From c4d49324b52f708d9e0d8fc6ef123cee84f68845 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 6 Jun 2023 16:08:50 -0400 Subject: [PATCH] various documentation updates - spelling fixes - formatting conventions - grammar fixes and clarifications - full integration into manual build procedure --- doc/src/Commands_pair.rst | 1 + doc/src/pair_aip_water_2dm.rst | 64 +++++++++++---------- doc/src/pair_style.rst | 1 + doc/utils/sphinx-config/false_positives.txt | 3 + 4 files changed, 39 insertions(+), 30 deletions(-) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 5f79015aaf..87d3129880 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -37,6 +37,7 @@ OPT. * * :doc:`adp (ko) ` * :doc:`agni (o) ` + * :doc:`aip/water/2dm (o) ` * :doc:`airebo (io) ` * :doc:`airebo/morse (io) ` * :doc:`amoeba (g) ` diff --git a/doc/src/pair_aip_water_2dm.rst b/doc/src/pair_aip_water_2dm.rst index 3ae63e1e45..5218db9c37 100644 --- a/doc/src/pair_aip_water_2dm.rst +++ b/doc/src/pair_aip_water_2dm.rst @@ -35,8 +35,8 @@ Description .. versionadded:: xxxx2023 -The *aip/water/2dm* style computes the anisotropic interfacial -potential (AIP) potential for interfaces of water with two-dimensinal (2D) +The *aip/water/2dm* style computes the anisotropic interfacial potential +(AIP) potential for interfaces of water with two-dimensional (2D) materials as described in :ref:`(Feng) `. .. math:: @@ -56,41 +56,45 @@ materials as described in :ref:`(Feng) `. Where :math:`\mathrm{Tap}(r_{ij})` is the taper function which provides a continuous cutoff (up to third derivative) for interatomic separations -larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn `. +larger than :math:`r_c` :doc:`pair_style ilp_graphene_hbn +`. It is important to include all the pairs to build the neighbor list for calculating the normals. .. note:: - Since each water molecule contains one oxygen atom and two hydrogen atoms, - a new definition is proposed (see In :ref:`(Feng) `),the atomic - normal vectors of hydrogen atoms are assumed to lie along the corresponding - oxygen-hydrogen bonds and the normal vector of the central oxygen atom - is defined as their average. + Since each water molecule contains one oxygen atom and two hydrogen + atoms, a new definition is proposed (see In :ref:`(Feng) `),the + atomic normal vectors of hydrogen atoms are assumed to lie along the + corresponding oxygen-hydrogen bonds and the normal vector of the + central oxygen atom is defined as their average. -The parameter file (e.g. COH.aip.water.2dm), is intended for use with *metal* -:doc:`units `, with energies in meV. Two additional parameters, -*S*, and *rcut* are included in the parameter file. *S* is designed to -facilitate scaling of energies. *rcut* is designed to build the neighbor -list for calculating the normals for each atom pair. +The provided parameter file, ``COH.aip.water.2dm``, is intended for use +with *metal* :doc:`units `, with energies in meV. Two additional +parameters, *S*, and *rcut* are included in the parameter file. *S* is +designed to facilitate scaling of energies; *rcut* is designed to build +the neighbor list for calculating the normals for each atom pair. .. note:: - The parameters presented in the parameter file (e.g. COH.aip.water.2dm), - are fitted with taper function by setting the cutoff equal to 16.0 - Angstrom. Using different cutoff or taper function should be careful. - These parameters provide a good description in both short- and long-range - interaction regimes. This feature is essential for simulations in high pressure - regime (i.e., the interlayer distance is smaller than the equilibrium - distance). + The parameters presented in the provided parameter file, + ``COH.aip.water.2dm``, are fitted with the taper function enabled by + setting the cutoff equal to 16.0 Angstrom. Using a different cutoff + or taper function setting should be carefully checked as they can + lead to significant errors. These parameters provide a good + description in both short- and long-range interaction regimes. This + feature is essential for simulations in high pressure regime (i.e., + the interlayer distance is smaller than the equilibrium distance). -This potential must be used in combination with hybrid/overlay. -Other interactions can be set to zero using pair_style *none*\ . +This potential must be used in combination with hybrid/overlay. Other +interactions can be set to zero using :doc:`pair_coeff settings +` with the pair style set to *none*\ . This pair style tallies a breakdown of the total interlayer potential -energy into sub-categories, which can be accessed via the :doc:`compute pair ` command as a vector of values of length 2. -The 2 values correspond to the following sub-categories: +energy into sub-categories, which can be accessed via the :doc:`compute +pair ` command as a vector of values of length 2. The 2 +values correspond to the following sub-categories: 1. *E_vdW* = vdW (attractive) energy 2. *E_Rep* = Repulsive energy @@ -132,11 +136,11 @@ if LAMMPS was built with that package. See the :doc:`Build package This pair style requires the newton setting to be *on* for pair interactions. -The COH.aip.water.2dm potential file provided with LAMMPS (see the potentials -directory) are parameterized for *metal* units. You can use this -potential with any LAMMPS units, but you would need to create your -COH.aip.water.2dm potential file with coefficients listed in the appropriate -units, if your simulation does not use *metal* units. +The ``COH.aip.water.2dm`` potential file provided with LAMMPS is +parameterized for *metal* units. You can use this pair style with any +LAMMPS units, but you would need to create your own potential file with +parameters in the appropriate units, if your simulation does not use +*metal* units. Related commands """""""""""""""" @@ -158,8 +162,8 @@ Default tap_flag = 1 - ---------- .. _Feng: + **(Feng)** Z. Feng and W. Ouyang et al., J. Phys. Chem. C. 127, 8704-8713 (2023). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 441313b0b8..494a26aacf 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -114,6 +114,7 @@ accelerated styles exist. * :doc:`adp ` - angular dependent potential (ADP) of Mishin * :doc:`agni ` - AGNI machine-learning potential +* :doc:`aip/water/2dm ` - anisotropic interfacial potential for water in 2d geometries * :doc:`airebo ` - AIREBO potential of Stuart * :doc:`airebo/morse ` - AIREBO with Morse instead of LJ * :doc:`amoeba ` - diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index d2d15633af..ad2a255447 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -55,6 +55,7 @@ Ai Aidan aij aimd +aip airebo Aj ajaramil @@ -528,6 +529,7 @@ collisional Columic colvars Colvars +COH COLVARS comID Commun @@ -1090,6 +1092,7 @@ Fellinger femtosecond femtoseconds fene +Feng Fennell fep FEP