update pair_pod
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exapde
@ -414,134 +414,134 @@ void CPairPOD::podNeighPairs(int *atomtypes, int start, int end)
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numneighsum[ii+1] = numneighsum[ii+1] + numneighsum[ii];
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}
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double CPairPOD::podenergy(double *x, double *a1, double *a2, double *a3, int *atomtypes, int inum)
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{
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// determine computation blocks
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this->get_atomblocks(inum);
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// check and allocate memory for atom/pair arrays, and create full neighbor list
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this->check_pairmemory(x, a1, a2, a3, inum);
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// initialize global descriptors to zero
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int nd1234 = podptr->pod.nd1234;
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podptr->podArraySetValue(gd, 0.0, nd1234);
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for (int i = 0; i< numblocks; i++) {
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// number of atoms in this computation block
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int nat = atomblocks[i+1] - atomblocks[i];
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// get POD neighbor pairs for this computation block
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podNeighPairs(atomtypes, atomblocks[i], atomblocks[i+1]);
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// compute global POD descriptors for this computation block
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podptr->linear_descriptors_ij(gd, tmpmem, rij, &tmpmem[nat*nd1234], numneighsum,
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typeai, idxi, ti, tj, nat, nij);
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}
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// compute energy and effective coefficients
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energy = podptr->calculate_energy(energycoeff, forcecoeff, gd, podcoeff);
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return energy;
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}
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double CPairPOD::podeatom(double *eatom, double *x, double *a1, double *a2, double *a3, int *atomtypes, int inum)
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{
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int nd1234 = podptr->pod.nd1234;
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// compute energy and effective coefficients
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energy = this->podenergy(x, a1, a2, a3, atomtypes, inum);
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// initialize force to zero
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podptr->podArraySetValue(eatom, 0.0, inum);
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for (int i = 0; i< numblocks; i++) { // loop over each computation block
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// # of atoms in this computation block
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int nat = atomblocks[i+1] - atomblocks[i];
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// get POD neighbor pairs for this computation block
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podNeighPairs(atomtypes, atomblocks[i], atomblocks[i+1]);
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// compute global POD descriptors for this computation block
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podptr->linear_descriptors_ij(gd, tmpmem, rij, &tmpmem[nat*nd1234], numneighsum,
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typeai, idxi, ti, tj, nat, nij);
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// calculate eatom = ld * energycoeff
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char chn = 'N';
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double one = 1.0, zero = 0.0;
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int inc1 = 1;
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DGEMV(&chn, &nat, &nd1234, &one, tmpmem, &nat, energycoeff, &inc1, &zero, &eatom[atomblocks[i]], &inc1);
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}
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return energy;
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}
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void CPairPOD::podforce(double *f, double *x, double *a1, double *a2, double *a3, int *atomtypes, int inum)
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{
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// initialize force to zero
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podptr->podArraySetValue(f, 0.0, dim*inum);
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for (int i = 0; i< numblocks; i++) { // loop over each computation block
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// # of atoms in this computation block
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int nat = atomblocks[i+1] - atomblocks[i];
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// get POD neighbor pairs for this computation block
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podNeighPairs(atomtypes, atomblocks[i], atomblocks[i+1]);
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// compute atomic force for this computation block
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podptr->calculate_force(f, forcecoeff, rij, tmpmem, numneighsum,
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typeai, idxi, ai, aj, ti, tj, nat, nij);
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}
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}
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double CPairPOD::podenergyforce(double *f, double *x, double *a1, double *a2, double *a3, int *atomtypes, int inum)
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{
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// compute energy and effective coefficients
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energy = this->podenergy(x, a1, a2, a3, atomtypes, inum);
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// initialize force to zero
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podptr->podArraySetValue(f, 0.0, dim*inum);
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for (int i = 0; i< numblocks; i++) { // loop over each computation block
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// # of atoms in this computation block
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int nat = atomblocks[i+1] - atomblocks[i];
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// get POD neighbor pairs for this computation block
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podNeighPairs(atomtypes, atomblocks[i], atomblocks[i+1]);
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// compute atomic force for this computation block
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podptr->calculate_force(f, forcecoeff, rij, tmpmem, numneighsum,
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typeai, idxi, ai, aj, ti, tj, nat, nij);
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}
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return energy;
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}
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// double CPairPOD::podenergy(double *x, double *a1, double *a2, double *a3, int *atomtypes, int inum)
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// {
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// // determine computation blocks
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//
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// this->get_atomblocks(inum);
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//
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// // check and allocate memory for atom/pair arrays, and create full neighbor list
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//
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// this->check_pairmemory(x, a1, a2, a3, inum);
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//
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// // initialize global descriptors to zero
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//
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// int nd1234 = podptr->pod.nd1234;
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// podptr->podArraySetValue(gd, 0.0, nd1234);
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//
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// for (int i = 0; i< numblocks; i++) {
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//
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// // number of atoms in this computation block
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//
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// int nat = atomblocks[i+1] - atomblocks[i];
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//
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// // get POD neighbor pairs for this computation block
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//
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// podNeighPairs(atomtypes, atomblocks[i], atomblocks[i+1]);
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//
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// // compute global POD descriptors for this computation block
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//
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// podptr->linear_descriptors_ij(gd, tmpmem, rij, &tmpmem[nat*nd1234], numneighsum,
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// typeai, idxi, ti, tj, nat, nij);
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//
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// }
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//
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// // compute energy and effective coefficients
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//
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// energy = podptr->calculate_energy(energycoeff, forcecoeff, gd, podcoeff);
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//
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// return energy;
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// }
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//
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// double CPairPOD::podeatom(double *eatom, double *x, double *a1, double *a2, double *a3, int *atomtypes, int inum)
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// {
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// int nd1234 = podptr->pod.nd1234;
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//
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// // compute energy and effective coefficients
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//
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// energy = this->podenergy(x, a1, a2, a3, atomtypes, inum);
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//
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// // initialize force to zero
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//
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// podptr->podArraySetValue(eatom, 0.0, inum);
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//
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// for (int i = 0; i< numblocks; i++) { // loop over each computation block
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//
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// // # of atoms in this computation block
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//
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// int nat = atomblocks[i+1] - atomblocks[i];
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//
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// // get POD neighbor pairs for this computation block
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//
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// podNeighPairs(atomtypes, atomblocks[i], atomblocks[i+1]);
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//
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// // compute global POD descriptors for this computation block
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//
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// podptr->linear_descriptors_ij(gd, tmpmem, rij, &tmpmem[nat*nd1234], numneighsum,
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// typeai, idxi, ti, tj, nat, nij);
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//
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// // calculate eatom = ld * energycoeff
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//
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// char chn = 'N';
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// double one = 1.0, zero = 0.0;
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// int inc1 = 1;
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// DGEMV(&chn, &nat, &nd1234, &one, tmpmem, &nat, energycoeff, &inc1, &zero, &eatom[atomblocks[i]], &inc1);
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// }
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//
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// return energy;
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// }
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//
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// void CPairPOD::podforce(double *f, double *x, double *a1, double *a2, double *a3, int *atomtypes, int inum)
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// {
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// // initialize force to zero
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//
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// podptr->podArraySetValue(f, 0.0, dim*inum);
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//
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// for (int i = 0; i< numblocks; i++) { // loop over each computation block
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//
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// // # of atoms in this computation block
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//
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// int nat = atomblocks[i+1] - atomblocks[i];
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//
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// // get POD neighbor pairs for this computation block
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//
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// podNeighPairs(atomtypes, atomblocks[i], atomblocks[i+1]);
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//
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// // compute atomic force for this computation block
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//
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// podptr->calculate_force(f, forcecoeff, rij, tmpmem, numneighsum,
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// typeai, idxi, ai, aj, ti, tj, nat, nij);
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// }
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// }
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//
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// double CPairPOD::podenergyforce(double *f, double *x, double *a1, double *a2, double *a3, int *atomtypes, int inum)
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// {
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// // compute energy and effective coefficients
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//
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// energy = this->podenergy(x, a1, a2, a3, atomtypes, inum);
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//
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// // initialize force to zero
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//
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// podptr->podArraySetValue(f, 0.0, dim*inum);
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//
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// for (int i = 0; i< numblocks; i++) { // loop over each computation block
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//
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// // # of atoms in this computation block
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//
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// int nat = atomblocks[i+1] - atomblocks[i];
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//
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// // get POD neighbor pairs for this computation block
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//
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// podNeighPairs(atomtypes, atomblocks[i], atomblocks[i+1]);
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//
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// // compute atomic force for this computation block
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//
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// podptr->calculate_force(f, forcecoeff, rij, tmpmem, numneighsum,
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// typeai, idxi, ai, aj, ti, tj, nat, nij);
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// }
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//
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// return energy;
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// }
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void CPairPOD::lammpsNeighPairs(double **x, int **firstneigh, int *atomtypes, int *map, int *numneigh, int gi)
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{
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