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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
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< |
* 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 |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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< |
* 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 |
|
* |
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< |
* 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 |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
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+ |
* 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). |
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+ |
* [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). |
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+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "restraints/ObjectRestraint.hpp" |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
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void ObjectRestraint::calcForce(Vector3d struc) { |
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|
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pot_ = 0.0; |
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– |
|
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if (restType_ & rtDisplacement) { |
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Vector3d del = struc - refPos_; |
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< |
RealType r = del.length(); |
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> |
RealType r = del.length(); |
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Vector3d frc = -kDisp_ * del; |
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RealType p = 0.5 * kDisp_ * del.lengthSquare(); |
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< |
pot_ += p; |
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> |
|
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> |
pot_ = p; |
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|
force_ = frc * scaleFactor_; |
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< |
restInfo_[rtDisplacement] = std::make_pair(r,p); |
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> |
if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r,p); |
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|
} |
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} |
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|
| 70 |
|
|
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RotMat3x3d temp = A * refA_.transpose(); |
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|
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+ |
Vector3d euler = temp.toEulerAngles(); |
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+ |
|
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Quat4d quat = temp.toQuaternion(); |
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|
|
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< |
RealType twistAngle, swingAngle; |
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> |
RealType twistAngle; |
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|
Vector3d swingAxis; |
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< |
RealType tw, swingX, swingY; |
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> |
RealType swingX, swingY; |
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|
|
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< |
quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis); |
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< |
quat.toSwingTwist(tw, swingX, swingY); |
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< |
|
| 81 |
< |
RealType dVdtwist, dVdswingX, dVdswingY; |
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< |
RealType dTwist, dSwingX, dSwingY; |
| 81 |
> |
quat.toSwingTwist(swingX, swingY, twistAngle); |
| 82 |
> |
|
| 83 |
> |
|
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|
RealType p; |
| 85 |
|
Vector3d tTwist, tSwing; |
| 86 |
|
|
| 87 |
|
if (restType_ & rtTwist){ |
| 88 |
< |
dTwist = twistAngle - twist0_; |
| 89 |
< |
dVdtwist = kTwist_ * sin(dTwist); |
| 90 |
< |
p = kTwist_ * (1.0 - cos(dTwist) ); |
| 88 |
> |
RealType dTwist = twistAngle - twist0_; |
| 89 |
> |
/// RealType dVdtwist = kTwist_ * sin(dTwist); |
| 90 |
> |
/// p = kTwist_ * (1.0 - cos(dTwist) ); |
| 91 |
> |
RealType dVdtwist = kTwist_ * dTwist; |
| 92 |
> |
p = 0.5 * kTwist_ * dTwist * dTwist; |
| 93 |
|
pot_ += p; |
| 94 |
|
tBody -= dVdtwist * V3Z; |
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< |
restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 95 |
> |
if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 96 |
|
} |
| 97 |
|
|
| 98 |
|
if (restType_ & rtSwingX){ |
| 99 |
< |
dSwingX = swingX - swingX0_; |
| 100 |
< |
dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX); |
| 101 |
< |
p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
| 99 |
> |
RealType dSwingX = swingX - swingX0_; |
| 100 |
> |
/// RealType dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX); |
| 101 |
> |
/// p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
| 102 |
> |
RealType dVdswingX = kSwingX_ * dSwingX; |
| 103 |
> |
p = 0.5 * kSwingX_ * dSwingX * dSwingX; |
| 104 |
|
pot_ += p; |
| 105 |
|
tBody -= dVdswingX * V3X; |
| 106 |
< |
restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 106 |
> |
if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 107 |
|
} |
| 108 |
|
|
| 109 |
|
if (restType_ & rtSwingY){ |
| 110 |
< |
dSwingY = swingY - swingY0_; |
| 111 |
< |
dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY); |
| 112 |
< |
p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
| 110 |
> |
RealType dSwingY = swingY - swingY0_; |
| 111 |
> |
/// RealType dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY); |
| 112 |
> |
/// p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
| 113 |
> |
RealType dVdswingY = kSwingY_ * dSwingY; |
| 114 |
> |
p = 0.5 * kSwingX_ * dSwingY * dSwingY; |
| 115 |
|
pot_ += p; |
| 116 |
|
tBody -= dVdswingY * V3Y; |
| 117 |
< |
restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 117 |
> |
if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 118 |
|
} |
| 119 |
|
|
| 120 |
|
Vector3d tLab = A.transpose() * tBody; |
