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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 |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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/** |
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#include "primitives/StuntDouble.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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#include "types/AtomStamp.hpp" |
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namespace oopse{ |
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> |
namespace OpenMD{ |
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class RigidBody : public StuntDouble { |
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public: |
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|
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|
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virtual std::string getType() { return name_;} |
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|
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/** Sets the name of this stuntdouble*/ |
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/** Sets the name of this stuntRealType*/ |
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virtual void setType(const std::string& name) { name_ = name;} |
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|
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|
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|
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|
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/** Sets the internal unit frame of this stuntdouble by three euler angles */ |
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void setElectroFrameFromEuler(double phi, double theta, double psi); |
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> |
void setElectroFrameFromEuler(RealType phi, RealType theta, RealType psi); |
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|
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/** |
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* Returns the gradient of this stuntdouble |
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* @return the inertia tensor of this stuntdouble |
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* @see #setI |
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*/ |
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virtual std::vector<double> getGrad(); |
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virtual std::vector<RealType> getGrad(); |
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|
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virtual void accept(BaseVisitor* v); |
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|
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void addAtom(Atom* at, AtomStamp* ats); |
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|
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/** calculate the reference coordinates */ |
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/** calculates the reference coordinates */ |
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void calcRefCoords(); |
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|
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/** Convert Atomic forces and torques to total forces and torques */ |
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/** Converts Atomic forces and torques to total forces and torques */ |
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void calcForcesAndTorques(); |
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|
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/** Converts Atomic forces and torques to total forces and torques and computes the rigid body contribution to the virial. Returns the rigid body contribution to the virial as a 3x3 matrix. */ |
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Mat3x3d calcForcesAndTorquesAndVirial(); |
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|
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/** update the positions of atoms belong to this rigidbody */ |
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void updateAtoms(); |
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|
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std::vector<RotMat3x3d> refOrients_; |
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}; |
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|
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}//namepace oopse |
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> |
}//namespace OpenMD |
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|
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#endif //PRIMITIVES_RIGIDBODY_HPP |
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|
