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]  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;

    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;

    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::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:	1755
Committed:	Thu Jun 14 01:58:35 2012 UTC (12 years, 10 months ago) by gezelter
Original Path:	*branches/development/src/parallel/ForceDecomposition.cpp*
File size:	6641 byte(s)
Log Message:	general bugfixes
#	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, 24107 (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	#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	ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan), needVelocities_(false) {
52
53	sman_ = info_->getSnapshotManager();
54	storageLayout_ = sman_->getStorageLayout();
55	ff_ = info_->getForceField();
56	userChoseCutoff_ = false;
57
58	Globals* simParams_ = info_->getSimParams();
59	if (simParams_->havePrintHeatFlux()) {
60	if (simParams_->getPrintHeatFlux()) {
61	needVelocities_ = true;
62	}
63	}
64
65	if (simParams_->haveSkinThickness()) {
66	skinThickness_ = simParams_->getSkinThickness();
67	} else {
68	skinThickness_ = 1.0;
69	sprintf(painCave.errMsg,
70	"ForceDecomposition: No value was set for the skinThickness.\n"
71	"\tOpenMD will use a default value of %f Angstroms\n"
72	"\tfor this simulation\n", skinThickness_);
73	painCave.severity = OPENMD_INFO;
74	painCave.isFatal = 0;
75	simError();
76	}
77
78	// cellOffsets are the partial space for the cell lists used in
79	// constructing the neighbor lists
80	cellOffsets_.clear();
81	cellOffsets_.push_back( Vector3i(0, 0, 0) );
82	cellOffsets_.push_back( Vector3i(1, 0, 0) );
83	cellOffsets_.push_back( Vector3i(1, 1, 0) );
84	cellOffsets_.push_back( Vector3i(0, 1, 0) );
85	cellOffsets_.push_back( Vector3i(-1,1, 0) );
86	cellOffsets_.push_back( Vector3i(0, 0, 1) );
87	cellOffsets_.push_back( Vector3i(1, 0, 1) );
88	cellOffsets_.push_back( Vector3i(1, 1, 1) );
89	cellOffsets_.push_back( Vector3i(0, 1, 1) );
90	cellOffsets_.push_back( Vector3i(-1,1, 1) );
91	cellOffsets_.push_back( Vector3i(-1,0, 1) );
92	cellOffsets_.push_back( Vector3i(-1,-1,1) );
93	cellOffsets_.push_back( Vector3i(0, -1,1) );
94	cellOffsets_.push_back( Vector3i(1, -1,1) );
95	}
96
97	void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
98
99	sdat.atype = atypesLocal[atom1];
100
101	sdat.pot = &embeddingPot;
102
103	if (storageLayout_ & DataStorage::dslElectroFrame) {
104	sdat.eFrame = &(snap_->atomData.electroFrame[atom1]);
105	}
106
107	if (storageLayout_ & DataStorage::dslTorque) {
108	sdat.t = &(snap_->atomData.torque[atom1]);
109	}
110
111	if (storageLayout_ & DataStorage::dslDensity) {
112	sdat.rho = &(snap_->atomData.density[atom1]);
113	}
114
115	if (storageLayout_ & DataStorage::dslFunctional) {
116	sdat.frho = &(snap_->atomData.functional[atom1]);
117	}
118
119	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
120	sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
121	}
122
123	if (storageLayout_ & DataStorage::dslSkippedCharge) {
124	sdat.skippedCharge = &(snap_->atomData.skippedCharge[atom1]);
125	}
126
127	if (storageLayout_ & DataStorage::dslParticlePot) {
128	sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
129	}
130
131	if (storageLayout_ & DataStorage::dslFlucQPosition) {
132	sdat.flucQ = &(snap_->atomData.flucQPos[atom1]);
133	}
134
135	if (storageLayout_ & DataStorage::dslFlucQForce) {
136	sdat.dVdFQ = &(snap_->atomData.flucQFrc[atom1]);
137	}
138	}
139
140	bool ForceDecomposition::checkNeighborList() {
141
142	int nGroups = snap_->cgData.position.size();
143	if (needVelocities_)
144	snap_->cgData.setStorageLayout(DataStorage::dslPosition \| DataStorage::dslVelocity);
145
146	// if we have changed the group identities or haven't set up the
147	// saved positions we automatically will need a neighbor list update:
148
149	if ( saved_CG_positions_.size() != nGroups ) return true;
150
151	RealType dispmax = 0.0;
152	Vector3d disp;
153
154	for (int i = 0; i < nGroups; i++) {
155	disp = snap_->cgData.position[i] - saved_CG_positions_[i];
156	for (int j = 0; j < 3; j++)
157	dispmax = max( abs(disp[j]), dispmax);
158	}
159
160	#ifdef IS_MPI
161	MPI::COMM_WORLD.Allreduce(&dispmax, &dispmax, 1, MPI::REALTYPE, MPI::MAX);
162	#endif
163
164	// a conservative test of list skin crossings
165	dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);
166
167
168	if (dispmax > skinThickness_)
169	return (dispmax > skinThickness_);
170
171	return false;
172	}
173
174	void ForceDecomposition::addToHeatFlux(Vector3d hf) {
175	Vector3d chf = snap_->getConductiveHeatFlux();
176	chf += hf;
177	snap_->setConductiveHeatFlux(chf);
178	}
179	void ForceDecomposition::setHeatFlux(Vector3d hf) {
180	snap_->setConductiveHeatFlux(hf);
181	}
182
183	}