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/dports/math/cppad/CppAD-20210000.8/include/cppad/local/sweep/
H A Dfor_hes.hpp457 atom_j = 0; in for_hes()
484 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in for_hes()
487 atom_x[atom_j] = parameter[arg[0]]; in for_hes()
490 type_x[atom_j] = dynamic_enum; in for_hes()
492 type_x[atom_j] = constant_enum; in for_hes()
495 ++atom_j; in for_hes()
496 if( atom_j == atom_n ) in for_hes()
505 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in for_hes()
509 type_x[atom_j] = variable_enum; in for_hes()
512 ++atom_j; in for_hes()
[all …]
H A Dreverse.hpp657 atom_j = atom_n; in reverse()
669 CPPAD_ASSERT_UNKNOWN( atom_j == 0 ); in reverse()
697 CPPAD_ASSERT_UNKNOWN( atom_j <= atom_n ); in reverse()
700 --atom_j; in reverse()
701 atom_ix[atom_j] = 0; in reverse()
711 if( atom_j == 0 ) in reverse()
722 --atom_j; in reverse()
723 atom_ix[atom_j] = size_t( arg[0] ); in reverse()
724 atom_type_x[atom_j] = variable_enum; in reverse()
727 atom_tx[atom_j*atom_k1 + ell] = in reverse()
[all …]
H A Drev_jac.hpp648 atom_j = atom_n; in rev_jac()
681 --atom_j; in rev_jac()
683 atom_x[atom_j] = parameter[arg[0]]; in rev_jac()
686 type_x[atom_j] = dynamic_enum; in rev_jac()
688 type_x[atom_j] = constant_enum; in rev_jac()
690 atom_ix[atom_j] = 0; in rev_jac()
692 if( atom_j == 0 ) in rev_jac()
703 --atom_j; in rev_jac()
706 type_x[atom_j] = variable_enum; in rev_jac()
708 atom_ix[atom_j] = size_t(arg[0]); in rev_jac()
[all …]
H A Dfor_jac.hpp623 atom_j = 0; in for_jac()
656 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in for_jac()
659 atom_x[atom_j] = parameter[arg[0]]; in for_jac()
662 type_x[atom_j] = dynamic_enum; in for_jac()
664 type_x[atom_j] = constant_enum; in for_jac()
667 ++atom_j; in for_jac()
668 if( atom_j == atom_n ) in for_jac()
677 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in for_jac()
681 type_x[atom_j] = variable_enum; in for_jac()
684 ++atom_j; in for_jac()
[all …]
H A Drev_hes.hpp632 atom_j = atom_n; in rev_hes()
660 --atom_j; in rev_hes()
662 atom_x[atom_j] = parameter[arg[0]]; in rev_hes()
665 type_x[atom_j] = dynamic_enum; in rev_hes()
667 type_x[atom_j] = constant_enum; in rev_hes()
669 atom_ix[atom_j] = 0; in rev_hes()
671 if( atom_j == 0 ) in rev_hes()
682 --atom_j; in rev_hes()
685 type_x[atom_j] = variable_enum; in rev_hes()
687 atom_ix[atom_j] = size_t(arg[0]); in rev_hes()
[all …]
H A Dforward2.hpp535 atom_j = 0; in forward2()
608 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in forward2()
612 atom_type_x[atom_j] = dynamic_enum; in forward2()
614 atom_type_x[atom_j] = constant_enum; in forward2()
621 ++atom_j; in forward2()
622 if( atom_j == atom_n ) in forward2()
631 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in forward2()
633 atom_type_x[atom_j] = variable_enum; in forward2()
635 atom_tx_all[atom_j*(q*r+1)+0] = in forward2()
644 ++atom_j; in forward2()
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H A Dforward0.hpp816 atom_j = 0; in forward0()
841 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in forward0()
845 atom_type_x[atom_j] = dynamic_enum; in forward0()
847 atom_type_x[atom_j] = constant_enum; in forward0()
848 atom_par_x[atom_j] = parameter[ arg[0] ]; in forward0()
849 atom_tx[atom_j++] = parameter[ arg[0] ]; in forward0()
851 if( atom_j == atom_n ) in forward0()
866 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in forward0()
868 atom_type_x[atom_j] = variable_enum; in forward0()
872 if( atom_j == atom_n ) in forward0()
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H A Dforward1.hpp900 atom_j = 0; in forward1()
934 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in forward1()
938 atom_type_x[atom_j] = dynamic_enum; in forward1()
940 atom_type_x[atom_j] = constant_enum; in forward1()
946 ++atom_j; in forward1()
947 if( atom_j == atom_n ) in forward1()
956 CPPAD_ASSERT_UNKNOWN( atom_j < atom_n ); in forward1()
958 atom_type_x[atom_j] = variable_enum; in forward1()
963 ++atom_j; in forward1()
964 if( atom_j == atom_n ) in forward1()
[all …]
/dports/math/cppad/CppAD-20210000.8/include/cppad/local/optimize/
H A Dget_par_usage.hpp332 atom_j = 0; in get_par_usage()
347 CPPAD_ASSERT_UNKNOWN( atom_j == atom_n ); in get_par_usage()
368 atom_ix[atom_j] = 0; in get_par_usage()
370 type_x[atom_j] = variable_enum; in get_par_usage()
371 ++atom_j; in get_par_usage()
372 if( atom_j == atom_n ) in get_par_usage()
379 atom_ix[atom_j] = size_t( arg[0] ); in get_par_usage()
382 type_x[atom_j] = dynamic_enum; in get_par_usage()
384 type_x[atom_j] = dynamic_enum; in get_par_usage()
385 ++atom_j; in get_par_usage()
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H A Dget_op_usage.hpp702 atom_j = atom_n; in get_op_usage()
778 CPPAD_ASSERT_UNKNOWN( 0 < atom_j && atom_j <= atom_n ); in get_op_usage()
779 --atom_j; in get_op_usage()
780 if( atom_j == 0 ) in get_op_usage()
783 atom_ix[atom_j] = 0; in get_op_usage()
788 type_x[atom_j] = dynamic_enum; in get_op_usage()
800 CPPAD_ASSERT_UNKNOWN( 0 < atom_j && atom_j <= atom_n ); in get_op_usage()
801 --atom_j; in get_op_usage()
802 if( atom_j == 0 ) in get_op_usage()
805 atom_ix[atom_j] = size_t(arg[0]); in get_op_usage()
[all …]
/dports/science/lammps/lammps-stable_29Sep2021/lib/gpu/
H A Dlal_neighbor_gpu.cu258 numtyp4 atom_i, atom_j; in calc_neigh_list_cell() local
303 fetch4(atom_j,lpid_j,pos_tex); in calc_neigh_list_cell()
306 pos_sh[tid].x = atom_j.x; in calc_neigh_list_cell()
307 pos_sh[tid].y = atom_j.y; in calc_neigh_list_cell()
308 pos_sh[tid].z = atom_j.z; in calc_neigh_list_cell()
326 diff.x = atom_i.x - simd_broadcast_d(atom_j.x, j, simd_size); in calc_neigh_list_cell()
395 numtyp4 atom_i, atom_j; in calc_neigh_list_cell() local
438 fetch4(atom_j,pid_j,pos_tex); //[pid_j]; in calc_neigh_list_cell()
439 pos_sh[tid].x = atom_j.x; in calc_neigh_list_cell()
440 pos_sh[tid].y = atom_j.y; in calc_neigh_list_cell()
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/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_KP__MD_527786671773_000/
H A DThreeBodyCluster.c125 int atom_j; in compute_routine() local
231 atom_j = neigh_list_of_current_part[neigh_count]; /* get neighbor ID */ in compute_routine()
233 if (atom_j == atom_i) continue; in compute_routine()
240 r_ij[d] = coords[atom_j * DIM + d] - coords[atom_i * DIM + d]; in compute_routine()
251 if (!(particle_contributing[atom_j] in compute_routine()
252 && atom_j < atom_i)) /* effective half-list */ in compute_routine()
256 phi2_contrib_prefactor = (particle_contributing[atom_j]) ? 1.0 : 0.5; in compute_routine()
281 force[atom_j * DIM + d] in compute_routine()
320 = coords[atom_k * DIM + d] - coords[atom_j * DIM + d]; in compute_routine()
366 force[atom_j * DIM + d] in compute_routine()
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_BH__MD_043141570610_000/
H A DThreeBodyCluster.c125 int atom_j; in compute_routine() local
231 atom_j = neigh_list_of_current_part[neigh_count]; /* get neighbor ID */ in compute_routine()
233 if (atom_j == atom_i) continue; in compute_routine()
240 r_ij[d] = coords[atom_j * DIM + d] - coords[atom_i * DIM + d]; in compute_routine()
251 if (!(particle_contributing[atom_j] in compute_routine()
252 && atom_j < atom_i)) /* effective half-list */ in compute_routine()
256 phi2_contrib_prefactor = (particle_contributing[atom_j]) ? 1.0 : 0.5; in compute_routine()
281 force[atom_j * DIM + d] in compute_routine()
320 = coords[atom_k * DIM + d] - coords[atom_j * DIM + d]; in compute_routine()
366 force[atom_j * DIM + d] in compute_routine()
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_KDS__MD_697985444380_000/
H A DThreeBodyBondOrder.c137 int atom_j; in compute_routine() local
269 atom_j = neigh_list_of_current_part[neigh_count]; /* get ID */ in compute_routine()
276 r_ij[dim] = coords[atom_j * DIM + dim] - coords[atom_i * DIM + dim]; in compute_routine()
305 atom_j = neigh_list_of_current_part[neigh_count]; /* get ID */ in compute_routine()
312 r_ij[dim] = coords[atom_j * DIM + dim] - coords[atom_i * DIM + dim]; in compute_routine()
332 if (atom_k == atom_j) { continue; } in compute_routine()
357 = coords[atom_k * DIM + dim] - coords[atom_j * DIM + dim]; in compute_routine()
404 force[atom_j * DIM + dim] in compute_routine()
453 if (atom_k == atom_j) { continue; } in compute_routine()
478 = coords[atom_k * DIM + dim] - coords[atom_j * DIM + dim]; in compute_routine()
[all …]
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_Gong__MD_065419309200_000/
H A DThreeBodyCluster.c125 int atom_j; in compute_routine() local
231 atom_j = neigh_list_of_current_part[neigh_count]; /* get neighbor ID */ in compute_routine()
235 phi2_contrib_prefactor = (particle_contributing[atom_j]) ? 1.0 : 0.5; in compute_routine()
242 r_ij[d] = coords[atom_j * DIM + d] - coords[atom_i * DIM + d]; in compute_routine()
253 if (!(particle_contributing[atom_j] in compute_routine()
254 && atom_j < atom_i)) /* effective half-list */ in compute_routine()
279 force[atom_j * DIM + d] in compute_routine()
316 = coords[atom_k * DIM + d] - coords[atom_j * DIM + d]; in compute_routine()
362 force[atom_j * DIM + d] in compute_routine()
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_SRS__MD_814842199451_000/
H A DThreeBodyCluster.c125 int atom_j; in compute_routine() local
231 atom_j = neigh_list_of_current_part[neigh_count]; /* get neighbor ID */ in compute_routine()
235 phi2_contrib_prefactor = (particle_contributing[atom_j]) ? 1.0 : 0.5; in compute_routine()
242 r_ij[d] = coords[atom_j * DIM + d] - coords[atom_i * DIM + d]; in compute_routine()
253 if (!(particle_contributing[atom_j] in compute_routine()
254 && atom_j < atom_i)) /* effective half-list */ in compute_routine()
279 force[atom_j * DIM + d] in compute_routine()
316 = coords[atom_k * DIM + d] - coords[atom_j * DIM + d]; in compute_routine()
362 force[atom_j * DIM + d] in compute_routine()
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_PPM__MD_184422512875_000/
H A DThreeBodyBondOrder.c128 int atom_j; in compute_routine() local
234 atom_j = neigh_list_of_current_part[neigh_count]; /* get ID */ in compute_routine()
241 r_ij[dim] = coords[atom_j * DIM + dim] - coords[atom_i * DIM + dim]; in compute_routine()
261 if (atom_k == atom_j) { continue; } in compute_routine()
286 = coords[atom_k * DIM + dim] - coords[atom_j * DIM + dim]; in compute_routine()
332 force[atom_j * DIM + dim] in compute_routine()
343 if (atom_k == atom_j) { continue; } in compute_routine()
368 = coords[atom_k * DIM + dim] - coords[atom_j * DIM + dim]; in compute_routine()
401 force[atom_j * DIM + dim] in compute_routine()
/dports/science/lammps/lammps-stable_29Sep2021/src/REAXFF/
H A Dreaxff_forces.cpp141 reax_atom *atom_i, *atom_j; in Init_Forces_noQEq() local
187 atom_j = &(system->my_atoms[j]); in Init_Forces_noQEq()
194 type_j = atom_j->type; in Init_Forces_noQEq()
213 jhb_top = End_Index(atom_j->Hindex, hbonds); in Init_Forces_noQEq()
217 Set_End_Index(atom_j->Hindex, jhb_top+1, hbonds); in Init_Forces_noQEq()
268 reax_atom *atom_i, *atom_j; in Estimate_Storages() local
302 atom_j = &(system->my_atoms[j]); in Estimate_Storages()
312 if (j < system->n || atom_i->orig_id < atom_j->orig_id) //tryQEq ||1 in Estimate_Storages()
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_WR__MD_817691861922_000/
H A DThreeBodyBondOrder.c132 int atom_j; in compute_routine() local
238 atom_j = neigh_list_of_current_part[neigh_count]; /* get ID */ in compute_routine()
245 r_ij[dim] = coords[atom_j * DIM + dim] - coords[atom_i * DIM + dim]; in compute_routine()
265 if (atom_k == atom_j) { continue; } in compute_routine()
290 = coords[atom_k * DIM + dim] - coords[atom_j * DIM + dim]; in compute_routine()
343 force[atom_j * DIM + dim] in compute_routine()
354 if (atom_k == atom_j) { continue; } in compute_routine()
379 = coords[atom_k * DIM + dim] - coords[atom_j * DIM + dim]; in compute_routine()
412 force[atom_j * DIM + dim] in compute_routine()
/dports/biology/protomol/protomol/framework/base/
H A DreducedHessBond.cpp5 const Vector3D& atom_j, in reducedHessBond() argument
9 Vector3D rij(atom_j - atom_i); in reducedHessBond()
/dports/science/lammps/lammps-stable_29Sep2021/src/OPENMP/
H A Dreaxff_forces_omp.cpp232 reax_atom *atom_i, *atom_j; in Init_Forces_noQEq_OMP() local
254 atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp) in Init_Forces_noQEq_OMP()
278 atom_j = &(system->my_atoms[j]); in Init_Forces_noQEq_OMP()
279 type_j = atom_j->type; in Init_Forces_noQEq_OMP()
395 atom_j = &(system->my_atoms[j]); in Init_Forces_noQEq_OMP()
396 type_j = atom_j->type; in Init_Forces_noQEq_OMP()
413 jhb_top = End_Index(atom_j->Hindex, hbonds); in Init_Forces_noQEq_OMP()
414 Set_End_Index(atom_j->Hindex, jhb_top+1, hbonds); in Init_Forces_noQEq_OMP()
/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/lib/gpu/
H A Dlal_neighbor_gpu.cu159 numtyp4 atom_i, atom_j; in calc_neigh_list_cell() local
202 fetch4(atom_j,pid_j,pos_tex); //[pid_j]; in calc_neigh_list_cell()
203 pos_sh[tid].x = atom_j.x; in calc_neigh_list_cell()
204 pos_sh[tid].y = atom_j.y; in calc_neigh_list_cell()
205 pos_sh[tid].z = atom_j.z; in calc_neigh_list_cell()
/dports/science/cp2k-data/cp2k-7.1.0/src/
H A Dqs_dftb3_methods.F86 … INTEGER :: atom_i, atom_j, blk, handle, i, ia, iac, & local
174 atom_j = atom_of_kind(icol)
190 force(jkind)%rho_elec(i, atom_j) = force(jkind)%rho_elec(i, atom_j) - fi
262 atom_j = atom_of_kind(jatom)
282 force(jkind)%rho_elec(i, atom_j) = force(jkind)%rho_elec(i, atom_j) - fi
/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/
H A Dqs_dftb3_methods.F86 … INTEGER :: atom_i, atom_j, blk, handle, i, ia, iac, & local
174 atom_j = atom_of_kind(icol)
190 force(jkind)%rho_elec(i, atom_j) = force(jkind)%rho_elec(i, atom_j) - fi
262 atom_j = atom_of_kind(jatom)
282 force(jkind)%rho_elec(i, atom_j) = force(jkind)%rho_elec(i, atom_j) - fi
H A Dtopology_coordinate_util.F101 INTEGER :: atom_i, atom_j, counter, dim0, dim1, & local
450 atom_j = ex_bond_list(iatom)%array1(j)
456 IF (ex_bond_list(atom_i)%array1(counter) == atom_j) THEN
468 pairs(N, 2) = atom_j
497 atom_j = ex_bend_list(iatom)%array1(j)
500 IF (atom_i == atom_j) CYCLE
504 IF (ex_bond_list(atom_i)%array1(counter) == atom_j) THEN
513 IF (ex_bend_list(atom_i)%array1(counter) == atom_j) THEN
525 pairs(N, 2) = atom_j

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