From 82bb3661267e08bf7ecb7014c83b80949e420f8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mateo=20Rodr=C3=ADguez?= Date: Thu, 17 Apr 2025 14:06:14 +0200 Subject: [PATCH] Delete doc/pair_ilj_cut.rst --- doc/pair_ilj_cut.rst | 152 ------------------------------------------- 1 file changed, 152 deletions(-) delete mode 100644 doc/pair_ilj_cut.rst diff --git a/doc/pair_ilj_cut.rst b/doc/pair_ilj_cut.rst deleted file mode 100644 index 47fdc31b44..0000000000 --- a/doc/pair_ilj_cut.rst +++ /dev/null @@ -1,152 +0,0 @@ -.. index:: pair_style ilj/cut - -pair_style ilj/cut command -============================= - -Syntax -"""""" - -.. code-block:: LAMMPS - - pair_style ilj/cut cutoff - -* ilj/cut = name of the pair style -* cutoff = global cutoff (distance units) - -Examples -"""""""" - -.. code-block:: LAMMPS - - pair_style ilj/cut 10.0 - pair_coeff 1 1 4.0 7.0 6.0 3.5 0.0045 - -Description -""""""""""" - -.. versionadded:: 29Aug2024 - -Pair style *ilj/cut* computes pairwise interactions from an Improved Lennard-Jones (ILJ) potential according to :ref:`(Pirani) `: - - -.. math:: - - x = r/R_m \\ - n_x = \alpha*x^2 + \beta \\ - \gamma \equiv m \\ - - V(x) = \epsilon \cdot \left( \frac{\gamma}{n_x - \gamma} \left(\frac{1}{x} \right)^{n_x} - \frac{n_x}{n_x - \gamma} \left(\frac{1}{x} \right)^{\gamma} \right) - \qquad r < r_c -:math:`r_c` is the cutoff. - - -An additional parameter, :math:`\alpha`, has been introduced in order to be able to recover the traditional LJ 12-6 with an adequate choice of parameters. With -:math:`R_m \equiv r_0 = \sigma \cdot 2^{1/6}`, :math:`\alpha = 0`, :math:`\beta = 12` and :math:`\gamma = 6` it is straightforward -to prove that LJ 12-6 is obtained. - - -This potential provides some advantages with respect to the Lennard-Jones (LJ) potential and can be really useful for molecular dynamics simulations, as one can see from :ref:`(Pirani) `. -It can be used for neutral-neutral (:math:`\gamma = 6`), ion-neutral (:math:`\gamma = 4`) or ion-ion systems (:math:`\gamma = 1`). -It removes most of the issues at short- and long-range of the LJ model. - - -It is possible to verify that using (:math:`\alpha= 4`), (:math:`\beta= 6`) and (:math:`\gamma = 6`), at the equilibrium distance, -the first and second derivatives of ILJ coincide with those of LJ 12-6 ( and the reduced force constant amounts to the typical 72). -In this case, LJ provides a long-range coefficient with a factor of 2 compared with the ILJ. Also, the short-range interaction is overestimated by LJ. -The ILJ potential solves both problems. - - -The analysis of a diverse amount of systems verified that (:math:`\alpha= 4`) works very well. -In some special cases (e.g. those involving very small multiple charged ions) this factor may take a slightly different value. -The parameter (:math:`\beta`) codifies the hardness (polarizability) of the interacting partners, and for neutral-neutral systems it ranges from 6 to 11. -Moreover, the modulation of (:math:`\beta`) permits to indirectly consider the role of further interaction components (such as the charge transfer int he perturbative limit) -and mitigates the effect of some uncertainty in the data. - - -A couple of examples of the applications of the ILJ potential should be useful to show its wide variety of uses: - -- The ILJ potential has been successfully used to model the interaction between a graphdiyne (GDY) membrane and molecular hydrogen (:ref:`(Arroyo) `). - -- The ILJ model and the phenomenological approach have been recently adopted by the NASA Laboratory to evaluate transport properties in gaseous mixtures (:ref:`(Chatzigeorgis) `) - - -The following coefficients must be defined for each pair of atoms -types via the :doc:`pair_coeff ` command as in the examples -above, or in the data file or restart files read by the -:doc:`read_data ` or :doc:`read_restart ` -commands: - -* :math:`\alpha` (dimensionless) -* :math:`\beta` (dimensionless) -* :math:`\gamma` (dimensionless) -* :math:`R_m` (distance units) -* :math:`\epsilon` (energy units) -* cutoff (distance units) - -The last coefficient is optional. If not specified, the global cutoff is used. - ----------- - -Mixing, shift, table, tail correction, restart, rRESPA info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" - -This pair style does not support mixing. Thus, coefficients for all I,J -pairs must be specified explicitly. - -This pair style supports the :doc:`pair_modify ` shift -option for the energy of the pair interaction. - -The :doc:`pair_modify ` table options are not relevant for -this pair style. - -This pair style does not support the :doc:`pair_modify ` -tail option for adding long-range tail corrections to energy and -pressure. - -This pair style writes its information to :doc:`binary restart files -`, so pair_style and pair_coeff commands do not need to be -specified in an input script that reads a restart file. - -This pair style supports the use of the *inner*, *middle*, and -*outer* keywords of the :doc:`run_style respa ` command, -meaning the pairwise forces can be partitioned by distance at different -levels of the rRESPA hierarchy. See the :doc:`run_style ` -command for details. - - ----------- - -Restrictions -"""""""""""" - -This pair style is only enabled if LAMMPS was built with the EXTRA-PAIR -package. See the :doc:`Build package ` page for more -info. - -Related commands -"""""""""""""""" - -* :doc:`pair_coeff ` -* :doc:`pair_style lj/cut ` - -Default -""""""" - -none - --------------- - -.. _Pirani: - -**(Pirani)** F. Pirani, S. Brizi, L. Roncaratti, P. Casavecchia, D. Cappelletti and F. Vecchiocattivi, Phys. Chem. Chem. Phys., 2008, 10, 5489–5503. - - -.. _Arroyo: - -**(Arroyo)** E. García-Arroyo, J. Campos-Martínez, M. Bartolomei, F. Pirani and M. Hernández, Phys. Chem. Chem. Phys., 2022,24, 15840-15850 - - -.. _Chatzigeorgis: - -**(Chatzigeorgis)** G. Bellas-Chatzigeorgis, J. Haskins and J. Scoggins , Physics of Fluids 1 August 2022; 34 (8): 087106. -