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Searched refs:atom_i (Results 1 – 25 of 57) sorted by relevance

123

/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_KP__MD_527786671773_000/
H A DThreeBodyCluster.c122 int atom_i; in compute_routine() local
186 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
188 if (SPECCODE != particle_species_codes[atom_i]) in compute_routine()
201 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
210 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
212 if (particle_contributing[atom_i]) in compute_routine()
217 atom_i, in compute_routine()
233 if (atom_j == atom_i) continue; in compute_routine()
279 force[atom_i * DIM + d] in compute_routine()
296 if (atom_k == atom_i) continue; in compute_routine()
[all …]
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_BH__MD_043141570610_000/
H A DThreeBodyCluster.c122 int atom_i; in compute_routine() local
186 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
188 if (SPECCODE != particle_species_codes[atom_i]) in compute_routine()
201 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
210 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
212 if (particle_contributing[atom_i]) in compute_routine()
217 atom_i, in compute_routine()
233 if (atom_j == atom_i) continue; in compute_routine()
279 force[atom_i * DIM + d] in compute_routine()
296 if (atom_k == atom_i) continue; in compute_routine()
[all …]
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_Gong__MD_065419309200_000/
H A DThreeBodyCluster.c122 int atom_i; in compute_routine() local
186 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
188 if (SPECCODE != particle_species_codes[atom_i]) in compute_routine()
201 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
203 for (d = 0; d < DIM; ++d) { force[atom_i * DIM + d] = 0.0; } in compute_routine()
210 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
212 if (particle_contributing[atom_i]) in compute_routine()
217 atom_i, in compute_routine()
254 && atom_j < atom_i)) /* effective half-list */ in compute_routine()
277 force[atom_i * DIM + d] in compute_routine()
[all …]
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_SRS__MD_814842199451_000/
H A DThreeBodyCluster.c122 int atom_i; in compute_routine() local
186 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
188 if (SPECCODE != particle_species_codes[atom_i]) in compute_routine()
201 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
203 for (d = 0; d < DIM; ++d) { force[atom_i * DIM + d] = 0.0; } in compute_routine()
210 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
212 if (particle_contributing[atom_i]) in compute_routine()
217 atom_i, in compute_routine()
254 && atom_j < atom_i)) /* effective half-list */ in compute_routine()
277 force[atom_i * DIM + d] in compute_routine()
[all …]
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_KDS__MD_697985444380_000/
H A DThreeBodyBondOrder.c134 int atom_i; in compute_routine() local
200 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
202 if (SPECCODE != particle_species_codes[atom_i]) in compute_routine()
215 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
217 for (dim = 0; dim < DIM; ++dim) { force[atom_i * DIM + dim] = 0.0; } in compute_routine()
229 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
231 if (particle_contributing[atom_i]) in compute_routine()
236 atom_i, in compute_routine()
402 force[atom_i * DIM + dim] in compute_routine()
437 force[atom_i * DIM + dim] in compute_routine()
[all …]
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_PPM__MD_184422512875_000/
H A DThreeBodyBondOrder.c125 int atom_i; in compute_routine() local
189 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
191 if (SPECCODE != particle_species_codes[atom_i]) in compute_routine()
204 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
206 for (dim = 0; dim < DIM; ++dim) { force[atom_i * DIM + dim] = 0.0; } in compute_routine()
213 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
215 if (particle_contributing[atom_i]) in compute_routine()
220 atom_i, in compute_routine()
269 = coords[atom_k * DIM + dim] - coords[atom_i * DIM + dim]; in compute_routine()
330 force[atom_i * DIM + dim] in compute_routine()
[all …]
/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_WR__MD_817691861922_000/
H A DThreeBodyBondOrder.c129 int atom_i; in compute_routine() local
193 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
195 if (SPECCODE != particle_species_codes[atom_i]) in compute_routine()
208 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
210 for (dim = 0; dim < DIM; ++dim) { force[atom_i * DIM + dim] = 0.0; } in compute_routine()
217 for (atom_i = 0; atom_i < *n_parts; ++atom_i) in compute_routine()
219 if (particle_contributing[atom_i]) in compute_routine()
224 atom_i, in compute_routine()
273 = coords[atom_k * DIM + dim] - coords[atom_i * DIM + dim]; in compute_routine()
341 force[atom_i * DIM + dim] in compute_routine()
[all …]
/dports/math/cppad/CppAD-20210000.8/include/cppad/local/sweep/
H A Dfor_hes.hpp456 atom_i = 0; in for_hes()
468 { CPPAD_ASSERT_UNKNOWN( atom_i == atom_m ); in for_hes()
483 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in for_hes()
504 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in for_hes()
521 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in for_hes()
528 atom_funrp[atom_i] = arg[0]; in for_hes()
530 ++atom_i; in for_hes()
531 if( atom_i == atom_m ) in for_hes()
539 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in for_hes()
544 ++atom_i; in for_hes()
[all …]
H A Dreverse.hpp656 atom_i = atom_m; in reverse()
668 { CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in reverse()
696 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in reverse()
719 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in reverse()
738 CPPAD_ASSERT_UNKNOWN( atom_i <= atom_m ); in reverse()
742 --atom_i; in reverse()
749 if( atom_i == 0 ) in reverse()
760 --atom_i; in reverse()
762 { atom_py[atom_i * atom_k1 + ell] = in reverse()
764 atom_ty[atom_i * atom_k1 + ell] = in reverse()
[all …]
H A Dfor_jac.hpp622 atom_i = 0; in for_jac()
634 { CPPAD_ASSERT_UNKNOWN( atom_i == atom_m ); in for_jac()
655 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in for_jac()
676 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in for_jac()
693 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in for_jac()
700 atom_funrp[atom_i] = arg[0]; in for_jac()
702 ++atom_i; in for_jac()
703 if( atom_i == atom_m ) in for_jac()
711 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in for_jac()
716 ++atom_i; in for_jac()
[all …]
H A Drev_jac.hpp647 atom_i = atom_m; in rev_jac()
656 { CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in rev_jac()
677 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in rev_jac()
700 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in rev_jac()
718 CPPAD_ASSERT_UNKNOWN( atom_i <= atom_m ); in rev_jac()
722 --atom_i; in rev_jac()
725 if( atom_i == 0 ) in rev_jac()
733 CPPAD_ASSERT_UNKNOWN( atom_i <= atom_m ); in rev_jac()
736 --atom_i; in rev_jac()
737 atom_iy[atom_i] = i_var; // variable for this result in rev_jac()
[all …]
H A Dforward2.hpp534 atom_i = 0; in forward2()
607 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in forward2()
630 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in forward2()
653 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in forward2()
656 atom_iy[atom_i] = 0; in forward2()
662 ++atom_i; in forward2()
663 if( atom_i == atom_m ) in forward2()
671 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in forward2()
674 atom_iy[atom_i] = i_var; in forward2()
682 ++atom_i; in forward2()
[all …]
H A Drev_hes.hpp631 atom_i = atom_m; in rev_hes()
640 { CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in rev_hes()
656 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in rev_hes()
679 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in rev_hes()
697 CPPAD_ASSERT_UNKNOWN( atom_i <= atom_m ); in rev_hes()
701 --atom_i; in rev_hes()
704 if( atom_i == 0 ) in rev_hes()
712 CPPAD_ASSERT_UNKNOWN( atom_i <= atom_m ); in rev_hes()
715 --atom_i; in rev_hes()
716 atom_iy[atom_i] = i_var; // variable for this result in rev_hes()
[all …]
H A Dforward1.hpp899 atom_i = 0; in forward1()
933 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in forward1()
955 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in forward1()
972 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in forward1()
976 atom_iy[atom_i] = 0; in forward1()
981 ++atom_i; in forward1()
982 if( atom_i == atom_m ) in forward1()
990 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in forward1()
993 atom_iy[atom_i] = i_var; in forward1()
997 ++atom_i; in forward1()
[all …]
H A Dforward0.hpp815 atom_i = 0; in forward0()
840 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in forward0()
865 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in forward0()
886 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in forward0()
890 atom_iy[atom_i] = 0; in forward0()
892 atom_i++; in forward0()
893 if( atom_i == atom_m ) in forward0()
901 CPPAD_ASSERT_UNKNOWN( atom_i < atom_m ); in forward0()
904 atom_iy[atom_i] = i_var; in forward0()
906 taylor[ i_var * J + 0 ] = atom_ty[atom_i++]; in forward0()
[all …]
/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/topology/
H A Dtest_top.py62 assert len(u.atoms[[self.atom_i]].bonds) == self.expected_n_i_bonds
67 assert len(u.atoms[[self.atom_i]].angles) == self.expected_n_i_angles
72 assert len(u.atoms[[self.atom_i]].dihedrals) == \
78 assert len(u.atoms[[self.atom_i]].impropers) == \
137 atom_i = 79 variable in TestPRMParser
194 atom_i = 335 variable in TestPRM12Parser
235 atom_i = 135 variable in TestParm7Parser
292 atom_i = 14 variable in TestPRM2
331 atom_i = 4 variable in TestPRMNCRST
/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
266 fetch4(atom_i,pid_i,pos_tex); //pos[i]; in calc_neigh_list_cell()
320 diff.x = atom_i.x - pos_sh[offset+j].x; in calc_neigh_list_cell()
321 diff.y = atom_i.y - pos_sh[offset+j].y; in calc_neigh_list_cell()
322 diff.z = atom_i.z - pos_sh[offset+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
403 fetch4(atom_i,pid_i,pos_tex); //pos[i]; in calc_neigh_list_cell()
449 diff.x = atom_i.x - pos_sh[j].x; in calc_neigh_list_cell()
450 diff.y = atom_i.y - pos_sh[j].y; in calc_neigh_list_cell()
[all …]
/dports/math/cppad/CppAD-20210000.8/include/cppad/local/optimize/
H A Dget_par_usage.hpp153 size_t atom_index=0, atom_old=0, atom_m=0, atom_n=0, atom_i=0, atom_j=0; in get_par_usage() local
333 atom_i = 0; in get_par_usage()
348 CPPAD_ASSERT_UNKNOWN( atom_i == atom_m ); in get_par_usage()
393 depend_y[atom_i] = op_usage[i_op] != usage_t(no_usage); in get_par_usage()
394 ++atom_i; in get_par_usage()
395 if( atom_i == atom_m ) in get_par_usage()
402 depend_y[atom_i] = op_usage[i_op] != usage_t(no_usage); in get_par_usage()
403 ++atom_i; in get_par_usage()
404 if( atom_i == atom_m ) in get_par_usage()
H A Dget_op_usage.hpp288 size_t atom_index=0, atom_old=0, atom_m=0, atom_n=0, atom_i=0, atom_j=0; in get_op_usage() local
703 atom_i = atom_m; in get_op_usage()
735 CPPAD_ASSERT_UNKNOWN( atom_i == 0 ); in get_op_usage()
818 CPPAD_ASSERT_UNKNOWN( 0 < atom_i && atom_i <= atom_m ); in get_op_usage()
819 --atom_i; in get_op_usage()
820 if( atom_i == 0 ) in get_op_usage()
824 { depend_y[atom_i] = true; in get_op_usage()
836 CPPAD_ASSERT_UNKNOWN( 0 < atom_i && atom_i <= atom_m ); in get_op_usage()
837 --atom_i; in get_op_usage()
838 if( atom_i == 0 ) in get_op_usage()
/dports/science/lammps/lammps-stable_29Sep2021/src/REAXFF/
H A Dreaxff_forces.cpp141 reax_atom *atom_i, *atom_j; in Init_Forces_noQEq() local
158 atom_i = &(system->my_atoms[i]); in Init_Forces_noQEq()
159 type_i = atom_i->type; in Init_Forces_noQEq()
179 ihb_top = End_Index(atom_i->Hindex, hbonds); in Init_Forces_noQEq()
241 Set_End_Index(atom_i->Hindex, ihb_top, hbonds); in Init_Forces_noQEq()
268 reax_atom *atom_i, *atom_j; in Estimate_Storages() local
281 atom_i = &(system->my_atoms[i]); in Estimate_Storages()
282 type_i = atom_i->type; in Estimate_Storages()
312 if (j < system->n || atom_i->orig_id < atom_j->orig_id) //tryQEq ||1 in Estimate_Storages()
/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/
H A Dxtb_coulomb.F357 atom_i = atom_of_kind(iatom)
365 force(ikind)%rho_elec(1, atom_i) = force(ikind)%rho_elec(1, atom_i) - fij(1)
366 force(ikind)%rho_elec(2, atom_i) = force(ikind)%rho_elec(2, atom_i) - fij(2)
367 force(ikind)%rho_elec(3, atom_i) = force(ikind)%rho_elec(3, atom_i) - fij(3)
372 force(ikind)%rho_elec(1, atom_i) = force(ikind)%rho_elec(1, atom_i) - fij(1)
373 force(ikind)%rho_elec(2, atom_i) = force(ikind)%rho_elec(2, atom_i) - fij(2)
374 force(ikind)%rho_elec(3, atom_i) = force(ikind)%rho_elec(3, atom_i) - fij(3)
451 force(ikind)%rho_elec(i, atom_i) = force(ikind)%rho_elec(i, atom_i) + fi
456 force(ikind)%rho_elec(i, atom_i) = force(ikind)%rho_elec(i, atom_i) + fi
595 force(ikind)%rho_elec(i, atom_i) = force(ikind)%rho_elec(i, atom_i) + fi
[all …]
H A Dtopology_coordinate_util.F447 atom_i = ex_bond_list(iatom)%array1(i)
455 DO counter = 1, SIZE(ex_bond_list(atom_i)%array1)
456 IF (ex_bond_list(atom_i)%array1(counter) == atom_j) THEN
467 pairs(N, 1) = atom_i
494 atom_i = ex_bond_list(iatom)%array1(i)
500 IF (atom_i == atom_j) CYCLE
503 DO counter = 1, SIZE(ex_bond_list(atom_i)%array1)
504 IF (ex_bond_list(atom_i)%array1(counter) == atom_j) THEN
512 DO counter = 1, SIZE(ex_bend_list(atom_i)%array1)
513 IF (ex_bend_list(atom_i)%array1(counter) == atom_j) THEN
[all …]
/dports/science/cp2k-data/cp2k-7.1.0/src/
H A Dxtb_coulomb.F357 atom_i = atom_of_kind(iatom)
365 force(ikind)%rho_elec(1, atom_i) = force(ikind)%rho_elec(1, atom_i) - fij(1)
366 force(ikind)%rho_elec(2, atom_i) = force(ikind)%rho_elec(2, atom_i) - fij(2)
367 force(ikind)%rho_elec(3, atom_i) = force(ikind)%rho_elec(3, atom_i) - fij(3)
372 force(ikind)%rho_elec(1, atom_i) = force(ikind)%rho_elec(1, atom_i) - fij(1)
373 force(ikind)%rho_elec(2, atom_i) = force(ikind)%rho_elec(2, atom_i) - fij(2)
374 force(ikind)%rho_elec(3, atom_i) = force(ikind)%rho_elec(3, atom_i) - fij(3)
451 force(ikind)%rho_elec(i, atom_i) = force(ikind)%rho_elec(i, atom_i) + fi
456 force(ikind)%rho_elec(i, atom_i) = force(ikind)%rho_elec(i, atom_i) + fi
595 force(ikind)%rho_elec(i, atom_i) = force(ikind)%rho_elec(i, atom_i) + fi
[all …]
H A Dtopology_coordinate_util.F447 atom_i = ex_bond_list(iatom)%array1(i)
455 DO counter = 1, SIZE(ex_bond_list(atom_i)%array1)
456 IF (ex_bond_list(atom_i)%array1(counter) == atom_j) THEN
467 pairs(N, 1) = atom_i
494 atom_i = ex_bond_list(iatom)%array1(i)
500 IF (atom_i == atom_j) CYCLE
503 DO counter = 1, SIZE(ex_bond_list(atom_i)%array1)
504 IF (ex_bond_list(atom_i)%array1(counter) == atom_j) THEN
512 DO counter = 1, SIZE(ex_bend_list(atom_i)%array1)
513 IF (ex_bend_list(atom_i)%array1(counter) == atom_j) THEN
[all …]
/dports/biology/protomol/protomol/framework/base/
H A DreducedHessBond.cpp4 Matrix3by3 reducedHessBond(const Vector3D& atom_i, in reducedHessBond() argument
9 Vector3D rij(atom_j - atom_i); in reducedHessBond()

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