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Searched refs:atom_pos (Results 1 – 25 of 92) sorted by relevance

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/dports/science/liggghts/LIGGGHTS-PUBLIC-3.8.0-26-g6e873439/lib/colvars/
H A Dcolvarproxy.h73 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 …]
H A Dcolvaratoms.h38 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 …]
H A Dcolvarmodule.h75 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 …]
H A Dcolvaratoms.cpp462 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 …]
/dports/science/lammps/lammps-stable_29Sep2021/lib/colvars/
H A Dcolvaratoms.h48 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()
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H A Dcolvarcomp_gpath.cpp55 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 …]
H A Dcolvaratoms.cpp196 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 …]
H A Dcolvarcomp_angles.cpp55 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()
/dports/lang/erlang-runtime23/otp-OTP-23.3.4.10/erts/emulator/test/
H A Dpseudoknot_SUITE.erl2789 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)).
/dports/lang/erlang-runtime24/otp-OTP-24.1.7/lib/compiler/test/inline_SUITE_data/
H A Dpseudoknot.erl2190 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)).
/dports/lang/erlang-runtime24/otp-OTP-24.1.7/erts/emulator/test/
H A Dpseudoknot_SUITE.erl2789 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)).
/dports/lang/erlang-runtime23/otp-OTP-23.3.4.10/lib/compiler/test/inline_SUITE_data/
H A Dpseudoknot.erl2190 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)).
/dports/lang/erlang-runtime22/otp-OTP-22.3.4.24/lib/compiler/test/inline_SUITE_data/
H A Dpseudoknot.erl2190 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)).
/dports/lang/erlang-runtime22/otp-OTP-22.3.4.24/erts/emulator/test/
H A Dpseudoknot_SUITE.erl2789 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)).
/dports/lang/erlang-wx/otp-OTP-24.1.7/lib/compiler/test/inline_SUITE_data/
H A Dpseudoknot.erl2190 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)).
/dports/lang/erlang-wx/otp-OTP-24.1.7/erts/emulator/test/
H A Dpseudoknot_SUITE.erl2789 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)).
/dports/lang/erlang/otp-OTP-24.1.7/erts/emulator/test/
H A Dpseudoknot_SUITE.erl2789 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)).
/dports/lang/erlang/otp-OTP-24.1.7/lib/compiler/test/inline_SUITE_data/
H A Dpseudoknot.erl2190 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)).
/dports/lang/erlang-java/otp-OTP-24.1.7/erts/emulator/test/
H A Dpseudoknot_SUITE.erl2789 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)).
/dports/lang/erlang-runtime21/otp-OTP-21.3.8.24/erts/emulator/test/
H A Dpseudoknot_SUITE.erl2789 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)).
/dports/lang/erlang-java/otp-OTP-24.1.7/lib/compiler/test/inline_SUITE_data/
H A Dpseudoknot.erl2190 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)).
/dports/lang/erlang-runtime21/otp-OTP-21.3.8.24/lib/compiler/test/inline_SUITE_data/
H A Dpseudoknot.erl2190 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)).
/dports/science/cp2k-data/cp2k-7.1.0/src/
H A Dintegration_grid_types.F29 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…
/dports/science/cp2k/cp2k-2e995eec7fd208c8a72d9544807bd8b8ba8cd1cc/src/
H A Dintegration_grid_types.F29 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…
/dports/science/quantum-espresso/q-e-qe-6.7.0/PW/src/
H A Dintersite_V.f90538 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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