| 1 |
< |
/* |
| 1 |
> |
/* |
| 2 |
|
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
|
* |
| 4 |
|
* The University of Notre Dame grants you ("Licensee") a |
| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include <cmath> |
| 46 |
|
#include "io/StatWriter.hpp" |
| 47 |
|
#include "minimizers/Minimizer.hpp" |
| 48 |
|
#include "primitives/Molecule.hpp" |
| 49 |
< |
namespace oopse { |
| 50 |
< |
double dotProduct(const std::vector<double>& v1, const std::vector<double>& v2) { |
| 49 |
> |
#ifdef IS_MPI |
| 50 |
> |
#include <mpi.h> |
| 51 |
> |
#endif |
| 52 |
> |
namespace OpenMD { |
| 53 |
> |
RealType dotProduct(const std::vector<RealType>& v1, const std::vector<RealType>& v2) { |
| 54 |
|
if (v1.size() != v2.size()) { |
| 55 |
|
|
| 56 |
|
} |
| 57 |
|
|
| 58 |
|
|
| 59 |
< |
double result = 0.0; |
| 59 |
> |
RealType result = 0.0; |
| 60 |
|
for (unsigned int i = 0; i < v1.size(); ++i) { |
| 61 |
< |
result += v1[i] * v2[i]; |
| 61 |
> |
result += v1[i] * v2[i]; |
| 62 |
|
} |
| 63 |
|
|
| 64 |
|
return result; |
| 65 |
< |
} |
| 65 |
> |
} |
| 66 |
|
|
| 67 |
< |
Minimizer::Minimizer(SimInfo* rhs) : |
| 67 |
> |
Minimizer::Minimizer(SimInfo* rhs) : |
| 68 |
|
info(rhs), usingShake(false) { |
| 69 |
|
|
| 70 |
< |
forceMan = new ForceManager(info); |
| 71 |
< |
paramSet= new MinimizerParameterSet(info), |
| 72 |
< |
calcDim(); |
| 73 |
< |
curX = getCoor(); |
| 70 |
< |
curG.resize(ndim); |
| 70 |
> |
forceMan = new ForceManager(info); |
| 71 |
> |
paramSet= new MinimizerParameterSet(info), calcDim(); |
| 72 |
> |
curX = getCoor(); |
| 73 |
> |
curG.resize(ndim); |
| 74 |
|
|
| 75 |
< |
} |
| 75 |
> |
} |
| 76 |
|
|
| 77 |
< |
Minimizer::~Minimizer() { |
| 77 |
> |
Minimizer::~Minimizer() { |
| 78 |
|
delete forceMan; |
| 79 |
|
delete paramSet; |
| 80 |
< |
} |
| 80 |
> |
} |
| 81 |
|
|
| 82 |
< |
void Minimizer::calcEnergyGradient(std::vector<double> &x, |
| 83 |
< |
std::vector<double> &grad, double&energy, int&status) { |
| 82 |
> |
void Minimizer::calcEnergyGradient(std::vector<RealType> &x, |
| 83 |
> |
std::vector<RealType> &grad, RealType&energy, int&status) { |
| 84 |
|
|
| 85 |
|
SimInfo::MoleculeIterator i; |
| 86 |
|
Molecule::IntegrableObjectIterator j; |
| 87 |
|
Molecule* mol; |
| 88 |
|
StuntDouble* integrableObject; |
| 89 |
< |
std::vector<double> myGrad; |
| 89 |
> |
std::vector<RealType> myGrad; |
| 90 |
|
int shakeStatus; |
| 91 |
|
|
| 92 |
|
status = 1; |
| 94 |
|
setCoor(x); |
| 95 |
|
|
| 96 |
|
if (usingShake) { |
| 97 |
< |
shakeStatus = shakeR(); |
| 97 |
> |
shakeStatus = shakeR(); |
| 98 |
|
} |
| 99 |
|
|
| 100 |
|
energy = calcPotential(); |
| 101 |
|
|
| 102 |
|
if (usingShake) { |
| 103 |
< |
shakeStatus = shakeF(); |
| 103 |
> |
shakeStatus = shakeF(); |
| 104 |
|
} |
| 105 |
|
|
| 106 |
|
x = getCoor(); |
| 108 |
|
int index = 0; |
| 109 |
|
|
| 110 |
|
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 111 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 112 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 111 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 112 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 113 |
|
|
| 114 |
< |
myGrad = integrableObject->getGrad(); |
| 115 |
< |
for (unsigned int k = 0; k < myGrad.size(); ++k) { |
| 116 |
< |
//gradient is equal to -f |
| 117 |
< |
grad[index++] = -myGrad[k]; |
| 118 |
< |
} |
| 119 |
< |
} |
| 114 |
> |
myGrad = integrableObject->getGrad(); |
| 115 |
> |
for (unsigned int k = 0; k < myGrad.size(); ++k) { |
| 116 |
> |
|
| 117 |
> |
grad[index++] = myGrad[k]; |
| 118 |
> |
} |
| 119 |
> |
} |
| 120 |
|
} |
| 121 |
|
|
| 122 |
< |
} |
| 122 |
> |
} |
| 123 |
|
|
| 124 |
< |
void Minimizer::setCoor(std::vector<double> &x) { |
| 124 |
> |
void Minimizer::setCoor(std::vector<RealType> &x) { |
| 125 |
|
Vector3d position; |
| 126 |
|
Vector3d eulerAngle; |
| 127 |
|
SimInfo::MoleculeIterator i; |
| 131 |
|
int index = 0; |
| 132 |
|
|
| 133 |
|
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 134 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 135 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 134 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 135 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 136 |
|
|
| 137 |
< |
position[0] = x[index++]; |
| 138 |
< |
position[1] = x[index++]; |
| 139 |
< |
position[2] = x[index++]; |
| 137 |
> |
position[0] = x[index++]; |
| 138 |
> |
position[1] = x[index++]; |
| 139 |
> |
position[2] = x[index++]; |
| 140 |
|
|
| 141 |
< |
integrableObject->setPos(position); |
| 141 |
> |
integrableObject->setPos(position); |
| 142 |
|
|
| 143 |
< |
if (integrableObject->isDirectional()) { |
| 144 |
< |
eulerAngle[0] = x[index++]; |
| 145 |
< |
eulerAngle[1] = x[index++]; |
| 146 |
< |
eulerAngle[2] = x[index++]; |
| 143 |
> |
if (integrableObject->isDirectional()) { |
| 144 |
> |
eulerAngle[0] = x[index++]; |
| 145 |
> |
eulerAngle[1] = x[index++]; |
| 146 |
> |
eulerAngle[2] = x[index++]; |
| 147 |
|
|
| 148 |
< |
integrableObject->setEuler(eulerAngle); |
| 149 |
< |
} |
| 150 |
< |
} |
| 148 |
> |
integrableObject->setEuler(eulerAngle); |
| 149 |
> |
} |
| 150 |
> |
} |
| 151 |
|
} |
| 152 |
|
|
| 153 |
< |
} |
| 153 |
> |
} |
| 154 |
|
|
| 155 |
< |
std::vector<double> Minimizer::getCoor() { |
| 155 |
> |
std::vector<RealType> Minimizer::getCoor() { |
| 156 |
|
Vector3d position; |
| 157 |
|
Vector3d eulerAngle; |
| 158 |
|
SimInfo::MoleculeIterator i; |
| 160 |
|
Molecule* mol; |
| 161 |
|
StuntDouble* integrableObject; |
| 162 |
|
int index = 0; |
| 163 |
< |
std::vector<double> x(getDim()); |
| 163 |
> |
std::vector<RealType> x(getDim()); |
| 164 |
|
|
| 165 |
|
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 166 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 167 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 166 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 167 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 168 |
|
|
| 169 |
< |
position = integrableObject->getPos(); |
| 170 |
< |
x[index++] = position[0]; |
| 171 |
< |
x[index++] = position[1]; |
| 172 |
< |
x[index++] = position[2]; |
| 169 |
> |
position = integrableObject->getPos(); |
| 170 |
> |
x[index++] = position[0]; |
| 171 |
> |
x[index++] = position[1]; |
| 172 |
> |
x[index++] = position[2]; |
| 173 |
|
|
| 174 |
< |
if (integrableObject->isDirectional()) { |
| 175 |
< |
eulerAngle = integrableObject->getEuler(); |
| 176 |
< |
x[index++] = eulerAngle[0]; |
| 177 |
< |
x[index++] = eulerAngle[1]; |
| 178 |
< |
x[index++] = eulerAngle[2]; |
| 179 |
< |
} |
| 180 |
< |
} |
| 174 |
> |
if (integrableObject->isDirectional()) { |
| 175 |
> |
eulerAngle = integrableObject->getEuler(); |
| 176 |
> |
x[index++] = eulerAngle[0]; |
| 177 |
> |
x[index++] = eulerAngle[1]; |
| 178 |
> |
x[index++] = eulerAngle[2]; |
| 179 |
> |
} |
| 180 |
> |
} |
| 181 |
|
} |
| 182 |
|
return x; |
| 183 |
< |
} |
| 183 |
> |
} |
| 184 |
|
|
| 185 |
|
|
| 186 |
< |
/* |
| 187 |
< |
int Minimizer::shakeR() { |
| 186 |
> |
/* |
| 187 |
> |
int Minimizer::shakeR() { |
| 188 |
|
int i, j; |
| 189 |
|
|
| 190 |
|
int done; |
| 191 |
|
|
| 192 |
< |
double posA[3], posB[3]; |
| 192 |
> |
RealType posA[3], posB[3]; |
| 193 |
|
|
| 194 |
< |
double velA[3], velB[3]; |
| 194 |
> |
RealType velA[3], velB[3]; |
| 195 |
|
|
| 196 |
< |
double pab[3]; |
| 196 |
> |
RealType pab[3]; |
| 197 |
|
|
| 198 |
< |
double rab[3]; |
| 198 |
> |
RealType rab[3]; |
| 199 |
|
|
| 200 |
|
int a, b, |
| 201 |
< |
ax, ay, |
| 202 |
< |
az, bx, |
| 203 |
< |
by, bz; |
| 201 |
> |
ax, ay, |
| 202 |
> |
az, bx, |
| 203 |
> |
by, bz; |
| 204 |
|
|
| 205 |
< |
double rma, rmb; |
| 205 |
> |
RealType rma, rmb; |
| 206 |
|
|
| 207 |
< |
double dx, dy, |
| 208 |
< |
dz; |
| 207 |
> |
RealType dx, dy, |
| 208 |
> |
dz; |
| 209 |
|
|
| 210 |
< |
double rpab; |
| 210 |
> |
RealType rpab; |
| 211 |
|
|
| 212 |
< |
double rabsq, pabsq, |
| 213 |
< |
rpabsq; |
| 212 |
> |
RealType rabsq, pabsq, |
| 213 |
> |
rpabsq; |
| 214 |
|
|
| 215 |
< |
double diffsq; |
| 215 |
> |
RealType diffsq; |
| 216 |
|
|
| 217 |
< |
double gab; |
| 217 |
> |
RealType gab; |
| 218 |
|
|
| 219 |
|
int iteration; |
| 220 |
|
|
| 221 |
|
for(i = 0; i < nAtoms; i++) { |
| 222 |
< |
moving[i] = 0; |
| 222 |
> |
moving[i] = 0; |
| 223 |
|
|
| 224 |
< |
moved[i] = 1; |
| 224 |
> |
moved[i] = 1; |
| 225 |
|
} |
| 226 |
|
|
| 227 |
|
iteration = 0; |
| 229 |
|
done = 0; |
| 230 |
|
|
| 231 |
|
while (!done && (iteration < maxIteration)) { |
| 232 |
< |
done = 1; |
| 232 |
> |
done = 1; |
| 233 |
|
|
| 234 |
< |
for(i = 0; i < nConstrained; i++) { |
| 235 |
< |
a = constrainedA[i]; |
| 234 |
> |
for(i = 0; i < nConstrained; i++) { |
| 235 |
> |
a = constrainedA[i]; |
| 236 |
|
|
| 237 |
< |
b = constrainedB[i]; |
| 237 |
> |
b = constrainedB[i]; |
| 238 |
|
|
| 239 |
< |
ax = (a * 3) + 0; |
| 239 |
> |
ax = (a * 3) + 0; |
| 240 |
|
|
| 241 |
< |
ay = (a * 3) + 1; |
| 241 |
> |
ay = (a * 3) + 1; |
| 242 |
|
|
| 243 |
< |
az = (a * 3) + 2; |
| 243 |
> |
az = (a * 3) + 2; |
| 244 |
|
|
| 245 |
< |
bx = (b * 3) + 0; |
| 245 |
> |
bx = (b * 3) + 0; |
| 246 |
|
|
| 247 |
< |
by = (b * 3) + 1; |
| 247 |
> |
by = (b * 3) + 1; |
| 248 |
|
|
| 249 |
< |
bz = (b * 3) + 2; |
| 247 |
< |
|
| 248 |
< |
if (moved[a] || moved[b]) { |
| 249 |
< |
posA = atoms[a]->getPos(); |
| 249 |
> |
bz = (b * 3) + 2; |
| 250 |
|
|
| 251 |
< |
posB = atoms[b]->getPos(); |
| 251 |
> |
if (moved[a] || moved[b]) { |
| 252 |
> |
posA = atoms[a]->getPos(); |
| 253 |
|
|
| 254 |
< |
for(j = 0; j < 3; j++) |
| 254 |
< |
pab[j] = posA[j] - posB[j]; |
| 254 |
> |
posB = atoms[b]->getPos(); |
| 255 |
|
|
| 256 |
< |
//periodic boundary condition |
| 256 |
> |
for(j = 0; j < 3; j++) |
| 257 |
> |
pab[j] = posA[j] - posB[j]; |
| 258 |
|
|
| 259 |
< |
info->wrapVector(pab); |
| 259 |
> |
//periodic boundary condition |
| 260 |
|
|
| 261 |
< |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
| 261 |
> |
info->wrapVector(pab); |
| 262 |
|
|
| 263 |
< |
rabsq = constrainedDsqr[i]; |
| 263 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
| 264 |
|
|
| 265 |
< |
diffsq = rabsq - pabsq; |
| 265 |
> |
rabsq = constrainedDsqr[i]; |
| 266 |
|
|
| 267 |
< |
// the original rattle code from alan tidesley |
| 267 |
> |
diffsq = rabsq - pabsq; |
| 268 |
|
|
| 269 |
< |
if (fabs(diffsq) > (tol * rabsq * 2)) { |
| 269 |
< |
rab[0] = oldPos[ax] - oldPos[bx]; |
| 269 |
> |
// the original rattle code from alan tidesley |
| 270 |
|
|
| 271 |
< |
rab[1] = oldPos[ay] - oldPos[by]; |
| 271 |
> |
if (fabs(diffsq) > (tol * rabsq * 2)) { |
| 272 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
| 273 |
|
|
| 274 |
< |
rab[2] = oldPos[az] - oldPos[bz]; |
| 274 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
| 275 |
|
|
| 276 |
< |
info->wrapVector(rab); |
| 276 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
| 277 |
|
|
| 278 |
< |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 278 |
> |
info->wrapVector(rab); |
| 279 |
|
|
| 280 |
< |
rpabsq = rpab * rpab; |
| 280 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 281 |
|
|
| 282 |
< |
if (rpabsq < (rabsq * -diffsq)) { |
| 282 |
> |
rpabsq = rpab * rpab; |
| 283 |
|
|
| 284 |
< |
#ifdef IS_MPI |
| 284 |
> |
if (rpabsq < (rabsq * -diffsq)) { |
| 285 |
|
|
| 286 |
< |
a = atoms[a]->getGlobalIndex(); |
| 286 |
> |
#ifdef IS_MPI |
| 287 |
|
|
| 288 |
< |
b = atoms[b]->getGlobalIndex(); |
| 288 |
> |
a = atoms[a]->getGlobalIndex(); |
| 289 |
|
|
| 290 |
< |
#endif //is_mpi |
| 290 |
> |
b = atoms[b]->getGlobalIndex(); |
| 291 |
|
|
| 292 |
< |
//std::cerr << "Waring: constraint failure" << std::endl; |
| 292 |
> |
#endif //is_mpi |
| 293 |
|
|
| 294 |
< |
gab = sqrt(rabsq / pabsq); |
| 294 |
> |
//std::cerr << "Waring: constraint failure" << std::endl; |
| 295 |
|
|
| 296 |
< |
rab[0] = (posA[0] - posB[0]) |
| 296 |
< |
* gab; |
| 296 |
> |
gab = sqrt(rabsq / pabsq); |
| 297 |
|
|
| 298 |
< |
rab[1] = (posA[1] - posB[1]) |
| 299 |
< |
* gab; |
| 298 |
> |
rab[0] = (posA[0] - posB[0]) |
| 299 |
> |
* gab; |
| 300 |
|
|
| 301 |
< |
rab[2] = (posA[2] - posB[2]) |
| 302 |
< |
* gab; |
| 301 |
> |
rab[1] = (posA[1] - posB[1]) |
| 302 |
> |
* gab; |
| 303 |
|
|
| 304 |
< |
info->wrapVector(rab); |
| 304 |
> |
rab[2] = (posA[2] - posB[2]) |
| 305 |
> |
* gab; |
| 306 |
|
|
| 307 |
< |
rpab = |
| 307 |
< |
rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 308 |
< |
} |
| 307 |
> |
info->wrapVector(rab); |
| 308 |
|
|
| 309 |
< |
//rma = 1.0 / atoms[a]->getMass(); |
| 309 |
> |
rpab = |
| 310 |
> |
rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
| 311 |
> |
} |
| 312 |
|
|
| 313 |
< |
//rmb = 1.0 / atoms[b]->getMass(); |
| 313 |
> |
//rma = 1.0 / atoms[a]->getMass(); |
| 314 |
|
|
| 315 |
< |
rma = 1.0; |
| 315 |
> |
//rmb = 1.0 / atoms[b]->getMass(); |
| 316 |
|
|
| 317 |
< |
rmb = 1.0; |
| 317 |
> |
rma = 1.0; |
| 318 |
|
|
| 319 |
< |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 319 |
> |
rmb = 1.0; |
| 320 |
|
|
| 321 |
< |
dx = rab[0]* |
| 321 |
< |
gab; |
| 321 |
> |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
| 322 |
|
|
| 323 |
< |
dy = rab[1]* |
| 324 |
< |
gab; |
| 323 |
> |
dx = rab[0]* |
| 324 |
> |
gab; |
| 325 |
|
|
| 326 |
< |
dz = rab[2]* |
| 327 |
< |
gab; |
| 326 |
> |
dy = rab[1]* |
| 327 |
> |
gab; |
| 328 |
|
|
| 329 |
< |
posA[0] += rma *dx; |
| 329 |
> |
dz = rab[2]* |
| 330 |
> |
gab; |
| 331 |
|
|
| 332 |
< |
posA[1] += rma *dy; |
| 332 |
> |
posA[0] += rma *dx; |
| 333 |
|
|
| 334 |
< |
posA[2] += rma *dz; |
| 334 |
> |
posA[1] += rma *dy; |
| 335 |
|
|
| 336 |
< |
atoms[a]->setPos(posA); |
| 336 |
> |
posA[2] += rma *dz; |
| 337 |
|
|
| 338 |
< |
posB[0] -= rmb *dx; |
| 338 |
> |
atoms[a]->setPos(posA); |
| 339 |
|
|
| 340 |
< |
posB[1] -= rmb *dy; |
| 340 |
> |
posB[0] -= rmb *dx; |
| 341 |
|
|
| 342 |
< |
posB[2] -= rmb *dz; |
| 342 |
> |
posB[1] -= rmb *dy; |
| 343 |
|
|
| 344 |
< |
atoms[b]->setPos(posB); |
| 344 |
> |
posB[2] -= rmb *dz; |
| 345 |
|
|
| 346 |
< |
moving[a] = 1; |
| 346 |
> |
atoms[b]->setPos(posB); |
| 347 |
|
|
| 348 |
< |
moving[b] = 1; |
| 348 |
> |
moving[a] = 1; |
| 349 |
|
|
| 350 |
< |
done = 0; |
| 351 |
< |
} |
| 352 |
< |
} |
| 353 |
< |
} |
| 350 |
> |
moving[b] = 1; |
| 351 |
> |
|
| 352 |
> |
done = 0; |
| 353 |
> |
} |
| 354 |
> |
} |
| 355 |
> |
} |
| 356 |
|
|
| 357 |
< |
for(i = 0; i < nAtoms; i++) { |
| 358 |
< |
moved[i] = moving[i]; |
| 357 |
> |
for(i = 0; i < nAtoms; i++) { |
| 358 |
> |
moved[i] = moving[i]; |
| 359 |
|
|
| 360 |
< |
moving[i] = 0; |
| 361 |
< |
} |
| 360 |
> |
moving[i] = 0; |
| 361 |
> |
} |
| 362 |
|
|
| 363 |
< |
iteration++; |
| 363 |
> |
iteration++; |
| 364 |
|
} |
| 365 |
|
|
| 366 |
|
if (!done) { |
| 367 |
< |
std::cerr << "Waring: can not constraint within maxIteration" |
| 368 |
< |
<< std::endl; |
| 367 |
> |
std::cerr << "Waring: can not constraint within maxIteration" |
| 368 |
> |
<< std::endl; |
| 369 |
|
|
| 370 |
< |
return -1; |
| 370 |
> |
return -1; |
| 371 |
|
} else |
| 372 |
< |
return 1; |
| 373 |
< |
} |
| 372 |
> |
return 1; |
| 373 |
> |
} |
| 374 |
|
|
| 375 |
< |
//remove constraint force along the bond direction |
| 375 |
> |
//remove constraint force along the bond direction |
| 376 |
|
|
| 377 |
|
|
| 378 |
< |
int Minimizer::shakeF() { |
| 378 |
> |
int Minimizer::shakeF() { |
| 379 |
|
int i, j; |
| 380 |
|
|
| 381 |
|
int done; |
| 382 |
|
|
| 383 |
< |
double posA[3], posB[3]; |
| 383 |
> |
RealType posA[3], posB[3]; |
| 384 |
|
|
| 385 |
< |
double frcA[3], frcB[3]; |
| 385 |
> |
RealType frcA[3], frcB[3]; |
| 386 |
|
|
| 387 |
< |
double rab[3], fpab[3]; |
| 387 |
> |
RealType rab[3], fpab[3]; |
| 388 |
|
|
| 389 |
|
int a, b, |
| 390 |
< |
ax, ay, |
| 391 |
< |
az, bx, |
| 392 |
< |
by, bz; |
| 390 |
> |
ax, ay, |
| 391 |
> |
az, bx, |
| 392 |
> |
by, bz; |
| 393 |
|
|
| 394 |
< |
double rma, rmb; |
| 394 |
> |
RealType rma, rmb; |
| 395 |
|
|
| 396 |
< |
double rvab; |
| 396 |
> |
RealType rvab; |
| 397 |
|
|
| 398 |
< |
double gab; |
| 398 |
> |
RealType gab; |
| 399 |
|
|
| 400 |
< |
double rabsq; |
| 400 |
> |
RealType rabsq; |
| 401 |
|
|
| 402 |
< |
double rfab; |
| 402 |
> |
RealType rfab; |
| 403 |
|
|
| 404 |
|
int iteration; |
| 405 |
|
|
| 406 |
|
for(i = 0; i < nAtoms; i++) { |
| 407 |
< |
moving[i] = 0; |
| 407 |
> |
moving[i] = 0; |
| 408 |
|
|
| 409 |
< |
moved[i] = 1; |
| 409 |
> |
moved[i] = 1; |
| 410 |
|
} |
| 411 |
|
|
| 412 |
|
done = 0; |
| 414 |
|
iteration = 0; |
| 415 |
|
|
| 416 |
|
while (!done && (iteration < maxIteration)) { |
| 417 |
< |
done = 1; |
| 417 |
> |
done = 1; |
| 418 |
|
|
| 419 |
< |
for(i = 0; i < nConstrained; i++) { |
| 420 |
< |
a = constrainedA[i]; |
| 419 |
> |
for(i = 0; i < nConstrained; i++) { |
| 420 |
> |
a = constrainedA[i]; |
| 421 |
|
|
| 422 |
< |
b = constrainedB[i]; |
| 422 |
> |
b = constrainedB[i]; |
| 423 |
|
|
| 424 |
< |
ax = (a * 3) + 0; |
| 424 |
> |
ax = (a * 3) + 0; |
| 425 |
|
|
| 426 |
< |
ay = (a * 3) + 1; |
| 426 |
> |
ay = (a * 3) + 1; |
| 427 |
|
|
| 428 |
< |
az = (a * 3) + 2; |
| 428 |
> |
az = (a * 3) + 2; |
| 429 |
|
|
| 430 |
< |
bx = (b * 3) + 0; |
| 430 |
> |
bx = (b * 3) + 0; |
| 431 |
|
|
| 432 |
< |
by = (b * 3) + 1; |
| 432 |
> |
by = (b * 3) + 1; |
| 433 |
|
|
| 434 |
< |
bz = (b * 3) + 2; |
| 434 |
> |
bz = (b * 3) + 2; |
| 435 |
|
|
| 436 |
< |
if (moved[a] || moved[b]) { |
| 437 |
< |
posA = atoms[a]->getPos(); |
| 436 |
> |
if (moved[a] || moved[b]) { |
| 437 |
> |
posA = atoms[a]->getPos(); |
| 438 |
|
|
| 439 |
< |
posB = atoms[b]->getPos(); |
| 439 |
> |
posB = atoms[b]->getPos(); |
| 440 |
|
|
| 441 |
< |
for(j = 0; j < 3; j++) |
| 442 |
< |
rab[j] = posA[j] - posB[j]; |
| 441 |
> |
for(j = 0; j < 3; j++) |
| 442 |
> |
rab[j] = posA[j] - posB[j]; |
| 443 |
|
|
| 444 |
< |
info->wrapVector(rab); |
| 444 |
> |
info->wrapVector(rab); |
| 445 |
|
|
| 446 |
< |
atoms[a]->getFrc(frcA); |
| 446 |
> |
atoms[a]->getFrc(frcA); |
| 447 |
|
|
| 448 |
< |
atoms[b]->getFrc(frcB); |
| 448 |
> |
atoms[b]->getFrc(frcB); |
| 449 |
|
|
| 450 |
< |
//rma = 1.0 / atoms[a]->getMass(); |
| 450 |
> |
//rma = 1.0 / atoms[a]->getMass(); |
| 451 |
|
|
| 452 |
< |
//rmb = 1.0 / atoms[b]->getMass(); |
| 452 |
> |
//rmb = 1.0 / atoms[b]->getMass(); |
| 453 |
|
|
| 454 |
< |
rma = 1.0; |
| 454 |
> |
rma = 1.0; |
| 455 |
|
|
| 456 |
< |
rmb = 1.0; |
| 456 |
> |
rmb = 1.0; |
| 457 |
|
|
| 458 |
< |
fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
| 458 |
> |
fpab[0] = frcA[0] * rma - frcB[0] * rmb; |
| 459 |
|
|
| 460 |
< |
fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
| 460 |
> |
fpab[1] = frcA[1] * rma - frcB[1] * rmb; |
| 461 |
|
|
| 462 |
< |
fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
| 462 |
> |
fpab[2] = frcA[2] * rma - frcB[2] * rmb; |
| 463 |
|
|
| 464 |
< |
gab = fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
| 464 |
> |
gab = fpab[0] * fpab[0] + fpab[1] * fpab[1] + fpab[2] * fpab[2]; |
| 465 |
|
|
| 466 |
< |
if (gab < 1.0) |
| 467 |
< |
gab = 1.0; |
| 466 |
> |
if (gab < 1.0) |
| 467 |
> |
gab = 1.0; |
| 468 |
|
|
| 469 |
< |
rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
| 469 |
> |
rabsq = rab[0] * rab[0] + rab[1] * rab[1] + rab[2] * rab[2]; |
| 470 |
|
|
| 471 |
< |
rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
| 471 |
> |
rfab = rab[0] * fpab[0] + rab[1] * fpab[1] + rab[2] * fpab[2]; |
| 472 |
|
|
| 473 |
< |
if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001) { |
| 474 |
< |
gab = -rfab / (rabsq * (rma + rmb)); |
| 473 |
> |
if (fabs(rfab) > sqrt(rabsq*gab) * 0.00001) { |
| 474 |
> |
gab = -rfab / (rabsq * (rma + rmb)); |
| 475 |
|
|
| 476 |
< |
frcA[0] = rab[0]* |
| 477 |
< |
gab; |
| 476 |
> |
frcA[0] = rab[0]* |
| 477 |
> |
gab; |
| 478 |
|
|
| 479 |
< |
frcA[1] = rab[1]* |
| 480 |
< |
gab; |
| 479 |
> |
frcA[1] = rab[1]* |
| 480 |
> |
gab; |
| 481 |
|
|
| 482 |
< |
frcA[2] = rab[2]* |
| 483 |
< |
gab; |
| 482 |
> |
frcA[2] = rab[2]* |
| 483 |
> |
gab; |
| 484 |
|
|
| 485 |
< |
atoms[a]->addFrc(frcA); |
| 485 |
> |
atoms[a]->addFrc(frcA); |
| 486 |
|
|
| 487 |
< |
frcB[0] = -rab[0]*gab; |
| 487 |
> |
frcB[0] = -rab[0]*gab; |
| 488 |
|
|
| 489 |
< |
frcB[1] = -rab[1]*gab; |
| 489 |
> |
frcB[1] = -rab[1]*gab; |
| 490 |
|
|
| 491 |
< |
frcB[2] = -rab[2]*gab; |
| 491 |
> |
frcB[2] = -rab[2]*gab; |
| 492 |
|
|
| 493 |
< |
atoms[b]->addFrc(frcB); |
| 493 |
> |
atoms[b]->addFrc(frcB); |
| 494 |
|
|
| 495 |
< |
moving[a] = 1; |
| 495 |
> |
moving[a] = 1; |
| 496 |
|
|
| 497 |
< |
moving[b] = 1; |
| 497 |
> |
moving[b] = 1; |
| 498 |
|
|
| 499 |
< |
done = 0; |
| 500 |
< |
} |
| 501 |
< |
} |
| 502 |
< |
} |
| 499 |
> |
done = 0; |
| 500 |
> |
} |
| 501 |
> |
} |
| 502 |
> |
} |
| 503 |
|
|
| 504 |
< |
for(i = 0; i < nAtoms; i++) { |
| 505 |
< |
moved[i] = moving[i]; |
| 504 |
> |
for(i = 0; i < nAtoms; i++) { |
| 505 |
> |
moved[i] = moving[i]; |
| 506 |
|
|
| 507 |
< |
moving[i] = 0; |
| 508 |
< |
} |
| 507 |
> |
moving[i] = 0; |
| 508 |
> |
} |
| 509 |
|
|
| 510 |
< |
iteration++; |
| 510 |
> |
iteration++; |
| 511 |
|
} |
| 512 |
|
|
| 513 |
|
if (!done) { |
| 514 |
< |
std::cerr << "Waring: can not constraint within maxIteration" |
| 515 |
< |
<< std::endl; |
| 514 |
> |
std::cerr << "Waring: can not constraint within maxIteration" |
| 515 |
> |
<< std::endl; |
| 516 |
|
|
| 517 |
< |
return -1; |
| 517 |
> |
return -1; |
| 518 |
|
} else |
| 519 |
< |
return 1; |
| 520 |
< |
} |
| 519 |
> |
return 1; |
| 520 |
> |
} |
| 521 |
|
|
| 522 |
< |
*/ |
| 522 |
> |
*/ |
| 523 |
|
|
| 524 |
< |
//calculate the value of object function |
| 524 |
> |
//calculate the value of object function |
| 525 |
|
|
| 526 |
< |
void Minimizer::calcF() { |
| 526 |
> |
void Minimizer::calcF() { |
| 527 |
|
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
| 528 |
< |
} |
| 528 |
> |
} |
| 529 |
|
|
| 530 |
< |
void Minimizer::calcF(std::vector < double > &x, double&f, int&status) { |
| 531 |
< |
std::vector < double > tempG; |
| 530 |
> |
void Minimizer::calcF(std::vector < RealType > &x, RealType&f, int&status) { |
| 531 |
> |
std::vector < RealType > tempG; |
| 532 |
|
|
| 533 |
|
tempG.resize(x.size()); |
| 534 |
|
|
| 535 |
|
calcEnergyGradient(x, tempG, f, status); |
| 536 |
< |
} |
| 536 |
> |
} |
| 537 |
|
|
| 538 |
< |
//calculate the gradient |
| 538 |
> |
//calculate the gradient |
| 539 |
|
|
| 540 |
< |
void Minimizer::calcG() { |
| 540 |
> |
void Minimizer::calcG() { |
| 541 |
|
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
| 542 |
< |
} |
| 542 |
> |
} |
| 543 |
|
|
| 544 |
< |
void Minimizer::calcG(std::vector<double>& x, std::vector<double>& g, double&f, int&status) { |
| 544 |
> |
void Minimizer::calcG(std::vector<RealType>& x, std::vector<RealType>& g, RealType&f, int&status) { |
| 545 |
|
calcEnergyGradient(x, g, f, status); |
| 546 |
< |
} |
| 546 |
> |
} |
| 547 |
|
|
| 548 |
< |
void Minimizer::calcDim() { |
| 548 |
> |
void Minimizer::calcDim() { |
| 549 |
|
|
| 550 |
|
SimInfo::MoleculeIterator i; |
| 551 |
|
Molecule::IntegrableObjectIterator j; |
| 554 |
|
ndim = 0; |
| 555 |
|
|
| 556 |
|
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 557 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 558 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 557 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 558 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 559 |
|
|
| 560 |
< |
ndim += 3; |
| 560 |
> |
ndim += 3; |
| 561 |
|
|
| 562 |
< |
if (integrableObject->isDirectional()) { |
| 563 |
< |
ndim += 3; |
| 564 |
< |
} |
| 565 |
< |
} |
| 562 |
> |
if (integrableObject->isDirectional()) { |
| 563 |
> |
ndim += 3; |
| 564 |
> |
} |
| 565 |
> |
} |
| 566 |
|
|
| 567 |
|
} |
| 568 |
< |
} |
| 568 |
> |
} |
| 569 |
|
|
| 570 |
< |
void Minimizer::setX(std::vector < double > &x) { |
| 570 |
> |
void Minimizer::setX(std::vector < RealType > &x) { |
| 571 |
|
if (x.size() != ndim) { |
| 572 |
< |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of x and curX does not match\n"); |
| 573 |
< |
painCave.isFatal = 1; |
| 574 |
< |
simError(); |
| 572 |
> |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of x and curX does not match\n"); |
| 573 |
> |
painCave.isFatal = 1; |
| 574 |
> |
simError(); |
| 575 |
|
} |
| 576 |
|
|
| 577 |
|
curX = x; |
| 578 |
< |
} |
| 578 |
> |
} |
| 579 |
|
|
| 580 |
< |
void Minimizer::setG(std::vector < double > &g) { |
| 580 |
> |
void Minimizer::setG(std::vector < RealType > &g) { |
| 581 |
|
if (g.size() != ndim) { |
| 582 |
< |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of g and curG does not match\n"); |
| 583 |
< |
painCave.isFatal = 1; |
| 584 |
< |
simError(); |
| 582 |
> |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of g and curG does not match\n"); |
| 583 |
> |
painCave.isFatal = 1; |
| 584 |
> |
simError(); |
| 585 |
|
} |
| 586 |
|
|
| 587 |
|
curG = g; |
| 588 |
< |
} |
| 588 |
> |
} |
| 589 |
|
|
| 590 |
|
|
| 591 |
< |
/** |
| 591 |
> |
/** |
| 592 |
|
|
| 593 |
< |
* In thoery, we need to find the minimum along the search direction |
| 594 |
< |
* However, function evaluation is too expensive. |
| 595 |
< |
* At the very begining of the problem, we check the search direction and make sure |
| 596 |
< |
* it is a descent direction |
| 597 |
< |
* we will compare the energy of two end points, |
| 598 |
< |
* if the right end point has lower energy, we just take it |
| 599 |
< |
* @todo optimize this line search algorithm |
| 600 |
< |
*/ |
| 593 |
> |
* In thoery, we need to find the minimum along the search direction |
| 594 |
> |
* However, function evaluation is too expensive. |
| 595 |
> |
* At the very begining of the problem, we check the search direction and make sure |
| 596 |
> |
* it is a descent direction |
| 597 |
> |
* we will compare the energy of two end points, |
| 598 |
> |
* if the right end point has lower energy, we just take it |
| 599 |
> |
* @todo optimize this line search algorithm |
| 600 |
> |
*/ |
| 601 |
|
|
| 602 |
< |
int Minimizer::doLineSearch(std::vector<double> &direction, |
| 603 |
< |
double stepSize) { |
| 602 |
> |
int Minimizer::doLineSearch(std::vector<RealType> &direction, |
| 603 |
> |
RealType stepSize) { |
| 604 |
|
|
| 605 |
< |
std::vector<double> xa; |
| 606 |
< |
std::vector<double> xb; |
| 607 |
< |
std::vector<double> xc; |
| 608 |
< |
std::vector<double> ga; |
| 609 |
< |
std::vector<double> gb; |
| 610 |
< |
std::vector<double> gc; |
| 611 |
< |
double fa; |
| 612 |
< |
double fb; |
| 613 |
< |
double fc; |
| 614 |
< |
double a; |
| 615 |
< |
double b; |
| 616 |
< |
double c; |
| 605 |
> |
std::vector<RealType> xa; |
| 606 |
> |
std::vector<RealType> xb; |
| 607 |
> |
std::vector<RealType> xc; |
| 608 |
> |
std::vector<RealType> ga; |
| 609 |
> |
std::vector<RealType> gb; |
| 610 |
> |
std::vector<RealType> gc; |
| 611 |
> |
RealType fa; |
| 612 |
> |
RealType fb; |
| 613 |
> |
RealType fc; |
| 614 |
> |
RealType a; |
| 615 |
> |
RealType b; |
| 616 |
> |
RealType c; |
| 617 |
|
int status; |
| 618 |
< |
double initSlope; |
| 619 |
< |
double slopeA; |
| 620 |
< |
double slopeB; |
| 621 |
< |
double slopeC; |
| 618 |
> |
RealType initSlope; |
| 619 |
> |
RealType slopeA; |
| 620 |
> |
RealType slopeB; |
| 621 |
> |
RealType slopeC; |
| 622 |
|
bool foundLower; |
| 623 |
|
int iter; |
| 624 |
|
int maxLSIter; |
| 625 |
< |
double mu; |
| 626 |
< |
double eta; |
| 627 |
< |
double ftol; |
| 628 |
< |
double lsTol; |
| 625 |
> |
RealType mu; |
| 626 |
> |
RealType eta; |
| 627 |
> |
RealType ftol; |
| 628 |
> |
RealType lsTol; |
| 629 |
|
|
| 630 |
|
xa.resize(ndim); |
| 631 |
|
xb.resize(ndim); |
| 653 |
|
slopeA = 0; |
| 654 |
|
|
| 655 |
|
for(size_t i = 0; i < ndim; i++) { |
| 656 |
< |
slopeA += curG[i] * direction[i]; |
| 656 |
> |
slopeA += curG[i] * direction[i]; |
| 657 |
|
} |
| 658 |
|
|
| 659 |
|
initSlope = slopeA; |
| 662 |
|
|
| 663 |
|
if (slopeA > 0) { |
| 664 |
|
|
| 665 |
< |
for(size_t i = 0; i < ndim; i++) { |
| 666 |
< |
direction[i] = -curG[i]; |
| 667 |
< |
} |
| 665 |
> |
for(size_t i = 0; i < ndim; i++) { |
| 666 |
> |
direction[i] = -curG[i]; |
| 667 |
> |
} |
| 668 |
|
|
| 669 |
< |
for(size_t i = 0; i < ndim; i++) { |
| 670 |
< |
slopeA += curG[i] * direction[i]; |
| 671 |
< |
} |
| 669 |
> |
for(size_t i = 0; i < ndim; i++) { |
| 670 |
> |
slopeA += curG[i] * direction[i]; |
| 671 |
> |
} |
| 672 |
|
|
| 673 |
< |
initSlope = slopeA; |
| 673 |
> |
initSlope = slopeA; |
| 674 |
|
} |
| 675 |
|
|
| 676 |
|
// Take a trial step |
| 677 |
|
|
| 678 |
|
for(size_t i = 0; i < ndim; i++) { |
| 679 |
< |
xc[i] = curX[i] + direction[i]* c; |
| 679 |
> |
xc[i] = curX[i] + direction[i]* c; |
| 680 |
|
} |
| 681 |
|
|
| 682 |
|
calcG(xc, gc, fc, status); |
| 683 |
|
|
| 684 |
|
if (status < 0) { |
| 685 |
< |
if (bVerbose) |
| 686 |
< |
std::cerr << "Function Evaluation Error" << std::endl; |
| 685 |
> |
if (bVerbose) |
| 686 |
> |
std::cerr << "Function Evaluation Error" << std::endl; |
| 687 |
|
} |
| 688 |
|
|
| 689 |
|
//calculate the derivative at c |
| 691 |
|
slopeC = 0; |
| 692 |
|
|
| 693 |
|
for(size_t i = 0; i < ndim; i++) { |
| 694 |
< |
slopeC += gc[i] * direction[i]; |
| 694 |
> |
slopeC += gc[i] * direction[i]; |
| 695 |
|
} |
| 696 |
|
// found a lower point |
| 697 |
|
|
| 698 |
|
if (fc < fa) { |
| 699 |
< |
curX = xc; |
| 699 |
> |
curX = xc; |
| 700 |
|
|
| 701 |
< |
curG = gc; |
| 701 |
> |
curG = gc; |
| 702 |
|
|
| 703 |
< |
curF = fc; |
| 703 |
> |
curF = fc; |
| 704 |
|
|
| 705 |
< |
return LS_SUCCEED; |
| 705 |
> |
return LS_SUCCEED; |
| 706 |
|
} else { |
| 707 |
< |
if (slopeC > 0) |
| 708 |
< |
stepSize *= 0.618034; |
| 707 |
> |
if (slopeC > 0) |
| 708 |
> |
stepSize *= 0.618034; |
| 709 |
|
} |
| 710 |
|
|
| 711 |
|
maxLSIter = paramSet->getLineSearchMaxIteration(); |
| 714 |
|
|
| 715 |
|
do { |
| 716 |
|
|
| 717 |
< |
// Select a new trial point. |
| 717 |
> |
// Select a new trial point. |
| 718 |
|
|
| 719 |
< |
// If the derivatives at points a & c have different sign we use cubic interpolate |
| 719 |
> |
// If the derivatives at points a & c have different sign we use cubic interpolate |
| 720 |
|
|
| 721 |
< |
//if (slopeC > 0){ |
| 721 |
> |
//if (slopeC > 0){ |
| 722 |
|
|
| 723 |
< |
eta = 3 * (fa - fc) / (c - a) + slopeA + slopeC; |
| 723 |
> |
eta = 3 * (fa - fc) / (c - a) + slopeA + slopeC; |
| 724 |
|
|
| 725 |
< |
mu = sqrt(eta * eta - slopeA * slopeC); |
| 725 |
> |
mu = sqrt(eta * eta - slopeA * slopeC); |
| 726 |
|
|
| 727 |
< |
b = a + (c - a) |
| 728 |
< |
* (1 - (slopeC + mu - eta) / (slopeC - slopeA + 2 * mu)); |
| 727 |
> |
b = a + (c - a) |
| 728 |
> |
* (1 - (slopeC + mu - eta) / (slopeC - slopeA + 2 * mu)); |
| 729 |
|
|
| 730 |
< |
if (b < lsTol) { |
| 731 |
< |
break; |
| 732 |
< |
} |
| 730 |
> |
if (b < lsTol) { |
| 731 |
> |
break; |
| 732 |
> |
} |
| 733 |
|
|
| 734 |
< |
//} |
| 734 |
> |
//} |
| 735 |
|
|
| 736 |
< |
// Take a trial step to this new point - new coords in xb |
| 736 |
> |
// Take a trial step to this new point - new coords in xb |
| 737 |
|
|
| 738 |
< |
for(size_t i = 0; i < ndim; i++) { |
| 739 |
< |
xb[i] = curX[i] + direction[i]* b; |
| 740 |
< |
} |
| 738 |
> |
for(size_t i = 0; i < ndim; i++) { |
| 739 |
> |
xb[i] = curX[i] + direction[i]* b; |
| 740 |
> |
} |
| 741 |
|
|
| 742 |
< |
//function evaluation |
| 742 |
> |
//function evaluation |
| 743 |
|
|
| 744 |
< |
calcG(xb, gb, fb, status); |
| 744 |
> |
calcG(xb, gb, fb, status); |
| 745 |
|
|
| 746 |
< |
if (status < 0) { |
| 747 |
< |
if (bVerbose) |
| 748 |
< |
std::cerr << "Function Evaluation Error" << std::endl; |
| 749 |
< |
} |
| 746 |
> |
if (status < 0) { |
| 747 |
> |
if (bVerbose) |
| 748 |
> |
std::cerr << "Function Evaluation Error" << std::endl; |
| 749 |
> |
} |
| 750 |
|
|
| 751 |
< |
//calculate the derivative at c |
| 751 |
> |
//calculate the derivative at c |
| 752 |
|
|
| 753 |
< |
slopeB = 0; |
| 753 |
> |
slopeB = 0; |
| 754 |
|
|
| 755 |
< |
for(size_t i = 0; i < ndim; i++) { |
| 756 |
< |
slopeB += gb[i] * direction[i]; |
| 757 |
< |
} |
| 755 |
> |
for(size_t i = 0; i < ndim; i++) { |
| 756 |
> |
slopeB += gb[i] * direction[i]; |
| 757 |
> |
} |
| 758 |
|
|
| 759 |
< |
//Amijo Rule to stop the line search |
| 759 |
> |
//Amijo Rule to stop the line search |
| 760 |
|
|
| 761 |
< |
if (fb <= curF + initSlope * ftol * b) { |
| 762 |
< |
curF = fb; |
| 761 |
> |
if (fb <= curF + initSlope * ftol * b) { |
| 762 |
> |
curF = fb; |
| 763 |
|
|
| 764 |
< |
curX = xb; |
| 764 |
> |
curX = xb; |
| 765 |
|
|
| 766 |
< |
curG = gb; |
| 766 |
> |
curG = gb; |
| 767 |
|
|
| 768 |
< |
return LS_SUCCEED; |
| 769 |
< |
} |
| 767 |
< |
|
| 768 |
< |
if (slopeB < 0 && fb < fa) { |
| 768 |
> |
return LS_SUCCEED; |
| 769 |
> |
} |
| 770 |
|
|
| 771 |
< |
//replace a by b |
| 771 |
> |
if (slopeB < 0 && fb < fa) { |
| 772 |
|
|
| 773 |
< |
fa = fb; |
| 773 |
> |
//replace a by b |
| 774 |
|
|
| 775 |
< |
a = b; |
| 775 |
> |
fa = fb; |
| 776 |
|
|
| 777 |
< |
slopeA = slopeB; |
| 777 |
> |
a = b; |
| 778 |
|
|
| 779 |
< |
// swap coord a/b |
| 779 |
> |
slopeA = slopeB; |
| 780 |
|
|
| 781 |
< |
std::swap(xa, xb); |
| 781 |
> |
// swap coord a/b |
| 782 |
|
|
| 783 |
< |
std::swap(ga, gb); |
| 783 |
< |
} else { |
| 783 |
> |
std::swap(xa, xb); |
| 784 |
|
|
| 785 |
< |
//replace c by b |
| 785 |
> |
std::swap(ga, gb); |
| 786 |
> |
} else { |
| 787 |
|
|
| 788 |
< |
fc = fb; |
| 788 |
> |
//replace c by b |
| 789 |
|
|
| 790 |
< |
c = b; |
| 790 |
> |
fc = fb; |
| 791 |
|
|
| 792 |
< |
slopeC = slopeB; |
| 792 |
> |
c = b; |
| 793 |
|
|
| 794 |
< |
// swap coord b/c |
| 794 |
> |
slopeC = slopeB; |
| 795 |
|
|
| 796 |
< |
std::swap(gb, gc); |
| 796 |
> |
// swap coord b/c |
| 797 |
|
|
| 798 |
< |
std::swap(xb, xc); |
| 798 |
< |
} |
| 798 |
> |
std::swap(gb, gc); |
| 799 |
|
|
| 800 |
< |
iter++; |
| 800 |
> |
std::swap(xb, xc); |
| 801 |
> |
} |
| 802 |
> |
|
| 803 |
> |
iter++; |
| 804 |
|
} while ((fb > fa || fb > fc) && (iter < maxLSIter)); |
| 805 |
|
|
| 806 |
|
if (fb < curF || iter >= maxLSIter) { |
| 807 |
|
|
| 808 |
< |
//could not find a lower value, we might just go uphill. |
| 808 |
> |
//could not find a lower value, we might just go uphill. |
| 809 |
|
|
| 810 |
< |
return LS_ERROR; |
| 810 |
> |
return LS_ERROR; |
| 811 |
|
} |
| 812 |
|
|
| 813 |
|
//select the end point |
| 814 |
|
|
| 815 |
|
if (fa <= fc) { |
| 816 |
< |
curX = xa; |
| 816 |
> |
curX = xa; |
| 817 |
|
|
| 818 |
< |
curG = ga; |
| 818 |
> |
curG = ga; |
| 819 |
|
|
| 820 |
< |
curF = fa; |
| 820 |
> |
curF = fa; |
| 821 |
|
} else { |
| 822 |
< |
curX = xc; |
| 822 |
> |
curX = xc; |
| 823 |
|
|
| 824 |
< |
curG = gc; |
| 824 |
> |
curG = gc; |
| 825 |
|
|
| 826 |
< |
curF = fc; |
| 826 |
> |
curF = fc; |
| 827 |
|
} |
| 828 |
|
|
| 829 |
|
return LS_SUCCEED; |
| 830 |
< |
} |
| 830 |
> |
} |
| 831 |
|
|
| 832 |
< |
void Minimizer::minimize() { |
| 832 |
> |
void Minimizer::minimize() { |
| 833 |
|
int convgStatus; |
| 834 |
|
int stepStatus; |
| 835 |
|
int maxIter; |
| 836 |
< |
int writeFrq; |
| 836 |
> |
int writeFreq; |
| 837 |
|
int nextWriteIter; |
| 838 |
|
Snapshot* curSnapshot =info->getSnapshotManager()->getCurrentSnapshot(); |
| 839 |
|
DumpWriter dumpWriter(info); |
| 844 |
|
|
| 845 |
|
init(); |
| 846 |
|
|
| 847 |
< |
writeFrq = paramSet->getWriteFrq(); |
| 847 |
> |
writeFreq = paramSet->getWriteFreq(); |
| 848 |
|
|
| 849 |
< |
nextWriteIter = writeFrq; |
| 849 |
> |
nextWriteIter = writeFreq; |
| 850 |
|
|
| 851 |
|
maxIter = paramSet->getMaxIteration(); |
| 852 |
|
|
| 853 |
|
for(curIter = 1; curIter <= maxIter; curIter++) { |
| 854 |
< |
stepStatus = step(); |
| 854 |
> |
stepStatus = step(); |
| 855 |
|
|
| 856 |
< |
//if (usingShake) |
| 857 |
< |
// preMove(); |
| 856 |
> |
//if (usingShake) |
| 857 |
> |
// preMove(); |
| 858 |
|
|
| 859 |
< |
if (stepStatus < 0) { |
| 860 |
< |
saveResult(); |
| 859 |
> |
if (stepStatus < 0) { |
| 860 |
> |
saveResult(); |
| 861 |
|
|
| 862 |
< |
minStatus = MIN_LSERROR; |
| 862 |
> |
minStatus = MIN_LSERROR; |
| 863 |
|
|
| 864 |
< |
std::cerr |
| 865 |
< |
<< "Minimizer Error: line search error, please try a small stepsize" |
| 866 |
< |
<< std::endl; |
| 864 |
> |
std::cerr |
| 865 |
> |
<< "Minimizer Error: line search error, please try a small stepsize" |
| 866 |
> |
<< std::endl; |
| 867 |
|
|
| 868 |
< |
return; |
| 869 |
< |
} |
| 868 |
> |
return; |
| 869 |
> |
} |
| 870 |
|
|
| 871 |
< |
//save snapshot |
| 872 |
< |
info->getSnapshotManager()->advance(); |
| 873 |
< |
//increase time |
| 874 |
< |
curSnapshot->increaseTime(1); |
| 871 |
> |
//save snapshot |
| 872 |
> |
info->getSnapshotManager()->advance(); |
| 873 |
> |
//increase time |
| 874 |
> |
curSnapshot->increaseTime(1); |
| 875 |
|
|
| 876 |
< |
if (curIter == nextWriteIter) { |
| 877 |
< |
nextWriteIter += writeFrq; |
| 878 |
< |
calcF(); |
| 879 |
< |
dumpWriter.writeDump(); |
| 880 |
< |
statWriter.writeStat(curSnapshot->statData); |
| 881 |
< |
} |
| 876 |
> |
if (curIter == nextWriteIter) { |
| 877 |
> |
nextWriteIter += writeFreq; |
| 878 |
> |
calcF(); |
| 879 |
> |
dumpWriter.writeDumpAndEor(); |
| 880 |
> |
statWriter.writeStat(curSnapshot->statData); |
| 881 |
> |
} |
| 882 |
|
|
| 883 |
< |
convgStatus = checkConvg(); |
| 883 |
> |
convgStatus = checkConvg(); |
| 884 |
|
|
| 885 |
< |
if (convgStatus > 0) { |
| 886 |
< |
saveResult(); |
| 885 |
> |
if (convgStatus > 0) { |
| 886 |
> |
saveResult(); |
| 887 |
|
|
| 888 |
< |
minStatus = MIN_CONVERGE; |
| 888 |
> |
minStatus = MIN_CONVERGE; |
| 889 |
|
|
| 890 |
< |
return; |
| 891 |
< |
} |
| 890 |
> |
return; |
| 891 |
> |
} |
| 892 |
|
|
| 893 |
< |
prepareStep(); |
| 893 |
> |
prepareStep(); |
| 894 |
|
} |
| 895 |
|
|
| 896 |
|
if (bVerbose) { |
| 897 |
< |
std::cout << "Minimizer Warning: " << minimizerName |
| 898 |
< |
<< " algorithm did not converge within " << maxIter << " iteration" |
| 899 |
< |
<< std::endl; |
| 897 |
> |
std::cout << "Minimizer Warning: " << minimizerName |
| 898 |
> |
<< " algorithm did not converge within " << maxIter << " iteration" |
| 899 |
> |
<< std::endl; |
| 900 |
|
} |
| 901 |
|
|
| 902 |
|
minStatus = MIN_MAXITER; |
| 903 |
|
|
| 904 |
|
saveResult(); |
| 905 |
< |
} |
| 905 |
> |
} |
| 906 |
|
|
| 907 |
|
|
| 908 |
< |
double Minimizer::calcPotential() { |
| 909 |
< |
forceMan->calcForces(true, false); |
| 908 |
> |
RealType Minimizer::calcPotential() { |
| 909 |
> |
forceMan->calcForces(); |
| 910 |
|
|
| 911 |
|
Snapshot* curSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 912 |
< |
double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
| 913 |
< |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 914 |
< |
double potential; |
| 912 |
> |
RealType potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
| 913 |
> |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 914 |
> |
RealType potential; |
| 915 |
|
|
| 916 |
|
#ifdef IS_MPI |
| 917 |
< |
MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM, |
| 917 |
> |
MPI_Allreduce(&potential_local, &potential, 1, MPI_REALTYPE, MPI_SUM, |
| 918 |
|
MPI_COMM_WORLD); |
| 919 |
|
#else |
| 920 |
|
potential = potential_local; |
| 923 |
|
//save total potential |
| 924 |
|
curSnapshot->statData[Stats::POTENTIAL_ENERGY] = potential; |
| 925 |
|
return potential; |
| 926 |
< |
} |
| 926 |
> |
} |
| 927 |
|
|
| 928 |
|
} |
