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

using namespace std;
namespace OpenMD {

  void ForceDecomposition::distributeInitialData() {
#ifdef IS_MPI
    Snapshot* snap = sman_->getCurrentSnapshot();
    int nAtoms = snap->getNumberOfAtoms();
    int nGroups = snap->getNumberOfCutoffGroups();

    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);

    int nInRow = AtomCommRealI.getSize();
    int nInCol = AtomCommRealJ.getSize();

    vector<vector<RealType> > pot_row(LR_POT_TYPES, 
                                      vector<RealType> (nInRow, 0.0));
    vector<vector<RealType> > pot_col(LR_POT_TYPES,
                                      vector<RealType> (nInCol, 0.0));

    vector<vector<RealType> > pot_local(LR_POT_TYPES, 
                                        vector<RealType> (nAtoms, 0.0));

#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);

      int n = snap->atomData.density.size();
      std::vector<RealType> rho_tmp(n, 0.0);
      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->atomData.force.size();
    std::vector<Vector3d> frc_tmp(n, 0.0);
    
    AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
    for (int i = 0; i < n; i++) {
      snap->atomData.force[i] += frc_tmp[i];
      frc_tmp[i] = 0.0;
    }
    
    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) {

      int nt = snap->atomData.force.size();
      std::vector<Vector3d> trq_tmp(nt, 0.0);

      AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
      for (int i = 0; i < n; i++) {
        snap->atomData.torque[i] += trq_tmp[i];
        trq_tmp[i] = 0.0;
      }
      
      AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
      for (int i = 0; i < n; i++)
        snap->atomData.torque[i] += trq_tmp[i];
    }
    
    
    vector<vector<RealType> > pot_temp(LR_POT_TYPES, 
                                       vector<RealType> (nAtoms, 0.0));
    
    for (int i = 0; i < LR_POT_TYPES; i++) {
      AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
      for (int ii = 0;  ii < pot_temp[i].size(); ii++ ) {
        pot_local[i] += pot_temp[i][ii];
      }
    }
    

#endif
  }
  
} //end namespace OpenMD
Revision:	1541
Committed:	Fri Feb 4 20:04:56 2011 UTC (14 years, 2 months ago) by gezelter
File size:	7637 byte(s)
Log Message:	working on communicators
#	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	1541	using namespace std;
46	gezelter	1539	namespace OpenMD {
47	chuckv	1538
48	gezelter	1539	void ForceDecomposition::distributeInitialData() {
49	chuckv	1538	#ifdef IS_MPI
50	gezelter	1541	Snapshot* snap = sman_->getCurrentSnapshot();
51			int nAtoms = snap->getNumberOfAtoms();
52			int nGroups = snap->getNumberOfCutoffGroups();
53	chuckv	1538
54	gezelter	1540	AtomCommRealI = new Communicator<Row,RealType>(nAtoms);
55			AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms);
56			AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nAtoms);
57	chuckv	1538
58	gezelter	1540	AtomCommRealJ = new Communicator<Column,RealType>(nAtoms);
59			AtomCommVectorJ = new Communicator<Column,Vector3d>(nAtoms);
60			AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nAtoms);
61	chuckv	1538
62	gezelter	1540	cgCommVectorI = new Communicator<Row,Vector3d>(nGroups);
63			cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups);
64	gezelter	1541
65			int nInRow = AtomCommRealI.getSize();
66			int nInCol = AtomCommRealJ.getSize();
67
68			vector<vector<RealType> > pot_row(LR_POT_TYPES,
69			vector<RealType> (nInRow, 0.0));
70			vector<vector<RealType> > pot_col(LR_POT_TYPES,
71			vector<RealType> (nInCol, 0.0));
72
73			vector<vector<RealType> > pot_local(LR_POT_TYPES,
74			vector<RealType> (nAtoms, 0.0));
75
76	chuckv	1538	#endif
77	gezelter	1539	}
78
79	chuckv	1538
80
81	gezelter	1539	void ForceDecomposition::distributeData() {
82	chuckv	1538	#ifdef IS_MPI
83	gezelter	1539	Snapshot* snap = sman_->getCurrentSnapshot();
84	gezelter	1540
85	gezelter	1539	// gather up the atomic positions
86			AtomCommVectorI->gather(snap->atomData.position,
87			snap->atomIData.position);
88			AtomCommVectorJ->gather(snap->atomData.position,
89	gezelter	1540	snap->atomJData.position);
90	gezelter	1539
91			// gather up the cutoff group positions
92			cgCommVectorI->gather(snap->cgData.position,
93	gezelter	1540	snap->cgIData.position);
94	gezelter	1539	cgCommVectorJ->gather(snap->cgData.position,
95	gezelter	1540	snap->cgJData.position);
96	gezelter	1539
97			// if needed, gather the atomic rotation matrices
98			if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
99			AtomCommMatrixI->gather(snap->atomData.aMat,
100	gezelter	1540	snap->atomIData.aMat);
101	gezelter	1539	AtomCommMatrixJ->gather(snap->atomData.aMat,
102	gezelter	1540	snap->atomJData.aMat);
103	gezelter	1539	}
104
105			// if needed, gather the atomic eletrostatic frames
106			if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
107			AtomCommMatrixI->gather(snap->atomData.electroFrame,
108	gezelter	1540	snap->atomIData.electroFrame);
109	gezelter	1539	AtomCommMatrixJ->gather(snap->atomData.electroFrame,
110	gezelter	1540	snap->atomJData.electroFrame);
111	gezelter	1539	}
112			#endif
113			}
114
115			void ForceDecomposition::collectIntermediateData() {
116			#ifdef IS_MPI
117			Snapshot* snap = sman_->getCurrentSnapshot();
118
119			if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
120	gezelter	1541
121	gezelter	1539	AtomCommRealI->scatter(snap->atomIData.density,
122	gezelter	1540	snap->atomData.density);
123	gezelter	1541
124			int n = snap->atomData.density.size();
125			std::vector<RealType> rho_tmp(n, 0.0);
126	gezelter	1539	AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp);
127			for (int i = 0; i < n; i++)
128			snap->atomData.density[i] += rho_tmp[i];
129			}
130	chuckv	1538	#endif
131	gezelter	1539	}
132
133			void ForceDecomposition::distributeIntermediateData() {
134	chuckv	1538	#ifdef IS_MPI
135	gezelter	1539	Snapshot* snap = sman_->getCurrentSnapshot();
136			if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
137			AtomCommRealI->gather(snap->atomData.functional,
138	gezelter	1540	snap->atomIData.functional);
139	gezelter	1539	AtomCommRealJ->gather(snap->atomData.functional,
140	gezelter	1540	snap->atomJData.functional);
141	gezelter	1539	}
142
143			if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
144			AtomCommRealI->gather(snap->atomData.functionalDerivative,
145	gezelter	1540	snap->atomIData.functionalDerivative);
146	gezelter	1539	AtomCommRealJ->gather(snap->atomData.functionalDerivative,
147	gezelter	1540	snap->atomJData.functionalDerivative);
148	gezelter	1539	}
149	chuckv	1538	#endif
150			}
151	gezelter	1539
152
153			void ForceDecomposition::collectData() {
154			#ifdef IS_MPI
155	gezelter	1540	Snapshot* snap = sman_->getCurrentSnapshot();
156
157	gezelter	1541	int n = snap->atomData.force.size();
158			std::vector<Vector3d> frc_tmp(n, 0.0);
159
160	gezelter	1540	AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp);
161	gezelter	1541	for (int i = 0; i < n; i++) {
162	gezelter	1540	snap->atomData.force[i] += frc_tmp[i];
163	gezelter	1541	frc_tmp[i] = 0.0;
164			}
165	gezelter	1540
166			AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp);
167			for (int i = 0; i < n; i++)
168			snap->atomData.force[i] += frc_tmp[i];
169
170
171			if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
172	gezelter	1541
173			int nt = snap->atomData.force.size();
174			std::vector<Vector3d> trq_tmp(nt, 0.0);
175
176	gezelter	1540	AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp);
177	gezelter	1541	for (int i = 0; i < n; i++) {
178	gezelter	1540	snap->atomData.torque[i] += trq_tmp[i];
179	gezelter	1541	trq_tmp[i] = 0.0;
180			}
181	gezelter	1540
182			AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp);
183			for (int i = 0; i < n; i++)
184			snap->atomData.torque[i] += trq_tmp[i];
185			}
186
187
188	gezelter	1541	vector<vector<RealType> > pot_temp(LR_POT_TYPES,
189			vector<RealType> (nAtoms, 0.0));
190
191			for (int i = 0; i < LR_POT_TYPES; i++) {
192			AtomCommRealI->scatter(pot_row[i], pot_temp[i]);
193			for (int ii = 0; ii < pot_temp[i].size(); ii++ ) {
194			pot_local[i] += pot_temp[i][ii];
195			}
196			}
197
198	gezelter	1540
199
200	gezelter	1539	#endif
201	chuckv	1538	}
202
203	gezelter	1539	} //end namespace OpenMD