forked from lijiext/lammps
fix up and integrate documentation for contributed pair styles
This commit is contained in:
Axel Kohlmeyer
parent
6415befb5b
commit
04c968362f
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@ -1040,6 +1040,7 @@ package"_Section_start.html#start_3.
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"coul/cut/soft (o)"_pair_lj_soft.html,
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"coul/diel (o)"_pair_coul_diel.html,
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"coul/long/soft (o)"_pair_lj_soft.html,
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"coul/shield"_pair_coul_shield.html,
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"dpd/fdt"_pair_dpd_fdt.html,
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"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
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"eam/cd (o)"_pair_eam.html,
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@ -1050,6 +1051,8 @@ package"_Section_start.html#start_3.
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"exp6/rx (k)"_pair_exp6_rx.html,
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"extep"_pair_extep.html,
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"gauss/cut"_pair_gauss.html,
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"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
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"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
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"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
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"lennard/mdf"_pair_mdf.html,
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"list"_pair_list.html,
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@ -437,6 +437,7 @@ pair_colloid.html
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pair_comb.html
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pair_coul.html
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pair_coul_diel.html
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pair_coul_shield.html
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pair_cs.html
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pair_dipole.html
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pair_dpd.html
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@ -453,9 +454,11 @@ pair_gayberne.html
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pair_gran.html
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pair_gromacs.html
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pair_gw.html
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pair_ilp_graphene_hbn.html
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pair_hbond_dreiding.html
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pair_hybrid.html
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pair_kim.html
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pair_kolmogorov_crespi_full.html
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pair_kolmogorov_crespi_z.html
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pair_lcbop.html
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pair_line_lj.html
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@ -13,7 +13,7 @@ pair_style coul/shield command :h3
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pair_style coul/shield cutoff tap_flag :pre
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cutoff = global cutoff (distance units)
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tap_flag = 0/1 to turn off/on the Tapper function
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tap_flag = 0/1 to turn off/on the taper function
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[Examples:]
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@ -23,27 +23,29 @@ pair_coeff 1 2 0.70 :pre
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[Description:]
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Style {coul/shield} computes a Coulomb interaction for boron and nitrigon
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atoms locate in different layers of hexagonal boron nitride. This potential must
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be used in combination with the potential "pair_style pair_ilp_gr_hBN"_pair_ilp_gr_hBN.html
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Style {coul/shield} computes a Coulomb interaction for boron and
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nitrogen atoms located in different layers of hexagonal boron
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nitride. This potential is designed be used in combination with
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the pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html
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NOTE: This potential is intended for electrostatic interactions between two different
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layers of hexagonal boron nitride. Therefore, to avoid interaction within the same layers,
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each layer should have a separate molecule id and is recommended to use
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"full" atom style in the data file.
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NOTE: This potential is intended for electrostatic interactions between
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two different layers of hexagonal boron nitride. Therefore, to avoid
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interaction within the same layers, each layer should have a separate
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molecule id and is recommended to use the "full" atom style, so that
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charge and molecule ID information is included.
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:c,image(Eqs/pair_coul_shield.jpg)
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Where Tap(r_ij) is the tapper function which provides a continuous cutoff (up to third derivative)
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for interatomic separations larger than r_c "(Maaravi)"_#Maaravi. Here \lambda is the shielding
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parameter that eliminates the short-range sigularity of the classical monopolar electrostatic
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interaction expression "(Maaravi)"_#Maaravi.
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Where Tap(r_ij) is the taper function which provides a continuous cutoff
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(up to third derivative) for inter-atomic separations larger than r_c
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"(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
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eliminates the short-range singularity of the classical mono-polar
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electrostatic interaction expression "(Maaravi)"_#Maaravi1.
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The shielding parameter \lambda (1/distance units) must be defined for each pair of atom
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types via the "pair_coeff"_pair_coeff.html command as in the example
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above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands:
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The shielding parameter {lambda} (1/distance units) must be defined for
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each pair of atom types via the "pair_coeff"_pair_coeff.html command as
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in the example above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html commands:
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The global cutoff (r_c) specified in the pair_style command is used.
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@ -51,13 +53,14 @@ The global cutoff (r_c) specified in the pair_style command is used.
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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This pair style does not support parameter mixing. Coefficients must be given explicitly for each type of particle pairs.
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This pair style does not support parameter mixing. Coefficients must
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be given explicitly for each type of particle pairs.
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The "pair_modify"_pair_modify.html table option is not relevant
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The "pair_modify"_pair_modify.html {table} option is not relevant
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for this pair style.
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This pair style does not support the "pair_modify"_pair_modify.html
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tail option for adding long-range tail corrections to energy and
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{tail} option for adding long-range tail corrections to energy and
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pressure.
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This pair style can only be used via the {pair} keyword of the
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@ -66,18 +69,18 @@ This pair style can only be used via the {pair} keyword of the
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[Restrictions:]
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This style is part of the "user-misc" package. It is only enabled
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This style is part of the USER-MISC package. It is only enabled
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if LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_2_3 section for more info.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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"pair_style pair_ilp_gr_hBN"_pair_ilp_gr_hBN.html
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"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html
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[Default:] tap_flag = 1
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:line
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:link(Maaravi)
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:link(Maaravi1)
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[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
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@ -6,64 +6,68 @@
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:line
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pair_style ILP/graphene/hBN command :h3
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pair_style ilp/graphene/hbn command :h3
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[Syntax:]
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pair_style hybrid/overlay ILP/graphene/hBN cutoff tap_flag :pre
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pair_style hybrid/overlay ilp/graphene/hbn cutoff tap_flag :pre
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cutoff = global cutoff (distance units)
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tap_flag = 0/1 to turn off/on the Tapper function
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tap_flag = 0/1 to turn off/on the taper function
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[Examples:]
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pair_style hybrid/overlay ILP/graphene/hBN 16.0 1
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pair_coeff * * ILP/graphene/hBN BNCH.ILP B N C :pre
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pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
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pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre
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pair_style hybrid/overlay rebo tersoff ILP/graphene/hBN 16.0 coul/shield 16.0
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pair_style hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
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pair_coeff * * rebo CH.airebo NULL NULL C
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pair_coeff * * tersoff BNC.tersoff B N NULL
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pair_coeff * * ILP/graphene/hBN BNCH.ILP B N C :pre
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pair_coeff * * ilp/graphene/hbn BNCH.ILP B N C :pre
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pair_coeff 1 1 coul/shield 0.70
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pair_coeff 1 2 coul/shield 0.69498201415576216335
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pair_coeff 2 2 coul/shield 0.69
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[Description:]
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The {ILP/graphene/hBN} style computes the registry-dependent interlayer potential (RDILP)
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potential as described in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi. The normals are calculated in
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the way as described in "(Kolmogorov)"_#Kolmogorov.
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The {ILP/graphene/hBN} style computes the registry-dependent interlayer
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potential (RDILP) potential as described in "(Leven)"_#Leven and
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"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
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in "(Kolmogorov)"_#Kolmogorov2.
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:c,image(Eqs/pair_ilp_gr_hBN.jpg)
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Where Tap(r_ij) is the tapper function which provides a continuous cutoff (up to third derivative)
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for interatomic separations larger than r_c "(Maaravi)"_#Maaravi. The definitons of each parameter
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in the above equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi.
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Where Tap(r_ij) is the taper function which provides a continuous
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cutoff (up to third derivative) for interatomic separations larger than
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r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above
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equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2.
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It is important to include all the pairs to build the neighbor list for
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calculating the normals.
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NOTE: This potential is intended for interactions between two different layers
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of graphene or hexagonal boron nitride. Therefore, to avoid interaction within
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the same layers, each layer should have a separate molecule id and is recommended
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to use "full" atom style in the data file.
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NOTE: This potential is intended for interactions between two different
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layers of graphene or hexagonal boron nitride. Therefore, to avoid
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interaction within the same layers, each layer should have a separate
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molecule id and is recommended to use "full" atom style in the data
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file.
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The parameter file (e.g. BNCH.ILP), is intended for use with metal
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"units"_units.html, with energies in meV. Two additional parameters, {S},
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and {rcut} are included in the parameter file. {S} is designed to
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The parameter file (e.g. BNCH.ILP), is intended for use with {metal}
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"units"_units.html, with energies in meV. Two additional parameters,
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{S}, and {rcut} are included in the parameter file. {S} is designed to
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facilitate scaling of energies. {rcut} is designed to build the neighbor
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list for calculating the normals for each atom pair.
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NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP), are
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fitted with tapper function by setting the cutoff equal to 16.0 Angstrom.
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Using different cutoff or tapper function should be careful.
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NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
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are fitted with taper function by setting the cutoff equal to 16.0
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Angstrom. Using different cutoff or taper function should be careful.
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NOTE: Two parameter files (BNCH.ILP and BNCH-old.ILP) are presented, BNCH-old.ILP
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contains the paramters published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi, which
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is only suitable for long-range interaction. The paramters in BNCH.ILP provides
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a good description both for short- and long-range interaction. This is useful for
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simulations in the high pressure (small interlayer distances) regime. The comparison of
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two sets of paramters can be found in "(Ouyang)"_#Ouyang.
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NOTE: Two parameter files (BNCH.ILP and BNCH-old.ILP) are presented,
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BNCH-old.ILP contains the parameters published in "(Leven)"_#Leven and
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"(Maaravi)"_#Maaravi2, which is only suitable for long-range
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interaction. The parameters in BNCH.ILP provides a good description both
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for short- and long-range interaction. This is useful for simulations in
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the high pressure (small interlayer distances) regime. The comparison of
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two sets of parameters can be found in "(Ouyang)"_#Ouyang.
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This potential must be used in combination with hybrid/overlay.
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Other interactions can be set to zero using pair_style {none}.
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@ -72,11 +76,13 @@ Other interactions can be set to zero using pair_style {none}.
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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This pair style does not support the pair_modify mix, shift, table, and tail options.
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This pair style does not support the pair_modify mix, shift, table, and
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tail options.
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This pair style does not write their information to binary restart files,
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since it is stored in potential files. Thus, you need to re-specify the
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pair_style and pair_coeff commands in an input script that reads a restart file.
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This pair style does not write their information to binary restart
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files, since it is stored in potential files. Thus, you need to
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re-specify the pair_style and pair_coeff commands in an input script
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that reads a restart file.
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[Restrictions:]
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@ -84,11 +90,14 @@ This fix is part of the USER-MISC package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
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This pair potential requires the newton setting to be “on” for pair interactions.
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This pair potential requires the newton setting to be {on} for pair
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interactions.
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The BNCH.ILP potential file provided with LAMMPS (see the potentials directory) are parameterized for metal units.
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You can use this potential with any LAMMPS units, but you would need to create your BNCH.ILP potential file with
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coefficients listed in the appropriate units, if your simulation doesn’t use “metal” units.
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The BNCH.ILP potential file provided with LAMMPS (see the potentials
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directory) are parameterized for {metal} units. You can use this
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potential with any LAMMPS units, but you would need to create your
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BNCH.ILP potential file with coefficients listed in the appropriate
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units, if your simulation does not use {metal} units.
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[Related commands:]
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@ -106,10 +115,10 @@ coefficients listed in the appropriate units, if your simulation doesn’t use
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:link(Leven)
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[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016)
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:link(Maaravi)
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:link(Maaravi2)
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[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
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:link(Kolmogorov)
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:link(Kolmogorov2)
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[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
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:link(Ouyang)
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@ -13,7 +13,7 @@ pair_style kolmogorov/crespi/full command :h3
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pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre
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cutoff = global cutoff (distance units)
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tap_flag = 0/1 to turn off/on the Tapper function
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tap_flag = 0/1 to turn off/on the taper function
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[Examples:]
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@ -27,23 +27,25 @@ pair_coeff * * kolmogorov/crespi/full CC.KC C C :pre
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[Description:]
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The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi interaction
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potential as described in "(Kolmogorov)"_#Kolmogorov. No simplification is made,
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The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi
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interaction potential as described in "(Kolmogorov)"_#Kolmogorov1.
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No simplification is made,
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:c,image(Eqs/pair_kolmogorov_crespi_full.jpg)
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It is important to have a suffiently large cutoff to ensure smooth forces and
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to include all the pairs to build the neighbor list for calculating the normals.
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Energies are shifted so that they go continously to zero at the cutoff assuming
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that the exponential part of {Vij} (first term) decays sufficiently fast.
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This shift is achieved by the last term in the equation for {Vij} above.
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It is important to have a sufficiently large cutoff to ensure smooth
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forces and to include all the pairs to build the neighbor list for
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calculating the normals. Energies are shifted so that they go
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continuously to zero at the cutoff assuming that the exponential part of
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{Vij} (first term) decays sufficiently fast. This shift is achieved by
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the last term in the equation for {Vij} above.
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NOTE: This potential is intended for interactions between two different graphene
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layers. Therefore, to avoid interaction within the same layers, each layer
|
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should have a separate molecule id and is recommended to use
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NOTE: This potential is intended for interactions between two different
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graphene layers. Therefore, to avoid interaction within the same layers,
|
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each layer should have a separate molecule id and is recommended to use
|
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"full" atom style in the data file.
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The parameter file (e.g. CC.KC), is intended for use with metal
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The parameter file (e.g. CC.KC), is intended for use with {metal}
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"units"_units.html, with energies in meV. Two additional parameters, {S},
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and {rcut} are included in the parameter file. {S} is designed to
|
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facilitate scaling of energies. {rcut} is designed to build the neighbor
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@ -56,11 +58,13 @@ Other interactions can be set to zero using pair_style {none}.
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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This pair style does not support the pair_modify mix, shift, table, and tail options.
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This pair style does not support the pair_modify mix, shift, table,
|
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and tail options.
|
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|
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This pair style does not write their information to binary restart files,
|
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since it is stored in potential files. Thus, you need to re-specify the
|
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pair_style and pair_coeff commands in an input script that reads a restart file.
|
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This pair style does not write their information to binary restart
|
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files, since it is stored in potential files. Thus, you need to
|
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re-specify the pair_style and pair_coeff commands in an input script
|
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that reads a restart file.
|
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[Restrictions:]
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@ -68,23 +72,26 @@ This fix is part of the USER-MISC package. It is only enabled if
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LAMMPS was built with that package. See the "Making
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LAMMPS"_Section_start.html#start_3 section for more info.
|
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|
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This pair potential requires the newton setting to be “on” for pair interactions.
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This pair potential requires the newton setting to be {on} for pair
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interactions.
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The CC.KC potential file provided with LAMMPS (see the potentials directory) are parameterized for metal units.
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You can use this potential with any LAMMPS units, but you would need to create your CC.KC potential file with
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coefficients listed in the appropriate units, if your simulation doesn’t use “metal” units.
|
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The CC.KC potential file provided with LAMMPS (see the potentials
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folder) are parameterized for metal units. You can use this potential
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with any LAMMPS units, but you would need to create your own custom
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CC.KC potential file with all coefficients converted to the appropriate
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units.
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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"pair_none"_pair_none.html
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"pair_style hybrid/overlay"_pair_hybrid.html
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"pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html
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"pair_style pair_ilp_gr_hBN"_pair_ilp_gr_hBN.html
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"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html
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"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html
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[Default:] tap_flag = 0
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:line
|
||||
|
||||
:link(Kolmogorov)
|
||||
:link(Kolmogorov1)
|
||||
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
|
||||
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|
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|
@ -25,7 +25,7 @@ pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
|
|||
[Description:]
|
||||
|
||||
The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
|
||||
potential as described in "(KC05)"_#KC05. An important simplification is made,
|
||||
potential as described in "(Kolmogorov)"_#KC05. An important simplification is made,
|
||||
which is to take all normals along the z-axis.
|
||||
|
||||
:c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
|
||||
|
|
@ -65,7 +65,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
|||
:line
|
||||
|
||||
:link(KC05)
|
||||
[(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
|
||||
[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
|
||||
|
||||
:link(vanWijk)
|
||||
[(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino,
|
||||
|
|
|
|||
|
|
@ -24,6 +24,7 @@ Pair Styles :h1
|
|||
pair_comb
|
||||
pair_coul
|
||||
pair_coul_diel
|
||||
pair_coul_shield
|
||||
pair_cs
|
||||
pair_dipole
|
||||
pair_dpd
|
||||
|
|
@ -42,7 +43,9 @@ Pair Styles :h1
|
|||
pair_gw
|
||||
pair_hbond_dreiding
|
||||
pair_hybrid
|
||||
pair_ilp_graphene_hbn
|
||||
pair_kim
|
||||
pair_kolmogorov_crespi_full
|
||||
pair_kolmogorov_crespi_z
|
||||
pair_lcbop
|
||||
pair_line_lj
|
||||
|
|
|
|||
Loading…
Reference in New Issue