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#define _FILE_OFFSET_BITS 64 |
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#include <cstring> |
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#include <iostream> |
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#include <fstream> |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
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int i, j, which_node, done, which_atom, local_index; |
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int i; |
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#ifdef IS_MPI |
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int j, which_node, done, which_atom, local_index; |
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#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
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#endif //is_mpi |
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|
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double q[4]; |
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DirectionalAtom* dAtom; |
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int nAtoms = entry_plug->n_atoms; |
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Atom** atoms = entry_plug->atoms; |
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double pos[3], vel[3]; |
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|
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|
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// write current frame to the eor file |
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|
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this->writeFinal( currentTime ); |
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|
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#ifndef IS_MPI |
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|
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outFile << nAtoms << "\n"; |
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|
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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outFile << currentTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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|
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";\n"; |
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|
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for( i=0; i<nAtoms; i++ ){ |
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atoms[i]->getPos(pos); |
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atoms[i]->getVel(vel); |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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atoms[i]->getX(), |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[i]->isDirectional() ){ |
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if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\n"; |
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|
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outFile << currentTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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|
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";\n"; |
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|
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outFile << currentTime << "\t" |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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outFile.flush(); |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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// Get the Node number which has this atom; |
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} |
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if (local_index != -1) { |
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//format the line |
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|
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atoms[local_index]->getPos(pos); |
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atoms[local_index]->getVel(vel); |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[local_index]->getType(), |
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atoms[local_index]->getX(), |
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atoms[local_index]->getY(), |
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atoms[local_index]->getZ(), |
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atoms[local_index]->get_vx(), |
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atoms[local_index]->get_vy(), |
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atoms[local_index]->get_vz()); // check here. |
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pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); // check here. |
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strcpy( writeLine, tempBuffer ); |
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if( atoms[local_index]->isDirectional() ){ |
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} |
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if (local_index != -1) { |
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//format the line |
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|
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atoms[local_index]->getPos(pos); |
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atoms[local_index]->getVel(vel); |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[local_index]->getType(), |
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atoms[local_index]->getX(), |
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atoms[local_index]->getY(), |
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atoms[local_index]->getZ(), |
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atoms[local_index]->get_vx(), |
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atoms[local_index]->get_vy(), |
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atoms[local_index]->get_vz()); // check here. |
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pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); // check here. |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[local_index]->isDirectional() ){ |
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#endif // is_mpi |
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} |
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void DumpWriter::writeFinal(){ |
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void DumpWriter::writeFinal(double finalTime){ |
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char finalName[500]; |
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ofstream finalOut; |
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|
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double q[4]; |
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DirectionalAtom* dAtom; |
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int nAtoms = entry_plug->n_atoms; |
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Atom** atoms = entry_plug->atoms; |
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int i, j, which_node, done, game_over, which_atom, local_index; |
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int i; |
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#ifdef IS_MPI |
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int j, which_node, done, which_atom, local_index; |
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#else //is_mpi |
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int nAtoms = entry_plug->n_atoms; |
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#endif //is_mpi |
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|
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double pos[3], vel[3]; |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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|
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finalOut << nAtoms << "\n"; |
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|
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finalOut << entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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finalOut << finalTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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|
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";\n"; |
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for( i=0; i<nAtoms; i++ ){ |
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atoms[i]->getPos(pos); |
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atoms[i]->getVel(vel); |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
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atoms[i]->getX(), |
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atoms[i]->getY(), |
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atoms[i]->getZ(), |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[i]->isDirectional() ){ |
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if( worldRank == 0 ){ |
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finalOut << mpiSim->getTotAtoms() << "\n"; |
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|
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finalOut << entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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finalOut << finalTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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|
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";\n"; |
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|
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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// Get the Node number which has this molecule: |
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for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
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if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
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} |
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if (local_index != -1) { |
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if (local_index != -1) { |
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|
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atoms[local_index]->getPos(pos); |
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atoms[local_index]->getVel(vel); |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[local_index]->getType(), |
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atoms[local_index]->getX(), |
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atoms[local_index]->getY(), |
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atoms[local_index]->getZ(), |
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atoms[local_index]->get_vx(), |
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atoms[local_index]->get_vy(), |
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atoms[local_index]->get_vz()); |
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pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[local_index]->isDirectional() ){ |
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} |
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if (local_index != -1) { |
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|
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atoms[local_index]->getPos(pos); |
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atoms[local_index]->getVel(vel); |
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|
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//format the line |
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[local_index]->getType(), |
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atoms[local_index]->getX(), |
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atoms[local_index]->getY(), |
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atoms[local_index]->getZ(), |
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atoms[local_index]->get_vx(), |
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atoms[local_index]->get_vy(), |
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atoms[local_index]->get_vz()); // check here. |
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pos[0], |
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pos[1], |
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pos[2], |
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vel[0], |
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vel[1], |
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vel[2]); // check here. |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[local_index]->isDirectional() ){ |