forked from lijiext/lammps
more changes to new polygon/hedron docs and command names
This commit is contained in:
Steven J. Plimpton
parent
de69e24551
commit
843b96e8dd
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@ -664,6 +664,8 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
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"vector"_fix_vector.html,
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"viscosity"_fix_viscosity.html,
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"viscous"_fix_viscous.html,
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"wall/body/polygon"_fix_wall_body_polygon.html,
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"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
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"wall/colloid"_fix_wall.html,
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"wall/gran"_fix_wall_gran.html,
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"wall/gran/region"_fix_wall_gran_region.html,
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@ -914,7 +916,9 @@ KOKKOS, o = USER-OMP, t = OPT.
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"airebo (oi)"_pair_airebo.html,
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"airebo/morse (oi)"_pair_airebo.html,
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"beck (go)"_pair_beck.html,
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"body"_pair_body.html,
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"body/nparticle"_pair_body_nparticle.html,
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"body/rounded/polygon"_pair_body_rounded/polygon.html,
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"body/rounded/polyhedron"_pair_body_rounded/polyhedron.html,
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"bop"_pair_bop.html,
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"born (go)"_pair_born.html,
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"born/coul/dsf"_pair_born.html,
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@ -286,12 +286,10 @@ polyhedron with a variable number of N vertices, E edges and F faces.
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This style can only be used for 3d models; see the
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"boundary"_boundary.html command. See the "pair_style
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body/rounded/polygon" doc page for a diagram of a two 2d squares with
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rounded circles at the vertices. A 3d cube with rounded spheres
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at the 8 vertices and 12 rounded edges would be similar.
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TRUNG: What are the special cases allowed for 3d, if any? Similar to
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the N=1 (sphere) and N=2 (rod) special cases for 2d, descibed in
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previous section.
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rounded circles at the vertices. A 3d cube with rounded spheres at
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the 8 vertices and 12 rounded edges would be similar. Special cases
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for N = 1 (sphere) and N = 2 (rod with rounded ends) can also be
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specified.
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This body style is for 3d discrete element models, as described in
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"Wang"_#Wang.
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@ -10,21 +10,21 @@ pair_style body command :h3
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[Syntax:]
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pair_style body cutoff :pre
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pair_style body/nparticle cutoff :pre
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cutoff = global cutoff for interactions (distance units)
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[Examples:]
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pair_style body 3.0
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pair_style body/nparticle 3.0
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pair_coeff * * 1.0 1.0
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pair_coeff 1 1 1.0 1.5 2.5 :pre
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[Description:]
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Style {body} is for use with body particles and calculates pairwise
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body/body interactions as well as interactions between body and
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point-particles. See "Section 6.14"_Section_howto.html#howto_14
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Style {body/nparticle} is for use with body particles and calculates
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pairwise body/body interactions as well as interactions between body
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and point-particles. See "Section 6.14"_Section_howto.html#howto_14
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of the manual and the "body"_body.html doc page for more details on
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using body particles.
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@ -28,11 +28,11 @@ pair_coeff 1 1 100.0 1.0 :pre
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Style {body/rounded/polygon} is for use with 2d models of body
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particles of style {rounded/polygon}. It calculates pairwise
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body/body interactions as well as interactions between body and point
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particles (modeled as disks with a specified diameter).
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See "Section 6.14"_Section_howto.html#howto_14 of the
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manual and the "body"_body.html doc page for more details on using
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body rounded/polygon particles.
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body/body interactions which can include body particles modeled as
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1-vertex circular disks with a specified diameter. See "Section
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6.14"_Section_howto.html#howto_14 of the manual and the
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"body"_body.html doc page for more details on using body
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rounded/polygon particles.
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This pairwise interaction between rounded polygons is described in
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"Fraige"_#Fraige, where a polygon does not have sharp corners, but is
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@ -51,8 +51,21 @@ between two particles are defined with respect to the separation of
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their respective rounded surfaces, not by the separation of the
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vertices and edges themselves.
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This means that the specified cutoff in the pair_style command is
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the cutoff distance, r_c, for the surface separation, \delta_n (see figure below).
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This means that the specified cutoff in the pair_style command is the
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cutoff distance, r_c, for the surface separation, \delta_n (see figure
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below). This is the distance at which two particles no longer
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interact. If r_c is specified as 0.0, then it is a contact-only
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interaction. I.e. the two particles must overlap in order to exert a
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repulsive force on each other. If r_c > 0.0, then the force between
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two particles will be attractive for surface separations from 0 to
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r_c, and repulsive once the particles overlap.
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Note that unlike for other pair styles, the specified cutoff is not
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the distance between the centers of two particles at which they stop
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interacting. This center-to-center distance depends on the shape and
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size of the two particles and their relative orientation. LAMMPS
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takes that into account when computing the surface separation distance
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and applying the r_c cutoff.
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The forces between vertex-vertex, vertex-edge, and edge-edge overlaps
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are given by:
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@ -61,25 +74,10 @@ are given by:
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:c,image(JPG/pair_body_rounded.jpg)
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TRUNG: The diagram label "cohesive regions" confuses me. Are you
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saying there is some distance d for which the force is attractive,
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i.e. the particles are cohesive? I think when d > Ri + Rj, since Ri +
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Rj is the surface/surface overlap discussed above? If so, then the
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discussion above about the specified cutoff is wrong? I.e. you can
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specify a large cutoff than the surface/surface overlap to get
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cohesive interactions? If so, this should be explained up above.
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But an additional confusion is that the specied cutoff (Rc in diagram?)
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is a single number, but depedning on the orientiation of the 2
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particles they might have a suface/surface overlap at a much
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smaller value of Ri + Rj. So what is Rc then? - I added
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the following paragraph to address this.
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Note that F_n and F_t are functions of the surface separation
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\delta_n = d - (R_i + R_j).
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In this model, when (R_i + R_j) < d < (R_i + R_j) + r_c, that is,
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0 < \delta_n < r_c, the cohesive region of the two surfaces overlap
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and the two surfaces are attractive to each other.
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Note that F_n and F_t are functions of the surface separation \delta_n
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= d - (R_i + R_j). In this model, when (R_i + R_j) < d < (R_i + R_j)
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+ r_c, that is, 0 < \delta_n < r_c, the cohesive region of the two
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surfaces overlap and the two surfaces are attractive to each other.
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In "Fraige"_#Fraige, the tangential friction force between two
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particles that are in contact is modeled differently prior to gross
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@ -92,7 +90,6 @@ contact nor calculate the tangential deformation. Instead, we assume
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that gross sliding takes place as soon as two particles are in
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contact.
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The following coefficients must be defined for each pair of atom types
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via the "pair_coeff"_pair_coeff.html command as in the examples above,
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or in the data file read by the "read_data"_read_data.html command:
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@ -101,12 +98,8 @@ k_n (energy/distance^2 units)
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k_na (energy/distance^2 units) :ul
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Effectively, k_n and k_na are the slopes of the red lines in the plot
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above for force versus surface separation, for \delta_n < 0 and 0 < \delta_n < r_c
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respectively. (TRUNG: is this sentence correct? - it should read delta_n,
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instead of r)
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TRUNG: reminder to copy any change in this file
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to the pair polyhedron file as well (and vice versa)
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above for force versus surface separation, for \delta_n < 0 and 0 <
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\delta_n < r_c respectively.
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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@ -28,28 +28,11 @@ pair_coeff 1 1 100.0 1.0 :pre
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Style {body/rounded/polygon} is for use with 3d models of body
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particles of style {rounded/polyhedron}. It calculates pairwise
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body/body interactions as well as interactions between body and
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point-particles (modeled as spheres with a specified diameter).
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See "Section 6.14"_Section_howto.html#howto_14 of
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the manual and the "body"_body.html doc page for more details on using
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body rounded/polyhedron particles.
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TRUNG: I think we need a paragraph here about how body/sphere
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interactions are handled. Does this pair style only do body/body but
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allow for a body = sphere or rod or some other degenerate case? Or
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does this pair style allow you to model a simulation of mixed body and
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point particles, where point particles are spheroids. If so, does
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this pair style do body/body and body/point, and you use one of the
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other granular pair styles to do point/point? I.e. a pair hybrid
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model? Or does everything have to be defined as bodies. Actually
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this paragraph would make more sense in the body.txt file about how to
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create a model that includes non-body particles (spheres). And in
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this pair style file just a couple lines about which part of the
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interactions this pair style computes. Ditto in the pair body polygon
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file. - The pair style supports body/sphere and sphere/sphere
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given that all the atoms should be of body rounded/polyhedron.
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I updated the above paragraph and added examples in body.txt for
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specifying the special objects (i.e. spheres and rods).
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body/body interactions which can include body particles modeled as
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1-vertex spheres with a specified diameter. See "Section
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6.14"_Section_howto.html#howto_14 of the manual and the
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"body"_body.html doc page for more details on using body
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rounded/polyhedron particles.
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This pairwise interaction between the rounded polyhedra is described in
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"Wang"_#Wang, where a polyhedron does not have sharp corners and
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@ -61,7 +44,6 @@ in the data file read by the "read data"_read_data.html command. This
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is a discrete element model (DEM) which allows for multiple contact
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points.
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Note that when two particles interact, the effective surface of each
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polyhedron particle is displaced outward from each of its vertices,
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edges, and faces by half its sphere diameter. The interaction forces
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@ -69,8 +51,21 @@ and energies between two particles are defined with respect to the
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separation of their respective rounded surfaces, not by the separation
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of the vertices, edges, and faces themselves.
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This means that the specified cutoff in the pair_style command is
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the cutoff distance, r_c, for the surface separation, \delta_n (see figure below).
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This means that the specified cutoff in the pair_style command is the
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cutoff distance, r_c, for the surface separation, \delta_n (see figure
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below). This is the distance at which two particles no longer
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interact. If r_c is specified as 0.0, then it is a contact-only
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interaction. I.e. the two particles must overlap in order to exert a
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repulsive force on each other. If r_c > 0.0, then the force between
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two particles will be attractive for surface separations from 0 to
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r_c, and repulsive once the particles overlap.
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Note that unlike for other pair styles, the specified cutoff is not
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the distance between the centers of two particles at which they stop
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interacting. This center-to-center distance depends on the shape and
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size of the two particles and their relative orientation. LAMMPS
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takes that into account when computing the surface separation distance
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and applying the r_c cutoff.
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The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge,
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and edge-face overlaps are given by:
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@ -97,9 +92,8 @@ k_n (energy/distance^2 units)
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k_na (energy/distance^2 units) :ul
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Effectively, k_n and k_na are the slopes of the red lines in the plot
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above for force versus surface separation, for \delta_n < 0 and 0 < \delta_n < r_c
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respectively. (TRUNG: is this sentence correct? - it should read delta_n,
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instead of r)
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above for force versus surface separation, for \delta_n < 0 and 0 <
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\delta_n < r_c respectively.
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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@ -8,7 +8,7 @@ read_data data.body
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velocity all create 1.44 87287 loop geom
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pair_style body 5.0
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pair_style body/nparticle 5.0
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pair_coeff * * 1.0 1.0
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neighbor 0.5 bin
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@ -15,7 +15,7 @@
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#include <cstdio>
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#include <cstdlib>
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#include <cstring>
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#include "pair_body.h"
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#include "pair_body_nparticle.h"
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#include "math_extra.h"
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#include "atom.h"
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#include "atom_vec_body.h"
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@ -32,7 +32,7 @@ using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairBody::PairBody(LAMMPS *lmp) : Pair(lmp)
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PairBodyNparticle::PairBodyNparticle(LAMMPS *lmp) : Pair(lmp)
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{
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dmax = nmax = 0;
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discrete = NULL;
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@ -44,7 +44,7 @@ PairBody::PairBody(LAMMPS *lmp) : Pair(lmp)
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/* ---------------------------------------------------------------------- */
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PairBody::~PairBody()
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PairBodyNparticle::~PairBodyNparticle()
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{
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memory->destroy(discrete);
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memory->destroy(dnum);
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@ -66,7 +66,7 @@ PairBody::~PairBody()
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/* ---------------------------------------------------------------------- */
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void PairBody::compute(int eflag, int vflag)
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void PairBodyNparticle::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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int ni,nj,npi,npj,ifirst,jfirst;
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@ -336,7 +336,7 @@ void PairBody::compute(int eflag, int vflag)
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairBody::allocate()
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void PairBodyNparticle::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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@ -361,7 +361,7 @@ void PairBody::allocate()
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global settings
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------------------------------------------------------------------------- */
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void PairBody::settings(int narg, char **arg)
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void PairBodyNparticle::settings(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Illegal pair_style command");
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@ -381,7 +381,7 @@ void PairBody::settings(int narg, char **arg)
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairBody::coeff(int narg, char **arg)
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void PairBodyNparticle::coeff(int narg, char **arg)
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{
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if (narg < 4 || narg > 5)
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error->all(FLERR,"Incorrect args for pair coefficients");
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@ -415,12 +415,12 @@ void PairBody::coeff(int narg, char **arg)
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairBody::init_style()
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void PairBodyNparticle::init_style()
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{
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avec = (AtomVecBody *) atom->style_match("body");
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if (!avec) error->all(FLERR,"Pair body requires atom style body");
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if (!avec) error->all(FLERR,"Pair body/nparticle requires atom style body");
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if (strcmp(avec->bptr->style,"nparticle") != 0)
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error->all(FLERR,"Pair body requires body style nparticle");
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error->all(FLERR,"Pair body/nparticle requires body style nparticle");
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bptr = (BodyNparticle *) avec->bptr;
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neighbor->request(this,instance_me);
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@ -430,7 +430,7 @@ void PairBody::init_style()
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairBody::init_one(int i, int j)
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double PairBodyNparticle::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
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@ -459,7 +459,7 @@ double PairBody::init_one(int i, int j)
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store sub-particle space-frame displacements from COM in discrete list
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------------------------------------------------------------------------- */
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void PairBody::body2space(int i)
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void PairBodyNparticle::body2space(int i)
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{
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int ibonus = atom->body[i];
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AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
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@ -13,21 +13,21 @@
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#ifdef PAIR_CLASS
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PairStyle(body,PairBody)
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PairStyle(body/nparticle,PairBodyNparticle)
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#else
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#ifndef LMP_PAIR_BODY_H
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#define LMP_PAIR_BODY_H
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#ifndef LMP_PAIR_BODY_NPARTICLE_H
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#define LMP_PAIR_BODY_NPARTICLE_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairBody : public Pair {
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class PairBodyNparticle : public Pair {
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public:
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PairBody(class LAMMPS *);
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~PairBody();
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PairBodyNparticle(class LAMMPS *);
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~PairBodyNparticle();
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void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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