| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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 ForceField.cpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/04/2004 |
| 46 |
– |
* @time 22:51am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 50 |
|
#include <algorithm> |
| 51 |
< |
#include "UseTheForce/ForceField.hpp" |
| 51 |
> |
#include "brains/ForceField.hpp" |
| 52 |
|
#include "utils/simError.h" |
| 53 |
< |
#include "utils/Tuple.hpp" |
| 53 |
> |
|
| 54 |
> |
#include "io/OptionSectionParser.hpp" |
| 55 |
> |
#include "io/BaseAtomTypesSectionParser.hpp" |
| 56 |
> |
#include "io/DirectionalAtomTypesSectionParser.hpp" |
| 57 |
> |
#include "io/AtomTypesSectionParser.hpp" |
| 58 |
> |
#include "io/BendTypesSectionParser.hpp" |
| 59 |
> |
#include "io/BondTypesSectionParser.hpp" |
| 60 |
> |
#include "io/ChargeAtomTypesSectionParser.hpp" |
| 61 |
> |
#include "io/EAMAtomTypesSectionParser.hpp" |
| 62 |
> |
#include "io/FluctuatingChargeAtomTypesSectionParser.hpp" |
| 63 |
> |
#include "io/GayBerneAtomTypesSectionParser.hpp" |
| 64 |
> |
#include "io/InversionTypesSectionParser.hpp" |
| 65 |
> |
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
| 66 |
> |
#include "io/MultipoleAtomTypesSectionParser.hpp" |
| 67 |
> |
#include "io/NonBondedInteractionsSectionParser.hpp" |
| 68 |
> |
#include "io/PolarizableAtomTypesSectionParser.hpp" |
| 69 |
> |
#include "io/SCAtomTypesSectionParser.hpp" |
| 70 |
> |
#include "io/ShapeAtomTypesSectionParser.hpp" |
| 71 |
> |
#include "io/StickyAtomTypesSectionParser.hpp" |
| 72 |
> |
#include "io/StickyPowerAtomTypesSectionParser.hpp" |
| 73 |
> |
#include "io/TorsionTypesSectionParser.hpp" |
| 74 |
> |
|
| 75 |
> |
#include "types/LennardJonesAdapter.hpp" |
| 76 |
> |
#include "types/EAMAdapter.hpp" |
| 77 |
> |
#include "types/SuttonChenAdapter.hpp" |
| 78 |
> |
#include "types/GayBerneAdapter.hpp" |
| 79 |
> |
#include "types/StickyAdapter.hpp" |
| 80 |
> |
|
| 81 |
|
namespace OpenMD { |
| 82 |
|
|
| 83 |
< |
ForceField::ForceField() { |
| 83 |
> |
ForceField::ForceField(std::string ffName) { |
| 84 |
|
|
| 85 |
|
char* tempPath; |
| 86 |
|
tempPath = getenv("FORCE_PARAM_PATH"); |
| 90 |
|
STR_DEFINE(ffPath_, FRC_PATH ); |
| 91 |
|
} else { |
| 92 |
|
ffPath_ = tempPath; |
| 93 |
+ |
} |
| 94 |
+ |
|
| 95 |
+ |
setForceFieldFileName(ffName + ".frc"); |
| 96 |
+ |
|
| 97 |
+ |
/** |
| 98 |
+ |
* The order of adding section parsers is important. |
| 99 |
+ |
* |
| 100 |
+ |
* OptionSectionParser must come first to set options for other |
| 101 |
+ |
* parsers |
| 102 |
+ |
* |
| 103 |
+ |
* DirectionalAtomTypesSectionParser should be added before |
| 104 |
+ |
* AtomTypesSectionParser, and these two section parsers will |
| 105 |
+ |
* actually create "real" AtomTypes (AtomTypesSectionParser will |
| 106 |
+ |
* create AtomType and DirectionalAtomTypesSectionParser will |
| 107 |
+ |
* create DirectionalAtomType, which is a subclass of AtomType and |
| 108 |
+ |
* should come first). |
| 109 |
+ |
* |
| 110 |
+ |
* Other AtomTypes Section Parsers will not create the "real" |
| 111 |
+ |
* AtomType, they only add and set some attributes of the AtomType |
| 112 |
+ |
* (via the Adapters). Thus ordering of these is not important. |
| 113 |
+ |
* AtomTypesSectionParser should be added before other atom type |
| 114 |
+ |
* |
| 115 |
+ |
* The order of BondTypesSectionParser, BendTypesSectionParser and |
| 116 |
+ |
* TorsionTypesSectionParser, etc. are not important. |
| 117 |
+ |
*/ |
| 118 |
+ |
|
| 119 |
+ |
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 120 |
+ |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 121 |
+ |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
| 122 |
+ |
spMan_.push_back(new AtomTypesSectionParser()); |
| 123 |
+ |
|
| 124 |
+ |
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
| 125 |
+ |
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
| 126 |
+ |
spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
| 127 |
+ |
spMan_.push_back(new FluctuatingChargeAtomTypesSectionParser(forceFieldOptions_)); |
| 128 |
+ |
spMan_.push_back(new PolarizableAtomTypesSectionParser(forceFieldOptions_)); |
| 129 |
+ |
spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_)); |
| 130 |
+ |
spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_)); |
| 131 |
+ |
spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_)); |
| 132 |
+ |
spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_)); |
| 133 |
+ |
spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); |
| 134 |
+ |
spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_)); |
| 135 |
+ |
|
| 136 |
+ |
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
| 137 |
+ |
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
| 138 |
+ |
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
| 139 |
+ |
spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_)); |
| 140 |
+ |
|
| 141 |
+ |
spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_)); |
| 142 |
+ |
} |
| 143 |
+ |
|
| 144 |
+ |
void ForceField::parse(const std::string& filename) { |
| 145 |
+ |
ifstrstream* ffStream; |
| 146 |
+ |
|
| 147 |
+ |
ffStream = openForceFieldFile(filename); |
| 148 |
+ |
|
| 149 |
+ |
spMan_.parse(*ffStream, *this); |
| 150 |
+ |
|
| 151 |
+ |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 152 |
+ |
AtomType* at; |
| 153 |
+ |
|
| 154 |
+ |
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 155 |
+ |
at = atomTypeCont_.nextType(i)) { |
| 156 |
+ |
|
| 157 |
+ |
// useBase sets the responsibilities, and these have to be done |
| 158 |
+ |
// after the atomTypes and Base types have all been scanned: |
| 159 |
+ |
|
| 160 |
+ |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 161 |
+ |
if (ayb.size() > 1) { |
| 162 |
+ |
for (int j = ayb.size()-1; j > 0; j--) { |
| 163 |
+ |
|
| 164 |
+ |
ayb[j-1]->useBase(ayb[j]); |
| 165 |
+ |
|
| 166 |
+ |
} |
| 167 |
+ |
} |
| 168 |
|
} |
| 169 |
+ |
|
| 170 |
+ |
delete ffStream; |
| 171 |
|
} |
| 172 |
|
|
| 173 |
|
/** |
| 227 |
|
|
| 228 |
|
std::vector<std::pair<int, std::vector<std::string> > > foundBonds; |
| 229 |
|
|
| 230 |
< |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 230 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); ++i) { |
| 231 |
|
jj = 0; |
| 232 |
< |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 232 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); ++j) { |
| 233 |
|
|
| 234 |
|
bondTypeScore = ii + jj; |
| 235 |
|
|
| 247 |
|
} |
| 248 |
|
|
| 249 |
|
|
| 250 |
< |
if (foundBonds.size() > 0) { |
| 250 |
> |
if (!foundBonds.empty()) { |
| 251 |
|
// sort the foundBonds by the score: |
| 252 |
|
std::sort(foundBonds.begin(), foundBonds.end()); |
| 253 |
|
|
| 150 |
– |
int bestScore = foundBonds[0].first; |
| 254 |
|
std::vector<std::string> theKeys = foundBonds[0].second; |
| 255 |
|
|
| 256 |
|
BondType* bestType = bondTypeCont_.find(theKeys); |
| 308 |
|
|
| 309 |
|
std::vector<tuple3<int, int, std::vector<std::string> > > foundBends; |
| 310 |
|
|
| 311 |
< |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 311 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); ++j) { |
| 312 |
|
ii = 0; |
| 313 |
< |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 313 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); ++i) { |
| 314 |
|
kk = 0; |
| 315 |
< |
for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
| 315 |
> |
for (k = at3Chain.begin(); k != at3Chain.end(); ++k) { |
| 316 |
|
|
| 317 |
|
IKscore = ii + kk; |
| 318 |
|
|
| 332 |
|
jj++; |
| 333 |
|
} |
| 334 |
|
|
| 335 |
< |
if (foundBends.size() > 0) { |
| 335 |
> |
if (!foundBends.empty()) { |
| 336 |
|
std::sort(foundBends.begin(), foundBends.end()); |
| 234 |
– |
int jscore = foundBends[0].first; |
| 235 |
– |
int ikscore = foundBends[0].second; |
| 337 |
|
std::vector<std::string> theKeys = foundBends[0].third; |
| 338 |
|
|
| 339 |
|
BendType* bestType = bendTypeCont_.find(theKeys); |
| 402 |
|
|
| 403 |
|
std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions; |
| 404 |
|
|
| 405 |
< |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 405 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); ++j) { |
| 406 |
|
kk = 0; |
| 407 |
< |
for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
| 407 |
> |
for (k = at3Chain.begin(); k != at3Chain.end(); ++k) { |
| 408 |
|
ii = 0; |
| 409 |
< |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 409 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); ++i) { |
| 410 |
|
ll = 0; |
| 411 |
< |
for (l = at4Chain.begin(); l != at4Chain.end(); l++) { |
| 411 |
> |
for (l = at4Chain.begin(); l != at4Chain.end(); ++l) { |
| 412 |
|
|
| 413 |
|
ILscore = ii + ll; |
| 414 |
|
JKscore = jj + kk; |
| 432 |
|
jj++; |
| 433 |
|
} |
| 434 |
|
|
| 435 |
< |
if (foundTorsions.size() > 0) { |
| 435 |
> |
if (!foundTorsions.empty()) { |
| 436 |
|
std::sort(foundTorsions.begin(), foundTorsions.end()); |
| 336 |
– |
int jkscore = foundTorsions[0].first; |
| 337 |
– |
int ilscore = foundTorsions[0].second; |
| 437 |
|
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 438 |
|
|
| 439 |
|
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 501 |
|
|
| 502 |
|
std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions; |
| 503 |
|
|
| 504 |
< |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 504 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); ++j) { |
| 505 |
|
kk = 0; |
| 506 |
< |
for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
| 506 |
> |
for (k = at3Chain.begin(); k != at3Chain.end(); ++k) { |
| 507 |
|
ii = 0; |
| 508 |
< |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 508 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); ++i) { |
| 509 |
|
ll = 0; |
| 510 |
< |
for (l = at4Chain.begin(); l != at4Chain.end(); l++) { |
| 510 |
> |
for (l = at4Chain.begin(); l != at4Chain.end(); ++l) { |
| 511 |
|
|
| 512 |
|
Iscore = ii; |
| 513 |
|
JKLscore = jj + kk + ll; |
| 531 |
|
jj++; |
| 532 |
|
} |
| 533 |
|
|
| 534 |
< |
if (foundInversions.size() > 0) { |
| 534 |
> |
if (!foundInversions.empty()) { |
| 535 |
|
std::sort(foundInversions.begin(), foundInversions.end()); |
| 437 |
– |
int iscore = foundInversions[0].first; |
| 438 |
– |
int jklscore = foundInversions[0].second; |
| 536 |
|
std::vector<std::string> theKeys = foundInversions[0].third; |
| 537 |
|
|
| 538 |
|
InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys); |
| 545 |
|
} |
| 546 |
|
|
| 547 |
|
NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) { |
| 548 |
+ |
|
| 549 |
|
std::vector<std::string> keys; |
| 550 |
|
keys.push_back(at1); |
| 551 |
|
keys.push_back(at2); |
| 552 |
< |
|
| 552 |
> |
|
| 553 |
|
//try exact match first |
| 554 |
|
NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys); |
| 555 |
|
if (nbiType) { |
| 556 |
|
return nbiType; |
| 557 |
|
} else { |
| 558 |
< |
//if no exact match found, try wild card match |
| 559 |
< |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 560 |
< |
} |
| 558 |
> |
AtomType* atype1; |
| 559 |
> |
AtomType* atype2; |
| 560 |
> |
std::vector<std::string> at1key; |
| 561 |
> |
at1key.push_back(at1); |
| 562 |
> |
atype1 = atomTypeCont_.find(at1key); |
| 563 |
> |
|
| 564 |
> |
std::vector<std::string> at2key; |
| 565 |
> |
at2key.push_back(at2); |
| 566 |
> |
atype2 = atomTypeCont_.find(at2key); |
| 567 |
> |
|
| 568 |
> |
// query atom types for their chains of responsibility |
| 569 |
> |
std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 570 |
> |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 571 |
> |
|
| 572 |
> |
std::vector<AtomType*>::iterator i; |
| 573 |
> |
std::vector<AtomType*>::iterator j; |
| 574 |
> |
|
| 575 |
> |
int ii = 0; |
| 576 |
> |
int jj = 0; |
| 577 |
> |
int nbiTypeScore; |
| 578 |
> |
|
| 579 |
> |
std::vector<std::pair<int, std::vector<std::string> > > foundNBI; |
| 580 |
> |
|
| 581 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); ++i) { |
| 582 |
> |
jj = 0; |
| 583 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); ++j) { |
| 584 |
> |
|
| 585 |
> |
nbiTypeScore = ii + jj; |
| 586 |
> |
|
| 587 |
> |
std::vector<std::string> myKeys; |
| 588 |
> |
myKeys.push_back((*i)->getName()); |
| 589 |
> |
myKeys.push_back((*j)->getName()); |
| 590 |
> |
|
| 591 |
> |
NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys); |
| 592 |
> |
if (nbiType) { |
| 593 |
> |
foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys)); |
| 594 |
> |
} |
| 595 |
> |
jj++; |
| 596 |
> |
} |
| 597 |
> |
ii++; |
| 598 |
> |
} |
| 599 |
> |
|
| 600 |
> |
|
| 601 |
> |
if (!foundNBI.empty()) { |
| 602 |
> |
// sort the foundNBI by the score: |
| 603 |
> |
std::sort(foundNBI.begin(), foundNBI.end()); |
| 604 |
> |
std::vector<std::string> theKeys = foundNBI[0].second; |
| 605 |
> |
|
| 606 |
> |
NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys); |
| 607 |
> |
return bestType; |
| 608 |
> |
} else { |
| 609 |
> |
//if no exact match found, try wild card match |
| 610 |
> |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 611 |
> |
} |
| 612 |
> |
} |
| 613 |
|
} |
| 614 |
|
|
| 615 |
|
BondType* ForceField::getExactBondType(const std::string &at1, |
| 729 |
|
} |
| 730 |
|
|
| 731 |
|
RealType ForceField::getRcutFromAtomType(AtomType* at) { |
| 732 |
< |
/**@todo */ |
| 583 |
< |
GenericData* data; |
| 584 |
< |
RealType rcut = 0.0; |
| 732 |
> |
RealType rcut(0.0); |
| 733 |
|
|
| 734 |
< |
if (at->isLennardJones()) { |
| 735 |
< |
data = at->getPropertyByName("LennardJones"); |
| 736 |
< |
if (data != NULL) { |
| 589 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 590 |
< |
|
| 591 |
< |
if (ljData != NULL) { |
| 592 |
< |
LJParam ljParam = ljData->getData(); |
| 593 |
< |
|
| 594 |
< |
//by default use 2.5*sigma as cutoff radius |
| 595 |
< |
rcut = 2.5 * ljParam.sigma; |
| 596 |
< |
|
| 597 |
< |
} else { |
| 598 |
< |
sprintf( painCave.errMsg, |
| 599 |
< |
"Can not cast GenericData to LJParam\n"); |
| 600 |
< |
painCave.severity = OPENMD_ERROR; |
| 601 |
< |
painCave.isFatal = 1; |
| 602 |
< |
simError(); |
| 603 |
< |
} |
| 604 |
< |
} else { |
| 605 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 606 |
< |
painCave.severity = OPENMD_ERROR; |
| 607 |
< |
painCave.isFatal = 1; |
| 608 |
< |
simError(); |
| 609 |
< |
} |
| 734 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(at); |
| 735 |
> |
if (lja.isLennardJones()) { |
| 736 |
> |
rcut = 2.5 * lja.getSigma(); |
| 737 |
|
} |
| 738 |
+ |
EAMAdapter ea = EAMAdapter(at); |
| 739 |
+ |
if (ea.isEAM()) { |
| 740 |
+ |
rcut = max(rcut, ea.getRcut()); |
| 741 |
+ |
} |
| 742 |
+ |
SuttonChenAdapter sca = SuttonChenAdapter(at); |
| 743 |
+ |
if (sca.isSuttonChen()) { |
| 744 |
+ |
rcut = max(rcut, 2.0 * sca.getAlpha()); |
| 745 |
+ |
} |
| 746 |
+ |
GayBerneAdapter gba = GayBerneAdapter(at); |
| 747 |
+ |
if (gba.isGayBerne()) { |
| 748 |
+ |
rcut = max(rcut, 2.5 * sqrt(2.0) * max(gba.getD(), gba.getL())); |
| 749 |
+ |
} |
| 750 |
+ |
StickyAdapter sa = StickyAdapter(at); |
| 751 |
+ |
if (sa.isSticky()) { |
| 752 |
+ |
rcut = max(rcut, max(sa.getRu(), sa.getRup())); |
| 753 |
+ |
} |
| 754 |
+ |
|
| 755 |
|
return rcut; |
| 756 |
|
} |
| 757 |
|
|
