| 1 |
/* |
| 2 |
* Copyright (c) 2008 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. Acknowledgement of the program authors must be made in any |
| 10 |
* publication of scientific results based in part on use of the |
| 11 |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
* the article in which the program was described (Matthew |
| 13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
* |
| 18 |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
#include <fstream> |
| 42 |
#include <iostream> |
| 43 |
#include "integrators/SMIPDForceManager.hpp" |
| 44 |
#include "math/CholeskyDecomposition.hpp" |
| 45 |
#include "utils/OOPSEConstant.hpp" |
| 46 |
#include "math/ConvexHull.hpp" |
| 47 |
#include "math/Triangle.hpp" |
| 48 |
|
| 49 |
namespace oopse { |
| 50 |
|
| 51 |
SMIPDForceManager::SMIPDForceManager(SimInfo* info) : ForceManager(info) { |
| 52 |
|
| 53 |
simParams = info->getSimParams(); |
| 54 |
veloMunge = new Velocitizer(info); |
| 55 |
|
| 56 |
// Create Hull, Convex Hull for now, other options later. |
| 57 |
|
| 58 |
surfaceMesh_ = new ConvexHull(); |
| 59 |
|
| 60 |
/* Check that the simulation has target pressure and target |
| 61 |
temperature set */ |
| 62 |
|
| 63 |
if (!simParams->haveTargetTemp()) { |
| 64 |
sprintf(painCave.errMsg, |
| 65 |
"SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 66 |
" without a targetTemp!\n"); |
| 67 |
painCave.isFatal = 1; |
| 68 |
painCave.severity = OOPSE_ERROR; |
| 69 |
simError(); |
| 70 |
} else { |
| 71 |
targetTemp_ = simParams->getTargetTemp(); |
| 72 |
} |
| 73 |
|
| 74 |
if (!simParams->haveTargetPressure()) { |
| 75 |
sprintf(painCave.errMsg, |
| 76 |
"SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 77 |
" without a targetPressure!\n"); |
| 78 |
painCave.isFatal = 1; |
| 79 |
simError(); |
| 80 |
} else { |
| 81 |
// Convert pressure from atm -> amu/(fs^2*Ang) |
| 82 |
targetPressure_ = simParams->getTargetPressure() / |
| 83 |
OOPSEConstant::pressureConvert; |
| 84 |
} |
| 85 |
|
| 86 |
if (simParams->getUsePeriodicBoundaryConditions()) { |
| 87 |
sprintf(painCave.errMsg, |
| 88 |
"SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 89 |
" with periodic boundary conditions!\n"); |
| 90 |
painCave.isFatal = 1; |
| 91 |
simError(); |
| 92 |
} |
| 93 |
|
| 94 |
if (!simParams->haveViscosity()) { |
| 95 |
sprintf(painCave.errMsg, |
| 96 |
"SMIPDynamics error: You can't use the SMIPD integrator\n" |
| 97 |
" without a viscosity!\n"); |
| 98 |
painCave.isFatal = 1; |
| 99 |
painCave.severity = OOPSE_ERROR; |
| 100 |
simError(); |
| 101 |
}else{ |
| 102 |
viscosity_ = simParams->getViscosity(); |
| 103 |
} |
| 104 |
|
| 105 |
dt_ = simParams->getDt(); |
| 106 |
|
| 107 |
variance_ = 2.0 * OOPSEConstant::kb * targetTemp_ / dt_; |
| 108 |
|
| 109 |
// Build a vector of integrable objects to determine if the are |
| 110 |
// surface atoms |
| 111 |
Molecule* mol; |
| 112 |
StuntDouble* integrableObject; |
| 113 |
SimInfo::MoleculeIterator i; |
| 114 |
Molecule::IntegrableObjectIterator j; |
| 115 |
|
| 116 |
for (mol = info_->beginMolecule(i); mol != NULL; |
| 117 |
mol = info_->nextMolecule(i)) { |
| 118 |
for (integrableObject = mol->beginIntegrableObject(j); |
| 119 |
integrableObject != NULL; |
| 120 |
integrableObject = mol->nextIntegrableObject(j)) { |
| 121 |
localSites_.push_back(integrableObject); |
| 122 |
} |
| 123 |
} |
| 124 |
} |
| 125 |
|
| 126 |
void SMIPDForceManager::postCalculation(bool needStress){ |
| 127 |
SimInfo::MoleculeIterator i; |
| 128 |
Molecule::IntegrableObjectIterator j; |
| 129 |
Molecule* mol; |
| 130 |
StuntDouble* integrableObject; |
| 131 |
|
| 132 |
// Compute surface Mesh |
| 133 |
surfaceMesh_->computeHull(localSites_); |
| 134 |
|
| 135 |
// Get total area and number of surface stunt doubles |
| 136 |
RealType area = surfaceMesh_->getArea(); |
| 137 |
int nSurfaceSDs = surfaceMesh_->getNs(); |
| 138 |
std::vector<Triangle> sMesh = surfaceMesh_->getMesh(); |
| 139 |
int nTriangles = sMesh.size(); |
| 140 |
|
| 141 |
// Generate all of the necessary random forces |
| 142 |
std::vector<Vector3d> randNums = genTriangleForces(nTriangles, variance_); |
| 143 |
|
| 144 |
// Loop over the mesh faces and apply external pressure to each |
| 145 |
// of the faces |
| 146 |
std::vector<Triangle>::iterator face; |
| 147 |
std::vector<StuntDouble*>::iterator vertex; |
| 148 |
int thisFacet = 0; |
| 149 |
for (face = sMesh.begin(); face != sMesh.end(); ++face){ |
| 150 |
|
| 151 |
Triangle thisTriangle = *face; |
| 152 |
std::vector<StuntDouble*> vertexSDs = thisTriangle.getVertices(); |
| 153 |
RealType thisArea = thisTriangle.getArea(); |
| 154 |
Vector3d unitNormal = thisTriangle.getNormal(); |
| 155 |
unitNormal.normalize(); |
| 156 |
Vector3d centroid = thisTriangle.getCentroid(); |
| 157 |
Vector3d facetVel = thisTriangle.getFacetVelocity(); |
| 158 |
|
| 159 |
Mat3x3d hydroTensor = thisTriangle.computeHydrodynamicTensor(viscosity_); |
| 160 |
|
| 161 |
hydroTensor *= OOPSEConstant::viscoConvert; |
| 162 |
Mat3x3d S; |
| 163 |
CholeskyDecomposition(hydroTensor, S); |
| 164 |
|
| 165 |
Vector3d extPressure = -unitNormal*(targetPressure_ * thisArea)/OOPSEConstant::energyConvert; |
| 166 |
Vector3d randomForce = S * randNums[thisFacet++]; |
| 167 |
Vector3d dragForce = -hydroTensor * facetVel; |
| 168 |
|
| 169 |
Vector3d langevinForce = (extPressure + randomForce + dragForce); |
| 170 |
|
| 171 |
// Apply triangle force to stuntdouble vertices |
| 172 |
for (vertex = vertexSDs.begin(); vertex != vertexSDs.end(); ++vertex){ |
| 173 |
if ((*vertex) != NULL){ |
| 174 |
Vector3d vertexForce = langevinForce / 3.0; |
| 175 |
(*vertex)->addFrc(vertexForce); |
| 176 |
if ((*vertex)->isDirectional()){ |
| 177 |
Vector3d vertexPos = (*vertex)->getPos(); |
| 178 |
Vector3d vertexCentroidVector = vertexPos - centroid; |
| 179 |
(*vertex)->addTrq(cross(vertexCentroidVector,vertexForce)); |
| 180 |
} |
| 181 |
} |
| 182 |
} |
| 183 |
} |
| 184 |
|
| 185 |
veloMunge->removeComDrift(); |
| 186 |
veloMunge->removeAngularDrift(); |
| 187 |
|
| 188 |
Snapshot* currSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 189 |
currSnapshot->setVolume(surfaceMesh_->getVolume()); |
| 190 |
ForceManager::postCalculation(needStress); |
| 191 |
} |
| 192 |
|
| 193 |
|
| 194 |
std::vector<Vector3d> SMIPDForceManager::genTriangleForces(int nTriangles, |
| 195 |
RealType variance) |
| 196 |
{ |
| 197 |
|
| 198 |
// zero fill the random vector before starting: |
| 199 |
std::vector<Vector3d> gaussRand; |
| 200 |
gaussRand.resize(nTriangles); |
| 201 |
std::fill(gaussRand.begin(), gaussRand.end(), V3Zero); |
| 202 |
|
| 203 |
#ifdef IS_MPI |
| 204 |
if (worldRank == 0) { |
| 205 |
#endif |
| 206 |
RealType rx, ry, rz; |
| 207 |
for (int i = 0; i < nTriangles; i++) { |
| 208 |
rx = randNumGen_.randNorm(0.0, variance); |
| 209 |
ry = randNumGen_.randNorm(0.0, variance); |
| 210 |
rz = randNumGen_.randNorm(0.0, variance); |
| 211 |
gaussRand[i][0] = rx; |
| 212 |
gaussRand[i][1] = ry; |
| 213 |
gaussRand[i][2] = rz; |
| 214 |
} |
| 215 |
#ifdef IS_MPI |
| 216 |
} |
| 217 |
#endif |
| 218 |
|
| 219 |
// push these out to the other processors |
| 220 |
|
| 221 |
#ifdef IS_MPI |
| 222 |
if (worldRank == 0) { |
| 223 |
MPI_Bcast(&gaussRand[0], nTriangles*3 , MPI_REALTYPE, 0, MPI_COMM_WORLD); |
| 224 |
} else { |
| 225 |
MPI_Bcast(&gaussRand[0], nTriangles*3, MPI_REALTYPE, 0, MPI_COMM_WORLD); |
| 226 |
} |
| 227 |
#endif |
| 228 |
|
| 229 |
return gaussRand; |
| 230 |
} |
| 231 |
} |
