consolidate the documentation for lj/switch3/coulgauss/long and mm3/switch3/coulgauss/long into a single file
This commit is contained in:
Axel Kohlmeyer
@ -187,7 +187,7 @@ OPT.
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* :doc:`mgpt <pair_mgpt>`
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* :doc:`mie/cut (g) <pair_mie>`
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* :doc:`mliap <pair_mliap>`
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* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
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* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
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* :doc:`momb <pair_momb>`
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* :doc:`morse (gkot) <pair_morse>`
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* :doc:`morse/smooth/linear (o) <pair_morse>`
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@ -2456,6 +2456,6 @@ which discuss the `QuickFF <quickff_>`_ methodology.
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* :doc:`bond_style mm3 <bond_mm3>`
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* :doc:`improper_style distharm <improper_distharm>`
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* :doc:`improper_style sqdistharm <improper_sqdistharm>`
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* :doc:`pair_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
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* :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
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* :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
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* examples/USER/yaff
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@ -1,8 +1,12 @@
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.. index:: pair_style lj/switch3/coulgauss/long
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.. index:: pair_style mm3/switch3/coulgauss/long
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pair_style lj/switch3/coulgauss/long command
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============================================
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pair_style mm3/switch3/coulgauss/long command
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=============================================
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Syntax
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""""""
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@ -10,7 +14,7 @@ Syntax
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pair_style style args
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* style = *lj/switch3/coulgauss/long*
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* style = *lj/switch3/coulgauss/long* or *mm3/switch3/coulgauss/long*
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* args = list of arguments for a particular style
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.. parsed-literal::
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@ -20,6 +24,11 @@ Syntax
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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width = width parameter of the smoothing function (distance units)
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*mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
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cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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width = width parameter of the smoothing function (distance units)
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Examples
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""""""""
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@ -31,6 +40,12 @@ Examples
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pair_style lj/switch3/coulgauss/long 12.0 10.0 3.0
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pair_coeff 1 0.2 2.5 1.2
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pair_style mm3/switch3/coulgauss/long 12.0 3.0
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pair_coeff 1 0.2 2.5 1.2
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pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0
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pair_coeff 1 0.2 2.5 1.2
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Description
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"""""""""""
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@ -41,8 +56,17 @@ vdW potential
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E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
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, which goes smoothly to zero at the cutoff r_c as defined
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by the switching function
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The *mm3/switch3/coulgauss/long* style evaluates the MM3
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vdW potential :ref:`(Allinger) <mm3-allinger1989>`
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.. math::
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E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
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r_{v,ij} & = r_{v,i} + r_{v,j} \\
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\epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
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Both potentials go smoothly to zero at the cutoff r_c as defined by the
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switching function
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.. math::
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@ -85,14 +109,35 @@ commands:
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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 epsilon and sigma coefficients
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and cutoff distance for all of the lj/long pair styles can be mixed.
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The default mix value is *geometric*\ . See the "pair_modify" command
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for details.
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Shifting the potential energy is not necessary because the switching
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function ensures that the potential is zero at the cut-off.
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These pair styles support the :doc:`pair_modify <pair_modify>` table and
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options since they can tabulate the short-range portion of the
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long-range Coulombic interactions.
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Thes pair styles do not support the :doc:`pair_modify <pair_modify>`
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tail option for adding a long-range tail correction to the
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Lennard-Jones portion of the energy and pressure.
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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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Restrictions
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""""""""""""
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These styles are part of the USER-YAFF package. They are only
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enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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These styles are part of the USER-YAFF package. They are only enabled
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if LAMMPS was built with that package. See the :doc:`Build package
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<Build_package>` doc page for more info.
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Related commands
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""""""""""""""""
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@ -1,109 +0,0 @@
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.. index:: pair_style mm3/switch3/coulgauss/long
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pair_style mm3/switch3/coulgauss/long command
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=============================================
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Syntax
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""""""
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.. code-block:: LAMMPS
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pair_style style args
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* style = *mm3/switch3/coulgauss/long*
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* args = list of arguments for a particular style
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.. parsed-literal::
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*mm3/switch3/coulgauss/long* args = cutoff (cutoff2) width
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cutoff = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
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cutoff2 = global cutoff for Coulombic (optional) (distance units)
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width = width parameter of the smoothing function (distance units)
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style mm3/switch3/coulgauss/long 12.0 3.0
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pair_coeff 1 0.2 2.5 1.2
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pair_style mm3/switch3/coulgauss/long 12.0 10.0 3.0
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pair_coeff 1 0.2 2.5 1.2
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Description
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"""""""""""
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The *mm3/switch3/coulgauss/long* style evaluates the MM3
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vdW potential :ref:`(Allinger) <mm3-allinger1989>`
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.. math::
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E & = \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
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r_{v,ij} & = r_{v,i} + r_{v,j} \\
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\epsilon_{ij} & = \sqrt{\epsilon_i \epsilon_j}
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, which goes smoothly to zero at the cutoff r_c as defined
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by the switching function
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.. math::
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S_3(r) = \left\lbrace \begin{array}{ll}
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1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
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3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
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0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
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\end{array} \right.
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where w is the width defined in the arguments. This potential
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is combined with Coulomb interaction between Gaussian charge densities:
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.. math::
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E = \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
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where :math:`q_i` and :math:`q_j` are the charges on the 2 atoms,
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epsilon is the dielectric constant which can be set by the
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:doc:`dielectric <dielectric>` command, ::math:`\gamma_i` and
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:math:`\gamma_j` are the widths of the Gaussian charge distribution and
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erf() is the error-function. This style has to be used in conjunction
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with the :doc:`kspace_style <kspace_style>` command
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If one cutoff is specified it is used for both the vdW and Coulomb
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terms. If two cutoffs are specified, the first is used as the cutoff
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for the vdW terms, and the second is the cutoff for the Coulombic term.
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The following coefficients must be defined for each pair of atoms
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types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
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above, 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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* :math:`\epsilon` (energy)
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* :math:`r_v` (distance)
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* :math:`\gamma` (distance)
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----------
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Mixing, shift, table, tail correction, restart, rRESPA info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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Mixing rules are fixed for this style as defined above.
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Shifting the potential energy is not necessary because the switching
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function ensures that the potential is zero at the cut-off.
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Restrictions
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""""""""""""
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These styles are part of the USER-YAFF package. They are only
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enabled if LAMMPS was built 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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Default
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"""""""
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none
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@ -250,7 +250,7 @@ accelerated styles exist.
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* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
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* :doc:`mesont/tpm <pair_mesont_tpm>` - nanotubes mesoscopic force field
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* :doc:`mie/cut <pair_mie>` - Mie potential
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* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
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* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
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* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
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* :doc:`morse <pair_morse>` - Morse potential
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* :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential
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