| 6 |
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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 |
|
* |
| 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 |
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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 |
|
* 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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|
#include <algorithm> |
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#include <mpi.h> |
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#endif |
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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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ZConsWriter::ZConsWriter(SimInfo* info, const std::string& filename) : info_(info) { |
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//use master - slave mode, only master node writes to disk |
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#ifdef IS_MPI |
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output_ << i->mol->getGlobalIndex() <<"\t" << i->fz << "\t" << i->zpos << "\t" << i->param.zTargetPos <<std::endl; |
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} |
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#else |
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int nproc; |
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MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
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> |
int nproc = MPI::COMM_WORLD.Get_size(); |
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const int masterNode = 0; |
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int myNode = worldRank; |
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std::vector<int> tmpNFixedZmols(nproc, 0); |
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std::vector<int> nFixedZmolsInProc(nproc, 0); |
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tmpNFixedZmols[myNode] = fixedZmols.size(); |
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|
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< |
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
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< |
MPI_Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], nproc, MPI_INT, |
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< |
MPI_SUM, MPI_COMM_WORLD); |
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> |
//do MPI_ALLREDUCE to exchange the total number of atoms, |
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> |
//rigidbodies and cutoff groups |
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> |
MPI::COMM_WORLD.Allreduce(&tmpNFixedZmols[0], &nFixedZmolsInProc[0], |
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> |
nproc, MPI::INT, MPI::SUM); |
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|
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< |
MPI_Status ierr; |
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> |
MPI::Status ierr; |
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int zmolIndex; |
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|
RealType data[3]; |
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|
|
| 132 |
|
|
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|
} else { |
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for(int k =0 ; k < nFixedZmolsInProc[i]; ++k) { |
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< |
MPI_Recv(&zmolIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr); |
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< |
MPI_Recv(data, 3, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr); |
| 135 |
> |
MPI::COMM_WORLD.Recv(&zmolIndex, 1, MPI::INT, i, 0, ierr); |
| 136 |
> |
MPI::COMM_WORLD.Recv(data, 3, MPI::REALTYPE, i, 0, ierr); |
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|
tmpData.zmolIndex = zmolIndex; |
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|
tmpData.zforce= data[0]; |
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tmpData.zpos = data[1]; |
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|
data[0] = j->fz; |
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data[1] = j->zpos; |
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data[2] = j->param.zTargetPos; |
| 164 |
< |
MPI_Send(&zmolIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 165 |
< |
MPI_Send(data, 3, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD); |
| 164 |
> |
MPI::COMM_WORLD.Send(&zmolIndex, 1, MPI::INT, masterNode, 0); |
| 165 |
> |
MPI::COMM_WORLD.Send(data, 3, MPI::REALTYPE, masterNode, 0); |
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|
|
| 167 |
|
} |
| 168 |
|
} |
