
107			if (storageLayout_ & DataStorage::dslFunctional) {
108			sdat.frho = &(snap_->atomData.functional[atom1]);
109			}
110
111			if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
112			sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
113			}
114
115	gezelter	1575	if (storageLayout_ & DataStorage::dslParticlePot) {
116			sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
117			}
118	gezelter	1572	}
119
120			bool ForceDecomposition::checkNeighborList() {
121
122			int nGroups = snap_->cgData.position.size();
123
124			// if we have changed the group identities or haven't set up the
125			// saved positions we automatically will need a neighbor list update:
126
127	gezelter	1582	if ( saved_CG_positions_.size() != nGroups ) {
128			cerr << "build because size\n";
129			return true;
130			}
131	gezelter	1572
132			RealType dispmax = 0.0;
133			Vector3d disp;
134
135			for (int i = 0; i < nGroups; i++) {
136			disp = snap_->cgData.position[i] - saved_CG_positions_[i];
137			for (int j = 0; j < 3; j++)
138			dispmax = max( abs(disp[j]), dispmax);
139			}
140
141			#ifdef IS_MPI
142			MPI::COMM_WORLD.Allreduce(&dispmax, &dispmax, 1, MPI::REALTYPE, MPI::MAX);
143			#endif
144
145			// a conservative test of list skin crossings
146			dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);
147
148	gezelter	1582
149			if (dispmax > skinThickness_) {
150			cerr << "build because movement\n";
151			return (dispmax > skinThickness_);
152	gezelter	1583	} else {
153			cerr << "not rebuilding\n";
154	gezelter	1582	}
155			return false;
156	gezelter	1572	}
157			}