| 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010). | 
| 40 | * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). | 
| 41 | */ | 
| 42 |  | 
| 43 | /** | 
| 44 | * @file Polynomial.hpp | 
| 45 | * @author    teng lin | 
| 46 | * @date  11/16/2004 | 
| 47 | * @version 1.0 | 
| 48 | */ | 
| 49 |  | 
| 50 | #ifndef MATH_POLYNOMIAL_HPP | 
| 51 | #define MATH_POLYNOMIAL_HPP | 
| 52 |  | 
| 53 | #include <iostream> | 
| 54 | #include <list> | 
| 55 | #include <map> | 
| 56 | #include <utility> | 
| 57 | #include <complex> | 
| 58 | #include "config.h" | 
| 59 | #include "math/Eigenvalue.hpp" | 
| 60 |  | 
| 61 | namespace OpenMD { | 
| 62 |  | 
| 63 | template<typename Real> Real fastpow(Real x, int N) { | 
| 64 | Real result(1); //or 1.0? | 
| 65 |  | 
| 66 | for (int i = 0; i < N; ++i) { | 
| 67 | result *= x; | 
| 68 | } | 
| 69 |  | 
| 70 | return result; | 
| 71 | } | 
| 72 |  | 
| 73 | /** | 
| 74 | * @class Polynomial Polynomial.hpp "math/Polynomial.hpp" | 
| 75 | * A generic Polynomial class | 
| 76 | */ | 
| 77 | template<typename Real> | 
| 78 | class Polynomial { | 
| 79 |  | 
| 80 | public: | 
| 81 | typedef Polynomial<Real> PolynomialType; | 
| 82 | typedef int ExponentType; | 
| 83 | typedef Real CoefficientType; | 
| 84 | typedef std::map<ExponentType, CoefficientType> PolynomialPairMap; | 
| 85 | typedef typename PolynomialPairMap::iterator iterator; | 
| 86 | typedef typename PolynomialPairMap::const_iterator const_iterator; | 
| 87 |  | 
| 88 | Polynomial() {} | 
| 89 | Polynomial(Real v) {setCoefficient(0, v);} | 
| 90 | /** | 
| 91 | * Calculates the value of this Polynomial evaluated at the given x value. | 
| 92 | * @return The value of this Polynomial evaluates at the given x value | 
| 93 | * @param x the value of the independent variable for this | 
| 94 | * Polynomial function | 
| 95 | */ | 
| 96 | Real evaluate(const Real& x) { | 
| 97 | Real result = Real(); | 
| 98 | ExponentType exponent; | 
| 99 | CoefficientType coefficient; | 
| 100 |  | 
| 101 | for (iterator i = polyPairMap_.begin(); i != polyPairMap_.end(); ++i) { | 
| 102 | exponent = i->first; | 
| 103 | coefficient = i->second; | 
| 104 | result  += fastpow(x, exponent) * coefficient; | 
| 105 | } | 
| 106 |  | 
| 107 | return result; | 
| 108 | } | 
| 109 |  | 
| 110 | /** | 
| 111 | * Returns the first derivative of this polynomial. | 
| 112 | * @return the first derivative of this polynomial | 
| 113 | * @param x | 
| 114 | */ | 
| 115 | Real evaluateDerivative(const Real& x) { | 
| 116 | Real result = Real(); | 
| 117 | ExponentType exponent; | 
| 118 | CoefficientType coefficient; | 
| 119 |  | 
| 120 | for (iterator i = polyPairMap_.begin(); i != polyPairMap_.end(); ++i) { | 
| 121 | exponent = i->first; | 
| 122 | coefficient = i->second; | 
| 123 | result  += fastpow(x, exponent - 1) * coefficient * exponent; | 
| 124 | } | 
| 125 |  | 
| 126 | return result; | 
| 127 | } | 
| 128 |  | 
| 129 |  | 
| 130 | /** | 
| 131 | * Set the coefficent of the specified exponent, if the | 
| 132 | * coefficient is already there, it will be overwritten. | 
| 133 | * @param exponent exponent of a term in this Polynomial | 
| 134 | * @param coefficient multiplier of a term in this Polynomial | 
| 135 | */ | 
| 136 | void setCoefficient(int exponent, const Real& coefficient) { | 
| 137 | polyPairMap_[exponent] = coefficient; | 
| 138 | } | 
| 139 |  | 
| 140 | /** | 
| 141 | * Set the coefficent of the specified exponent. If the | 
| 142 | * coefficient is already there, just add the new coefficient to | 
| 143 | * the old one, otherwise, just call setCoefficent | 
| 144 | * @param exponent exponent of a term in this Polynomial | 
| 145 | * @param coefficient multiplier of a term in this Polynomial | 
| 146 | */ | 
| 147 | void addCoefficient(int exponent, const Real& coefficient) { | 
| 148 | iterator i = polyPairMap_.find(exponent); | 
| 149 |  | 
| 150 | if (i != end()) { | 
| 151 | i->second += coefficient; | 
| 152 | } else { | 
| 153 | setCoefficient(exponent, coefficient); | 
| 154 | } | 
| 155 | } | 
| 156 |  | 
| 157 | /** | 
| 158 | * Returns the coefficient associated with the given power for | 
| 159 | * this Polynomial. | 
| 160 | * @return the coefficient associated with the given power for | 
| 161 | * this Polynomial | 
| 162 | * @exponent exponent of any term in this Polynomial | 
| 163 | */ | 
| 164 | Real getCoefficient(ExponentType exponent) { | 
| 165 | iterator i = polyPairMap_.find(exponent); | 
| 166 |  | 
| 167 | if (i != end()) { | 
| 168 | return i->second; | 
| 169 | } else { | 
| 170 | return Real(0); | 
| 171 | } | 
| 172 | } | 
| 173 |  | 
| 174 | iterator begin() { | 
| 175 | return polyPairMap_.begin(); | 
| 176 | } | 
| 177 |  | 
| 178 | const_iterator begin() const{ | 
| 179 | return polyPairMap_.begin(); | 
| 180 | } | 
| 181 |  | 
| 182 | iterator end() { | 
| 183 | return polyPairMap_.end(); | 
| 184 | } | 
| 185 |  | 
| 186 | const_iterator end() const{ | 
| 187 | return polyPairMap_.end(); | 
| 188 | } | 
| 189 |  | 
| 190 | iterator find(ExponentType exponent) { | 
| 191 | return polyPairMap_.find(exponent); | 
| 192 | } | 
| 193 |  | 
| 194 | size_t size() { | 
| 195 | return polyPairMap_.size(); | 
| 196 | } | 
| 197 |  | 
| 198 | int degree() { | 
| 199 | int deg = 0; | 
| 200 | for (iterator i = polyPairMap_.begin(); i != polyPairMap_.end(); ++i) { | 
| 201 | if (i->first > deg) | 
| 202 | deg = i->first; | 
| 203 | } | 
| 204 | return deg; | 
| 205 | } | 
| 206 |  | 
| 207 | PolynomialType& operator = (const PolynomialType& p) { | 
| 208 |  | 
| 209 | if (this != &p)  // protect against invalid self-assignment | 
| 210 | { | 
| 211 | typename Polynomial<Real>::const_iterator i; | 
| 212 |  | 
| 213 | polyPairMap_.clear();  // clear out the old map | 
| 214 |  | 
| 215 | for (i =  p.begin(); i != p.end(); ++i) { | 
| 216 | this->setCoefficient(i->first, i->second); | 
| 217 | } | 
| 218 | } | 
| 219 | // by convention, always return *this | 
| 220 | return *this; | 
| 221 | } | 
| 222 |  | 
| 223 | PolynomialType& operator += (const PolynomialType& p) { | 
| 224 | typename Polynomial<Real>::const_iterator i; | 
| 225 |  | 
| 226 | for (i =  p.begin(); i  != p.end(); ++i) { | 
| 227 | this->addCoefficient(i->first, i->second); | 
| 228 | } | 
| 229 |  | 
| 230 | return *this; | 
| 231 | } | 
| 232 |  | 
| 233 | PolynomialType& operator -= (const PolynomialType& p) { | 
| 234 | typename Polynomial<Real>::const_iterator i; | 
| 235 | for (i =  p.begin(); i  != p.end(); ++i) { | 
| 236 | this->addCoefficient(i->first, -i->second); | 
| 237 | } | 
| 238 | return *this; | 
| 239 | } | 
| 240 |  | 
| 241 | PolynomialType& operator *= (const PolynomialType& p) { | 
| 242 | typename Polynomial<Real>::const_iterator i; | 
| 243 | typename Polynomial<Real>::const_iterator j; | 
| 244 | Polynomial<Real> p2(*this); | 
| 245 |  | 
| 246 | polyPairMap_.clear();  // clear out old map | 
| 247 | for (i = p2.begin(); i !=p2.end(); ++i) { | 
| 248 | for (j = p.begin(); j !=p.end(); ++j) { | 
| 249 | this->addCoefficient( i->first + j->first, i->second * j->second); | 
| 250 | } | 
| 251 | } | 
| 252 | return *this; | 
| 253 | } | 
| 254 |  | 
| 255 | //PolynomialType& operator *= (const Real v) | 
| 256 | PolynomialType& operator *= (const Real v) { | 
| 257 | typename Polynomial<Real>::const_iterator i; | 
| 258 | //Polynomial<Real> result; | 
| 259 |  | 
| 260 | for (i = this->begin(); i != this->end(); ++i) { | 
| 261 | this->setCoefficient( i->first, i->second*v); | 
| 262 | } | 
| 263 |  | 
| 264 | return *this; | 
| 265 | } | 
| 266 |  | 
| 267 | PolynomialType& operator += (const Real v) { | 
| 268 | this->addCoefficient( 0, v); | 
| 269 | return *this; | 
| 270 | } | 
| 271 |  | 
| 272 | /** | 
| 273 | * Returns the first derivative of this polynomial. | 
| 274 | * @return the first derivative of this polynomial | 
| 275 | */ | 
| 276 | PolynomialType & getDerivative() { | 
| 277 | Polynomial<Real> p; | 
| 278 |  | 
| 279 | typename Polynomial<Real>::const_iterator i; | 
| 280 | ExponentType exponent; | 
| 281 | CoefficientType coefficient; | 
| 282 |  | 
| 283 | for (i =  this->begin(); i  != this->end(); ++i) { | 
| 284 | exponent = i->first; | 
| 285 | coefficient = i->second; | 
| 286 | p.setCoefficient(exponent-1, coefficient * exponent); | 
| 287 | } | 
| 288 |  | 
| 289 | return p; | 
| 290 | } | 
| 291 |  | 
| 292 | // Creates the Companion matrix for a given polynomial | 
| 293 | DynamicRectMatrix<Real> CreateCompanion() { | 
| 294 | int rank = degree(); | 
| 295 | DynamicRectMatrix<Real> mat(rank, rank); | 
| 296 | Real majorCoeff = getCoefficient(rank); | 
| 297 | for(int i = 0; i < rank; ++i) { | 
| 298 | for(int j = 0; j < rank; ++j) { | 
| 299 | if(i - j == 1) { | 
| 300 | mat(i, j) = 1; | 
| 301 | } else if(j == rank-1) { | 
| 302 | mat(i, j) = -1 * getCoefficient(i) / majorCoeff; | 
| 303 | } | 
| 304 | } | 
| 305 | } | 
| 306 | return mat; | 
| 307 | } | 
| 308 |  | 
| 309 | // Find the Roots of a given polynomial | 
| 310 | std::vector<complex<Real> > FindRoots() { | 
| 311 | int rank = degree(); | 
| 312 | DynamicRectMatrix<Real> companion = CreateCompanion(); | 
| 313 | JAMA::Eigenvalue<Real> eig(companion); | 
| 314 | DynamicVector<Real> reals, imags; | 
| 315 | eig.getRealEigenvalues(reals); | 
| 316 | eig.getImagEigenvalues(imags); | 
| 317 |  | 
| 318 | std::vector<complex<Real> > roots; | 
| 319 | for (int i = 0; i < rank; i++) { | 
| 320 | roots.push_back(complex<Real>(reals(i), imags(i))); | 
| 321 | } | 
| 322 |  | 
| 323 | return roots; | 
| 324 | } | 
| 325 |  | 
| 326 | std::vector<Real> FindRealRoots() { | 
| 327 |  | 
| 328 | const Real fEpsilon = 1.0e-8; | 
| 329 | std::vector<Real> roots; | 
| 330 | roots.clear(); | 
| 331 |  | 
| 332 | const int deg = degree(); | 
| 333 |  | 
| 334 | switch (deg) { | 
| 335 | case 1: { | 
| 336 | Real fC1 = getCoefficient(1); | 
| 337 | Real fC0 = getCoefficient(0); | 
| 338 | roots.push_back( -fC0 / fC1); | 
| 339 | return roots; | 
| 340 | } | 
| 341 | break; | 
| 342 | case 2: { | 
| 343 | Real fC2 = getCoefficient(2); | 
| 344 | Real fC1 = getCoefficient(1); | 
| 345 | Real fC0 = getCoefficient(0); | 
| 346 | Real fDiscr = fC1*fC1 - 4.0*fC0*fC2; | 
| 347 | if (abs(fDiscr) <= fEpsilon) { | 
| 348 | fDiscr = (Real)0.0; | 
| 349 | } | 
| 350 |  | 
| 351 | if (fDiscr < (Real)0.0) {  // complex roots only | 
| 352 | return roots; | 
| 353 | } | 
| 354 |  | 
| 355 | Real fTmp = ((Real)0.5)/fC2; | 
| 356 |  | 
| 357 | if (fDiscr > (Real)0.0) { // 2 real roots | 
| 358 | fDiscr = sqrt(fDiscr); | 
| 359 | roots.push_back(fTmp*(-fC1 - fDiscr)); | 
| 360 | roots.push_back(fTmp*(-fC1 + fDiscr)); | 
| 361 | } else { | 
| 362 | roots.push_back(-fTmp * fC1);  // 1 real root | 
| 363 | } | 
| 364 | } | 
| 365 | return roots; | 
| 366 | break; | 
| 367 |  | 
| 368 | case 3: { | 
| 369 | Real fC3 = getCoefficient(3); | 
| 370 | Real fC2 = getCoefficient(2); | 
| 371 | Real fC1 = getCoefficient(1); | 
| 372 | Real fC0 = getCoefficient(0); | 
| 373 |  | 
| 374 | // make polynomial monic, x^3+c2*x^2+c1*x+c0 | 
| 375 | Real fInvC3 = ((Real)1.0)/fC3; | 
| 376 | fC0 *= fInvC3; | 
| 377 | fC1 *= fInvC3; | 
| 378 | fC2 *= fInvC3; | 
| 379 |  | 
| 380 | // convert to y^3+a*y+b = 0 by x = y-c2/3 | 
| 381 | const Real fThird = (Real)1.0/(Real)3.0; | 
| 382 | const Real fTwentySeventh = (Real)1.0/(Real)27.0; | 
| 383 | Real fOffset = fThird*fC2; | 
| 384 | Real fA = fC1 - fC2*fOffset; | 
| 385 | Real fB = fC0+fC2*(((Real)2.0)*fC2*fC2-((Real)9.0)*fC1)*fTwentySeventh; | 
| 386 | Real fHalfB = ((Real)0.5)*fB; | 
| 387 |  | 
| 388 | Real fDiscr = fHalfB*fHalfB + fA*fA*fA*fTwentySeventh; | 
| 389 | if (fabs(fDiscr) <= fEpsilon) { | 
| 390 | fDiscr = (Real)0.0; | 
| 391 | } | 
| 392 |  | 
| 393 | if (fDiscr > (Real)0.0) {  // 1 real, 2 complex roots | 
| 394 |  | 
| 395 | fDiscr = sqrt(fDiscr); | 
| 396 | Real fTemp = -fHalfB + fDiscr; | 
| 397 | Real root; | 
| 398 | if (fTemp >= (Real)0.0) { | 
| 399 | root = pow(fTemp,fThird); | 
| 400 | } else { | 
| 401 | root = -pow(-fTemp,fThird); | 
| 402 | } | 
| 403 | fTemp = -fHalfB - fDiscr; | 
| 404 | if ( fTemp >= (Real)0.0 ) { | 
| 405 | root += pow(fTemp,fThird); | 
| 406 | } else { | 
| 407 | root -= pow(-fTemp,fThird); | 
| 408 | } | 
| 409 | root -= fOffset; | 
| 410 |  | 
| 411 | roots.push_back(root); | 
| 412 | } else if (fDiscr < (Real)0.0) { | 
| 413 | const Real fSqrt3 = sqrt((Real)3.0); | 
| 414 | Real fDist = sqrt(-fThird*fA); | 
| 415 | Real fAngle = fThird*atan2(sqrt(-fDiscr), -fHalfB); | 
| 416 | Real fCos = cos(fAngle); | 
| 417 | Real fSin = sin(fAngle); | 
| 418 | roots.push_back(((Real)2.0)*fDist*fCos-fOffset); | 
| 419 | roots.push_back(-fDist*(fCos+fSqrt3*fSin)-fOffset); | 
| 420 | roots.push_back(-fDist*(fCos-fSqrt3*fSin)-fOffset); | 
| 421 | } else { | 
| 422 | Real fTemp; | 
| 423 | if (fHalfB >= (Real)0.0) { | 
| 424 | fTemp = -pow(fHalfB,fThird); | 
| 425 | } else { | 
| 426 | fTemp = pow(-fHalfB,fThird); | 
| 427 | } | 
| 428 | roots.push_back(((Real)2.0)*fTemp-fOffset); | 
| 429 | roots.push_back(-fTemp-fOffset); | 
| 430 | roots.push_back(-fTemp-fOffset); | 
| 431 | } | 
| 432 | } | 
| 433 | return roots; | 
| 434 | break; | 
| 435 | case 4: { | 
| 436 | Real fC4 = getCoefficient(4); | 
| 437 | Real fC3 = getCoefficient(3); | 
| 438 | Real fC2 = getCoefficient(2); | 
| 439 | Real fC1 = getCoefficient(1); | 
| 440 | Real fC0 = getCoefficient(0); | 
| 441 |  | 
| 442 | // make polynomial monic, x^4+c3*x^3+c2*x^2+c1*x+c0 | 
| 443 | Real fInvC4 = ((Real)1.0)/fC4; | 
| 444 | fC0 *= fInvC4; | 
| 445 | fC1 *= fInvC4; | 
| 446 | fC2 *= fInvC4; | 
| 447 | fC3 *= fInvC4; | 
| 448 |  | 
| 449 | // reduction to resolvent cubic polynomial y^3+r2*y^2+r1*y+r0 = 0 | 
| 450 | Real fR0 = -fC3*fC3*fC0 + ((Real)4.0)*fC2*fC0 - fC1*fC1; | 
| 451 | Real fR1 = fC3*fC1 - ((Real)4.0)*fC0; | 
| 452 | Real fR2 = -fC2; | 
| 453 | Polynomial<Real> tempCubic; | 
| 454 | tempCubic.setCoefficient(0, fR0); | 
| 455 | tempCubic.setCoefficient(1, fR1); | 
| 456 | tempCubic.setCoefficient(2, fR2); | 
| 457 | tempCubic.setCoefficient(3, 1.0); | 
| 458 | std::vector<Real> cubeRoots = tempCubic.FindRealRoots(); // always | 
| 459 | // produces | 
| 460 | // at | 
| 461 | // least | 
| 462 | // one | 
| 463 | // root | 
| 464 | Real fY = cubeRoots[0]; | 
| 465 |  | 
| 466 | Real fDiscr = ((Real)0.25)*fC3*fC3 - fC2 + fY; | 
| 467 | if (fabs(fDiscr) <= fEpsilon) { | 
| 468 | fDiscr = (Real)0.0; | 
| 469 | } | 
| 470 |  | 
| 471 | if (fDiscr > (Real)0.0) { | 
| 472 | Real fR = sqrt(fDiscr); | 
| 473 | Real fT1 = ((Real)0.75)*fC3*fC3 - fR*fR - ((Real)2.0)*fC2; | 
| 474 | Real fT2 = (((Real)4.0)*fC3*fC2 - ((Real)8.0)*fC1 - fC3*fC3*fC3) / | 
| 475 | (((Real)4.0)*fR); | 
| 476 |  | 
| 477 | Real fTplus = fT1+fT2; | 
| 478 | Real fTminus = fT1-fT2; | 
| 479 | if (fabs(fTplus) <= fEpsilon) { | 
| 480 | fTplus = (Real)0.0; | 
| 481 | } | 
| 482 | if (fabs(fTminus) <= fEpsilon) { | 
| 483 | fTminus = (Real)0.0; | 
| 484 | } | 
| 485 |  | 
| 486 | if (fTplus >= (Real)0.0) { | 
| 487 | Real fD = sqrt(fTplus); | 
| 488 | roots.push_back(-((Real)0.25)*fC3+((Real)0.5)*(fR+fD)); | 
| 489 | roots.push_back(-((Real)0.25)*fC3+((Real)0.5)*(fR-fD)); | 
| 490 | } | 
| 491 | if (fTminus >= (Real)0.0) { | 
| 492 | Real fE = sqrt(fTminus); | 
| 493 | roots.push_back(-((Real)0.25)*fC3+((Real)0.5)*(fE-fR)); | 
| 494 | roots.push_back(-((Real)0.25)*fC3-((Real)0.5)*(fE+fR)); | 
| 495 | } | 
| 496 | } else if (fDiscr < (Real)0.0) { | 
| 497 | //roots.clear(); | 
| 498 | } else { | 
| 499 | Real fT2 = fY*fY-((Real)4.0)*fC0; | 
| 500 | if (fT2 >= -fEpsilon) { | 
| 501 | if (fT2 < (Real)0.0) { // round to zero | 
| 502 | fT2 = (Real)0.0; | 
| 503 | } | 
| 504 | fT2 = ((Real)2.0)*sqrt(fT2); | 
| 505 | Real fT1 = ((Real)0.75)*fC3*fC3 - ((Real)2.0)*fC2; | 
| 506 | if (fT1+fT2 >= fEpsilon) { | 
| 507 | Real fD = sqrt(fT1+fT2); | 
| 508 | roots.push_back( -((Real)0.25)*fC3+((Real)0.5)*fD); | 
| 509 | roots.push_back( -((Real)0.25)*fC3-((Real)0.5)*fD); | 
| 510 | } | 
| 511 | if (fT1-fT2 >= fEpsilon) { | 
| 512 | Real fE = sqrt(fT1-fT2); | 
| 513 | roots.push_back( -((Real)0.25)*fC3+((Real)0.5)*fE); | 
| 514 | roots.push_back( -((Real)0.25)*fC3-((Real)0.5)*fE); | 
| 515 | } | 
| 516 | } | 
| 517 | } | 
| 518 | } | 
| 519 | return roots; | 
| 520 | break; | 
| 521 | default: { | 
| 522 | DynamicRectMatrix<Real> companion = CreateCompanion(); | 
| 523 | JAMA::Eigenvalue<Real> eig(companion); | 
| 524 | DynamicVector<Real> reals, imags; | 
| 525 | eig.getRealEigenvalues(reals); | 
| 526 | eig.getImagEigenvalues(imags); | 
| 527 |  | 
| 528 | for (int i = 0; i < deg; i++) { | 
| 529 | if (fabs(imags(i)) < fEpsilon) | 
| 530 | roots.push_back(reals(i)); | 
| 531 | } | 
| 532 | } | 
| 533 | return roots; | 
| 534 | break; | 
| 535 | } | 
| 536 |  | 
| 537 | return roots; // should be empty if you got here | 
| 538 | } | 
| 539 |  | 
| 540 | private: | 
| 541 |  | 
| 542 | PolynomialPairMap polyPairMap_; | 
| 543 | }; | 
| 544 |  | 
| 545 |  | 
| 546 | /** | 
| 547 | * Generates and returns the product of two given Polynomials. | 
| 548 | * @return A Polynomial containing the product of the two given Polynomial parameters | 
| 549 | */ | 
| 550 | template<typename Real> | 
| 551 | Polynomial<Real> operator *(const Polynomial<Real>& p1, const Polynomial<Real>& p2) { | 
| 552 | typename Polynomial<Real>::const_iterator i; | 
| 553 | typename Polynomial<Real>::const_iterator j; | 
| 554 | Polynomial<Real> p; | 
| 555 |  | 
| 556 | for (i = p1.begin(); i !=p1.end(); ++i) { | 
| 557 | for (j = p2.begin(); j !=p2.end(); ++j) { | 
| 558 | p.addCoefficient( i->first + j->first, i->second * j->second); | 
| 559 | } | 
| 560 | } | 
| 561 |  | 
| 562 | return p; | 
| 563 | } | 
| 564 |  | 
| 565 | template<typename Real> | 
| 566 | Polynomial<Real> operator *(const Polynomial<Real>& p, const Real v) { | 
| 567 | typename Polynomial<Real>::const_iterator i; | 
| 568 | Polynomial<Real> result; | 
| 569 |  | 
| 570 | for (i = p.begin(); i !=p.end(); ++i) { | 
| 571 | result.setCoefficient( i->first , i->second * v); | 
| 572 | } | 
| 573 |  | 
| 574 | return result; | 
| 575 | } | 
| 576 |  | 
| 577 | template<typename Real> | 
| 578 | Polynomial<Real> operator *( const Real v, const Polynomial<Real>& p) { | 
| 579 | typename Polynomial<Real>::const_iterator i; | 
| 580 | Polynomial<Real> result; | 
| 581 |  | 
| 582 | for (i = p.begin(); i !=p.end(); ++i) { | 
| 583 | result.setCoefficient( i->first , i->second * v); | 
| 584 | } | 
| 585 |  | 
| 586 | return result; | 
| 587 | } | 
| 588 |  | 
| 589 | /** | 
| 590 | * Generates and returns the sum of two given Polynomials. | 
| 591 | * @param p1 the first polynomial | 
| 592 | * @param p2 the second polynomial | 
| 593 | */ | 
| 594 | template<typename Real> | 
| 595 | Polynomial<Real> operator +(const Polynomial<Real>& p1, const Polynomial<Real>& p2) { | 
| 596 | Polynomial<Real> p(p1); | 
| 597 |  | 
| 598 | typename Polynomial<Real>::const_iterator i; | 
| 599 |  | 
| 600 | for (i =  p2.begin(); i  != p2.end(); ++i) { | 
| 601 | p.addCoefficient(i->first, i->second); | 
| 602 | } | 
| 603 |  | 
| 604 | return p; | 
| 605 |  | 
| 606 | } | 
| 607 |  | 
| 608 | /** | 
| 609 | * Generates and returns the difference of two given Polynomials. | 
| 610 | * @return | 
| 611 | * @param p1 the first polynomial | 
| 612 | * @param p2 the second polynomial | 
| 613 | */ | 
| 614 | template<typename Real> | 
| 615 | Polynomial<Real> operator -(const Polynomial<Real>& p1, const Polynomial<Real>& p2) { | 
| 616 | Polynomial<Real> p(p1); | 
| 617 |  | 
| 618 | typename Polynomial<Real>::const_iterator i; | 
| 619 |  | 
| 620 | for (i =  p2.begin(); i  != p2.end(); ++i) { | 
| 621 | p.addCoefficient(i->first, -i->second); | 
| 622 | } | 
| 623 |  | 
| 624 | return p; | 
| 625 |  | 
| 626 | } | 
| 627 |  | 
| 628 | /** | 
| 629 | * Returns the first derivative of this polynomial. | 
| 630 | * @return the first derivative of this polynomial | 
| 631 | */ | 
| 632 | template<typename Real> | 
| 633 | Polynomial<Real> getDerivative(const Polynomial<Real>& p1) { | 
| 634 | Polynomial<Real> p; | 
| 635 |  | 
| 636 | typename Polynomial<Real>::const_iterator i; | 
| 637 | int exponent; | 
| 638 | Real coefficient; | 
| 639 |  | 
| 640 | for (i =  p1.begin(); i  != p1.end(); ++i) { | 
| 641 | exponent = i->first; | 
| 642 | coefficient = i->second; | 
| 643 | p.setCoefficient(exponent-1, coefficient * exponent); | 
| 644 | } | 
| 645 |  | 
| 646 | return p; | 
| 647 | } | 
| 648 |  | 
| 649 | /** | 
| 650 | * Tests if two polynomial have the same exponents | 
| 651 | * @return true if all of the exponents in these Polynomial are identical | 
| 652 | * @param p1 the first polynomial | 
| 653 | * @param p2 the second polynomial | 
| 654 | * @note this function does not compare the coefficient | 
| 655 | */ | 
| 656 | template<typename Real> | 
| 657 | bool equal(const Polynomial<Real>& p1, const Polynomial<Real>& p2) { | 
| 658 |  | 
| 659 | typename Polynomial<Real>::const_iterator i; | 
| 660 | typename Polynomial<Real>::const_iterator j; | 
| 661 |  | 
| 662 | if (p1.size() != p2.size() ) { | 
| 663 | return false; | 
| 664 | } | 
| 665 |  | 
| 666 | for (i =  p1.begin(), j = p2.begin(); i  != p1.end() && j != p2.end(); ++i, ++j) { | 
| 667 | if (i->first != j->first) { | 
| 668 | return false; | 
| 669 | } | 
| 670 | } | 
| 671 |  | 
| 672 | return true; | 
| 673 | } | 
| 674 |  | 
| 675 |  | 
| 676 |  | 
| 677 | typedef Polynomial<RealType> DoublePolynomial; | 
| 678 |  | 
| 679 | } //end namespace OpenMD | 
| 680 | #endif //MATH_POLYNOMIAL_HPP |