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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 |
| 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)) |
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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 |
| 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 |
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* 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 |
| 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, 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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|
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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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f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA)); |
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f3 = dVdcosPhi * cross(dcosdB, r43); |
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|
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< |
// In OOPSE's version of an improper torsion, the central atom |
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> |
// In OpenMD's version of an improper torsion, the central atom |
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// comes first. However, to get the planarity in a typical cosine |
| 100 |
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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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// AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon) |
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// OOPSE: I - (J - K - L) (e.g. I is sp2 hybridized carbon) |
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> |
// OpenMD: I - (J - K - L) (e.g. I is sp2 hybridized carbon) |
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|
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// Confusing enough? Good. |
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|
