From ce13f687840d66f08ee5d32167cd9c7e5e77d251 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 22 Oct 2007 21:43:55 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1086 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 4 +- doc/Section_commands.txt | 1 + doc/pair_coeff.html | 1 + doc/pair_coeff.txt | 1 + doc/pair_resquared.html | 201 ++++++++++++++++++++++++++++++++++++++ doc/pair_resquared.txt | 194 ++++++++++++++++++++++++++++++++++++ doc/pair_style.html | 1 + doc/pair_style.txt | 1 + doc/pair_tersoff.html | 52 ++++++++-- 9 files changed, 448 insertions(+), 8 deletions(-) create mode 100644 doc/pair_resquared.html create mode 100755 doc/pair_resquared.txt diff --git a/doc/Section_commands.html b/doc/Section_commands.html index 8a166919c0..df055aeddd 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -363,8 +363,8 @@ full description: lj/class2/coul/longlj/cutlj/cut/optlj/cut/coul/cut lj/cut/coul/debyelj/cut/coul/longlj/cut/coul/long/tip4plj/expand lj/smoothlubricatemeammorse -morse/optsoftswtable -tersoffyukawa +morse/optresquaredsoftsw +tabletersoffyukawa

These are pair styles contributed by users, which can be used if diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 8c2d81c48e..390d97eefc 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -511,6 +511,7 @@ full description: "meam"_pair_meam.html, "morse"_pair_morse.html, "morse/opt"_pair_morse.html, +"resquared"_pair_resquared.html, "soft"_pair_soft.html, "sw"_pair_sw.html, "table"_pair_table.html, diff --git a/doc/pair_coeff.html b/doc/pair_coeff.html index 172e449300..1ad76ba0cb 100644 --- a/doc/pair_coeff.html +++ b/doc/pair_coeff.html @@ -126,6 +126,7 @@ the pair_style command, and coefficients specified by the associated

  • pair_style meam - modified embedded atom method (MEAM)
  • pair_style morse - Morse potential
  • pair_style morse - optimized version of Morse potential +
  • pair_style resquared - Everaers RE-Squared ellipsoidal potential
  • pair_style soft - Soft (cosine) potential
  • pair_style sw - Stillinger-Weber 3-body potential
  • pair_style table - tabulated pair potential diff --git a/doc/pair_coeff.txt b/doc/pair_coeff.txt index f4c7de1b3d..299fd3f4b3 100644 --- a/doc/pair_coeff.txt +++ b/doc/pair_coeff.txt @@ -122,6 +122,7 @@ the pair_style command, and coefficients specified by the associated "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) "pair_style morse"_pair_morse.html - Morse potential "pair_style morse"_pair_morse.html - optimized version of Morse potential +"pair_style resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential "pair_style soft"_pair_soft.html - Soft (cosine) potential "pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential "pair_style table"_pair_table.html - tabulated pair potential diff --git a/doc/pair_resquared.html b/doc/pair_resquared.html new file mode 100644 index 0000000000..1374ef7d9c --- /dev/null +++ b/doc/pair_resquared.html @@ -0,0 +1,201 @@ + +
    LAMMPS WWW Site - LAMMPS Documentation - LAMMPS Commands +
    + + + + + + +
    + +

    pair_style resquared command +

    +

    Syntax: +

    +
    pair_style resquared cutoff 
+
    + +

    Examples: +

    +
    pair_style resquared 10.0
+pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 
+
    +

    Description: +

    +

    Style resquared computes the RE-squared anisotropic interaction +(Everaers,Babadi) between pairs of ellipsoidal and/or +spherical Lennard-Jones particles. For ellipsoidal interactions, +the potential considers the ellipsoid as being comprised of small +spheres of size sigma. LJ particles are a single sphere of size +sigma. The distinction is made to allow the pair style to make +efficient calculations of ellipsoid/solvent interactions. +

    + + +

    Details for the equations used are given in the references below +and this document. +

    +

    Use of this pair style requires the NVE, NVT, or NPT fixes +with the asphere extension (e.g. fix +nve/asphere) in order to integrate particle +rotation. Additionally, atom_style ellipsoid should +be used since it defines the rotational state of the ellipsoidal +particles and the shape command should be used to +specify ellipsoid diameters. +

    +

    The following coefficients must be defined for each pair of atoms +types via the pair_coeff command as in the examples +above, or in the data file or restart files read by the +read_data or read_restart +commands: +

    + +

    The parameters used depend on the type of particles interacting - +ellipsoid or LJ sphere. The type of particle is determined by +the diameters specified with the shape +command. LJ spheres have diameters equal to zero and thus +represent a single particle with size sigma. The epsilon_i_* or +epsilon_j_* parameters are ignored for LJ sphere interactions. +The interactions between two LJ sphere particles are computed +using the standard Lennard-Jones formula. +

    +

    A12 specifies the energy prefactor which depends on +the type of particles interacting. For ellipsoid-ellipsoid +interactions, A12 is the Hamaker constant as described in +(Everaers). In LJ units: +

    +
    +
    +

    where rho gives the number density of the spherical particles +composing the ellipsoids and epsilon_LJ determines the +interaction strength of the spherical particles. +

    +

    For ellipsoid-LJ sphere interactions, A12 gives the energy +prefactor (see here for details: +

    +
    +
    +

    For LJ sphere-LJ sphere interactions, A12 is the standard +epsilon used in Lennard-Jones pair styles: +

    +
    +
    +

    sigma specifies the diameter of the continuous distribution of +constituent particles within each ellipsoid used to model +the RE-squared potential. Therefore, the effective shape +of an ellipsoid is given by the specified diameters +(see the shape command) plus sigma. +

    +

    For large uniform molecules it has been shown that the epsilon_*_* +energy parameters are approximately representable in terms of +local contact curvatures (Everaers): +

    +
    +
    +

    where a, b, and c give the particle diameters. +

    +

    The last coefficient is optional. If not specified, the global +cutoff specified in the pair_style command is used. +

    +

    The epsilon_i and epsilon_j coefficients are actually defined for atom +types, not for pairs of atom types. Thus, in a series of pair_coeff +commands, they only need to be specified once for each atom type. +

    +

    Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are +non-zero, the three values are assigned to atom type I. If all the +epsilon_i values are zero, they are ignored. If any of epsilon_j_a, +epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned +to atom type J. If all three epsilon_i values are zero, they are +ignored. Thus the typical way to define the epsilon_i and epsilon_j +coefficients is to list their values in "pair_coeff I J" commands when +I = J, but set them to 0.0 when I != J. If you do list them when I != +J, you should insure they are consistent with their values in other +pair_coeff commands. +

    +

    Note that if this potential is being used as a sub-style of +pair_style hybrid, and there is no "pair_coeff I I" +setting made for RE-squared for a particular type I (because I-I +interactions are computed by another hybrid pair potential), then you +still need to insure the epsilon a,b,c coefficients are assigned to +that type in a "pair_coeff I J" command. +

    +
    + +

    Mixing, shift, table, tail correction, per-atom energy/stress, +restart, rRESPA info: +

    +

    Automatic mixing is supported only between LJ sphere +pairs due to the different meanings of the energy prefactors used +to calculate the interactions and the implicit dependance of +the ellipsoid-LJ sphere interaction on the equation for the +Hamaker constant presented here. Mixing of sigma and epsilon +followed by calculation of the energy prefactors using the +equations above is recommended. +

    +

    This pair styles supports the pair_modify shift +option for the energy of the Lennard-Jones portion of the pair +interaction, but only for sphere-sphere interactions. There is no +shifting performed for ellipsoidal interactions due to the anisotropic +dependence of the interaction. +

    +

    The pair_modify table option is not relevant +for this pair style. +

    +

    This pair style does not support the pair_modify +tail option for adding long-range tail corrections to energy and +pressure. +

    +

    This pair style does not calculate per-atom energy and stress, as used +by the compute epair/atom, compute +stress/atom, and dump custom +commands. +

    +

    This pair style writes its information to 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 can only be used via the pair keyword of the +run_style respa command. It does not support the +inner, middle, outer keywords of the run_style +command. +

    +
    + +

    Restrictions: +

    +

    This style is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the Making +LAMMPS section for more info. +

    +

    The distance-of-closest-approach approximation used by LAMMPS becomes +less accurate when high-aspect ratio ellipsoids are used. +

    +

    Related commands: +

    +

    pair_coeff, fix nve/asphere, +compute temp/asphere +

    +

    Default: none +

    +
    + + + +

    (Everaers) Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). +

    + + +

    (Berardi) Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006). +

    + diff --git a/doc/pair_resquared.txt b/doc/pair_resquared.txt new file mode 100755 index 0000000000..c3e3ff0864 --- /dev/null +++ b/doc/pair_resquared.txt @@ -0,0 +1,194 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style resquared command :h3 + +[Syntax:] + +pair_style resquared cutoff :pre + +cutoff = global cutoff for interactions (distance units) :ul + +[Examples:] + +pair_style resquared 10.0 +pair_coeff * * 1.0 1.0 1.7 3.4 3.4 1.0 1.0 1.0 :pre + +[Description:] + +Style {resquared} computes the RE-squared anisotropic interaction +"(Everaers,Babadi)"_#Everaers between pairs of ellipsoidal and/or +spherical Lennard-Jones particles. For ellipsoidal interactions, +the potential considers the ellipsoid as being comprised of small +spheres of size sigma. LJ particles are a single sphere of size +sigma. The distinction is made to allow the pair style to make +efficient calculations of ellipsoid/solvent interactions. + +:link(redoc,Eqs/pair_resquared_extra.pdf) + +Details for the equations used are given in the references below +and "this document"_#redoc. + +Use of this pair style requires the NVE, NVT, or NPT fixes +with the {asphere} extension (e.g. "fix +nve/asphere"_fix_nve_asphere.html) in order to integrate particle +rotation. Additionally, "atom_style ellipsoid"_atom_style.html should +be used since it defines the rotational state of the ellipsoidal +particles and the "shape"_shape.html command should be used to +specify ellipsoid diameters. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the examples +above, or in the data file or restart files read by the +"read_data"_read_data.html or "read_restart"_read_restart.html +commands: + +A12 = Energy Prefactor/Hamaker constant (energy units) +sigma = atomic interaction diameter (distance units) +epsilon_i_a = relative well depth of type I for side-to-side interactions +epsilon_i_b = relative well depth of type I for face-to-face interactions +epsilon_i_c = relative well depth of type I for end-to-end interactions +epsilon_j_a = relative well depth of type J for side-to-side interactions +epsilon_j_b = relative well depth of type J for face-to-face interactions +epsilon_j_c = relative well depth of type J for end-to-end interactions +cutoff (distance units) :ul + +The parameters used depend on the type of particles interacting - +ellipsoid or LJ sphere. The type of particle is determined by +the diameters specified with the "shape"_shape.html +command. LJ spheres have diameters equal to zero and thus +represent a single particle with size sigma. The epsilon_i_* or +epsilon_j_* parameters are ignored for LJ sphere interactions. +The interactions between two LJ sphere particles are computed +using the standard Lennard-Jones formula. + +A12 specifies the energy prefactor which depends on +the type of particles interacting. For ellipsoid-ellipsoid +interactions, A12 is the Hamaker constant as described in +"(Everaers)"_#Everaers. In LJ units: + +:c,image(Eqs/pair_resquared.jpg) + +where rho gives the number density of the spherical particles +composing the ellipsoids and epsilon_LJ determines the +interaction strength of the spherical particles. + +For ellipsoid-LJ sphere interactions, A12 gives the energy +prefactor (see "here"_Eqs/pair_resquared_extra.pdf for details: + +:c,image(Eqs/pair_resquared2.jpg) + +For LJ sphere-LJ sphere interactions, A12 is the standard +epsilon used in Lennard-Jones pair styles: + +:c,image(Eqs/pair_resquared3.jpg) + +sigma specifies the diameter of the continuous distribution of +constituent particles within each ellipsoid used to model +the RE-squared potential. Therefore, the effective shape +of an ellipsoid is given by the specified diameters +(see the "shape"_shape.html command) plus sigma. + +For large uniform molecules it has been shown that the epsilon_*_* +energy parameters are approximately representable in terms of +local contact curvatures "(Everaers)"_#Everaers: + +:c,image(Eqs/pair_resquared4.jpg) + +where a, b, and c give the particle diameters. + +The last coefficient is optional. If not specified, the global +cutoff specified in the pair_style command is used. + +The epsilon_i and epsilon_j coefficients are actually defined for atom +types, not for pairs of atom types. Thus, in a series of pair_coeff +commands, they only need to be specified once for each atom type. + +Specifically, if any of epsilon_i_a, epsilon_i_b, epsilon_i_c are +non-zero, the three values are assigned to atom type I. If all the +epsilon_i values are zero, they are ignored. If any of epsilon_j_a, +epsilon_j_b, epsilon_j_c are non-zero, the three values are assigned +to atom type J. If all three epsilon_i values are zero, they are +ignored. Thus the typical way to define the epsilon_i and epsilon_j +coefficients is to list their values in "pair_coeff I J" commands when +I = J, but set them to 0.0 when I != J. If you do list them when I != +J, you should insure they are consistent with their values in other +pair_coeff commands. + +Note that if this potential is being used as a sub-style of +"pair_style hybrid"_pair_hybrid.html, and there is no "pair_coeff I I" +setting made for RE-squared for a particular type I (because I-I +interactions are computed by another hybrid pair potential), then you +still need to insure the epsilon a,b,c coefficients are assigned to +that type in a "pair_coeff I J" command. + +:line + +[Mixing, shift, table, tail correction, per-atom energy/stress, +restart, rRESPA info]: + +Automatic mixing is supported only between LJ sphere +pairs due to the different meanings of the energy prefactors used +to calculate the interactions and the implicit dependance of +the ellipsoid-LJ sphere interaction on the equation for the +Hamaker constant presented here. Mixing of sigma and epsilon +followed by calculation of the energy prefactors using the +equations above is recommended. + +This pair styles supports the "pair_modify"_pair_modify.html shift +option for the energy of the Lennard-Jones portion of the pair +interaction, but only for sphere-sphere interactions. There is no +shifting performed for ellipsoidal interactions due to the anisotropic +dependence of the interaction. + +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. + +This pair style does not support the "pair_modify"_pair_modify.html +tail option for adding long-range tail corrections to energy and +pressure. + +This pair style does not calculate per-atom energy and stress, as used +by the "compute epair/atom"_compute_epair_atom.html, "compute +stress/atom"_compute_stress_atom.html, and "dump custom"_dump.html +commands. + +This pair style writes its information to "binary restart +files"_restart.html, 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 can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords of the "run_style +command"_run_style.html. + +:line + +[Restrictions:] + +This style is part of the "asphere" package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#2_3 section for more info. + +The distance-of-closest-approach approximation used by LAMMPS becomes +less accurate when high-aspect ratio ellipsoids are used. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "fix nve/asphere"_fix_nve_asphere.html, +"compute temp/asphere"_compute_temp_asphere.html + +[Default:] none + +:line + +:link(Everaers) +[(Everaers)] Everaers and Ejtehadi, Phys Rev E, 67, 041710 (2003). + +:link(Babadi) +[(Berardi)] Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006). diff --git a/doc/pair_style.html b/doc/pair_style.html index 22bae93db1..7bd27d802b 100644 --- a/doc/pair_style.html +++ b/doc/pair_style.html @@ -131,6 +131,7 @@ the pair_style command, and coefficients specified by the associated
  • pair_style meam - modified embedded atom method (MEAM)
  • pair_style morse - Morse potential
  • pair_style morse - optimized version of Morse potential +
  • pair_style resquared - Everaers RE-Squared ellipsoidal potential
  • pair_style soft - Soft (cosine) potential
  • pair_style sw - Stillinger-Weber 3-body potential
  • pair_style table - tabulated pair potential diff --git a/doc/pair_style.txt b/doc/pair_style.txt index 6a546a5cbf..7d45954397 100644 --- a/doc/pair_style.txt +++ b/doc/pair_style.txt @@ -127,6 +127,7 @@ the pair_style command, and coefficients specified by the associated "pair_style meam"_pair_meam.html - modified embedded atom method (MEAM) "pair_style morse"_pair_morse.html - Morse potential "pair_style morse"_pair_morse.html - optimized version of Morse potential +"pair_style resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential "pair_style soft"_pair_soft.html - Soft (cosine) potential "pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential "pair_style table"_pair_table.html - tabulated pair potential diff --git a/doc/pair_tersoff.html b/doc/pair_tersoff.html index 7565f7c734..68af7aa633 100644 --- a/doc/pair_tersoff.html +++ b/doc/pair_tersoff.html @@ -23,14 +23,14 @@ pair_coeff * * SiC.tersoff Si C Si

    Description:

    -

    The tersoff style computes a 3-body Tersoff potential +

    The tersoff style computes a 3-body Tersoff potential for the energy E of a system of atoms as

    -
    +

    where f_R is a two-body term and f_A includes three-body interactions. The summations in the formula are over all neighbors J and K of atom I -within a cutoff distance = R + D. +within a cutoff distance = R + D.

    Only a single pair_coeff command is used with the tersoff style which specifies a Tersoff potential file with parameters for all @@ -66,6 +66,8 @@ above:

    • element 1 (the center atom in a 3-body interaction)
    • element 2 (the atom bonded to the center atom)
    • element 3 (the atom influencing the 1-2 bond in a bond-order sense) +
    • m +
    • gamma
    • lambda3 (1/distance units)
    • c
    • d @@ -80,7 +82,7 @@ above:
    • A (energy units)

    The n, beta, lambda2, B, lambda1, and A parameters are only used for -two-body interactions. The lambda3, c, d, and costheta0 parameters +two-body interactions. The m, gamma, lambda3, c, d, and costheta0 parameters are only used for three-body interactions. The R and D parameters are used for both two-body and three-body interactions. The non-annotated parameters are unitless. @@ -113,6 +115,38 @@ The parameters used only for two-body interactions in entries whose 2nd and 3rd element are different (e.g. SiCSi) are not used for anything and can be set to 0.0 if desired.

    +

    We chose the above form so as to enable users to define +all commonly used variants of the Tersoff potential. +In particular, our form reduces to the original +Tersoff form when m = 3 and gamma = 1, while it reduces to the form of Albe +et al. when beta = 1 and m = 1. Tersoff used a slightly +different but equivalent form for alloys, which we will refer to +as Tersoff_2. +

    +

    LAMMPS parameter values for Tersoff_2 can be obtained as follows. +The parameters for species i and j can be calculated +using the Tersoff_2 mixing rules: +

    +
    +
    +

    Values not shown are determined by the first atom type. Finally, the +Tersoff_2 parameters R and S must be converted to the LAMMPS parameters +R and D (R is different in both forms), using the following relations: +R=(R'+S')/2 and D=(S'-R')/2, where the primes indicate the Tersoff_2 parameters. +

    +

    In the potentials directory, the file SiCGe.tersoff +provides the LAMMPS parameters for Tersoff's various versions of Si, as well +as his alloy paramters for Si, C, and Ge. This file can be +used for pure Si, (three different versions), pure C, pure Ge, binary SiC, and binary SiGe. +LAMMPS will generate an error +if this file is used with any combination involving C and Ge, since there are no entries for +the GeC interactions (Tersoff did not publish parameters for this cross-interaction.) +Tersoff files are also provided for the SiC alloy (SiC.tersoff) and the GaN (GaN.tersoff) +alloys. +

    +

    Many thanks to Rutuparna Narulkar, David Farrell, and Xiaowang Zhou for helping clarify +how Tersoff parameters for alloys have been defined in various papers. +

    Mixing, shift, table, tail correction, per-atom energy/stress, @@ -164,8 +198,14 @@ appropriate units if your simulation doesn't use "metal" units.

    - + -

    (Tersoff) Tersoff, Phys Rev B, 37, 6991 (1988). +(Tersoff_1) J. Tersoff, Phys Rev B, 37, 6991 (1988). + + +(Albe) J. Nord, K. Albe, P. Erhartand K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003). + + +

    (Tersoff_2) J. Tersoff, Phys Rev B, 39, 5566 (1989)