213 lines
6.6 KiB
ReStructuredText
213 lines
6.6 KiB
ReStructuredText
.. index:: pair\_style gauss
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pair\_style gauss command
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=========================
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pair\_style gauss/gpu command
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=============================
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pair\_style gauss/omp command
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=============================
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pair\_style gauss/cut command
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=============================
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pair\_style gauss/cut/omp command
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=================================
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Syntax
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""""""
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.. parsed-literal::
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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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.. parsed-literal::
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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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.. image:: Eqs/pair_gauss.jpg
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:align: center
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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. Rc 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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.. image:: Eqs/pair_gauss_cut.jpg
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:align: center
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where H determines together with the standard deviation sigma\_h the
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peak height of the Gaussian function, and r\_mh the peak position.
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Examples of the use of the Gaussian potentials include implicit
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solvent simulations of salt ions :ref:`(Lenart) <Lenart2>` and of surfactants
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:ref:`(Jusufi) <Jusufi2>`. In these instances the Gaussian potential mimics
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the hydration barrier between a pair of particles. The hydration
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barrier is located at r\_mh and has a width of sigma\_h. The prefactor
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determines the height of the 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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* r\_mh (distance units)
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* 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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Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
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page. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
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:doc:`suffix <suffix>` command in your input script.
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See the :doc:`Speed packages <Speed_packages>` doc page for more
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instructions on how to use the accelerated styles effectively.
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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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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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.. parsed-literal::
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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/cut* style is part of the "user-misc" package. It is only
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enabled if LAMMPS is build with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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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:** 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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