| 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) { |
| 51 |
< |
if (v1.size() != v2.size()) { |
| 49 |
> |
#ifdef IS_MPI |
| 50 |
> |
#include <mpi.h> |
| 51 |
> |
#endif |
| 52 |
> |
namespace OpenMD { |
| 53 |
|
|
| 52 |
– |
} |
| 53 |
– |
|
| 54 |
– |
|
| 55 |
– |
double result = 0.0; |
| 56 |
– |
for (unsigned int i = 0; i < v1.size(); ++i) { |
| 57 |
– |
result += v1[i] * v2[i]; |
| 58 |
– |
} |
| 59 |
– |
|
| 60 |
– |
return result; |
| 61 |
– |
} |
| 62 |
– |
|
| 54 |
|
Minimizer::Minimizer(SimInfo* rhs) : |
| 55 |
|
info(rhs), usingShake(false) { |
| 56 |
< |
|
| 57 |
< |
forceMan = new ForceManager(info); |
| 58 |
< |
paramSet= new MinimizerParameterSet(info), |
| 59 |
< |
calcDim(); |
| 60 |
< |
curX = getCoor(); |
| 61 |
< |
curG.resize(ndim); |
| 62 |
< |
|
| 72 |
< |
} |
| 73 |
< |
|
| 56 |
> |
|
| 57 |
> |
forceMan = new ForceManager(info); |
| 58 |
> |
paramSet= new MinimizerParameterSet(info), calcDim(); |
| 59 |
> |
curX = getCoor(); |
| 60 |
> |
curG.resize(ndim); |
| 61 |
> |
} |
| 62 |
> |
|
| 63 |
|
Minimizer::~Minimizer() { |
| 64 |
|
delete forceMan; |
| 65 |
|
delete paramSet; |
| 66 |
|
} |
| 67 |
+ |
|
| 68 |
+ |
// void Minimizer::calcEnergyGradient(std::vector<RealType> &x, |
| 69 |
+ |
// std::vector<RealType> &grad, |
| 70 |
+ |
// RealType&energy, int&status) { |
| 71 |
|
|
| 72 |
< |
void Minimizer::calcEnergyGradient(std::vector<double> &x, |
| 73 |
< |
std::vector<double> &grad, double&energy, int&status) { |
| 72 |
> |
// SimInfo::MoleculeIterator i; |
| 73 |
> |
// Molecule::IntegrableObjectIterator j; |
| 74 |
> |
// Molecule* mol; |
| 75 |
> |
// StuntDouble* integrableObject; |
| 76 |
> |
// std::vector<RealType> myGrad; |
| 77 |
> |
// int shakeStatus; |
| 78 |
|
|
| 79 |
< |
SimInfo::MoleculeIterator i; |
| 83 |
< |
Molecule::IntegrableObjectIterator j; |
| 84 |
< |
Molecule* mol; |
| 85 |
< |
StuntDouble* integrableObject; |
| 86 |
< |
std::vector<double> myGrad; |
| 87 |
< |
int shakeStatus; |
| 79 |
> |
// status = 1; |
| 80 |
|
|
| 81 |
< |
status = 1; |
| 81 |
> |
// setCoor(x); |
| 82 |
|
|
| 83 |
< |
setCoor(x); |
| 83 |
> |
// if (usingShake) { |
| 84 |
> |
// shakeStatus = shakeR(); |
| 85 |
> |
// } |
| 86 |
|
|
| 87 |
< |
if (usingShake) { |
| 94 |
< |
shakeStatus = shakeR(); |
| 95 |
< |
} |
| 87 |
> |
// energy = calcPotential(); |
| 88 |
|
|
| 89 |
< |
energy = calcPotential(); |
| 89 |
> |
// if (usingShake) { |
| 90 |
> |
// shakeStatus = shakeF(); |
| 91 |
> |
// } |
| 92 |
|
|
| 93 |
< |
if (usingShake) { |
| 100 |
< |
shakeStatus = shakeF(); |
| 101 |
< |
} |
| 93 |
> |
// x = getCoordinates(); |
| 94 |
|
|
| 95 |
< |
x = getCoor(); |
| 95 |
> |
// int index = 0; |
| 96 |
|
|
| 97 |
< |
int index = 0; |
| 98 |
< |
|
| 99 |
< |
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 100 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 101 |
< |
integrableObject = mol->nextIntegrableObject(j)) { |
| 102 |
< |
|
| 103 |
< |
myGrad = integrableObject->getGrad(); |
| 104 |
< |
for (unsigned int k = 0; k < myGrad.size(); ++k) { |
| 105 |
< |
|
| 106 |
< |
grad[index++] = myGrad[k]; |
| 107 |
< |
} |
| 108 |
< |
} |
| 117 |
< |
} |
| 118 |
< |
|
| 119 |
< |
} |
| 97 |
> |
// for (mol = info->beginMolecule(i); mol != NULL; |
| 98 |
> |
// mol = info->nextMolecule(i)) { |
| 99 |
> |
// for (integrableObject = mol->beginIntegrableObject(j); |
| 100 |
> |
// integrableObject != NULL; |
| 101 |
> |
// integrableObject = mol->nextIntegrableObject(j)) { |
| 102 |
> |
// myGrad = integrableObject->getGrad(); |
| 103 |
> |
// for (unsigned int k = 0; k < myGrad.size(); ++k) { |
| 104 |
> |
// grad[index++] = myGrad[k]; |
| 105 |
> |
// } |
| 106 |
> |
// } |
| 107 |
> |
// } |
| 108 |
> |
// } |
| 109 |
|
|
| 110 |
< |
void Minimizer::setCoor(std::vector<double> &x) { |
| 110 |
> |
void Minimizer::setCoor(std::vector<RealType> &x) { |
| 111 |
|
Vector3d position; |
| 112 |
|
Vector3d eulerAngle; |
| 113 |
|
SimInfo::MoleculeIterator i; |
| 116 |
|
StuntDouble* integrableObject; |
| 117 |
|
int index = 0; |
| 118 |
|
|
| 119 |
< |
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 120 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 119 |
> |
for (mol = info->beginMolecule(i); mol != NULL; |
| 120 |
> |
mol = info->nextMolecule(i)) { |
| 121 |
> |
for (integrableObject = mol->beginIntegrableObject(j); |
| 122 |
> |
integrableObject != NULL; |
| 123 |
|
integrableObject = mol->nextIntegrableObject(j)) { |
| 124 |
< |
|
| 124 |
> |
|
| 125 |
|
position[0] = x[index++]; |
| 126 |
|
position[1] = x[index++]; |
| 127 |
|
position[2] = x[index++]; |
| 128 |
< |
|
| 128 |
> |
|
| 129 |
|
integrableObject->setPos(position); |
| 130 |
< |
|
| 130 |
> |
|
| 131 |
|
if (integrableObject->isDirectional()) { |
| 132 |
|
eulerAngle[0] = x[index++]; |
| 133 |
|
eulerAngle[1] = x[index++]; |
| 134 |
|
eulerAngle[2] = x[index++]; |
| 135 |
< |
|
| 135 |
> |
|
| 136 |
|
integrableObject->setEuler(eulerAngle); |
| 137 |
|
} |
| 138 |
|
} |
| 139 |
< |
} |
| 149 |
< |
|
| 139 |
> |
} |
| 140 |
|
} |
| 141 |
|
|
| 142 |
< |
std::vector<double> Minimizer::getCoor() { |
| 142 |
> |
std::vector<RealType> Minimizer::getCoor() { |
| 143 |
|
Vector3d position; |
| 144 |
|
Vector3d eulerAngle; |
| 145 |
|
SimInfo::MoleculeIterator i; |
| 147 |
|
Molecule* mol; |
| 148 |
|
StuntDouble* integrableObject; |
| 149 |
|
int index = 0; |
| 150 |
< |
std::vector<double> x(getDim()); |
| 150 |
> |
std::vector<RealType> x(getDim()); |
| 151 |
|
|
| 152 |
< |
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 153 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 152 |
> |
for (mol = info->beginMolecule(i); mol != NULL; |
| 153 |
> |
mol = info->nextMolecule(i)) { |
| 154 |
> |
for (integrableObject = mol->beginIntegrableObject(j); |
| 155 |
> |
integrableObject != NULL; |
| 156 |
|
integrableObject = mol->nextIntegrableObject(j)) { |
| 157 |
< |
|
| 157 |
> |
|
| 158 |
|
position = integrableObject->getPos(); |
| 159 |
|
x[index++] = position[0]; |
| 160 |
|
x[index++] = position[1]; |
| 161 |
|
x[index++] = position[2]; |
| 162 |
< |
|
| 162 |
> |
|
| 163 |
|
if (integrableObject->isDirectional()) { |
| 164 |
|
eulerAngle = integrableObject->getEuler(); |
| 165 |
|
x[index++] = eulerAngle[0]; |
| 170 |
|
} |
| 171 |
|
return x; |
| 172 |
|
} |
| 173 |
< |
|
| 174 |
< |
|
| 173 |
> |
|
| 174 |
> |
|
| 175 |
|
/* |
| 176 |
|
int Minimizer::shakeR() { |
| 177 |
|
int i, j; |
| 178 |
< |
|
| 178 |
> |
|
| 179 |
|
int done; |
| 180 |
|
|
| 181 |
< |
double posA[3], posB[3]; |
| 181 |
> |
RealType posA[3], posB[3]; |
| 182 |
|
|
| 183 |
< |
double velA[3], velB[3]; |
| 183 |
> |
RealType velA[3], velB[3]; |
| 184 |
|
|
| 185 |
< |
double pab[3]; |
| 185 |
> |
RealType pab[3]; |
| 186 |
|
|
| 187 |
< |
double rab[3]; |
| 187 |
> |
RealType rab[3]; |
| 188 |
|
|
| 189 |
|
int a, b, |
| 190 |
|
ax, ay, |
| 191 |
|
az, bx, |
| 192 |
|
by, bz; |
| 193 |
|
|
| 194 |
< |
double rma, rmb; |
| 194 |
> |
RealType rma, rmb; |
| 195 |
|
|
| 196 |
< |
double dx, dy, |
| 196 |
> |
RealType dx, dy, |
| 197 |
|
dz; |
| 198 |
|
|
| 199 |
< |
double rpab; |
| 199 |
> |
RealType rpab; |
| 200 |
|
|
| 201 |
< |
double rabsq, pabsq, |
| 201 |
> |
RealType rabsq, pabsq, |
| 202 |
|
rpabsq; |
| 203 |
|
|
| 204 |
< |
double diffsq; |
| 204 |
> |
RealType diffsq; |
| 205 |
|
|
| 206 |
< |
double gab; |
| 206 |
> |
RealType gab; |
| 207 |
|
|
| 208 |
|
int iteration; |
| 209 |
|
|
| 369 |
|
|
| 370 |
|
int done; |
| 371 |
|
|
| 372 |
< |
double posA[3], posB[3]; |
| 372 |
> |
RealType posA[3], posB[3]; |
| 373 |
|
|
| 374 |
< |
double frcA[3], frcB[3]; |
| 374 |
> |
RealType frcA[3], frcB[3]; |
| 375 |
|
|
| 376 |
< |
double rab[3], fpab[3]; |
| 376 |
> |
RealType rab[3], fpab[3]; |
| 377 |
|
|
| 378 |
|
int a, b, |
| 379 |
|
ax, ay, |
| 380 |
|
az, bx, |
| 381 |
|
by, bz; |
| 382 |
|
|
| 383 |
< |
double rma, rmb; |
| 383 |
> |
RealType rma, rmb; |
| 384 |
|
|
| 385 |
< |
double rvab; |
| 385 |
> |
RealType rvab; |
| 386 |
|
|
| 387 |
< |
double gab; |
| 387 |
> |
RealType gab; |
| 388 |
|
|
| 389 |
< |
double rabsq; |
| 389 |
> |
RealType rabsq; |
| 390 |
|
|
| 391 |
< |
double rfab; |
| 391 |
> |
RealType rfab; |
| 392 |
|
|
| 393 |
|
int iteration; |
| 394 |
|
|
| 513 |
|
//calculate the value of object function |
| 514 |
|
|
| 515 |
|
void Minimizer::calcF() { |
| 516 |
< |
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
| 516 |
> |
egEvalStatus = calcEnergyGradient(curX, curG, curF); |
| 517 |
|
} |
| 518 |
< |
|
| 519 |
< |
void Minimizer::calcF(std::vector < double > &x, double&f, int&status) { |
| 520 |
< |
std::vector < double > tempG; |
| 521 |
< |
|
| 518 |
> |
|
| 519 |
> |
void Minimizer::calcF(std::vector < RealType > &x, RealType&f, int&status) { |
| 520 |
> |
std::vector < RealType > tempG; |
| 521 |
> |
|
| 522 |
|
tempG.resize(x.size()); |
| 523 |
< |
|
| 524 |
< |
calcEnergyGradient(x, tempG, f, status); |
| 523 |
> |
|
| 524 |
> |
status = calcEnergyGradient(x, tempG, f); |
| 525 |
|
} |
| 526 |
< |
|
| 526 |
> |
|
| 527 |
|
//calculate the gradient |
| 528 |
< |
|
| 528 |
> |
|
| 529 |
|
void Minimizer::calcG() { |
| 530 |
< |
calcEnergyGradient(curX, curG, curF, egEvalStatus); |
| 530 |
> |
egEvalStatus = calcEnergyGradient(curX, curG, curF); |
| 531 |
|
} |
| 532 |
< |
|
| 533 |
< |
void Minimizer::calcG(std::vector<double>& x, std::vector<double>& g, double&f, int&status) { |
| 534 |
< |
calcEnergyGradient(x, g, f, status); |
| 532 |
> |
|
| 533 |
> |
void Minimizer::calcG(std::vector<RealType>& x, |
| 534 |
> |
std::vector<RealType>& g, RealType&f, int&status) { |
| 535 |
> |
status = calcEnergyGradient(x, g, f); |
| 536 |
|
} |
| 537 |
< |
|
| 537 |
> |
|
| 538 |
|
void Minimizer::calcDim() { |
| 539 |
< |
|
| 539 |
> |
|
| 540 |
|
SimInfo::MoleculeIterator i; |
| 541 |
|
Molecule::IntegrableObjectIterator j; |
| 542 |
|
Molecule* mol; |
| 543 |
|
StuntDouble* integrableObject; |
| 544 |
|
ndim = 0; |
| 545 |
< |
|
| 546 |
< |
for (mol = info->beginMolecule(i); mol != NULL; mol = info->nextMolecule(i)) { |
| 547 |
< |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 545 |
> |
|
| 546 |
> |
for (mol = info->beginMolecule(i); mol != NULL; |
| 547 |
> |
mol = info->nextMolecule(i)) { |
| 548 |
> |
for (integrableObject = mol->beginIntegrableObject(j); |
| 549 |
> |
integrableObject != NULL; |
| 550 |
|
integrableObject = mol->nextIntegrableObject(j)) { |
| 551 |
< |
|
| 551 |
> |
|
| 552 |
|
ndim += 3; |
| 553 |
< |
|
| 553 |
> |
|
| 554 |
|
if (integrableObject->isDirectional()) { |
| 555 |
|
ndim += 3; |
| 556 |
|
} |
| 557 |
< |
} |
| 563 |
< |
|
| 557 |
> |
} |
| 558 |
|
} |
| 559 |
|
} |
| 560 |
|
|
| 561 |
< |
void Minimizer::setX(std::vector < double > &x) { |
| 561 |
> |
void Minimizer::setX(std::vector<RealType> &x) { |
| 562 |
|
if (x.size() != ndim) { |
| 563 |
< |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of x and curX does not match\n"); |
| 563 |
> |
sprintf(painCave.errMsg, |
| 564 |
> |
"Minimizer setX: dimensions of x and curX do not match\n"); |
| 565 |
|
painCave.isFatal = 1; |
| 566 |
|
simError(); |
| 567 |
|
} |
| 569 |
|
curX = x; |
| 570 |
|
} |
| 571 |
|
|
| 572 |
< |
void Minimizer::setG(std::vector < double > &g) { |
| 572 |
> |
void Minimizer::setG(std::vector <RealType> &g) { |
| 573 |
|
if (g.size() != ndim) { |
| 574 |
< |
sprintf(painCave.errMsg, "Minimizer Error: dimesion of g and curG does not match\n"); |
| 574 |
> |
sprintf(painCave.errMsg, |
| 575 |
> |
"Minimizer setG: dimensions of g and curG do not match\n"); |
| 576 |
|
painCave.isFatal = 1; |
| 577 |
|
simError(); |
| 578 |
|
} |
| 579 |
< |
|
| 579 |
> |
|
| 580 |
|
curG = g; |
| 581 |
|
} |
| 582 |
|
|
| 583 |
|
|
| 584 |
|
/** |
| 585 |
< |
|
| 586 |
< |
* In thoery, we need to find the minimum along the search direction |
| 587 |
< |
* However, function evaluation is too expensive. |
| 588 |
< |
* At the very begining of the problem, we check the search direction and make sure |
| 589 |
< |
* it is a descent direction |
| 590 |
< |
* we will compare the energy of two end points, |
| 595 |
< |
* if the right end point has lower energy, we just take it |
| 596 |
< |
* @todo optimize this line search algorithm |
| 585 |
> |
* In theory, we need to find the minimum along the search direction |
| 586 |
> |
* However, function evaluation is usually too expensive. At the |
| 587 |
> |
* very begining of the problem, we check the search direction and |
| 588 |
> |
* make sure it is a descent direction we will compare the energy of |
| 589 |
> |
* two end points, if the right end point has lower energy, we'll |
| 590 |
> |
* just take it. |
| 591 |
|
*/ |
| 592 |
|
|
| 593 |
< |
int Minimizer::doLineSearch(std::vector<double> &direction, |
| 594 |
< |
double stepSize) { |
| 593 |
> |
int Minimizer::doLineSearch(std::vector<RealType> &direction, |
| 594 |
> |
RealType stepSize) { |
| 595 |
|
|
| 596 |
< |
std::vector<double> xa; |
| 597 |
< |
std::vector<double> xb; |
| 598 |
< |
std::vector<double> xc; |
| 599 |
< |
std::vector<double> ga; |
| 600 |
< |
std::vector<double> gb; |
| 601 |
< |
std::vector<double> gc; |
| 602 |
< |
double fa; |
| 603 |
< |
double fb; |
| 604 |
< |
double fc; |
| 605 |
< |
double a; |
| 606 |
< |
double b; |
| 607 |
< |
double c; |
| 596 |
> |
std::vector<RealType> xa; |
| 597 |
> |
std::vector<RealType> xb; |
| 598 |
> |
std::vector<RealType> xc; |
| 599 |
> |
std::vector<RealType> ga; |
| 600 |
> |
std::vector<RealType> gb; |
| 601 |
> |
std::vector<RealType> gc; |
| 602 |
> |
RealType fa; |
| 603 |
> |
RealType fb; |
| 604 |
> |
RealType fc; |
| 605 |
> |
RealType a; |
| 606 |
> |
RealType b; |
| 607 |
> |
RealType c; |
| 608 |
|
int status; |
| 609 |
< |
double initSlope; |
| 610 |
< |
double slopeA; |
| 611 |
< |
double slopeB; |
| 612 |
< |
double slopeC; |
| 609 |
> |
RealType initSlope; |
| 610 |
> |
RealType slopeA; |
| 611 |
> |
RealType slopeB; |
| 612 |
> |
RealType slopeC; |
| 613 |
|
bool foundLower; |
| 614 |
|
int iter; |
| 615 |
|
int maxLSIter; |
| 616 |
< |
double mu; |
| 617 |
< |
double eta; |
| 618 |
< |
double ftol; |
| 619 |
< |
double lsTol; |
| 616 |
> |
RealType mu; |
| 617 |
> |
RealType eta; |
| 618 |
> |
RealType ftol; |
| 619 |
> |
RealType lsTol; |
| 620 |
|
|
| 621 |
|
xa.resize(ndim); |
| 622 |
|
xb.resize(ndim); |
| 626 |
|
gc.resize(ndim); |
| 627 |
|
|
| 628 |
|
a = 0.0; |
| 635 |
– |
|
| 629 |
|
fa = curF; |
| 637 |
– |
|
| 630 |
|
xa = curX; |
| 639 |
– |
|
| 631 |
|
ga = curG; |
| 632 |
|
|
| 633 |
|
c = a + stepSize; |
| 634 |
|
|
| 635 |
|
ftol = paramSet->getFTol(); |
| 645 |
– |
|
| 636 |
|
lsTol = paramSet->getLineSearchTol(); |
| 637 |
|
|
| 638 |
|
//calculate the derivative at a = 0 |
| 642 |
|
for(size_t i = 0; i < ndim; i++) { |
| 643 |
|
slopeA += curG[i] * direction[i]; |
| 644 |
|
} |
| 645 |
< |
|
| 645 |
> |
|
| 646 |
> |
#ifdef IS_MPI |
| 647 |
> |
// in parallel, we need to add up the contributions from all |
| 648 |
> |
// processors: |
| 649 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &slopeA, 1, MPI::REALTYPE, |
| 650 |
> |
MPI::SUM); |
| 651 |
> |
#endif |
| 652 |
> |
|
| 653 |
|
initSlope = slopeA; |
| 654 |
|
|
| 655 |
|
// if going uphill, use negative gradient as searching direction |
| 664 |
|
slopeA += curG[i] * direction[i]; |
| 665 |
|
} |
| 666 |
|
|
| 667 |
+ |
#ifdef IS_MPI |
| 668 |
+ |
// in parallel, we need to add up the contributions from all |
| 669 |
+ |
// processors: |
| 670 |
+ |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &slopeA, 1, MPI::REALTYPE, |
| 671 |
+ |
MPI::SUM); |
| 672 |
+ |
#endif |
| 673 |
|
initSlope = slopeA; |
| 674 |
|
} |
| 675 |
|
|
| 697 |
|
|
| 698 |
|
if (fc < fa) { |
| 699 |
|
curX = xc; |
| 697 |
– |
|
| 700 |
|
curG = gc; |
| 699 |
– |
|
| 701 |
|
curF = fc; |
| 701 |
– |
|
| 702 |
|
return LS_SUCCEED; |
| 703 |
|
} else { |
| 704 |
|
if (slopeC > 0) |
| 830 |
|
int convgStatus; |
| 831 |
|
int stepStatus; |
| 832 |
|
int maxIter; |
| 833 |
< |
int writeFrq; |
| 833 |
> |
int writeFreq; |
| 834 |
|
int nextWriteIter; |
| 835 |
|
Snapshot* curSnapshot =info->getSnapshotManager()->getCurrentSnapshot(); |
| 836 |
|
DumpWriter dumpWriter(info); |
| 841 |
|
|
| 842 |
|
init(); |
| 843 |
|
|
| 844 |
< |
writeFrq = paramSet->getWriteFrq(); |
| 844 |
> |
writeFreq = paramSet->getWriteFreq(); |
| 845 |
|
|
| 846 |
< |
nextWriteIter = writeFrq; |
| 846 |
> |
nextWriteIter = writeFreq; |
| 847 |
|
|
| 848 |
|
maxIter = paramSet->getMaxIteration(); |
| 849 |
|
|
| 871 |
|
curSnapshot->increaseTime(1); |
| 872 |
|
|
| 873 |
|
if (curIter == nextWriteIter) { |
| 874 |
< |
nextWriteIter += writeFrq; |
| 874 |
> |
nextWriteIter += writeFreq; |
| 875 |
|
calcF(); |
| 876 |
< |
dumpWriter.writeDump(); |
| 876 |
> |
dumpWriter.writeDumpAndEor(); |
| 877 |
|
statWriter.writeStat(curSnapshot->statData); |
| 878 |
|
} |
| 879 |
|
|
| 902 |
|
} |
| 903 |
|
|
| 904 |
|
|
| 905 |
< |
double Minimizer::calcPotential() { |
| 906 |
< |
forceMan->calcForces(true, false); |
| 905 |
> |
RealType Minimizer::calcPotential() { |
| 906 |
> |
forceMan->calcForces(); |
| 907 |
|
|
| 908 |
|
Snapshot* curSnapshot = info->getSnapshotManager()->getCurrentSnapshot(); |
| 909 |
< |
double potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
| 909 |
> |
RealType potential_local = curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] + |
| 910 |
|
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] ; |
| 911 |
< |
double potential; |
| 911 |
> |
RealType potential; |
| 912 |
|
|
| 913 |
|
#ifdef IS_MPI |
| 914 |
< |
MPI_Allreduce(&potential_local, &potential, 1, MPI_DOUBLE, MPI_SUM, |
| 914 |
> |
MPI_Allreduce(&potential_local, &potential, 1, MPI_REALTYPE, MPI_SUM, |
| 915 |
|
MPI_COMM_WORLD); |
| 916 |
|
#else |
| 917 |
|
potential = potential_local; |
