| /dports/science/lammps/lammps-stable_29Sep2021/src/MOLECULE/ |
| H A D | atom_vec_template.cpp | 67 onemols = &atom->molecules[imol]; in process_args()
74 if (onemols[i]->bondflag) bonds_allow = 1; in process_args()
75 if (onemols[i]->angleflag) angles_allow = 1; in process_args()
76 if (onemols[i]->dihedralflag) dihedrals_allow = 1; in process_args()
77 if (onemols[i]->improperflag) impropers_allow = 1; in process_args()
84 atom->nbondtypes = MAX(atom->nbondtypes,onemols[i]->nbondtypes); in process_args()
85 atom->nangletypes = MAX(atom->nangletypes,onemols[i]->nangletypes); in process_args()
86 atom->ndihedraltypes = MAX(atom->ndihedraltypes,onemols[i]->ndihedraltypes); in process_args()
87 atom->nimpropertypes = MAX(atom->nimpropertypes,onemols[i]->nimpropertypes); in process_args()
145 if ((molatom_one < -1) || ((molindex_one >= 0) && (molatom_one >= onemols[molindex_one]->natoms))) in data_atom_post()
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| /dports/science/lammps/lammps-stable_29Sep2021/src/ |
| H A D | ntopo_dihedral_template.cpp | 52 Molecule **onemols = atom->avec->onemols; in build() local
69 num_dihedral = onemols[imol]->num_dihedral; in build()
70 dihedral_atom1 = onemols[imol]->dihedral_atom1; in build()
71 dihedral_atom2 = onemols[imol]->dihedral_atom2; in build()
72 dihedral_atom3 = onemols[imol]->dihedral_atom3; in build()
73 dihedral_atom4 = onemols[imol]->dihedral_atom4; in build()
74 dihedral_type = onemols[imol]->dihedral_type; in build()
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| H A D | ntopo_improper_template.cpp | 52 Molecule **onemols = atom->avec->onemols; in build() local
69 num_improper = onemols[imol]->num_improper; in build()
70 improper_atom1 = onemols[imol]->improper_atom1; in build()
71 improper_atom2 = onemols[imol]->improper_atom2; in build()
72 improper_atom3 = onemols[imol]->improper_atom3; in build()
73 improper_atom4 = onemols[imol]->improper_atom4; in build()
74 improper_type = onemols[imol]->improper_type; in build()
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| H A D | fix_deposit.cpp | 109 if (onemols[i]->xflag == 0) in FixDeposit()
111 if (onemols[i]->typeflag == 0) in FixDeposit()
113 if (ntype+onemols[i]->ntypes <= 0 || in FixDeposit()
117 if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols) in FixDeposit()
120 onemols[i]->check_attributes(0); in FixDeposit()
124 onemols[i]->compute_center(); in FixDeposit()
283 if (onemols[i]->radiusflag) in init()
429 natom = onemols[imol]->natoms; in pre_exchange()
706 onemols = &atom->molecules[imol]; in options()
707 nmol = onemols[0]->nset; in options()
[all …]
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| H A D | ntopo_angle_template.cpp | 51 Molecule **onemols = atom->avec->onemols; in build() local
68 num_angle = onemols[imol]->num_angle; in build()
69 angle_atom1 = onemols[imol]->angle_atom1; in build()
70 angle_atom2 = onemols[imol]->angle_atom2; in build()
71 angle_atom3 = onemols[imol]->angle_atom3; in build()
72 angle_type = onemols[imol]->angle_type; in build()
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| H A D | ntopo_bond_template.cpp | 51 Molecule **onemols = atom->avec->onemols; in build() local
68 num_bond = onemols[imol]->num_bond; in build()
69 bond_atom = onemols[imol]->bond_atom; in build()
70 bond_type = onemols[imol]->bond_type; in build()
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| H A D | npair_half_bin_newton.cpp | 55 Molecule **onemols = atom->avec->onemols; in build() local
107 which = find_special(onemols[imol]->special[iatom], in build()
108 onemols[imol]->nspecial[iatom], in build()
138 which = find_special(onemols[imol]->special[iatom], in build()
139 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_half_multi_old_newton.cpp | 58 Molecule **onemols = atom->avec->onemols; in build() local
110 which = find_special(onemols[imol]->special[iatom], in build()
111 onemols[imol]->nspecial[iatom], in build()
147 which = find_special(onemols[imol]->special[iatom], in build()
148 onemols[imol]->nspecial[iatom], in build()
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| H A D | compute_improper_local.cpp | 129 Molecule **onemols = atom->avec->onemols; in compute_impropers() local
152 ni = onemols[imol]->num_improper[iatom]; in compute_impropers()
162 if (tag[atom2] != onemols[imol]->improper_atom2[atom2][i]) continue; in compute_impropers()
164 atom1 = atom->map(onemols[imol]->improper_atom1[atom2][i]+tagprev); in compute_impropers()
165 atom3 = atom->map(onemols[imol]->improper_atom3[atom2][i]+tagprev); in compute_impropers()
166 atom4 = atom->map(onemols[imol]->improper_atom4[atom2][i]+tagprev); in compute_impropers()
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| H A D | npair_half_multi_newton.cpp | 60 Molecule **onemols = atom->avec->onemols; in build() local
133 which = find_special(onemols[imol]->special[iatom], in build()
134 onemols[imol]->nspecial[iatom], in build()
171 which = find_special(onemols[imol]->special[iatom], in build()
172 onemols[imol]->nspecial[iatom], in build()
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| H A D | compute_angle_local.cpp | 214 Molecule **onemols = atom->avec->onemols; in compute_angles() local
232 na = onemols[imol]->num_angle[iatom]; in compute_angles()
242 if (tag[atom2] != onemols[imol]->angle_atom2[atom2][i]) continue; in compute_angles()
243 atype = onemols[imol]->angle_type[atom2][i]; in compute_angles()
245 atom1 = atom->map(onemols[imol]->angle_atom1[atom2][i]+tagprev); in compute_angles()
246 atom3 = atom->map(onemols[imol]->angle_atom3[atom2][i]+tagprev); in compute_angles()
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| H A D | npair_full_nsq.cpp | 59 Molecule **onemols = atom->avec->onemols; in build() local
103 which = find_special(onemols[imol]->special[iatom], in build()
104 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_half_nsq_newtoff.cpp | 60 Molecule **onemols = atom->avec->onemols; in build() local
104 which = find_special(onemols[imol]->special[iatom], in build()
105 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_half_bin_newtoff.cpp | 56 Molecule **onemols = atom->avec->onemols; in build() local
106 which = find_special(onemols[imol]->special[iatom], in build()
107 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_full_bin.cpp | 54 Molecule **onemols = atom->avec->onemols; in build() local
102 which = find_special(onemols[imol]->special[iatom], in build()
103 onemols[imol]->nspecial[iatom], in build()
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| /dports/science/lammps/lammps-stable_29Sep2021/src/GRANULAR/ |
| H A D | fix_pour.cpp | 131 if (onemols[i]->xflag == 0) in FixPour()
133 if (onemols[i]->typeflag == 0) in FixPour()
135 if (ntype+onemols[i]->ntypes <= 0 || in FixPour()
139 if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols) in FixPour()
142 onemols[i]->check_attributes(0); in FixPour()
146 onemols[i]->compute_center(); in FixPour()
521 natom = onemols[imol]->natoms; in pre_exchange()
544 if (onemols[imol]->radiusflag) in pre_exchange()
936 onemols = &atom->molecules[imol]; in options()
937 nmol = onemols[0]->nset; in options()
[all …]
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| /dports/science/lammps/lammps-stable_29Sep2021/src/MC/ |
| H A D | fix_widom.cpp | 148 if (onemols[imol]->xflag == 0) in FixWidom()
157 if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols) in FixWidom()
219 onemols = atom->molecules; in options()
220 nmol = onemols[imol]->nset; in options()
367 onemols[imol]->compute_com(); in init()
370 onemols[imol]->x[i][0] -= onemols[imol]->com[0]; in init()
371 onemols[imol]->x[i][1] -= onemols[imol]->com[1]; in init()
372 onemols[imol]->x[i][2] -= onemols[imol]->com[2]; in init()
374 onemols[imol]->com[0] = 0; in init()
375 onemols[imol]->com[1] = 0; in init()
[all …]
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| H A D | fix_gcmc.cpp | 166 if (onemols[imol]->xflag == 0) in FixGCMC()
175 if (atom->molecular == Atom::TEMPLATE && onemols != atom->avec->onemols) in FixGCMC()
287 onemols = atom->molecules; in options()
288 nmol = onemols[imol]->nset; in options()
608 onemols[imol]->compute_com(); in init()
611 onemols[imol]->x[i][0] -= onemols[imol]->com[0]; in init()
612 onemols[imol]->x[i][1] -= onemols[imol]->com[1]; in init()
613 onemols[imol]->x[i][2] -= onemols[imol]->com[2]; in init()
615 onemols[imol]->com[0] = 0; in init()
616 onemols[imol]->com[1] = 0; in init()
[all …]
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| /dports/science/lammps/lammps-stable_29Sep2021/src/OPENMP/ |
| H A D | npair_half_bin_newton_omp.cpp | 67 Molecule **onemols = atom->avec->onemols; in build() local
118 which = find_special(onemols[imol]->special[iatom], in build()
119 onemols[imol]->nspecial[iatom], in build()
149 which = find_special(onemols[imol]->special[iatom], in build()
150 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_half_multi_old_newton_omp.cpp | 69 Molecule **onemols = atom->avec->onemols; in build() local
120 which = find_special(onemols[imol]->special[iatom], in build()
121 onemols[imol]->nspecial[iatom], in build()
157 which = find_special(onemols[imol]->special[iatom], in build()
158 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_half_multi_newton_omp.cpp | 71 Molecule **onemols = atom->avec->onemols; in build() local
144 which = find_special(onemols[imol]->special[iatom], in build()
145 onemols[imol]->nspecial[iatom], in build()
182 which = find_special(onemols[imol]->special[iatom], in build()
183 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_full_bin_omp.cpp | 63 Molecule **onemols = atom->avec->onemols; in build() local
112 which = find_special(onemols[imol]->special[iatom], in build()
113 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_half_bin_newtoff_omp.cpp | 68 Molecule **onemols = atom->avec->onemols; in build() local
117 which = find_special(onemols[imol]->special[iatom], in build()
118 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_half_nsq_newtoff_omp.cpp | 68 Molecule **onemols = atom->avec->onemols; in build() local
113 which = find_special(onemols[imol]->special[iatom], in build()
114 onemols[imol]->nspecial[iatom], in build()
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| H A D | npair_full_nsq_omp.cpp | 67 Molecule **onemols = atom->avec->onemols; in build() local
112 which = find_special(onemols[imol]->special[iatom], in build()
113 onemols[imol]->nspecial[iatom], in build()
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