/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/lib/colvars/ |
H A D | colvarproxy.h | 73 virtual cvm::rvector position_distance (cvm::atom_pos const &pos1, 74 cvm::atom_pos const &pos2) = 0; 78 virtual cvm::real position_dist2 (cvm::atom_pos const &pos1, 79 cvm::atom_pos const &pos2); 84 virtual void select_closest_image (cvm::atom_pos &pos, 85 cvm::atom_pos const &ref_pos) = 0; 91 void select_closest_images (std::vector<cvm::atom_pos> &pos, 92 cvm::atom_pos const &ref_pos); 121 std::vector<cvm::atom_pos> &pos, 135 for (std::vector<cvm::atom_pos>::iterator pi = pos.begin(); in select_closest_images() [all …]
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H A D | colvaratoms.h | 38 cvm::atom_pos pos; 85 pos = atom_pos (0.0); in reset_data() 133 cvm::atom_pos dummy_atom_pos; 168 std::vector<cvm::atom_pos> ref_pos; 173 cvm::atom_pos ref_pos_cog; 254 std::vector<cvm::atom_pos> positions() const; 257 std::vector<cvm::atom_pos> positions_shifted (cvm::rvector const &shift) const; 261 cvm::atom_pos center_of_geometry() const; 265 cvm::atom_pos center_of_mass() const; 268 std::vector<cvm::atom_pos> old_pos; [all …]
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H A D | colvarmodule.h | 75 typedef rvector atom_pos; typedef 276 static rvector position_distance (atom_pos const &pos1, 277 atom_pos const &pos2); 286 static real position_dist2 (atom_pos const &pos1, 287 atom_pos const &pos2); 292 static void select_closest_image (atom_pos &pos, 293 atom_pos const &ref_pos); 300 atom_pos const &ref_pos); 325 std::vector<atom_pos> &pos, 333 std::vector<atom_pos> &pos, [all …]
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H A D | colvaratoms.cpp | 462 ref_pos_cog = cvm::atom_pos (0.0, 0.0, 0.0); in center_ref_pos() 583 cvm::atom_pos cvm::atom_group::center_of_geometry() const in center_of_geometry() 588 cvm::atom_pos cog (0.0, 0.0, 0.0); in center_of_geometry() 597 cvm::atom_pos cvm::atom_group::center_of_mass() const in center_of_mass() 602 cvm::atom_pos com (0.0, 0.0, 0.0); in center_of_mass() 682 std::vector<cvm::atom_pos> x (this->size(), 0.0); in positions() 684 std::vector<cvm::atom_pos>::iterator xi = x.begin(); in positions() 697 std::vector<cvm::atom_pos> x (this->size(), 0.0); in positions_shifted() 699 std::vector<cvm::atom_pos>::iterator xi = x.begin(); in positions_shifted() 714 std::vector<cvm::atom_pos>::iterator vi = v.begin(); in velocities() [all …]
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/dports/science/lammps/lammps-stable_29Sep2021/lib/colvars/ |
H A D | colvaratoms.h | 48 cvm::atom_pos pos; 96 pos = cvm::atom_pos(0.0); in reset_data() 210 int set_dummy_pos(cvm::atom_pos const &pos); 252 cvm::atom_pos dummy_atom_pos; 336 std::vector<cvm::atom_pos> ref_pos; 341 cvm::atom_pos ref_pos_cog; 413 cvm::atom_pos cog; 416 cvm::atom_pos cog_orig; 433 cvm::atom_pos com; 443 inline cvm::atom_pos center_of_mass() const in center_of_mass() [all …]
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H A D | colvarcomp_gpath.cpp | 55 std::vector<cvm::atom_pos> reference_position(atoms->size()); in CartesianBasedPath() 168 cvm::atom_pos reference_cog_1, reference_cog_2; in prepareVectors() 182 cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2; in prepareVectors() 203 cvm::atom_pos reference_cog_1, reference_cog_3; in prepareVectors() 217 cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_3; in prepareVectors() 307 cvm::atom_pos reference_cog_1, reference_cog_2; in prepareVectors() 321 std::vector<cvm::atom_pos> tmp_reference_fitting_frame_1; in prepareVectors() 322 std::vector<cvm::atom_pos> tmp_reference_fitting_frame_2; in prepareVectors() 324 cvm::atom_pos reference_fitting_cog_1, reference_fitting_cog_2; in prepareVectors() 351 cvm::atom_pos reference_cog_3; in prepareVectors() [all …]
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H A D | colvaratoms.cpp | 196 int cvm::atom_group::set_dummy_pos(cvm::atom_pos const &pos) in set_dummy_pos() 957 ref_pos_cog = cvm::atom_pos(0.0, 0.0, 0.0); in center_ref_pos() 958 std::vector<cvm::atom_pos>::iterator pi; in center_ref_pos() 1021 cvm::atom_pos const rpg_cog = fitting_group ? in calc_apply_roto_translation() 1213 cvm::atom_pos const pos_orig = in calc_fit_gradients() 1246 std::vector<cvm::atom_pos> x(this->size(), 0.0); in positions() 1248 std::vector<cvm::atom_pos>::iterator xi = x.begin(); in positions() 1267 std::vector<cvm::atom_pos> x(this->size(), 0.0); in positions_shifted() 1269 std::vector<cvm::atom_pos>::iterator xi = x.begin(); in positions_shifted() 1290 std::vector<cvm::atom_pos>::iterator vi = v.begin(); in velocities() [all …]
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H A D | colvarcomp_angles.cpp | 55 cvm::atom_pos const g1_pos = group1->center_of_mass(); in calc_value() 56 cvm::atom_pos const g2_pos = group2->center_of_mass(); in calc_value() 57 cvm::atom_pos const g3_pos = group3->center_of_mass(); in calc_value() 181 cvm::atom_pos const g1_pos = group1->center_of_mass(); in calc_value() 182 cvm::atom_pos const g2_pos = group2->center_of_mass(); in calc_value() 183 cvm::atom_pos const g3_pos = group3->center_of_mass(); in calc_value() 318 cvm::atom_pos const g1_pos = group1->center_of_mass(); in calc_value() 319 cvm::atom_pos const g2_pos = group2->center_of_mass(); in calc_value() 320 cvm::atom_pos const g3_pos = group3->center_of_mass(); in calc_value() 321 cvm::atom_pos const g4_pos = group4->center_of_mass(); in calc_value()
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/dports/lang/erlang-runtime23/otp-OTP-23.3.4.10/erts/emulator/test/ |
H A D | pseudoknot_SUITE.erl | 2789 atom_pos(Atom, {I,T,N}) -> function 3045 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 3047 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 3049 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 3051 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 3145 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 3146 atom_pos(nuc_C3_,Ref), 3147 atom_pos(nuc_C4_,Ref))), 3189 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 3190 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-runtime24/otp-OTP-24.1.7/lib/compiler/test/inline_SUITE_data/ |
H A D | pseudoknot.erl | 2190 atom_pos(Atom, {I,T,N}) -> function 2271 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 2273 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 2275 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 2277 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 2371 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 2372 atom_pos(nuc_C3_,Ref), 2373 atom_pos(nuc_C4_,Ref))), 2415 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 2416 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-runtime24/otp-OTP-24.1.7/erts/emulator/test/ |
H A D | pseudoknot_SUITE.erl | 2789 atom_pos(Atom, {I,T,N}) -> function 3045 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 3047 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 3049 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 3051 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 3145 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 3146 atom_pos(nuc_C3_,Ref), 3147 atom_pos(nuc_C4_,Ref))), 3189 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 3190 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-runtime23/otp-OTP-23.3.4.10/lib/compiler/test/inline_SUITE_data/ |
H A D | pseudoknot.erl | 2190 atom_pos(Atom, {I,T,N}) -> function 2271 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 2273 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 2275 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 2277 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 2371 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 2372 atom_pos(nuc_C3_,Ref), 2373 atom_pos(nuc_C4_,Ref))), 2415 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 2416 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-runtime22/otp-OTP-22.3.4.24/lib/compiler/test/inline_SUITE_data/ |
H A D | pseudoknot.erl | 2190 atom_pos(Atom, {I,T,N}) -> function 2271 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 2273 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 2275 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 2277 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 2371 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 2372 atom_pos(nuc_C3_,Ref), 2373 atom_pos(nuc_C4_,Ref))), 2415 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 2416 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-runtime22/otp-OTP-22.3.4.24/erts/emulator/test/ |
H A D | pseudoknot_SUITE.erl | 2789 atom_pos(Atom, {I,T,N}) -> function 3045 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 3047 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 3049 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 3051 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 3145 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 3146 atom_pos(nuc_C3_,Ref), 3147 atom_pos(nuc_C4_,Ref))), 3189 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 3190 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-wx/otp-OTP-24.1.7/lib/compiler/test/inline_SUITE_data/ |
H A D | pseudoknot.erl | 2190 atom_pos(Atom, {I,T,N}) -> function 2271 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 2273 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 2275 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 2277 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 2371 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 2372 atom_pos(nuc_C3_,Ref), 2373 atom_pos(nuc_C4_,Ref))), 2415 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 2416 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-wx/otp-OTP-24.1.7/erts/emulator/test/ |
H A D | pseudoknot_SUITE.erl | 2789 atom_pos(Atom, {I,T,N}) -> function 3045 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 3047 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 3049 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 3051 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 3145 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 3146 atom_pos(nuc_C3_,Ref), 3147 atom_pos(nuc_C4_,Ref))), 3189 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 3190 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang/otp-OTP-24.1.7/erts/emulator/test/ |
H A D | pseudoknot_SUITE.erl | 2789 atom_pos(Atom, {I,T,N}) -> function 3045 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 3047 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 3049 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 3051 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 3145 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 3146 atom_pos(nuc_C3_,Ref), 3147 atom_pos(nuc_C4_,Ref))), 3189 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 3190 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang/otp-OTP-24.1.7/lib/compiler/test/inline_SUITE_data/ |
H A D | pseudoknot.erl | 2190 atom_pos(Atom, {I,T,N}) -> function 2271 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 2273 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 2275 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 2277 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 2371 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 2372 atom_pos(nuc_C3_,Ref), 2373 atom_pos(nuc_C4_,Ref))), 2415 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 2416 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-java/otp-OTP-24.1.7/erts/emulator/test/ |
H A D | pseudoknot_SUITE.erl | 2789 atom_pos(Atom, {I,T,N}) -> function 3045 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 3047 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 3049 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 3051 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 3145 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 3146 atom_pos(nuc_C3_,Ref), 3147 atom_pos(nuc_C4_,Ref))), 3189 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 3190 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-runtime21/otp-OTP-21.3.8.24/erts/emulator/test/ |
H A D | pseudoknot_SUITE.erl | 2789 atom_pos(Atom, {I,T,N}) -> function 3045 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 3047 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 3049 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 3051 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 3145 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 3146 atom_pos(nuc_C3_,Ref), 3147 atom_pos(nuc_C4_,Ref))), 3189 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 3190 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-java/otp-OTP-24.1.7/lib/compiler/test/inline_SUITE_data/ |
H A D | pseudoknot.erl | 2190 atom_pos(Atom, {I,T,N}) -> function 2271 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 2273 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 2275 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 2277 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 2371 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 2372 atom_pos(nuc_C3_,Ref), 2373 atom_pos(nuc_C4_,Ref))), 2415 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 2416 atom_pos(nuc_O3_,V)).
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/dports/lang/erlang-runtime21/otp-OTP-21.3.8.24/lib/compiler/test/inline_SUITE_data/ |
H A D | pseudoknot.erl | 2190 atom_pos(Atom, {I,T,N}) -> function 2271 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rA_N9, V),atom_pos(nuc_C4, V)); 2273 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)); 2275 tfo_align(atom_pos(nuc_C1_, V),atom_pos(rG_N9, V),atom_pos(nuc_C4, V)); 2277 tfo_align(atom_pos(nuc_C1_, V),atom_pos(nuc_N1, V),atom_pos(nuc_C2, V)). 2371 Align = tfo_inv_ortho(tfo_align(atom_pos(nuc_O3_,Ref), 2372 atom_pos(nuc_C3_,Ref), 2373 atom_pos(nuc_C4_,Ref))), 2415 pt_dist(atom_pos(nuc_P, get_var(J,Partial_inst)), 2416 atom_pos(nuc_O3_,V)).
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/dports/science/cp2k-data/cp2k-7.1.0/src/ |
H A D | integration_grid_types.F | 29 REAL(KIND=dp), DIMENSION(:, :), ALLOCATABLE :: atom_pos component 109 …IF (ALLOCATED(int_grid%grid_batch(i)%gnlist%atom_pos)) DEALLOCATE (int_grid%grid_batch(i)%gnlist%a…
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/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/ |
H A D | integration_grid_types.F | 29 REAL(KIND=dp), DIMENSION(:, :), ALLOCATABLE :: atom_pos component 109 …IF (ALLOCATED(int_grid%grid_batch(i)%gnlist%atom_pos)) DEALLOCATE (int_grid%grid_batch(i)%gnlist%a…
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/dports/science/quantum-espresso/q-e-qe-6.7.0/PW/src/ |
H A D | intersite_V.f90 | 538 USE ldaU, ONLY : atom_pos, at_sc, sc_at, num_uc 571 x2(i) = atom_pos(at_sc(at2)%at,i) + DBLE(at_sc(at2)%n(i)) 584 r1(i) = r1(i) + atom_pos(at1,j) * ss(j,i) 607 dx(i) = r2(i) - atom_pos(at,i) 635 dx(i) = r1(i) - atom_pos(at,i) 661 dr(i) = NINT(r2(i) - atom_pos(rat2,i)) 782 USE ldaU, ONLY : atom_pos 788 ALLOCATE(atom_pos(nat,3)) 792 atom_pos(na,ipol) = bg(1,ipol)*tau(1,na) + &
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