| 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, 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 |
#ifndef NONBONDED_NONBONDEDINTERACTION_HPP |
| 44 |
#define NONBONDED_NONBONDEDINTERACTION_HPP |
| 45 |
|
| 46 |
#include "types/AtomType.hpp" |
| 47 |
#include "math/SquareMatrix3.hpp" |
| 48 |
|
| 49 |
using namespace std; |
| 50 |
namespace OpenMD { |
| 51 |
|
| 52 |
/** |
| 53 |
* The InteractionFamily enum. |
| 54 |
* |
| 55 |
* This is used to sort different types of non-bonded interaction |
| 56 |
* and to prevent multiple interactions in the same family from |
| 57 |
* being applied to any given pair of atom types. |
| 58 |
*/ |
| 59 |
enum InteractionFamily { |
| 60 |
NO_FAMILY = 0, /**< No family defined */ |
| 61 |
VANDERWAALS_FAMILY = 1, /**< Long-range dispersion and short-range pauli repulsion */ |
| 62 |
ELECTROSTATIC_FAMILY = 2, /**< Coulombic and point-multipole interactions */ |
| 63 |
METALLIC_FAMILY = 3, /**< Transition metal interactions involving electron density */ |
| 64 |
HYDROGENBONDING_FAMILY = 4,/**< Short-range directional interactions */ |
| 65 |
N_INTERACTION_FAMILIES = 5 |
| 66 |
}; |
| 67 |
|
| 68 |
/** |
| 69 |
* Boolean flags for the iHash_ and sHash_ data structures. These |
| 70 |
* are used to greatly increase the speed of looking up the |
| 71 |
* low-level interaction for any given pair: |
| 72 |
*/ |
| 73 |
const static int ELECTROSTATIC_INTERACTION = (1 << 0); |
| 74 |
const static int LJ_INTERACTION = (1 << 1); |
| 75 |
const static int EAM_INTERACTION = (1 << 2); |
| 76 |
const static int SC_INTERACTION = (1 << 3); |
| 77 |
const static int STICKY_INTERACTION = (1 << 4); |
| 78 |
const static int GB_INTERACTION = (1 << 5); |
| 79 |
const static int MORSE_INTERACTION = (1 << 6); |
| 80 |
const static int REPULSIVEPOWER_INTERACTION = (1 << 7); |
| 81 |
const static int MAW_INTERACTION = (1 << 8); |
| 82 |
|
| 83 |
typedef Vector<RealType, N_INTERACTION_FAMILIES> potVec; |
| 84 |
|
| 85 |
/** |
| 86 |
* The InteractionData struct. |
| 87 |
* |
| 88 |
* This is used to pass pointers to data to specific non-bonded |
| 89 |
* interactions for force calculations. Not all of the struct |
| 90 |
* members are utilized by any given interaction. |
| 91 |
*/ |
| 92 |
struct InteractionData { |
| 93 |
//pair<AtomType*, AtomType*> atypes; /**< pair of atom types interacting */ |
| 94 |
int atid1; /**< atomType ident for atom 1 */ |
| 95 |
int atid2; /**< atomType ident for atom 2 */ |
| 96 |
Vector3d* d; /**< interatomic vector (already wrapped into box) */ |
| 97 |
RealType* rij; /**< interatomic separation */ |
| 98 |
RealType* r2; /**< square of rij */ |
| 99 |
RealType* rcut; /**< cutoff radius for this interaction */ |
| 100 |
bool shiftedPot; /**< shift the potential up inside the cutoff? */ |
| 101 |
bool shiftedForce; /**< shifted forces smoothly inside the cutoff? */ |
| 102 |
RealType* sw; /**< switching function value at rij */ |
| 103 |
int* topoDist; /**< topological distance between atoms */ |
| 104 |
bool excluded; /**< is this excluded from *direct* pairwise interactions? (some indirect interactions may still apply) */ |
| 105 |
bool sameRegion; /**< are these atoms specified to be in the same region? */ |
| 106 |
RealType* vdwMult; /**< multiplier for van der Waals interactions */ |
| 107 |
RealType* electroMult; /**< multiplier for electrostatic interactions */ |
| 108 |
potVec* pot; /**< total potential */ |
| 109 |
potVec* excludedPot; /**< potential energy excluded from the overall calculation */ |
| 110 |
RealType* vpair; /**< pair potential */ |
| 111 |
bool doParticlePot; /**< should we bother with the particle pot? */ |
| 112 |
bool doElectricField; /**< should we bother with the electric field? */ |
| 113 |
bool doSitePotential; /**< should we bother with electrostatic site potential */ |
| 114 |
RealType* particlePot1; /**< pointer to particle potential for atom1 */ |
| 115 |
RealType* particlePot2; /**< pointer to particle potential for atom2 */ |
| 116 |
Vector3d* f1; /**< force between the two atoms */ |
| 117 |
RotMat3x3d* A1; /**< pointer to rotation matrix of first atom */ |
| 118 |
RotMat3x3d* A2; /**< pointer to rotation matrix of second atom */ |
| 119 |
Vector3d* dipole1; /**< pointer to dipole vector of first atom */ |
| 120 |
Vector3d* dipole2; /**< pointer to dipole vector of first atom */ |
| 121 |
Mat3x3d* quadrupole1; /**< pointer to quadrupole tensor of first atom */ |
| 122 |
Mat3x3d* quadrupole2; /**< pointer to quadrupole tensor of first atom */ |
| 123 |
Vector3d* t1; /**< pointer to torque on first atom */ |
| 124 |
Vector3d* t2; /**< pointer to torque on second atom */ |
| 125 |
RealType* rho1; /**< total electron density at first atom */ |
| 126 |
RealType* rho2; /**< total electron density at second atom */ |
| 127 |
RealType* frho1; /**< density functional at first atom */ |
| 128 |
RealType* frho2; /**< density functional at second atom */ |
| 129 |
RealType* dfrho1; /**< derivative of functional for atom 1 */ |
| 130 |
RealType* dfrho2; /**< derivative of functional for atom 2 */ |
| 131 |
RealType* flucQ1; /**< fluctuating charge on atom1 */ |
| 132 |
RealType* flucQ2; /**< fluctuating charge on atom2 */ |
| 133 |
RealType* dVdFQ1; /**< fluctuating charge force on atom1 */ |
| 134 |
RealType* dVdFQ2; /**< fluctuating charge force on atom2 */ |
| 135 |
Vector3d* eField1; /**< pointer to electric field on first atom */ |
| 136 |
Vector3d* eField2; /**< pointer to electric field on second atom */ |
| 137 |
RealType* skippedCharge1; /**< charge skipped on atom1 in pairwise interaction loop with atom2 */ |
| 138 |
RealType* skippedCharge2; /**< charge skipped on atom2 in pairwise interaction loop with atom1 */ |
| 139 |
RealType* sPot1; /**< site potential on first atom */ |
| 140 |
RealType* sPot2; /**< site potential on second atom */ |
| 141 |
}; |
| 142 |
|
| 143 |
/** |
| 144 |
* The SelfData struct. |
| 145 |
* |
| 146 |
* This is used to pass pointers to data for the self-interaction or |
| 147 |
* derived information on a single atom after a pass through all |
| 148 |
* other interactions. This is used by electrostatic methods that |
| 149 |
* have long-range corrections involving interactions with a medium |
| 150 |
* or a boundary and also by specific metal interactions for |
| 151 |
* electron density functional calculations. Not all of the struct |
| 152 |
* members are utilized by any given self interaction. |
| 153 |
*/ |
| 154 |
struct SelfData { |
| 155 |
//AtomType* atype; /**< pointer to AtomType of the atom */ |
| 156 |
int atid; /**< atomType ident for the atom */ |
| 157 |
Vector3d* dipole; /**< pointer to dipole vector of the atom */ |
| 158 |
Mat3x3d* quadrupole; /**< pointer to quadrupole tensor of the atom */ |
| 159 |
RealType* skippedCharge;/**< charge skipped in pairwise interaction loop */ |
| 160 |
potVec* pot; /**< total potential */ |
| 161 |
potVec* excludedPot; /**< potential energy excluded from the overall calculation */ |
| 162 |
bool doParticlePot; /**< should we bother with the particle pot? */ |
| 163 |
RealType* particlePot; /**< contribution to potential from this particle */ |
| 164 |
Vector3d* t; /**< pointer to resultant torque on atom */ |
| 165 |
RealType* rho; /**< electron density */ |
| 166 |
RealType* frho; /**< value of density functional for atom */ |
| 167 |
RealType* dfrhodrho; /**< derivative of density functional for atom */ |
| 168 |
RealType* flucQ; /**< current value of atom's fluctuating charge */ |
| 169 |
RealType* flucQfrc; /**< fluctuating charge derivative */ |
| 170 |
}; |
| 171 |
|
| 172 |
|
| 173 |
/** |
| 174 |
* The basic interface for non-bonded interactions. |
| 175 |
*/ |
| 176 |
class NonBondedInteraction { |
| 177 |
public: |
| 178 |
NonBondedInteraction() {} |
| 179 |
virtual ~NonBondedInteraction() {} |
| 180 |
virtual void calcForce(InteractionData &idat) = 0; |
| 181 |
virtual InteractionFamily getFamily() = 0; |
| 182 |
virtual int getHash() = 0; |
| 183 |
virtual RealType getSuggestedCutoffRadius(pair<AtomType*, AtomType*> atypes) = 0; |
| 184 |
virtual string getName() = 0; |
| 185 |
}; |
| 186 |
|
| 187 |
/** |
| 188 |
* The basic interface for van der Waals interactions. |
| 189 |
*/ |
| 190 |
class VanDerWaalsInteraction : public NonBondedInteraction { |
| 191 |
public: |
| 192 |
VanDerWaalsInteraction() : NonBondedInteraction() { } |
| 193 |
virtual ~VanDerWaalsInteraction() {} |
| 194 |
virtual InteractionFamily getFamily() {return VANDERWAALS_FAMILY;} |
| 195 |
}; |
| 196 |
|
| 197 |
/** |
| 198 |
* The basic interface for electrostatic interactions. |
| 199 |
*/ |
| 200 |
class ElectrostaticInteraction : public NonBondedInteraction { |
| 201 |
public: |
| 202 |
ElectrostaticInteraction() : NonBondedInteraction() { } |
| 203 |
virtual ~ElectrostaticInteraction() {} |
| 204 |
virtual void calcSelfCorrection(SelfData &sdat) = 0; |
| 205 |
virtual InteractionFamily getFamily() {return ELECTROSTATIC_FAMILY;} |
| 206 |
virtual int getHash() {return ELECTROSTATIC_INTERACTION;} |
| 207 |
}; |
| 208 |
|
| 209 |
/** |
| 210 |
* The basic interface for metallic interactions. |
| 211 |
*/ |
| 212 |
class MetallicInteraction : public NonBondedInteraction { |
| 213 |
public: |
| 214 |
MetallicInteraction() : NonBondedInteraction() { } |
| 215 |
virtual ~MetallicInteraction() {} |
| 216 |
virtual void calcDensity(InteractionData &idat) = 0; |
| 217 |
virtual void calcFunctional(SelfData &sdat) = 0; |
| 218 |
virtual InteractionFamily getFamily() {return METALLIC_FAMILY;} |
| 219 |
}; |
| 220 |
|
| 221 |
/** |
| 222 |
* The basic interface for hydrogen bonding interactions. |
| 223 |
*/ |
| 224 |
class HydrogenBondingInteraction : public NonBondedInteraction { |
| 225 |
public: |
| 226 |
HydrogenBondingInteraction() : NonBondedInteraction() { } |
| 227 |
virtual ~HydrogenBondingInteraction() {} |
| 228 |
virtual InteractionFamily getFamily() {return HYDROGENBONDING_FAMILY;} |
| 229 |
}; |
| 230 |
|
| 231 |
} //end namespace OpenMD |
| 232 |
#endif |
