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/ForceMatrixDecomposition.hpp"
#include "math/SquareMatrix3.hpp"
#include "nonbonded/NonBondedInteraction.hpp"
#include "brains/SnapshotManager.hpp"

using namespace std;
namespace OpenMD {

  /**
   * distributeInitialData is essentially a copy of the older fortran 
   * SimulationSetup
   */
  
  void ForceMatrixDecomposition::distributeInitialData() {
#ifdef IS_MPI    
    Snapshot* snap = sman_->getCurrentSnapshot();
    int nLocal = snap->getNumberOfAtoms();
    int nGroups = snap->getNumberOfCutoffGroups();

    AtomCommIntRow = new Communicator<Row,int>(nLocal);
    AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
    AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
    AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);

    AtomCommIntColumn = new Communicator<Column,int>(nLocal);
    AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
    AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
    AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);

    cgCommIntRow = new Communicator<Row,int>(nGroups);
    cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
    cgCommIntColumn = new Communicator<Column,int>(nGroups);
    cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);

    int nAtomsInRow = AtomCommIntRow->getSize();
    int nAtomsInCol = AtomCommIntColumn->getSize();
    int nGroupsInRow = cgCommIntRow->getSize();
    int nGroupsInCol = cgCommIntColumn->getSize();
    
    vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, 
                                      vector<RealType> (nAtomsInRow, 0.0));
    vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
                                      vector<RealType> (nAtomsInCol, 0.0));
    
    vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
    
    // gather the information for atomtype IDs (atids):
    vector<int> identsLocal = info_->getIdentArray();
    identsRow.reserve(nAtomsInRow);
    identsCol.reserve(nAtomsInCol);
    
    AtomCommIntRow->gather(identsLocal, identsRow);
    AtomCommIntColumn->gather(identsLocal, identsCol);
    
    AtomLocalToGlobal = info_->getGlobalAtomIndices();
    AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
    AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
    
    cgLocalToGlobal = info_->getGlobalGroupIndices();
    cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
    cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);

    // still need:
    // topoDist
    // exclude
#endif
  }
    

  void ForceMatrixDecomposition::distributeData()  {
#ifdef IS_MPI
    Snapshot* snap = sman_->getCurrentSnapshot();
    
    // gather up the atomic positions
    AtomCommVectorRow->gather(snap->atomData.position, 
                            snap->atomIData.position);
    AtomCommVectorColumn->gather(snap->atomData.position, 
                            snap->atomJData.position);
    
    // gather up the cutoff group positions
    cgCommVectorRow->gather(snap->cgData.position, 
                          snap->cgIData.position);
    cgCommVectorColumn->gather(snap->cgData.position, 
                          snap->cgJData.position);
    
    // if needed, gather the atomic rotation matrices
    if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
      AtomCommMatrixRow->gather(snap->atomData.aMat, 
                              snap->atomIData.aMat);
      AtomCommMatrixColumn->gather(snap->atomData.aMat, 
                              snap->atomJData.aMat);
    }
    
    // if needed, gather the atomic eletrostatic frames
    if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
      AtomCommMatrixRow->gather(snap->atomData.electroFrame, 
                              snap->atomIData.electroFrame);
      AtomCommMatrixColumn->gather(snap->atomData.electroFrame, 
                              snap->atomJData.electroFrame);
    }
#endif      
  }
  
  void ForceMatrixDecomposition::collectIntermediateData() {
#ifdef IS_MPI
    Snapshot* snap = sman_->getCurrentSnapshot();
    
    if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {

      AtomCommRealRow->scatter(snap->atomIData.density, 
                             snap->atomData.density);

      int n = snap->atomData.density.size();
      std::vector<RealType> rho_tmp(n, 0.0);
      AtomCommRealColumn->scatter(snap->atomJData.density, rho_tmp);
      for (int i = 0; i < n; i++)
        snap->atomData.density[i] += rho_tmp[i];
    }
#endif
  }
  
  void ForceMatrixDecomposition::distributeIntermediateData() {
#ifdef IS_MPI
    Snapshot* snap = sman_->getCurrentSnapshot();
    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
      AtomCommRealRow->gather(snap->atomData.functional, 
                            snap->atomIData.functional);
      AtomCommRealColumn->gather(snap->atomData.functional, 
                            snap->atomJData.functional);
    }
    
    if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
      AtomCommRealRow->gather(snap->atomData.functionalDerivative, 
                            snap->atomIData.functionalDerivative);
      AtomCommRealColumn->gather(snap->atomData.functionalDerivative, 
                            snap->atomJData.functionalDerivative);
    }
#endif
  }
  
  
  void ForceMatrixDecomposition::collectData() {
#ifdef IS_MPI
    Snapshot* snap = sman_->getCurrentSnapshot();
    
    int n = snap->atomData.force.size();
    vector<Vector3d> frc_tmp(n, V3Zero);
    
    AtomCommVectorRow->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;
    }
    
    AtomCommVectorColumn->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();
      vector<Vector3d> trq_tmp(nt, V3Zero);

      AtomCommVectorRow->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;
      }
      
      AtomCommVectorColumn->scatter(snap->atomJData.torque, trq_tmp);
      for (int i = 0; i < n; i++)
        snap->atomData.torque[i] += trq_tmp[i];
    }
    
    int nLocal = snap->getNumberOfAtoms();

    vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, 
                                       vector<RealType> (nLocal, 0.0));
    
    for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
      AtomCommRealRow->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:	1549
Committed:	Wed Apr 27 18:38:15 2011 UTC (14 years, 6 months ago) by gezelter
Original Path:	*branches/development/src/parallel/ForceMatrixDecomposition.cpp*
File size:	9011 byte(s)
Log Message:	a few more tweaks We're getting somewhat closer to deleting fortran.
#	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	1549	#include "parallel/ForceMatrixDecomposition.hpp"
42	gezelter	1539	#include "math/SquareMatrix3.hpp"
43	gezelter	1544	#include "nonbonded/NonBondedInteraction.hpp"
44			#include "brains/SnapshotManager.hpp"
45	chuckv	1538
46	gezelter	1541	using namespace std;
47	gezelter	1539	namespace OpenMD {
48	chuckv	1538
49	gezelter	1544	/**
50			* distributeInitialData is essentially a copy of the older fortran
51			* SimulationSetup
52			*/
53
54	gezelter	1549	void ForceMatrixDecomposition::distributeInitialData() {
55	gezelter	1544	#ifdef IS_MPI
56	gezelter	1541	Snapshot* snap = sman_->getCurrentSnapshot();
57	gezelter	1544	int nLocal = snap->getNumberOfAtoms();
58	gezelter	1541	int nGroups = snap->getNumberOfCutoffGroups();
59	chuckv	1538
60	gezelter	1549	AtomCommIntRow = new Communicator<Row,int>(nLocal);
61			AtomCommRealRow = new Communicator<Row,RealType>(nLocal);
62			AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal);
63			AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal);
64	chuckv	1538
65	gezelter	1549	AtomCommIntColumn = new Communicator<Column,int>(nLocal);
66			AtomCommRealColumn = new Communicator<Column,RealType>(nLocal);
67			AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal);
68			AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal);
69	chuckv	1538
70	gezelter	1549	cgCommIntRow = new Communicator<Row,int>(nGroups);
71			cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups);
72			cgCommIntColumn = new Communicator<Column,int>(nGroups);
73			cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups);
74	gezelter	1541
75	gezelter	1549	int nAtomsInRow = AtomCommIntRow->getSize();
76			int nAtomsInCol = AtomCommIntColumn->getSize();
77			int nGroupsInRow = cgCommIntRow->getSize();
78			int nGroupsInCol = cgCommIntColumn->getSize();
79
80	gezelter	1544	vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES,
81			vector<RealType> (nAtomsInRow, 0.0));
82			vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES,
83			vector<RealType> (nAtomsInCol, 0.0));
84
85			vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0);
86	gezelter	1549
87	gezelter	1544	// gather the information for atomtype IDs (atids):
88	gezelter	1547	vector<int> identsLocal = info_->getIdentArray();
89			identsRow.reserve(nAtomsInRow);
90			identsCol.reserve(nAtomsInCol);
91	gezelter	1549
92			AtomCommIntRow->gather(identsLocal, identsRow);
93			AtomCommIntColumn->gather(identsLocal, identsCol);
94
95			AtomLocalToGlobal = info_->getGlobalAtomIndices();
96			AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal);
97			AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal);
98
99			cgLocalToGlobal = info_->getGlobalGroupIndices();
100			cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal);
101			cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal);
102	gezelter	1541
103	gezelter	1544	// still need:
104			// topoDist
105			// exclude
106	chuckv	1538	#endif
107	gezelter	1539	}
108
109	chuckv	1538
110
111	gezelter	1549	void ForceMatrixDecomposition::distributeData() {
112	chuckv	1538	#ifdef IS_MPI
113	gezelter	1539	Snapshot* snap = sman_->getCurrentSnapshot();
114	gezelter	1540
115	gezelter	1539	// gather up the atomic positions
116	gezelter	1549	AtomCommVectorRow->gather(snap->atomData.position,
117	gezelter	1539	snap->atomIData.position);
118	gezelter	1549	AtomCommVectorColumn->gather(snap->atomData.position,
119	gezelter	1540	snap->atomJData.position);
120	gezelter	1539
121			// gather up the cutoff group positions
122	gezelter	1549	cgCommVectorRow->gather(snap->cgData.position,
123	gezelter	1540	snap->cgIData.position);
124	gezelter	1549	cgCommVectorColumn->gather(snap->cgData.position,
125	gezelter	1540	snap->cgJData.position);
126	gezelter	1539
127			// if needed, gather the atomic rotation matrices
128			if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) {
129	gezelter	1549	AtomCommMatrixRow->gather(snap->atomData.aMat,
130	gezelter	1540	snap->atomIData.aMat);
131	gezelter	1549	AtomCommMatrixColumn->gather(snap->atomData.aMat,
132	gezelter	1540	snap->atomJData.aMat);
133	gezelter	1539	}
134
135			// if needed, gather the atomic eletrostatic frames
136			if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) {
137	gezelter	1549	AtomCommMatrixRow->gather(snap->atomData.electroFrame,
138	gezelter	1540	snap->atomIData.electroFrame);
139	gezelter	1549	AtomCommMatrixColumn->gather(snap->atomData.electroFrame,
140	gezelter	1540	snap->atomJData.electroFrame);
141	gezelter	1539	}
142			#endif
143			}
144
145	gezelter	1549	void ForceMatrixDecomposition::collectIntermediateData() {
146	gezelter	1539	#ifdef IS_MPI
147			Snapshot* snap = sman_->getCurrentSnapshot();
148
149			if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) {
150	gezelter	1541
151	gezelter	1549	AtomCommRealRow->scatter(snap->atomIData.density,
152	gezelter	1540	snap->atomData.density);
153	gezelter	1541
154			int n = snap->atomData.density.size();
155			std::vector<RealType> rho_tmp(n, 0.0);
156	gezelter	1549	AtomCommRealColumn->scatter(snap->atomJData.density, rho_tmp);
157	gezelter	1539	for (int i = 0; i < n; i++)
158			snap->atomData.density[i] += rho_tmp[i];
159			}
160	chuckv	1538	#endif
161	gezelter	1539	}
162
163	gezelter	1549	void ForceMatrixDecomposition::distributeIntermediateData() {
164	chuckv	1538	#ifdef IS_MPI
165	gezelter	1539	Snapshot* snap = sman_->getCurrentSnapshot();
166			if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) {
167	gezelter	1549	AtomCommRealRow->gather(snap->atomData.functional,
168	gezelter	1540	snap->atomIData.functional);
169	gezelter	1549	AtomCommRealColumn->gather(snap->atomData.functional,
170	gezelter	1540	snap->atomJData.functional);
171	gezelter	1539	}
172
173			if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) {
174	gezelter	1549	AtomCommRealRow->gather(snap->atomData.functionalDerivative,
175	gezelter	1540	snap->atomIData.functionalDerivative);
176	gezelter	1549	AtomCommRealColumn->gather(snap->atomData.functionalDerivative,
177	gezelter	1540	snap->atomJData.functionalDerivative);
178	gezelter	1539	}
179	chuckv	1538	#endif
180			}
181	gezelter	1539
182
183	gezelter	1549	void ForceMatrixDecomposition::collectData() {
184	gezelter	1539	#ifdef IS_MPI
185	gezelter	1540	Snapshot* snap = sman_->getCurrentSnapshot();
186
187	gezelter	1541	int n = snap->atomData.force.size();
188	gezelter	1544	vector<Vector3d> frc_tmp(n, V3Zero);
189	gezelter	1541
190	gezelter	1549	AtomCommVectorRow->scatter(snap->atomIData.force, frc_tmp);
191	gezelter	1541	for (int i = 0; i < n; i++) {
192	gezelter	1540	snap->atomData.force[i] += frc_tmp[i];
193	gezelter	1541	frc_tmp[i] = 0.0;
194			}
195	gezelter	1540
196	gezelter	1549	AtomCommVectorColumn->scatter(snap->atomJData.force, frc_tmp);
197	gezelter	1540	for (int i = 0; i < n; i++)
198			snap->atomData.force[i] += frc_tmp[i];
199
200
201			if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) {
202	gezelter	1541
203			int nt = snap->atomData.force.size();
204	gezelter	1544	vector<Vector3d> trq_tmp(nt, V3Zero);
205	gezelter	1541
206	gezelter	1549	AtomCommVectorRow->scatter(snap->atomIData.torque, trq_tmp);
207	gezelter	1541	for (int i = 0; i < n; i++) {
208	gezelter	1540	snap->atomData.torque[i] += trq_tmp[i];
209	gezelter	1541	trq_tmp[i] = 0.0;
210			}
211	gezelter	1540
212	gezelter	1549	AtomCommVectorColumn->scatter(snap->atomJData.torque, trq_tmp);
213	gezelter	1540	for (int i = 0; i < n; i++)
214			snap->atomData.torque[i] += trq_tmp[i];
215			}
216
217	gezelter	1544	int nLocal = snap->getNumberOfAtoms();
218
219			vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES,
220			vector<RealType> (nLocal, 0.0));
221	gezelter	1540
222	gezelter	1544	for (int i = 0; i < N_INTERACTION_FAMILIES; i++) {
223	gezelter	1549	AtomCommRealRow->scatter(pot_row[i], pot_temp[i]);
224	gezelter	1541	for (int ii = 0; ii < pot_temp[i].size(); ii++ ) {
225			pot_local[i] += pot_temp[i][ii];
226			}
227			}
228	gezelter	1539	#endif
229	chuckv	1538	}
230
231	gezelter	1539	} //end namespace OpenMD