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).
 */

#ifdef IS_MPI
#include <mpi.h>
#endif

#include "parallel/ForceDecomposition.hpp"
#include "math/Vector3.hpp"

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.atid = idents[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.flucQfrc = &(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_Allreduce(&dispmax, &dispmax, 1, MPI_REALTYPE, MPI_MAX, MPI_COMM_WORLD);
#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:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 8 months ago) by gezelter
File size:	6927 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	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 "parallel/ForceDecomposition.hpp"
48	#include "math/Vector3.hpp"
49
50	using namespace std;
51	namespace OpenMD {
52
53	ForceDecomposition::ForceDecomposition(SimInfo* info, InteractionManager* iMan) : info_(info), interactionMan_(iMan), needVelocities_(false) {
54
55	sman_ = info_->getSnapshotManager();
56	storageLayout_ = sman_->getStorageLayout();
57	ff_ = info_->getForceField();
58	userChoseCutoff_ = false;
59
60	usePeriodicBoundaryConditions_ = info->getSimParams()->getUsePeriodicBoundaryConditions();
61
62	Globals* simParams_ = info_->getSimParams();
63	if (simParams_->havePrintHeatFlux()) {
64	if (simParams_->getPrintHeatFlux()) {
65	needVelocities_ = true;
66	}
67	}
68
69	if (simParams_->haveSkinThickness()) {
70	skinThickness_ = simParams_->getSkinThickness();
71	} else {
72	skinThickness_ = 1.0;
73	sprintf(painCave.errMsg,
74	"ForceDecomposition: No value was set for the skinThickness.\n"
75	"\tOpenMD will use a default value of %f Angstroms\n"
76	"\tfor this simulation\n", skinThickness_);
77	painCave.severity = OPENMD_INFO;
78	painCave.isFatal = 0;
79	simError();
80	}
81
82	// cellOffsets are the partial space for the cell lists used in
83	// constructing the neighbor lists
84	cellOffsets_.clear();
85	cellOffsets_.push_back( Vector3i(0, 0, 0) );
86	cellOffsets_.push_back( Vector3i(1, 0, 0) );
87	cellOffsets_.push_back( Vector3i(1, 1, 0) );
88	cellOffsets_.push_back( Vector3i(0, 1, 0) );
89	cellOffsets_.push_back( Vector3i(-1,1, 0) );
90	cellOffsets_.push_back( Vector3i(0, 0, 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	cellOffsets_.push_back( Vector3i(-1,0, 1) );
96	cellOffsets_.push_back( Vector3i(-1,-1,1) );
97	cellOffsets_.push_back( Vector3i(0, -1,1) );
98	cellOffsets_.push_back( Vector3i(1, -1,1) );
99	}
100
101	void ForceDecomposition::fillSelfData(SelfData &sdat, int atom1) {
102
103	//sdat.atype = atypesLocal[atom1];
104	sdat.atid = idents[atom1];
105
106	sdat.pot = &embeddingPot;
107	sdat.excludedPot = &excludedSelfPot;
108
109	if (storageLayout_ & DataStorage::dslDipole) {
110	sdat.dipole = &(snap_->atomData.dipole[atom1]);
111	}
112
113	if (storageLayout_ & DataStorage::dslQuadrupole) {
114	sdat.quadrupole = &(snap_->atomData.quadrupole[atom1]);
115	}
116
117	if (storageLayout_ & DataStorage::dslTorque) {
118	sdat.t = &(snap_->atomData.torque[atom1]);
119	}
120
121	if (storageLayout_ & DataStorage::dslDensity) {
122	sdat.rho = &(snap_->atomData.density[atom1]);
123	}
124
125	if (storageLayout_ & DataStorage::dslFunctional) {
126	sdat.frho = &(snap_->atomData.functional[atom1]);
127	}
128
129	if (storageLayout_ & DataStorage::dslFunctionalDerivative) {
130	sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]);
131	}
132
133	if (storageLayout_ & DataStorage::dslSkippedCharge) {
134	sdat.skippedCharge = &(snap_->atomData.skippedCharge[atom1]);
135	}
136
137	if (storageLayout_ & DataStorage::dslParticlePot) {
138	sdat.particlePot = &(snap_->atomData.particlePot[atom1]);
139	}
140
141	if (storageLayout_ & DataStorage::dslFlucQPosition) {
142	sdat.flucQ = &(snap_->atomData.flucQPos[atom1]);
143	}
144
145	if (storageLayout_ & DataStorage::dslFlucQForce) {
146	sdat.flucQfrc = &(snap_->atomData.flucQFrc[atom1]);
147	}
148	}
149
150	bool ForceDecomposition::checkNeighborList() {
151
152	int nGroups = snap_->cgData.position.size();
153	if (needVelocities_)
154	snap_->cgData.setStorageLayout(DataStorage::dslPosition \| DataStorage::dslVelocity);
155
156	// if we have changed the group identities or haven't set up the
157	// saved positions we automatically will need a neighbor list update:
158
159	if ( saved_CG_positions_.size() != nGroups ) return true;
160
161	RealType dispmax = 0.0;
162	Vector3d disp;
163
164	for (int i = 0; i < nGroups; i++) {
165	disp = snap_->cgData.position[i] - saved_CG_positions_[i];
166	for (int j = 0; j < 3; j++)
167	dispmax = max( abs(disp[j]), dispmax);
168	}
169
170	#ifdef IS_MPI
171	MPI_Allreduce(&dispmax, &dispmax, 1, MPI_REALTYPE, MPI_MAX, MPI_COMM_WORLD);
172	#endif
173
174	// a conservative test of list skin crossings
175	dispmax = 2.0 * sqrt (3.0 * dispmax * dispmax);
176
177
178	if (dispmax > skinThickness_)
179	return (dispmax > skinThickness_);
180
181	return false;
182	}
183
184	void ForceDecomposition::addToHeatFlux(Vector3d hf) {
185	Vector3d chf = snap_->getConductiveHeatFlux();
186	chf += hf;
187	snap_->setConductiveHeatFlux(chf);
188	}
189	void ForceDecomposition::setHeatFlux(Vector3d hf) {
190	snap_->setConductiveHeatFlux(hf);
191	}
192
193	}