| 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 |
+ |
#include "config.h" |
| 44 |
+ |
#include <cmath> |
| 45 |
+ |
|
| 46 |
|
#include "primitives/Torsion.hpp" |
| 47 |
|
|
| 48 |
< |
namespace oopse { |
| 48 |
> |
namespace OpenMD { |
| 49 |
|
|
| 50 |
|
Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4, |
| 51 |
|
TorsionType *tt) : |
| 52 |
|
atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { } |
| 53 |
|
|
| 54 |
< |
void Torsion::calcForce() { |
| 54 |
> |
void Torsion::calcForce(RealType& angle, bool doParticlePot) { |
| 55 |
> |
|
| 56 |
|
Vector3d pos1 = atom1_->getPos(); |
| 57 |
|
Vector3d pos2 = atom2_->getPos(); |
| 58 |
|
Vector3d pos3 = atom3_->getPos(); |
| 64 |
|
|
| 65 |
|
// Calculate the cross products and distances |
| 66 |
|
Vector3d A = cross(r21, r32); |
| 67 |
< |
double rA = A.length(); |
| 67 |
> |
RealType rA = A.length(); |
| 68 |
|
Vector3d B = cross(r32, r43); |
| 69 |
< |
double rB = B.length(); |
| 65 |
< |
Vector3d C = cross(r32, A); |
| 66 |
< |
double rC = C.length(); |
| 69 |
> |
RealType rB = B.length(); |
| 70 |
|
|
| 71 |
+ |
/* |
| 72 |
+ |
If either of the two cross product vectors is tiny, that means |
| 73 |
+ |
the three atoms involved are colinear, and the torsion angle is |
| 74 |
+ |
going to be undefined. The easiest check for this problem is |
| 75 |
+ |
to use the product of the two lengths. |
| 76 |
+ |
*/ |
| 77 |
+ |
if (rA * rB < OpenMD::epsilon) return; |
| 78 |
+ |
|
| 79 |
|
A.normalize(); |
| 80 |
< |
B.normalize(); |
| 70 |
< |
C.normalize(); |
| 80 |
> |
B.normalize(); |
| 81 |
|
|
| 82 |
|
// Calculate the sin and cos |
| 83 |
< |
double cos_phi = dot(A, B) ; |
| 84 |
< |
double sin_phi = dot(C, B); |
| 85 |
< |
|
| 86 |
< |
double dVdPhi; |
| 87 |
< |
torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi); |
| 88 |
< |
|
| 89 |
< |
Vector3d f1; |
| 90 |
< |
Vector3d f2; |
| 91 |
< |
Vector3d f3; |
| 92 |
< |
|
| 83 |
< |
if (fabs(sin_phi) > 0.5) { |
| 84 |
< |
//use the sin version to prevent potential singularities |
| 85 |
< |
|
| 83 |
> |
RealType cos_phi = dot(A, B) ; |
| 84 |
> |
if (cos_phi > 1.0) cos_phi = 1.0; |
| 85 |
> |
if (cos_phi < -1.0) cos_phi = -1.0; |
| 86 |
> |
|
| 87 |
> |
RealType dVdcosPhi; |
| 88 |
> |
torsionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
| 89 |
> |
Vector3d f1 ; |
| 90 |
> |
Vector3d f2 ; |
| 91 |
> |
Vector3d f3 ; |
| 92 |
> |
|
| 93 |
|
Vector3d dcosdA = (cos_phi * A - B) /rA; |
| 94 |
|
Vector3d dcosdB = (cos_phi * B - A) /rB; |
| 95 |
< |
|
| 89 |
< |
double dVdcosPhi = -dVdPhi / sin_phi; |
| 90 |
< |
|
| 95 |
> |
|
| 96 |
|
f1 = dVdcosPhi * cross(r32, dcosdA); |
| 97 |
|
f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
| 98 |
|
f3 = dVdcosPhi * cross(dcosdB, r32); |
| 99 |
< |
|
| 95 |
< |
} else { |
| 96 |
< |
//use the cos version to prevent potential singularities |
| 97 |
< |
|
| 98 |
< |
double dVdsinPhi = dVdPhi /cos_phi; |
| 99 |
< |
Vector3d dsindB = (sin_phi * B - C) /rB; |
| 100 |
< |
Vector3d dsindC = (sin_phi * C - B) /rC; |
| 101 |
< |
|
| 102 |
< |
f1.x() = dVdsinPhi*((r32.y()*r32.y() + r32.z()*r32.z())*dsindC.x() - r32.x()*r32.y()*dsindC.y() - r32.x()*r32.z()*dsindC.z()); |
| 103 |
< |
|
| 104 |
< |
f1.y() = dVdsinPhi*((r32.z()*r32.z() + r32.x()*r32.x())*dsindC.y() - r32.y()*r32.z()*dsindC.z() - r32.y()*r32.x()*dsindC.x()); |
| 105 |
< |
|
| 106 |
< |
f1.z() = dVdsinPhi*((r32.x()*r32.x() + r32.y()*r32.y())*dsindC.z() - r32.z()*r32.x()*dsindC.x() - r32.z()*r32.y()*dsindC.y()); |
| 107 |
< |
|
| 108 |
< |
f2.x() = dVdsinPhi*(-(r32.y()*r21.y() + r32.z()*r21.z())*dsindC.x() + (2.0*r32.x()*r21.y() - r21.x()*r32.y())*dsindC.y() |
| 109 |
< |
+ (2.0*r32.x()*r21.z() - r21.x()*r32.z())*dsindC.z() + dsindB.z()*r43.y() - dsindB.y()*r43.z()); |
| 110 |
< |
|
| 111 |
< |
f2.y() = dVdsinPhi*(-(r32.z()*r21.z() + r32.x()*r21.x())*dsindC.y() + (2.0*r32.y()*r21.z() - r21.y()*r32.z())*dsindC.z() |
| 112 |
< |
+ (2.0*r32.y()*r21.x() - r21.y()*r32.x())*dsindC.x() + dsindB.x()*r43.z() - dsindB.z()*r43.x()); |
| 113 |
< |
|
| 114 |
< |
f2.z() = dVdsinPhi*(-(r32.x()*r21.x() + r32.y()*r21.y())*dsindC.z() + (2.0*r32.z()*r21.x() - r21.z()*r32.x())*dsindC.x() |
| 115 |
< |
+(2.0*r32.z()*r21.y() - r21.z()*r32.y())*dsindC.y() + dsindB.y()*r43.x() - dsindB.x()*r43.y()); |
| 116 |
< |
|
| 117 |
< |
f3 = dVdsinPhi * cross(dsindB, r32); |
| 118 |
< |
} |
| 119 |
< |
|
| 99 |
> |
|
| 100 |
|
atom1_->addFrc(f1); |
| 101 |
|
atom2_->addFrc(f2 - f1); |
| 102 |
|
atom3_->addFrc(f3 - f2); |
| 103 |
|
atom4_->addFrc(-f3); |
| 104 |
< |
} |
| 105 |
< |
|
| 104 |
> |
|
| 105 |
> |
if (doParticlePot) { |
| 106 |
> |
atom1_->addParticlePot(potential_); |
| 107 |
> |
atom2_->addParticlePot(potential_); |
| 108 |
> |
atom3_->addParticlePot(potential_); |
| 109 |
> |
atom4_->addParticlePot(potential_); |
| 110 |
> |
} |
| 111 |
> |
|
| 112 |
> |
angle = acos(cos_phi) /M_PI * 180.0; |
| 113 |
> |
} |
| 114 |
|
} |
