| 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, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include "primitives/Inversion.hpp" |
| 43 |
|
|
| 44 |
< |
namespace oopse { |
| 44 |
> |
namespace OpenMD { |
| 45 |
|
|
| 46 |
|
Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, |
| 47 |
|
Atom *atom4, InversionType *it) : |
| 50 |
|
|
| 51 |
|
void Inversion::calcForce(RealType& angle) { |
| 52 |
|
|
| 53 |
< |
// In OOPSE's version of an inversion, the central atom |
| 53 |
> |
// In OpenMD's version of an inversion, the central atom |
| 54 |
|
// comes first. However, to get the planarity in a typical cosine |
| 55 |
|
// version of this potential (i.e. Amber-style), the central atom |
| 56 |
|
// is treated as atom *3* in a standard torsion form: |
| 94 |
|
f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA)); |
| 95 |
|
f3 = dVdcosPhi * cross(dcosdB, r43); |
| 96 |
|
|
| 97 |
< |
// In OOPSE's version of an improper torsion, the central atom |
| 97 |
> |
// In OpenMD's version of an improper torsion, the central atom |
| 98 |
|
// comes first. However, to get the planarity in a typical cosine |
| 99 |
|
// version of this potential (i.e. Amber-style), the central atom |
| 100 |
|
// is treated as atom *3* in a standard torsion form: |
| 101 |
|
|
| 102 |
|
// AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon) |
| 103 |
< |
// OOPSE: I - (J - K - L) (e.g. I is sp2 hybridized carbon) |
| 103 |
> |
// OpenMD: I - (J - K - L) (e.g. I is sp2 hybridized carbon) |
| 104 |
|
|
| 105 |
|
// Confusing enough? Good. |
| 106 |
|
|
