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/dports/science/mpqc/mpqc-2.3.1/src/lib/chemistry/qc/basis/
H A Dgpetite.cc96 int **atom_map; in GenPetite4() local
110 atom_map = compute_atom_map(b1); in GenPetite4()
111 shell_map_i_ = compute_shell_map(atom_map,b1); in GenPetite4()
112 delete_atom_map(atom_map,b1); in GenPetite4()
114 atom_map = compute_atom_map(b2); in GenPetite4()
115 shell_map_j_ = compute_shell_map(atom_map,b2); in GenPetite4()
116 delete_atom_map(atom_map,b2); in GenPetite4()
118 atom_map = compute_atom_map(b3); in GenPetite4()
120 delete_atom_map(atom_map,b3); in GenPetite4()
122 atom_map = compute_atom_map(b4); in GenPetite4()
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H A Dpetite.cc59 int **atom_map; in compute_atom_map() local
60 atom_map = new int*[natom]; in compute_atom_map()
61 for (int i=0; i < natom; i++) atom_map[i] = new int[ng]; in compute_atom_map()
81 atom_map[i][g] = mol.atom_at_position(np, 0.05); in compute_atom_map()
82 if (atom_map[i][g] < 0) { in compute_atom_map()
97 return atom_map; in compute_atom_map()
102 sc::delete_atom_map(int **atom_map, const Ref<GaussianBasisSet> &basis) in delete_atom_map() argument
104 if (atom_map) { in delete_atom_map()
107 delete[] atom_map[i]; in delete_atom_map()
108 delete[] atom_map; in delete_atom_map()
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H A Dpetite.h67 void delete_atom_map(int **atom_map, const Ref<GaussianBasisSet> &);
69 int **compute_shell_map(int **atom_map, const Ref<GaussianBasisSet> &);
152 int atom_map(int n, int g) const { return (c1_) ? n : atom_map_[n][g]; } in atom_map() function
/dports/science/py-avogadrolibs/avogadrolibs-1.94.0/scripts/
H A Dgetresdata.py155 atom_map = {} variable
161 atom_map[idx] = res.GetAtomID(atom).strip().rstrip(), atom.GetAtomicNum()
170 double_bonds.append((atom_map[begin][0], atom_map[end][0]))
172 single_bonds.append((atom_map[begin][0], atom_map[end][0]))
178 for atom in list(atom_map.values())[:-1]:
/dports/science/avogadrolibs/avogadrolibs-1.94.0/scripts/
H A Dgetresdata.py155 atom_map = {} variable
161 atom_map[idx] = res.GetAtomID(atom).strip().rstrip(), atom.GetAtomicNum()
170 double_bonds.append((atom_map[begin][0], atom_map[end][0]))
172 single_bonds.append((atom_map[begin][0], atom_map[end][0]))
178 for atom in list(atom_map.values())[:-1]:
/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/
H A Dnegf_matrix_utils.F527 IF (atom_map(iatom_row)%iatom > max_atom) max_atom = atom_map(iatom_row)%iatom
539 IF (atom_map(iatom_row)%iatom <= atom_map(iatom_col)%iatom) THEN
540 icol = atom_map(iatom_col)%iatom
541 irow = atom_map(iatom_row)%iatom
543 icol = atom_map(iatom_row)%iatom
544 irow = atom_map(iatom_col)%iatom
568 IF (atom_map(iatom_row)%iatom <= atom_map(iatom_col)%iatom) THEN
569 icol = atom_map(iatom_col)%iatom
570 irow = atom_map(iatom_row)%iatom
610 IF (atom_map(iatom_row)%iatom <= atom_map(iatom_col)%iatom) THEN
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H A Dnegf_atom_map.F73 …SUBROUTINE negf_map_atomic_indices(atom_map, atom_list, subsys_device, subsys_contact, eps_geometr… argument
75 INTENT(out) :: atom_map local
97 natoms = SIZE(atom_map, 1)
111 atom_map(iatom)%iatom = 0
127 … atom_map(iatom)%iatom = kind_groups_contact(ikind_contact)%atom_list(iatom_kind)
128 atom_map(iatom)%cell = NINT(coords_scaled)
135 IF (atom_map(iatom)%iatom == 0) THEN
H A Dnegf_env_types.F249 atom_map=map_contact(icontact)%atom_map, &
346 ALLOCATE (atom_map(natoms))
349 CALL negf_map_atomic_indices(atom_map=atom_map, &
360 atom_map=atom_map, &
370 atom_map=atom_map, &
1109 CPASSERT(SIZE(atom_map, 1) == natoms_bulk)
1125 dir_axis_min = atom_map(atom_min)%cell(direction_axis_abs)
1141 atom_map_cell0(natoms_cell0) = atom_map(iatom)
1190 CPASSERT(SIZE(atom_map, 1) == natoms_bulk)
1207 dir_axis_min = atom_map(atom_min)%cell(direction_axis_abs)
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/dports/science/cp2k-data/cp2k-7.1.0/src/
H A Dnegf_matrix_utils.F527 IF (atom_map(iatom_row)%iatom > max_atom) max_atom = atom_map(iatom_row)%iatom
539 IF (atom_map(iatom_row)%iatom <= atom_map(iatom_col)%iatom) THEN
540 icol = atom_map(iatom_col)%iatom
541 irow = atom_map(iatom_row)%iatom
543 icol = atom_map(iatom_row)%iatom
544 irow = atom_map(iatom_col)%iatom
568 IF (atom_map(iatom_row)%iatom <= atom_map(iatom_col)%iatom) THEN
569 icol = atom_map(iatom_col)%iatom
570 irow = atom_map(iatom_row)%iatom
610 IF (atom_map(iatom_row)%iatom <= atom_map(iatom_col)%iatom) THEN
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H A Dnegf_atom_map.F73 …SUBROUTINE negf_map_atomic_indices(atom_map, atom_list, subsys_device, subsys_contact, eps_geometr… argument
75 INTENT(out) :: atom_map local
97 natoms = SIZE(atom_map, 1)
111 atom_map(iatom)%iatom = 0
127 … atom_map(iatom)%iatom = kind_groups_contact(ikind_contact)%atom_list(iatom_kind)
128 atom_map(iatom)%cell = NINT(coords_scaled)
135 IF (atom_map(iatom)%iatom == 0) THEN
H A Dnegf_env_types.F249 atom_map=map_contact(icontact)%atom_map, &
346 ALLOCATE (atom_map(natoms))
349 CALL negf_map_atomic_indices(atom_map=atom_map, &
360 atom_map=atom_map, &
370 atom_map=atom_map, &
1109 CPASSERT(SIZE(atom_map, 1) == natoms_bulk)
1125 dir_axis_min = atom_map(atom_min)%cell(direction_axis_abs)
1141 atom_map_cell0(natoms_cell0) = atom_map(iatom)
1190 CPASSERT(SIZE(atom_map, 1) == natoms_bulk)
1207 dir_axis_min = atom_map(atom_min)%cell(direction_axis_abs)
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/dports/net-mgmt/lldpd/lldpd-1.0.8/src/lib/atoms/
H A Ddot3.c48 static struct atom_map port_dot3_power_pairs_map = {
58 static struct atom_map port_dot3_power_class_map = {
70 static struct atom_map port_dot3_power_priority_map = {
81 static struct atom_map port_dot3_power_pd_4pid_map = {
89 static struct atom_map port_dot3_power_pse_status_map = {
99 static struct atom_map port_dot3_power_pd_status_map = {
119 static struct atom_map port_dot3_power_class_a_map = {
133 static struct atom_map port_dot3_power_class_b_map = {
147 static struct atom_map port_dot3_power_class_ext_map = {
169 static struct atom_map port_dot3_power_type_ext_map = {
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/dports/lang/swi-pl/swipl-8.2.3/packages/semweb/
H A Datom_map.c102 } atom_map; typedef
594 atom_map *am = cd; in free_node_data()
657 { atom_map *m; in new_atom_map()
673 { atom_map *m; in destroy_atom_map()
700 { atom_map *map; in insert_atom_map4()
794 { atom_map *map; in delete_atom_map2()
817 { atom_map *map; in delete_atom_map3()
954 { atom_map *map; in find_atom_map()
1130 { atom_map *map; in rdf_keys_in_literal_map()
1150 { atom_map *map; in rdf_reset_literal_map()
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/dports/lang/yap/yap-6.2.2/packages/semweb/
H A Datom_map.c69 typedef struct atom_map struct
74 } atom_map; argument
621 { atom_map *m; in new_atom_map()
637 { atom_map *m; in destroy_atom_map()
660 { atom_map *map; in insert_atom_map4()
716 { atom_map *map; in delete_atom_map2()
744 { atom_map *map; in delete_atom_map3()
805 { atom_map *map; in find_atom_map()
973 { atom_map *map; in rdf_keys_in_literal_map()
1094 { atom_map *map; in rdf_reset_literal_map()
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/dports/science/p5-Chemistry-MidasPattern/Chemistry-MidasPattern-0.11/lib/Chemistry/
H A DMidasPattern.pm126 atom_map => [],
135 sub atom_map { subroutine
137 @{$self->{atom_map}};
315 $self->{atom_map} = \@ret;
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-MidasPattern-0.11/lib/Chemistry/
H A DMidasPattern.pm126 atom_map => [],
135 sub atom_map { subroutine
137 @{$self->{atom_map}};
315 $self->{atom_map} = \@ret;
/dports/science/lammps/lammps-stable_29Sep2021/tools/drude/
H A Dpolarizer.py450 atom_map = {}
463 atom_map[atom['n']] = len(atom_map) + 1
467 if bond['i'] in atom_map and bond['j'] in atom_map:
472 if bond['i'] in atom_map:
501 if atom['n'] not in atom_map:
505 atom['n'] = atom_map[atom['n']]
516 bond['i'] = atom_map[bond['i']]
517 bond['j'] = atom_map[bond['j']]
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-3DBuilder-0.10/t/
H A Dbuilder.t102 my $len = distance($bt->{patt}->atom_map);
114 my $ang = angle_deg($at->{patt}->atom_map);
126 my $dih = dihedral_deg($dt->{patt}->atom_map);
130 my $path = join("", map { $_->symbol } $dt->{patt}->atom_map)
/dports/science/p5-Chemistry-3DBuilder/Chemistry-3DBuilder-0.10/t/
H A Dbuilder.t102 my $len = distance($bt->{patt}->atom_map);
114 my $ang = angle_deg($at->{patt}->atom_map);
126 my $dih = dihedral_deg($dt->{patt}->atom_map);
130 my $path = join("", map { $_->symbol } $dt->{patt}->atom_map)
/dports/science/p5-PerlMol/PerlMol-0.3500/inc/BUNDLES/Chemistry-MidasPattern-0.11/t/
H A Dmidas.t29 } $patt->atom_map;
30 push @got, sprintf("%d atoms", 0+$patt->atom_map);
/dports/science/p5-Chemistry-MidasPattern/Chemistry-MidasPattern-0.11/t/
H A Dmidas.t29 } $patt->atom_map;
30 push @got, sprintf("%d atoms", 0+$patt->atom_map);
/dports/science/mpqc/mpqc-2.3.1/src/lib/chemistry/molecule/
H A Dhess.cc163 int **atom_map = new int*[natom]; in cartesian_to_symmetry() local
164 for (i=0; i < natom; i++) atom_map[i] = new int[ng]; in cartesian_to_symmetry()
177 atom_map[i][g] = mol->atom_at_position(np, 0.05); in cartesian_to_symmetry()
178 if (atom_map[i][g] < 0) { in cartesian_to_symmetry()
208 projmat.accumulate_element(atom_map[atom][g]*3+ii, in cartesian_to_symmetry()
280 for (i=0; i<natom; i++) delete[] atom_map[i]; in cartesian_to_symmetry()
281 delete[] atom_map; in cartesian_to_symmetry()
/dports/devel/py-tables/tables-3.6.1/tables/
H A Datom.py39 atom_map = {} # filled as atom classes are created variable
106 assert self.kind in atom_map
108 atomclass = atom_map[self.kind][itemsize]
111 atom_map[self.kind])
209 atom_map[kind] = class_
213 atom_map[kind] = {}
217 atom_map[kind][int(itemsize)] = class_
460 if kind not in atom_map:
477 kdata = atom_map[kind]
/dports/science/p5-PerlMol/PerlMol-0.3500/examples/combinatorial_enumeration/
H A Dcombinatorial_enumeration.pl49 my @nfg1 = $fg1_pat->atom_map;
51 my @nfg2 = $fg2_pat->atom_map;
/dports/science/py-qcelemental/qcelemental-0.24.0/qcelemental/models/
H A Dbasis.py167 atom_map: List[str] = Field( variable in BasisSet
210 def _calculate_nbf(cls, atom_map, center_data) -> int: argument
225 for center in atom_map:

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