214 lines
8.5 KiB
ReStructuredText
214 lines
8.5 KiB
ReStructuredText
.. index:: compute orientorder/atom
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.. index:: compute orientorder/atom/kk
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compute orientorder/atom command
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================================
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Accelerator Variants: *orientorder/atom/kk*
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Syntax
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""""""
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.. parsed-literal::
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compute ID group-ID orientorder/atom keyword values ...
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* ID, group-ID are documented in :doc:`compute <compute>` command
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* orientorder/atom = style name of this compute command
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* one or more keyword/value pairs may be appended
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.. parsed-literal::
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keyword = *cutoff* or *nnn* or *degrees* or *components* or *chunksize*
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*cutoff* value = distance cutoff
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*nnn* value = number of nearest neighbors
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*degrees* values = nlvalues, l1, l2,...
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*wl* value = yes or no
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*wl/hat* value = yes or no
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*components* value = ldegree
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*chunksize* value = number of atoms in each pass
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Examples
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""""""""
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.. code-block:: LAMMPS
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compute 1 all orientorder/atom
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compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
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compute 1 all orientorder/atom wl/hat yes
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compute 1 all orientorder/atom components 6
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Description
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"""""""""""
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Define a computation that calculates a set of bond-orientational
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order parameters :math:`Q_l` for each atom in a group. These order parameters
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were introduced by :ref:`Steinhardt et al. <Steinhardt>` as a way to
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characterize the local orientational order in atomic structures.
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For each atom, :math:`Q_l` is a real number defined as follows:
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.. math::
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\bar{Y}_{lm} = & \frac{1}{nnn}\sum_{j = 1}^{nnn} Y_{lm}( \theta( {\bf r}_{ij} ), \phi( {\bf r}_{ij} ) ) \\
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Q_l = & \sqrt{\frac{4 \pi}{2 l + 1} \sum_{m = -l}^{m = l} \bar{Y}_{lm} \bar{Y}^*_{lm}}
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The first equation defines the local order parameters as averages
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of the spherical harmonics :math:`Y_{lm}` for each neighbor.
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These are complex number components of the 3D analog of the 2D order
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parameter :math:`q_n`, which is implemented as LAMMPS compute
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:doc:`hexorder/atom <compute_hexorder_atom>`.
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The summation is over the *nnn* nearest
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neighbors of the central atom.
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The angles :math:`theta` and :math:`phi` are the standard spherical polar angles
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defining the direction of the bond vector :math:`r_{ij}`.
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The phase and sign of :math:`Y_{lm}` follow the standard conventions,
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so that :math:`{\rm sign}(Y_{ll}(0,0)) = (-1)^l`.
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The second equation defines :math:`Q_l`, which is a
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rotationally invariant non-negative amplitude obtained by summing
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over all the components of degree *l*\ .
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The optional keyword *cutoff* defines the distance cutoff
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used when searching for neighbors. The default value, also
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the maximum allowable value, is the cutoff specified
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by the pair style.
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The optional keyword *nnn* defines the number of nearest
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neighbors used to calculate :math:`Q_l`. The default value is 12.
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If the value is NULL, then all neighbors up to the
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specified distance cutoff are used.
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The optional keyword *degrees* defines the list of order parameters to
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be computed. The first argument *nlvalues* is the number of order
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parameters. This is followed by that number of non-negative integers giving the
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degree of each order parameter. Because :math:`Q_2` and all odd-degree order
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parameters are zero for atoms in cubic crystals (see
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:ref:`Steinhardt <Steinhardt>`), the default order parameters are :math:`Q_4`,
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:math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`. For the FCC
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crystal with *nnn* =12, :math:`Q_4 = \sqrt{\frac{7}{192}} = 0.19094...`.
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The numerical values of all order
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parameters up to :math:`Q_12` for a range of commonly encountered
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high-symmetry structures are given in Table I of :ref:`Mickel et al. <Mickel>`,
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and these can be reproduced with this compute.
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The optional keyword *wl* will output the third-order invariants :math:`W_l`
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(see Eq. 1.4 in :ref:`Steinhardt <Steinhardt>`) for the same degrees as
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for the :math:`Q_l` parameters. For the FCC crystal with *nnn* =12,
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:math:`W_4` = -sqrt(14/143).(49/4096)/Pi\^1.5 = -0.0006722136...
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The optional keyword *wl/hat* will output the normalized third-order
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invariants :math:`\hat{W}_l` (see Eq. 2.2 in :ref:`Steinhardt <Steinhardt>`)
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for the same degrees as for the :math:`Q_l` parameters. For the FCC crystal
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with *nnn* =12, :math:`\hat{W}_4 = -\frac{7}{3} \sqrt{\frac{2}{429}} = -0.159317...`
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The numerical
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values of :math:`\hat{W}_l` for a range of commonly encountered high-symmetry
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structures are given in Table I of :ref:`Steinhardt <Steinhardt>`, and these
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can be reproduced with this keyword.
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The optional keyword *components* will output the components of the
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*normalized* complex vector :math:`\hat{Y}_{lm} = \bar{Y}_{lm}/|\bar{Y}_{lm}|` of degree *ldegree*\,
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which must be included in the list of order parameters to be computed. This option can be used
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in conjunction with :doc:`compute coord_atom <compute_coord_atom>` to
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calculate the ten Wolde's criterion to identify crystal-like
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particles, as discussed in :ref:`ten Wolde <tenWolde2>`.
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The optional keyword *chunksize* is only applicable when using the
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the KOKKOS package and is ignored otherwise. This keyword controls
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the number of atoms in each pass used to compute the bond-orientational
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order parameters and is used to avoid running out of memory. For example
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if there are 4000 atoms in the simulation and the *chunksize*
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is set to 2000, the parameter calculation will be broken up
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into two passes.
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The value of :math:`Q_l` is set to zero for atoms not in the
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specified compute group, as well as for atoms that have less than
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*nnn* neighbors within the distance cutoff, unless *nnn* is NULL.
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The neighbor list needed to compute this quantity is constructed each
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time the calculation is performed (i.e. each time a snapshot of atoms
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is dumped). Thus it can be inefficient to compute/dump this quantity
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too frequently.
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.. note::
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If you have a bonded system, then the settings of
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:doc:`special_bonds <special_bonds>` command can remove pairwise
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interactions between atoms in the same bond, angle, or dihedral. This
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is the default setting for the :doc:`special_bonds <special_bonds>`
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command, and means those pairwise interactions do not appear in the
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neighbor list. Because this fix uses the neighbor list, it also means
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those pairs will not be included in the order parameter. This
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difficulty can be circumvented by writing a dump file, and using the
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:doc:`rerun <rerun>` command to compute the order parameter for
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snapshots in the dump file. The rerun script can use a
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:doc:`special_bonds <special_bonds>` command that includes all pairs in
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the neighbor list.
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----------
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.. include:: accel_styles.rst
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----------
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Output info
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"""""""""""
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This compute calculates a per-atom array with *nlvalues* columns,
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giving the :math:`Q_l` values for each atom, which are real numbers on the
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range :math:`0 <= Q_l <= 1`.
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If the keyword *wl* is set to yes, then the :math:`W_l` values for each
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atom will be added to the output array, which are real numbers.
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If the keyword *wl/hat* is set to yes, then the :math:`\hat{W}_l`
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values for each atom will be added to the output array, which are real numbers.
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If the keyword *components* is set, then the real and imaginary parts
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of each component of *normalized* :math:`\hat{Y}_{lm}` will be added to the
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output array in the following order: :math:`{\rm Re}(\hat{Y}_{-m}), {\rm Im}(\hat{Y}_{-m}),
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{\rm Re}(\hat{Y}_{-m+1}), {\rm Im}(\hat{Y}_{-m+1}), \dots , {\rm Re}(\hat{Y}_m), {\rm Im}(\hat{Y}_m)`.
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In summary, the per-atom array will contain *nlvalues* columns, followed by
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an additional *nlvalues* columns if *wl* is set to yes, followed by
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an additional *nlvalues* columns if *wl/hat* is set to yes, followed
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by an additional 2\*(2\* *ldegree*\ +1) columns if the *components*
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keyword is set.
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These values can be accessed by any command that uses per-atom values
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from a compute as input. See the :doc:`Howto output <Howto_output>` doc
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page for an overview of LAMMPS output options.
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Restrictions
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""""""""""""
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none
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Related commands
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""""""""""""""""
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:doc:`compute coord/atom <compute_coord_atom>`, :doc:`compute centro/atom <compute_centro_atom>`, :doc:`compute hexorder/atom <compute_hexorder_atom>`
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Default
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"""""""
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The option defaults are *cutoff* = pair style cutoff, *nnn* = 12,
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*degrees* = 5 4 6 8 10 12 i.e. :math:`Q_4`, :math:`Q_6`, :math:`Q_8`, :math:`Q_{10}`, and :math:`Q_{12}`,
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*wl* = no, *wl/hat* = no, *components* off, and *chunksize* = 2000
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----------
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.. _Steinhardt:
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**(Steinhardt)** P. Steinhardt, D. Nelson, and M. Ronchetti,
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Phys. Rev. B 28, 784 (1983).
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.. _Mickel:
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**(Mickel)** W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
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J. Chem. Phys. 138, 044501 (2013).
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.. _tenWolde2:
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**(tenWolde)** P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
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J. Chem. Phys. 104, 9932 (1996).
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