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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 |
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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 |
| 12 |
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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 |
| 15 |
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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 |
| 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 |
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* 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 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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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: |
| 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). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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+ |
* [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 "primitives/Inversion.hpp" |
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#include "fstream" |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, |
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Atom *atom4, InversionType *it) : |
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|
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void Inversion::calcForce(RealType& angle) { |
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|
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// In OOPSE's version of an inversion, the central atom |
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> |
// In OpenMD's version of an inversion, the central atom |
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// comes first. However, to get the planarity in a typical cosine |
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// version of this potential (i.e. Amber-style), the central atom |
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// is treated as atom *3* in a standard torsion form: |
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|
|
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Vector3d pos1 = atom2_->getPos(); |
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Vector3d pos2 = atom1_->getPos(); |
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< |
Vector3d pos3 = atom4_->getPos(); |
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Vector3d pos4 = atom3_->getPos(); |
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> |
Vector3d pos2 = atom3_->getPos(); |
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> |
Vector3d pos3 = atom1_->getPos(); |
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> |
Vector3d pos4 = atom4_->getPos(); |
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|
|
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/*std::ofstream myfile; |
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myfile.open("Inversion", std::ios::app); |
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myfile << atom1_->getType() << " - atom1; " |
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<< atom2_->getType() << " - atom2; " |
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<< atom3_->getType() << " - atom3; " |
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<< atom4_->getType() << " - atom4; " |
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<< std::endl; |
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*/ |
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Vector3d r21 = pos1 - pos2; |
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Vector3d r32 = pos2 - pos3; |
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Vector3d r42 = pos2 - pos4; |
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> |
Vector3d r31 = pos1 - pos3; |
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> |
Vector3d r23 = pos3 - pos2; |
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> |
Vector3d r43 = pos3 - pos4; |
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|
|
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// Calculate the cross products and distances |
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Vector3d A = cross(r21, r32); |
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> |
Vector3d A = cross(r31, r43); |
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RealType rA = A.length(); |
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< |
Vector3d B = cross(r32, r42); |
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> |
Vector3d B = cross(r43, r23); |
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RealType rB = B.length(); |
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//Vector3d C = cross(r23, A); |
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//RealType rC = C.length(); |
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|
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// Calculate the sin and cos |
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RealType cos_phi = dot(A, B) ; |
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if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0" |
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< |
<< std::endl;} |
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< |
if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0" |
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< |
<< std::endl;} |
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< |
//std::cout << "We actually use this inversion!!!!" << std::endl; |
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> |
if (cos_phi > 1.0) cos_phi = 1.0; |
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> |
if (cos_phi < -1.0) cos_phi = -1.0; |
| 84 |
|
|
| 85 |
|
RealType dVdcosPhi; |
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– |
//cos_phi = 2.0*cos_phi*cos_phi - 1.0; |
| 86 |
|
inversionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
| 87 |
|
Vector3d f1 ; |
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|
Vector3d f2 ; |
| 91 |
|
Vector3d dcosdA = (cos_phi * A - B) /rA; |
| 92 |
|
Vector3d dcosdB = (cos_phi * B - A) /rB; |
| 93 |
|
|
| 94 |
< |
f1 = dVdcosPhi * cross(r32, dcosdA); |
| 95 |
< |
f2 = dVdcosPhi * ( cross(r42, dcosdB) - cross(r21, dcosdA)); |
| 96 |
< |
f3 = dVdcosPhi * cross(dcosdB, r32); |
| 94 |
> |
f1 = dVdcosPhi * cross(r43, dcosdA); |
| 95 |
> |
f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA)); |
| 96 |
> |
f3 = dVdcosPhi * cross(dcosdB, r43); |
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|
|
| 98 |
< |
// In OOPSE's version of an improper torsion, the central atom |
| 98 |
> |
// In OpenMD's version of an improper torsion, the central atom |
| 99 |
|
// comes first. However, to get the planarity in a typical cosine |
| 100 |
|
// version of this potential (i.e. Amber-style), the central atom |
| 101 |
|
// is treated as atom *3* in a standard torsion form: |
| 102 |
|
|
| 103 |
|
// AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon) |
| 104 |
< |
// OOPSE: I - (J - K - L) (e.g. I is sp2 hybridized carbon) |
| 104 |
> |
// OpenMD: I - (J - K - L) (e.g. I is sp2 hybridized carbon) |
| 105 |
|
|
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|
// Confusing enough? Good. |
| 107 |
|
|
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|
atom4_->addFrc(-f2); |
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|
atom3_->addFrc(-f3); |
| 112 |
|
|
| 113 |
+ |
atom1_->addParticlePot(potential_); |
| 114 |
+ |
atom2_->addParticlePot(potential_); |
| 115 |
+ |
atom3_->addParticlePot(potential_); |
| 116 |
+ |
atom4_->addParticlePot(potential_); |
| 117 |
+ |
|
| 118 |
|
angle = acos(cos_phi) /M_PI * 180.0; |
| 119 |
|
} |
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|
