src/parallel/ForceMatrixDecomposition.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 "parallel/Communicator.hpp"
#include "math/SquareMatrix3.hpp"

namespace OpenMD {

  void ForceDecomposition::distributeInitialData() {
#ifdef IS_MPI

    int nAtoms;
    int nGroups;

    AtomCommRealI = new Communicator<Row,RealType>(nAtoms);
    AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms);
    AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nAtoms);

    AtomCommRealJ = new Communicator<Column,RealType>(nAtoms);
    AtomCommVectorJ = new Communicator<Column,Vector3d>(nAtoms);
    AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nAtoms);

    cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
    cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
    // more to come
#endif
  }
    

  void ForceDecomposition::distributeData()  {
#ifdef IS_MPI
    Snapshot* snap = sman_->getCurrentSnapshot();
    
    // gather up the atomic positions
    AtomCommVectorI->gather(snap->atomData.position, 
                            snap->atomIData.position);
    AtomCommVectorJ->gather(snap->atomData.position, 
                            snap->atomJData.position);
    
    // gather up the cutoff group positions
    cgCommVectorI->gather(snap->cgData.position, 
                          snap->cgIData.position);
    cgCommVectorJ->gather(snap->cgData.position, 
                          snap->cgJData.position);
    
    // if needed, gather the atomic rotation matrices
    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
      AtomCommMatrixI->gather(snap->atomData.aMat, 
                              snap->atomIData.aMat);
      AtomCommMatrixJ->gather(snap->atomData.aMat, 
                              snap->atomJData.aMat);
    }
    
    // if needed, gather the atomic eletrostatic frames
    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
      AtomCommMatrixI->gather(snap->atomData.electroFrame, 
                              snap->atomIData.electroFrame);
      AtomCommMatrixJ->gather(snap->atomData.electroFrame, 
                              snap->atomJData.electroFrame);
    }
#endif      
  }
  
  void ForceDecomposition::collectIntermediateData() {
#ifdef IS_MPI
    Snapshot* snap = sman_->getCurrentSnapshot();
    
    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
      AtomCommRealI->scatter(snap->atomIData.density, 
                             snap->atomData.density);
      std::vector<RealType> rho_tmp;
      int n = snap->getNumberOfAtoms();
      rho_tmp.reserve( n );
      AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
      for (int i = 0; i < n; i++)
        snap->atomData.density[i] += rho_tmp[i];
    }
#endif
  }
  
  void ForceDecomposition::distributeIntermediateData() {
#ifdef IS_MPI
    Snapshot* snap = sman_->getCurrentSnapshot();
    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
      AtomCommRealI->gather(snap->atomData.functional, 
                            snap->atomIData.functional);
      AtomCommRealJ->gather(snap->atomData.functional, 
                            snap->atomJData.functional);
    }
    
    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
      AtomCommRealI->gather(snap->atomData.functionalDerivative, 
                            snap->atomIData.functionalDerivative);
      AtomCommRealJ->gather(snap->atomData.functionalDerivative, 
                            snap->atomJData.functionalDerivative);
    }
#endif
  }
  
  
  void ForceDecomposition::collectData() {
#ifdef IS_MPI
    Snapshot* snap = sman_->getCurrentSnapshot();
    int n = snap->getNumberOfAtoms();

    std::vector<Vector3d> frc_tmp;
    frc_tmp.reserve( n );
    
    AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
    for (int i = 0; i < n; i++)
      snap->atomData.force[i] += frc_tmp[i];
    
    AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
    for (int i = 0; i < n; i++)
      snap->atomData.force[i] += frc_tmp[i];
    
    
    if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
      std::vector<Vector3d> trq_tmp;
      trq_tmp.reserve( n );
      
      AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
      for (int i = 0; i < n; i++)
        snap->atomData.torque[i] += trq_tmp[i];
      
      AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
      for (int i = 0; i < n; i++)
        snap->atomData.torque[i] += trq_tmp[i];
    }
    
    // Still need pot!
    

#endif
  }
  
} //end namespace OpenMD
Revision:	1540
Committed:	Mon Jan 17 21:34:36 2011 UTC (14 years, 9 months ago) by gezelter
Original Path:	*branches/development/src/parallel/ForceDecomposition.cpp*
File size:	6673 byte(s)
Log Message:	changes for new parallel architecture
#	User	Rev	Content
1	gezelter	1539	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	chuckv	1538	*
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	gezelter	1539	#include "parallel/ForceDecomposition.hpp"
42			#include "parallel/Communicator.hpp"
43			#include "math/SquareMatrix3.hpp"
44	chuckv	1538
45	gezelter	1539	namespace OpenMD {
46	chuckv	1538
47	gezelter	1539	void ForceDecomposition::distributeInitialData() {
48	chuckv	1538	#ifdef IS_MPI
49
50	gezelter	1539	int nAtoms;
51			int nGroups;
52	chuckv	1538
53	gezelter	1540	AtomCommRealI = new Communicator<Row,RealType>(nAtoms);
54			AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms);
55			AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nAtoms);
56	chuckv	1538
57	gezelter	1540	AtomCommRealJ = new Communicator<Column,RealType>(nAtoms);
58			AtomCommVectorJ = new Communicator<Column,Vector3d>(nAtoms);
59			AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nAtoms);
60	chuckv	1538
61	gezelter	1540	cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
62			cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
63	gezelter	1539	// more to come
64	chuckv	1538	#endif
65	gezelter	1539	}
66
67	chuckv	1538
68
69	gezelter	1539	void ForceDecomposition::distributeData() {
70	chuckv	1538	#ifdef IS_MPI
71	gezelter	1539	Snapshot* snap = sman_->getCurrentSnapshot();
72	gezelter	1540
73	gezelter	1539	// gather up the atomic positions
74			AtomCommVectorI->gather(snap->atomData.position,
75			snap->atomIData.position);
76			AtomCommVectorJ->gather(snap->atomData.position,
77	gezelter	1540	snap->atomJData.position);
78	gezelter	1539
79			// gather up the cutoff group positions
80			cgCommVectorI->gather(snap->cgData.position,
81	gezelter	1540	snap->cgIData.position);
82	gezelter	1539	cgCommVectorJ->gather(snap->cgData.position,
83	gezelter	1540	snap->cgJData.position);
84	gezelter	1539
85			// if needed, gather the atomic rotation matrices
86			if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
87			AtomCommMatrixI->gather(snap->atomData.aMat,
88	gezelter	1540	snap->atomIData.aMat);
89	gezelter	1539	AtomCommMatrixJ->gather(snap->atomData.aMat,
90	gezelter	1540	snap->atomJData.aMat);
91	gezelter	1539	}
92
93			// if needed, gather the atomic eletrostatic frames
94			if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
95			AtomCommMatrixI->gather(snap->atomData.electroFrame,
96	gezelter	1540	snap->atomIData.electroFrame);
97	gezelter	1539	AtomCommMatrixJ->gather(snap->atomData.electroFrame,
98	gezelter	1540	snap->atomJData.electroFrame);
99	gezelter	1539	}
100			#endif
101			}
102
103			void ForceDecomposition::collectIntermediateData() {
104			#ifdef IS_MPI
105			Snapshot* snap = sman_->getCurrentSnapshot();
106
107			if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
108			AtomCommRealI->scatter(snap->atomIData.density,
109	gezelter	1540	snap->atomData.density);
110	gezelter	1539	std::vector<RealType> rho_tmp;
111			int n = snap->getNumberOfAtoms();
112			rho_tmp.reserve( n );
113			AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
114			for (int i = 0; i < n; i++)
115			snap->atomData.density[i] += rho_tmp[i];
116			}
117	chuckv	1538	#endif
118	gezelter	1539	}
119
120			void ForceDecomposition::distributeIntermediateData() {
121	chuckv	1538	#ifdef IS_MPI
122	gezelter	1539	Snapshot* snap = sman_->getCurrentSnapshot();
123			if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
124			AtomCommRealI->gather(snap->atomData.functional,
125	gezelter	1540	snap->atomIData.functional);
126	gezelter	1539	AtomCommRealJ->gather(snap->atomData.functional,
127	gezelter	1540	snap->atomJData.functional);
128	gezelter	1539	}
129
130			if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
131			AtomCommRealI->gather(snap->atomData.functionalDerivative,
132	gezelter	1540	snap->atomIData.functionalDerivative);
133	gezelter	1539	AtomCommRealJ->gather(snap->atomData.functionalDerivative,
134	gezelter	1540	snap->atomJData.functionalDerivative);
135	gezelter	1539	}
136	chuckv	1538	#endif
137			}
138	gezelter	1539
139
140			void ForceDecomposition::collectData() {
141			#ifdef IS_MPI
142	gezelter	1540	Snapshot* snap = sman_->getCurrentSnapshot();
143			int n = snap->getNumberOfAtoms();
144
145			std::vector<Vector3d> frc_tmp;
146			frc_tmp.reserve( n );
147
148			AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
149			for (int i = 0; i < n; i++)
150			snap->atomData.force[i] += frc_tmp[i];
151
152			AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
153			for (int i = 0; i < n; i++)
154			snap->atomData.force[i] += frc_tmp[i];
155
156
157			if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
158			std::vector<Vector3d> trq_tmp;
159			trq_tmp.reserve( n );
160
161			AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
162			for (int i = 0; i < n; i++)
163			snap->atomData.torque[i] += trq_tmp[i];
164
165			AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
166			for (int i = 0; i < n; i++)
167			snap->atomData.torque[i] += trq_tmp[i];
168			}
169
170			// Still need pot!
171
172
173
174	gezelter	1539	#endif
175	chuckv	1538	}
176
177	gezelter	1539	} //end namespace OpenMD