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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#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), needVelocities_(false) {

    sman_ = info_->getSnapshotManager();
    storageLayout_ = sman_->getStorageLayout();
    ff_ = info_->getForceField();
    userChoseCutoff_ = false;

    usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions();

    Globals* simParams_ = info_->getSimParams();    
    if (simParams_->havePrintHeatFlux()) {
      if (simParams_->getPrintHeatFlux()) {
        needVelocities_ = true;
      }
    }

    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 = atypesLocal[atom1];

    sdat.pot = &embeddingPot;
    sdat.excludedPot = &excludedSelfPot;

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

    if (storageLayout_ & DataStorage::dslQuadrupole) {
      sdat.quadrupole = &(snap_->atomData.quadrupole[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::dslSkippedCharge) {
      sdat.skippedCharge = &(snap_->atomData.skippedCharge[atom1]);
    }

    if (storageLayout_ & DataStorage::dslParticlePot) {
      sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
    }
    
    if (storageLayout_ & DataStorage::dslFlucQPosition) {
      sdat.flucQ = &(snap_->atomData.flucQPos[atom1]);
    }
    
    if (storageLayout_ & DataStorage::dslFlucQForce) {
      sdat.dVdFQ = &(snap_->atomData.flucQFrc[atom1]);
    }
  }

  bool ForceDecomposition::checkNeighborList() {

    int nGroups = snap_->cgData.position.size();
    if (needVelocities_) 
      snap_->cgData.setStorageLayout(DataStorage::dslPosition | DataStorage::dslVelocity);
    
    // 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 ) 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_) 
      return (dispmax > skinThickness_);   

    return false;
  }

  void ForceDecomposition::addToHeatFlux(Vector3d hf) {
    Vector3d chf = snap_->getConductiveHeatFlux();
    chf += hf;
    snap_->setConductiveHeatFlux(chf);
  }
  void ForceDecomposition::setHeatFlux(Vector3d hf) {
    snap_->setConductiveHeatFlux(hf);
  }

}
Revision:	1856
Committed:	Tue Apr 2 21:30:34 2013 UTC (12 years ago) by gezelter
File size:	6887 byte(s)
Log Message:	Bug fixes to get new parallel decomposition methods working without periodic boundary conditions. Updated volume in stats file correctly. LangevinHull fixes for low viscosity values.
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1572	*/
42			#include "parallel/ForceDecomposition.hpp"
43			#include "math/Vector3.hpp"
44			#ifdef IS_MPI
45			#include <mpi.h>
46			#endif
47
48			using namespace std;
49			namespace OpenMD {
50
51	gezelter	1723	ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan), needVelocities_(false) {
52	gezelter	1755
53	gezelter	1572	sman_ = info_->getSnapshotManager();
54			storageLayout_ = sman_->getStorageLayout();
55			ff_ = info_->getForceField();
56	gezelter	1576	userChoseCutoff_ = false;
57	gezelter	1572
58	gezelter	1856	usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions();
59
60	gezelter	1572	Globals* simParams_ = info_->getSimParams();
61	gezelter	1723	if (simParams_->havePrintHeatFlux()) {
62			if (simParams_->getPrintHeatFlux()) {
63			needVelocities_ = true;
64			}
65			}
66
67	gezelter	1572	if (simParams_->haveSkinThickness()) {
68			skinThickness_ = simParams_->getSkinThickness();
69			} else {
70			skinThickness_ = 1.0;
71			sprintf(painCave.errMsg,
72			"ForceDecomposition: No value was set for the skinThickness.\n"
73			"\tOpenMD will use a default value of %f Angstroms\n"
74			"\tfor this simulation\n", skinThickness_);
75			painCave.severity = OPENMD_INFO;
76			painCave.isFatal = 0;
77			simError();
78			}
79
80			// cellOffsets are the partial space for the cell lists used in
81			// constructing the neighbor lists
82			cellOffsets_.clear();
83			cellOffsets_.push_back( Vector3i(0, 0, 0) );
84			cellOffsets_.push_back( Vector3i(1, 0, 0) );
85			cellOffsets_.push_back( Vector3i(1, 1, 0) );
86			cellOffsets_.push_back( Vector3i(0, 1, 0) );
87			cellOffsets_.push_back( Vector3i(-1,1, 0) );
88			cellOffsets_.push_back( Vector3i(0, 0, 1) );
89			cellOffsets_.push_back( Vector3i(1, 0, 1) );
90			cellOffsets_.push_back( Vector3i(1, 1, 1) );
91			cellOffsets_.push_back( Vector3i(0, 1, 1) );
92			cellOffsets_.push_back( Vector3i(-1,1, 1) );
93			cellOffsets_.push_back( Vector3i(-1,0, 1) );
94			cellOffsets_.push_back( Vector3i(-1,-1,1) );
95			cellOffsets_.push_back( Vector3i(0, -1,1) );
96			cellOffsets_.push_back( Vector3i(1, -1,1) );
97			}
98
99	gezelter	1582	void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
100	gezelter	1583
101	gezelter	1591	sdat.atype = atypesLocal[atom1];
102	gezelter	1613
103			sdat.pot = &embeddingPot;
104	gezelter	1761	sdat.excludedPot = &excludedSelfPot;
105	gezelter	1629
106	gezelter	1787	if (storageLayout_ & DataStorage::dslDipole) {
107			sdat.dipole = &(snap_->atomData.dipole[atom1]);
108	gezelter	1572	}
109	gezelter	1787
110			if (storageLayout_ & DataStorage::dslQuadrupole) {
111			sdat.quadrupole = &(snap_->atomData.quadrupole[atom1]);
112			}
113
114	gezelter	1572	if (storageLayout_ & DataStorage::dslTorque) {
115			sdat.t = &(snap_->atomData.torque[atom1]);
116			}
117
118			if (storageLayout_ & DataStorage::dslDensity) {
119			sdat.rho = &(snap_->atomData.density[atom1]);
120			}
121
122			if (storageLayout_ & DataStorage::dslFunctional) {
123			sdat.frho = &(snap_->atomData.functional[atom1]);
124			}
125
126			if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
127			sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
128			}
129
130	gezelter	1586	if (storageLayout_ & DataStorage::dslSkippedCharge) {
131			sdat.skippedCharge = &(snap_->atomData.skippedCharge[atom1]);
132			}
133
134	gezelter	1575	if (storageLayout_ & DataStorage::dslParticlePot) {
135			sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
136			}
137	jmichalk	1736
138			if (storageLayout_ & DataStorage::dslFlucQPosition) {
139			sdat.flucQ = &(snap_->atomData.flucQPos[atom1]);
140			}
141
142			if (storageLayout_ & DataStorage::dslFlucQForce) {
143			sdat.dVdFQ = &(snap_->atomData.flucQFrc[atom1]);
144			}
145	gezelter	1572	}
146
147			bool ForceDecomposition::checkNeighborList() {
148
149			int nGroups = snap_->cgData.position.size();
150	gezelter	1723	if (needVelocities_)
151			snap_->cgData.setStorageLayout(DataStorage::dslPosition \| DataStorage::dslVelocity);
152
153	gezelter	1572	// if we have changed the group identities or haven't set up the
154			// saved positions we automatically will need a neighbor list update:
155
156	gezelter	1587	if ( saved_CG_positions_.size() != nGroups ) return true;
157	gezelter	1572
158			RealType dispmax = 0.0;
159			Vector3d disp;
160
161			for (int i = 0; i < nGroups; i++) {
162			disp = snap_->cgData.position[i] - saved_CG_positions_[i];
163			for (int j = 0; j < 3; j++)
164			dispmax = max( abs(disp[j]), dispmax);
165			}
166
167			#ifdef IS_MPI
168			MPI::COMM_WORLD.Allreduce(&dispmax, &dispmax, 1, MPI::REALTYPE, MPI::MAX);
169			#endif
170
171			// a conservative test of list skin crossings
172			dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);
173
174	gezelter	1582
175	gezelter	1587	if (dispmax > skinThickness_)
176	gezelter	1582	return (dispmax > skinThickness_);
177	gezelter	1587
178	gezelter	1582	return false;
179	gezelter	1572	}
180	gezelter	1723
181			void ForceDecomposition::addToHeatFlux(Vector3d hf) {
182	gezelter	1744	Vector3d chf = snap_->getConductiveHeatFlux();
183			chf += hf;
184			snap_->setConductiveHeatFlux(chf);
185	gezelter	1723	}
186			void ForceDecomposition::setHeatFlux(Vector3d hf) {
187	gezelter	1744	snap_->setConductiveHeatFlux(hf);
188	gezelter	1723	}
189
190	gezelter	1572	}