forked from lijiext/lammps
373 lines
12 KiB
C++
373 lines
12 KiB
C++
#include "PerPairQuantity.h"
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#include "PerAtomQuantity.h"
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#include "KernelFunction.h"
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#include "FE_Mesh.h"
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#include "Utility.h"
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#include "Quadrature.h"
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using ATC::HeartBeat;
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using std::pair;
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using std::map;
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namespace ATC {
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//==========================================================
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PairMap::PairMap(LammpsInterface * lammpsInterface, int groupbit ):
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lammpsInterface_(lammpsInterface),
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groupbit_(groupbit),
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nPairs_(0), nBonds_(0)
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{
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};
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PairMap::~PairMap(void)
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{
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};
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//==========================================================
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PairMapNeighbor::PairMapNeighbor(LammpsInterface * lammpsInterface, int groupbit):
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PairMap(lammpsInterface,groupbit)
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{
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};
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void PairMapNeighbor::reset(void) const
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{
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int inum = lammpsInterface_->neighbor_list_inum();
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int *ilist = lammpsInterface_->neighbor_list_ilist();
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int *numneigh = lammpsInterface_->neighbor_list_numneigh();
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int **firstneigh = lammpsInterface_->neighbor_list_firstneigh();
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const int * mask = lammpsInterface_->atom_mask();
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pairMap_.clear();
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int pairIndex = nBonds_;
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std::pair< int,int > pair_ij;
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for (int i = 0; i < inum; i++) {
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int lammps_i = ilist[i];
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if (mask[lammps_i] & groupbit_) {
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for (int j = 0; j < numneigh[lammps_i]; j++) {
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int lammps_j = firstneigh[lammps_i][j];
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lammpsInterface_->neighbor_remap(lammps_j);
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pair_ij.first = lammps_i; // alpha
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pair_ij.second = lammps_j; // beta
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pairMap_[pair_ij] = pairIndex;
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pairIndex++;
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}
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}
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}
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nPairs_ = pairIndex;
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needReset_ = false;
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}
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//==========================================================
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PairMapBond::PairMapBond(LammpsInterface * lammpsInterface, int groupbit):
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PairMap(lammpsInterface,groupbit)
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{
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};
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//==========================================================
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PairMapBoth::PairMapBoth(LammpsInterface * lammpsInterface, int groupbit):
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PairMapNeighbor(lammpsInterface,groupbit)
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{
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};
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//==========================================================
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DensePerPairMatrix::DensePerPairMatrix(LammpsInterface * lammpsInterface,
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const PairMap & pairMap,
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int nCols):
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lammpsInterface_(lammpsInterface),
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pairMap_(pairMap),
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nCols_(nCols)
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{
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};
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//==========================================================
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PairVirial::PairVirial(LammpsInterface * lammpsInterface,
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const PairMap & pairMap, int nCols):
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DensePerPairMatrix(lammpsInterface,pairMap,nCols)
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{
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};
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//==========================================================
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PairVirialEulerian::PairVirialEulerian(LammpsInterface * lammpsInterface,
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const PairMap & pairMap):
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PairVirial(lammpsInterface,pairMap,6)
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{
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};
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void PairVirialEulerian::reset(void) const
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{
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int nPairs = pairMap_.size();
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quantity_.reset(nPairs,nCols_);
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double **xatom = lammpsInterface_->xatom();
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for (ATOM_PAIR apair = pairMap_.start();
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! pairMap_.finished(); apair=pairMap_++){
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int lammps_a = (apair.first).first ;
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int lammps_b = (apair.first).second;
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int pairIndex = apair.second;
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double * xa = xatom[lammps_a];
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double * xb = xatom[lammps_b];
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double delx = xa[0] - xb[0];
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double dely = xa[1] - xb[1];
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double delz = xa[2] - xb[2];
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double rsq = delx*delx + dely*dely + delz*delz;
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double fforce = 0;
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lammpsInterface_->pair_force(apair,rsq,fforce);
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quantity_(pairIndex,0)=-delx*delx*fforce;
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quantity_(pairIndex,1)=-dely*dely*fforce;
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quantity_(pairIndex,2)=-delz*delz*fforce;
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quantity_(pairIndex,3)=-delx*dely*fforce;
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quantity_(pairIndex,4)=-delx*delz*fforce;
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quantity_(pairIndex,5)=-dely*delz*fforce;
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}
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}
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//==========================================================
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PairVirialLagrangian::PairVirialLagrangian(LammpsInterface * lammpsInterface,
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const PairMap & pairMap,
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double ** xRef):
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// const PerAtomQuantity<double> * xRef):
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PairVirial(lammpsInterface,pairMap,9),
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xRef_(xRef)
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{
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};
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void PairVirialLagrangian::reset(void) const
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{
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int nPairs = pairMap_.size();
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quantity_.reset(nPairs,nCols_);
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double **xatom = lammpsInterface_->xatom();
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double ** xref = xRef_;
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for (ATOM_PAIR apair = pairMap_.start();
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! pairMap_.finished(); apair=pairMap_++){
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int lammps_a = (apair.first).first ;
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int lammps_b = (apair.first).second;
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int pairIndex = apair.second;
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double * xa = xatom[lammps_a];
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double * xb = xatom[lammps_b];
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double delx = xa[0] - xb[0];
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double dely = xa[1] - xb[1];
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double delz = xa[2] - xb[2];
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double * Xa = xref[lammps_a];
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double * Xb = xref[lammps_b];
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double delX = Xa[0] - Xb[0];
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double delY = Xa[1] - Xb[1];
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double delZ = Xa[2] - Xb[2];
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double rsq = delx*delx + dely*dely + delz*delz;
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double fforce = 0;
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lammpsInterface_->pair_force(apair,rsq,fforce);
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quantity_(pairIndex,0)=-delx*fforce*delX;
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quantity_(pairIndex,1)=-delx*fforce*delY;
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quantity_(pairIndex,2)=-delx*fforce*delZ;
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quantity_(pairIndex,3)=-dely*fforce*delX;
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quantity_(pairIndex,4)=-dely*fforce*delY;
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quantity_(pairIndex,5)=-dely*fforce*delZ;
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quantity_(pairIndex,6)=-delz*fforce*delX;
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quantity_(pairIndex,7)=-delz*fforce*delY;
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quantity_(pairIndex,8)=-delz*fforce*delZ;
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}
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}
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//==========================================================
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PairPotentialHeatFlux::PairPotentialHeatFlux(LammpsInterface * lammpsInterface,
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const PairMap & pairMap):
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DensePerPairMatrix(lammpsInterface,pairMap,3)
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{
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};
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//==========================================================
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PairPotentialHeatFluxEulerian::PairPotentialHeatFluxEulerian(LammpsInterface * lammpsInterface,
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const PairMap & pairMap):
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PairPotentialHeatFlux(lammpsInterface,pairMap)
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{
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};
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void PairPotentialHeatFluxEulerian::reset(void) const
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{
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int nPairs = pairMap_.size();
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quantity_.reset(nPairs,nCols_);
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double **xatom = lammpsInterface_->xatom();
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double **vatom = lammpsInterface_->vatom();
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for (ATOM_PAIR apair = pairMap_.start();
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! pairMap_.finished(); apair=pairMap_++){
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int lammps_a = (apair.first).first ;
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int lammps_b = (apair.first).second;
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int pairIndex = apair.second;
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double * xa = xatom[lammps_a];
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double * xb = xatom[lammps_b];
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double delx = xa[0] - xb[0];
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double dely = xa[1] - xb[1];
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double delz = xa[2] - xb[2];
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double rsq = delx*delx + dely*dely + delz*delz;
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double fforce = 0;
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lammpsInterface_->pair_force(apair,rsq,fforce);
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double* v = vatom[lammps_a];
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fforce *=delx*v[0] + dely*v[1] + delz*v[2];
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quantity_(pairIndex,0)=fforce*delx;
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quantity_(pairIndex,1)=fforce*dely;
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quantity_(pairIndex,2)=fforce*delz;
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}
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}
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//==========================================================
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PairPotentialHeatFluxLagrangian::PairPotentialHeatFluxLagrangian(LammpsInterface * lammpsInterface,
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const PairMap & pairMap, double ** xRef):
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PairPotentialHeatFlux(lammpsInterface,pairMap),
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xRef_(xRef)
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{
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};
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void PairPotentialHeatFluxLagrangian::reset(void) const
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{
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int nPairs = pairMap_.size();
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quantity_.reset(nPairs,nCols_);
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double **xatom = lammpsInterface_->xatom();
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double **vatom = lammpsInterface_->vatom();
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for (ATOM_PAIR apair = pairMap_.start();
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! pairMap_.finished(); apair=pairMap_++){
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int lammps_a = (apair.first).first ;
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int lammps_b = (apair.first).second;
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int pairIndex = apair.second;
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double * xa = xatom[lammps_a];
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double * xb = xatom[lammps_b];
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double delx = xa[0] - xb[0];
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double dely = xa[1] - xb[1];
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double delz = xa[2] - xb[2];
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double * Xa = xRef_[lammps_a];
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double * Xb = xRef_[lammps_b];
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double delX = Xa[0] - Xb[0];
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double delY = Xa[1] - Xb[1];
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double delZ = Xa[2] - Xb[2];
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double rsq = delx*delx + dely*dely + delz*delz;
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double fforce = 0;
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lammpsInterface_->pair_force(apair,rsq,fforce);
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double* v = vatom[lammps_a];
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fforce *=delx*v[0] + dely*v[1] + delz*v[2];
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quantity_(pairIndex,0)=fforce*delX;
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quantity_(pairIndex,1)=fforce*delY;
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quantity_(pairIndex,2)=fforce*delZ;
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}
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}
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//==========================================================
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SparsePerPairMatrix::SparsePerPairMatrix(LammpsInterface * lammpsInterface,
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const PairMap & pairMap):
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lammpsInterface_(lammpsInterface),
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pairMap_(pairMap)
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{
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};
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//==========================================================
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BondMatrix::BondMatrix(LammpsInterface * lammpsInterface,
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const PairMap & pairMap, double ** x, const FE_Mesh * feMesh):
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SparsePerPairMatrix(lammpsInterface,pairMap), x_(x), feMesh_(feMesh)
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{
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};
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//==========================================================
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BondMatrixKernel::BondMatrixKernel(LammpsInterface * lammpsInterface,
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const PairMap & pairMap,
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double ** x,
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const FE_Mesh * feMesh,
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const KernelFunction * kernelFunction):
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BondMatrix(lammpsInterface,pairMap,x,feMesh),
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kernelFunction_(kernelFunction)
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{
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if (kernelFunction_ == NULL)
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throw ATC_Error("No AtC kernel function initialized");
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};
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void BondMatrixKernel::reset(void) const
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{
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int nPairs = pairMap_.size(); // needs to come after quantity for reset
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int nNodes = feMesh_->num_nodes_unique();
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quantity_.reset(nNodes,nPairs);
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double lam1,lam2;
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std::pair< int,int > pair_jk;
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int heartbeatFreq = (nNodes <= 10 ? 1 : (int) nNodes / 10);
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HeartBeat beat("computing bond matrix ",heartbeatFreq);
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beat.start();
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DENS_VEC xa(3),xI(3),xaI(3),xb(3),xbI(3),xba(3);
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double invVol = kernelFunction_->inv_vol();
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for (int I = 0; I < nNodes; I++) {
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beat.next();
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xI = feMesh_->nodal_coordinates(I);
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if (!kernelFunction_->node_contributes(xI)) { continue; }
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for (ATOM_PAIR apair = pairMap_.start();
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! pairMap_.finished(); apair=pairMap_++){
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int lammps_a = (apair.first).first ;
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int lammps_b = (apair.first).second;
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xa.copy(x_[lammps_a],3);
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xaI = xa - xI;
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lammpsInterface_->periodicity_correction(xaI.ptr());
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xb.copy(x_[lammps_b],3);
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xba = xb - xa;
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xbI = xba + xaI;
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kernelFunction_->bond_intercepts(xaI,xbI,lam1,lam2);
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if (lam1 < lam2) {
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double bondValue = invVol*(kernelFunction_->bond(xaI,xbI,lam1,lam2));
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int pairIndex = apair.second;
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quantity_.add(I,pairIndex,bondValue);
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} // if lam1 < lam2
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} // pair map
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} // end nodes loop
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quantity_.compress();
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beat.finish();
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}
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//==========================================================
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BondMatrixPartitionOfUnity::BondMatrixPartitionOfUnity(LammpsInterface * lammpsInterface,
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const PairMap & pairMap, double ** x, const FE_Mesh * feMesh,
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const DIAG_MAN * invVols):
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BondMatrix(lammpsInterface,pairMap,x,feMesh),
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invVols_(invVols)
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{
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ATC::Quadrature::instance()->set_line_quadrature(lineNgauss_,lineXg_,lineWg_);
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double lam1 = 0.0, lam2 = 1.0;
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double del_lambda = 0.5*(lam2 - lam1);
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double avg_lambda = 0.5*(lam2 + lam1);
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for (int i = 0; i < lineNgauss_; i++) {
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double lambda = del_lambda*lineXg_[i] +avg_lambda;
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lineXg_[i] = lambda;
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lineWg_[i] *= 0.5;
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}
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};
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void BondMatrixPartitionOfUnity::reset(void) const
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{
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int nNodes = feMesh_->num_nodes_unique();
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int nPairs = pairMap_.size();
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quantity_.reset(nNodes,nPairs);
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int nodes_per_element = feMesh_->num_nodes_per_element();
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Array<int> node_list(nodes_per_element);
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DENS_VEC shp(nodes_per_element);
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std::pair< int,int > pair_jk;
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int heartbeatFreq = (int) nPairs / 10;
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HeartBeat beat("computing bond matrix ",heartbeatFreq);
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beat.start();
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DENS_VEC xa(3),xb(3),xab(3),xlambda(3);
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for (ATOM_PAIR apair = pairMap_.start();
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! pairMap_.finished(); apair=pairMap_++){
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beat.next();
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int lammps_a = (apair.first).first ;
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int lammps_b = (apair.first).second;
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int pairIndex = apair.second;
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xa.copy(x_[lammps_a],3);
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xb.copy(x_[lammps_b],3);
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xab = xa - xb;
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for (int i = 0; i < lineNgauss_; i++) {
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double lambda = lineXg_[i];
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xlambda = lambda*xab + xb;
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lammpsInterface_->periodicity_correction(xlambda.ptr());
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feMesh_->shape_functions(xlambda,shp,node_list);
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// accumulate to nodes whose support overlaps the integration point
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for (int I = 0; I < nodes_per_element; I++) {
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int Inode = node_list(I);
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double inv_vol = (invVols_->quantity())(Inode,Inode);
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double val = inv_vol*shp(I)*lineWg_[i];
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quantity_.add(Inode,pairIndex,val);
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}
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}
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}
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quantity_.compress();
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beat.finish();
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}
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//==========================================================
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}
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