[CP2K-user] [CP2K:14439] GEOMETRY wrong or EMAX_SPLINE too small!
Travis
polla... at gmail.com
Fri Jan 1 18:51:22 UTC 2021
Hi,
The CIF file is converting to a structure with extra atoms that overlap
(red below) causing the error you see in both graphite and gold cases. CP2K
shifts the structure to a different origin internally, it doesn't matter
that some of the coordinates are negative.
WARNING| Particles: 114 10 at distance [au]: 0.00000000 less
than: 0.01889726; increase EMAX_SPLINE.
You should be able to fix the graphite one by loading the CIF file in
Avogadro and saving as XYZ to remove equivalent atoms.
-T
On Friday, January 1, 2021 at 5:23:56 AM UTC-5 dre... at gmail.com wrote:
> Thank you for reply. I need to optimize 4 layers graphite. I got cif file
> below which I convert to xyz file and then I use it for cp2k.in. However,
> I can not find out right abc for the optimisation, for example, if I use
> abc from cif (14.80620; 17.09680; 17.37000) I get same "GEOMETRY wrong or
> EMAX_SPLINE too small!" error. If I use those one from xyz, for example, I
> have edged coordinates in x as 16.040001 and -1.233800, so, I decide that x
> should be their absolute sum 17.273801. I do same job for both xy
> dimensions. Could you please guide me how to chose right abc for
> optimisation from this cif example.
>
> Regards,
> Dmitrii
>
> #CIF file:
>
> data_C_mp-48_conventional_standard.cif_6x4x2_1
>
> _audit_creation_date 2020-12-05
> _audit_creation_method 'generated by MedeA 3.0.3'
>
> _chemical_formula_sum 'C'
>
> _symmetry_space_group_name_H-M 'P1'
> _symmetry_Int_Tables_number 1
>
> _cell_length_a 14.80620
> _cell_length_b 17.09680
> _cell_length_c 17.37000
> _cell_angle_alpha 90.00
> _cell_angle_beta 90.00
> _cell_angle_gamma 90.00
> _cell_volume 4397.02
> _cell_formula_units_Z 384
>
> loop_
> _atom_site_label
> _atom_site_symmetry_multiplicity
> _atom_site_Wyckoff_symbol
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> _atom_site_occupancy
> C1 1 a 0.00000 0.00000 0.12500 1.0
> C2 1 a 0.08333 0.12500 0.12500 1.0
> C3 1 a 0.00000 0.00000 0.37500 1.0
> C4 1 a 0.08333 0.12500 0.37500 1.0
> C5 1 a 0.08333 0.04167 0.12500 1.0
> C6 1 a 0.00000 0.16667 0.12500 1.0
> C7 1 a 0.00000 0.08333 0.37500 1.0
> C8 1 a 0.08333 0.20833 0.37500 1.0
> C9 1 a 0.00000 0.00000 0.62500 1.0
> C10 1 a 0.08333 0.12500 0.62500 1.0
> C11 1 a 0.00000 0.00000 0.87500 1.0
> C12 1 a 0.08333 0.12500 0.87500 1.0
> C13 1 a 0.08333 0.04167 0.62500 1.0
> C14 1 a 0.00000 0.16667 0.62500 1.0
> C15 1 a 0.00000 0.08333 0.87500 1.0
> C16 1 a 0.08333 0.20833 0.87500 1.0
> C17 1 a 0.00000 0.25000 0.12500 1.0
> C18 1 a 0.08333 0.37500 0.12500 1.0
> C19 1 a 0.00000 0.25000 0.37500 1.0
> C20 1 a 0.08333 0.37500 0.37500 1.0
> C21 1 a 0.08333 0.29167 0.12500 1.0
> C22 1 a 0.00000 0.41667 0.12500 1.0
> C23 1 a 0.00000 0.33333 0.37500 1.0
> C24 1 a 0.08333 0.45833 0.37500 1.0
> C25 1 a 0.00000 0.25000 0.62500 1.0
> C26 1 a 0.08333 0.37500 0.62500 1.0
> C27 1 a 0.00000 0.25000 0.87500 1.0
> C28 1 a 0.08333 0.37500 0.87500 1.0
> C29 1 a 0.08333 0.29167 0.62500 1.0
> C30 1 a 0.00000 0.41667 0.62500 1.0
> C31 1 a 0.00000 0.33333 0.87500 1.0
> C32 1 a 0.08333 0.45833 0.87500 1.0
> C33 1 a 0.00000 0.50000 0.12500 1.0
> C34 1 a 0.08333 0.62500 0.12500 1.0
> C35 1 a 0.00000 0.50000 0.37500 1.0
> C36 1 a 0.08333 0.62500 0.37500 1.0
> C37 1 a 0.08333 0.54167 0.12500 1.0
> C38 1 a 0.00000 0.66667 0.12500 1.0
> C39 1 a 0.00000 0.58333 0.37500 1.0
> C40 1 a 0.08333 0.70833 0.37500 1.0
> C41 1 a 0.00000 0.50000 0.62500 1.0
> C42 1 a 0.08333 0.62500 0.62500 1.0
> C43 1 a 0.00000 0.50000 0.87500 1.0
> C44 1 a 0.08333 0.62500 0.87500 1.0
> C45 1 a 0.08333 0.54167 0.62500 1.0
> C46 1 a 0.00000 0.66667 0.62500 1.0
> C47 1 a 0.00000 0.58333 0.87500 1.0
> C48 1 a 0.08333 0.70833 0.87500 1.0
> C49 1 a 0.00000 0.75000 0.12500 1.0
> C50 1 a 0.08333 0.87500 0.12500 1.0
> C51 1 a 0.00000 0.75000 0.37500 1.0
> C52 1 a 0.08333 0.87500 0.37500 1.0
> C53 1 a 0.08333 0.79167 0.12500 1.0
> C54 1 a 0.00000 0.91667 0.12500 1.0
> C55 1 a 0.00000 0.83333 0.37500 1.0
> C56 1 a 0.08333 0.95833 0.37500 1.0
> C57 1 a 0.00000 0.75000 0.62500 1.0
> C58 1 a 0.08333 0.87500 0.62500 1.0
> C59 1 a 0.00000 0.75000 0.87500 1.0
> C60 1 a 0.08333 0.87500 0.87500 1.0
> C61 1 a 0.08333 0.79167 0.62500 1.0
> C62 1 a 0.00000 0.91667 0.62500 1.0
> C63 1 a 0.00000 0.83333 0.87500 1.0
> C64 1 a 0.08333 0.95833 0.87500 1.0
> C65 1 a 0.16667 0.00000 0.12500 1.0
> C66 1 a 0.25000 0.12500 0.12500 1.0
> C67 1 a 0.16667 0.00000 0.37500 1.0
> C68 1 a 0.25000 0.12500 0.37500 1.0
> C69 1 a 0.25000 0.04167 0.12500 1.0
> C70 1 a 0.16667 0.16667 0.12500 1.0
> C71 1 a 0.16667 0.08333 0.37500 1.0
> C72 1 a 0.25000 0.20833 0.37500 1.0
> C73 1 a 0.16667 0.00000 0.62500 1.0
> C74 1 a 0.25000 0.12500 0.62500 1.0
> C75 1 a 0.16667 0.00000 0.87500 1.0
> C76 1 a 0.25000 0.12500 0.87500 1.0
> C77 1 a 0.25000 0.04167 0.62500 1.0
> C78 1 a 0.16667 0.16667 0.62500 1.0
> C79 1 a 0.16667 0.08333 0.87500 1.0
> C80 1 a 0.25000 0.20833 0.87500 1.0
> C81 1 a 0.16667 0.25000 0.12500 1.0
> C82 1 a 0.25000 0.37500 0.12500 1.0
> C83 1 a 0.16667 0.25000 0.37500 1.0
> C84 1 a 0.25000 0.37500 0.37500 1.0
> C85 1 a 0.25000 0.29167 0.12500 1.0
> C86 1 a 0.16667 0.41667 0.12500 1.0
> C87 1 a 0.16667 0.33333 0.37500 1.0
> C88 1 a 0.25000 0.45833 0.37500 1.0
> C89 1 a 0.16667 0.25000 0.62500 1.0
> C90 1 a 0.25000 0.37500 0.62500 1.0
> C91 1 a 0.16667 0.25000 0.87500 1.0
> C92 1 a 0.25000 0.37500 0.87500 1.0
> C93 1 a 0.25000 0.29167 0.62500 1.0
> C94 1 a 0.16667 0.41667 0.62500 1.0
> C95 1 a 0.16667 0.33333 0.87500 1.0
> C96 1 a 0.25000 0.45833 0.87500 1.0
> C97 1 a 0.16667 0.50000 0.12500 1.0
> C98 1 a 0.25000 0.62500 0.12500 1.0
> C99 1 a 0.16667 0.50000 0.37500 1.0
> C100 1 a 0.25000 0.62500 0.37500 1.0
> C101 1 a 0.25000 0.54167 0.12500 1.0
> C102 1 a 0.16667 0.66667 0.12500 1.0
> C103 1 a 0.16667 0.58333 0.37500 1.0
> C104 1 a 0.25000 0.70833 0.37500 1.0
> C105 1 a 0.16667 0.50000 0.62500 1.0
> C106 1 a 0.25000 0.62500 0.62500 1.0
> C107 1 a 0.16667 0.50000 0.87500 1.0
> C108 1 a 0.25000 0.62500 0.87500 1.0
> C109 1 a 0.25000 0.54167 0.62500 1.0
> C110 1 a 0.16667 0.66667 0.62500 1.0
> C111 1 a 0.16667 0.58333 0.87500 1.0
> C112 1 a 0.25000 0.70833 0.87500 1.0
> C113 1 a 0.16667 0.75000 0.12500 1.0
> C114 1 a 0.25000 0.87500 0.12500 1.0
> C115 1 a 0.16667 0.75000 0.37500 1.0
> C116 1 a 0.25000 0.87500 0.37500 1.0
> C117 1 a 0.25000 0.79167 0.12500 1.0
> C118 1 a 0.16667 0.91667 0.12500 1.0
> C119 1 a 0.16667 0.83333 0.37500 1.0
> C120 1 a 0.25000 0.95833 0.37500 1.0
> C121 1 a 0.16667 0.75000 0.62500 1.0
> C122 1 a 0.25000 0.87500 0.62500 1.0
> C123 1 a 0.16667 0.75000 0.87500 1.0
> C124 1 a 0.25000 0.87500 0.87500 1.0
> C125 1 a 0.25000 0.79167 0.62500 1.0
> C126 1 a 0.16667 0.91667 0.62500 1.0
> C127 1 a 0.16667 0.83333 0.87500 1.0
> C128 1 a 0.25000 0.95833 0.87500 1.0
> C129 1 a 0.33333 0.00000 0.12500 1.0
> C130 1 a 0.41667 0.12500 0.12500 1.0
> C131 1 a 0.33333 0.00000 0.37500 1.0
> C132 1 a 0.41667 0.12500 0.37500 1.0
> C133 1 a 0.41667 0.04167 0.12500 1.0
> C134 1 a 0.33333 0.16667 0.12500 1.0
> C135 1 a 0.33333 0.08333 0.37500 1.0
> C136 1 a 0.41667 0.20833 0.37500 1.0
> C137 1 a 0.33333 0.00000 0.62500 1.0
> C138 1 a 0.41667 0.12500 0.62500 1.0
> C139 1 a 0.33333 0.00000 0.87500 1.0
> C140 1 a 0.41667 0.12500 0.87500 1.0
> C141 1 a 0.41667 0.04167 0.62500 1.0
> C142 1 a 0.33333 0.16667 0.62500 1.0
> C143 1 a 0.33333 0.08333 0.87500 1.0
> C144 1 a 0.41667 0.20833 0.87500 1.0
> C145 1 a 0.33333 0.25000 0.12500 1.0
> C146 1 a 0.41667 0.37500 0.12500 1.0
> C147 1 a 0.33333 0.25000 0.37500 1.0
> C148 1 a 0.41667 0.37500 0.37500 1.0
> C149 1 a 0.41667 0.29167 0.12500 1.0
> C150 1 a 0.33333 0.41667 0.12500 1.0
> C151 1 a 0.33333 0.33333 0.37500 1.0
> C152 1 a 0.41667 0.45833 0.37500 1.0
> C153 1 a 0.33333 0.25000 0.62500 1.0
> C154 1 a 0.41667 0.37500 0.62500 1.0
> C155 1 a 0.33333 0.25000 0.87500 1.0
> C156 1 a 0.41667 0.37500 0.87500 1.0
> C157 1 a 0.41667 0.29167 0.62500 1.0
> C158 1 a 0.33333 0.41667 0.62500 1.0
> C159 1 a 0.33333 0.33333 0.87500 1.0
> C160 1 a 0.41667 0.45833 0.87500 1.0
> C161 1 a 0.33333 0.50000 0.12500 1.0
> C162 1 a 0.41667 0.62500 0.12500 1.0
> C163 1 a 0.33333 0.50000 0.37500 1.0
> C164 1 a 0.41667 0.62500 0.37500 1.0
> C165 1 a 0.41667 0.54167 0.12500 1.0
> C166 1 a 0.33333 0.66667 0.12500 1.0
> C167 1 a 0.33333 0.58333 0.37500 1.0
> C168 1 a 0.41667 0.70833 0.37500 1.0
> C169 1 a 0.33333 0.50000 0.62500 1.0
> C170 1 a 0.41667 0.62500 0.62500 1.0
> C171 1 a 0.33333 0.50000 0.87500 1.0
> C172 1 a 0.41667 0.62500 0.87500 1.0
> C173 1 a 0.41667 0.54167 0.62500 1.0
> C174 1 a 0.33333 0.66667 0.62500 1.0
> C175 1 a 0.33333 0.58333 0.87500 1.0
> C176 1 a 0.41667 0.70833 0.87500 1.0
> C177 1 a 0.33333 0.75000 0.12500 1.0
> C178 1 a 0.41667 0.87500 0.12500 1.0
> C179 1 a 0.33333 0.75000 0.37500 1.0
> C180 1 a 0.41667 0.87500 0.37500 1.0
> C181 1 a 0.41667 0.79167 0.12500 1.0
> C182 1 a 0.33333 0.91667 0.12500 1.0
> C183 1 a 0.33333 0.83333 0.37500 1.0
> C184 1 a 0.41667 0.95833 0.37500 1.0
> C185 1 a 0.33333 0.75000 0.62500 1.0
> C186 1 a 0.41667 0.87500 0.62500 1.0
> C187 1 a 0.33333 0.75000 0.87500 1.0
> C188 1 a 0.41667 0.87500 0.87500 1.0
> C189 1 a 0.41667 0.79167 0.62500 1.0
> C190 1 a 0.33333 0.91667 0.62500 1.0
> C191 1 a 0.33333 0.83333 0.87500 1.0
> C192 1 a 0.41667 0.95833 0.87500 1.0
> C193 1 a 0.50000 0.00000 0.12500 1.0
> C194 1 a 0.58333 0.12500 0.12500 1.0
> C195 1 a 0.50000 0.00000 0.37500 1.0
> C196 1 a 0.58333 0.12500 0.37500 1.0
> C197 1 a 0.58333 0.04167 0.12500 1.0
> C198 1 a 0.50000 0.16667 0.12500 1.0
> C199 1 a 0.50000 0.08333 0.37500 1.0
> C200 1 a 0.58333 0.20833 0.37500 1.0
> C201 1 a 0.50000 0.00000 0.62500 1.0
> C202 1 a 0.58333 0.12500 0.62500 1.0
> C203 1 a 0.50000 0.00000 0.87500 1.0
> C204 1 a 0.58333 0.12500 0.87500 1.0
> C205 1 a 0.58333 0.04167 0.62500 1.0
> C206 1 a 0.50000 0.16667 0.62500 1.0
> C207 1 a 0.50000 0.08333 0.87500 1.0
> C208 1 a 0.58333 0.20833 0.87500 1.0
> C209 1 a 0.50000 0.25000 0.12500 1.0
> C210 1 a 0.58333 0.37500 0.12500 1.0
> C211 1 a 0.50000 0.25000 0.37500 1.0
> C212 1 a 0.58333 0.37500 0.37500 1.0
> C213 1 a 0.58333 0.29167 0.12500 1.0
> C214 1 a 0.50000 0.41667 0.12500 1.0
> C215 1 a 0.50000 0.33333 0.37500 1.0
> C216 1 a 0.58333 0.45833 0.37500 1.0
> C217 1 a 0.50000 0.25000 0.62500 1.0
> C218 1 a 0.58333 0.37500 0.62500 1.0
> C219 1 a 0.50000 0.25000 0.87500 1.0
> C220 1 a 0.58333 0.37500 0.87500 1.0
> C221 1 a 0.58333 0.29167 0.62500 1.0
> C222 1 a 0.50000 0.41667 0.62500 1.0
> C223 1 a 0.50000 0.33333 0.87500 1.0
> C224 1 a 0.58333 0.45833 0.87500 1.0
> C225 1 a 0.50000 0.50000 0.12500 1.0
> C226 1 a 0.58333 0.62500 0.12500 1.0
> C227 1 a 0.50000 0.50000 0.37500 1.0
> C228 1 a 0.58333 0.62500 0.37500 1.0
> C229 1 a 0.58333 0.54167 0.12500 1.0
> C230 1 a 0.50000 0.66667 0.12500 1.0
> C231 1 a 0.50000 0.58333 0.37500 1.0
> C232 1 a 0.58333 0.70833 0.37500 1.0
> C233 1 a 0.50000 0.50000 0.62500 1.0
> C234 1 a 0.58333 0.62500 0.62500 1.0
> C235 1 a 0.50000 0.50000 0.87500 1.0
> C236 1 a 0.58333 0.62500 0.87500 1.0
> C237 1 a 0.58333 0.54167 0.62500 1.0
> C238 1 a 0.50000 0.66667 0.62500 1.0
> C239 1 a 0.50000 0.58333 0.87500 1.0
> C240 1 a 0.58333 0.70833 0.87500 1.0
> C241 1 a 0.50000 0.75000 0.12500 1.0
> C242 1 a 0.58333 0.87500 0.12500 1.0
> C243 1 a 0.50000 0.75000 0.37500 1.0
> C244 1 a 0.58333 0.87500 0.37500 1.0
> C245 1 a 0.58333 0.79167 0.12500 1.0
> C246 1 a 0.50000 0.91667 0.12500 1.0
> C247 1 a 0.50000 0.83333 0.37500 1.0
> C248 1 a 0.58333 0.95833 0.37500 1.0
> C249 1 a 0.50000 0.75000 0.62500 1.0
> C250 1 a 0.58333 0.87500 0.62500 1.0
> C251 1 a 0.50000 0.75000 0.87500 1.0
> C252 1 a 0.58333 0.87500 0.87500 1.0
> C253 1 a 0.58333 0.79167 0.62500 1.0
> C254 1 a 0.50000 0.91667 0.62500 1.0
> C255 1 a 0.50000 0.83333 0.87500 1.0
> C256 1 a 0.58333 0.95833 0.87500 1.0
> C257 1 a 0.66667 0.00000 0.12500 1.0
> C258 1 a 0.75000 0.12500 0.12500 1.0
> C259 1 a 0.66667 0.00000 0.37500 1.0
> C260 1 a 0.75000 0.12500 0.37500 1.0
> C261 1 a 0.75000 0.04167 0.12500 1.0
> C262 1 a 0.66667 0.16667 0.12500 1.0
> C263 1 a 0.66667 0.08333 0.37500 1.0
> C264 1 a 0.75000 0.20833 0.37500 1.0
> C265 1 a 0.66667 0.00000 0.62500 1.0
> C266 1 a 0.75000 0.12500 0.62500 1.0
> C267 1 a 0.66667 0.00000 0.87500 1.0
> C268 1 a 0.75000 0.12500 0.87500 1.0
> C269 1 a 0.75000 0.04167 0.62500 1.0
> C270 1 a 0.66667 0.16667 0.62500 1.0
> C271 1 a 0.66667 0.08333 0.87500 1.0
> C272 1 a 0.75000 0.20833 0.87500 1.0
> C273 1 a 0.66667 0.25000 0.12500 1.0
> C274 1 a 0.75000 0.37500 0.12500 1.0
> C275 1 a 0.66667 0.25000 0.37500 1.0
> C276 1 a 0.75000 0.37500 0.37500 1.0
> C277 1 a 0.75000 0.29167 0.12500 1.0
> C278 1 a 0.66667 0.41667 0.12500 1.0
> C279 1 a 0.66667 0.33333 0.37500 1.0
> C280 1 a 0.75000 0.45833 0.37500 1.0
> C281 1 a 0.66667 0.25000 0.62500 1.0
> C282 1 a 0.75000 0.37500 0.62500 1.0
> C283 1 a 0.66667 0.25000 0.87500 1.0
> C284 1 a 0.75000 0.37500 0.87500 1.0
> C285 1 a 0.75000 0.29167 0.62500 1.0
> C286 1 a 0.66667 0.41667 0.62500 1.0
> C287 1 a 0.66667 0.33333 0.87500 1.0
> C288 1 a 0.75000 0.45833 0.87500 1.0
> C289 1 a 0.66667 0.50000 0.12500 1.0
> C290 1 a 0.75000 0.62500 0.12500 1.0
> C291 1 a 0.66667 0.50000 0.37500 1.0
> C292 1 a 0.75000 0.62500 0.37500 1.0
> C293 1 a 0.75000 0.54167 0.12500 1.0
> C294 1 a 0.66667 0.66667 0.12500 1.0
> C295 1 a 0.66667 0.58333 0.37500 1.0
> C296 1 a 0.75000 0.70833 0.37500 1.0
> C297 1 a 0.66667 0.50000 0.62500 1.0
> C298 1 a 0.75000 0.62500 0.62500 1.0
> C299 1 a 0.66667 0.50000 0.87500 1.0
> C300 1 a 0.75000 0.62500 0.87500 1.0
> C301 1 a 0.75000 0.54167 0.62500 1.0
> C302 1 a 0.66667 0.66667 0.62500 1.0
> C303 1 a 0.66667 0.58333 0.87500 1.0
> C304 1 a 0.75000 0.70833 0.87500 1.0
> C305 1 a 0.66667 0.75000 0.12500 1.0
> C306 1 a 0.75000 0.87500 0.12500 1.0
> C307 1 a 0.66667 0.75000 0.37500 1.0
> C308 1 a 0.75000 0.87500 0.37500 1.0
> C309 1 a 0.75000 0.79167 0.12500 1.0
> C310 1 a 0.66667 0.91667 0.12500 1.0
> C311 1 a 0.66667 0.83333 0.37500 1.0
> C312 1 a 0.75000 0.95833 0.37500 1.0
> C313 1 a 0.66667 0.75000 0.62500 1.0
> C314 1 a 0.75000 0.87500 0.62500 1.0
> C315 1 a 0.66667 0.75000 0.87500 1.0
> C316 1 a 0.75000 0.87500 0.87500 1.0
> C317 1 a 0.75000 0.79167 0.62500 1.0
> C318 1 a 0.66667 0.91667 0.62500 1.0
> C319 1 a 0.66667 0.83333 0.87500 1.0
> C320 1 a 0.75000 0.95833 0.87500 1.0
> C321 1 a 0.83333 0.00000 0.12500 1.0
> C322 1 a 0.91667 0.12500 0.12500 1.0
> C323 1 a 0.83333 0.00000 0.37500 1.0
> C324 1 a 0.91667 0.12500 0.37500 1.0
> C325 1 a 0.91667 0.04167 0.12500 1.0
> C326 1 a 0.83333 0.16667 0.12500 1.0
> C327 1 a 0.83333 0.08333 0.37500 1.0
> C328 1 a 0.91667 0.20833 0.37500 1.0
> C329 1 a 0.83333 0.00000 0.62500 1.0
> C330 1 a 0.91667 0.12500 0.62500 1.0
> C331 1 a 0.83333 0.00000 0.87500 1.0
> C332 1 a 0.91667 0.12500 0.87500 1.0
> C333 1 a 0.91667 0.04167 0.62500 1.0
> C334 1 a 0.83333 0.16667 0.62500 1.0
> C335 1 a 0.83333 0.08333 0.87500 1.0
> C336 1 a 0.91667 0.20833 0.87500 1.0
> C337 1 a 0.83333 0.25000 0.12500 1.0
> C338 1 a 0.91667 0.37500 0.12500 1.0
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>
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> C 13.572400 7.835977 6.513750
> C 12.338450 4.274200 10.856251
> C 13.572400 6.411300 10.856251
> C 12.338450 4.274200 15.198750
> C 13.572400 6.411300 15.198750
> C 13.572400 4.986623 10.856251
> C 12.338450 7.123724 10.856251
> C 12.338450 5.698876 15.198750
> C 13.572400 7.835977 15.198750
> C 12.338450 8.548400 2.171250
> C 13.572400 10.685500 2.171250
> C 12.338450 8.548400 6.513750
> C 13.572400 10.685500 6.513750
> C 13.572400 9.260824 2.171250
> C 12.338450 11.397924 2.171250
> C 12.338450 9.973076 6.513750
> C 13.572400 12.110176 6.513750
> C 12.338450 8.548400 10.856251
> C 13.572400 10.685500 10.856251
> C 12.338450 8.548400 15.198750
> C 13.572400 10.685500 15.198750
> C 13.572400 9.260824 10.856251
> C 12.338450 11.397924 10.856251
> C 12.338450 9.973076 15.198750
> C 13.572400 12.110176 15.198750
> C 12.338450 12.822599 2.171250
> C 13.572400 14.959700 2.171250
> C 12.338450 12.822599 6.513750
> C 13.572400 14.959700 6.513750
> C 13.572400 13.535024 2.171250
> C 12.338450 15.672124 2.171250
> C 12.338450 14.247275 6.513750
> C 13.572400 16.384377 6.513750
> C 12.338450 12.822599 10.856251
> C 13.572400 14.959700 10.856251
> C 12.338450 12.822599 15.198750
> C 13.572400 14.959700 15.198750
> C 13.572400 13.535024 10.856251
> C 12.338450 15.672124 10.856251
> C 12.338450 14.247275 15.198750
> C 13.572400 16.384377 15.198750
> C -1.233800 0.712424 2.171250
> C 0.000000 -1.424676 2.171250
> C -1.233800 17.809223 2.171250
> C 1.233801 17.809223 2.171250
> C 14.806200 -1.424676 2.171250
> C 16.040001 0.712424 2.171250
> C 13.572400 17.809223 2.171250
> C 16.040001 17.809223 2.171250
> C -1.233800 -0.712423 6.513750
> C 1.233801 -0.712423 6.513750
> C -1.233800 16.384377 6.513750
> C 0.000000 18.521477 6.513750
> C 13.572400 -0.712423 6.513750
> C 16.040001 -0.712423 6.513750
> C 16.040001 16.384377 6.513750
> C 14.806200 18.521477 6.513750
> C 16.040001 2.137100 2.171250
> C -1.233800 0.712424 10.856251
> C 0.000000 -1.424676 10.856251
> C -1.233800 17.809223 10.856251
> C 1.233801 17.809223 10.856251
> C 14.806200 -1.424676 10.856251
> C 16.040001 0.712424 10.856251
> C 13.572400 17.809223 10.856251
> C 16.040001 17.809223 10.856251
> C -1.233800 -0.712423 15.198750
> C 1.233801 -0.712423 15.198750
> C -1.233800 16.384377 15.198750
> C 0.000000 18.521477 15.198750
> C 13.572400 -0.712423 15.198750
> C 16.040001 -0.712423 15.198750
> C 16.040001 16.384377 15.198750
> C 14.806200 18.521477 15.198750
> C 16.040001 2.137100 10.856251
> C -1.233800 4.986623 2.171250
> C -1.233800 3.561776 6.513750
> C 16.040001 3.561776 6.513750
> C 16.040001 6.411300 2.171250
> C -1.233800 4.986623 10.856251
> C -1.233800 3.561776 15.198750
> C 16.040001 3.561776 15.198750
> C 16.040001 6.411300 10.856251
> C -1.233800 9.260824 2.171250
> C -1.233800 7.835977 6.513750
> C 16.040001 7.835977 6.513750
> C 16.040001 10.685500 2.171250
> C -1.233800 9.260824 10.856251
> C -1.233800 7.835977 15.198750
> C 16.040001 7.835977 15.198750
> C 16.040001 10.685500 10.856251
> C -1.233800 13.535024 2.171250
> C -1.233800 12.110176 6.513750
> C 16.040001 12.110176 6.513750
> C -1.233800 13.535024 10.856251
> C -1.233800 12.110176 15.198750
> C 16.040001 12.110176 15.198750
> C 2.467749 -1.424676 2.171250
> C 3.701550 17.809223 2.171250
> C 3.701550 -0.712423 6.513750
> C 2.467749 18.521477 6.513750
> C 2.467749 -1.424676 10.856251
> C 3.701550 17.809223 10.856251
> C 3.701550 -0.712423 15.198750
> C 2.467749 18.521477 15.198750
> C 4.935351 -1.424676 2.171250
> C 6.169299 17.809223 2.171250
> C 6.169299 -0.712423 6.513750
> C 4.935351 18.521477 6.513750
> C 4.935351 -1.424676 10.856251
> C 6.169299 17.809223 10.856251
> C 6.169299 -0.712423 15.198750
> C 4.935351 18.521477 15.198750
> C 7.403100 -1.424676 2.171250
> C 8.636900 17.809223 2.171250
> C 8.636900 -0.712423 6.513750
> C 7.403100 18.521477 6.513750
> C 7.403100 -1.424676 10.856251
> C 8.636900 17.809223 10.856251
> C 8.636900 -0.712423 15.198750
> C 7.403100 18.521477 15.198750
> C 9.870850 -1.424676 2.171250
> C 11.104650 17.809223 2.171250
> C 11.104650 -0.712423 6.513750
> C 9.870850 18.521477 6.513750
> C 9.870850 -1.424676 10.856251
> C 11.104650 17.809223 10.856251
> C 11.104650 -0.712423 15.198750
> C 9.870850 18.521477 15.198750
> C 12.338450 -1.424676 2.171250
> C 12.338450 18.521477 6.513750
> C 12.338450 -1.424676 10.856251
> C 12.338450 18.521477 15.198750
>
> On Monday, December 28, 2020 at 9:48:12 PM UTC+11 tkuehne wrote:
>
>> Dear Dmitrii,
>>
>> Should I just take absolute sum of CELL_TOP| by Vector a, b, and c for
>> correct abc cell parameters (see output with error and cell_top section
>> below)?
>>
>>
>> no this is definitely not the way to go. How did you obtain the given
>> lattice vectors in the first place?
>> Since the cell has to be commensurate wrt to your periodic boundary
>> conditions, they can not be
>> simply obtained by "visual inspection“.
>>
>> Greetings,
>> Thomas
>>
>>
>> Thank you,
>> Dmitrii
>>
>> ...
>> [a.u./Bohr**2] -> [1/cm]
>> 5.14048714338585E+03
>>
>>
>> CELL_TOP| Volume [angstrom^3]:
>> 21621.753
>> CELL_TOP| Vector a [angstrom 23.070 0.000 0.000 |a| =
>> 23.070
>> CELL_TOP| Vector b [angstrom -10.822 18.744 0.000 |b| =
>> 21.644
>> CELL_TOP| Vector c [angstrom 0.000 0.000 50.000 |c| =
>> 50.000
>> CELL_TOP| Angle (b,c), alpha [degree]:
>> 90.000
>> CELL_TOP| Angle (a,c), beta [degree]:
>> 90.000
>> CELL_TOP| Angle (a,b), gamma [degree]:
>> 120.000
>> CELL_TOP| Numerically orthorhombic:
>> NO
>> WARNING| Particles: 114 10 at distance [au]: 0.00000000 less
>> than: 0.01889726; increase EMAX_SPLINE.
>>
>>
>> *******************************************************************************
>> * ___
>> *
>> * / \
>> *
>> * [ABORT]
>> *
>> * \___/ GEOMETRY wrong or EMAX_SPLINE too small!
>> *
>> * |
>> *
>> * O/|
>> *
>> * /| |
>> *
>> * / \
>> fist_neighbor_lists.F:607 *
>>
>> *******************************************************************************
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "cp2k" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to cp... at googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/219773d5-1896-4798-9aaa-c6bd8fbce1acn%40googlegroups.com
>> <https://groups.google.com/d/msgid/cp2k/219773d5-1896-4798-9aaa-c6bd8fbce1acn%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>> <Au111_geometry.inp>
>>
>>
>>
>>
>> ==============================
>> Thomas D. Kühne
>> Dynamics of Condensed Matter
>> Chair of Theoretical Chemistry
>> University of Paderborn
>> Warburger Str. 100
>> D-33098 Paderborn
>> Germany
>> td... at mail.upb.de
>> +49/(0)5251/60-5726 <+49%205251%20605726>
>>
>>
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