| 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, 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 |
+ |
#include "config.h" |
| 44 |
+ |
#include <cmath> |
| 45 |
+ |
|
| 46 |
|
#include "primitives/Inversion.hpp" |
| 43 |
– |
#include "fstream" |
| 47 |
|
|
| 48 |
< |
namespace oopse { |
| 48 |
> |
namespace OpenMD { |
| 49 |
|
|
| 50 |
|
Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, |
| 51 |
< |
Atom *atom4, InversionType *it) : |
| 52 |
< |
atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), |
| 53 |
< |
inversionType_(it) { } |
| 51 |
> |
Atom *atom4, InversionType *it) : |
| 52 |
> |
ShortRangeInteraction(), inversionType_(it) { |
| 53 |
> |
|
| 54 |
> |
atoms_.resize(4); |
| 55 |
> |
atoms_[0] = atom1; |
| 56 |
> |
atoms_[1] = atom2; |
| 57 |
> |
atoms_[2] = atom3; |
| 58 |
> |
atoms_[3] = atom4; |
| 59 |
> |
|
| 60 |
> |
inversionKey_ = inversionType_->getKey(); |
| 61 |
> |
} |
| 62 |
|
|
| 63 |
< |
void Inversion::calcForce(RealType& angle) { |
| 63 |
> |
void Inversion::calcForce(RealType& angle, bool doParticlePot) { |
| 64 |
|
|
| 65 |
< |
// In OOPSE's version of an inversion, the central atom |
| 65 |
> |
// In OpenMD's version of an inversion, the central atom |
| 66 |
|
// comes first. However, to get the planarity in a typical cosine |
| 67 |
|
// version of this potential (i.e. Amber-style), the central atom |
| 68 |
|
// is treated as atom *3* in a standard torsion form: |
| 69 |
|
|
| 70 |
< |
Vector3d pos1 = atom2_->getPos(); |
| 71 |
< |
Vector3d pos2 = atom3_->getPos(); |
| 72 |
< |
Vector3d pos3 = atom1_->getPos(); |
| 73 |
< |
Vector3d pos4 = atom4_->getPos(); |
| 70 |
> |
Vector3d pos1 = atoms_[1]->getPos(); |
| 71 |
> |
Vector3d pos2 = atoms_[2]->getPos(); |
| 72 |
> |
Vector3d pos3 = atoms_[0]->getPos(); |
| 73 |
> |
Vector3d pos4 = atoms_[3]->getPos(); |
| 74 |
|
|
| 64 |
– |
/*std::ofstream myfile; |
| 65 |
– |
myfile.open("Inversion", std::ios::app); |
| 66 |
– |
myfile << atom1_->getType() << " - atom1; " |
| 67 |
– |
<< atom2_->getType() << " - atom2; " |
| 68 |
– |
<< atom3_->getType() << " - atom3; " |
| 69 |
– |
<< atom4_->getType() << " - atom4; " |
| 70 |
– |
<< std::endl; |
| 71 |
– |
*/ |
| 75 |
|
Vector3d r31 = pos1 - pos3; |
| 76 |
|
Vector3d r23 = pos3 - pos2; |
| 77 |
|
Vector3d r43 = pos3 - pos4; |
| 90 |
|
|
| 91 |
|
// Calculate the sin and cos |
| 92 |
|
RealType cos_phi = dot(A, B) ; |
| 93 |
< |
if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0" |
| 94 |
< |
<< std::endl;} |
| 92 |
< |
if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0" |
| 93 |
< |
<< std::endl;} |
| 94 |
< |
//std::cout << "We actually use this inversion!!!!" << std::endl; |
| 93 |
> |
if (cos_phi > 1.0) cos_phi = 1.0; |
| 94 |
> |
if (cos_phi < -1.0) cos_phi = -1.0; |
| 95 |
|
|
| 96 |
|
RealType dVdcosPhi; |
| 97 |
< |
//cos_phi = 2.0*cos_phi*cos_phi - 1.0; |
| 98 |
< |
inversionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
| 97 |
> |
switch (inversionKey_) { |
| 98 |
> |
case itCosAngle: |
| 99 |
> |
inversionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
| 100 |
> |
break; |
| 101 |
> |
case itAngle: |
| 102 |
> |
RealType phi = acos(cos_phi); |
| 103 |
> |
RealType dVdPhi; |
| 104 |
> |
inversionType_->calcForce(phi, potential_, dVdPhi); |
| 105 |
> |
RealType sin_phi = sqrt(1.0 - cos_phi * cos_phi); |
| 106 |
> |
if (fabs(sin_phi) < 1.0E-6) { |
| 107 |
> |
sin_phi = 1.0E-6; |
| 108 |
> |
} |
| 109 |
> |
dVdcosPhi = dVdPhi / sin_phi; |
| 110 |
> |
break; |
| 111 |
> |
} |
| 112 |
> |
|
| 113 |
|
Vector3d f1 ; |
| 114 |
|
Vector3d f2 ; |
| 115 |
|
Vector3d f3 ; |
| 121 |
|
f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA)); |
| 122 |
|
f3 = dVdcosPhi * cross(dcosdB, r43); |
| 123 |
|
|
| 124 |
< |
// In OOPSE's version of an improper torsion, the central atom |
| 124 |
> |
// In OpenMD's version of an improper torsion, the central atom |
| 125 |
|
// comes first. However, to get the planarity in a typical cosine |
| 126 |
|
// version of this potential (i.e. Amber-style), the central atom |
| 127 |
|
// is treated as atom *3* in a standard torsion form: |
| 128 |
|
|
| 129 |
|
// AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon) |
| 130 |
< |
// OOPSE: I - (J - K - L) (e.g. I is sp2 hybridized carbon) |
| 130 |
> |
// OpenMD: I - (J - K - L) (e.g. I is sp2 hybridized carbon) |
| 131 |
|
|
| 132 |
|
// Confusing enough? Good. |
| 133 |
|
|
| 134 |
< |
atom2_->addFrc(f1); |
| 135 |
< |
atom1_->addFrc(f2 - f1 + f3); |
| 136 |
< |
atom4_->addFrc(-f2); |
| 137 |
< |
atom3_->addFrc(-f3); |
| 134 |
> |
atoms_[1]->addFrc(f1); |
| 135 |
> |
atoms_[0]->addFrc(f2 - f1 + f3); |
| 136 |
> |
atoms_[3]->addFrc(-f2); |
| 137 |
> |
atoms_[2]->addFrc(-f3); |
| 138 |
|
|
| 139 |
+ |
if (doParticlePot) { |
| 140 |
+ |
atoms_[0]->addParticlePot(potential_); |
| 141 |
+ |
atoms_[1]->addParticlePot(potential_); |
| 142 |
+ |
atoms_[2]->addParticlePot(potential_); |
| 143 |
+ |
atoms_[3]->addParticlePot(potential_); |
| 144 |
+ |
} |
| 145 |
+ |
|
| 146 |
|
angle = acos(cos_phi) /M_PI * 180.0; |
| 147 |
|
} |
| 148 |
|
|
