Coordinates
Coordinates
Section System::Coordinates
Type block
If XYZCoordinates, PDBCoordinates, and XSFCoordinates were not found,
Octopus tries to read the coordinates for the atoms from the block Coordinates. The
format is quite straightforward:
%Coordinates
  ‘C’ | -0.56415 | 0.0 | 0.0 | no
  ‘O’ |  0.56415 | 0.0 | 0.0 | no
%
The first line defines a carbon atom at coordinates (-0.56415, 0.0, 0.0),
that is not allowed to move during dynamical simulations. The second line has
a similar meaning. This block obviously defines a carbon monoxide molecule, if the
input units are eV_Angstrom. The number of coordinates for each species
must be equal to the dimension of your space (generally 3).
Note that in this way it is possible to fix some of the atoms (this
is not possible when specifying the coordinates through a PDBCoordinates or
XYZCoordinates file). The last column is optional, and the default is yes.
It is always possible to fix all atoms using the MoveIons directive.
- components/01-derivatives_1d.01.inp
- components/01-derivatives_1d.02-fortran.inp
- components/02-derivatives_2d.01.inp
- components/03-derivatives_3d.01.inp
- components/03-derivatives_3d.02-unpacked.inp
- components/04-hartree_3d_cg.01-cg_corrected.inp
- components/05-hartree_3d_fft.01-fft.inp
- components/05-hartree_3d_fft.02-fft_corrected.inp
- components/05-hartree_3d_fft.03-3d_1d_periodic.inp
- components/05-hartree_3d_fft.04-3d_3d_periodic.inp
- components/05-hartree_3d_fft.05-3d_2d_periodic.inp
- components/06-hartree_3d_isf.01-isf.inp
- components/07-cholesky_serial.01-real.inp
- components/07-cholesky_serial.02-complex.inp
- components/07-cholesky_serial.03-parindep.inp
- components/08-gs.01-cgs_real.inp
- components/08-gs.02-cgs_complex.inp
- components/08-gs.03-mgs_real.inp
- components/08-gs.04-mgs_complex.inp
- components/08-gs.05-drcgs_real.inp
- components/08-gs.06-drcgs_complex.inp
- components/10-hartree_pfft.01-fft.inp
- components/10-hartree_pfft.02-fft_corrected.inp
- components/10-hartree_pfft.03-3d_1d_periodic.inp
- components/10-hartree_pfft.04-3d_3d_periodic.inp
- components/10-hartree_pfft.05-3d_2d_periodic.inp
- components/10-hartree_pfft.06-fft-parstates.inp
- components/11-hartree_cl.01-fft.inp
- components/12-hartree_direct_3d.01.inp
- components/13-hartree_3d_mg.01-multigrid.inp
- components/13-hartree_3d_mg.02-curvilinear.inp
- components/14-center-geom.01-run.inp
- components/15-cholesky_parallel.01-real.inp
- components/15-cholesky_parallel.02-complex.inp
- components/16-hartree_3d_psolver.01-psolver.inp
- components/16-hartree_3d_psolver.02-psolver.inp
- components/18-interpolation.01-1d.inp
- components/18-interpolation.02-2d.inp
- components/18-interpolation.03-3d.inp
- components/19-hgh_soc.01-3d.inp
- components/23-exponential_apply.01-jellium.inp
- components/24-boundaries.01-jellium.inp
- components/25-subspace.01-jellium.inp
- components/26-batch_ops.01-jellium.inp
- components/26-batch_ops.02-jellium-complex.inp
- components/26-batch_ops.03-jellium-spinor.inp
- components/29-linear_solver.01-real.inp
- components/31-grid_interpolation.01.inp
- components/34-regridding.01-samespacing-mixed.inp
- components/34-regridding.02-samespacing-parstates.inp
- components/34-regridding.03-samespacing-pardomains.inp
- components/34-regridding.04-spacing-ratio3-mixed.inp
- components/34-regridding.05-spacing-ratio3-parstates.inp
- components/34-regridding.06-spacing-ratio3-pardomains.inp
- components/34-regridding.07-spacing-ratio3-nearestneighbor-mixed.inp
- components/34-regridding.08-spacing-ratio3-nearestneighbor-parstates.inp
- components/34-regridding.09-spacing-ratio3-nearestneighbor-pardomains.inp
- components/35-helmholtz_decom.01-large_box_no_surf_corr.inp
- components/35-helmholtz_decom.02-small_box_no_surf_corr.inp
- components/35-helmholtz_decom.03-parallelepiped_small_box_with_surf_corr.inp
- components/35-helmholtz_decom.04-cylinder_small_box_with_surf_corr.inp
- components/35-helmholtz_decom.05-sphere_small_box_with_surf_corr.inp
- components/36-maxwell_vector_potential.inp
- components/37-current-density.inp
- errors/01-run_mode.01-one_shot.inp
- errors/02-scf_errors.01-rdmft.inp
- finite_systems_1d/01-hydrogen.01-ground_state.inp
- finite_systems_1d/01-hydrogen.02-excited_state.inp
- finite_systems_1d/01-hydrogen.03-dummy.inp
- finite_systems_1d/01-hydrogen.04-absorbing_boundaries.inp
- finite_systems_1d/02-neon_mpi.01-ground_state-IP_par_domains.inp
- finite_systems_1d/02-neon_mpi.02-ground_state-kli_par_domains.inp
- finite_systems_1d/02-neon_mpi.03-td_calc-kli_par_states.inp
- finite_systems_1d/03-He-Hartree-Fock.01-gs.inp
- finite_systems_1d/04-lithium.01-ground_state.inp
- finite_systems_1d/04-lithium.02-absorbing_boundaries.inp
- finite_systems_1d/09-morse.01-gs.inp
- finite_systems_1d/09-morse.02-unocc.inp
- finite_systems_1d/09-morse.03-td.inp
- finite_systems_2d/01-quadratic_box.01-ground_state.inp
- finite_systems_2d/01-quadratic_box.02-hartree.inp
- finite_systems_2d/01-quadratic_box.03-hartree+xc.inp
- finite_systems_2d/01-quadratic_box.04-spin_polarized.inp
- finite_systems_2d/02-fock-darwin.01-ground_state.inp
- finite_systems_2d/02-fock-darwin.02-ground_state.inp
- finite_systems_2d/02-fock-darwin.03-ground_state.inp
- finite_systems_2d/02-fock-darwin.04-ground_state.inp
- finite_systems_2d/03-helium_atom.01-ground_state.inp
- finite_systems_2d/03-helium_atom.02-ground_state.inp
- finite_systems_2d/04-biot_savart.01-gs.inp
- finite_systems_2d/05-spin_precession.01-ground_state.inp
- finite_systems_2d/05-spin_precession.02-time_propagation.inp
- finite_systems_2d/06-gdlib.01-gs.inp
- finite_systems_2d/07-user_def_box.01-gs.inp
- finite_systems_2d/08-constrain.01-gs.inp
- finite_systems_2d/08-constrain.02-gs_dir.inp
- finite_systems_2d/08-constrain.03-polarized.inp
- finite_systems_2d/09-magnetic_2d.01-no_field.inp
- finite_systems_2d/09-magnetic_2d.02-gs_gauge_xy.inp
- finite_systems_2d/09-magnetic_2d.03-gs_gauge_y.inp
- finite_systems_3d/01-carbon_atom.01-psf_l0.inp
- finite_systems_3d/01-carbon_atom.02-psf_l1.inp
- finite_systems_3d/01-carbon_atom.03-static_field.inp
- finite_systems_3d/01-carbon_atom.04-smear.inp
- finite_systems_3d/02-curvilinear_coordinates.01-gygi.inp
- finite_systems_3d/03-magnetic.01-gs-unpolarized.inp
- finite_systems_3d/03-magnetic.02-td-unpolarized.inp
- finite_systems_3d/03-magnetic.03-gs-polarized.inp
- finite_systems_3d/03-magnetic.04-td-polarized.inp
- finite_systems_3d/03-magnetic.05-gs-spinors.inp
- finite_systems_3d/03-magnetic.06-td-spinors.inp
- finite_systems_3d/04-jellium.01-ground_state.inp
- finite_systems_3d/05-output.01-gs-set1.inp
- finite_systems_3d/05-output.02-gs.inp
- finite_systems_3d/05-output.03-convert.inp
- finite_systems_3d/05-output.04-convert-op.inp
- finite_systems_3d/06-restart.01-gs_mixrho.inp
- finite_systems_3d/06-restart.02-restart_gs_mixrho.inp
- finite_systems_3d/06-restart.03-gs_mixvhxc.inp
- finite_systems_3d/06-restart.04-restart_gs_mixvhxc.inp
- finite_systems_3d/06-restart.05-restart_gs.inp
- finite_systems_3d/06-restart.06-td_calc.inp
- finite_systems_3d/06-restart.07-restart_td_calc.inp
- finite_systems_3d/07-spin_orbit_coupling.01-hgh.inp
- finite_systems_3d/07-spin_orbit_coupling.02-rkb.inp
- finite_systems_3d/08-spin_orbit_coupling_full.01-hgh.inp
- finite_systems_3d/08-spin_orbit_coupling_full.02-rkb.inp
- finite_systems_3d/08-spin_orbit_coupling_full.03-unocc.inp
- finite_systems_3d/09-spinors.01-ground_state.inp
- finite_systems_3d/09-spinors.02-rmmdiis.inp
- finite_systems_3d/09-spinors.03-rmmdiis_extra_states.inp
- finite_systems_3d/12-forces.01-N2_gs.inp
- finite_systems_3d/12-forces.02-N2_gs.inp
- finite_systems_3d/12-forces.03-N2_gs.inp
- finite_systems_3d/13-full_potential_hydrogen.01-gs.inp
- finite_systems_3d/13-full_potential_hydrogen.02-gs-cg.inp
- finite_systems_3d/14-fullerene_unpacked.01-gs.inp
- finite_systems_3d/14-fullerene_unpacked.02-td-unpacked.inp
- finite_systems_3d/14-fullerene_unpacked.03-td-packed.inp
- finite_systems_3d/15-fullerene_stdlcao.01-gs.inp
- finite_systems_3d/16-scfinlcao_std.01-gs.inp
- finite_systems_3d/17-scfinlcao_alt.01-gs.inp
- finite_systems_3d/18-preconditioner_poisson.01-poisson.inp
- finite_systems_3d/20-eigensolver.01-cg.inp
- finite_systems_3d/20-eigensolver.03-plan.inp
- finite_systems_3d/20-eigensolver.04-evolution.inp
- finite_systems_3d/20-eigensolver.05-rmmdiis.inp
- finite_systems_3d/20-eigensolver.06-rmmdiis-noscalapack.inp
- finite_systems_3d/20-eigensolver.07-chebyshev.inp
- finite_systems_3d/20-eigensolver.08-evolution-chebyshev.inp
- finite_systems_3d/22-preconditioner.01-none.inp
- finite_systems_3d/22-preconditioner.02-filter.inp
- finite_systems_3d/22-preconditioner.03-jacobi.inp
- finite_systems_3d/22-preconditioner.04-multigrid.inp
- finite_systems_3d/22-preconditioner.05-multigrid_rmmdiis.inp
- finite_systems_3d/23-go-na2.01-steep.inp
- finite_systems_3d/23-go-na2.02-simplex.inp
- finite_systems_3d/23-go-na2.03-fire.inp
- finite_systems_3d/23-go-na2.04-fire_restart.inp
- finite_systems_3d/23-go-na2.05-constrains.inp
- finite_systems_3d/24-o2-spin.01-gs.inp
- finite_systems_3d/28-carbon_big_box.01-ground_state.inp
- finite_systems_3d/29-pcm_chlorine_anion.01-ground_state-n60.inp
- finite_systems_3d/29-pcm_chlorine_anion.02-td_prop-n60.inp
- finite_systems_3d/29-pcm_chlorine_anion.03-ground_state-n60-poisson.inp
- finite_systems_3d/29-pcm_chlorine_anion.04-ground_state-n240.inp
- finite_systems_3d/30-local_multipoles.01-gs.inp
- finite_systems_3d/30-local_multipoles.02-multipoles.inp
- finite_systems_3d/30-local_multipoles.03-multipoles_restart.inp
- finite_systems_3d/31-acetylene_b3lyp.01-gs.inp
- finite_systems_3d/32-tdpcm_methane.01-ground_state.inp
- finite_systems_3d/32-tdpcm_methane.02-td_prop_neq.inp
- finite_systems_3d/32-tdpcm_methane.03-td_prop_eom.inp
- finite_systems_3d/33-cg.01-orthogonalize_all.inp
- finite_systems_3d/33-cg.02-additional_terms.inp
- finite_systems_3d/33-cg.03-cg_direction.inp
- finite_systems_3d/34-walltime.01-gs_walltime.inp
- finite_systems_3d/34-walltime.02-restart_gs.inp
- finite_systems_3d/34-walltime.03-td_walltime.inp
- finite_systems_3d/34-walltime.04-restart_td.inp
- finite_systems_3d/35-slater_x.01-gs.inp
- finite_systems_3d/35-slater_x.02-gs_spinors.inp
- finite_systems_3d/36-kli_x.01-gs.inp
- finite_systems_3d/36-kli_x.02-gs_spinors.inp
- finite_systems_3d/37-sternheimer_polarized.01-gs.inp
- finite_systems_3d/37-sternheimer_polarized.02-em_resp.inp
- finite_systems_3d/38-carbon_atom_cgal_box.01-gs.inp
- finite_systems_3d/39-adsic.01-unpolarized.inp
- finite_systems_3d/39-adsic.02-polarized.inp
- finite_systems_3d/40-evo.01-par_domains.inp
- finite_systems_3d/40-evo.02-par_states.inp
- finite_systems_3d/41-gpu-bug.01-C.inp
- finite_systems_3d/42-full_potential_anc.01-gs.inp
- finite_systems_3d/42-full_potential_anc.02-sc-zora.inp
- finite_systems_3d/42-full_potential_anc.03-sf-zora.inp
- finite_systems_3d/42-full_potential_anc.04-fr-zora.inp
- finite_systems_3d/42-full_potential_anc.05-zora-error.inp
- finite_systems_3d/43-gga_spinors.01-H.inp
- functionals/01-xc_1d.01-wfs-lda.inp
- functionals/01-xc_1d.02-wfs-hf.inp
- functionals/01-xc_1d.lda_csc.inp
- functionals/01-xc_1d.oep_exx.inp
- functionals/01-xc_1d.oep_kli.inp
- functionals/02-xc_2d.01-hartree.inp
- functionals/02-xc_2d.02-hf.inp
- functionals/02-xc_2d.gga_b86.inp
- functionals/02-xc_2d.gga_b86_mgc.inp
- functionals/02-xc_2d.gga_b88.inp
- functionals/02-xc_2d.gga_pbe.inp
- functionals/02-xc_2d.lda_amgb.inp
- functionals/02-xc_2d.lda_prm.inp
- functionals/03-xc.01-gs.inp
- functionals/03-xc.b3lyp_fock.inp
- functionals/03-xc.b3lyp_oep.inp
- functionals/03-xc.exx.inp
- functionals/03-xc.fbex.inp
- functionals/03-xc.fbex_sl.inp
- functionals/03-xc.gga_c_am05.inp
- functionals/03-xc.gga_c_lm.inp
- functionals/03-xc.gga_c_lyp.inp
- functionals/03-xc.gga_c_p86.inp
- functionals/03-xc.gga_c_pbe.inp
- functionals/03-xc.gga_c_pbe_jrgx.inp
- functionals/03-xc.gga_c_pbe_sol.inp
- functionals/03-xc.gga_c_pw91.inp
- functionals/03-xc.gga_c_xpbe.inp
- functionals/03-xc.gga_x_am05.inp
- functionals/03-xc.gga_x_b86.inp
- functionals/03-xc.gga_x_b86_mgc.inp
- functionals/03-xc.gga_x_b88.inp
- functionals/03-xc.gga_x_bayesian.inp
- functionals/03-xc.gga_x_dk87_r1.inp
- functionals/03-xc.gga_x_dk87_r2.inp
- functionals/03-xc.gga_x_ft97_a.inp
- functionals/03-xc.gga_x_ft97_b.inp
- functionals/03-xc.gga_x_g96.inp
- functionals/03-xc.gga_x_lb.inp
- functionals/03-xc.gga_x_lg93.inp
- functionals/03-xc.gga_x_mpbe.inp
- functionals/03-xc.gga_x_mpw91.inp
- functionals/03-xc.gga_x_optb88_vdw.inp
- functionals/03-xc.gga_x_optpbe_vdw.inp
- functionals/03-xc.gga_x_optx.inp
- functionals/03-xc.gga_x_pbe.inp
- functionals/03-xc.gga_x_pbe_jsjr.inp
- functionals/03-xc.gga_x_pbe_r.inp
- functionals/03-xc.gga_x_pbe_sol.inp
- functionals/03-xc.gga_x_pbea.inp
- functionals/03-xc.gga_x_pbek1_vdw.inp
- functionals/03-xc.gga_x_pw86.inp
- functionals/03-xc.gga_x_pw91.inp
- functionals/03-xc.gga_x_rpbe.inp
- functionals/03-xc.gga_x_wc.inp
- functionals/03-xc.gga_x_xpbe.inp
- functionals/03-xc.gga_xc_b97_d.inp
- functionals/03-xc.gga_xc_edf1.inp
- functionals/03-xc.gga_xc_hcth_120.inp
- functionals/03-xc.gga_xc_hcth_147.inp
- functionals/03-xc.gga_xc_hcth_407.inp
- functionals/03-xc.gga_xc_hcth_93.inp
- functionals/03-xc.gga_xc_mpwlyp1w.inp
- functionals/03-xc.gga_xc_pbe1w.inp
- functionals/03-xc.gga_xc_pbelyp1w.inp
- functionals/03-xc.gga_xc_xlyp.inp
- functionals/03-xc.kli.inp
- functionals/03-xc.lda_c_fbe.inp
- functionals/03-xc.lda_c_gl.inp
- functionals/03-xc.lda_c_hl.inp
- functionals/03-xc.lda_c_ob_pw.inp
- functionals/03-xc.lda_c_ob_pz.inp
- functionals/03-xc.lda_c_pw.inp
- functionals/03-xc.lda_c_pw_mod.inp
- functionals/03-xc.lda_c_pz.inp
- functionals/03-xc.lda_c_pz_mod.inp
- functionals/03-xc.lda_c_rpa.inp
- functionals/03-xc.lda_c_vbh.inp
- functionals/03-xc.lda_c_vwn.inp
- functionals/03-xc.lda_c_vwn_rpa.inp
- functionals/03-xc.lda_c_wigner.inp
- functionals/03-xc.lda_c_xalpha.inp
- functionals/03-xc.lda_x.inp
- functionals/03-xc.lda_xc_teter93.inp
- functionals/03-xc.mvorb_hse06_fock.inp
- functionals/03-xc.pbe0_fock.inp
- functionals/03-xc.pbe0_oep.inp
- functionals/03-xc.sic_pz.inp
- functionals/03-xc.slater.inp
- functionals/04-oep.01-jellium-lsda.inp
- functionals/04-oep.02-jellium-exx_kli.inp
- functionals/04-oep.03-jellium-full_exx.inp
- functionals/05-ks_inversion.01-target_density.inp
- functionals/05-ks_inversion.02-two_particle.inp
- functionals/05-ks_inversion.03-inversion.inp
- functionals/05-ks_inversion.04-inv_godby.inp
- functionals/06-rdmft.01-ip.inp
- functionals/06-rdmft.02-gs_basis.inp
- functionals/06-rdmft.03-gs_grid.inp
- functionals/07-sic.01-gs.inp
- functionals/07-sic.02-scdm.inp
- functionals/08-vdw_ts.01-gs.inp
- functionals/09-vdw_ts_sc.01-gs.inp
- functionals/11-vdw_d3.01-gs.inp
- functionals/13-libvdwxc_h2o.01-vdwdfcx.inp
- functionals/14-libvdwxc_Be_hcp.01-vdwdfcx.inp
- functionals/15-oep-CG.01-kli.inp
- functionals/15-oep-CG.02-oep-dens.inp
- functionals/16-dressed-rdmft.01-ip.inp
- functionals/16-dressed-rdmft.02-hf.inp
- functionals/16-dressed-rdmft.03-rdmft.inp
- functionals/17-oep-photons.01-kli-spinpolarized.inp
- functionals/17-oep-photons.02-kli.inp
- functionals/17-oep-photons.03-oep.inp
- functionals/18-mgga.01-br89.inp
- functionals/18-mgga.02-br89_oep.inp
- functionals/18-mgga.03-lda.inp
- functionals/18-mgga.04-ncbr.inp
- functionals/18-mgga.05-ncbr_oep.inp
- functionals/18-mgga.06_nccs.inp
- functionals/19-qedft-breit-1d.01-etac-px.inp
- functionals/19-qedft-breit-1d.02-pxlda.inp
- functionals/20-qedft-breit-2d.01-etac-px.inp
- functionals/20-qedft-breit-2d.02-pxlda-weak.inp
- functionals/20-qedft-breit-2d.03-pxlda-strong.inp
- functionals/21-qedft-breit-3d.01-pxlda-hydrogen.inp
- functionals/21-qedft-breit-3d.02-pxlda-helium.inp
- functionals/22-vdw_d3_stress.01-Be_hpc.inp
- functionals/23-xc_lrx.inp
- lda_u/04-ACBN0_isolated.01-H_unpacked.inp
- lda_u/04-ACBN0_isolated.02-H_packed.inp
- lda_u/05-forces.01-Na2.inp
- lda_u/05-forces.02-Na2_go.inp
- lda_u/05-forces.03-Na2_go_ACBN0.inp
- lda_u/06-laser.01-gs.inp
- lda_u/06-laser.02-length_gauge.inp
- lda_u/06-laser.03-velocity_gauge.inp
- lda_u/10-intersite.01-Na2.inp
- lda_u/11-full_delta.01-gs.inp
- lda_u/12-intersite_spinors.01-Na2_gs.inp
- lda_u/12-intersite_spinors.02-Na2_td.inp
- linear_response/01-casida.01-gs.inp
- linear_response/01-casida.02-vib_modes.inp
- linear_response/01-casida.03-unocc.inp
- linear_response/01-casida.04-unocc_restart.inp
- linear_response/01-casida.05-casida.inp
- linear_response/01-casida.06-casida_scalapack.inp
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