/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_KP__MD_527786671773_000/ |
H A D | ThreeBodyCluster.c | 122 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 …]
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/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_BH__MD_043141570610_000/ |
H A D | ThreeBodyCluster.c | 122 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 …]
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/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_Gong__MD_065419309200_000/ |
H A D | ThreeBodyCluster.c | 122 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 …]
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/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyCluster_SRS__MD_814842199451_000/ |
H A D | ThreeBodyCluster.c | 122 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 …]
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/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_KDS__MD_697985444380_000/ |
H A D | ThreeBodyBondOrder.c | 134 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 …]
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/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_PPM__MD_184422512875_000/ |
H A D | ThreeBodyBondOrder.c | 125 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 …]
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/dports/science/openkim-models/openkim-models-2021-01-28/model-drivers/ThreeBodyBondOrder_WR__MD_817691861922_000/ |
H A D | ThreeBodyBondOrder.c | 129 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 …]
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/dports/math/cppad/CppAD-20210000.8/include/cppad/local/sweep/ |
H A D | for_hes.hpp | 456 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 …]
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H A D | reverse.hpp | 656 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 …]
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H A D | for_jac.hpp | 622 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 …]
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H A D | rev_jac.hpp | 647 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 …]
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H A D | forward2.hpp | 534 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 …]
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H A D | rev_hes.hpp | 631 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 …]
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H A D | forward1.hpp | 899 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 …]
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H A D | forward0.hpp | 815 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 …]
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/dports/science/py-MDAnalysisTests/MDAnalysisTests-0.19.2/MDAnalysisTests/topology/ |
H A D | test_top.py | 62 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
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/dports/science/lammps/lammps-stable_29Sep2021/lib/gpu/ |
H A D | lal_neighbor_gpu.cu | 258 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 …]
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/dports/math/cppad/CppAD-20210000.8/include/cppad/local/optimize/ |
H A D | get_par_usage.hpp | 153 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()
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H A D | get_op_usage.hpp | 288 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()
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/dports/science/lammps/lammps-stable_29Sep2021/src/REAXFF/ |
H A D | reaxff_forces.cpp | 141 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()
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/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/ |
H A D | xtb_coulomb.F | 357 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 …]
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H A D | topology_coordinate_util.F | 447 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 …]
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/dports/science/cp2k-data/cp2k-7.1.0/src/ |
H A D | xtb_coulomb.F | 357 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 …]
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H A D | topology_coordinate_util.F | 447 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 …]
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/dports/biology/protomol/protomol/framework/base/ |
H A D | reducedHessBond.cpp | 4 Matrix3by3 reducedHessBond(const Vector3D& atom_i, in reducedHessBond() argument 9 Vector3D rij(atom_j - atom_i); in reducedHessBond()
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