| 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 "restraints/ObjectRestraint.hpp" |
| 44 |
|
|
| 45 |
< |
namespace oopse { |
| 45 |
> |
namespace OpenMD { |
| 46 |
|
|
| 47 |
|
void ObjectRestraint::calcForce(Vector3d struc) { |
| 48 |
|
|
| 49 |
|
pot_ = 0.0; |
| 49 |
– |
|
| 50 |
|
if (restType_ & rtDisplacement) { |
| 51 |
|
Vector3d del = struc - refPos_; |
| 52 |
< |
RealType r = del.length(); |
| 52 |
> |
RealType r = del.length(); |
| 53 |
|
Vector3d frc = -kDisp_ * del; |
| 54 |
|
RealType p = 0.5 * kDisp_ * del.lengthSquare(); |
| 55 |
< |
pot_ += p; |
| 55 |
> |
|
| 56 |
> |
pot_ = p; |
| 57 |
|
force_ = frc * scaleFactor_; |
| 58 |
< |
restInfo_[rtDisplacement] = std::make_pair(r,p); |
| 58 |
> |
if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r,p); |
| 59 |
|
} |
| 60 |
|
} |
| 61 |
|
|
| 69 |
|
Vector3d tBody(0.0); |
| 70 |
|
|
| 71 |
|
RotMat3x3d temp = A * refA_.transpose(); |
| 71 |
– |
|
| 72 |
|
Quat4d quat = temp.toQuaternion(); |
| 73 |
|
|
| 74 |
< |
RealType twistAngle, swingAngle; |
| 74 |
> |
RealType twistAngle; |
| 75 |
|
Vector3d swingAxis; |
| 76 |
< |
RealType tw, swingX, swingY; |
| 76 |
> |
RealType swingX, swingY; |
| 77 |
|
|
| 78 |
< |
quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis); |
| 79 |
< |
quat.toSwingTwist(tw, swingX, swingY); |
| 80 |
< |
|
| 81 |
< |
RealType dVdtwist, dVdswingX, dVdswingY; |
| 82 |
< |
RealType dTwist, dSwingX, dSwingY; |
| 78 |
> |
quat.toSwingTwist(swingX, swingY, twistAngle); |
| 79 |
> |
|
| 80 |
> |
|
| 81 |
|
RealType p; |
| 82 |
|
Vector3d tTwist, tSwing; |
| 83 |
|
|
| 84 |
|
if (restType_ & rtTwist){ |
| 85 |
< |
dTwist = twistAngle - twist0_; |
| 86 |
< |
dVdtwist = kTwist_ * sin(dTwist); |
| 87 |
< |
p = kTwist_ * (1.0 - cos(dTwist) ); |
| 85 |
> |
RealType dTwist = twistAngle - twist0_; |
| 86 |
> |
/// RealType dVdtwist = kTwist_ * sin(dTwist); |
| 87 |
> |
/// p = kTwist_ * (1.0 - cos(dTwist) ); |
| 88 |
> |
RealType dVdtwist = kTwist_ * dTwist; |
| 89 |
> |
p = 0.5 * kTwist_ * dTwist * dTwist; |
| 90 |
|
pot_ += p; |
| 91 |
|
tBody -= dVdtwist * V3Z; |
| 92 |
< |
restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 92 |
> |
if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 93 |
|
} |
| 94 |
|
|
| 95 |
|
if (restType_ & rtSwingX){ |
| 96 |
< |
dSwingX = swingX - swingX0_; |
| 97 |
< |
dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX); |
| 98 |
< |
p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
| 96 |
> |
RealType dSwingX = swingX - swingX0_; |
| 97 |
> |
/// RealType dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX); |
| 98 |
> |
/// p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
| 99 |
> |
RealType dVdswingX = kSwingX_ * dSwingX; |
| 100 |
> |
p = 0.5 * kSwingX_ * dSwingX * dSwingX; |
| 101 |
|
pot_ += p; |
| 102 |
|
tBody -= dVdswingX * V3X; |
| 103 |
< |
restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 103 |
> |
if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 104 |
|
} |
| 105 |
|
|
| 106 |
|
if (restType_ & rtSwingY){ |
| 107 |
< |
dSwingY = swingY - swingY0_; |
| 108 |
< |
dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY); |
| 109 |
< |
p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
| 107 |
> |
RealType dSwingY = swingY - swingY0_; |
| 108 |
> |
/// RealType dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY); |
| 109 |
> |
/// p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
| 110 |
> |
RealType dVdswingY = kSwingY_ * dSwingY; |
| 111 |
> |
p = 0.5 * kSwingX_ * dSwingY * dSwingY; |
| 112 |
|
pot_ += p; |
| 113 |
|
tBody -= dVdswingY * V3Y; |
| 114 |
< |
restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 114 |
> |
if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 115 |
|
} |
| 116 |
|
|
| 117 |
|
Vector3d tLab = A.transpose() * tBody; |
