| 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 |
|
|
| 49 |
|
#include <mpi.h> |
| 50 |
|
#endif |
| 51 |
|
|
| 52 |
< |
namespace oopse { |
| 52 |
> |
namespace OpenMD { |
| 53 |
|
RestWriter::RestWriter(SimInfo* info, const std::string& filename, |
| 54 |
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std::vector<Restraint*> restraints ) : |
| 55 |
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info_(info){ |
| 74 |
|
// TODO: get Restraint info from slave nodes: |
| 75 |
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std::vector<Restraint*>::const_iterator resti; |
| 76 |
|
for(resti=restraints.begin(); resti != restraints.end(); ++resti){ |
| 77 |
< |
std::string myName = (*resti)->getRestraintName(); |
| 78 |
< |
int myType = (*resti)->getRestraintType(); |
| 79 |
< |
|
| 80 |
< |
output_ << myName << ":"; |
| 81 |
< |
|
| 82 |
< |
if (myType & Restraint::rtDisplacement) |
| 83 |
< |
output_ << "\tPosition(angstroms)\tEnergy(kcal/mol)"; |
| 84 |
< |
|
| 85 |
< |
if (myType & Restraint::rtTwist) |
| 86 |
< |
output_ << "\tTwistAngle(radians)\tEnergy(kcal/mol)"; |
| 87 |
< |
|
| 88 |
< |
if (myType & Restraint::rtSwingX) |
| 89 |
< |
output_ << "\tSwingXAngle(radians)\tEnergy(kcal/mol)"; |
| 90 |
< |
|
| 91 |
< |
if (myType & Restraint::rtSwingY) |
| 92 |
< |
output_ << "\tSwingYAngle(radians)\tEnergy(kcal/mol)"; |
| 93 |
< |
|
| 77 |
> |
|
| 78 |
> |
if ((*resti)->getPrintRestraint()) { |
| 79 |
> |
std::string myName = (*resti)->getRestraintName(); |
| 80 |
> |
int myType = (*resti)->getRestraintType(); |
| 81 |
> |
|
| 82 |
> |
output_ << myName << ":"; |
| 83 |
> |
|
| 84 |
> |
if (myType & Restraint::rtDisplacement) |
| 85 |
> |
output_ << "\tPosition(angstroms)\tEnergy(kcal/mol)"; |
| 86 |
> |
|
| 87 |
> |
if (myType & Restraint::rtTwist) |
| 88 |
> |
output_ << "\tTwistAngle(radians)\tEnergy(kcal/mol)"; |
| 89 |
> |
|
| 90 |
> |
if (myType & Restraint::rtSwingX) |
| 91 |
> |
output_ << "\tSwingXAngle(radians)\tEnergy(kcal/mol)"; |
| 92 |
> |
|
| 93 |
> |
if (myType & Restraint::rtSwingY) |
| 94 |
> |
output_ << "\tSwingYAngle(radians)\tEnergy(kcal/mol)"; |
| 95 |
> |
|
| 96 |
> |
} |
| 97 |
|
} |
| 98 |
|
output_ << "\n"; |
| 99 |
|
#ifdef IS_MPI |
| 127 |
|
} |
| 128 |
|
} |
| 129 |
|
|
| 130 |
< |
}// end oopse |
| 130 |
> |
}// end namespace OpenMD |
| 131 |
|
|
