| 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 |
|
/** |
| 49 |
|
*/ |
| 50 |
|
|
| 51 |
|
#include <algorithm> |
| 52 |
< |
#include "UseTheForce/ForceField.hpp" |
| 52 |
> |
#include "brains/ForceField.hpp" |
| 53 |
|
#include "utils/simError.h" |
| 53 |
– |
#include "utils/Tuple.hpp" |
| 54 |
– |
#include "UseTheForce/DarkSide/atype_interface.h" |
| 55 |
– |
#include "UseTheForce/DarkSide/fForceOptions_interface.h" |
| 56 |
– |
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
| 57 |
– |
namespace oopse { |
| 54 |
|
|
| 55 |
< |
ForceField::ForceField() { |
| 55 |
> |
#include "io/OptionSectionParser.hpp" |
| 56 |
> |
#include "io/BaseAtomTypesSectionParser.hpp" |
| 57 |
> |
#include "io/DirectionalAtomTypesSectionParser.hpp" |
| 58 |
> |
#include "io/AtomTypesSectionParser.hpp" |
| 59 |
> |
#include "io/BendTypesSectionParser.hpp" |
| 60 |
> |
#include "io/BondTypesSectionParser.hpp" |
| 61 |
> |
#include "io/ChargeAtomTypesSectionParser.hpp" |
| 62 |
> |
#include "io/EAMAtomTypesSectionParser.hpp" |
| 63 |
> |
#include "io/FluctuatingChargeAtomTypesSectionParser.hpp" |
| 64 |
> |
#include "io/GayBerneAtomTypesSectionParser.hpp" |
| 65 |
> |
#include "io/InversionTypesSectionParser.hpp" |
| 66 |
> |
#include "io/LennardJonesAtomTypesSectionParser.hpp" |
| 67 |
> |
#include "io/MultipoleAtomTypesSectionParser.hpp" |
| 68 |
> |
#include "io/NonBondedInteractionsSectionParser.hpp" |
| 69 |
> |
#include "io/PolarizableAtomTypesSectionParser.hpp" |
| 70 |
> |
#include "io/SCAtomTypesSectionParser.hpp" |
| 71 |
> |
#include "io/ShapeAtomTypesSectionParser.hpp" |
| 72 |
> |
#include "io/StickyAtomTypesSectionParser.hpp" |
| 73 |
> |
#include "io/StickyPowerAtomTypesSectionParser.hpp" |
| 74 |
> |
#include "io/TorsionTypesSectionParser.hpp" |
| 75 |
> |
|
| 76 |
> |
#include "types/LennardJonesAdapter.hpp" |
| 77 |
> |
#include "types/EAMAdapter.hpp" |
| 78 |
> |
#include "types/SuttonChenAdapter.hpp" |
| 79 |
> |
#include "types/GayBerneAdapter.hpp" |
| 80 |
> |
#include "types/StickyAdapter.hpp" |
| 81 |
> |
|
| 82 |
> |
namespace OpenMD { |
| 83 |
> |
|
| 84 |
> |
ForceField::ForceField(std::string ffName) { |
| 85 |
> |
|
| 86 |
|
char* tempPath; |
| 87 |
|
tempPath = getenv("FORCE_PARAM_PATH"); |
| 88 |
< |
|
| 88 |
> |
|
| 89 |
|
if (tempPath == NULL) { |
| 90 |
|
//convert a macro from compiler to a string in c++ |
| 91 |
|
STR_DEFINE(ffPath_, FRC_PATH ); |
| 92 |
|
} else { |
| 93 |
|
ffPath_ = tempPath; |
| 94 |
|
} |
| 95 |
+ |
|
| 96 |
+ |
setForceFieldFileName(ffName + ".frc"); |
| 97 |
+ |
|
| 98 |
+ |
/** |
| 99 |
+ |
* The order of adding section parsers is important. |
| 100 |
+ |
* |
| 101 |
+ |
* OptionSectionParser must come first to set options for other |
| 102 |
+ |
* parsers |
| 103 |
+ |
* |
| 104 |
+ |
* DirectionalAtomTypesSectionParser should be added before |
| 105 |
+ |
* AtomTypesSectionParser, and these two section parsers will |
| 106 |
+ |
* actually create "real" AtomTypes (AtomTypesSectionParser will |
| 107 |
+ |
* create AtomType and DirectionalAtomTypesSectionParser will |
| 108 |
+ |
* create DirectionalAtomType, which is a subclass of AtomType and |
| 109 |
+ |
* should come first). |
| 110 |
+ |
* |
| 111 |
+ |
* Other AtomTypes Section Parsers will not create the "real" |
| 112 |
+ |
* AtomType, they only add and set some attributes of the AtomType |
| 113 |
+ |
* (via the Adapters). Thus ordering of these is not important. |
| 114 |
+ |
* AtomTypesSectionParser should be added before other atom type |
| 115 |
+ |
* |
| 116 |
+ |
* The order of BondTypesSectionParser, BendTypesSectionParser and |
| 117 |
+ |
* TorsionTypesSectionParser, etc. are not important. |
| 118 |
+ |
*/ |
| 119 |
+ |
|
| 120 |
+ |
spMan_.push_back(new OptionSectionParser(forceFieldOptions_)); |
| 121 |
+ |
spMan_.push_back(new BaseAtomTypesSectionParser()); |
| 122 |
+ |
spMan_.push_back(new DirectionalAtomTypesSectionParser(forceFieldOptions_)); |
| 123 |
+ |
spMan_.push_back(new AtomTypesSectionParser()); |
| 124 |
+ |
|
| 125 |
+ |
spMan_.push_back(new LennardJonesAtomTypesSectionParser(forceFieldOptions_)); |
| 126 |
+ |
spMan_.push_back(new ChargeAtomTypesSectionParser(forceFieldOptions_)); |
| 127 |
+ |
spMan_.push_back(new MultipoleAtomTypesSectionParser(forceFieldOptions_)); |
| 128 |
+ |
spMan_.push_back(new FluctuatingChargeAtomTypesSectionParser(forceFieldOptions_)); |
| 129 |
+ |
spMan_.push_back(new PolarizableAtomTypesSectionParser(forceFieldOptions_)); |
| 130 |
+ |
spMan_.push_back(new GayBerneAtomTypesSectionParser(forceFieldOptions_)); |
| 131 |
+ |
spMan_.push_back(new EAMAtomTypesSectionParser(forceFieldOptions_)); |
| 132 |
+ |
spMan_.push_back(new SCAtomTypesSectionParser(forceFieldOptions_)); |
| 133 |
+ |
spMan_.push_back(new ShapeAtomTypesSectionParser(forceFieldOptions_)); |
| 134 |
+ |
spMan_.push_back(new StickyAtomTypesSectionParser(forceFieldOptions_)); |
| 135 |
+ |
spMan_.push_back(new StickyPowerAtomTypesSectionParser(forceFieldOptions_)); |
| 136 |
+ |
|
| 137 |
+ |
spMan_.push_back(new BondTypesSectionParser(forceFieldOptions_)); |
| 138 |
+ |
spMan_.push_back(new BendTypesSectionParser(forceFieldOptions_)); |
| 139 |
+ |
spMan_.push_back(new TorsionTypesSectionParser(forceFieldOptions_)); |
| 140 |
+ |
spMan_.push_back(new InversionTypesSectionParser(forceFieldOptions_)); |
| 141 |
+ |
|
| 142 |
+ |
spMan_.push_back(new NonBondedInteractionsSectionParser(forceFieldOptions_)); |
| 143 |
|
} |
| 144 |
|
|
| 145 |
+ |
void ForceField::parse(const std::string& filename) { |
| 146 |
+ |
ifstrstream* ffStream; |
| 147 |
|
|
| 148 |
< |
ForceField::~ForceField() { |
| 149 |
< |
deleteAtypes(); |
| 150 |
< |
deleteSwitch(); |
| 148 |
> |
ffStream = openForceFieldFile(filename); |
| 149 |
> |
|
| 150 |
> |
spMan_.parse(*ffStream, *this); |
| 151 |
> |
|
| 152 |
> |
ForceField::AtomTypeContainer::MapTypeIterator i; |
| 153 |
> |
AtomType* at; |
| 154 |
> |
|
| 155 |
> |
for (at = atomTypeCont_.beginType(i); at != NULL; |
| 156 |
> |
at = atomTypeCont_.nextType(i)) { |
| 157 |
> |
|
| 158 |
> |
// useBase sets the responsibilities, and these have to be done |
| 159 |
> |
// after the atomTypes and Base types have all been scanned: |
| 160 |
> |
|
| 161 |
> |
std::vector<AtomType*> ayb = at->allYourBase(); |
| 162 |
> |
if (ayb.size() > 1) { |
| 163 |
> |
for (int j = ayb.size()-1; j > 0; j--) { |
| 164 |
> |
|
| 165 |
> |
ayb[j-1]->useBase(ayb[j]); |
| 166 |
> |
|
| 167 |
> |
} |
| 168 |
> |
} |
| 169 |
> |
} |
| 170 |
> |
|
| 171 |
> |
delete ffStream; |
| 172 |
|
} |
| 173 |
|
|
| 174 |
+ |
/** |
| 175 |
+ |
* getAtomType by string |
| 176 |
+ |
* |
| 177 |
+ |
* finds the requested atom type in this force field using the string |
| 178 |
+ |
* name of the atom type. |
| 179 |
+ |
*/ |
| 180 |
|
AtomType* ForceField::getAtomType(const std::string &at) { |
| 181 |
|
std::vector<std::string> keys; |
| 182 |
|
keys.push_back(at); |
| 183 |
|
return atomTypeCont_.find(keys); |
| 184 |
+ |
} |
| 185 |
+ |
|
| 186 |
+ |
/** |
| 187 |
+ |
* getAtomType by ident |
| 188 |
+ |
* |
| 189 |
+ |
* finds the requested atom type in this force field using the |
| 190 |
+ |
* integer ident instead of the string name of the atom type. |
| 191 |
+ |
*/ |
| 192 |
+ |
AtomType* ForceField::getAtomType(int ident) { |
| 193 |
+ |
std::string at = atypeIdentToName.find(ident)->second; |
| 194 |
+ |
return getAtomType(at); |
| 195 |
|
} |
| 196 |
|
|
| 197 |
|
BondType* ForceField::getBondType(const std::string &at1, |
| 553 |
|
} |
| 554 |
|
|
| 555 |
|
NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) { |
| 556 |
+ |
|
| 557 |
|
std::vector<std::string> keys; |
| 558 |
|
keys.push_back(at1); |
| 559 |
|
keys.push_back(at2); |
| 563 |
|
if (nbiType) { |
| 564 |
|
return nbiType; |
| 565 |
|
} else { |
| 566 |
< |
//if no exact match found, try wild card match |
| 567 |
< |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 568 |
< |
} |
| 566 |
> |
AtomType* atype1; |
| 567 |
> |
AtomType* atype2; |
| 568 |
> |
std::vector<std::string> at1key; |
| 569 |
> |
at1key.push_back(at1); |
| 570 |
> |
atype1 = atomTypeCont_.find(at1key); |
| 571 |
> |
|
| 572 |
> |
std::vector<std::string> at2key; |
| 573 |
> |
at2key.push_back(at2); |
| 574 |
> |
atype2 = atomTypeCont_.find(at2key); |
| 575 |
> |
|
| 576 |
> |
// query atom types for their chains of responsibility |
| 577 |
> |
std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 578 |
> |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 579 |
> |
|
| 580 |
> |
std::vector<AtomType*>::iterator i; |
| 581 |
> |
std::vector<AtomType*>::iterator j; |
| 582 |
> |
|
| 583 |
> |
int ii = 0; |
| 584 |
> |
int jj = 0; |
| 585 |
> |
int nbiTypeScore; |
| 586 |
> |
|
| 587 |
> |
std::vector<std::pair<int, std::vector<std::string> > > foundNBI; |
| 588 |
> |
|
| 589 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 590 |
> |
jj = 0; |
| 591 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 592 |
> |
|
| 593 |
> |
nbiTypeScore = ii + jj; |
| 594 |
> |
|
| 595 |
> |
std::vector<std::string> myKeys; |
| 596 |
> |
myKeys.push_back((*i)->getName()); |
| 597 |
> |
myKeys.push_back((*j)->getName()); |
| 598 |
> |
|
| 599 |
> |
NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(myKeys); |
| 600 |
> |
if (nbiType) { |
| 601 |
> |
foundNBI.push_back(std::make_pair(nbiTypeScore, myKeys)); |
| 602 |
> |
} |
| 603 |
> |
jj++; |
| 604 |
> |
} |
| 605 |
> |
ii++; |
| 606 |
> |
} |
| 607 |
> |
|
| 608 |
> |
|
| 609 |
> |
if (foundNBI.size() > 0) { |
| 610 |
> |
// sort the foundNBI by the score: |
| 611 |
> |
std::sort(foundNBI.begin(), foundNBI.end()); |
| 612 |
> |
|
| 613 |
> |
int bestScore = foundNBI[0].first; |
| 614 |
> |
std::vector<std::string> theKeys = foundNBI[0].second; |
| 615 |
> |
|
| 616 |
> |
NonBondedInteractionType* bestType = nonBondedInteractionTypeCont_.find(theKeys); |
| 617 |
> |
return bestType; |
| 618 |
> |
} else { |
| 619 |
> |
//if no exact match found, try wild card match |
| 620 |
> |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 621 |
> |
} |
| 622 |
> |
} |
| 623 |
|
} |
| 624 |
|
|
| 625 |
|
BondType* ForceField::getExactBondType(const std::string &at1, |
| 675 |
|
bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { |
| 676 |
|
std::vector<std::string> keys; |
| 677 |
|
keys.push_back(at); |
| 678 |
+ |
atypeIdentToName[atomType->getIdent()] = at; |
| 679 |
|
return atomTypeCont_.add(keys, atomType); |
| 680 |
|
} |
| 681 |
|
|
| 682 |
|
bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { |
| 683 |
|
std::vector<std::string> keys; |
| 684 |
|
keys.push_back(at); |
| 685 |
+ |
atypeIdentToName[atomType->getIdent()] = at; |
| 686 |
|
return atomTypeCont_.replace(keys, atomType); |
| 687 |
|
} |
| 688 |
|
|
| 739 |
|
} |
| 740 |
|
|
| 741 |
|
RealType ForceField::getRcutFromAtomType(AtomType* at) { |
| 742 |
< |
/**@todo */ |
| 572 |
< |
GenericData* data; |
| 573 |
< |
RealType rcut = 0.0; |
| 742 |
> |
RealType rcut(0.0); |
| 743 |
|
|
| 744 |
< |
if (at->isLennardJones()) { |
| 745 |
< |
data = at->getPropertyByName("LennardJones"); |
| 746 |
< |
if (data != NULL) { |
| 578 |
< |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 579 |
< |
|
| 580 |
< |
if (ljData != NULL) { |
| 581 |
< |
LJParam ljParam = ljData->getData(); |
| 582 |
< |
|
| 583 |
< |
//by default use 2.5*sigma as cutoff radius |
| 584 |
< |
rcut = 2.5 * ljParam.sigma; |
| 585 |
< |
|
| 586 |
< |
} else { |
| 587 |
< |
sprintf( painCave.errMsg, |
| 588 |
< |
"Can not cast GenericData to LJParam\n"); |
| 589 |
< |
painCave.severity = OOPSE_ERROR; |
| 590 |
< |
painCave.isFatal = 1; |
| 591 |
< |
simError(); |
| 592 |
< |
} |
| 593 |
< |
} else { |
| 594 |
< |
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 595 |
< |
painCave.severity = OOPSE_ERROR; |
| 596 |
< |
painCave.isFatal = 1; |
| 597 |
< |
simError(); |
| 598 |
< |
} |
| 744 |
> |
LennardJonesAdapter lja = LennardJonesAdapter(at); |
| 745 |
> |
if (lja.isLennardJones()) { |
| 746 |
> |
rcut = 2.5 * lja.getSigma(); |
| 747 |
|
} |
| 748 |
+ |
EAMAdapter ea = EAMAdapter(at); |
| 749 |
+ |
if (ea.isEAM()) { |
| 750 |
+ |
rcut = max(rcut, ea.getRcut()); |
| 751 |
+ |
} |
| 752 |
+ |
SuttonChenAdapter sca = SuttonChenAdapter(at); |
| 753 |
+ |
if (sca.isSuttonChen()) { |
| 754 |
+ |
rcut = max(rcut, 2.0 * sca.getAlpha()); |
| 755 |
+ |
} |
| 756 |
+ |
GayBerneAdapter gba = GayBerneAdapter(at); |
| 757 |
+ |
if (gba.isGayBerne()) { |
| 758 |
+ |
rcut = max(rcut, 2.5 * sqrt(2.0) * max(gba.getD(), gba.getL())); |
| 759 |
+ |
} |
| 760 |
+ |
StickyAdapter sa = StickyAdapter(at); |
| 761 |
+ |
if (sa.isSticky()) { |
| 762 |
+ |
rcut = max(rcut, max(sa.getRu(), sa.getRup())); |
| 763 |
+ |
} |
| 764 |
+ |
|
| 765 |
|
return rcut; |
| 766 |
|
} |
| 767 |
|
|
| 787 |
|
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 788 |
|
"variable?\n", |
| 789 |
|
forceFieldFilename.c_str() ); |
| 790 |
< |
painCave.severity = OOPSE_ERROR; |
| 790 |
> |
painCave.severity = OPENMD_ERROR; |
| 791 |
|
painCave.isFatal = 1; |
| 792 |
|
simError(); |
| 793 |
|
} |
| 795 |
|
return ffStream; |
| 796 |
|
} |
| 797 |
|
|
| 798 |
< |
void ForceField::setFortranForceOptions(){ |
| 634 |
< |
ForceOptions theseFortranOptions; |
| 635 |
< |
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
| 636 |
< |
setfForceOptions(&theseFortranOptions); |
| 637 |
< |
} |
| 638 |
< |
} //end namespace oopse |
| 798 |
> |
} //end namespace OpenMD |
