| 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] Vardeman & Gezelter, in progress (2009). |
| 40 |
*/ |
| 41 |
#include "parallel/ForceDecomposition.hpp" |
| 42 |
#include "math/SquareMatrix3.hpp" |
| 43 |
#include "nonbonded/NonBondedInteraction.hpp" |
| 44 |
#include "brains/SnapshotManager.hpp" |
| 45 |
|
| 46 |
using namespace std; |
| 47 |
namespace OpenMD { |
| 48 |
|
| 49 |
/** |
| 50 |
* distributeInitialData is essentially a copy of the older fortran |
| 51 |
* SimulationSetup |
| 52 |
*/ |
| 53 |
|
| 54 |
void ForceDecomposition::distributeInitialData() { |
| 55 |
#ifdef IS_MPI |
| 56 |
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 57 |
int nLocal = snap->getNumberOfAtoms(); |
| 58 |
int nGroups = snap->getNumberOfCutoffGroups(); |
| 59 |
|
| 60 |
AtomCommIntI = new Communicator<Row,int>(nLocal); |
| 61 |
AtomCommRealI = new Communicator<Row,RealType>(nLocal); |
| 62 |
AtomCommVectorI = new Communicator<Row,Vector3d>(nLocal); |
| 63 |
AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nLocal); |
| 64 |
|
| 65 |
AtomCommIntJ = new Communicator<Column,int>(nLocal); |
| 66 |
AtomCommRealJ = new Communicator<Column,RealType>(nLocal); |
| 67 |
AtomCommVectorJ = new Communicator<Column,Vector3d>(nLocal); |
| 68 |
AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nLocal); |
| 69 |
|
| 70 |
cgCommIntI = new Communicator<Row,int>(nGroups); |
| 71 |
cgCommVectorI = new Communicator<Row,Vector3d>(nGroups); |
| 72 |
cgCommIntJ = new Communicator<Column,int>(nGroups); |
| 73 |
cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups); |
| 74 |
|
| 75 |
int nAtomsInRow = AtomCommIntI->getSize(); |
| 76 |
int nAtomsInCol = AtomCommIntJ->getSize(); |
| 77 |
int nGroupsInRow = cgCommIntI->getSize(); |
| 78 |
int nGroupsInCol = cgCommIntJ->getSize(); |
| 79 |
|
| 80 |
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 |
|
| 87 |
// gather the information for atomtype IDs (atids): |
| 88 |
vector<int> identsLocal = info_->getIdentArray(); |
| 89 |
identsRow.reserve(nAtomsInRow); |
| 90 |
identsCol.reserve(nAtomsInCol); |
| 91 |
|
| 92 |
AtomCommIntI->gather(identsLocal, identsRow); |
| 93 |
AtomCommIntJ->gather(identsLocal, identsCol); |
| 94 |
|
| 95 |
AtomLocalToGlobal = info_->getLocalToGlobalAtomIndex(); |
| 96 |
AtomCommIntI->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 97 |
AtomCommIntJ->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 98 |
|
| 99 |
cgLocalToGlobal = info_->getLocalToGlobalCutoffGroupIndex(); |
| 100 |
cgCommIntI->gather(cgLocalToGlobal, cgRowToGlobal); |
| 101 |
cgCommIntJ->gather(cgLocalToGlobal, cgColToGlobal); |
| 102 |
|
| 103 |
|
| 104 |
|
| 105 |
// still need: |
| 106 |
// topoDist |
| 107 |
// exclude |
| 108 |
#endif |
| 109 |
} |
| 110 |
|
| 111 |
|
| 112 |
|
| 113 |
void ForceDecomposition::distributeData() { |
| 114 |
#ifdef IS_MPI |
| 115 |
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 116 |
|
| 117 |
// gather up the atomic positions |
| 118 |
AtomCommVectorI->gather(snap->atomData.position, |
| 119 |
snap->atomIData.position); |
| 120 |
AtomCommVectorJ->gather(snap->atomData.position, |
| 121 |
snap->atomJData.position); |
| 122 |
|
| 123 |
// gather up the cutoff group positions |
| 124 |
cgCommVectorI->gather(snap->cgData.position, |
| 125 |
snap->cgIData.position); |
| 126 |
cgCommVectorJ->gather(snap->cgData.position, |
| 127 |
snap->cgJData.position); |
| 128 |
|
| 129 |
// if needed, gather the atomic rotation matrices |
| 130 |
if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) { |
| 131 |
AtomCommMatrixI->gather(snap->atomData.aMat, |
| 132 |
snap->atomIData.aMat); |
| 133 |
AtomCommMatrixJ->gather(snap->atomData.aMat, |
| 134 |
snap->atomJData.aMat); |
| 135 |
} |
| 136 |
|
| 137 |
// if needed, gather the atomic eletrostatic frames |
| 138 |
if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) { |
| 139 |
AtomCommMatrixI->gather(snap->atomData.electroFrame, |
| 140 |
snap->atomIData.electroFrame); |
| 141 |
AtomCommMatrixJ->gather(snap->atomData.electroFrame, |
| 142 |
snap->atomJData.electroFrame); |
| 143 |
} |
| 144 |
#endif |
| 145 |
} |
| 146 |
|
| 147 |
void ForceDecomposition::collectIntermediateData() { |
| 148 |
#ifdef IS_MPI |
| 149 |
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 150 |
|
| 151 |
if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) { |
| 152 |
|
| 153 |
AtomCommRealI->scatter(snap->atomIData.density, |
| 154 |
snap->atomData.density); |
| 155 |
|
| 156 |
int n = snap->atomData.density.size(); |
| 157 |
std::vector<RealType> rho_tmp(n, 0.0); |
| 158 |
AtomCommRealJ->scatter(snap->atomJData.density, rho_tmp); |
| 159 |
for (int i = 0; i < n; i++) |
| 160 |
snap->atomData.density[i] += rho_tmp[i]; |
| 161 |
} |
| 162 |
#endif |
| 163 |
} |
| 164 |
|
| 165 |
void ForceDecomposition::distributeIntermediateData() { |
| 166 |
#ifdef IS_MPI |
| 167 |
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 168 |
if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) { |
| 169 |
AtomCommRealI->gather(snap->atomData.functional, |
| 170 |
snap->atomIData.functional); |
| 171 |
AtomCommRealJ->gather(snap->atomData.functional, |
| 172 |
snap->atomJData.functional); |
| 173 |
} |
| 174 |
|
| 175 |
if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) { |
| 176 |
AtomCommRealI->gather(snap->atomData.functionalDerivative, |
| 177 |
snap->atomIData.functionalDerivative); |
| 178 |
AtomCommRealJ->gather(snap->atomData.functionalDerivative, |
| 179 |
snap->atomJData.functionalDerivative); |
| 180 |
} |
| 181 |
#endif |
| 182 |
} |
| 183 |
|
| 184 |
|
| 185 |
void ForceDecomposition::collectData() { |
| 186 |
#ifdef IS_MPI |
| 187 |
Snapshot* snap = sman_->getCurrentSnapshot(); |
| 188 |
|
| 189 |
int n = snap->atomData.force.size(); |
| 190 |
vector<Vector3d> frc_tmp(n, V3Zero); |
| 191 |
|
| 192 |
AtomCommVectorI->scatter(snap->atomIData.force, frc_tmp); |
| 193 |
for (int i = 0; i < n; i++) { |
| 194 |
snap->atomData.force[i] += frc_tmp[i]; |
| 195 |
frc_tmp[i] = 0.0; |
| 196 |
} |
| 197 |
|
| 198 |
AtomCommVectorJ->scatter(snap->atomJData.force, frc_tmp); |
| 199 |
for (int i = 0; i < n; i++) |
| 200 |
snap->atomData.force[i] += frc_tmp[i]; |
| 201 |
|
| 202 |
|
| 203 |
if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) { |
| 204 |
|
| 205 |
int nt = snap->atomData.force.size(); |
| 206 |
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 207 |
|
| 208 |
AtomCommVectorI->scatter(snap->atomIData.torque, trq_tmp); |
| 209 |
for (int i = 0; i < n; i++) { |
| 210 |
snap->atomData.torque[i] += trq_tmp[i]; |
| 211 |
trq_tmp[i] = 0.0; |
| 212 |
} |
| 213 |
|
| 214 |
AtomCommVectorJ->scatter(snap->atomJData.torque, trq_tmp); |
| 215 |
for (int i = 0; i < n; i++) |
| 216 |
snap->atomData.torque[i] += trq_tmp[i]; |
| 217 |
} |
| 218 |
|
| 219 |
int nLocal = snap->getNumberOfAtoms(); |
| 220 |
|
| 221 |
vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
| 222 |
vector<RealType> (nLocal, 0.0)); |
| 223 |
|
| 224 |
for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
| 225 |
AtomCommRealI->scatter(pot_row[i], pot_temp[i]); |
| 226 |
for (int ii = 0; ii < pot_temp[i].size(); ii++ ) { |
| 227 |
pot_local[i] += pot_temp[i][ii]; |
| 228 |
} |
| 229 |
} |
| 230 |
#endif |
| 231 |
} |
| 232 |
|
| 233 |
} //end namespace OpenMD |
