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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
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* |
| 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 |
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* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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* 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 |
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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 |
| 13 |
|
* 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. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
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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). |
| 37 |
+ |
* [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] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include <cmath> |
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#include "visitors/ZconsVisitor.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/StringUtils.hpp" |
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namespace oopse { |
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> |
#include "types/ZconsStamp.hpp" |
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> |
namespace OpenMD { |
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|
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ZConsVisitor::ZConsVisitor(SimInfo* info) : BaseVisitor(), info_(info), zconsReader_(NULL){ |
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|
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currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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Globals* simParam = info_->getSimParams(); |
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|
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if (simParam->haveZconstraintTime()){ |
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> |
if (simParam->haveZconsTime()){ |
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zconsTime_ = simParam->getZconsTime(); |
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} |
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else{ |
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zconsTol_ = 0.01; |
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sprintf(painCave.errMsg, |
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"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n" |
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"\tOOPSE will use a default value of %f.\n" |
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> |
"\tOpenMD will use a default value of %f.\n" |
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"\tTo set the tolerance, use the zconsTol variable.\n", |
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zconsTol_); |
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painCave.isFatal = 0; |
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simError(); |
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} |
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|
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int nZconstraints = simParam->getNzConstraints(); |
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ZconStamp** stamp = simParam->getZconStamp(); |
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> |
int nZconstraints = simParam->getNZconsStamps(); |
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> |
std::vector<ZConsStamp*> stamp = simParam->getZconsStamps(); |
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for (int i = 0; i < nZconstraints; i++){ |
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int zmolIndex = stamp[i]->getMolIndex(); |
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zmolStates_.insert(std::make_pair(zmolIndex, zsMoving)); |
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|
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} |
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|
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< |
void ZConsVisitor::readZconsFile(double time) { |
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< |
double tempTime; |
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> |
void ZConsVisitor::readZconsFile(RealType time) { |
| 161 |
> |
RealType tempTime; |
| 162 |
|
while(zconsReader_->hasNextFrame()){ |
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tempTime = zconsReader_->getCurTime(); |
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if(tempTime >= time) { |
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sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str()); |
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result += buffer; |
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|
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< |
sprintf(buffer , "number of zconstraint molecule: %d\n", zmolStates_.size()); |
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> |
sprintf(buffer , "number of zconstraint molecule: %d\n", (int) zmolStates_.size()); |
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|
result += buffer; |
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|
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|
sprintf(buffer , "zconstraint tolerance = %lf\n", zconsTol_); |
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|
} |
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|
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|
|
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< |
}//namespace oopse |
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> |
}//namespace OpenMD |
