199 lines
6.3 KiB
ReStructuredText
199 lines
6.3 KiB
ReStructuredText
.. index:: pair_style gauss
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.. index:: pair_style gauss/gpu
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.. index:: pair_style gauss/omp
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.. index:: pair_style gauss/cut
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.. index:: pair_style gauss/cut/omp
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pair_style gauss command
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========================
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Accelerator Variants: *gauss/gpu*, *gauss/omp*
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pair_style gauss/cut command
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============================
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Accelerator Variants: *gauss/cut/omp*
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Syntax
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""""""
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.. code-block:: LAMMPS
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pair_style gauss cutoff
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pair_style gauss/cut cutoff
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* cutoff = global cutoff for Gauss interactions (distance units)
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style gauss 12.0
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pair_coeff * * 1.0 0.9
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pair_coeff 1 4 1.0 0.9 10.0
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pair_style gauss/cut 3.5
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pair_coeff 1 4 0.2805 1.45 0.112
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Description
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"""""""""""
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Style *gauss* computes a tethering potential of the form
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.. math::
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E = - A \exp(-B r^2) \qquad r < r_c
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between an atom and its corresponding tether site which will typically
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be a frozen atom in the simulation. :math:`r_c` is the cutoff.
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The following coefficients must be defined for each pair of atom types
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via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
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or in the data file or restart files read by the
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:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
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commands:
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* A (energy units)
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* B (1/distance\^2 units)
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* cutoff (distance units)
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The last coefficient is optional. If not specified, the global cutoff
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is used.
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Style *gauss/cut* computes a generalized Gaussian interaction potential
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between pairs of particles:
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.. math::
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E = \frac{H}{\sigma_h\sqrt{2\pi}} \exp\left[-\frac{(r-r_{mh})^2}{2\sigma_h^2}\right]
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where H determines together with the standard deviation :math:`\sigma_h`
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the peak height of the Gaussian function, and :math:`r_{mh}` the peak
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position. Examples of the use of the Gaussian potentials include
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implicit solvent simulations of salt ions :ref:`(Lenart) <Lenart2>` and
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of surfactants :ref:`(Jusufi) <Jusufi2>`. In these instances the
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Gaussian potential mimics the hydration barrier between a pair of
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particles. The hydration barrier is located at :math:`r_{mh}` and has a
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width of :math:`\sigma_h`. The prefactor determines the height of the
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potential barrier.
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The following coefficients must be defined for each pair of atom types
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via the :doc:`pair_coeff <pair_coeff>` command as in the example above,
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or in the data file or restart files read by the
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:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
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commands:
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* H (energy \* distance units)
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* :math:`r_{mh}` (distance units)
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* :math:`\sigma_h` (distance units)
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* cutoff (distance units)
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The last coefficient is optional. If not specified, the global cutoff
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is used.
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----------
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.. include:: accel_styles.rst
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----------
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Mixing, shift, table, tail correction, restart, rRESPA info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh
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parameters, and the cutoff distance for these pair styles can be mixed:
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A (energy units)
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sqrt(1/B) (distance units, see below)
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H (energy units)
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sigma_h (distance units)
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r_mh (distance units)
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cutoff (distance units):ul
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The default mix value is *geometric*\ .
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Only *arithmetic* and *geometric* mix values are supported.
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See the "pair_modify" command for details.
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The A and H parameters are mixed using the same rules normally
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used to mix the "epsilon" parameter in a Lennard Jones interaction.
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The sigma_h, r_mh, and the cutoff distance are mixed using the same
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rules used to mix the "sigma" parameter in a Lennard Jones interaction.
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The B parameter is converted to a distance (sigma), before mixing
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(using sigma=B\^-0.5), and converted back to a coefficient
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afterwards (using B=sigma\^2).
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Negative A values are converted to positive A values (using abs(A))
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before mixing, and converted back after mixing
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(by multiplying by min(sign(Ai),sign(Aj))).
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This way, if either particle is repulsive (if Ai<0 or Aj<0),
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then the default interaction between both particles will be repulsive.
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The *gauss* style does not support the :doc:`pair_modify <pair_modify>`
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shift option. There is no effect due to the Gaussian well beyond the
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cutoff; hence reasonable cutoffs need to be specified.
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The *gauss/cut* style supports the :doc:`pair_modify <pair_modify>` shift
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option for the energy of the Gauss-potential portion of the pair
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interaction.
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The :doc:`pair_modify <pair_modify>` table and tail options are not
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relevant for these pair styles.
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These pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need
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to be specified in an input script that reads a restart file.
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These pair styles can only be used via the *pair* keyword of the
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:doc:`run_style respa <run_style>` command. They do not support the
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*inner*, *middle*, *outer* keywords.
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The *gauss* pair style tallies an "occupancy" count of how many Gaussian-well
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sites have an atom within the distance at which the force is a maximum
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= sqrt(0.5/b). This quantity can be accessed via the :doc:`compute pair <compute_pair>` command as a vector of values of length 1.
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To print this quantity to the log file (with a descriptive column
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heading) the following commands could be included in an input script:
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.. code-block:: LAMMPS
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compute gauss all pair gauss
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variable occ equal c_gauss[1]
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thermo_style custom step temp epair v_occ
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----------
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Restrictions
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""""""""""""
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The *gauss* and *gauss/cut* styles are part of the EXTRA-PAIR package.
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They are only enabled if LAMMPS is build with that package. See the
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:doc:`Build package <Build_package>` page for more info.
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The *gauss* style does not apply :doc:`special_bonds <special_bonds>`
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factors. When using this pair style on a system that has bonds, the
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special_bonds factors, if using the default setting of 0.0, may need to
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be adjusted to some very small number (e.g. 1.0e-100), so that those
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special pairs are not completely excluded from the neighbor lists, but
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won't contribute forces or energies from styles (e.g. when used in
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combination with a :doc:`hybrid pair style <pair_hybrid>`) that do
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apply those factors.
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`,
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:doc:`pair_style coul/diel <pair_coul_diel>`
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Default
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"""""""
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none
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.. _Lenart2:
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**(Lenart)** Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126,
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044509 (2007).
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.. _Jusufi2:
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**(Jusufi)** Jusufi, Hynninen, and Panagiotopoulos, J Phys Chem B, 112,
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13783 (2008).
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