mirror of https://github.com/lammps/lammps.git
Merge pull request #962 from ndtrung81/body-dem
Discrete element models for the BODY package
This commit is contained in:
Steve Plimpton
GitHub
commit
5c21d2aff9
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@ -0,0 +1,13 @@
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\documentstyle[12pt]{article}
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\begin{document}
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\begin{eqnarray*}
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F_n &=& k_n \delta_n - c_n v_n, \qquad \delta_n \le 0 \\
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&=& -k_{na} \delta_n - c_n v_n, \qquad 0 < \delta_n \le r_c \\
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&=& 0 \qquad \qquad \qquad \qquad \delta_n > r_c \\
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F_t &=& \mu k_n \delta_n - c_t v_t, \qquad \delta_n \le 0 \\
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&=& 0 \qquad \qquad \qquad \qquad \delta_n > 0
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\end{eqnarray*}
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\end{document}
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@ -678,6 +678,8 @@ 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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@ -930,7 +932,9 @@ 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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|
|
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260
doc/src/body.txt
260
doc/src/body.txt
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|
@ -27,18 +27,16 @@ styles supported by LAMMPS are as follows. The name in the first
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column is used as the {bstyle} argument for the "atom_style
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body"_atom_style.html command.
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{nparticle} | rigid body with N sub-particles |
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{rounded/polygon} | 2d convex polygon with N vertices :tb(c=2,s=|)
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{nparticle} : rigid body with N sub-particles
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{rounded/polygon} : 2d polygons with N vertices
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{rounded/polyhedron} : 3d polyhedra with N vertices, E edges and F faces :tb(s=:)
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The body style determines what attributes are stored for each body and
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thus how they can be used to compute pairwise body/body or
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bond/non-body (point particle) interactions. More details of each
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style are described below.
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NOTE: The rounded/polygon style listed in the table above and
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described below has not yet been relesed in LAMMPS. It will be soon.
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We hope to add more styles in the future. See "Section
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More styles may be added in the future. See "Section
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10.12"_Section_modify.html#mod_12 for details on how to add a new body
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style to the code.
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@ -61,7 +59,7 @@ the simple particles.
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By contrast, when body particles are used, LAMMPS treats an entire
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body as a single particle for purposes of computing pairwise
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interactions, building neighbor lists, migrating particles between
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processors, outputting particles to a dump file, etc. This means that
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processors, output of particles to a dump file, etc. This means that
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interactions between pairs of bodies or between a body and non-body
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(point) particle need to be encoded in an appropriate pair style. If
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such a pair style were to mimic the "fix rigid"_fix_rigid.html model,
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@ -72,17 +70,20 @@ single body/body interaction was computed.
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Thus it only makes sense to use body particles and develop such a pair
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style, when particle/particle interactions are more complex than what
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the "fix rigid"_fix_rigid.html command can already calculate. For
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example, if particles have one or more of the following attributes:
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example, consider particles with one or more of the following
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attributes:
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represented by a surface mesh
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represented by a collection of geometric entities (e.g. planes + spheres)
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deformable
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internal stress that induces fragmentation :ul
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then the interaction between pairs of particles is likely to be more
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complex than the summation of simple sub-particle interactions. An
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example is contact or frictional forces between particles with planar
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surfaces that inter-penetrate.
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For these models, the interaction between pairs of particles is likely
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to be more complex than the summation of simple pairwise interactions.
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An example is contact or frictional forces between particles with
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planar surfaces that inter-penetrate. Likewise, the body particle may
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store internal state, such as a stress tensor used to compute a
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fracture criterion.
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These are additional LAMMPS commands that can be used with body
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particles of different styles
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@ -130,7 +131,9 @@ x1 y1 z1
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...
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xN yN zN :pre
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N is the number of sub-particles in the body particle. M = 6 + 3*N.
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where M = 6 + 3*N, and N is the number of sub-particles in the body
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particle.
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The integer line has a single value N. The floating point line(s)
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list 6 moments of inertia followed by the coordinates of the N
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sub-particles (x1 to zN) as 3N values. These values can be listed on
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@ -175,15 +178,18 @@ The {bflag2} argument is ignored.
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[Specifics of body style rounded/polygon:]
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NOTE: Aug 2016 - This body style has not yet been added to LAMMPS.
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The info below is a placeholder.
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The {rounded/polygon} body style represents body particles as a 2d
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polygon with a variable number of N vertices. This style can only be
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used for 2d models; see the "boundary"_boundary.html command. See the
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"pair_style body/rounded/polygon" doc page for a diagram of two
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squares with rounded circles at the vertices. Special cases for N = 1
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(circle) and N = 2 (rod with rounded ends) can also be specified.
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The {rounded/polygon} body style represents body particles as a convex
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polygon with a variable number N > 2 of vertices, which can only be
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used for 2d models. One example use of this body style is for 2d
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discrete element models, as described in "Fraige"_#Fraige. Similar to
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body style {nparticle}, the atom_style body command for this body
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style takes two additional arguments:
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One use of this body style is for 2d discrete element models, as
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described in "Fraige"_#body-Fraige.
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Similar to body style {nparticle}, the atom_style body command for
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this body style takes two additional arguments:
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atom_style body rounded/polygon Nmin Nmax
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Nmin = minimum # of vertices in any body in the system
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@ -203,17 +209,20 @@ x1 y1 z1
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...
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xN yN zN
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i j j k k ...
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radius :pre
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diameter :pre
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N is the number of vertices in the body particle. M = 6 + 3*N + 2*N +
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1. The integer line has a single value N. The floating point line(s)
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where M = 6 + 3*N + 2*N + 1, and N is the number of vertices in the
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body particle.
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The integer line has a single value N. The floating point line(s)
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list 6 moments of inertia followed by the coordinates of the N
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vertices (x1 to zN) as 3N values, followed by 2N vertex indices
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corresponding to the end points of the N edges, followed by a single
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radius value = the smallest circle encompassing the polygon. That
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last value is used to facilitate the body/body contact detection.
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These floating-point values can be listed on as many lines as you
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wish; see the "read_data"_read_data.html command for more details.
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vertices (x1 to zN) as 3N values (with z = 0.0 for each), followed by
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2N vertex indices corresponding to the end points of the N edges,
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followed by a single diameter value = the rounded diameter of the
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circle that surrounds each vertex. The diameter value can be different
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for each body particle. These floating-point values can be listed on
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as many lines as you wish; see the "read_data"_read_data.html command
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for more details.
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The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
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values consistent with the current orientation of the rigid body
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@ -225,8 +234,11 @@ from the center-of-mass of the body particle. The center-of-mass
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position of the particle is specified by the x,y,z values in the
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{Atoms} section of the data file.
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For example, the following information would specify a square
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particles whose edge length is sqrt(2):
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For example, the following information would specify a square particle
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whose edge length is sqrt(2) and rounded diameter is 1.0. The
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orientation of the square is aligned with the xy coordinate axes which
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is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
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1 1 4 0 0 0. Note that only Izz matters in 2D simulations.
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3 1 27
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4
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@ -235,12 +247,178 @@ particles whose edge length is sqrt(2):
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-0.7071 0.7071 0
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0.7071 0.7071 0
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0.7071 -0.7071 0
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0 1 1 2 2 3 3 0
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0 1
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1 2
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2 3
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3 0
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1.0 :pre
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A rod in 2D, whose length is 4.0, mass 1.0, rounded at two ends
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by circles of diameter 0.5, is specified as follows:
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1 1 13
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2
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1 1 1.33333 0 0 0
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-2 0 0
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2 0 0
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0.5 :pre
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A disk, whose diameter is 3.0, mass 1.0, is specified as follows:
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1 1 10
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1
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1 1 4.5 0 0 0
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0 0 0
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3.0 :pre
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The "pair_style body/rounded/polygon"_pair_body_rounded_polygon.html
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command can be used with this body style to compute body/body
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interactions.
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interactions. The "fix wall/body/polygon"_fix_wall_body_polygon.html
|
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command can be used with this body style to compute the interaction of
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body particles with a wall.
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:line
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[Specifics of body style rounded/polyhedron:]
|
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The {rounded/polyhedron} body style represents body particles as a 3d
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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 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"_#body-Wang.
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Similar to body style {rounded/polygon}, the atom_style body command
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for this body style takes two additional arguments:
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atom_style body rounded/polyhedron Nmin Nmax
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Nmin = minimum # of vertices in any body in the system
|
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Nmax = maximum # of vertices in any body in the system :pre
|
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|
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The Nmin and Nmax arguments are used to bound the size of data
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structures used internally by each particle.
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|
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When the "read_data"_read_data.html command reads a data file for this
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body style, the following information must be provided for each entry
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in the {Bodies} section of the data file:
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atom-ID 3 M
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N E F
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ixx iyy izz ixy ixz iyz
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x1 y1 z1
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...
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xN yN zN
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0 1
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1 2
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2 3
|
||||
...
|
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0 1 2 -1
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0 2 3 -1
|
||||
...
|
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1 2 3 4
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diameter :pre
|
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|
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where M = 6 + 3*N + 2*E + 4*F + 1, and N is the number of vertices in
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the body particle, E = number of edges, F = number of faces.
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|
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The integer line has three values: number of vertices (N), number of
|
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edges (E) and number of faces (F). The floating point line(s) list 6
|
||||
moments of inertia followed by the coordinates of the N vertices (x1
|
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to zN) as 3N values, followed by 2N vertex indices corresponding to
|
||||
the end points of the E edges, then 4*F vertex indices defining F
|
||||
faces. The last value is the diameter value = the rounded diameter of
|
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the sphere that surrounds each vertex. The diameter value can be
|
||||
different for each body particle. These floating-point values can be
|
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listed on as many lines as you wish; see the
|
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"read_data"_read_data.html command for more details. Because the
|
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maxmimum vertices per face is hard-coded to be 4
|
||||
(i.e. quadrilaterals), faces with more than 4 vertices need to be
|
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split into triangles or quadrilaterals. For triangular faces, the
|
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last vertex index should be set to -1.
|
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|
||||
The ordering of the 4 vertices within a face should follow
|
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the right-hand rule so that the normal vector of the face points
|
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outwards from the center of mass.
|
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|
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The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
|
||||
values consistent with the current orientation of the rigid body
|
||||
around its center of mass. The values are with respect to the
|
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simulation box XYZ axes, not with respect to the principal axes of the
|
||||
rigid body itself. LAMMPS performs the latter calculation internally.
|
||||
The coordinates of each vertex are specified as its x,y,z displacement
|
||||
from the center-of-mass of the body particle. The center-of-mass
|
||||
position of the particle is specified by the x,y,z values in the
|
||||
{Atoms} section of the data file.
|
||||
|
||||
For example, the following information would specify a cubic particle
|
||||
whose edge length is 2.0 and rounded diameter is 0.5.
|
||||
The orientation of the cube is aligned with the xyz coordinate axes
|
||||
which is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz
|
||||
iyz = 0.667 0.667 0.667 0 0 0.
|
||||
|
||||
1 3 79
|
||||
8 12 6
|
||||
0.667 0.667 0.667 0 0 0
|
||||
1 1 1
|
||||
1 -1 1
|
||||
-1 -1 1
|
||||
-1 1 1
|
||||
1 1 -1
|
||||
1 -1 -1
|
||||
-1 -1 -1
|
||||
-1 1 -1
|
||||
0 1
|
||||
1 2
|
||||
2 3
|
||||
3 0
|
||||
4 5
|
||||
5 6
|
||||
6 7
|
||||
7 4
|
||||
0 4
|
||||
1 5
|
||||
2 6
|
||||
3 7
|
||||
0 1 2 3
|
||||
4 5 6 7
|
||||
0 1 5 4
|
||||
1 2 6 5
|
||||
2 3 7 6
|
||||
3 0 4 7
|
||||
0.5 :pre
|
||||
|
||||
A rod in 3D, whose length is 4.0, mass 1.0 and rounded at two ends
|
||||
by circles of diameter 0.5, is specified as follows:
|
||||
|
||||
1 1 13
|
||||
2
|
||||
0 1.33333 1.33333 0 0 0
|
||||
-2 0 0
|
||||
2 0 0
|
||||
0.5 :pre
|
||||
|
||||
A sphere whose diameter is 3.0 and mass 1.0, is specified as follows:
|
||||
|
||||
1 1 10
|
||||
1
|
||||
0.9 0.9 0.9 0 0 0
|
||||
0 0 0
|
||||
3.0 :pre
|
||||
|
||||
The "pair_style
|
||||
body/rounded/polhedron"_pair_body_rounded_polyhedron.html command can
|
||||
be used with this body style to compute body/body interactions. The
|
||||
"fix wall/body/polyhedron"_fix_wall_body_polygon.html command can be
|
||||
used with this body style to compute the interaction of body particles
|
||||
with a wall.
|
||||
|
||||
:line
|
||||
|
||||
For output purposes via the "compute
|
||||
body/local"_compute_body_local.html and "dump local"_dump.html
|
||||
|
|
@ -257,10 +435,10 @@ the body particle itself. These values are calculated using the
|
|||
current COM and orientation of the body particle.
|
||||
|
||||
For images created by the "dump image"_dump_image.html command, if the
|
||||
{body} keyword is set, then each body particle is drawn as a convex
|
||||
polygon consisting of N line segments. Note that the line segments
|
||||
are drawn between the N vertices, which does not correspond exactly to
|
||||
the physical extent of the body (because the "pair_style
|
||||
{body} keyword is set, then each body particle is drawn as a polygon
|
||||
consisting of N line segments. Note that the line segments are drawn
|
||||
between the N vertices, which does not correspond exactly to the
|
||||
physical extent of the body (because the "pair_style
|
||||
rounded/polygon"_pair_body_rounded_polygon.html defines finite-size
|
||||
spheres at those point and the line segments between the spheres are
|
||||
tangent to the spheres). The drawn diameter of each line segment is
|
||||
|
|
@ -269,6 +447,10 @@ determined by the {bflag1} parameter for the {body} keyword. The
|
|||
|
||||
:line
|
||||
|
||||
:link(Fraige)
|
||||
:link(body-Fraige)
|
||||
[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
|
||||
Particuology, 6, 455 (2008).
|
||||
|
||||
:link(body-Wang)
|
||||
[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
|
||||
Matter, 13, 1 (2011).
|
||||
|
|
|
|||
|
|
@ -0,0 +1,104 @@
|
|||
"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
|
||||
|
||||
fix wall/body/polygon command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID wall/body/polygon k_n c_n c_t wallstyle args keyword values ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
wall/body/polygon = style name of this fix command :l
|
||||
k_n = normal repulsion strength (force/distance or pressure units) :l
|
||||
c_n = normal damping coefficient (force/distance or pressure units) :l
|
||||
c_t = tangential damping coefficient (force/distance or pressure units) :l
|
||||
wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
|
||||
args = list of arguments for a particular style :l
|
||||
{xplane} or {yplane} args = lo hi
|
||||
lo,hi = position of lower and upper plane (distance units), either can be NULL)
|
||||
{zcylinder} args = radius
|
||||
radius = cylinder radius (distance units) :pre
|
||||
zero or more keyword/value pairs may be appended to args :l
|
||||
keyword = {wiggle} :l
|
||||
{wiggle} values = dim amplitude period
|
||||
dim = {x} or {y} or {z}
|
||||
amplitude = size of oscillation (distance units)
|
||||
period = time of oscillation (time units) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all wall/body/polygon 1000.0 20.0 5.0 xplane -10.0 10.0
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix is for use with 2d models of body particles of style
|
||||
{rounded/polygon}. It bounds the simulation domain with wall(s). All
|
||||
particles in the group interact with the wall when they are close
|
||||
enough to touch it. The nature of the interaction between the wall
|
||||
and the polygon particles is the same as that between the polygon
|
||||
particles themselves, which is similar to a Hookean potential. See
|
||||
"Section 6.14"_Section_howto.html#howto_14 of the manual and the
|
||||
"body"_body.html doc page for more details on using body particles.
|
||||
|
||||
The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as
|
||||
those specified with the "pair_style
|
||||
body/rounded/polygon"_pair_body_rounded_polygon.html command.
|
||||
|
||||
The {wallstyle} can be planar or cylindrical. The 2 planar options
|
||||
specify a pair of walls in a dimension. Wall positions are given by
|
||||
{lo} and {hi}. Either of the values can be specified as NULL if a
|
||||
single wall is desired. For a {zcylinder} wallstyle, the cylinder's
|
||||
axis is at x = y = 0.0, and the radius of the cylinder is specified.
|
||||
|
||||
Optionally, the wall can be moving, if the {wiggle} keyword is
|
||||
appended.
|
||||
|
||||
For the {wiggle} keyword, the wall oscillates sinusoidally, similar to
|
||||
the oscillations of particles which can be specified by the "fix
|
||||
move"_fix_move.html command. This is useful in packing simulations of
|
||||
particles. The arguments to the {wiggle} keyword specify a dimension
|
||||
for the motion, as well as it's {amplitude} and {period}. Note that
|
||||
if the dimension is in the plane of the wall, this is effectively a
|
||||
shearing motion. If the dimension is perpendicular to the wall, it is
|
||||
more of a shaking motion. A {zcylinder} wall can only be wiggled in
|
||||
the z dimension.
|
||||
|
||||
Each timestep, the position of a wiggled wall in the appropriate {dim}
|
||||
is set according to this equation:
|
||||
|
||||
position = coord + A - A cos (omega * delta) :pre
|
||||
|
||||
where {coord} is the specified initial position of the wall, {A} is
|
||||
the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time
|
||||
elapsed since the fix was specified. The velocity of the wall is set
|
||||
to the derivative of this expression.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||
fix. No global or per-atom quantities are stored by this fix for
|
||||
access by various "output commands"_Section_howto.html#howto_15. No
|
||||
parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the BODY package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Any dimension (xy) that has a wall must be non-periodic.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"atom_style body"_atom_style.html, "pair_style
|
||||
body/rounded/polygon"_pair_body_rounded_polygon.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -0,0 +1,103 @@
|
|||
"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
|
||||
|
||||
fix wall/body/polyhedron command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID wall/body/polyhedron k_n c_n c_t wallstyle args keyword values ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
wall/body/polyhedron = style name of this fix command :l
|
||||
k_n = normal repulsion strength (force/distance units or pressure units - see discussion below) :l
|
||||
c_n = normal damping coefficient (force/distance units or pressure units - see discussion below) :l
|
||||
c_t = tangential damping coefficient (force/distance units or pressure units - see discussion below) :l
|
||||
wallstyle = {xplane} or {yplane} or {zplane} or {zcylinder} :l
|
||||
args = list of arguments for a particular style :l
|
||||
{xplane} or {yplane} args = lo hi
|
||||
lo,hi = position of lower and upper plane (distance units), either can be NULL)
|
||||
{zcylinder} args = radius
|
||||
radius = cylinder radius (distance units) :pre
|
||||
zero or more keyword/value pairs may be appended to args :l
|
||||
keyword = {wiggle} :l
|
||||
{wiggle} values = dim amplitude period
|
||||
dim = {x} or {y} or {z}
|
||||
amplitude = size of oscillation (distance units)
|
||||
period = time of oscillation (time units) :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all wall/body/polyhedron 1000.0 20.0 5.0 xplane -10.0 10.0
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix is for use with 3d models of body particles of style
|
||||
{rounded/polyhedron}. It bounds the simulation domain with wall(s).
|
||||
All particles in the group interact with the wall when they are close
|
||||
enough to touch it. The nature of the interaction between the wall
|
||||
and the polygon particles is the same as that between the polygon
|
||||
particles themselves, which is similar to a Hookean potential. See
|
||||
"Section 6.14"_Section_howto.html#howto_14 of the manual and the
|
||||
"body"_body.html doc page for more details on using body particles.
|
||||
|
||||
The parameters {k_n}, {c_n}, {c_t} have the same meaning and units as
|
||||
those specified with the "pair_style
|
||||
body/rounded/polyhedron"_pair_body_rounded_polyhedron.html command.
|
||||
|
||||
The {wallstyle} can be planar or cylindrical. The 3 planar options
|
||||
specify a pair of walls in a dimension. Wall positions are given by
|
||||
{lo} and {hi}. Either of the values can be specified as NULL if a
|
||||
single wall is desired. For a {zcylinder} wallstyle, the cylinder's
|
||||
axis is at x = y = 0.0, and the radius of the cylinder is specified.
|
||||
|
||||
Optionally, the wall can be moving, if the {wiggle} keyword is appended.
|
||||
|
||||
For the {wiggle} keyword, the wall oscillates sinusoidally, similar to
|
||||
the oscillations of particles which can be specified by the "fix
|
||||
move"_fix_move.html command. This is useful in packing simulations of
|
||||
particles. The arguments to the {wiggle} keyword specify a dimension
|
||||
for the motion, as well as it's {amplitude} and {period}. Note that
|
||||
if the dimension is in the plane of the wall, this is effectively a
|
||||
shearing motion. If the dimension is perpendicular to the wall, it is
|
||||
more of a shaking motion. A {zcylinder} wall can only be wiggled in
|
||||
the z dimension.
|
||||
|
||||
Each timestep, the position of a wiggled wall in the appropriate {dim}
|
||||
is set according to this equation:
|
||||
|
||||
position = coord + A - A cos (omega * delta) :pre
|
||||
|
||||
where {coord} is the specified initial position of the wall, {A} is
|
||||
the {amplitude}, {omega} is 2 PI / {period}, and {delta} is the time
|
||||
elapsed since the fix was specified. The velocity of the wall is set
|
||||
to the derivative of this expression.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
None of the "fix_modify"_fix_modify.html options are relevant to this
|
||||
fix. No global or per-atom quantities are stored by this fix for
|
||||
access by various "output commands"_Section_howto.html#howto_15. No
|
||||
parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the BODY package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Any dimension (xyz) that has a wall must be non-periodic.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"atom_style body"_atom_style.html, "pair_style
|
||||
body/rounded/polyhedron"_pair_body_rounded_polyhedron.html
|
||||
|
||||
[Default:] none
|
||||
|
|
@ -283,6 +283,8 @@ fix_vector.html
|
|||
fix_viscosity.html
|
||||
fix_viscous.html
|
||||
fix_wall.html
|
||||
fix_wall_body_polygon.html
|
||||
fix_wall_body_polyhedron.html
|
||||
fix_wall_ees.html
|
||||
fix_wall_gran.html
|
||||
fix_wall_gran_region.html
|
||||
|
|
@ -424,8 +426,9 @@ pair_agni.html
|
|||
pair_airebo.html
|
||||
pair_awpmd.html
|
||||
pair_beck.html
|
||||
pair_body.html
|
||||
pair_body_nparticle.html
|
||||
pair_body_rounded_polygon.html
|
||||
pair_body_rounded_polyhedron.html
|
||||
pair_bop.html
|
||||
pair_born.html
|
||||
pair_brownian.html
|
||||
|
|
|
|||
|
|
@ -10,21 +10,21 @@ pair_style body command :h3
|
|||
|
||||
[Syntax:]
|
||||
|
||||
pair_style body cutoff :pre
|
||||
pair_style body/nparticle cutoff :pre
|
||||
|
||||
cutoff = global cutoff for interactions (distance units)
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style body 3.0
|
||||
pair_style body/nparticle 3.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_coeff 1 1 1.0 1.5 2.5 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {body} is for use with body particles and calculates pairwise
|
||||
body/body interactions as well as interactions between body and
|
||||
point-particles. See "Section 6.14"_Section_howto.html#howto_14
|
||||
Style {body/nparticle} is for use with body particles and calculates
|
||||
pairwise body/body interactions as well as interactions between body
|
||||
and point-particles. See "Section 6.14"_Section_howto.html#howto_14
|
||||
of the manual and the "body"_body.html doc page for more details on
|
||||
using body particles.
|
||||
|
||||
|
|
@ -8,12 +8,127 @@
|
|||
|
||||
pair_style body/rounded/polygon command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style body/rounded/polygon c_n c_t mu delta_ua cutoff :pre
|
||||
|
||||
c_n = normal damping coefficient
|
||||
c_t = tangential damping coefficient
|
||||
mu = normal friction coefficient during gross sliding
|
||||
delta_ua = multiple contact scaling factor
|
||||
cutoff = global separation cutoff for interactions (distance units), see below for definition :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style body/rounded/polygon 20.0 5.0 0.0 1.0 0.5
|
||||
pair_coeff * * 100.0 1.0
|
||||
pair_coeff 1 1 100.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Note: This feature is not yet implemented.
|
||||
Style {body/rounded/polygon} is for use with 2d models of body
|
||||
particles of style {rounded/polygon}. It calculates pairwise
|
||||
body/body interactions which can include body particles modeled as
|
||||
1-vertex circular disks with a specified diameter. See "Section
|
||||
6.14"_Section_howto.html#howto_14 of the manual and the
|
||||
"body"_body.html doc page for more details on using body
|
||||
rounded/polygon particles.
|
||||
|
||||
This pairwise interaction between rounded polygons is described in
|
||||
"Fraige"_#pair-Fraige, where a polygon does not have sharp corners,
|
||||
but is rounded at its vertices by circles centered on each vertex with
|
||||
a specified diameter. The edges of the polygon are defined between
|
||||
pairs of adjacent vertices. The circle diameter for each polygon is
|
||||
specified in the data file read by the "read data"_read_data.html
|
||||
command. This is a 2d discrete element model (DEM) which allows for
|
||||
multiple contact points.
|
||||
|
||||
Note that when two particles interact, the effective surface of each
|
||||
polygon particle is displaced outward from each of its vertices and
|
||||
edges by half its circle diameter (as in the diagram below of a gray
|
||||
and yellow square particle). The interaction forces and energies
|
||||
between two particles are defined with respect to the separation of
|
||||
their respective rounded surfaces, not by the separation of the
|
||||
vertices and edges themselves.
|
||||
|
||||
This means that the specified cutoff in the pair_style command is the
|
||||
cutoff distance, r_c, for the surface separation, \delta_n (see figure
|
||||
below). This is the distance at which two particles no longer
|
||||
interact. If r_c is specified as 0.0, then it is a contact-only
|
||||
interaction. I.e. the two particles must overlap in order to exert a
|
||||
repulsive force on each other. If r_c > 0.0, then the force between
|
||||
two particles will be attractive for surface separations from 0 to
|
||||
r_c, and repulsive once the particles overlap.
|
||||
|
||||
Note that unlike for other pair styles, the specified cutoff is not
|
||||
the distance between the centers of two particles at which they stop
|
||||
interacting. This center-to-center distance depends on the shape and
|
||||
size of the two particles and their relative orientation. LAMMPS
|
||||
takes that into account when computing the surface separation distance
|
||||
and applying the r_c cutoff.
|
||||
|
||||
The forces between vertex-vertex, vertex-edge, and edge-edge overlaps
|
||||
are given by:
|
||||
|
||||
:c,image(Eqs/pair_body_rounded.jpg)
|
||||
|
||||
:c,image(JPG/pair_body_rounded.jpg)
|
||||
|
||||
Note that F_n and F_t are functions of the surface separation \delta_n
|
||||
= d - (R_i + R_j). In this model, when (R_i + R_j) < d < (R_i + R_j)
|
||||
+ r_c, that is, 0 < \delta_n < r_c, the cohesive region of the two
|
||||
surfaces overlap and the two surfaces are attractive to each other.
|
||||
|
||||
In "Fraige"_#pair-Fraige, the tangential friction force between two
|
||||
particles that are in contact is modeled differently prior to gross
|
||||
sliding (i.e. static friction) and during gross-sliding (kinetic
|
||||
friction). The latter takes place when the tangential deformation
|
||||
exceeds the Coulomb frictional limit. In the current implementation,
|
||||
however, we do not take into account frictional history, i.e. we do
|
||||
not keep track of how many time steps the two particles have been in
|
||||
contact nor calculate the tangential deformation. Instead, we assume
|
||||
that gross sliding takes place as soon as two particles are in
|
||||
contact.
|
||||
|
||||
The following coefficients must be defined for each pair of atom types
|
||||
via the "pair_coeff"_pair_coeff.html command as in the examples above,
|
||||
or in the data file read by the "read_data"_read_data.html command:
|
||||
|
||||
k_n (energy/distance^2 units)
|
||||
k_na (energy/distance^2 units) :ul
|
||||
|
||||
Effectively, k_n and k_na are the slopes of the red lines in the plot
|
||||
above for force versus surface separation, for \delta_n < 0 and 0 <
|
||||
\delta_n < r_c respectively.
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
mix, shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to "binary restart
|
||||
files"_restart.html. Thus, you need to re-specify the pair_style and
|
||||
pair_coeff commands 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.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
These pair styles are part of the BODY package. They are only enabled
|
||||
if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
This pair style requires the "newton"_newton.html setting to be "on"
|
||||
for pair interactions.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style body"_pair_body.html
|
||||
"pair_coeff"_pair_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:link(pair-Fraige)
|
||||
[(Fraige)] F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
|
||||
Particuology, 6, 455 (2008).
|
||||
|
|
|
|||
|
|
@ -0,0 +1,130 @@
|
|||
"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 body/rounded/polyhedron command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style body/rounded/polyhedron c_n c_t mu delta_ua cutoff :pre
|
||||
|
||||
c_n = normal damping coefficient
|
||||
c_t = tangential damping coefficient
|
||||
mu = normal friction coefficient during gross sliding
|
||||
delta_ua = multiple contact scaling factor
|
||||
cutoff = global separation cutoff for interactions (distance units), see below for definition :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style body/rounded/polyhedron 20.0 5.0 0.0 1.0 0.5
|
||||
pair_coeff * * 100.0 1.0
|
||||
pair_coeff 1 1 100.0 1.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Style {body/rounded/polygon} is for use with 3d models of body
|
||||
particles of style {rounded/polyhedron}. It calculates pairwise
|
||||
body/body interactions which can include body particles modeled as
|
||||
1-vertex spheres with a specified diameter. See "Section
|
||||
6.14"_Section_howto.html#howto_14 of the manual and the
|
||||
"body"_body.html doc page for more details on using body
|
||||
rounded/polyhedron particles.
|
||||
|
||||
This pairwise interaction between the rounded polyhedra is described
|
||||
in "Wang"_#pair-Wang, where a polyhedron does not have sharp corners
|
||||
and edges, but is rounded at its vertices and edges by spheres
|
||||
centered on each vertex with a specified diameter. The edges if the
|
||||
polyhedron are defined between pairs of adjacent vertices. Its faces
|
||||
are defined by a loop of edges. The sphere diameter for each polygon
|
||||
is specified in the data file read by the "read data"_read_data.html
|
||||
command. This is a discrete element model (DEM) which allows for
|
||||
multiple contact points.
|
||||
|
||||
Note that when two particles interact, the effective surface of each
|
||||
polyhedron particle is displaced outward from each of its vertices,
|
||||
edges, and faces by half its sphere diameter. The interaction forces
|
||||
and energies between two particles are defined with respect to the
|
||||
separation of their respective rounded surfaces, not by the separation
|
||||
of the vertices, edges, and faces themselves.
|
||||
|
||||
This means that the specified cutoff in the pair_style command is the
|
||||
cutoff distance, r_c, for the surface separation, \delta_n (see figure
|
||||
below). This is the distance at which two particles no longer
|
||||
interact. If r_c is specified as 0.0, then it is a contact-only
|
||||
interaction. I.e. the two particles must overlap in order to exert a
|
||||
repulsive force on each other. If r_c > 0.0, then the force between
|
||||
two particles will be attractive for surface separations from 0 to
|
||||
r_c, and repulsive once the particles overlap.
|
||||
|
||||
Note that unlike for other pair styles, the specified cutoff is not
|
||||
the distance between the centers of two particles at which they stop
|
||||
interacting. This center-to-center distance depends on the shape and
|
||||
size of the two particles and their relative orientation. LAMMPS
|
||||
takes that into account when computing the surface separation distance
|
||||
and applying the r_c cutoff.
|
||||
|
||||
The forces between vertex-vertex, vertex-edge, vertex-face, edge-edge,
|
||||
and edge-face overlaps are given by:
|
||||
|
||||
:c,image(Eqs/pair_body_rounded.jpg)
|
||||
|
||||
:c,image(JPG/pair_body_rounded.jpg)
|
||||
|
||||
In "Wang"_#pair-Wang, the tangential friction force between two
|
||||
particles that are in contact is modeled differently prior to gross
|
||||
sliding (i.e. static friction) and during gross-sliding (kinetic
|
||||
friction). The latter takes place when the tangential deformation
|
||||
exceeds the Coulomb frictional limit. In the current implementation,
|
||||
however, we do not take into account frictional history, i.e. we do
|
||||
not keep track of how many time steps the two particles have been in
|
||||
contact nor calculate the tangential deformation. Instead, we assume
|
||||
that gross sliding takes place as soon as two particles are in
|
||||
contact.
|
||||
|
||||
The following coefficients must be defined for each pair of atom types
|
||||
via the "pair_coeff"_pair_coeff.html command as in the examples above,
|
||||
or in the data file read by the "read_data"_read_data.html command:
|
||||
|
||||
k_n (energy/distance^2 units)
|
||||
k_na (energy/distance^2 units) :ul
|
||||
|
||||
Effectively, k_n and k_na are the slopes of the red lines in the plot
|
||||
above for force versus surface separation, for \delta_n < 0 and 0 <
|
||||
\delta_n < r_c respectively.
|
||||
|
||||
[Mixing, shift, table, tail correction, restart, rRESPA info]:
|
||||
|
||||
This pair style does not support the "pair_modify"_pair_modify.html
|
||||
mix, shift, table, and tail options.
|
||||
|
||||
This pair style does not write its information to "binary restart
|
||||
files"_restart.html. Thus, you need to re-specify the pair_style and
|
||||
pair_coeff commands 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.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
These pair styles are part of the BODY package. They are only enabled
|
||||
if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
This pair style requires the "newton"_newton.html setting to be "on"
|
||||
for pair interactions.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:link(pair-Wang)
|
||||
[(Wang)] J. Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular
|
||||
Matter, 13, 1 (2011).
|
||||
|
||||
|
|
@ -0,0 +1,76 @@
|
|||
LAMMPS data file for polygons: cubes, moment of inertia I = m edge^2/ 6
|
||||
2 atoms
|
||||
2 bodies
|
||||
1 atom types
|
||||
0 6 xlo xhi
|
||||
0 6 ylo yhi
|
||||
0 6 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 1 1.5 1.5 1.5
|
||||
2 1 1 1 4.0 4.0 4.0
|
||||
|
||||
Bodies
|
||||
|
||||
1 3 79
|
||||
8 12 6
|
||||
0.667 0.667 0.667 0 0 0
|
||||
1 1 1
|
||||
1 -1 1
|
||||
-1 -1 1
|
||||
-1 1 1
|
||||
1 1 -1
|
||||
1 -1 -1
|
||||
-1 -1 -1
|
||||
-1 1 -1
|
||||
0 1
|
||||
1 2
|
||||
2 3
|
||||
3 0
|
||||
4 5
|
||||
5 6
|
||||
6 7
|
||||
7 4
|
||||
0 4
|
||||
1 5
|
||||
2 6
|
||||
3 7
|
||||
0 1 2 3
|
||||
4 5 6 7
|
||||
0 1 5 4
|
||||
1 2 6 5
|
||||
2 3 7 6
|
||||
3 0 4 7
|
||||
0.5
|
||||
2 3 79
|
||||
8 12 6
|
||||
0.667 0.667 0.667 0 0 0
|
||||
1 1 1
|
||||
1 -1 1
|
||||
-1 -1 1
|
||||
-1 1 1
|
||||
1 1 -1
|
||||
1 -1 -1
|
||||
-1 -1 -1
|
||||
-1 1 -1
|
||||
0 1
|
||||
1 2
|
||||
2 3
|
||||
3 0
|
||||
4 5
|
||||
5 6
|
||||
6 7
|
||||
7 4
|
||||
0 4
|
||||
1 5
|
||||
2 6
|
||||
3 7
|
||||
0 1 2 3
|
||||
4 5 6 7
|
||||
0 1 5 4
|
||||
1 2 6 5
|
||||
2 3 7 6
|
||||
3 0 4 7
|
||||
0.5
|
||||
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
LAMMPS data file for polygons: squares of edge length L: Izz = 1/6mL^2
|
||||
2 atoms
|
||||
2 bodies
|
||||
1 atom types
|
||||
0 12 xlo xhi
|
||||
0 12 ylo yhi
|
||||
-0.5 0.5 zlo zhi
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 1 4 5 0
|
||||
2 1 1 1 9 6 0
|
||||
|
||||
Bodies
|
||||
|
||||
1 1 19
|
||||
4
|
||||
1 1 2.67 0 0 0
|
||||
-2 -2 0
|
||||
-2 2 0
|
||||
2 2 0
|
||||
2 -2 0
|
||||
0.5
|
||||
2 1 19
|
||||
4
|
||||
1 1 2.67 0 0 0
|
||||
-2 -2 0
|
||||
-2 2 0
|
||||
2 2 0
|
||||
2 -2 0
|
||||
0.5
|
||||
|
||||
|
|
@ -8,7 +8,7 @@ read_data data.body
|
|||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style body 5.0
|
||||
pair_style body/nparticle 5.0
|
||||
pair_coeff * * 1.0 1.0
|
||||
|
||||
neighbor 0.5 bin
|
||||
|
|
|
|||
|
|
@ -0,0 +1,53 @@
|
|||
# 3d rounded cubes
|
||||
|
||||
variable r index 3
|
||||
variable steps index 10000
|
||||
|
||||
units lj
|
||||
dimension 3
|
||||
|
||||
atom_style body rounded/polyhedron 1 10
|
||||
|
||||
read_data data.cubes
|
||||
|
||||
replicate $r $r $r
|
||||
|
||||
velocity all create 1.2 187287 dist gaussian mom yes rot yes
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 1
|
||||
variable c_n equal 20
|
||||
variable c_t equal 5
|
||||
variable mu equal 0
|
||||
variable A_ua equal 1
|
||||
|
||||
pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#fix 1 all nve/body
|
||||
fix 1 all nvt/body temp 1.2 1.2 0.1
|
||||
#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0
|
||||
|
||||
compute p2 all pressure 1_temp
|
||||
|
||||
#compute 1 all body/local id 1 2 3
|
||||
#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type &
|
||||
# zoom 1.5 adiam 1.5 body type 0 0 view 60 15
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
thermo_style custom step ke pe etotal c_p2 c_1_temp
|
||||
|
||||
thermo 1000
|
||||
|
||||
run ${steps}
|
||||
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
# pouring 3d rounded polyhedron bodies
|
||||
|
||||
variable steps index 6000
|
||||
|
||||
units lj
|
||||
boundary p p fm
|
||||
comm_modify vel yes
|
||||
|
||||
atom_style body rounded/polyhedron 1 8
|
||||
atom_modify map array
|
||||
|
||||
region reg block 0 50 0 50 0 50 units box
|
||||
create_box 4 reg
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 5
|
||||
variable c_n equal 20
|
||||
variable c_t equal 5
|
||||
variable mu equal 0
|
||||
variable A_ua equal 1
|
||||
|
||||
pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/body
|
||||
fix 2 all gravity 1.0 spherical 0.0 -180.0
|
||||
|
||||
molecule object molecule.cube molecule.tetra toff 1 &
|
||||
molecule.rod3d toff 2 molecule.point3d toff 3
|
||||
|
||||
region slab block 5 45 5 45 25 35 units box
|
||||
fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object &
|
||||
molfrac 0.25 0.25 0.25 0.25
|
||||
|
||||
fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL
|
||||
|
||||
#compute 1 all body/local type 1 2 3
|
||||
#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
#dump 10 all custom 1000 tmp.dump id type x y z radius
|
||||
|
||||
thermo_style custom step atoms ke pe etotal press
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type &
|
||||
# zoom 1.5 adiam 1.5 body type 0 0 view 75 15
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
run ${steps}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
# 2d rounded polygon bodies
|
||||
|
||||
variable r index 4
|
||||
variable steps index 100000
|
||||
variable T index 0.5
|
||||
variable P index 0.1
|
||||
variable seed index 980411
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
|
||||
atom_style body rounded/polygon 1 6
|
||||
atom_modify map array
|
||||
read_data data.squares
|
||||
|
||||
replicate $r $r 1
|
||||
|
||||
velocity all create $T ${seed} dist gaussian mom yes rot yes
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 2
|
||||
variable c_n equal 1
|
||||
variable c_t equal 1
|
||||
variable mu equal 0.1
|
||||
variable delta_ua equal 0.5
|
||||
|
||||
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#fix 1 all nve/body
|
||||
#fix 1 all nvt/body temp $T $T 1.0
|
||||
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 &
|
||||
y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
||||
|
||||
fix 2 all enforce2d
|
||||
|
||||
#compute 1 all body/local id 1 2 3
|
||||
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
thermo_style custom step ke pe etotal press
|
||||
thermo 1000
|
||||
|
||||
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 &
|
||||
# adiam 1.5 body type 0 0
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
run ${steps}
|
||||
|
|
@ -0,0 +1,57 @@
|
|||
# 2d rounded polygon bodies
|
||||
|
||||
variable r index 4
|
||||
variable steps index 100000
|
||||
variable T index 0.5
|
||||
variable P index 0.1
|
||||
variable seed index 980411
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
|
||||
atom_style body rounded/polygon 1 6
|
||||
atom_modify map array
|
||||
read_data data.squares
|
||||
|
||||
replicate $r $r 1
|
||||
|
||||
velocity all create $T ${seed} dist gaussian mom yes rot yes
|
||||
|
||||
change_box all boundary p f p
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 2
|
||||
variable c_n equal 0.1
|
||||
variable c_t equal 0.1
|
||||
variable mu equal 0.1
|
||||
variable delta_ua equal 0.5
|
||||
|
||||
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#fix 1 all nve/body
|
||||
#fix 1 all nvt/body temp $T $T 1.0
|
||||
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
|
||||
|
||||
fix 2 all enforce2d
|
||||
fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
|
||||
|
||||
#compute 1 all body/local id 1 2 3
|
||||
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
thermo_style custom step ke pe etotal press
|
||||
thermo 1000
|
||||
|
||||
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 &
|
||||
# adiam 1.5 body type 0 0
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
run ${steps}
|
||||
|
|
@ -0,0 +1,125 @@
|
|||
LAMMPS (29 Jun 2018)
|
||||
# 3d rounded cubes
|
||||
|
||||
variable r index 3
|
||||
variable steps index 10000
|
||||
|
||||
units lj
|
||||
dimension 3
|
||||
|
||||
atom_style body rounded/polyhedron 1 10
|
||||
|
||||
read_data data.cubes
|
||||
orthogonal box = (0 0 0) to (6 6 6)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
2 bodies
|
||||
|
||||
replicate $r $r $r
|
||||
replicate 3 $r $r
|
||||
replicate 3 3 $r
|
||||
replicate 3 3 3
|
||||
orthogonal box = (0 0 0) to (18 18 18)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
54 atoms
|
||||
Time spent = 0.000217915 secs
|
||||
|
||||
velocity all create 1.2 187287 dist gaussian mom yes rot yes
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 1
|
||||
variable c_n equal 20
|
||||
variable c_t equal 5
|
||||
variable mu equal 0
|
||||
variable A_ua equal 1
|
||||
|
||||
pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 0 1 0.5
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
pair_coeff * * 100 ${k_na}
|
||||
pair_coeff * * 100 1
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#fix 1 all nve/body
|
||||
fix 1 all nvt/body temp 1.2 1.2 0.1
|
||||
#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0
|
||||
|
||||
compute p2 all pressure 1_temp
|
||||
|
||||
#compute 1 all body/local id 1 2 3
|
||||
#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
thermo_style custom step ke pe etotal c_p2 c_1_temp
|
||||
|
||||
thermo 1000
|
||||
|
||||
run ${steps}
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.9641
|
||||
ghost atom cutoff = 3.9641
|
||||
binsize = 1.98205, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair body/rounded/polyhedron, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.952 | 4.952 | 4.952 Mbytes
|
||||
Step KinEng PotEng TotEng c_p2 c_1_temp
|
||||
0 1.7666667 0 1.7666667 0.01090535 0.59439252
|
||||
1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694
|
||||
2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624
|
||||
3000 3.090491 0.16511199 3.255603 0.018691142 1.23672
|
||||
4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839
|
||||
5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154
|
||||
6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839
|
||||
7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326
|
||||
8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056
|
||||
9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914
|
||||
10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679
|
||||
Loop time of 38.5686 on 1 procs for 10000 steps with 54 atoms
|
||||
|
||||
Performance: 22401.653 tau/day, 259.278 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 38.426 | 38.426 | 38.426 | 0.0 | 99.63
|
||||
Neigh | 0.0043154 | 0.0043154 | 0.0043154 | 0.0 | 0.01
|
||||
Comm | 0.047616 | 0.047616 | 0.047616 | 0.0 | 0.12
|
||||
Output | 0.00017595 | 0.00017595 | 0.00017595 | 0.0 | 0.00
|
||||
Modify | 0.082948 | 0.082948 | 0.082948 | 0.0 | 0.22
|
||||
Other | | 0.007761 | | | 0.02
|
||||
|
||||
Nlocal: 54 ave 54 max 54 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 96 ave 96 max 96 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 100
|
||||
Ave neighs/atom = 1.85185
|
||||
Neighbor list builds = 268
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:38
|
||||
|
|
@ -0,0 +1,125 @@
|
|||
LAMMPS (29 Jun 2018)
|
||||
# 3d rounded cubes
|
||||
|
||||
variable r index 3
|
||||
variable steps index 10000
|
||||
|
||||
units lj
|
||||
dimension 3
|
||||
|
||||
atom_style body rounded/polyhedron 1 10
|
||||
|
||||
read_data data.cubes
|
||||
orthogonal box = (0 0 0) to (6 6 6)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
2 bodies
|
||||
|
||||
replicate $r $r $r
|
||||
replicate 3 $r $r
|
||||
replicate 3 3 $r
|
||||
replicate 3 3 3
|
||||
orthogonal box = (0 0 0) to (18 18 18)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
54 atoms
|
||||
Time spent = 0.00103807 secs
|
||||
|
||||
velocity all create 1.2 187287 dist gaussian mom yes rot yes
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 1
|
||||
variable c_n equal 20
|
||||
variable c_t equal 5
|
||||
variable mu equal 0
|
||||
variable A_ua equal 1
|
||||
|
||||
pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 0 1 0.5
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
pair_coeff * * 100 ${k_na}
|
||||
pair_coeff * * 100 1
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#fix 1 all nve/body
|
||||
fix 1 all nvt/body temp 1.2 1.2 0.1
|
||||
#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0
|
||||
|
||||
compute p2 all pressure 1_temp
|
||||
|
||||
#compute 1 all body/local id 1 2 3
|
||||
#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
thermo_style custom step ke pe etotal c_p2 c_1_temp
|
||||
|
||||
thermo 1000
|
||||
|
||||
run ${steps}
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3.9641
|
||||
ghost atom cutoff = 3.9641
|
||||
binsize = 1.98205, bins = 10 10 10
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair body/rounded/polyhedron, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.879 | 5.068 | 5.256 Mbytes
|
||||
Step KinEng PotEng TotEng c_p2 c_1_temp
|
||||
0 1.7666667 0 1.7666667 0.01090535 0.59439252
|
||||
1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694
|
||||
2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624
|
||||
3000 3.090491 0.16511199 3.255603 0.018691142 1.23672
|
||||
4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839
|
||||
5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154
|
||||
6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839
|
||||
7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326
|
||||
8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056
|
||||
9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914
|
||||
10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679
|
||||
Loop time of 20.5306 on 4 procs for 10000 steps with 54 atoms
|
||||
|
||||
Performance: 42083.509 tau/day, 487.078 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.5288 | 10.878 | 19.952 | 159.0 | 52.98
|
||||
Neigh | 0.0014424 | 0.0016552 | 0.0021195 | 0.7 | 0.01
|
||||
Comm | 0.50623 | 9.5805 | 12.93 | 169.4 | 46.66
|
||||
Output | 0.00011921 | 0.00014341 | 0.00021386 | 0.0 | 0.00
|
||||
Modify | 0.044663 | 0.047684 | 0.05382 | 1.6 | 0.23
|
||||
Other | | 0.023 | | | 0.11
|
||||
|
||||
Nlocal: 13.5 ave 17 max 9 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
Nghost: 63.5 ave 68 max 58 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 25 ave 38 max 6 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 100
|
||||
Ave neighs/atom = 1.85185
|
||||
Neighbor list builds = 268
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:20
|
||||
|
|
@ -0,0 +1,138 @@
|
|||
LAMMPS (29 Jun 2018)
|
||||
# pouring 3d rounded polyhedron bodies
|
||||
|
||||
variable steps index 6000
|
||||
|
||||
units lj
|
||||
boundary p p fm
|
||||
comm_modify vel yes
|
||||
|
||||
atom_style body rounded/polyhedron 1 8
|
||||
atom_modify map array
|
||||
|
||||
region reg block 0 50 0 50 0 50 units box
|
||||
create_box 4 reg
|
||||
Created orthogonal box = (0 0 0) to (50 50 50)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 5
|
||||
variable c_n equal 20
|
||||
variable c_t equal 5
|
||||
variable mu equal 0
|
||||
variable A_ua equal 1
|
||||
|
||||
pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
|
||||
pair_style body/rounded/polyhedron 20 5 0 1 0.5
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
pair_coeff * * 100 ${k_na}
|
||||
pair_coeff * * 100 5
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/body
|
||||
fix 2 all gravity 1.0 spherical 0.0 -180.0
|
||||
|
||||
molecule object molecule.cube molecule.tetra toff 1 molecule.rod3d toff 2 molecule.point3d toff 3
|
||||
Read molecule object:
|
||||
1 atoms with max type 1
|
||||
0 bonds with max type 0
|
||||
0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
Read molecule object:
|
||||
1 atoms with max type 2
|
||||
0 bonds with max type 0
|
||||
0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
Read molecule object:
|
||||
1 atoms with max type 3
|
||||
0 bonds with max type 0
|
||||
0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
Read molecule object:
|
||||
1 atoms with max type 4
|
||||
0 bonds with max type 0
|
||||
0 angles with max type 0
|
||||
0 dihedrals with max type 0
|
||||
0 impropers with max type 0
|
||||
|
||||
region slab block 5 45 5 45 25 35 units box
|
||||
fix ins all pour 500 0 4767548 vol 0.4 10 region slab mol object molfrac 0.25 0.25 0.25 0.25
|
||||
Particle insertion: 134 every 4472 steps, 500 by step 13417
|
||||
|
||||
fix 4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL
|
||||
|
||||
#compute 1 all body/local type 1 2 3
|
||||
#dump 1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
#dump 10 all custom 1000 tmp.dump id type x y z radius
|
||||
|
||||
thermo_style custom step atoms ke pe etotal press
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 75 15
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
run ${steps}
|
||||
run 6000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 5
|
||||
ghost atom cutoff = 5
|
||||
binsize = 2.5, bins = 20 20 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair body/rounded/polyhedron, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 0.5065 | 0.5065 | 0.5065 Mbytes
|
||||
Step Atoms KinEng PotEng TotEng Press
|
||||
0 0 -0 0 0 0
|
||||
1000 134 -0 0.00083010524 0.00083010524 -2.1515152e-06
|
||||
2000 134 -0 -0.00069962476 -0.00069962476 -1.4170663e-08
|
||||
3000 134 -0 -0.00069962687 -0.00069962687 -4.1478181e-11
|
||||
4000 134 -0 -0.00069962687 -0.00069962687 -1.2141026e-13
|
||||
5000 268 -0 0.014969705 0.014969705 3.0797164e-05
|
||||
6000 268 -0 0.042467887 0.042467887 0.00056148005
|
||||
Loop time of 0.634737 on 1 procs for 6000 steps with 268 atoms
|
||||
|
||||
Performance: 816716.196 tau/day, 9452.734 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41391 | 0.41391 | 0.41391 | 0.0 | 65.21
|
||||
Neigh | 0.010547 | 0.010547 | 0.010547 | 0.0 | 1.66
|
||||
Comm | 0.0030921 | 0.0030921 | 0.0030921 | 0.0 | 0.49
|
||||
Output | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 0.02
|
||||
Modify | 0.19736 | 0.19736 | 0.19736 | 0.0 | 31.09
|
||||
Other | | 0.009719 | | | 1.53
|
||||
|
||||
Nlocal: 268 ave 268 max 268 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3 ave 3 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 68 ave 68 max 68 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 68
|
||||
Ave neighs/atom = 0.253731
|
||||
Neighbor list builds = 168
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
Total wall time: 0:00:00
|
||||
|
|
@ -0,0 +1,221 @@
|
|||
LAMMPS (29 Jun 2018)
|
||||
# 2d rounded polygon bodies
|
||||
|
||||
variable r index 4
|
||||
variable steps index 100000
|
||||
variable T index 0.5
|
||||
variable P index 0.1
|
||||
variable seed index 980411
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
|
||||
atom_style body rounded/polygon 1 6
|
||||
atom_modify map array
|
||||
read_data data.squares
|
||||
orthogonal box = (0 0 -0.5) to (12 12 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
2 bodies
|
||||
|
||||
replicate $r $r 1
|
||||
replicate 4 $r 1
|
||||
replicate 4 4 1
|
||||
orthogonal box = (0 0 -0.5) to (48 48 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32 atoms
|
||||
Time spent = 0.00020504 secs
|
||||
|
||||
velocity all create $T ${seed} dist gaussian mom yes rot yes
|
||||
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
|
||||
velocity all create 0.5 980411 dist gaussian mom yes rot yes
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 2
|
||||
variable c_n equal 1
|
||||
variable c_t equal 1
|
||||
variable mu equal 0.1
|
||||
variable delta_ua equal 0.5
|
||||
|
||||
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
pair_coeff * * 100 ${k_na}
|
||||
pair_coeff * * 100 2
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#fix 1 all nve/body
|
||||
#fix 1 all nvt/body temp $T $T 1.0
|
||||
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
|
||||
|
||||
fix 2 all enforce2d
|
||||
|
||||
#compute 1 all body/local id 1 2 3
|
||||
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
thermo_style custom step ke pe etotal press
|
||||
thermo 1000
|
||||
|
||||
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
run ${steps}
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.15685
|
||||
ghost atom cutoff = 6.15685
|
||||
binsize = 3.07843, bins = 16 16 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair body/rounded/polygon, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.781 | 4.781 | 4.781 Mbytes
|
||||
Step KinEng PotEng TotEng Press
|
||||
0 0.484375 0.25 0.734375 0.0067274306
|
||||
1000 0.39423376 0.0017918048 0.39602557 0.0021941612
|
||||
2000 0.42284177 0.01346585 0.43630762 0.0029377883
|
||||
3000 0.58154405 0.011321689 0.59286574 0.003667871
|
||||
4000 0.73518304 0.034603175 0.76978621 0.0018689207
|
||||
5000 0.84367476 0.025292163 0.86896692 0.0089161373
|
||||
6000 0.70803236 0.0085631016 0.71659546 0.0045552895
|
||||
7000 0.56206452 0.10453031 0.66659483 0.010255161
|
||||
8000 0.64538994 0.088817673 0.73420761 0.0037633655
|
||||
9000 0.90540819 0.063696004 0.96910419 0.0077673359
|
||||
10000 0.68632042 0.093265016 0.77958544 0.0057864838
|
||||
11000 0.59118074 0.025654748 0.61683549 0.012518759
|
||||
12000 0.67522767 0.038176401 0.71340407 0.01741153
|
||||
13000 0.7644843 0.10429844 0.86878274 0.013161339
|
||||
14000 0.56152694 0.067836655 0.62936359 0.016852121
|
||||
15000 0.41895506 0.019513348 0.43846841 0.015225695
|
||||
16000 0.55799421 0.1564559 0.71445011 0.011703561
|
||||
17000 0.59391964 0.034450221 0.62836986 0.026215002
|
||||
18000 0.75911858 0.030885726 0.7900043 0.018396366
|
||||
19000 0.64417995 0.12110912 0.76528907 0.010247952
|
||||
20000 0.57751435 0.16965651 0.74717086 0.023392323
|
||||
21000 0.7613368 0.13405354 0.89539034 0.021498982
|
||||
22000 0.57676692 0.18011879 0.75688571 0.024469161
|
||||
23000 0.54043723 0.11842026 0.65885749 0.019799067
|
||||
24000 0.62276061 0.038967924 0.66172853 0.019080086
|
||||
25000 0.53157536 0.11651937 0.64809473 0.017019298
|
||||
26000 0.72213293 0.039012448 0.76114538 0.015434904
|
||||
27000 0.62157832 0.13697494 0.75855326 0.028711011
|
||||
28000 0.41323738 0.16301101 0.57624839 0.041792632
|
||||
29000 0.45774328 0.17569066 0.63343394 0.019975231
|
||||
30000 0.78901796 0.099791386 0.88880934 0.024116947
|
||||
31000 0.85205397 0.11977547 0.97182945 0.026667489
|
||||
32000 0.37137095 0.1232622 0.49463315 0.00087637364
|
||||
33000 0.26860871 0.26056381 0.52917252 0.036110517
|
||||
34000 0.3018636 0.21336905 0.51523265 0.040315549
|
||||
35000 0.39915129 0.28245957 0.68161085 0.034876856
|
||||
36000 0.25761236 0.2352705 0.49288286 0.022772767
|
||||
37000 0.1071233 0.31692858 0.42405188 0.017994666
|
||||
38000 0.083729577 0.28473145 0.36846103 -0.0045370431
|
||||
39000 0.070355565 0.26682083 0.33717639 0.017921556
|
||||
40000 0.075894079 0.20077896 0.27667304 0.014873186
|
||||
41000 0.05891028 0.15989064 0.21880092 0.025547873
|
||||
42000 0.1225107 0.16583605 0.28834675 0.038842785
|
||||
43000 0.17049189 0.14323991 0.3137318 0.029550161
|
||||
44000 0.26823939 0.15208257 0.42032196 0.028113612
|
||||
45000 0.10172203 0.1729706 0.27469264 -0.013769913
|
||||
46000 0.14841355 0.19085074 0.33926429 -0.00073741985
|
||||
47000 0.27654927 0.19097937 0.46752864 0.04021431
|
||||
48000 0.53432331 0.080769923 0.61509323 0.029932845
|
||||
49000 0.69111634 0.13064951 0.82176585 0.028985406
|
||||
50000 0.24520806 0.18317453 0.42838258 0.05179746
|
||||
51000 0.23541368 0.14281364 0.37822732 0.071884238
|
||||
52000 0.25464996 0.095730242 0.3503802 0.034488204
|
||||
53000 0.53677633 0.1058745 0.64265084 0.059932498
|
||||
54000 0.32970921 0.27979128 0.60950049 0.062869716
|
||||
55000 0.49094054 0.096735015 0.58767556 0.04728005
|
||||
56000 0.54398249 0.2216472 0.76562969 0.056712022
|
||||
57000 0.60869068 0.2338422 0.84253288 0.077143302
|
||||
58000 0.72175509 0.18687368 0.90862877 0.019357656
|
||||
59000 0.79442757 0.092502981 0.88693055 0.066882632
|
||||
60000 0.6810555 0.077699385 0.75875488 0.095975173
|
||||
61000 0.63178834 0.05071143 0.68249977 0.043586668
|
||||
62000 0.76589344 0.044615704 0.81050914 0.085718411
|
||||
63000 0.84815889 0.030527848 0.87868674 0.053072795
|
||||
64000 0.7309043 0.051938637 0.78284294 0.058887766
|
||||
65000 0.62498816 0.034474465 0.65946262 0.068446407
|
||||
66000 0.69817494 0.068546004 0.76672094 0.062634433
|
||||
67000 0.86444275 0.010184259 0.87462701 0.073635055
|
||||
68000 0.77820319 0.0079319524 0.78613515 0.090330925
|
||||
69000 0.56938919 0.0092629332 0.57865213 0.061838729
|
||||
70000 0.61870712 0.010047381 0.6287545 0.066501338
|
||||
71000 0.71651803 0.0088366199 0.72535465 0.079136316
|
||||
72000 0.76278925 0.008828151 0.77161741 0.063672771
|
||||
73000 0.75447428 0.0083985526 0.76287283 0.078256913
|
||||
74000 0.66185251 0.0091910052 0.67104351 0.069840511
|
||||
75000 0.58458829 0.0097671568 0.59435544 0.076123422
|
||||
76000 0.7487564 0.0100022 0.7587586 0.076171741
|
||||
77000 0.89505465 0.009250681 0.90430533 0.074921699
|
||||
78000 0.73738164 0.0092029279 0.74658457 0.078835344
|
||||
79000 0.65735281 0.010099528 0.66745233 0.077940627
|
||||
80000 0.70247542 0.010306464 0.71278189 0.079560093
|
||||
81000 0.74839505 0.010199092 0.75859415 0.080835104
|
||||
82000 0.75193767 0.010274058 0.76221173 0.081086684
|
||||
83000 0.71392598 0.010495573 0.72442156 0.082746145
|
||||
84000 0.58498928 0.011027388 0.59601667 0.08356465
|
||||
85000 0.59022869 0.011729474 0.60195817 0.084519397
|
||||
86000 0.81753578 0.011208964 0.82874475 0.085490261
|
||||
87000 0.83480682 0.010542579 0.8453494 0.086268527
|
||||
88000 0.67322538 0.011170734 0.68439611 0.08751623
|
||||
89000 0.62637389 0.012033316 0.6384072 0.088548094
|
||||
90000 0.92828557 0.011750388 0.94003596 0.089199823
|
||||
91000 0.96072564 0.010324509 0.97105015 0.090204803
|
||||
92000 0.72105071 0.011484152 0.73253486 0.09140819
|
||||
93000 0.65762527 0.012558219 0.67018349 0.092453474
|
||||
94000 0.73991591 0.01261909 0.752535 0.093373477
|
||||
95000 0.91791653 0.011980455 0.92989699 0.094182136
|
||||
96000 0.76562561 0.011807085 0.7774327 0.095323684
|
||||
97000 0.57292104 0.013610205 0.58653124 0.096505977
|
||||
98000 0.68141076 0.013863204 0.69527396 0.097380069
|
||||
99000 0.82390969 0.013002341 0.83691203 0.098235926
|
||||
100000 0.77639728 0.012989342 0.78938662 0.099274147
|
||||
Loop time of 3.88899 on 1 procs for 100000 steps with 32 atoms
|
||||
|
||||
Performance: 2221655.884 tau/day, 25713.610 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 3.056 | 3.056 | 3.056 | 0.0 | 78.58
|
||||
Neigh | 0.0051048 | 0.0051048 | 0.0051048 | 0.0 | 0.13
|
||||
Comm | 0.091444 | 0.091444 | 0.091444 | 0.0 | 2.35
|
||||
Output | 0.0011995 | 0.0011995 | 0.0011995 | 0.0 | 0.03
|
||||
Modify | 0.69909 | 0.69909 | 0.69909 | 0.0 | 17.98
|
||||
Other | | 0.03616 | | | 0.93
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21 ave 21 max 21 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 57 ave 57 max 57 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 57
|
||||
Ave neighs/atom = 1.78125
|
||||
Neighbor list builds = 1445
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:03
|
||||
|
|
@ -0,0 +1,221 @@
|
|||
LAMMPS (29 Jun 2018)
|
||||
# 2d rounded polygon bodies
|
||||
|
||||
variable r index 4
|
||||
variable steps index 100000
|
||||
variable T index 0.5
|
||||
variable P index 0.1
|
||||
variable seed index 980411
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
|
||||
atom_style body rounded/polygon 1 6
|
||||
atom_modify map array
|
||||
read_data data.squares
|
||||
orthogonal box = (0 0 -0.5) to (12 12 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
2 bodies
|
||||
|
||||
replicate $r $r 1
|
||||
replicate 4 $r 1
|
||||
replicate 4 4 1
|
||||
orthogonal box = (0 0 -0.5) to (48 48 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32 atoms
|
||||
Time spent = 0.000324011 secs
|
||||
|
||||
velocity all create $T ${seed} dist gaussian mom yes rot yes
|
||||
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
|
||||
velocity all create 0.5 980411 dist gaussian mom yes rot yes
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 2
|
||||
variable c_n equal 1
|
||||
variable c_t equal 1
|
||||
variable mu equal 0.1
|
||||
variable delta_ua equal 0.5
|
||||
|
||||
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 1 ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 1 0.1 ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 1 0.1 0.5 ${cut_inner}
|
||||
pair_style body/rounded/polygon 1 1 0.1 0.5 0.5
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
pair_coeff * * 100 ${k_na}
|
||||
pair_coeff * * 100 2
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#fix 1 all nve/body
|
||||
#fix 1 all nvt/body temp $T $T 1.0
|
||||
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 $P 1.0 couple xy fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 y 0.001 0.1 1.0 couple xy fixedpoint 0 0 0
|
||||
|
||||
fix 2 all enforce2d
|
||||
|
||||
#compute 1 all body/local id 1 2 3
|
||||
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
thermo_style custom step ke pe etotal press
|
||||
thermo 1000
|
||||
|
||||
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
run ${steps}
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.15685
|
||||
ghost atom cutoff = 6.15685
|
||||
binsize = 3.07843, bins = 16 16 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair body/rounded/polygon, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.774 | 4.774 | 4.774 Mbytes
|
||||
Step KinEng PotEng TotEng Press
|
||||
0 0.484375 0.25 0.734375 0.0067274306
|
||||
1000 0.39423376 0.0017918048 0.39602557 0.0021941612
|
||||
2000 0.42284177 0.01346585 0.43630762 0.0029377883
|
||||
3000 0.58154405 0.011321689 0.59286574 0.003667871
|
||||
4000 0.73518304 0.034603175 0.76978621 0.0018689207
|
||||
5000 0.84367476 0.025292163 0.86896692 0.0089161373
|
||||
6000 0.70803236 0.0085631016 0.71659546 0.0045552895
|
||||
7000 0.56206452 0.10453031 0.66659483 0.010255161
|
||||
8000 0.64538994 0.088817673 0.73420761 0.0037633655
|
||||
9000 0.90540819 0.063696004 0.96910419 0.0077673359
|
||||
10000 0.68632042 0.093265016 0.77958544 0.0057864837
|
||||
11000 0.59118074 0.025654748 0.61683549 0.012518759
|
||||
12000 0.67522767 0.038176401 0.71340407 0.01741153
|
||||
13000 0.7644843 0.10429844 0.86878274 0.013161339
|
||||
14000 0.56152694 0.067836656 0.6293636 0.016852113
|
||||
15000 0.41895505 0.019513353 0.43846841 0.015225696
|
||||
16000 0.55799443 0.15645637 0.7144508 0.011703646
|
||||
17000 0.59385248 0.03451986 0.62837234 0.025482966
|
||||
18000 0.75902169 0.031103586 0.79012527 0.018263354
|
||||
19000 0.64266826 0.12535314 0.76802141 0.014884119
|
||||
20000 0.57836261 0.16581188 0.74417449 0.024667165
|
||||
21000 0.78281936 0.11877527 0.90159464 -0.0090089213
|
||||
22000 0.5312006 0.13300874 0.66420934 0.025797278
|
||||
23000 0.56458861 0.084369128 0.64895774 0.024630917
|
||||
24000 0.65126875 0.06122992 0.71249867 0.034377198
|
||||
25000 0.55173441 0.15694886 0.70868327 0.021634086
|
||||
26000 0.59121615 0.17071182 0.76192797 0.024758366
|
||||
27000 0.6394843 0.17442949 0.81391378 0.034919937
|
||||
28000 0.31144221 0.41243036 0.72387256 0.074115225
|
||||
29000 0.13516917 0.3075419 0.44271107 0.023861298
|
||||
30000 0.14094934 0.24407203 0.38502137 0.037030438
|
||||
31000 0.26313749 0.087395422 0.35053291 0.042347005
|
||||
32000 0.51602457 0.063012079 0.57903664 0.018550299
|
||||
33000 0.55628829 0.200213 0.75650129 0.026507686
|
||||
34000 0.97399408 0.082504517 1.0564986 0.037889878
|
||||
35000 0.64710533 0.17662002 0.82372535 0.058295508
|
||||
36000 0.45769083 0.08241194 0.54010277 0.014957415
|
||||
37000 0.72850105 0.053874061 0.78237512 0.037194593
|
||||
38000 0.44177995 0.28939498 0.73117493 0.045194029
|
||||
39000 0.46828451 0.077630686 0.54591519 0.089849009
|
||||
40000 0.46786451 0.092828423 0.56069294 0.028042052
|
||||
41000 0.71861856 0.097085715 0.81570427 0.036473296
|
||||
42000 0.74121021 0.10553127 0.84674148 0.054058843
|
||||
43000 0.62945489 0.12770673 0.75716161 0.047267994
|
||||
44000 0.49900638 0.085150056 0.58415644 0.054798793
|
||||
45000 0.70199572 0.063415877 0.7654116 0.038363546
|
||||
46000 0.49513142 0.10649384 0.60162526 0.059392561
|
||||
47000 0.3858898 0.079458749 0.46534855 0.051825764
|
||||
48000 0.62585854 0.028585902 0.65444444 0.054074424
|
||||
49000 0.65934482 0.51865062 1.1779954 -0.035272836
|
||||
50000 0.5420438 0.082056756 0.62410056 0.031187494
|
||||
51000 0.36685223 0.14224019 0.50909241 0.073790397
|
||||
52000 0.19044627 0.15368389 0.34413016 0.059034266
|
||||
53000 0.26847678 0.075693324 0.3441701 0.032276915
|
||||
54000 0.3593711 0.19034549 0.54971659 0.070827883
|
||||
55000 0.21659198 0.1929074 0.40949939 0.035916364
|
||||
56000 0.28242715 0.12313241 0.40555956 0.062083926
|
||||
57000 0.34067475 0.14711992 0.48779467 0.059321458
|
||||
58000 0.4842796 0.16143425 0.64571385 0.059048247
|
||||
59000 0.84438871 0.076546849 0.92093556 0.048046901
|
||||
60000 0.92794849 0.054331626 0.98228012 0.058392272
|
||||
61000 0.6916736 0.076168342 0.76784194 0.058654987
|
||||
62000 0.63317965 0.094506389 0.72768604 0.061044719
|
||||
63000 0.63317266 0.038785593 0.67195825 0.097236147
|
||||
64000 0.81696668 0.121811 0.93877769 0.064935373
|
||||
65000 0.82644758 0.25188344 1.078331 0.093352359
|
||||
66000 0.64975019 0.17930857 0.82905876 0.058805254
|
||||
67000 0.63487678 0.16877059 0.80364737 0.070254696
|
||||
68000 0.79140717 0.11631004 0.9077172 0.064646394
|
||||
69000 0.85687272 0.057835331 0.91470805 0.071057291
|
||||
70000 0.67785976 0.040686768 0.71854653 0.074687222
|
||||
71000 0.60594577 0.032193155 0.63813893 0.069349268
|
||||
72000 0.77586745 0.024068533 0.79993598 0.083394193
|
||||
73000 0.88877625 0.025746326 0.91452258 0.081511105
|
||||
74000 0.73507888 0.036574786 0.77165367 0.075360233
|
||||
75000 0.68787782 0.042098622 0.72997644 0.068651098
|
||||
76000 0.72515745 0.04360868 0.76876613 0.069594624
|
||||
77000 0.77580944 0.041826702 0.81763614 0.071937144
|
||||
78000 0.76640394 0.039285046 0.80568899 0.074274921
|
||||
79000 0.62504309 0.039593585 0.66463667 0.076443295
|
||||
80000 0.60001642 0.043468215 0.64348464 0.094547719
|
||||
81000 0.82175037 0.045608873 0.86735924 0.080186295
|
||||
82000 0.85783276 0.042692576 0.90052534 0.081576548
|
||||
83000 0.71367707 0.042172193 0.75584926 0.08256625
|
||||
84000 0.68532406 0.044724759 0.73004882 0.083672013
|
||||
85000 0.72576789 0.046982462 0.77275035 0.084789331
|
||||
86000 0.75597701 0.04765086 0.80362787 0.085758056
|
||||
87000 0.74190598 0.047629096 0.78953507 0.086679976
|
||||
88000 0.60967704 0.049906172 0.65958321 0.085526191
|
||||
89000 0.54490288 0.054768238 0.59967112 0.090604027
|
||||
90000 0.75398341 0.057153453 0.81113686 0.091900858
|
||||
91000 0.84577472 0.052753512 0.89852823 0.091913909
|
||||
92000 0.7176235 0.050677427 0.76830093 0.092032507
|
||||
93000 0.61699446 0.054097013 0.67109147 0.092071275
|
||||
94000 0.76330752 0.057398618 0.82070614 0.092435043
|
||||
95000 0.98754458 0.053801311 1.0413459 0.093526707
|
||||
96000 0.7405897 0.052135628 0.79272533 0.095011929
|
||||
97000 0.65587599 0.057011962 0.71288795 0.096692123
|
||||
98000 0.72345634 0.060700171 0.78415651 0.097510345
|
||||
99000 0.88283624 0.061795247 0.94463149 0.09799633
|
||||
100000 0.86303812 0.058912988 0.92195111 0.09892993
|
||||
Loop time of 2.80074 on 4 procs for 100000 steps with 32 atoms
|
||||
|
||||
Performance: 3084895.573 tau/day, 35704.810 timesteps/s
|
||||
99.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.81169 | 0.89466 | 0.97669 | 8.4 | 31.94
|
||||
Neigh | 0.0017524 | 0.0018129 | 0.0018773 | 0.1 | 0.06
|
||||
Comm | 0.91307 | 0.99193 | 1.0691 | 7.3 | 35.42
|
||||
Output | 0.00076914 | 0.00093722 | 0.0013936 | 0.0 | 0.03
|
||||
Modify | 0.75335 | 0.75779 | 0.76346 | 0.4 | 27.06
|
||||
Other | | 0.1536 | | | 5.48
|
||||
|
||||
Nlocal: 8 ave 10 max 4 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 17.25 ave 19 max 15 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 13.5 ave 21 max 5 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 54
|
||||
Ave neighs/atom = 1.6875
|
||||
Neighbor list builds = 1443
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,223 @@
|
|||
LAMMPS (29 Jun 2018)
|
||||
# 2d rounded polygon bodies
|
||||
|
||||
variable r index 4
|
||||
variable steps index 100000
|
||||
variable T index 0.5
|
||||
variable P index 0.1
|
||||
variable seed index 980411
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
|
||||
atom_style body rounded/polygon 1 6
|
||||
atom_modify map array
|
||||
read_data data.squares
|
||||
orthogonal box = (0 0 -0.5) to (12 12 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
2 bodies
|
||||
|
||||
replicate $r $r 1
|
||||
replicate 4 $r 1
|
||||
replicate 4 4 1
|
||||
orthogonal box = (0 0 -0.5) to (48 48 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
32 atoms
|
||||
Time spent = 0.00029707 secs
|
||||
|
||||
velocity all create $T ${seed} dist gaussian mom yes rot yes
|
||||
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
|
||||
velocity all create 0.5 980411 dist gaussian mom yes rot yes
|
||||
|
||||
change_box all boundary p f p
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 2
|
||||
variable c_n equal 0.1
|
||||
variable c_t equal 0.1
|
||||
variable mu equal 0.1
|
||||
variable delta_ua equal 0.5
|
||||
|
||||
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
pair_coeff * * 100 ${k_na}
|
||||
pair_coeff * * 100 2
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#fix 1 all nve/body
|
||||
#fix 1 all nvt/body temp $T $T 1.0
|
||||
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
|
||||
|
||||
fix 2 all enforce2d
|
||||
fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
|
||||
|
||||
#compute 1 all body/local id 1 2 3
|
||||
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
thermo_style custom step ke pe etotal press
|
||||
thermo 1000
|
||||
|
||||
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
run ${steps}
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.15685
|
||||
ghost atom cutoff = 6.15685
|
||||
binsize = 3.07843, bins = 16 16 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair body/rounded/polygon, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.771 | 4.771 | 4.771 Mbytes
|
||||
Step KinEng PotEng TotEng Press
|
||||
0 0.484375 0.25 0.734375 0.0067274306
|
||||
1000 0.49241101 0.0031318767 0.49554289 0.017768281
|
||||
2000 0.56118632 0.0026068888 0.56379321 0.003410416
|
||||
3000 0.75565115 0.025578366 0.78122951 0.0071862988
|
||||
4000 0.72298647 0.093150646 0.81613712 0.003190158
|
||||
5000 0.51684166 0.049164868 0.56600653 0.0096960168
|
||||
6000 0.56627905 0.048132853 0.6144119 0.020733586
|
||||
7000 0.58122129 0.018223718 0.59944501 0.0038160759
|
||||
8000 0.64297977 0.025934821 0.66891459 0.0041091784
|
||||
9000 0.41748404 0.0077890042 0.42527305 0.0039270065
|
||||
10000 0.35738377 0.078487805 0.43587158 3.9079782e-05
|
||||
11000 0.41529308 0.13619284 0.55148592 -0.0067482285
|
||||
12000 0.43274718 0.071315497 0.50406268 0.007006378
|
||||
13000 0.4748331 0.069904647 0.54473775 0.0010384372
|
||||
14000 0.6287791 0.12721033 0.75598943 0.0047792448
|
||||
15000 0.4692413 0.12344005 0.59268136 0.018033616
|
||||
16000 0.43157074 0.14306789 0.57463862 0.042356676
|
||||
17000 0.53085999 0.22126296 0.75212294 0.027509646
|
||||
18000 0.52688968 0.13225282 0.6591425 0.0021558013
|
||||
19000 0.55032328 0.12513047 0.67545375 0.025036251
|
||||
20000 0.48465097 0.1431055 0.62775647 0.017193781
|
||||
21000 0.53166734 0.21928574 0.75095307 0.011564317
|
||||
22000 0.62177353 0.09296159 0.71473512 0.017660922
|
||||
23000 0.6972939 0.12434123 0.82163514 0.024432327
|
||||
24000 0.42767372 0.22152311 0.64919684 -0.013712449
|
||||
25000 0.4816037 0.19272865 0.67433236 0.052386055
|
||||
26000 0.72642579 0.19697046 0.92339625 0.020407694
|
||||
27000 0.39649144 0.15058326 0.5470747 0.023705766
|
||||
28000 0.44896324 0.18500106 0.6339643 -0.0089410286
|
||||
29000 0.5565759 0.11085772 0.66743362 0.048437166
|
||||
30000 0.58173584 0.21773281 0.79946865 0.0057357773
|
||||
31000 0.49199415 0.23601982 0.72801397 0.046744152
|
||||
32000 0.55665496 0.20542161 0.76207658 -0.0038756805
|
||||
33000 0.62730739 0.24460524 0.87191263 0.045330682
|
||||
34000 0.58107044 0.16395278 0.74502322 -0.0049496051
|
||||
35000 0.56838849 0.21842922 0.78681771 0.0062086036
|
||||
36000 0.45910273 0.28464172 0.74374445 -0.011700747
|
||||
37000 0.37092037 0.27646862 0.647389 0.022305679
|
||||
38000 0.7278047 0.30674438 1.0345491 0.07698342
|
||||
39000 0.5132923 0.27395066 0.78724295 0.026898634
|
||||
40000 0.62348649 0.24424644 0.86773293 0.039403899
|
||||
41000 0.3658401 0.15512326 0.52096337 0.022559003
|
||||
42000 0.4912253 0.35712978 0.84835508 -0.010336341
|
||||
43000 0.70225957 0.36314638 1.0654059 0.004148866
|
||||
44000 0.56958157 0.25488927 0.82447084 0.067537066
|
||||
45000 0.45854352 0.30149439 0.76003791 -0.017002401
|
||||
46000 0.62787247 0.34567995 0.97355242 0.11894801
|
||||
47000 0.61348914 0.29378625 0.90727539 0.067873976
|
||||
48000 0.71301829 0.34135284 1.0543711 0.021077736
|
||||
49000 0.53520804 0.30593196 0.84113999 0.0059257647
|
||||
50000 0.44966403 0.35370793 0.80337195 0.0020395669
|
||||
51000 0.5236113 0.32296924 0.84658054 -0.051011506
|
||||
52000 0.53905573 0.351771 0.89082672 0.013720106
|
||||
53000 0.55978158 0.41293947 0.97272106 0.068558589
|
||||
54000 0.52170459 0.2718066 0.7935112 0.0093138985
|
||||
55000 0.61078876 0.43353897 1.0443277 0.045377392
|
||||
56000 0.51300655 0.33182278 0.84482933 -0.018418487
|
||||
57000 0.54882822 0.38380093 0.93262915 0.10249946
|
||||
58000 0.72106212 0.45361279 1.1746749 0.030313481
|
||||
59000 0.55871447 0.63823029 1.1969448 0.019079703
|
||||
60000 0.49395192 0.58283102 1.0767829 0.0179349
|
||||
61000 0.45991079 0.62540573 1.0853165 0.074398804
|
||||
62000 0.4655788 0.60862262 1.0742014 0.11472976
|
||||
63000 0.55634524 0.63069255 1.1870378 -0.0025676135
|
||||
64000 0.57688903 0.45435264 1.0312417 0.0083813852
|
||||
65000 0.57168922 0.42217005 0.99385927 0.044931269
|
||||
66000 0.6206044 0.46727538 1.0878798 0.019686229
|
||||
67000 0.61037155 0.41840109 1.0287726 0.0195109
|
||||
68000 0.63848598 0.41305347 1.0515395 0.072940144
|
||||
69000 0.49244916 0.3834095 0.87585866 0.07963677
|
||||
70000 0.41847062 0.51907975 0.93755037 0.18447904
|
||||
71000 0.45198986 0.52973709 0.98172695 0.078419371
|
||||
72000 0.47064262 0.37808165 0.84872427 -0.00046308054
|
||||
73000 0.6690143 0.37549359 1.0445079 0.061208432
|
||||
74000 0.60444955 0.33779636 0.94224592 -0.068840321
|
||||
75000 0.61762382 0.3916421 1.0092659 0.16253292
|
||||
76000 0.63657961 0.50277989 1.1393595 0.013857508
|
||||
77000 0.52524028 0.43597896 0.96121924 -0.03296482
|
||||
78000 0.43803533 0.33172284 0.76975817 0.078763029
|
||||
79000 0.67156089 0.55272177 1.2242827 0.080822223
|
||||
80000 0.68678238 0.46061627 1.1473987 0.0027036992
|
||||
81000 0.64956678 0.44959229 1.0991591 0.11201483
|
||||
82000 0.51060477 0.43508342 0.9456882 0.028000608
|
||||
83000 0.59550548 0.69026083 1.2857663 -0.0015809004
|
||||
84000 0.64222145 0.38768816 1.0299096 0.014153173
|
||||
85000 0.7661229 0.43445261 1.2005755 0.048034534
|
||||
86000 0.60025257 0.53027929 1.1305319 0.0056865157
|
||||
87000 0.46220939 0.47470035 0.93690974 0.075311946
|
||||
88000 0.54123847 0.62899839 1.1702369 0.13260162
|
||||
89000 0.61212272 0.6114241 1.2235468 0.033284822
|
||||
90000 0.63924773 0.6916249 1.3308726 0.045088296
|
||||
91000 0.49316865 0.51037033 1.003539 0.023203598
|
||||
92000 0.57572123 0.43496319 1.0106844 0.297092
|
||||
93000 0.65187559 0.56815972 1.2200353 0.1538215
|
||||
94000 0.64107331 0.58948521 1.2305585 0.031117778
|
||||
95000 0.64584158 0.6364688 1.2823104 0.096154676
|
||||
96000 0.60509093 0.601487 1.2065779 0.03457172
|
||||
97000 0.68837218 0.77974186 1.468114 0.17801164
|
||||
98000 0.62725266 0.64137144 1.2686241 0.17449001
|
||||
99000 0.46861221 0.67000291 1.1386151 0.2429588
|
||||
100000 0.5879119 0.7140612 1.3019731 0.064634257
|
||||
Loop time of 2.50594 on 1 procs for 100000 steps with 32 atoms
|
||||
|
||||
Performance: 3447804.126 tau/day, 39905.140 timesteps/s
|
||||
100.0% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5639 | 1.5639 | 1.5639 | 0.0 | 62.41
|
||||
Neigh | 0.0086911 | 0.0086911 | 0.0086911 | 0.0 | 0.35
|
||||
Comm | 0.058926 | 0.058926 | 0.058926 | 0.0 | 2.35
|
||||
Output | 0.0012379 | 0.0012379 | 0.0012379 | 0.0 | 0.05
|
||||
Modify | 0.83537 | 0.83537 | 0.83537 | 0.0 | 33.34
|
||||
Other | | 0.03781 | | | 1.51
|
||||
|
||||
Nlocal: 32 ave 32 max 32 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 20 ave 20 max 20 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 57 ave 57 max 57 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 57
|
||||
Ave neighs/atom = 1.78125
|
||||
Neighbor list builds = 2705
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,223 @@
|
|||
LAMMPS (29 Jun 2018)
|
||||
# 2d rounded polygon bodies
|
||||
|
||||
variable r index 4
|
||||
variable steps index 100000
|
||||
variable T index 0.5
|
||||
variable P index 0.1
|
||||
variable seed index 980411
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
|
||||
atom_style body rounded/polygon 1 6
|
||||
atom_modify map array
|
||||
read_data data.squares
|
||||
orthogonal box = (0 0 -0.5) to (12 12 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2 atoms
|
||||
2 bodies
|
||||
|
||||
replicate $r $r 1
|
||||
replicate 4 $r 1
|
||||
replicate 4 4 1
|
||||
orthogonal box = (0 0 -0.5) to (48 48 0.5)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
32 atoms
|
||||
Time spent = 0.000386 secs
|
||||
|
||||
velocity all create $T ${seed} dist gaussian mom yes rot yes
|
||||
velocity all create 0.5 ${seed} dist gaussian mom yes rot yes
|
||||
velocity all create 0.5 980411 dist gaussian mom yes rot yes
|
||||
|
||||
change_box all boundary p f p
|
||||
|
||||
variable cut_inner equal 0.5
|
||||
variable k_n equal 100
|
||||
variable k_na equal 2
|
||||
variable c_n equal 0.1
|
||||
variable c_t equal 0.1
|
||||
variable mu equal 0.1
|
||||
variable delta_ua equal 0.5
|
||||
|
||||
pair_style body/rounded/polygon ${c_n} ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 ${c_t} ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 0.1 ${mu} ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 0.1 0.1 ${delta_ua} ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 ${cut_inner}
|
||||
pair_style body/rounded/polygon 0.1 0.1 0.1 0.5 0.5
|
||||
pair_coeff * * ${k_n} ${k_na}
|
||||
pair_coeff * * 100 ${k_na}
|
||||
pair_coeff * * 100 2
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
timestep 0.001
|
||||
|
||||
#fix 1 all nve/body
|
||||
#fix 1 all nvt/body temp $T $T 1.0
|
||||
fix 1 all npt/body temp $T $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 $T 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 $P 1.0 fixedpoint 0 0 0
|
||||
fix 1 all npt/body temp 0.5 0.5 1.0 x 0.001 0.1 1.0 fixedpoint 0 0 0
|
||||
|
||||
fix 2 all enforce2d
|
||||
fix 3 all wall/body/polygon 2000 50 50 yplane 0.0 48.0
|
||||
|
||||
#compute 1 all body/local id 1 2 3
|
||||
#dump 1 all local 100000 dump.polygon.* index c_1[1] c_1[2] c_1[3] c_1[4]
|
||||
|
||||
thermo_style custom step ke pe etotal press
|
||||
thermo 1000
|
||||
|
||||
#dump 2 all image 10000 image.*.jpg type type zoom 2.0 # adiam 1.5 body type 0 0
|
||||
#dump_modify 2 pad 6
|
||||
|
||||
run ${steps}
|
||||
run 100000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 6.15685
|
||||
ghost atom cutoff = 6.15685
|
||||
binsize = 3.07843, bins = 16 16 1
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair body/rounded/polygon, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/2d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.773 | 4.773 | 4.773 Mbytes
|
||||
Step KinEng PotEng TotEng Press
|
||||
0 0.484375 0.25 0.734375 0.0067274306
|
||||
1000 0.49241101 0.0031318767 0.49554289 0.017768281
|
||||
2000 0.56118632 0.0026068888 0.56379321 0.003410416
|
||||
3000 0.75565115 0.025578366 0.78122951 0.0071862988
|
||||
4000 0.72298647 0.093150646 0.81613712 0.003190158
|
||||
5000 0.51684166 0.049164868 0.56600653 0.0096960168
|
||||
6000 0.56627905 0.048132853 0.6144119 0.020733586
|
||||
7000 0.58122129 0.018223718 0.59944501 0.0038160759
|
||||
8000 0.64297977 0.025934821 0.66891459 0.0041091784
|
||||
9000 0.41748404 0.0077890042 0.42527305 0.0039270065
|
||||
10000 0.35738377 0.078487805 0.43587158 3.9079865e-05
|
||||
11000 0.41529307 0.13619284 0.55148591 -0.0067482285
|
||||
12000 0.43274718 0.071315527 0.50406271 0.007006369
|
||||
13000 0.4748324 0.069905666 0.54473807 0.0010385254
|
||||
14000 0.62603727 0.098905625 0.7249429 0.0048876764
|
||||
15000 0.44512086 0.10415235 0.54927321 0.01902062
|
||||
16000 0.47460177 0.18053316 0.65513493 0.045013976
|
||||
17000 0.52742676 0.10110706 0.62853382 0.013615471
|
||||
18000 0.46111734 0.096118795 0.55723613 0.0073676834
|
||||
19000 0.59668439 0.13652292 0.73320731 0.029403553
|
||||
20000 0.46840192 0.11611719 0.58451911 -0.00034412499
|
||||
21000 0.53550533 0.096457461 0.6319628 0.0019785732
|
||||
22000 0.46599715 0.13206373 0.59806087 0.031970672
|
||||
23000 0.49280776 0.20404726 0.69685501 0.03657433
|
||||
24000 0.60901688 0.18255214 0.79156902 0.044955017
|
||||
25000 0.47345185 0.13671357 0.61016542 0.020313539
|
||||
26000 0.47653832 0.12448225 0.60102057 0.01878099
|
||||
27000 0.50008212 0.24740634 0.74748845 0.021862639
|
||||
28000 0.41627204 0.2519463 0.66821834 0.054683701
|
||||
29000 0.55608273 0.23100212 0.78708485 -0.0043318497
|
||||
30000 0.53884537 0.3001584 0.83900377 -0.012838186
|
||||
31000 0.53036238 0.2300328 0.76039518 -0.0061688449
|
||||
32000 0.42666792 0.20536256 0.63203048 0.045305282
|
||||
33000 0.62908185 0.1652033 0.79428515 0.0072777588
|
||||
34000 0.47028154 0.388736 0.85901754 0.04332288
|
||||
35000 0.54602322 0.2775624 0.82358562 0.02898206
|
||||
36000 0.59860544 0.21824655 0.81685199 0.0025936194
|
||||
37000 0.62467827 0.11983499 0.74451326 0.050052743
|
||||
38000 0.72594229 0.36584781 1.0917901 0.04280621
|
||||
39000 0.51129656 0.23859043 0.74988699 0.050817447
|
||||
40000 0.53263836 0.24212889 0.77476725 0.036245922
|
||||
41000 0.50288088 0.36668283 0.86956371 0.018381415
|
||||
42000 0.46653688 0.21974887 0.68628574 0.012661062
|
||||
43000 0.61738785 0.32131037 0.93869821 0.012709433
|
||||
44000 0.56603903 0.26515554 0.83119457 0.03315102
|
||||
45000 0.56231638 0.32111693 0.88343331 0.06079756
|
||||
46000 0.7096208 0.2570131 0.96663391 0.048770468
|
||||
47000 0.588755 0.1880748 0.7768298 0.035962604
|
||||
48000 0.56296339 0.25783519 0.82079858 0.053019928
|
||||
49000 0.419885 0.42328618 0.84317118 0.038105269
|
||||
50000 0.63073351 0.41426285 1.0449964 0.0015271048
|
||||
51000 0.59357935 0.184222 0.77780136 0.015996218
|
||||
52000 0.60608471 0.36247533 0.96856003 0.10984665
|
||||
53000 0.5227842 0.27686739 0.79965159 0.02761699
|
||||
54000 0.39435923 0.34197355 0.73633278 0.061183263
|
||||
55000 0.46748455 0.34230903 0.80979358 0.077441382
|
||||
56000 0.59819827 0.29212061 0.89031889 0.043772353
|
||||
57000 0.61682559 0.32788566 0.94471124 0.03992069
|
||||
58000 0.52702478 0.24891506 0.77593984 0.058480883
|
||||
59000 0.66925719 0.4109031 1.0801603 0.072434423
|
||||
60000 0.66807714 0.39233068 1.0604078 0.082370324
|
||||
61000 0.5724275 0.43308567 1.0055132 0.0072945426
|
||||
62000 0.49433556 0.38453743 0.87887299 0.0036097443
|
||||
63000 0.57575143 0.54067119 1.1164226 0.073339638
|
||||
64000 0.68045383 0.38246533 1.0629192 0.025314593
|
||||
65000 0.59843527 0.42928622 1.0277215 -0.030096445
|
||||
66000 0.60274797 0.50186417 1.1046121 0.069797184
|
||||
67000 0.47450407 0.52689807 1.0014021 0.008758012
|
||||
68000 0.5514135 0.64113187 1.1925454 0.093863314
|
||||
69000 0.52008074 0.45749565 0.97757639 -0.066061381
|
||||
70000 0.69042662 0.50416006 1.1945867 0.014128617
|
||||
71000 0.63925854 0.35153425 0.9907928 -0.01134957
|
||||
72000 0.52088835 0.47626986 0.99715821 0.10198133
|
||||
73000 0.46333852 0.5515537 1.0148922 0.00060582772
|
||||
74000 0.53481418 0.50409531 1.0389095 0.00919451
|
||||
75000 0.67182749 0.50380162 1.1756291 0.043301985
|
||||
76000 0.70492289 0.4112122 1.1161351 0.14880484
|
||||
77000 0.59781817 0.50197661 1.0997948 -0.057111711
|
||||
78000 0.51677429 0.4348232 0.95159749 -0.0074619446
|
||||
79000 0.50663297 0.55000424 1.0566372 0.0052071216
|
||||
80000 0.59392006 0.48394003 1.0778601 -0.018990234
|
||||
81000 0.66323593 0.40358336 1.0668193 -0.02961345
|
||||
82000 0.61596979 0.49177944 1.1077492 0.1314853
|
||||
83000 0.63917554 0.61656584 1.2557414 0.11908351
|
||||
84000 0.49305291 0.46161646 0.95466937 0.033558488
|
||||
85000 0.52552044 0.54250555 1.068026 0.13015174
|
||||
86000 0.55140914 0.38924725 0.94065638 0.047412499
|
||||
87000 0.60952504 0.52603688 1.1355619 0.039230066
|
||||
88000 0.50119735 0.547539 1.0487364 0.019659933
|
||||
89000 0.40331401 0.50331134 0.90662535 -0.056906034
|
||||
90000 0.47067839 0.51306911 0.9837475 0.11918166
|
||||
91000 0.45564995 0.38693455 0.8425845 0.12040045
|
||||
92000 0.64163032 0.34232532 0.98395564 0.0057051641
|
||||
93000 0.70375593 0.53646186 1.2402178 0.16044241
|
||||
94000 0.53378112 0.51971406 1.0534952 0.11389004
|
||||
95000 0.47055342 0.50396004 0.97451346 0.079424215
|
||||
96000 0.59543473 0.40204536 0.99748009 0.096813093
|
||||
97000 0.64821917 0.50051728 1.1487365 0.054071312
|
||||
98000 0.55723937 0.4945909 1.0518303 0.047316424
|
||||
99000 0.56044424 0.50773312 1.0681774 0.0149959
|
||||
100000 0.68254229 0.32704484 1.0095871 0.0069212661
|
||||
Loop time of 2.20043 on 4 procs for 100000 steps with 32 atoms
|
||||
|
||||
Performance: 3926501.701 tau/day, 45445.622 timesteps/s
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41008 | 0.41366 | 0.41719 | 0.4 | 18.80
|
||||
Neigh | 0.0027823 | 0.0030481 | 0.0034747 | 0.5 | 0.14
|
||||
Comm | 0.74581 | 0.7675 | 0.78684 | 2.0 | 34.88
|
||||
Output | 0.00082111 | 0.0010884 | 0.0016899 | 1.1 | 0.05
|
||||
Modify | 0.83828 | 0.85329 | 0.86656 | 1.4 | 38.78
|
||||
Other | | 0.1618 | | | 7.36
|
||||
|
||||
Nlocal: 8 ave 9 max 7 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 12.75 ave 14 max 12 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 11 ave 19 max 5 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 44
|
||||
Ave neighs/atom = 1.375
|
||||
Neighbor list builds = 2663
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
|
|
@ -0,0 +1,52 @@
|
|||
# 3d polygon body: cubes, moment of inertia I = m edge^2/ 6
|
||||
|
||||
1 atoms
|
||||
3 79 body
|
||||
|
||||
Coords
|
||||
|
||||
1 0 0 0
|
||||
|
||||
Types
|
||||
|
||||
1 1
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
|
||||
Body Integers
|
||||
|
||||
8 12 6
|
||||
|
||||
Body Doubles
|
||||
|
||||
0.667 0.667 0.667 0 0 0
|
||||
1 1 1
|
||||
1 -1 1
|
||||
-1 -1 1
|
||||
-1 1 1
|
||||
1 1 -1
|
||||
1 -1 -1
|
||||
-1 -1 -1
|
||||
-1 1 -1
|
||||
0 1
|
||||
1 2
|
||||
2 3
|
||||
3 0
|
||||
4 5
|
||||
5 6
|
||||
6 7
|
||||
7 4
|
||||
0 4
|
||||
1 5
|
||||
2 6
|
||||
3 7
|
||||
0 1 2 3
|
||||
4 5 6 7
|
||||
0 1 5 4
|
||||
1 2 6 5
|
||||
2 3 7 6
|
||||
3 0 4 7
|
||||
0.5
|
||||
|
||||
|
|
@ -0,0 +1,26 @@
|
|||
# 2d polygon body: disks Izz = 1/2 m radius^2
|
||||
|
||||
1 atoms
|
||||
3 10 body
|
||||
|
||||
Coords
|
||||
|
||||
1 0 0 0
|
||||
|
||||
Types
|
||||
|
||||
1 1
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
|
||||
Body Integers
|
||||
|
||||
1 0 0
|
||||
|
||||
Body Doubles
|
||||
|
||||
1 1 1.125 0 0 0
|
||||
0 0 0
|
||||
3.0
|
||||
|
|
@ -0,0 +1,27 @@
|
|||
# 2d polygon body: rods Izz = 1/12 m length^2
|
||||
|
||||
1 atoms
|
||||
3 13 body
|
||||
|
||||
Coords
|
||||
|
||||
1 0 0 0
|
||||
|
||||
Types
|
||||
|
||||
1 1
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
|
||||
Body Integers
|
||||
|
||||
2 1 0
|
||||
|
||||
Body Doubles
|
||||
|
||||
1 1 1.333 0 0 0
|
||||
-2 0 0
|
||||
2 0 0
|
||||
0.5
|
||||
|
|
@ -0,0 +1,39 @@
|
|||
# 3d polygon body: regular tetrahedra, moment of inertia I = m edge^2/ 20
|
||||
|
||||
1 atoms
|
||||
3 47 body
|
||||
|
||||
Coords
|
||||
|
||||
1 0 0 0
|
||||
|
||||
Types
|
||||
|
||||
1 1
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
|
||||
Body Integers
|
||||
|
||||
4 6 4
|
||||
|
||||
Body Doubles
|
||||
|
||||
0.4 0.4 0.4 0 0 0
|
||||
1 1 1
|
||||
1 -1 -1
|
||||
-1 1 -1
|
||||
-1 -1 1
|
||||
0 1
|
||||
0 2
|
||||
0 3
|
||||
1 2
|
||||
2 3
|
||||
3 1
|
||||
0 1 2 -1
|
||||
0 1 3 -1
|
||||
0 2 3 -1
|
||||
1 2 3 -1
|
||||
0.5
|
||||
|
|
@ -0,0 +1,452 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cstdlib>
|
||||
#include "body_rounded_polygon.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "domain.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EPSILON 1.0e-7
|
||||
enum{SPHERE,LINE}; // also in DumpImage
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BodyRoundedPolygon::BodyRoundedPolygon(LAMMPS *lmp, int narg, char **arg) :
|
||||
Body(lmp, narg, arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Invalid body rounded/polygon command");
|
||||
|
||||
if (domain->dimension != 2)
|
||||
error->all(FLERR,"Atom_style body rounded/polygon "
|
||||
"can only be used in 2d simulations");
|
||||
|
||||
// nmin and nmax are minimum and maximum number of vertices
|
||||
|
||||
int nmin = force->inumeric(FLERR,arg[1]);
|
||||
int nmax = force->inumeric(FLERR,arg[2]);
|
||||
if (nmin <= 0 || nmin > nmax)
|
||||
error->all(FLERR,"Invalid body rounded/polygon command");
|
||||
|
||||
size_forward = 0;
|
||||
|
||||
// 1 integer for number of vertices,
|
||||
// 3*nmax doubles for vertex coordinates + 2*nmax doubles for edge ends
|
||||
// 1 double for the enclosing radius
|
||||
// 1 double for the rounded radius
|
||||
|
||||
size_border = 1 + 3*nmax + 2*nmax + 1 + 1;
|
||||
|
||||
// NOTE: need to set appropriate nnbin param for dcp
|
||||
|
||||
icp = new MyPoolChunk<int>(1,1);
|
||||
dcp = new MyPoolChunk<double>(3*nmin+2*nmin+1+1,3*nmax+2*nmax+1+1);
|
||||
|
||||
memory->create(imflag,nmax,"body/rounded/polygon:imflag");
|
||||
memory->create(imdata,nmax,7,"body/nparticle:imdata");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BodyRoundedPolygon::~BodyRoundedPolygon()
|
||||
{
|
||||
delete icp;
|
||||
delete dcp;
|
||||
memory->destroy(imflag);
|
||||
memory->destroy(imdata);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolygon::nsub(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
return bonus->ivalue[0];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double *BodyRoundedPolygon::coords(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
return bonus->dvalue;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolygon::nedges(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
int nvertices = bonus->ivalue[0];
|
||||
if (nvertices == 1) return 0;
|
||||
else if (nvertices == 2) return 1;
|
||||
return nvertices;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double *BodyRoundedPolygon::edges(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
return bonus->dvalue+3*nsub(bonus);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BodyRoundedPolygon::enclosing_radius(struct AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
int nvertices = bonus->ivalue[0];
|
||||
if (nvertices == 1 || nvertices == 2)
|
||||
return *(bonus->dvalue+3*nsub(bonus)+2);
|
||||
return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BodyRoundedPolygon::rounded_radius(struct AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
int nvertices = bonus->ivalue[0];
|
||||
if (nvertices == 1 || nvertices == 2)
|
||||
return *(bonus->dvalue+3*nsub(bonus)+2+1);
|
||||
return *(bonus->dvalue + 3*nsub(bonus) + 2*nsub(bonus)+1);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolygon::pack_border_body(AtomVecBody::Bonus *bonus, double *buf)
|
||||
{
|
||||
int nsub = bonus->ivalue[0];
|
||||
buf[0] = nsub;
|
||||
memcpy(&buf[1],bonus->dvalue,(3*nsub+2*nsub+1+1)*sizeof(double));
|
||||
return 1+(3*nsub+2*nsub+1+1);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolygon::unpack_border_body(AtomVecBody::Bonus *bonus,
|
||||
double *buf)
|
||||
{
|
||||
int nsub = static_cast<int> (buf[0]);
|
||||
bonus->ivalue[0] = nsub;
|
||||
memcpy(bonus->dvalue,&buf[1],(3*nsub+2*nsub+1+1)*sizeof(double));
|
||||
return 1+(3*nsub+2*nsub+1+1);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
populate bonus data structure with data file values
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BodyRoundedPolygon::data_body(int ibonus, int ninteger, int ndouble,
|
||||
int *ifile, double *dfile)
|
||||
{
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
|
||||
// set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles
|
||||
|
||||
if (ninteger != 1)
|
||||
error->one(FLERR,"Incorrect # of integer values in "
|
||||
"Bodies section of data file");
|
||||
int nsub = ifile[0];
|
||||
if (nsub < 1)
|
||||
error->one(FLERR,"Incorrect integer value in "
|
||||
"Bodies section of data file");
|
||||
|
||||
// nentries = number of double entries to be read from Body section:
|
||||
// 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius
|
||||
|
||||
int nentries = 6 + 3*nsub + 1;
|
||||
if (ndouble != nentries)
|
||||
error->one(FLERR,"Incorrect # of floating-point values in "
|
||||
"Bodies section of data file");
|
||||
|
||||
bonus->ninteger = 1;
|
||||
bonus->ivalue = icp->get(bonus->iindex);
|
||||
bonus->ivalue[0] = nsub;
|
||||
bonus->ndouble = 3*nsub + 2*nsub + 1 + 1;
|
||||
bonus->dvalue = dcp->get(bonus->ndouble,bonus->dindex);
|
||||
|
||||
// diagonalize inertia tensor
|
||||
|
||||
double tensor[3][3];
|
||||
tensor[0][0] = dfile[0];
|
||||
tensor[1][1] = dfile[1];
|
||||
tensor[2][2] = dfile[2];
|
||||
tensor[0][1] = tensor[1][0] = dfile[3];
|
||||
tensor[0][2] = tensor[2][0] = dfile[4];
|
||||
tensor[1][2] = tensor[2][1] = dfile[5];
|
||||
|
||||
double *inertia = bonus->inertia;
|
||||
double evectors[3][3];
|
||||
int ierror = MathExtra::jacobi(tensor,inertia,evectors);
|
||||
if (ierror) error->one(FLERR,
|
||||
"Insufficient Jacobi rotations for body nparticle");
|
||||
|
||||
// if any principal moment < scaled EPSILON, set to 0.0
|
||||
|
||||
double max;
|
||||
max = MAX(inertia[0],inertia[1]);
|
||||
max = MAX(max,inertia[2]);
|
||||
|
||||
if (inertia[0] < EPSILON*max) inertia[0] = 0.0;
|
||||
if (inertia[1] < EPSILON*max) inertia[1] = 0.0;
|
||||
if (inertia[2] < EPSILON*max) inertia[2] = 0.0;
|
||||
|
||||
// exyz_space = principal axes in space frame
|
||||
|
||||
double ex_space[3],ey_space[3],ez_space[3];
|
||||
|
||||
ex_space[0] = evectors[0][0];
|
||||
ex_space[1] = evectors[1][0];
|
||||
ex_space[2] = evectors[2][0];
|
||||
ey_space[0] = evectors[0][1];
|
||||
ey_space[1] = evectors[1][1];
|
||||
ey_space[2] = evectors[2][1];
|
||||
ez_space[0] = evectors[0][2];
|
||||
ez_space[1] = evectors[1][2];
|
||||
ez_space[2] = evectors[2][2];
|
||||
|
||||
// enforce 3 evectors as a right-handed coordinate system
|
||||
// flip 3rd vector if needed
|
||||
|
||||
double cross[3];
|
||||
MathExtra::cross3(ex_space,ey_space,cross);
|
||||
if (MathExtra::dot3(cross,ez_space) < 0.0) MathExtra::negate3(ez_space);
|
||||
|
||||
// create initial quaternion
|
||||
|
||||
MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus->quat);
|
||||
|
||||
// bonus->dvalue = the first 3*nsub elements are sub-particle displacements
|
||||
// find the enclosing radius of the body from the maximum displacement
|
||||
|
||||
int i,m;
|
||||
double delta[3], rsq, erad, rrad;
|
||||
double erad2 = 0;
|
||||
int j = 6;
|
||||
int k = 0;
|
||||
for (i = 0; i < nsub; i++) {
|
||||
delta[0] = dfile[j];
|
||||
delta[1] = dfile[j+1];
|
||||
delta[2] = dfile[j+2];
|
||||
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
|
||||
delta,&bonus->dvalue[k]);
|
||||
rsq = delta[0] * delta[0] + delta[1] * delta[1] +
|
||||
delta[2] * delta[2];
|
||||
if (rsq > erad2) erad2 = rsq;
|
||||
j += 3;
|
||||
k += 3;
|
||||
}
|
||||
|
||||
// .. the next 2*nsub elements are edge ends
|
||||
|
||||
int nedges;
|
||||
if (nsub == 1) { // spheres
|
||||
nedges = 0;
|
||||
bonus->dvalue[k] = 0;
|
||||
*(&bonus->dvalue[k]+1) = 0;
|
||||
k += 2;
|
||||
|
||||
// the last element of bonus->dvalue is the rounded & enclosing radius
|
||||
|
||||
rrad = 0.5 * dfile[j];
|
||||
bonus->dvalue[k] = rrad;
|
||||
erad = rrad;
|
||||
|
||||
k++;
|
||||
bonus->dvalue[k] = rrad;
|
||||
|
||||
atom->radius[bonus->ilocal] = erad;
|
||||
|
||||
} else if (nsub == 2) { // rods
|
||||
nedges = 1;
|
||||
for (i = 0; i < nedges; i++) {
|
||||
bonus->dvalue[k] = 0;
|
||||
*(&bonus->dvalue[k]+1) = 1;
|
||||
k += 2;
|
||||
}
|
||||
|
||||
erad = sqrt(erad2);
|
||||
bonus->dvalue[k] = erad;
|
||||
|
||||
// the last element of bonus->dvalue is the rounded radius
|
||||
|
||||
rrad = 0.5 * dfile[j];
|
||||
k++;
|
||||
bonus->dvalue[k] = rrad;
|
||||
|
||||
atom->radius[bonus->ilocal] = erad + rrad;
|
||||
|
||||
} else { // polygons
|
||||
nedges = nsub;
|
||||
for (i = 0; i < nedges; i++) {
|
||||
bonus->dvalue[k] = i;
|
||||
m = i+1;
|
||||
if (m == nedges) m = 0;
|
||||
*(&bonus->dvalue[k]+1) = m;
|
||||
k += 2;
|
||||
}
|
||||
|
||||
// the next to last element is the enclosing radius
|
||||
|
||||
erad = sqrt(erad2);
|
||||
bonus->dvalue[k] = erad;
|
||||
|
||||
// the last element of bonus->dvalue is the rounded radius
|
||||
|
||||
rrad = 0.5 * dfile[j];
|
||||
k++;
|
||||
bonus->dvalue[k] = rrad;
|
||||
|
||||
atom->radius[bonus->ilocal] = erad + rrad;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return radius of body particle defined by ifile/dfile params
|
||||
params are ordered as in data file
|
||||
called by Molecule class which needs single body size
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BodyRoundedPolygon::radius_body(int ninteger, int ndouble,
|
||||
int *ifile, double *dfile)
|
||||
{
|
||||
int nsub = ifile[0];
|
||||
if (nsub < 1)
|
||||
error->one(FLERR,"Incorrect integer value in "
|
||||
"Bodies section of data file");
|
||||
if (ndouble != 6 + 3*nsub + 1)
|
||||
error->one(FLERR,"Incorrect # of floating-point values in "
|
||||
"Bodies section of data file");
|
||||
|
||||
// sub-particle coords are relative to body center at (0,0,0)
|
||||
// offset = 6 for sub-particle coords
|
||||
|
||||
double onerad;
|
||||
double maxrad = 0.0;
|
||||
double delta[3];
|
||||
|
||||
int offset = 6;
|
||||
for (int i = 0; i < nsub; i++) {
|
||||
delta[0] = dfile[offset];
|
||||
delta[1] = dfile[offset+1];
|
||||
delta[2] = dfile[offset+2];
|
||||
offset += 3;
|
||||
onerad = MathExtra::len3(delta);
|
||||
maxrad = MAX(maxrad,onerad);
|
||||
}
|
||||
|
||||
// add in radius of rounded corners
|
||||
|
||||
return maxrad + 0.5*dfile[offset];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolygon::noutcol()
|
||||
{
|
||||
// the number of columns for the vertex coordinates
|
||||
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolygon::noutrow(int ibonus)
|
||||
{
|
||||
// only return the first nsub rows for the vertex coordinates
|
||||
|
||||
return avec->bonus[ibonus].ivalue[0];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BodyRoundedPolygon::output(int ibonus, int m, double *values)
|
||||
{
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
|
||||
double p[3][3];
|
||||
MathExtra::quat_to_mat(bonus->quat,p);
|
||||
MathExtra::matvec(p,&bonus->dvalue[3*m],values);
|
||||
|
||||
double *x = atom->x[bonus->ilocal];
|
||||
values[0] += x[0];
|
||||
values[1] += x[1];
|
||||
values[2] += x[2];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolygon::image(int ibonus, double flag1, double flag2,
|
||||
int *&ivec, double **&darray)
|
||||
{
|
||||
int j;
|
||||
double p[3][3];
|
||||
double *x, rrad;
|
||||
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
int n = bonus->ivalue[0];
|
||||
|
||||
if (n == 1) {
|
||||
for (int i = 0; i < n; i++) {
|
||||
imflag[i] = SPHERE;
|
||||
MathExtra::quat_to_mat(bonus->quat,p);
|
||||
MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]);
|
||||
|
||||
rrad = enclosing_radius(bonus);
|
||||
x = atom->x[bonus->ilocal];
|
||||
imdata[i][0] += x[0];
|
||||
imdata[i][1] += x[1];
|
||||
imdata[i][2] += x[2];
|
||||
if (flag1 <= 0) imdata[i][3] = 2*rrad;
|
||||
else imdata[i][3] = flag1;
|
||||
}
|
||||
|
||||
} else {
|
||||
|
||||
// first end pt of each line
|
||||
|
||||
for (int i = 0; i < n; i++) {
|
||||
imflag[i] = LINE;
|
||||
MathExtra::quat_to_mat(bonus->quat,p);
|
||||
MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]);
|
||||
|
||||
rrad = rounded_radius(bonus);
|
||||
x = atom->x[bonus->ilocal];
|
||||
imdata[i][0] += x[0];
|
||||
imdata[i][1] += x[1];
|
||||
imdata[i][2] += x[2];
|
||||
if (flag1 <= 0) imdata[i][6] = 2*rrad;
|
||||
else imdata[i][6] = flag1;
|
||||
}
|
||||
|
||||
// second end pt of each line
|
||||
|
||||
for (int i = 0; i < n; i++) {
|
||||
j = i+1;
|
||||
if (j == n) j = 0;
|
||||
imdata[i][3] = imdata[j][0];
|
||||
imdata[i][4] = imdata[j][1];
|
||||
imdata[i][5] = imdata[j][2];
|
||||
}
|
||||
}
|
||||
|
||||
ivec = imflag;
|
||||
darray = imdata;
|
||||
return n;
|
||||
}
|
||||
|
|
@ -0,0 +1,86 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BODY_CLASS
|
||||
|
||||
BodyStyle(rounded/polygon,BodyRoundedPolygon)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_BODY_ROUNDED_POLYGON_H
|
||||
#define LMP_BODY_ROUNDED_POLYGON_H
|
||||
|
||||
#include "body.h"
|
||||
#include "atom_vec_body.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BodyRoundedPolygon : public Body {
|
||||
public:
|
||||
BodyRoundedPolygon(class LAMMPS *, int, char **);
|
||||
~BodyRoundedPolygon();
|
||||
int nsub(struct AtomVecBody::Bonus *);
|
||||
double *coords(struct AtomVecBody::Bonus *);
|
||||
int nedges(struct AtomVecBody::Bonus *);
|
||||
double *edges(struct AtomVecBody::Bonus *);
|
||||
double enclosing_radius(struct AtomVecBody::Bonus *);
|
||||
double rounded_radius(struct AtomVecBody::Bonus *);
|
||||
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
double radius_body(int, int, int *, double *);
|
||||
|
||||
int noutrow(int);
|
||||
int noutcol();
|
||||
void output(int, int, double *);
|
||||
int image(int, double, double, int *&, double **&);
|
||||
|
||||
private:
|
||||
int *imflag;
|
||||
double **imdata;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Invalid body rounded/polygon command
|
||||
|
||||
Arguments in atom-style command are not correct.
|
||||
|
||||
E: Invalid format in Bodies section of data file
|
||||
|
||||
The specified number of integer or floating point values does not
|
||||
appear.
|
||||
|
||||
E: Incorrect # of integer values in Bodies section of data file
|
||||
|
||||
See doc page for body style.
|
||||
|
||||
E: Incorrect integer value in Bodies section of data file
|
||||
|
||||
See doc page for body style.
|
||||
|
||||
E: Incorrect # of floating-point values in Bodies section of data file
|
||||
|
||||
See doc page for body style.
|
||||
|
||||
E: Insufficient Jacobi rotations for body nparticle
|
||||
|
||||
Eigensolve for rigid body was not sufficiently accurate.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,526 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cstdlib>
|
||||
#include "body_rounded_polyhedron.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "domain.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EPSILON 1.0e-7
|
||||
#define MAX_FACE_SIZE 4 // maximum number of vertices per face (for now)
|
||||
|
||||
enum{SPHERE,LINE}; // also in DumpImage
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BodyRoundedPolyhedron::BodyRoundedPolyhedron(LAMMPS *lmp, int narg, char **arg) :
|
||||
Body(lmp, narg, arg)
|
||||
{
|
||||
if (narg != 3) error->all(FLERR,"Invalid body rounded/polygon command");
|
||||
|
||||
// nmin and nmax are minimum and maximum number of vertices
|
||||
|
||||
int nmin = force->inumeric(FLERR,arg[1]);
|
||||
int nmax = force->inumeric(FLERR,arg[2]);
|
||||
if (nmin <= 0 || nmin > nmax)
|
||||
error->all(FLERR,"Invalid body rounded/polyhedron command");
|
||||
|
||||
size_forward = 0;
|
||||
|
||||
// 3 integers: 1 for no. of vertices, 1 for no. of edges, 1 for no. of faces
|
||||
// 3*nmax doubles for vertex coordinates + 2*nmax doubles for edge ends +
|
||||
// (MAX_FACE_SIZE+1)*nmax for faces
|
||||
// 1 double for the enclosing radius
|
||||
// 1 double for the rounded radius
|
||||
|
||||
size_border = 3 + 3*nmax + 2*nmax + MAX_FACE_SIZE*nmax + 1 + 1;
|
||||
|
||||
// NOTE: need to set appropriate nnbin param for dcp
|
||||
|
||||
icp = new MyPoolChunk<int>(1,3);
|
||||
dcp = new MyPoolChunk<double>(3*nmin+2+1+1,
|
||||
3*nmax+2*nmax+MAX_FACE_SIZE*nmax+1+1);
|
||||
|
||||
memory->create(imflag,2*nmax,"body/rounded/polyhedron:imflag");
|
||||
memory->create(imdata,2*nmax,7,"body/polyhedron:imdata");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BodyRoundedPolyhedron::~BodyRoundedPolyhedron()
|
||||
{
|
||||
delete icp;
|
||||
delete dcp;
|
||||
memory->destroy(imflag);
|
||||
memory->destroy(imdata);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolyhedron::nsub(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
return bonus->ivalue[0];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double *BodyRoundedPolyhedron::coords(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
return bonus->dvalue;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolyhedron::nedges(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
int nvertices = bonus->ivalue[0];
|
||||
int nedges = bonus->ivalue[1];
|
||||
int nfaces = bonus->ivalue[2];
|
||||
if (nvertices == 1) return 0;
|
||||
else if (nvertices == 2) return 1;
|
||||
return nedges; //(nvertices+nfaces-2); // Euler's polyon formula: V-E+F=2
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double *BodyRoundedPolyhedron::edges(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
return bonus->dvalue+3*nsub(bonus);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolyhedron::nfaces(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
return bonus->ivalue[2];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double *BodyRoundedPolyhedron::faces(AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
int nvertices = bonus->ivalue[0];
|
||||
if (nvertices == 1 || nvertices == 2) return NULL;
|
||||
return bonus->dvalue+3*nsub(bonus)+2*nedges(bonus);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BodyRoundedPolyhedron::enclosing_radius(struct AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
int nvertices = bonus->ivalue[0];
|
||||
if (nvertices == 1 || nvertices == 2)
|
||||
return *(bonus->dvalue+3*nsub(bonus)+2);
|
||||
return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) +
|
||||
MAX_FACE_SIZE*nfaces(bonus));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BodyRoundedPolyhedron::rounded_radius(struct AtomVecBody::Bonus *bonus)
|
||||
{
|
||||
int nvertices = bonus->ivalue[0];
|
||||
if (nvertices == 1 || nvertices == 2)
|
||||
return *(bonus->dvalue+3*nsub(bonus)+2+1);
|
||||
return *(bonus->dvalue+3*nsub(bonus) + 2*nedges(bonus) +
|
||||
MAX_FACE_SIZE*nfaces(bonus)+1);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolyhedron::pack_border_body(AtomVecBody::Bonus *bonus, double *buf)
|
||||
{
|
||||
int nsub = bonus->ivalue[0];
|
||||
int ned = bonus->ivalue[1];
|
||||
int nfac = bonus->ivalue[2];
|
||||
buf[0] = nsub;
|
||||
buf[1] = ned;
|
||||
buf[2] = nfac;
|
||||
int ndouble;
|
||||
if (nsub == 1 || nsub == 2) ndouble = 3*nsub+2+MAX_FACE_SIZE*nfac+1+1;
|
||||
else ndouble = 3*nsub+2*ned+MAX_FACE_SIZE*nfac+1+1;
|
||||
memcpy(&buf[3],bonus->dvalue,ndouble*sizeof(double));
|
||||
return 3+ndouble;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolyhedron::unpack_border_body(AtomVecBody::Bonus *bonus,
|
||||
double *buf)
|
||||
{
|
||||
int nsub = static_cast<int> (buf[0]);
|
||||
int ned = static_cast<int> (buf[1]);
|
||||
int nfac = static_cast<int> (buf[2]);
|
||||
bonus->ivalue[0] = nsub;
|
||||
bonus->ivalue[1] = ned;
|
||||
bonus->ivalue[2] = nfac;
|
||||
int ndouble;
|
||||
if (nsub == 1 || nsub == 2) ndouble = 3*nsub+2+MAX_FACE_SIZE*nfac+1+1;
|
||||
else ndouble = 3*nsub+2*ned+MAX_FACE_SIZE*nfac+1+1;
|
||||
memcpy(bonus->dvalue,&buf[3],ndouble*sizeof(double));
|
||||
return 3+ndouble;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
populate bonus data structure with data file values
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BodyRoundedPolyhedron::data_body(int ibonus, int ninteger, int ndouble,
|
||||
int *ifile, double *dfile)
|
||||
{
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
|
||||
// set ninteger, ndouble in bonus and allocate 2 vectors of ints, doubles
|
||||
|
||||
if (ninteger != 3)
|
||||
error->one(FLERR,"Incorrect # of integer values in "
|
||||
"Bodies section of data file");
|
||||
int nsub = ifile[0];
|
||||
int ned = ifile[1];
|
||||
int nfac = ifile[2];
|
||||
if (nsub < 1)
|
||||
error->one(FLERR,"Incorrect integer value in "
|
||||
"Bodies section of data file");
|
||||
|
||||
// nentries = number of double entries to be read from Body section:
|
||||
// nsub == 1 || nsub == 2 || nsub == 3:
|
||||
// 6 for inertia + 3*nsub for vertex coords + 1 for rounded radius
|
||||
// nsub > 3:
|
||||
// 6 for inertia + 3*nsub for vertex coords + 2*nsub for edges +
|
||||
// 3*nfaces + 1 for rounded radius
|
||||
|
||||
int nedges,nentries;
|
||||
if (nsub == 1 || nsub == 2) {
|
||||
nentries = 6 + 3*nsub + 1;
|
||||
} else {
|
||||
nedges = ned; //nsub + nfac - 2;
|
||||
nentries = 6 + 3*nsub + 2*nedges + MAX_FACE_SIZE*nfac + 1;
|
||||
}
|
||||
if (ndouble != nentries)
|
||||
error->one(FLERR,"Incorrect # of floating-point values in "
|
||||
"Bodies section of data file");
|
||||
|
||||
bonus->ninteger = 3;
|
||||
bonus->ivalue = icp->get(bonus->iindex);
|
||||
bonus->ivalue[0] = nsub;
|
||||
bonus->ivalue[1] = ned;
|
||||
bonus->ivalue[2] = nfac;
|
||||
if (nsub == 1 || nsub == 2) bonus->ndouble = 3*nsub + 2*nsub + 1 + 1;
|
||||
else bonus->ndouble = 3*nsub + 2*nedges + MAX_FACE_SIZE*nfac + 1 + 1;
|
||||
bonus->dvalue = dcp->get(bonus->ndouble,bonus->dindex);
|
||||
|
||||
// diagonalize inertia tensor
|
||||
|
||||
double tensor[3][3];
|
||||
tensor[0][0] = dfile[0];
|
||||
tensor[1][1] = dfile[1];
|
||||
tensor[2][2] = dfile[2];
|
||||
tensor[0][1] = tensor[1][0] = dfile[3];
|
||||
tensor[0][2] = tensor[2][0] = dfile[4];
|
||||
tensor[1][2] = tensor[2][1] = dfile[5];
|
||||
|
||||
double *inertia = bonus->inertia;
|
||||
double evectors[3][3];
|
||||
int ierror = MathExtra::jacobi(tensor,inertia,evectors);
|
||||
if (ierror) error->one(FLERR,
|
||||
"Insufficient Jacobi rotations for body nparticle");
|
||||
|
||||
// if any principal moment < scaled EPSILON, set to 0.0
|
||||
|
||||
double max;
|
||||
max = MAX(inertia[0],inertia[1]);
|
||||
max = MAX(max,inertia[2]);
|
||||
|
||||
if (inertia[0] < EPSILON*max) inertia[0] = 0.0;
|
||||
if (inertia[1] < EPSILON*max) inertia[1] = 0.0;
|
||||
if (inertia[2] < EPSILON*max) inertia[2] = 0.0;
|
||||
|
||||
// exyz_space = principal axes in space frame
|
||||
|
||||
double ex_space[3],ey_space[3],ez_space[3];
|
||||
|
||||
ex_space[0] = evectors[0][0];
|
||||
ex_space[1] = evectors[1][0];
|
||||
ex_space[2] = evectors[2][0];
|
||||
ey_space[0] = evectors[0][1];
|
||||
ey_space[1] = evectors[1][1];
|
||||
ey_space[2] = evectors[2][1];
|
||||
ez_space[0] = evectors[0][2];
|
||||
ez_space[1] = evectors[1][2];
|
||||
ez_space[2] = evectors[2][2];
|
||||
|
||||
// enforce 3 evectors as a right-handed coordinate system
|
||||
// flip 3rd vector if needed
|
||||
|
||||
double cross[3];
|
||||
MathExtra::cross3(ex_space,ey_space,cross);
|
||||
if (MathExtra::dot3(cross,ez_space) < 0.0) MathExtra::negate3(ez_space);
|
||||
|
||||
// create initial quaternion
|
||||
|
||||
MathExtra::exyz_to_q(ex_space,ey_space,ez_space,bonus->quat);
|
||||
|
||||
// bonus->dvalue = the first 3*nsub elements are sub-particle displacements
|
||||
// find the enclosing radius of the body from the maximum displacement
|
||||
|
||||
int i,m;
|
||||
double delta[3], rsq, erad, rrad;
|
||||
double erad2 = 0;
|
||||
int j = 6;
|
||||
int k = 0;
|
||||
for (i = 0; i < nsub; i++) {
|
||||
delta[0] = dfile[j];
|
||||
delta[1] = dfile[j+1];
|
||||
delta[2] = dfile[j+2];
|
||||
MathExtra::transpose_matvec(ex_space,ey_space,ez_space,
|
||||
delta,&bonus->dvalue[k]);
|
||||
rsq = delta[0] * delta[0] + delta[1] * delta[1] +
|
||||
delta[2] * delta[2];
|
||||
if (rsq > erad2) erad2 = rsq;
|
||||
j += 3;
|
||||
k += 3;
|
||||
}
|
||||
|
||||
// .. the next 2*nsub elements are edge ends
|
||||
|
||||
if (nsub == 1) { // spheres
|
||||
nedges = 0;
|
||||
bonus->dvalue[k] = 0;
|
||||
*(&bonus->dvalue[k]+1) = 0;
|
||||
k += 2;
|
||||
|
||||
rrad = 0.5 * dfile[j];
|
||||
bonus->dvalue[k] = rrad;
|
||||
erad = rrad; // enclosing radius = rounded_radius
|
||||
|
||||
// the last element of bonus->dvalue is the rounded radius
|
||||
|
||||
k++;
|
||||
bonus->dvalue[k] = rrad;
|
||||
|
||||
atom->radius[bonus->ilocal] = erad;
|
||||
|
||||
} else if (nsub == 2) { // rods
|
||||
nedges = 1;
|
||||
for (i = 0; i < nedges; i++) {
|
||||
bonus->dvalue[k] = 0;
|
||||
*(&bonus->dvalue[k]+1) = 1;
|
||||
k += 2;
|
||||
}
|
||||
|
||||
erad = sqrt(erad2);
|
||||
bonus->dvalue[k] = erad;
|
||||
|
||||
// the last element of bonus->dvalue is the rounded radius
|
||||
|
||||
rrad = 0.5 * dfile[j];
|
||||
k++;
|
||||
bonus->dvalue[k] = rrad;
|
||||
|
||||
atom->radius[bonus->ilocal] = erad + rrad;
|
||||
|
||||
} else { // polyhedra
|
||||
|
||||
// edges
|
||||
|
||||
for (i = 0; i < nedges; i++) {
|
||||
bonus->dvalue[k] = dfile[j];
|
||||
*(&bonus->dvalue[k]+1) = dfile[j+1];
|
||||
k += 2;
|
||||
j += 2;
|
||||
}
|
||||
|
||||
// faces
|
||||
|
||||
for (i = 0; i < nfac; i++) {
|
||||
for (m = 0; m < MAX_FACE_SIZE; m++)
|
||||
*(&bonus->dvalue[k]+m) = dfile[j+m];
|
||||
k += MAX_FACE_SIZE;
|
||||
j += MAX_FACE_SIZE;
|
||||
}
|
||||
|
||||
// the next to last element is the enclosing radius
|
||||
|
||||
erad = sqrt(erad2);
|
||||
bonus->dvalue[k] = erad;
|
||||
|
||||
// the last element bonus-> dvalue is the rounded radius
|
||||
|
||||
rrad = 0.5 * dfile[j];
|
||||
k++;
|
||||
bonus->dvalue[k] = rrad;
|
||||
|
||||
atom->radius[bonus->ilocal] = erad + rrad;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return radius of body particle defined by ifile/dfile params
|
||||
params are ordered as in data file
|
||||
called by Molecule class which needs single body size
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BodyRoundedPolyhedron::radius_body(int ninteger, int ndouble,
|
||||
int *ifile, double *dfile)
|
||||
{
|
||||
int nsub = ifile[0];
|
||||
int ned = ifile[1];
|
||||
int nfac = ifile[2];
|
||||
int nedges = ned; //nsub + nfac - 2;
|
||||
|
||||
int nentries;
|
||||
if (nsub == 1 || nsub == 2) nentries = 6 + 3*nsub + 1;
|
||||
else nentries = 6 + 3*nsub + 2*nedges + MAX_FACE_SIZE*nfac + 1;
|
||||
|
||||
if (nsub < 1)
|
||||
error->one(FLERR,"Incorrect integer value in "
|
||||
"Bodies section of data file");
|
||||
if (ndouble != nentries)
|
||||
error->one(FLERR,"Incorrect # of floating-point values in "
|
||||
"Bodies section of data file");
|
||||
|
||||
// sub-particle coords are relative to body center at (0,0,0)
|
||||
// offset = 6 for sub-particle coords
|
||||
|
||||
double onerad;
|
||||
double maxrad = 0.0;
|
||||
double delta[3];
|
||||
|
||||
int offset = 6;
|
||||
for (int i = 0; i < nsub; i++) {
|
||||
delta[0] = dfile[offset];
|
||||
delta[1] = dfile[offset+1];
|
||||
delta[2] = dfile[offset+2];
|
||||
offset += 3;
|
||||
onerad = MathExtra::len3(delta);
|
||||
maxrad = MAX(maxrad,onerad);
|
||||
}
|
||||
|
||||
if (nsub > 2) offset += (2*nedges+MAX_FACE_SIZE*nfac);
|
||||
|
||||
// add in radius of rounded corners
|
||||
|
||||
return maxrad + 0.5*dfile[offset];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolyhedron::noutcol()
|
||||
{
|
||||
// the number of columns for the vertex coordinates
|
||||
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolyhedron::noutrow(int ibonus)
|
||||
{
|
||||
// only return the first nsub rows for the vertex coordinates
|
||||
|
||||
return avec->bonus[ibonus].ivalue[0];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BodyRoundedPolyhedron::output(int ibonus, int m, double *values)
|
||||
{
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
|
||||
double p[3][3];
|
||||
MathExtra::quat_to_mat(bonus->quat,p);
|
||||
MathExtra::matvec(p,&bonus->dvalue[3*m],values);
|
||||
|
||||
double *x = atom->x[bonus->ilocal];
|
||||
values[0] += x[0];
|
||||
values[1] += x[1];
|
||||
values[2] += x[2];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int BodyRoundedPolyhedron::image(int ibonus, double flag1, double flag2,
|
||||
int *&ivec, double **&darray)
|
||||
{
|
||||
int j, nelements;
|
||||
double p[3][3];
|
||||
double *x, rrad;
|
||||
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
int nvertices = bonus->ivalue[0];
|
||||
|
||||
if (nvertices == 1) { // spheres
|
||||
|
||||
for (int i = 0; i < nvertices; i++) {
|
||||
imflag[i] = SPHERE;
|
||||
MathExtra::quat_to_mat(bonus->quat,p);
|
||||
MathExtra::matvec(p,&bonus->dvalue[3*i],imdata[i]);
|
||||
|
||||
rrad = enclosing_radius(bonus);
|
||||
x = atom->x[bonus->ilocal];
|
||||
imdata[i][0] += x[0];
|
||||
imdata[i][1] += x[1];
|
||||
imdata[i][2] += x[2];
|
||||
if (flag1 <= 0) imdata[i][3] = 2*rrad;
|
||||
else imdata[i][3] = flag1;
|
||||
}
|
||||
|
||||
nelements = nvertices;
|
||||
} else {
|
||||
int nfaces = bonus->ivalue[2];
|
||||
int nedges = bonus->ivalue[1]; //nvertices + nfaces - 2;
|
||||
if (nvertices == 2) nedges = 1; // special case: rods
|
||||
double* edge_ends = &bonus->dvalue[3*nvertices];
|
||||
int pt1, pt2;
|
||||
|
||||
for (int i = 0; i < nedges; i++) {
|
||||
imflag[i] = LINE;
|
||||
|
||||
pt1 = static_cast<int>(edge_ends[2*i]);
|
||||
pt2 = static_cast<int>(edge_ends[2*i+1]);
|
||||
|
||||
MathExtra::quat_to_mat(bonus->quat,p);
|
||||
MathExtra::matvec(p,&bonus->dvalue[3*pt1],imdata[i]);
|
||||
MathExtra::matvec(p,&bonus->dvalue[3*pt2],&imdata[i][3]);
|
||||
|
||||
rrad = rounded_radius(bonus);
|
||||
x = atom->x[bonus->ilocal];
|
||||
imdata[i][0] += x[0];
|
||||
imdata[i][1] += x[1];
|
||||
imdata[i][2] += x[2];
|
||||
imdata[i][3] += x[0];
|
||||
imdata[i][4] += x[1];
|
||||
imdata[i][5] += x[2];
|
||||
|
||||
if (flag1 <= 0) imdata[i][6] = 2*rrad;
|
||||
else imdata[i][6] = flag1;
|
||||
}
|
||||
|
||||
nelements = nedges;
|
||||
}
|
||||
|
||||
ivec = imflag;
|
||||
darray = imdata;
|
||||
return nelements;
|
||||
}
|
||||
|
|
@ -0,0 +1,88 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BODY_CLASS
|
||||
|
||||
BodyStyle(rounded/polyhedron,BodyRoundedPolyhedron)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_BODY_ROUNDED_POLYHEDRON_H
|
||||
#define LMP_BODY_ROUNDED_POLYHEDRON_H
|
||||
|
||||
#include "body.h"
|
||||
#include "atom_vec_body.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BodyRoundedPolyhedron : public Body {
|
||||
public:
|
||||
BodyRoundedPolyhedron(class LAMMPS *, int, char **);
|
||||
~BodyRoundedPolyhedron();
|
||||
int nsub(struct AtomVecBody::Bonus *);
|
||||
double *coords(struct AtomVecBody::Bonus *);
|
||||
int nedges(struct AtomVecBody::Bonus *);
|
||||
double *edges(struct AtomVecBody::Bonus *);
|
||||
int nfaces(struct AtomVecBody::Bonus *);
|
||||
double *faces(struct AtomVecBody::Bonus *);
|
||||
double enclosing_radius(struct AtomVecBody::Bonus *);
|
||||
double rounded_radius(struct AtomVecBody::Bonus *);
|
||||
|
||||
int pack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
int unpack_border_body(struct AtomVecBody::Bonus *, double *);
|
||||
void data_body(int, int, int, int *, double *);
|
||||
double radius_body(int, int, int *, double *);
|
||||
|
||||
int noutrow(int);
|
||||
int noutcol();
|
||||
void output(int, int, double *);
|
||||
int image(int, double, double, int *&, double **&);
|
||||
|
||||
private:
|
||||
int *imflag;
|
||||
double **imdata;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Invalid body rounded/polyhedron command
|
||||
|
||||
Arguments in atom-style command are not correct.
|
||||
|
||||
E: Invalid format in Bodies section of data file
|
||||
|
||||
The specified number of integer or floating point values does not
|
||||
appear.
|
||||
|
||||
E: Incorrect # of integer values in Bodies section of data file
|
||||
|
||||
See doc page for body style.
|
||||
|
||||
E: Incorrect integer value in Bodies section of data file
|
||||
|
||||
See doc page for body style.
|
||||
|
||||
E: Incorrect # of floating-point values in Bodies section of data file
|
||||
|
||||
See doc page for body style.
|
||||
|
||||
E: Insufficient Jacobi rotations for body rounded/polyhedron
|
||||
|
||||
Eigensolve for rigid body was not sufficiently accurate.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,832 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cmath>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "fix_wall_body_polygon.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "body_rounded_polygon.h"
|
||||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "modify.h"
|
||||
#include "respa.h"
|
||||
#include "math_const.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
using namespace MathConst;
|
||||
|
||||
enum{XPLANE=0,YPLANE=1,ZCYLINDER}; // XYZ PLANE need to be 0,1,2
|
||||
enum{HOOKE,HOOKE_HISTORY};
|
||||
|
||||
enum {INVALID=0,NONE=1,VERTEX=2};
|
||||
enum {FAR=0,XLO,XHI,YLO,YHI};
|
||||
|
||||
//#define _POLYGON_DEBUG
|
||||
#define DELTA 10000
|
||||
#define EPSILON 1e-2
|
||||
#define BIG 1.0e20
|
||||
#define MAX_CONTACTS 4 // maximum number of contacts for 2D models
|
||||
#define EFF_CONTACTS 2 // effective contacts for 2D models
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixWallBodyPolygon::FixWallBodyPolygon(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 7) error->all(FLERR,"Illegal fix wall/body/polygon command");
|
||||
|
||||
if (!atom->body_flag)
|
||||
error->all(FLERR,"Fix wall/body/polygon requires "
|
||||
"atom style body/rounded/polygon");
|
||||
|
||||
restart_peratom = 1;
|
||||
create_attribute = 1;
|
||||
|
||||
// wall/particle coefficients
|
||||
|
||||
kn = force->numeric(FLERR,arg[3]);
|
||||
|
||||
c_n = force->numeric(FLERR,arg[4]);
|
||||
if (strcmp(arg[5],"NULL") == 0) c_t = 0.5 * c_n;
|
||||
else c_t = force->numeric(FLERR,arg[5]);
|
||||
|
||||
if (kn < 0.0 || c_n < 0.0 || c_t < 0.0)
|
||||
error->all(FLERR,"Illegal fix wall/body/polygon command");
|
||||
|
||||
// wallstyle args
|
||||
|
||||
int iarg = 6;
|
||||
if (strcmp(arg[iarg],"xplane") == 0) {
|
||||
if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polygon command");
|
||||
wallstyle = XPLANE;
|
||||
if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG;
|
||||
else lo = force->numeric(FLERR,arg[iarg+1]);
|
||||
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
|
||||
else hi = force->numeric(FLERR,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg],"yplane") == 0) {
|
||||
if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polygon command");
|
||||
wallstyle = YPLANE;
|
||||
if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG;
|
||||
else lo = force->numeric(FLERR,arg[iarg+1]);
|
||||
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
|
||||
else hi = force->numeric(FLERR,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg],"zcylinder") == 0) {
|
||||
if (narg < iarg+2) error->all(FLERR,"Illegal fix wall/body/polygon command");
|
||||
wallstyle = ZCYLINDER;
|
||||
lo = hi = 0.0;
|
||||
cylradius = force->numeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
}
|
||||
|
||||
// check for trailing keyword/values
|
||||
|
||||
wiggle = 0;
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"wiggle") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/body/polygon command");
|
||||
if (strcmp(arg[iarg+1],"x") == 0) axis = 0;
|
||||
else if (strcmp(arg[iarg+1],"y") == 0) axis = 1;
|
||||
else if (strcmp(arg[iarg+1],"z") == 0) axis = 2;
|
||||
else error->all(FLERR,"Illegal fix wall/body/polygon command");
|
||||
amplitude = force->numeric(FLERR,arg[iarg+2]);
|
||||
period = force->numeric(FLERR,arg[iarg+3]);
|
||||
wiggle = 1;
|
||||
iarg += 4;
|
||||
} else error->all(FLERR,"Illegal fix wall/body/polygon command");
|
||||
}
|
||||
|
||||
if (wallstyle == XPLANE && domain->xperiodic)
|
||||
error->all(FLERR,"Cannot use wall in periodic dimension");
|
||||
if (wallstyle == YPLANE && domain->yperiodic)
|
||||
error->all(FLERR,"Cannot use wall in periodic dimension");
|
||||
if (wallstyle == ZCYLINDER && (domain->xperiodic || domain->yperiodic))
|
||||
error->all(FLERR,"Cannot use wall in periodic dimension");
|
||||
|
||||
if (wiggle && wallstyle == ZCYLINDER && axis != 2)
|
||||
error->all(FLERR,"Invalid wiggle direction for fix wall/body/polygon");
|
||||
|
||||
// setup oscillations
|
||||
|
||||
if (wiggle) omega = 2.0*MY_PI / period;
|
||||
|
||||
time_origin = update->ntimestep;
|
||||
|
||||
dmax = nmax = 0;
|
||||
discrete = NULL;
|
||||
dnum = dfirst = NULL;
|
||||
|
||||
edmax = ednummax = 0;
|
||||
edge = NULL;
|
||||
ednum = edfirst = NULL;
|
||||
|
||||
enclosing_radius = NULL;
|
||||
rounded_radius = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixWallBodyPolygon::~FixWallBodyPolygon()
|
||||
{
|
||||
memory->destroy(discrete);
|
||||
memory->destroy(dnum);
|
||||
memory->destroy(dfirst);
|
||||
|
||||
memory->destroy(edge);
|
||||
memory->destroy(ednum);
|
||||
memory->destroy(edfirst);
|
||||
|
||||
memory->destroy(enclosing_radius);
|
||||
memory->destroy(rounded_radius);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallBodyPolygon::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= POST_FORCE;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolygon::init()
|
||||
{
|
||||
dt = update->dt;
|
||||
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
if (!avec)
|
||||
error->all(FLERR,"Pair body/rounded/polygon requires atom style body");
|
||||
if (strcmp(avec->bptr->style,"rounded/polygon") != 0)
|
||||
error->all(FLERR,"Pair body/rounded/polygon requires "
|
||||
"body style rounded/polygon");
|
||||
bptr = (BodyRoundedPolygon *) avec->bptr;
|
||||
|
||||
// set pairstyle from body/polygonular pair style
|
||||
|
||||
if (force->pair_match("body/rounded/polygon",1))
|
||||
pairstyle = HOOKE;
|
||||
else error->all(FLERR,"Fix wall/body/polygon is incompatible with Pair style");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolygon::setup(int vflag)
|
||||
{
|
||||
if (strstr(update->integrate_style,"verlet"))
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolygon::post_force(int vflag)
|
||||
{
|
||||
double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos;
|
||||
int i,ni,npi,ifirst,nei,iefirst,side;
|
||||
double facc[3];
|
||||
|
||||
// set position of wall to initial settings and velocity to 0.0
|
||||
// if wiggle, set wall position and velocity accordingly
|
||||
|
||||
double wlo = lo;
|
||||
double whi = hi;
|
||||
vwall[0] = vwall[1] = vwall[2] = 0.0;
|
||||
if (wiggle) {
|
||||
double arg = omega * (update->ntimestep - time_origin) * dt;
|
||||
if (wallstyle == axis) {
|
||||
wlo = lo + amplitude - amplitude*cos(arg);
|
||||
whi = hi + amplitude - amplitude*cos(arg);
|
||||
}
|
||||
vwall[axis] = amplitude*omega*sin(arg);
|
||||
}
|
||||
|
||||
// loop over all my atoms
|
||||
// rsq = distance from wall
|
||||
// dx,dy,dz = signed distance from wall
|
||||
// for rotating cylinder, reset vwall based on particle position
|
||||
// skip atom if not close enough to wall
|
||||
// if wall was set to NULL, it's skipped since lo/hi are infinity
|
||||
// compute force and torque on atom if close enough to wall
|
||||
// via wall potential matched to pair potential
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
int *body = atom->body;
|
||||
double *radius = atom->radius;
|
||||
double **torque = atom->torque;
|
||||
double **angmom = atom->angmom;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// grow the per-atom lists if necessary and initialize
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
memory->destroy(dnum);
|
||||
memory->destroy(dfirst);
|
||||
memory->destroy(ednum);
|
||||
memory->destroy(edfirst);
|
||||
memory->destroy(enclosing_radius);
|
||||
memory->destroy(rounded_radius);
|
||||
nmax = atom->nmax;
|
||||
memory->create(dnum,nmax,"fix:dnum");
|
||||
memory->create(dfirst,nmax,"fix:dfirst");
|
||||
memory->create(ednum,nmax,"fix:ednum");
|
||||
memory->create(edfirst,nmax,"fix:edfirst");
|
||||
memory->create(enclosing_radius,nmax,"fix:enclosing_radius");
|
||||
memory->create(rounded_radius,nmax,"fix:rounded_radius");
|
||||
}
|
||||
|
||||
ndiscrete = nedge = 0;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
dnum[i] = ednum[i] = 0;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
|
||||
if (body[i] < 0) continue;
|
||||
|
||||
dx = dy = dz = 0.0;
|
||||
side = FAR;
|
||||
if (wallstyle == XPLANE) {
|
||||
del1 = x[i][0] - wlo;
|
||||
del2 = whi - x[i][0];
|
||||
if (del1 < del2) {
|
||||
dx = del1;
|
||||
wall_pos = wlo;
|
||||
side = XLO;
|
||||
} else {
|
||||
dx = -del2;
|
||||
wall_pos = whi;
|
||||
side = XHI;
|
||||
}
|
||||
} else if (wallstyle == YPLANE) {
|
||||
del1 = x[i][1] - wlo;
|
||||
del2 = whi - x[i][1];
|
||||
if (del1 < del2) {
|
||||
dy = del1;
|
||||
wall_pos = wlo;
|
||||
side = YLO;
|
||||
} else {
|
||||
dy = -del2;
|
||||
wall_pos = whi;
|
||||
side = YHI;
|
||||
}
|
||||
} else if (wallstyle == ZCYLINDER) {
|
||||
delxy = sqrt(x[i][0]*x[i][0] + x[i][1]*x[i][1]);
|
||||
delr = cylradius - delxy;
|
||||
if (delr > eradi) dz = cylradius;
|
||||
else {
|
||||
dx = -delr/delxy * x[i][0];
|
||||
dy = -delr/delxy * x[i][1];
|
||||
}
|
||||
}
|
||||
|
||||
rsq = dx*dx + dy*dy + dz*dz;
|
||||
if (rsq > radius[i]*radius[i]) continue;
|
||||
|
||||
double r = sqrt(rsq);
|
||||
double rsqinv = 1.0 / rsq;
|
||||
|
||||
if (dnum[i] == 0) body2space(i);
|
||||
npi = dnum[i];
|
||||
ifirst = dfirst[i];
|
||||
nei = ednum[i];
|
||||
iefirst = edfirst[i];
|
||||
eradi = enclosing_radius[i];
|
||||
rradi = rounded_radius[i];
|
||||
|
||||
// reset vertex and edge forces
|
||||
|
||||
for (ni = 0; ni < npi; ni++) {
|
||||
discrete[ifirst+ni][3] = 0;
|
||||
discrete[ifirst+ni][4] = 0;
|
||||
discrete[ifirst+ni][5] = 0;
|
||||
}
|
||||
|
||||
for (ni = 0; ni < nei; ni++) {
|
||||
edge[iefirst+ni][2] = 0;
|
||||
edge[iefirst+ni][3] = 0;
|
||||
edge[iefirst+ni][4] = 0;
|
||||
}
|
||||
|
||||
int interact, num_contacts, done;
|
||||
double delta_a, delta_ua, j_a;
|
||||
Contact contact_list[MAX_CONTACTS];
|
||||
|
||||
num_contacts = 0;
|
||||
facc[0] = facc[1] = facc[2] = 0;
|
||||
interact = vertex_against_wall(i, wall_pos, x, f, torque, side,
|
||||
contact_list, num_contacts, facc);
|
||||
|
||||
if (num_contacts >= 2) {
|
||||
|
||||
// find the first two distinct contacts
|
||||
|
||||
done = 0;
|
||||
for (int m = 0; m < num_contacts-1; m++) {
|
||||
for (int n = m+1; n < num_contacts; n++) {
|
||||
delta_a = contact_separation(contact_list[m], contact_list[n]);
|
||||
if (delta_a > 0) {
|
||||
delta_ua = 1.0;
|
||||
j_a = delta_a / (EFF_CONTACTS * delta_ua);
|
||||
if (j_a < 1.0) j_a = 1.0;
|
||||
|
||||
// scale the force at both contacts
|
||||
|
||||
contact_forces(contact_list[m], j_a, x, v, angmom, f, torque,
|
||||
vwall, facc);
|
||||
contact_forces(contact_list[n], j_a, x, v, angmom, f, torque,
|
||||
vwall, facc);
|
||||
done = 1;
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (done == 1) break;
|
||||
}
|
||||
|
||||
} else if (num_contacts == 1) {
|
||||
|
||||
// if there's only one contact, it should be handled here
|
||||
// since forces/torques have not been accumulated from vertex2wall()
|
||||
|
||||
contact_forces(contact_list[0], 1.0, x, v, angmom, f, torque,
|
||||
vwall, facc);
|
||||
}
|
||||
} // group bit
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolygon::reset_dt()
|
||||
{
|
||||
dt = update->dt;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert N sub-particles in body I to space frame using current quaternion
|
||||
store sub-particle space-frame displacements from COM in discrete list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolygon::body2space(int i)
|
||||
{
|
||||
int ibonus = atom->body[i];
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
int nsub = bptr->nsub(bonus);
|
||||
double *coords = bptr->coords(bonus);
|
||||
int body_num_edges = bptr->nedges(bonus);
|
||||
double* vertices = bptr->edges(bonus);
|
||||
double eradius = bptr->enclosing_radius(bonus);
|
||||
double rradius = bptr->rounded_radius(bonus);
|
||||
|
||||
// get the number of sub-particles (vertices)
|
||||
// and the index of the first vertex of my body in the list
|
||||
|
||||
dnum[i] = nsub;
|
||||
dfirst[i] = ndiscrete;
|
||||
|
||||
// grow the vertex list if necessary
|
||||
// the first 3 columns are for coords, the last 3 for forces
|
||||
|
||||
if (ndiscrete + nsub > dmax) {
|
||||
dmax += DELTA;
|
||||
memory->grow(discrete,dmax,6,"fix:discrete");
|
||||
}
|
||||
|
||||
double p[3][3];
|
||||
MathExtra::quat_to_mat(bonus->quat,p);
|
||||
|
||||
for (int m = 0; m < nsub; m++) {
|
||||
MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]);
|
||||
discrete[ndiscrete][3] = 0;
|
||||
discrete[ndiscrete][4] = 0;
|
||||
discrete[ndiscrete][5] = 0;
|
||||
ndiscrete++;
|
||||
}
|
||||
|
||||
// get the number of edges (vertices)
|
||||
// and the index of the first edge of my body in the list
|
||||
|
||||
ednum[i] = body_num_edges;
|
||||
edfirst[i] = nedge;
|
||||
|
||||
// grow the edge list if necessary
|
||||
// the first 2 columns are for vertex indices within body,
|
||||
// the last 3 for forces
|
||||
|
||||
if (nedge + body_num_edges > edmax) {
|
||||
edmax += DELTA;
|
||||
memory->grow(edge,edmax,5,"fix:edge");
|
||||
}
|
||||
|
||||
for (int m = 0; m < body_num_edges; m++) {
|
||||
edge[nedge][0] = static_cast<int>(vertices[2*m+0]);
|
||||
edge[nedge][1] = static_cast<int>(vertices[2*m+1]);
|
||||
edge[nedge][2] = 0;
|
||||
edge[nedge][3] = 0;
|
||||
edge[nedge][4] = 0;
|
||||
nedge++;
|
||||
}
|
||||
|
||||
enclosing_radius[i] = eradius;
|
||||
rounded_radius[i] = rradius;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Determine the interaction mode between i's vertices against the wall
|
||||
|
||||
i = atom i (body i)
|
||||
x = atoms' coordinates
|
||||
f = atoms' forces
|
||||
torque = atoms' torques
|
||||
Return:
|
||||
contact_list = list of contacts between i and the wall
|
||||
num_contacts = number of contacts between i's vertices and the wall
|
||||
interact = 0 no interaction with the wall
|
||||
1 there's at least one vertex of i interacts
|
||||
with the wall
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos,
|
||||
double** x, double** f, double** torque, int side,
|
||||
Contact* contact_list, int &num_contacts, double* facc)
|
||||
{
|
||||
int ni, npi, ifirst, interact;
|
||||
double xpi[3], xpj[3], dist, eradi, rradi;
|
||||
double fx, fy, fz, rx, ry, rz;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
npi = dnum[i];
|
||||
ifirst = dfirst[i];
|
||||
eradi = enclosing_radius[i];
|
||||
rradi = rounded_radius[i];
|
||||
|
||||
interact = 0;
|
||||
|
||||
// loop through body i's vertices
|
||||
|
||||
for (ni = 0; ni < npi; ni++) {
|
||||
|
||||
// convert body-fixed coordinates to space-fixed, xi
|
||||
|
||||
xpi[0] = x[i][0] + discrete[ifirst+ni][0];
|
||||
xpi[1] = x[i][1] + discrete[ifirst+ni][1];
|
||||
xpi[2] = x[i][2] + discrete[ifirst+ni][2];
|
||||
|
||||
int mode, contact, p2vertex;
|
||||
double d, R, hi[3], t, delx, dely, delz, fpair, shift;
|
||||
double xj[3], rij;
|
||||
|
||||
// compute the distance from the vertex xpi to the wall
|
||||
|
||||
mode = compute_distance_to_wall(xpi, rradi, wall_pos, side,
|
||||
d, hi, contact);
|
||||
|
||||
if (mode == INVALID || mode == NONE) continue;
|
||||
|
||||
if (mode == VERTEX) {
|
||||
|
||||
interact = 1;
|
||||
|
||||
// vertex i interacts with the wall
|
||||
|
||||
delx = xpi[0] - hi[0];
|
||||
dely = xpi[1] - hi[1];
|
||||
delz = xpi[2] - hi[2];
|
||||
|
||||
// R = surface separation = d shifted by the rounded radius
|
||||
// R = d - p1.rounded_radius;
|
||||
// note: the force is defined for R, not for d
|
||||
// R > 0: no interaction
|
||||
// R <= 0: deformation between vertex i and the wall
|
||||
|
||||
rij = sqrt(delx*delx + dely*dely + delz*delz);
|
||||
R = rij - rradi;
|
||||
|
||||
// the normal frictional term -c_n * vn will be added later
|
||||
|
||||
if (R <= 0) { // deformation occurs
|
||||
fpair = -kn * R;
|
||||
} else fpair = 0.0;
|
||||
|
||||
fx = delx*fpair/rij;
|
||||
fy = dely*fpair/rij;
|
||||
fz = delz*fpair/rij;
|
||||
|
||||
#ifdef _POLYGON_DEBUG
|
||||
printf(" Interaction between vertex %d of %d and wall:", ni);
|
||||
printf(" mode = %d; contact = %d; d = %f; rij = %f\n",
|
||||
mode, contact, d, rij);
|
||||
printf(" R = %f\n", R);
|
||||
printf(" fpair = %f\n", fpair);
|
||||
#endif
|
||||
|
||||
if (contact == 1) {
|
||||
|
||||
// vertex ni of body i contacts with edge nj of body j
|
||||
|
||||
contact_list[num_contacts].ibody = i;
|
||||
contact_list[num_contacts].jbody = -1;
|
||||
contact_list[num_contacts].vertex = ni;
|
||||
contact_list[num_contacts].edge = -1;
|
||||
contact_list[num_contacts].xv[0] = xpi[0];
|
||||
contact_list[num_contacts].xv[1] = xpi[1];
|
||||
contact_list[num_contacts].xv[2] = xpi[2];
|
||||
contact_list[num_contacts].xe[0] = hi[0];
|
||||
contact_list[num_contacts].xe[1] = hi[1];
|
||||
contact_list[num_contacts].xe[2] = hi[2];
|
||||
contact_list[num_contacts].separation = R;
|
||||
num_contacts++;
|
||||
|
||||
// store forces to vertex ni to be rescaled later,
|
||||
// if there are 2 contacts
|
||||
|
||||
discrete[ifirst+ni][3] = fx;
|
||||
discrete[ifirst+ni][4] = fy;
|
||||
discrete[ifirst+ni][5] = fz;
|
||||
|
||||
#ifdef _POLYGON_DEBUG
|
||||
printf(" Stored forces at vertex and edge for accumulating later.\n");
|
||||
#endif
|
||||
|
||||
} else { // no contact
|
||||
|
||||
// accumulate force and torque to the body directly
|
||||
|
||||
f[i][0] += fx;
|
||||
f[i][1] += fy;
|
||||
f[i][2] += fz;
|
||||
sum_torque(x[i], xpi, fx, fy, fz, torque[i]);
|
||||
|
||||
} // end if contact
|
||||
|
||||
} // end if mode
|
||||
|
||||
} // end for looping through the vertices of body i
|
||||
|
||||
return interact;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------------
|
||||
Compute the distance between a vertex to the wall
|
||||
another body
|
||||
Input:
|
||||
x0 = coordinate of the tested vertex
|
||||
rradi = rounded radius of the vertex
|
||||
wall_pos = position of the wall
|
||||
Output:
|
||||
d = Distance from a point x0 to an wall
|
||||
hi = coordinates of the projection of x0 on the wall
|
||||
contact = 0 no contact between the queried vertex and the wall
|
||||
1 contact detected
|
||||
return NONE if there is no interaction
|
||||
EDGE if the tested vertex interacts with the wall
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixWallBodyPolygon::compute_distance_to_wall(double* x0, double rradi,
|
||||
double wall_pos, int side, double &d, double hi[3], int &contact)
|
||||
{
|
||||
int mode;
|
||||
double delxy;
|
||||
|
||||
// h0 = position of the projection of x0 on the wall
|
||||
if (wallstyle == XPLANE) {
|
||||
hi[0] = wall_pos;
|
||||
hi[1] = x0[1];
|
||||
hi[2] = x0[2];
|
||||
} else if (wallstyle == YPLANE) {
|
||||
hi[0] = x0[0];
|
||||
hi[1] = wall_pos;
|
||||
hi[2] = x0[2];
|
||||
} else if (wallstyle == ZCYLINDER) {
|
||||
delxy = sqrt(x0[0]*x0[0] + x0[1]*x0[1]);
|
||||
hi[0] = x0[0]*cylradius/delxy;
|
||||
hi[1] = x0[1]*cylradius/delxy;
|
||||
hi[2] = x0[2];
|
||||
}
|
||||
|
||||
// distance from x0 to the wall = distance from x0 to hi
|
||||
|
||||
distance(hi, x0, d);
|
||||
|
||||
// determine the interaction mode
|
||||
|
||||
if (d < rradi) {
|
||||
mode = VERTEX;
|
||||
contact = 1;
|
||||
} else {
|
||||
if (side == XLO) {
|
||||
if (x0[0] < wall_pos) mode = VERTEX;
|
||||
else mode = NONE;
|
||||
} else if (side == XHI) {
|
||||
if (x0[0] > wall_pos) mode = VERTEX;
|
||||
else mode = NONE;
|
||||
} else if (side == YLO) {
|
||||
if (x0[1] < wall_pos) mode = VERTEX;
|
||||
else mode = NONE;
|
||||
} else if (side == YHI) {
|
||||
if (x0[1] > wall_pos) mode = VERTEX;
|
||||
else mode = NONE;
|
||||
}
|
||||
}
|
||||
|
||||
if (mode == NONE) contact = 0;
|
||||
else contact = 1;
|
||||
|
||||
return mode;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Compute the contact forces between two bodies
|
||||
modify the force stored at the vertex and edge in contact by j_a
|
||||
sum forces and torque to the corresponding bodies
|
||||
fn = normal friction component
|
||||
ft = tangential friction component (-c_t * vrt)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolygon::contact_forces(Contact& contact, double j_a,
|
||||
double** x, double** v, double** angmom, double** f,
|
||||
double** torque, double* vwall, double* facc)
|
||||
{
|
||||
int ibody,ibonus,ifirst, jefirst, ni;
|
||||
double fx,fy,fz,delx,dely,delz,rsq,rsqinv;
|
||||
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
|
||||
double fn[3],ft[3],vi[3];
|
||||
double *quat, *inertia;
|
||||
AtomVecBody::Bonus *bonus;
|
||||
|
||||
ibody = contact.ibody;
|
||||
|
||||
// compute the velocity of the vertex in the space-fixed frame
|
||||
|
||||
ibonus = atom->body[ibody];
|
||||
bonus = &avec->bonus[ibonus];
|
||||
quat = bonus->quat;
|
||||
inertia = bonus->inertia;
|
||||
total_velocity(contact.xv, x[ibody], v[ibody], angmom[ibody],
|
||||
inertia, quat, vi);
|
||||
|
||||
// vector pointing from the vertex to the point on the wall
|
||||
|
||||
delx = contact.xv[0] - contact.xe[0];
|
||||
dely = contact.xv[1] - contact.xe[1];
|
||||
delz = contact.xv[2] - contact.xe[2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rsqinv = 1.0/rsq;
|
||||
|
||||
// relative translational velocity
|
||||
|
||||
vr1 = vi[0] - vwall[0];
|
||||
vr2 = vi[1] - vwall[1];
|
||||
vr3 = vi[2] - vwall[2];
|
||||
|
||||
// normal component
|
||||
|
||||
vnnr = vr1*delx + vr2*dely + vr3*delz;
|
||||
vn1 = delx*vnnr * rsqinv;
|
||||
vn2 = dely*vnnr * rsqinv;
|
||||
vn3 = delz*vnnr * rsqinv;
|
||||
|
||||
// tangential component
|
||||
|
||||
vt1 = vr1 - vn1;
|
||||
vt2 = vr2 - vn2;
|
||||
vt3 = vr3 - vn3;
|
||||
|
||||
// normal friction term at contact
|
||||
|
||||
fn[0] = -c_n * vn1;
|
||||
fn[1] = -c_n * vn2;
|
||||
fn[2] = -c_n * vn3;
|
||||
|
||||
// tangential friction term at contact
|
||||
// excluding the tangential deformation term for now
|
||||
|
||||
ft[0] = -c_t * vt1;
|
||||
ft[1] = -c_t * vt2;
|
||||
ft[2] = -c_t * vt3;
|
||||
|
||||
// only the cohesive force is scaled by j_a
|
||||
|
||||
ifirst = dfirst[ibody];
|
||||
ni = contact.vertex;
|
||||
|
||||
fx = discrete[ifirst+ni][3] * j_a + fn[0] + ft[0];
|
||||
fy = discrete[ifirst+ni][4] * j_a + fn[1] + ft[1];
|
||||
fz = discrete[ifirst+ni][5] * j_a + fn[2] + ft[2];
|
||||
f[ibody][0] += fx;
|
||||
f[ibody][1] += fy;
|
||||
f[ibody][2] += fz;
|
||||
sum_torque(x[ibody], contact.xv, fx, fy, fz, torque[ibody]);
|
||||
|
||||
// accumulate forces to the vertex only
|
||||
|
||||
facc[0] += fx; facc[1] += fy; facc[2] += fz;
|
||||
|
||||
#ifdef _POLYGON_DEBUG
|
||||
printf("From contact forces: vertex fx %f fy %f fz %f\n"
|
||||
" torque body %d: %f %f %f\n",
|
||||
discrete[ifirst+ni][3], discrete[ifirst+ni][4], discrete[ifirst+ni][5],
|
||||
atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2]);
|
||||
#endif
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Determine the length of the contact segment, i.e. the separation between
|
||||
2 contacts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixWallBodyPolygon::contact_separation(const Contact& c1,
|
||||
const Contact& c2)
|
||||
{
|
||||
double x1 = c1.xv[0];
|
||||
double y1 = c1.xv[1];
|
||||
double x2 = c1.xe[0];
|
||||
double y2 = c1.xe[1];
|
||||
double x3 = c2.xv[0];
|
||||
double y3 = c2.xv[1];
|
||||
|
||||
double delta_a = 0.0;
|
||||
if (fabs(x2 - x1) > EPSILON) {
|
||||
double A = (y2 - y1) / (x2 - x1);
|
||||
delta_a = fabs(y1 - A * x1 - y3 + A * x3) / sqrt(1 + A * A);
|
||||
} else {
|
||||
delta_a = fabs(x1 - x3);
|
||||
}
|
||||
|
||||
return delta_a;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Accumulate torque to body from the force f=(fx,fy,fz) acting at point x
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolygon::sum_torque(double* xm, double *x, double fx,
|
||||
double fy, double fz, double* torque)
|
||||
{
|
||||
double rx = x[0] - xm[0];
|
||||
double ry = x[1] - xm[1];
|
||||
double rz = x[2] - xm[2];
|
||||
double tx = ry * fz - rz * fy;
|
||||
double ty = rz * fx - rx * fz;
|
||||
double tz = rx * fy - ry * fx;
|
||||
torque[0] += tx;
|
||||
torque[1] += ty;
|
||||
torque[2] += tz;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Calculate the total velocity of a point (vertex, a point on an edge):
|
||||
vi = vcm + omega ^ (p - xcm)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolygon::total_velocity(double* p, double *xcm,
|
||||
double* vcm, double *angmom, double *inertia,
|
||||
double *quat, double* vi)
|
||||
{
|
||||
double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3];
|
||||
r[0] = p[0] - xcm[0];
|
||||
r[1] = p[1] - xcm[1];
|
||||
r[2] = p[2] - xcm[2];
|
||||
MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space);
|
||||
MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space,
|
||||
inertia,omega);
|
||||
vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0];
|
||||
vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1];
|
||||
vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolygon::distance(const double* x2, const double* x1,
|
||||
double& r) {
|
||||
r = sqrt((x2[0] - x1[0]) * (x2[0] - x1[0])
|
||||
+ (x2[1] - x1[1]) * (x2[1] - x1[1])
|
||||
+ (x2[2] - x1[2]) * (x2[2] - x1[2]));
|
||||
}
|
||||
|
|
@ -0,0 +1,131 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(wall/body/polygon,FixWallBodyPolygon)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_WALL_BODY_POLYGON_H
|
||||
#define LMP_FIX_WALL_BODY_POLYGON_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixWallBodyPolygon : public Fix {
|
||||
public:
|
||||
FixWallBodyPolygon(class LAMMPS *, int, char **);
|
||||
virtual ~FixWallBodyPolygon();
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
virtual void post_force(int);
|
||||
void reset_dt();
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int vertex; // vertex of the first polygon
|
||||
int edge; // edge of the second polygon
|
||||
double xv[3]; // coordinates of the vertex
|
||||
double xe[3]; // coordinates of the projection of the vertex on the edge
|
||||
double separation;// separation at contact
|
||||
};
|
||||
|
||||
protected:
|
||||
int wallstyle,pairstyle,wiggle,axis;
|
||||
double kn; // normal repulsion strength
|
||||
double c_n; // normal damping coefficient
|
||||
double c_t; // tangential damping coefficient
|
||||
double lo,hi,cylradius;
|
||||
double amplitude,period,omega;
|
||||
double dt;
|
||||
int time_origin;
|
||||
|
||||
class AtomVecBody *avec;
|
||||
class BodyRoundedPolygon *bptr;
|
||||
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
|
||||
void body2space(int);
|
||||
|
||||
int vertex_against_wall(int ibody, double wall_pos, double** x,
|
||||
double** f, double** torque, int side,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
double* facc);
|
||||
|
||||
int compute_distance_to_wall(double* x0, double rradi, double wall_pos,
|
||||
int side, double &d, double hi[3], int &contact);
|
||||
double contact_separation(const Contact& c1, const Contact& c2);
|
||||
void contact_forces(Contact& contact, double j_a, double** x,
|
||||
double** v, double** angmom, double** f, double** torque,
|
||||
double* vwall, double* facc);
|
||||
void sum_torque(double* xm, double *x, double fx,
|
||||
double fy, double fz, double* torque);
|
||||
void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
|
||||
double *inertia, double *quat, double* vi);
|
||||
void distance(const double* x2, const double* x1, double& r);
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Fix wall/body/polygon requires atom style body rounded/polygon
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot use wall in periodic dimension
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot wiggle and shear fix wall/body/polygon
|
||||
|
||||
Cannot specify both options at the same time.
|
||||
|
||||
E: Invalid wiggle direction for fix wall/body/polygon
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix wall/body/polygon is incompatible with Pair style
|
||||
|
||||
Must use a body pair style to define the parameters needed for
|
||||
this fix.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,945 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing author: Trung Dac Nguyen (ndactrung@gmail.com)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <cmath>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "fix_wall_body_polyhedron.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec_body.h"
|
||||
#include "body_rounded_polyhedron.h"
|
||||
#include "domain.h"
|
||||
#include "update.h"
|
||||
#include "force.h"
|
||||
#include "pair.h"
|
||||
#include "modify.h"
|
||||
#include "respa.h"
|
||||
#include "math_const.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
using namespace MathConst;
|
||||
|
||||
enum{XPLANE=0,YPLANE=1,ZPLANE}; // XYZ PLANE need to be 0,1,2
|
||||
enum{HOOKE,HOOKE_HISTORY};
|
||||
|
||||
enum {INVALID=0,NONE=1,VERTEX=2};
|
||||
enum {FAR=0,XLO,XHI,YLO,YHI,ZLO,ZHI};
|
||||
|
||||
//#define _POLYHEDRON_DEBUG
|
||||
#define DELTA 10000
|
||||
#define EPSILON 1e-2
|
||||
#define BIG 1.0e20
|
||||
#define MAX_CONTACTS 4 // maximum number of contacts for 2D models
|
||||
#define EFF_CONTACTS 2 // effective contacts for 2D models
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixWallBodyPolyhedron::FixWallBodyPolyhedron(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 7) error->all(FLERR,"Illegal fix wall/body/polyhedron command");
|
||||
|
||||
if (!atom->body_flag)
|
||||
error->all(FLERR,"Fix wall/body/polyhedron requires "
|
||||
"atom style body/rounded/polyhedron");
|
||||
|
||||
restart_peratom = 1;
|
||||
create_attribute = 1;
|
||||
|
||||
// wall/particle coefficients
|
||||
|
||||
kn = force->numeric(FLERR,arg[3]);
|
||||
|
||||
c_n = force->numeric(FLERR,arg[4]);
|
||||
if (strcmp(arg[5],"NULL") == 0) c_t = 0.5 * c_n;
|
||||
else c_t = force->numeric(FLERR,arg[5]);
|
||||
|
||||
if (kn < 0.0 || c_n < 0.0 || c_t < 0.0)
|
||||
error->all(FLERR,"Illegal fix wall/body/polyhedron command");
|
||||
|
||||
// wallstyle args
|
||||
|
||||
int iarg = 6;
|
||||
if (strcmp(arg[iarg],"xplane") == 0) {
|
||||
if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polyhedron command");
|
||||
wallstyle = XPLANE;
|
||||
if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG;
|
||||
else lo = force->numeric(FLERR,arg[iarg+1]);
|
||||
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
|
||||
else hi = force->numeric(FLERR,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg],"yplane") == 0) {
|
||||
if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polyhedron command");
|
||||
wallstyle = YPLANE;
|
||||
if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG;
|
||||
else lo = force->numeric(FLERR,arg[iarg+1]);
|
||||
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
|
||||
else hi = force->numeric(FLERR,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg],"zplane") == 0) {
|
||||
if (narg < iarg+3) error->all(FLERR,"Illegal fix wall/body/polyhedron command");
|
||||
wallstyle = ZPLANE;
|
||||
if (strcmp(arg[iarg+1],"NULL") == 0) lo = -BIG;
|
||||
else lo = force->numeric(FLERR,arg[iarg+1]);
|
||||
if (strcmp(arg[iarg+2],"NULL") == 0) hi = BIG;
|
||||
else hi = force->numeric(FLERR,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
}
|
||||
|
||||
// check for trailing keyword/values
|
||||
|
||||
wiggle = 0;
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"wiggle") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix wall/body/polyhedron command");
|
||||
if (strcmp(arg[iarg+1],"x") == 0) axis = 0;
|
||||
else if (strcmp(arg[iarg+1],"y") == 0) axis = 1;
|
||||
else if (strcmp(arg[iarg+1],"z") == 0) axis = 2;
|
||||
else error->all(FLERR,"Illegal fix wall/body/polyhedron command");
|
||||
amplitude = force->numeric(FLERR,arg[iarg+2]);
|
||||
period = force->numeric(FLERR,arg[iarg+3]);
|
||||
wiggle = 1;
|
||||
iarg += 4;
|
||||
} else error->all(FLERR,"Illegal fix wall/body/polyhedron command");
|
||||
}
|
||||
|
||||
if (wallstyle == XPLANE && domain->xperiodic)
|
||||
error->all(FLERR,"Cannot use wall in periodic dimension");
|
||||
if (wallstyle == YPLANE && domain->yperiodic)
|
||||
error->all(FLERR,"Cannot use wall in periodic dimension");
|
||||
if (wallstyle == ZPLANE && domain->zperiodic)
|
||||
error->all(FLERR,"Cannot use wall in periodic dimension");
|
||||
|
||||
// setup oscillations
|
||||
|
||||
if (wiggle) omega = 2.0*MY_PI / period;
|
||||
|
||||
time_origin = update->ntimestep;
|
||||
|
||||
dmax = nmax = 0;
|
||||
discrete = NULL;
|
||||
dnum = dfirst = NULL;
|
||||
|
||||
edmax = ednummax = 0;
|
||||
edge = NULL;
|
||||
ednum = edfirst = NULL;
|
||||
|
||||
facmax = facnummax = 0;
|
||||
face = NULL;
|
||||
facnum = facfirst = NULL;
|
||||
|
||||
enclosing_radius = NULL;
|
||||
rounded_radius = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixWallBodyPolyhedron::~FixWallBodyPolyhedron()
|
||||
{
|
||||
memory->destroy(discrete);
|
||||
memory->destroy(dnum);
|
||||
memory->destroy(dfirst);
|
||||
|
||||
memory->destroy(edge);
|
||||
memory->destroy(ednum);
|
||||
memory->destroy(edfirst);
|
||||
|
||||
memory->destroy(face);
|
||||
memory->destroy(facnum);
|
||||
memory->destroy(facfirst);
|
||||
|
||||
memory->destroy(enclosing_radius);
|
||||
memory->destroy(rounded_radius);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallBodyPolyhedron::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= POST_FORCE;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::init()
|
||||
{
|
||||
dt = update->dt;
|
||||
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
if (!avec)
|
||||
error->all(FLERR,"Pair body/rounded/polyhedron requires atom style body");
|
||||
if (strcmp(avec->bptr->style,"rounded/polyhedron") != 0)
|
||||
error->all(FLERR,"Pair body/rounded/polyhedron requires "
|
||||
"body style rounded/polyhedron");
|
||||
bptr = (BodyRoundedPolyhedron *) avec->bptr;
|
||||
|
||||
// set pairstyle from body/polyhedronular pair style
|
||||
|
||||
if (force->pair_match("body/rounded/polyhedron",1))
|
||||
pairstyle = HOOKE;
|
||||
else error->all(FLERR,"Fix wall/body/polyhedron is incompatible with Pair style");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::setup(int vflag)
|
||||
{
|
||||
if (strstr(update->integrate_style,"verlet"))
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::post_force(int vflag)
|
||||
{
|
||||
double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos;
|
||||
int i,ni,npi,ifirst,nei,iefirst,nfi,iffirst,side;
|
||||
double facc[3];
|
||||
|
||||
// set position of wall to initial settings and velocity to 0.0
|
||||
// if wiggle, set wall position and velocity accordingly
|
||||
|
||||
double wlo = lo;
|
||||
double whi = hi;
|
||||
vwall[0] = vwall[1] = vwall[2] = 0.0;
|
||||
if (wiggle) {
|
||||
double arg = omega * (update->ntimestep - time_origin) * dt;
|
||||
if (wallstyle == axis) {
|
||||
wlo = lo + amplitude - amplitude*cos(arg);
|
||||
whi = hi + amplitude - amplitude*cos(arg);
|
||||
}
|
||||
vwall[axis] = amplitude*omega*sin(arg);
|
||||
}
|
||||
|
||||
// loop over all my atoms
|
||||
// rsq = distance from wall
|
||||
// dx,dy,dz = signed distance from wall
|
||||
// for rotating cylinder, reset vwall based on particle position
|
||||
// skip atom if not close enough to wall
|
||||
// if wall was set to NULL, it's skipped since lo/hi are infinity
|
||||
// compute force and torque on atom if close enough to wall
|
||||
// via wall potential matched to pair potential
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
int *body = atom->body;
|
||||
double *radius = atom->radius;
|
||||
double **torque = atom->torque;
|
||||
double **angmom = atom->angmom;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// grow the per-atom lists if necessary and initialize
|
||||
|
||||
if (atom->nmax > nmax) {
|
||||
memory->destroy(dnum);
|
||||
memory->destroy(dfirst);
|
||||
memory->destroy(ednum);
|
||||
memory->destroy(edfirst);
|
||||
memory->destroy(facnum);
|
||||
memory->destroy(facfirst);
|
||||
memory->destroy(enclosing_radius);
|
||||
memory->destroy(rounded_radius);
|
||||
nmax = atom->nmax;
|
||||
memory->create(dnum,nmax,"fix:dnum");
|
||||
memory->create(dfirst,nmax,"fix:dfirst");
|
||||
memory->create(ednum,nmax,"fix:ednum");
|
||||
memory->create(edfirst,nmax,"fix:edfirst");
|
||||
memory->create(facnum,nmax,"fix:facnum");
|
||||
memory->create(facfirst,nmax,"fix:facfirst");
|
||||
memory->create(enclosing_radius,nmax,"fix:enclosing_radius");
|
||||
memory->create(rounded_radius,nmax,"fix:rounded_radius");
|
||||
}
|
||||
|
||||
ndiscrete = nedge = nface = 0;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
dnum[i] = ednum[i] = facnum[i] = 0;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
|
||||
if (body[i] < 0) continue;
|
||||
|
||||
dx = dy = dz = 0.0;
|
||||
side = FAR;
|
||||
if (wallstyle == XPLANE) {
|
||||
del1 = x[i][0] - wlo;
|
||||
del2 = whi - x[i][0];
|
||||
if (del1 < del2) {
|
||||
dx = del1;
|
||||
wall_pos = wlo;
|
||||
side = XLO;
|
||||
} else {
|
||||
dx = -del2;
|
||||
wall_pos = whi;
|
||||
side = XHI;
|
||||
}
|
||||
} else if (wallstyle == YPLANE) {
|
||||
del1 = x[i][1] - wlo;
|
||||
del2 = whi - x[i][1];
|
||||
if (del1 < del2) {
|
||||
dy = del1;
|
||||
wall_pos = wlo;
|
||||
side = YLO;
|
||||
} else {
|
||||
dy = -del2;
|
||||
wall_pos = whi;
|
||||
side = YHI;
|
||||
}
|
||||
} else if (wallstyle == ZPLANE) {
|
||||
del1 = x[i][2] - wlo;
|
||||
del2 = whi - x[i][2];
|
||||
if (del1 < del2) {
|
||||
dy = del1;
|
||||
wall_pos = wlo;
|
||||
side = ZLO;
|
||||
} else {
|
||||
dy = -del2;
|
||||
wall_pos = whi;
|
||||
side = ZHI;
|
||||
}
|
||||
}
|
||||
|
||||
rsq = dx*dx + dy*dy + dz*dz;
|
||||
if (rsq > radius[i]*radius[i]) continue;
|
||||
|
||||
double r = sqrt(rsq);
|
||||
double rsqinv = 1.0 / rsq;
|
||||
|
||||
if (dnum[i] == 0) body2space(i);
|
||||
npi = dnum[i];
|
||||
ifirst = dfirst[i];
|
||||
nei = ednum[i];
|
||||
iefirst = edfirst[i];
|
||||
nfi = facnum[i];
|
||||
iffirst = facfirst[i];
|
||||
eradi = enclosing_radius[i];
|
||||
rradi = rounded_radius[i];
|
||||
|
||||
if (npi == 1) {
|
||||
sphere_against_wall(i, wall_pos, side, vwall, x, v, f, angmom, torque);
|
||||
continue;
|
||||
}
|
||||
|
||||
// reset vertex and edge forces
|
||||
|
||||
for (ni = 0; ni < npi; ni++) {
|
||||
discrete[ifirst+ni][3] = 0;
|
||||
discrete[ifirst+ni][4] = 0;
|
||||
discrete[ifirst+ni][5] = 0;
|
||||
discrete[ifirst+ni][6] = 0;
|
||||
}
|
||||
|
||||
for (ni = 0; ni < nei; ni++) {
|
||||
edge[iefirst+ni][2] = 0;
|
||||
edge[iefirst+ni][3] = 0;
|
||||
edge[iefirst+ni][4] = 0;
|
||||
edge[iefirst+ni][5] = 0;
|
||||
}
|
||||
|
||||
int interact, num_contacts, done;
|
||||
double delta_a, delta_ua, j_a;
|
||||
Contact contact_list[MAX_CONTACTS];
|
||||
|
||||
num_contacts = 0;
|
||||
facc[0] = facc[1] = facc[2] = 0;
|
||||
interact = edge_against_wall(i, wall_pos, side, vwall, x, f, torque,
|
||||
contact_list, num_contacts, facc);
|
||||
|
||||
} // group bit
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::reset_dt()
|
||||
{
|
||||
dt = update->dt;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
convert N sub-particles in body I to space frame using current quaternion
|
||||
store sub-particle space-frame displacements from COM in discrete list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::body2space(int i)
|
||||
{
|
||||
int ibonus = atom->body[i];
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
int nsub = bptr->nsub(bonus);
|
||||
double *coords = bptr->coords(bonus);
|
||||
int body_num_edges = bptr->nedges(bonus);
|
||||
double* edge_ends = bptr->edges(bonus);
|
||||
int body_num_faces = bptr->nfaces(bonus);
|
||||
double* face_pts = bptr->faces(bonus);
|
||||
double eradius = bptr->enclosing_radius(bonus);
|
||||
double rradius = bptr->rounded_radius(bonus);
|
||||
|
||||
// get the number of sub-particles (vertices)
|
||||
// and the index of the first vertex of my body in the list
|
||||
|
||||
dnum[i] = nsub;
|
||||
dfirst[i] = ndiscrete;
|
||||
|
||||
// grow the vertex list if necessary
|
||||
// the first 3 columns are for coords, the last 3 for forces
|
||||
|
||||
if (ndiscrete + nsub > dmax) {
|
||||
dmax += DELTA;
|
||||
memory->grow(discrete,dmax,7,"fix:discrete");
|
||||
}
|
||||
|
||||
double p[3][3];
|
||||
MathExtra::quat_to_mat(bonus->quat,p);
|
||||
|
||||
for (int m = 0; m < nsub; m++) {
|
||||
MathExtra::matvec(p,&coords[3*m],discrete[ndiscrete]);
|
||||
discrete[ndiscrete][3] = 0;
|
||||
discrete[ndiscrete][4] = 0;
|
||||
discrete[ndiscrete][5] = 0;
|
||||
discrete[ndiscrete][6] = 0;
|
||||
ndiscrete++;
|
||||
}
|
||||
|
||||
// get the number of edges (vertices)
|
||||
// and the index of the first edge of my body in the list
|
||||
|
||||
ednum[i] = body_num_edges;
|
||||
edfirst[i] = nedge;
|
||||
|
||||
// grow the edge list if necessary
|
||||
// the first 2 columns are for vertex indices within body,
|
||||
// the last 3 for forces
|
||||
|
||||
if (nedge + body_num_edges > edmax) {
|
||||
edmax += DELTA;
|
||||
memory->grow(edge,edmax,6,"fix:edge");
|
||||
}
|
||||
|
||||
for (int m = 0; m < body_num_edges; m++) {
|
||||
edge[nedge][0] = static_cast<int>(edge_ends[2*m+0]);
|
||||
edge[nedge][1] = static_cast<int>(edge_ends[2*m+1]);
|
||||
edge[nedge][2] = 0;
|
||||
edge[nedge][3] = 0;
|
||||
edge[nedge][4] = 0;
|
||||
edge[nedge][5] = 0;
|
||||
nedge++;
|
||||
}
|
||||
|
||||
// get the number of faces and the index of the first face
|
||||
|
||||
facnum[i] = body_num_faces;
|
||||
facfirst[i] = nface;
|
||||
|
||||
// grow the face list if necessary
|
||||
// the first 3 columns are for vertex indices within body, the last 3 for forces
|
||||
|
||||
if (nface + body_num_faces > facmax) {
|
||||
facmax += DELTA;
|
||||
memory->grow(face,facmax,6,"pair:face");
|
||||
}
|
||||
|
||||
for (int m = 0; m < body_num_faces; m++) {
|
||||
face[nface][0] = static_cast<int>(face_pts[3*m+0]);
|
||||
face[nface][1] = static_cast<int>(face_pts[3*m+1]);
|
||||
face[nface][2] = static_cast<int>(face_pts[3*m+2]);
|
||||
face[nface][3] = 0;
|
||||
face[nface][4] = 0;
|
||||
face[nface][5] = 0;
|
||||
nface++;
|
||||
}
|
||||
|
||||
enclosing_radius[i] = eradius;
|
||||
rounded_radius[i] = rradius;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Determine the interaction mode between a sphere against the wall
|
||||
|
||||
i = atom i (body i)
|
||||
x = atoms' coordinates
|
||||
f = atoms' forces
|
||||
torque = atoms' torques
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallBodyPolyhedron::sphere_against_wall(int i, double wall_pos,
|
||||
int side, double* vwall, double** x, double** v, double** f,
|
||||
double** angmom, double** torque)
|
||||
{
|
||||
int mode;
|
||||
double rradi,hi[3],d,delx,dely,delz,R,fpair,fx,fy,fz;
|
||||
|
||||
rradi = rounded_radius[i];
|
||||
mode = NONE;
|
||||
|
||||
if (wallstyle == XPLANE) {
|
||||
hi[0] = wall_pos;
|
||||
hi[1] = x[i][1];
|
||||
hi[2] = x[i][2];
|
||||
} else if (wallstyle == YPLANE) {
|
||||
hi[0] = x[i][0];
|
||||
hi[1] = wall_pos;
|
||||
hi[2] = x[i][2];
|
||||
} else if (wallstyle == ZPLANE) {
|
||||
hi[0] = x[i][0];
|
||||
hi[1] = x[i][1];
|
||||
hi[2] = wall_pos;
|
||||
}
|
||||
|
||||
distance(hi, x[i], d);
|
||||
|
||||
if (d <= rradi) {
|
||||
delx = x[i][0] - hi[0];
|
||||
dely = x[i][1] - hi[1];
|
||||
delz = x[i][2] - hi[2];
|
||||
R = d - rradi;
|
||||
|
||||
fpair = -kn * R;
|
||||
|
||||
fx = delx*fpair/d;
|
||||
fy = dely*fpair/d;
|
||||
fz = delz*fpair/d;
|
||||
|
||||
contact_forces(i, 1.0, x[i], hi, delx, dely, delz,
|
||||
fx, fy, fz, x, v, angmom, f, torque, vwall);
|
||||
mode = VERTEX;
|
||||
}
|
||||
|
||||
return mode;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Determine the interaction mode between i's vertices against the wall
|
||||
|
||||
i = atom i (body i)
|
||||
x = atoms' coordinates
|
||||
f = atoms' forces
|
||||
torque = atoms' torques
|
||||
Output:
|
||||
contact_list = list of contacts between i and the wall
|
||||
num_contacts = number of contacts between i's vertices and the wall
|
||||
Return:
|
||||
number of contacts of the edge to the wall (0, 1 or 2)
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos,
|
||||
int side, double* vwall, double** x, double** f, double** torque,
|
||||
Contact* contact_list, int &num_contacts, double* facc)
|
||||
{
|
||||
int ni, nei, mode, contact;
|
||||
double rradi;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
nei = ednum[i];
|
||||
rradi = rounded_radius[i];
|
||||
|
||||
contact = 0;
|
||||
|
||||
// loop through body i's edges
|
||||
|
||||
for (ni = 0; ni < nei; ni++)
|
||||
mode = compute_distance_to_wall(i, ni, x[i], rradi, wall_pos, side, vwall,
|
||||
contact);
|
||||
|
||||
return contact;
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------------
|
||||
Compute the distance between a vertex to the wall
|
||||
another body
|
||||
Input:
|
||||
x0 = coordinate of the tested vertex
|
||||
rradi = rounded radius of the vertex
|
||||
wall_pos = position of the wall
|
||||
Output:
|
||||
d = Distance from a point x0 to an wall
|
||||
hi = coordinates of the projection of x0 on the wall
|
||||
contact = 0 no contact between the queried vertex and the wall
|
||||
1 contact detected
|
||||
return NONE if there is no interaction
|
||||
VERTEX if the tested vertex interacts with the wall
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int FixWallBodyPolyhedron::compute_distance_to_wall(int ibody, int edge_index,
|
||||
double *xmi, double rounded_radius_i, double wall_pos,
|
||||
int side, double* vwall, int &contact)
|
||||
{
|
||||
int mode,ifirst,iefirst,npi1,npi2;
|
||||
double d1,d2,xpi1[3],xpi2[3],hi[3];
|
||||
double fx,fy,fz,fpair,delx,dely,delz,R;
|
||||
|
||||
double** x = atom->x;
|
||||
double** v = atom->v;
|
||||
double** f = atom->f;
|
||||
double** torque = atom->torque;
|
||||
double** angmom = atom->angmom;
|
||||
|
||||
// two ends of the edge from body i
|
||||
|
||||
ifirst = dfirst[ibody];
|
||||
iefirst = edfirst[ibody];
|
||||
npi1 = static_cast<int>(edge[iefirst+edge_index][0]);
|
||||
npi2 = static_cast<int>(edge[iefirst+edge_index][1]);
|
||||
|
||||
xpi1[0] = xmi[0] + discrete[ifirst+npi1][0];
|
||||
xpi1[1] = xmi[1] + discrete[ifirst+npi1][1];
|
||||
xpi1[2] = xmi[2] + discrete[ifirst+npi1][2];
|
||||
|
||||
xpi2[0] = xmi[0] + discrete[ifirst+npi2][0];
|
||||
xpi2[1] = xmi[1] + discrete[ifirst+npi2][1];
|
||||
xpi2[2] = xmi[2] + discrete[ifirst+npi2][2];
|
||||
|
||||
// determine the intersection of the edge to the wall
|
||||
|
||||
mode = NONE;
|
||||
double j_a = 1.0;
|
||||
|
||||
if (wallstyle == XPLANE) {
|
||||
hi[0] = wall_pos;
|
||||
hi[1] = xpi1[1];
|
||||
hi[2] = xpi1[2];
|
||||
} else if (wallstyle == YPLANE) {
|
||||
hi[0] = xpi1[0];
|
||||
hi[1] = wall_pos;
|
||||
hi[2] = xpi1[2];
|
||||
} else if (wallstyle == ZPLANE) {
|
||||
hi[0] = xpi1[0];
|
||||
hi[1] = xpi1[1];
|
||||
hi[2] = wall_pos;
|
||||
}
|
||||
|
||||
distance(hi, xpi1, d1);
|
||||
|
||||
if (d1 <= rounded_radius_i && static_cast<int>(discrete[ifirst+npi1][6]) == 0) {
|
||||
delx = xpi1[0] - hi[0];
|
||||
dely = xpi1[1] - hi[1];
|
||||
delz = xpi1[2] - hi[2];
|
||||
R = d1 - rounded_radius_i;
|
||||
|
||||
fpair = -kn * R;
|
||||
|
||||
fx = delx*fpair/d1;
|
||||
fy = dely*fpair/d1;
|
||||
fz = delz*fpair/d1;
|
||||
|
||||
contact_forces(ibody, j_a, xpi1, hi, delx, dely, delz,
|
||||
fx, fy, fz, x, v, angmom, f, torque, vwall);
|
||||
discrete[ifirst+npi1][6] = 1;
|
||||
contact++;
|
||||
mode = VERTEX;
|
||||
}
|
||||
|
||||
if (wallstyle == XPLANE) {
|
||||
hi[0] = wall_pos;
|
||||
hi[1] = xpi2[1];
|
||||
hi[2] = xpi2[2];
|
||||
} else if (wallstyle == YPLANE) {
|
||||
hi[0] = xpi2[0];
|
||||
hi[1] = wall_pos;
|
||||
hi[2] = xpi2[2];
|
||||
} else if (wallstyle == ZPLANE) {
|
||||
hi[0] = xpi2[0];
|
||||
hi[1] = xpi2[1];
|
||||
hi[2] = wall_pos;
|
||||
}
|
||||
|
||||
distance(hi, xpi2, d2);
|
||||
|
||||
if (d2 <= rounded_radius_i && static_cast<int>(discrete[ifirst+npi2][6]) == 0) {
|
||||
delx = xpi2[0] - hi[0];
|
||||
dely = xpi2[1] - hi[1];
|
||||
delz = xpi2[2] - hi[2];
|
||||
R = d2 - rounded_radius_i;
|
||||
|
||||
fpair = -kn * R;
|
||||
|
||||
fx = delx*fpair/d2;
|
||||
fy = dely*fpair/d2;
|
||||
fz = delz*fpair/d2;
|
||||
|
||||
contact_forces(ibody, j_a, xpi2, hi, delx, dely, delz,
|
||||
fx, fy, fz, x, v, angmom, f, torque, vwall);
|
||||
discrete[ifirst+npi2][6] = 1;
|
||||
contact++;
|
||||
mode = VERTEX;
|
||||
}
|
||||
|
||||
return mode;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Compute contact forces between two bodies
|
||||
modify the force stored at the vertex and edge in contact by j_a
|
||||
sum forces and torque to the corresponding bodies
|
||||
fn = normal friction component
|
||||
ft = tangential friction component (-c_t * v_t)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::contact_forces(int ibody,
|
||||
double j_a, double *xi, double *xj, double delx, double dely, double delz,
|
||||
double fx, double fy, double fz, double** x, double** v, double** angmom,
|
||||
double** f, double** torque, double* vwall)
|
||||
{
|
||||
int ibonus,jbonus;
|
||||
double fxt,fyt,fzt,rsq,rsqinv;
|
||||
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
|
||||
double fn[3],ft[3],vi[3],vj[3];
|
||||
double *quat, *inertia;
|
||||
AtomVecBody::Bonus *bonus;
|
||||
|
||||
// compute the velocity of the vertex in the space-fixed frame
|
||||
|
||||
ibonus = atom->body[ibody];
|
||||
bonus = &avec->bonus[ibonus];
|
||||
quat = bonus->quat;
|
||||
inertia = bonus->inertia;
|
||||
total_velocity(xi, x[ibody], v[ibody], angmom[ibody],
|
||||
inertia, quat, vi);
|
||||
|
||||
// vector pointing from the contact point on ibody to the wall
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rsqinv = 1.0/rsq;
|
||||
|
||||
// relative translational velocity
|
||||
|
||||
vr1 = vi[0] - vwall[0];
|
||||
vr2 = vi[1] - vwall[1];
|
||||
vr3 = vi[2] - vwall[2];
|
||||
|
||||
// normal component
|
||||
|
||||
vnnr = vr1*delx + vr2*dely + vr3*delz;
|
||||
vn1 = delx*vnnr * rsqinv;
|
||||
vn2 = dely*vnnr * rsqinv;
|
||||
vn3 = delz*vnnr * rsqinv;
|
||||
|
||||
// tangential component
|
||||
|
||||
vt1 = vr1 - vn1;
|
||||
vt2 = vr2 - vn2;
|
||||
vt3 = vr3 - vn3;
|
||||
|
||||
// normal friction term at contact
|
||||
|
||||
fn[0] = -c_n * vn1;
|
||||
fn[1] = -c_n * vn2;
|
||||
fn[2] = -c_n * vn3;
|
||||
|
||||
// tangential friction term at contact
|
||||
// excluding the tangential deformation term for now
|
||||
|
||||
ft[0] = -c_t * vt1;
|
||||
ft[1] = -c_t * vt2;
|
||||
ft[2] = -c_t * vt3;
|
||||
|
||||
fxt = fx; fyt = fy; fzt = fz;
|
||||
fx = fxt * j_a + fn[0] + ft[0];
|
||||
fy = fyt * j_a + fn[1] + ft[1];
|
||||
fz = fzt * j_a + fn[2] + ft[2];
|
||||
|
||||
f[ibody][0] += fx;
|
||||
f[ibody][1] += fy;
|
||||
f[ibody][2] += fz;
|
||||
sum_torque(x[ibody], xi, fx, fy, fz, torque[ibody]);
|
||||
|
||||
#ifdef _POLYHEDRON_DEBUG
|
||||
printf("From contact forces: vertex fx %f fy %f fz %f\n"
|
||||
" torque body %d: %f %f %f\n"
|
||||
" torque body %d: %f %f %f\n",
|
||||
fxt, fyt, fzt,
|
||||
atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2],
|
||||
atom->tag[jbody],torque[jbody][0],torque[jbody][1],torque[jbody][2]);
|
||||
#endif
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Compute the contact forces between two bodies
|
||||
modify the force stored at the vertex and edge in contact by j_a
|
||||
sum forces and torque to the corresponding bodies
|
||||
fn = normal friction component
|
||||
ft = tangential friction component (-c_t * vrt)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::contact_forces(Contact& contact, double j_a,
|
||||
double** x, double** v, double** angmom, double** f,
|
||||
double** torque, double* vwall, double* facc)
|
||||
{
|
||||
int ibody,ibonus,ifirst, jefirst, ni;
|
||||
double fx,fy,fz,delx,dely,delz,rsq,rsqinv;
|
||||
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
|
||||
double fn[3],ft[3],vi[3];
|
||||
double *quat, *inertia;
|
||||
AtomVecBody::Bonus *bonus;
|
||||
|
||||
ibody = contact.ibody;
|
||||
|
||||
// compute the velocity of the vertex in the space-fixed frame
|
||||
|
||||
ibonus = atom->body[ibody];
|
||||
bonus = &avec->bonus[ibonus];
|
||||
quat = bonus->quat;
|
||||
inertia = bonus->inertia;
|
||||
total_velocity(contact.xv, x[ibody], v[ibody], angmom[ibody],
|
||||
inertia, quat, vi);
|
||||
|
||||
// vector pointing from the vertex to the point on the wall
|
||||
|
||||
delx = contact.xv[0] - contact.xe[0];
|
||||
dely = contact.xv[1] - contact.xe[1];
|
||||
delz = contact.xv[2] - contact.xe[2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
rsqinv = 1.0/rsq;
|
||||
|
||||
// relative translational velocity
|
||||
|
||||
vr1 = vi[0] - vwall[0];
|
||||
vr2 = vi[1] - vwall[1];
|
||||
vr3 = vi[2] - vwall[2];
|
||||
|
||||
// normal component
|
||||
|
||||
vnnr = vr1*delx + vr2*dely + vr3*delz;
|
||||
vn1 = delx*vnnr * rsqinv;
|
||||
vn2 = dely*vnnr * rsqinv;
|
||||
vn3 = delz*vnnr * rsqinv;
|
||||
|
||||
// tangential component
|
||||
|
||||
vt1 = vr1 - vn1;
|
||||
vt2 = vr2 - vn2;
|
||||
vt3 = vr3 - vn3;
|
||||
|
||||
// normal friction term at contact
|
||||
|
||||
fn[0] = -c_n * vn1;
|
||||
fn[1] = -c_n * vn2;
|
||||
fn[2] = -c_n * vn3;
|
||||
|
||||
// tangential friction term at contact
|
||||
// excluding the tangential deformation term for now
|
||||
|
||||
ft[0] = -c_t * vt1;
|
||||
ft[1] = -c_t * vt2;
|
||||
ft[2] = -c_t * vt3;
|
||||
|
||||
// only the cohesive force is scaled by j_a
|
||||
|
||||
ifirst = dfirst[ibody];
|
||||
ni = contact.vertex;
|
||||
|
||||
fx = discrete[ifirst+ni][3] * j_a + fn[0] + ft[0];
|
||||
fy = discrete[ifirst+ni][4] * j_a + fn[1] + ft[1];
|
||||
fz = discrete[ifirst+ni][5] * j_a + fn[2] + ft[2];
|
||||
f[ibody][0] += fx;
|
||||
f[ibody][1] += fy;
|
||||
f[ibody][2] += fz;
|
||||
sum_torque(x[ibody], contact.xv, fx, fy, fz, torque[ibody]);
|
||||
|
||||
// accumulate forces to the vertex only
|
||||
|
||||
facc[0] += fx; facc[1] += fy; facc[2] += fz;
|
||||
|
||||
#ifdef _POLYHEDRON_DEBUG
|
||||
printf("From contact forces: vertex fx %f fy %f fz %f\n"
|
||||
" torque body %d: %f %f %f\n",
|
||||
discrete[ifirst+ni][3], discrete[ifirst+ni][4], discrete[ifirst+ni][5],
|
||||
atom->tag[ibody],torque[ibody][0],torque[ibody][1],torque[ibody][2]);
|
||||
#endif
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Determine the length of the contact segment, i.e. the separation between
|
||||
2 contacts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixWallBodyPolyhedron::contact_separation(const Contact& c1,
|
||||
const Contact& c2)
|
||||
{
|
||||
double x1 = c1.xv[0];
|
||||
double y1 = c1.xv[1];
|
||||
double x2 = c1.xe[0];
|
||||
double y2 = c1.xe[1];
|
||||
double x3 = c2.xv[0];
|
||||
double y3 = c2.xv[1];
|
||||
|
||||
double delta_a = 0.0;
|
||||
if (fabs(x2 - x1) > EPSILON) {
|
||||
double A = (y2 - y1) / (x2 - x1);
|
||||
delta_a = fabs(y1 - A * x1 - y3 + A * x3) / sqrt(1 + A * A);
|
||||
} else {
|
||||
delta_a = fabs(x1 - x3);
|
||||
}
|
||||
|
||||
return delta_a;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Accumulate torque to body from the force f=(fx,fy,fz) acting at point x
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::sum_torque(double* xm, double *x, double fx,
|
||||
double fy, double fz, double* torque)
|
||||
{
|
||||
double rx = x[0] - xm[0];
|
||||
double ry = x[1] - xm[1];
|
||||
double rz = x[2] - xm[2];
|
||||
double tx = ry * fz - rz * fy;
|
||||
double ty = rz * fx - rx * fz;
|
||||
double tz = rx * fy - ry * fx;
|
||||
torque[0] += tx;
|
||||
torque[1] += ty;
|
||||
torque[2] += tz;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Calculate the total velocity of a point (vertex, a point on an edge):
|
||||
vi = vcm + omega ^ (p - xcm)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::total_velocity(double* p, double *xcm,
|
||||
double* vcm, double *angmom, double *inertia,
|
||||
double *quat, double* vi)
|
||||
{
|
||||
double r[3],omega[3],ex_space[3],ey_space[3],ez_space[3];
|
||||
r[0] = p[0] - xcm[0];
|
||||
r[1] = p[1] - xcm[1];
|
||||
r[2] = p[2] - xcm[2];
|
||||
MathExtra::q_to_exyz(quat,ex_space,ey_space,ez_space);
|
||||
MathExtra::angmom_to_omega(angmom,ex_space,ey_space,ez_space,
|
||||
inertia,omega);
|
||||
vi[0] = omega[1]*r[2] - omega[2]*r[1] + vcm[0];
|
||||
vi[1] = omega[2]*r[0] - omega[0]*r[2] + vcm[1];
|
||||
vi[2] = omega[0]*r[1] - omega[1]*r[0] + vcm[2];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixWallBodyPolyhedron::distance(const double* x2, const double* x1,
|
||||
double& r) {
|
||||
r = sqrt((x2[0] - x1[0]) * (x2[0] - x1[0])
|
||||
+ (x2[1] - x1[1]) * (x2[1] - x1[1])
|
||||
+ (x2[2] - x1[2]) * (x2[2] - x1[2]));
|
||||
}
|
||||
|
|
@ -0,0 +1,143 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(wall/body/polyhedron,FixWallBodyPolyhedron)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_WALL_BODY_POLYHERON_H
|
||||
#define LMP_FIX_WALL_BODY_POLYHERON_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixWallBodyPolyhedron : public Fix {
|
||||
public:
|
||||
FixWallBodyPolyhedron(class LAMMPS *, int, char **);
|
||||
virtual ~FixWallBodyPolyhedron();
|
||||
int setmask();
|
||||
void init();
|
||||
void setup(int);
|
||||
virtual void post_force(int);
|
||||
void reset_dt();
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int vertex; // vertex of the first polygon
|
||||
int edge; // edge of the second polygon
|
||||
double xv[3]; // coordinates of the vertex
|
||||
double xe[3]; // coordinates of the projection of the vertex on the edge
|
||||
double separation;// separation at contact
|
||||
};
|
||||
|
||||
protected:
|
||||
int wallstyle,pairstyle,wiggle,axis;
|
||||
double kn,c_n,c_t;
|
||||
double lo,hi,cylradius;
|
||||
double amplitude,period,omega;
|
||||
double dt;
|
||||
int time_origin;
|
||||
|
||||
class AtomVecBody *avec;
|
||||
class BodyRoundedPolyhedron *bptr;
|
||||
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
|
||||
double **face; // list of all edge for all bodies
|
||||
int nface; // number of faces in list
|
||||
int facmax; // allocated size of face list
|
||||
int *facnum; // number of faces per line, 0 if uninit
|
||||
int *facfirst; // index of first face per each line
|
||||
int facnummax; // allocated size of facnum,facfirst vectors
|
||||
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
|
||||
void body2space(int);
|
||||
|
||||
int edge_against_wall(int ibody, double wall_pos, int side, double* vwall,
|
||||
double** x, double** f, double** torque, Contact* contact_list,
|
||||
int &num_contacts, double* facc);
|
||||
int sphere_against_wall(int i, double wall_pos, int side, double* vwall,
|
||||
double** x, double** v, double** f, double** angmom, double** torque);
|
||||
|
||||
int compute_distance_to_wall(int ibody, int edge_index, double *xmi,
|
||||
double rounded_radius_i, double wall_pos, int side,
|
||||
double* vwall, int &contact);
|
||||
double contact_separation(const Contact& c1, const Contact& c2);
|
||||
void contact_forces(int ibody, double j_a, double *xi, double *xj,
|
||||
double delx, double dely, double delz,
|
||||
double fx, double fy, double fz, double** x, double** v,
|
||||
double** angmom, double** f, double** torque, double* vwall);
|
||||
|
||||
void contact_forces(Contact& contact, double j_a, double** x,
|
||||
double** v, double** angmom, double** f, double** torque,
|
||||
double* vwall, double* facc);
|
||||
void sum_torque(double* xm, double *x, double fx,
|
||||
double fy, double fz, double* torque);
|
||||
void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
|
||||
double *inertia, double *quat, double* vi);
|
||||
void distance(const double* x2, const double* x1, double& r);
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Fix wall/body/polyhedron requires atom style body rounded/polyhedron
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot use wall in periodic dimension
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Cannot wiggle and shear fix wall/body/polygon
|
||||
|
||||
Cannot specify both options at the same time.
|
||||
|
||||
E: Invalid wiggle direction for fix wall/body/polygon
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix wall/body/polygon is incompatible with Pair style
|
||||
|
||||
Must use a body pair style to define the parameters needed for
|
||||
this fix.
|
||||
|
||||
*/
|
||||
|
|
@ -15,7 +15,7 @@
|
|||
#include <cstdio>
|
||||
#include <cstdlib>
|
||||
#include <cstring>
|
||||
#include "pair_body.h"
|
||||
#include "pair_body_nparticle.h"
|
||||
#include "math_extra.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec_body.h"
|
||||
|
|
@ -32,7 +32,7 @@ using namespace LAMMPS_NS;
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairBody::PairBody(LAMMPS *lmp) : Pair(lmp)
|
||||
PairBodyNparticle::PairBodyNparticle(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
dmax = nmax = 0;
|
||||
discrete = NULL;
|
||||
|
|
@ -44,7 +44,7 @@ PairBody::PairBody(LAMMPS *lmp) : Pair(lmp)
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairBody::~PairBody()
|
||||
PairBodyNparticle::~PairBodyNparticle()
|
||||
{
|
||||
memory->destroy(discrete);
|
||||
memory->destroy(dnum);
|
||||
|
|
@ -66,7 +66,7 @@ PairBody::~PairBody()
|
|||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairBody::compute(int eflag, int vflag)
|
||||
void PairBodyNparticle::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
int ni,nj,npi,npj,ifirst,jfirst;
|
||||
|
|
@ -336,7 +336,7 @@ void PairBody::compute(int eflag, int vflag)
|
|||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBody::allocate()
|
||||
void PairBodyNparticle::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
|
@ -361,7 +361,7 @@ void PairBody::allocate()
|
|||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBody::settings(int narg, char **arg)
|
||||
void PairBodyNparticle::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
|
|
@ -381,7 +381,7 @@ void PairBody::settings(int narg, char **arg)
|
|||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBody::coeff(int narg, char **arg)
|
||||
void PairBodyNparticle::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 4 || narg > 5)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
|
|
@ -415,12 +415,12 @@ void PairBody::coeff(int narg, char **arg)
|
|||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBody::init_style()
|
||||
void PairBodyNparticle::init_style()
|
||||
{
|
||||
avec = (AtomVecBody *) atom->style_match("body");
|
||||
if (!avec) error->all(FLERR,"Pair body requires atom style body");
|
||||
if (!avec) error->all(FLERR,"Pair body/nparticle requires atom style body");
|
||||
if (strcmp(avec->bptr->style,"nparticle") != 0)
|
||||
error->all(FLERR,"Pair body requires body style nparticle");
|
||||
error->all(FLERR,"Pair body/nparticle requires body style nparticle");
|
||||
bptr = (BodyNparticle *) avec->bptr;
|
||||
|
||||
neighbor->request(this,instance_me);
|
||||
|
|
@ -430,7 +430,7 @@ void PairBody::init_style()
|
|||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairBody::init_one(int i, int j)
|
||||
double PairBodyNparticle::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
|
||||
|
|
@ -459,7 +459,7 @@ double PairBody::init_one(int i, int j)
|
|||
store sub-particle space-frame displacements from COM in discrete list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairBody::body2space(int i)
|
||||
void PairBodyNparticle::body2space(int i)
|
||||
{
|
||||
int ibonus = atom->body[i];
|
||||
AtomVecBody::Bonus *bonus = &avec->bonus[ibonus];
|
||||
|
|
@ -13,21 +13,21 @@
|
|||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(body,PairBody)
|
||||
PairStyle(body/nparticle,PairBodyNparticle)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BODY_H
|
||||
#define LMP_PAIR_BODY_H
|
||||
#ifndef LMP_PAIR_BODY_NPARTICLE_H
|
||||
#define LMP_PAIR_BODY_NPARTICLE_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairBody : public Pair {
|
||||
class PairBodyNparticle : public Pair {
|
||||
public:
|
||||
PairBody(class LAMMPS *);
|
||||
~PairBody();
|
||||
PairBodyNparticle(class LAMMPS *);
|
||||
~PairBodyNparticle();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,137 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(body/rounded/polygon,PairBodyRoundedPolygon)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BODY_ROUNDED_POLYGON_H
|
||||
#define LMP_PAIR_BODY_ROUNDED_POLYGON_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairBodyRoundedPolygon : public Pair {
|
||||
public:
|
||||
PairBodyRoundedPolygon(class LAMMPS *);
|
||||
~PairBodyRoundedPolygon();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int vertex; // vertex of the first polygon
|
||||
int edge; // edge of the second polygon
|
||||
double xv[3]; // coordinates of the vertex
|
||||
double xe[3]; // coordinates of the projection of the vertex on the edge
|
||||
double separation;// separation at contact
|
||||
};
|
||||
|
||||
protected:
|
||||
double **k_n; // normal repulsion strength
|
||||
double **k_na; // normal attraction strength
|
||||
double c_n; // normal damping coefficient
|
||||
double c_t; // tangential damping coefficient
|
||||
double mu; // normal friction coefficient during gross sliding
|
||||
double delta_ua; // contact line (area for 3D models) modification factor
|
||||
double cut_inner; // cutoff for interaction between vertex-edge surfaces
|
||||
|
||||
class AtomVecBody *avec;
|
||||
class BodyRoundedPolygon *bptr;
|
||||
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
double *maxerad; // per-type maximum enclosing radius
|
||||
|
||||
void allocate();
|
||||
void body2space(int);
|
||||
|
||||
// sphere-sphere interaction
|
||||
void sphere_against_sphere(int i, int j, double delx, double dely, double delz,
|
||||
double rsq, double k_n, double k_na,
|
||||
double** x, double** v, double** f, int evflag);
|
||||
// vertex-edge interaction
|
||||
int vertex_against_edge(int i, int j, double k_n, double k_na,
|
||||
double** x, double** f, double** torque,
|
||||
tagint* tag, Contact* contact_list,
|
||||
int &num_contacts, double &evdwl, double* facc);
|
||||
// compute distance between a point and an edge from another body
|
||||
int compute_distance_to_vertex(int ibody, int edge_index, double* xmi,
|
||||
double rounded_radius, double* x0,
|
||||
double x0_rounded_radius, double cut_inner,
|
||||
double &d, double hi[3], double &t,
|
||||
int &contact);
|
||||
// compute contact forces if contact points are detected
|
||||
void contact_forces(Contact& contact, double j_a,
|
||||
double** x, double** v, double** angmom, double** f,
|
||||
double** torque, double &evdwl, double* facc);
|
||||
|
||||
// compute the separation between two contacts
|
||||
double contact_separation(const Contact& c1, const Contact& c2);
|
||||
|
||||
// accumulate torque to a body given a force at a given point
|
||||
void sum_torque(double* xm, double *x, double fx,
|
||||
double fy, double fz, double* torque);
|
||||
// helper functions
|
||||
int opposite_sides(double* x1, double* x2, double* a, double* b);
|
||||
void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
|
||||
double *inertia, double *quat, double* vi);
|
||||
inline void distance(const double* x2, const double* x1, double& r);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair body/rounded/polygon requires atom style body rounded/polygon
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Pair body requires body style rounded/polygon
|
||||
|
||||
This pair style is specific to the rounded/polygon body style.
|
||||
|
||||
*/
|
||||
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|
|
@ -0,0 +1,200 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(body/rounded/polyhedron,PairBodyRoundedPolyhedron)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_BODY_ROUNDED_POLYHEDRON_H
|
||||
#define LMP_PAIR_BODY_ROUNDED_POLYHEDRON_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairBodyRoundedPolyhedron : public Pair {
|
||||
public:
|
||||
PairBodyRoundedPolyhedron(class LAMMPS *);
|
||||
~PairBodyRoundedPolyhedron();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
|
||||
virtual void kernel_force(double R, int itype, int jtype,
|
||||
double& energy, double& fpair);
|
||||
|
||||
struct Contact {
|
||||
int ibody, jbody; // body (i.e. atom) indices (not tags)
|
||||
int type; // 0 = VERTEX-FACE; 1 = EDGE-EDGE
|
||||
double fx,fy,fz; // unscaled cohesive forces at contact
|
||||
double xi[3]; // coordinates of the contact point on ibody
|
||||
double xj[3]; // coordinates of the contact point on jbody
|
||||
double separation; // contact surface separation
|
||||
int unique;
|
||||
};
|
||||
|
||||
protected:
|
||||
double **k_n; // normal repulsion strength
|
||||
double **k_na; // normal attraction strength
|
||||
double c_n; // normal damping coefficient
|
||||
double c_t; // tangential damping coefficient
|
||||
double mu; // normal friction coefficient during gross sliding
|
||||
double A_ua; // characteristic contact area
|
||||
double cut_inner; // cutoff for interaction between vertex-edge surfaces
|
||||
|
||||
class AtomVecBody *avec;
|
||||
class BodyRoundedPolyhedron *bptr;
|
||||
|
||||
double **discrete; // list of all sub-particles for all bodies
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
double **edge; // list of all edge for all bodies
|
||||
int nedge; // number of edge in list
|
||||
int edmax; // allocated size of edge list
|
||||
int *ednum; // number of edges per line, 0 if uninit
|
||||
int *edfirst; // index of first edge per each line
|
||||
int ednummax; // allocated size of ednum,edfirst vectors
|
||||
|
||||
double **face; // list of all edge for all bodies
|
||||
int nface; // number of faces in list
|
||||
int facmax; // allocated size of face list
|
||||
int *facnum; // number of faces per line, 0 if uninit
|
||||
int *facfirst; // index of first face per each line
|
||||
int facnummax; // allocated size of facnum,facfirst vectors
|
||||
|
||||
double *enclosing_radius; // enclosing radii for all bodies
|
||||
double *rounded_radius; // rounded radii for all bodies
|
||||
double *maxerad; // per-type maximum enclosing radius
|
||||
|
||||
void allocate();
|
||||
void body2space(int);
|
||||
|
||||
// sphere-sphere interaction
|
||||
void sphere_against_sphere(int ibody, int jbody, int itype, int jtype,
|
||||
double delx, double dely, double delz, double rsq,
|
||||
double** v, double** f, int evflag);
|
||||
// sphere-edge interaction
|
||||
void sphere_against_edge(int ibody, int jbody, int itype, int jtype,
|
||||
double** x, double** v, double** f, double** torque,
|
||||
double** angmom, int evflag);
|
||||
// sphere-face interaction
|
||||
void sphere_against_face(int ibody, int jbody, int itype, int jtype,
|
||||
double** x, double** v, double** f, double** torque,
|
||||
double** angmom, int evflag);
|
||||
// edge-edge interactions
|
||||
int edge_against_edge(int ibody, int jbody, int itype, int jtype,
|
||||
double** x,Contact* contact_list, int &num_contacts,
|
||||
double &evdwl, double* facc);
|
||||
// edge-face interactions
|
||||
int edge_against_face(int ibody, int jbody, int itype, int jtype,
|
||||
double** x, Contact* contact_list, int &num_contacts,
|
||||
double &evdwl, double* facc);
|
||||
|
||||
// a face vs. a single edge
|
||||
int interaction_face_to_edge(int ibody, int face_index, double* xmi,
|
||||
double rounded_radius_i, int jbody, int edge_index,
|
||||
double* xmj, double rounded_radius_j,
|
||||
int itype, int jtype, double cut_inner,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
double& energy, double* facc);
|
||||
// an edge vs. an edge from another body
|
||||
int interaction_edge_to_edge(int ibody, int edge_index_i, double* xmi,
|
||||
double rounded_radius_i, int jbody, int edge_index_j,
|
||||
double* xmj, double rounded_radius_j,
|
||||
int itype, int jtype, double cut_inner,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
double& energy, double* facc);
|
||||
|
||||
// compute contact forces if contact points are detected
|
||||
void contact_forces(int ibody, int jbody, double *xi, double *xj,
|
||||
double delx, double dely, double delz, double fx, double fy, double fz,
|
||||
double** x, double** v, double** angmom, double** f, double** torque,
|
||||
double* facc);
|
||||
|
||||
// compute force and torque between two bodies given a pair of interacting points
|
||||
void pair_force_and_torque(int ibody, int jbody, double* pi, double* pj,
|
||||
double r, double contact_dist, int itype, int jtype,
|
||||
double** x, double** v, double** f, double** torque,
|
||||
double** angmom, int jflag, double& energy, double* facc);
|
||||
|
||||
// rescale the cohesive forces if a contact area is detected
|
||||
void rescale_cohesive_forces(double** x, double** f, double** torque,
|
||||
Contact* contact_list, int &num_contacts,
|
||||
int itype, int jtype, double* facc);
|
||||
|
||||
// compute the separation between two contacts
|
||||
double contact_separation(const Contact& c1, const Contact& c2);
|
||||
|
||||
// detect the unique contact points (as there may be double counts)
|
||||
void find_unique_contacts(Contact* contact_list, int& num_contacts);
|
||||
|
||||
// accumulate torque to a body given a force at a given point
|
||||
void sum_torque(double* xm, double *x, double fx, double fy, double fz, double* torque);
|
||||
|
||||
// find the intersection point (if any) between an edge and a face
|
||||
int edge_face_intersect(double* x1, double* x2, double* x3, double* a, double* b,
|
||||
double* hi1, double* hi2, double& d1, double& d2,
|
||||
int& inside_a, int& inside_b);
|
||||
// helper functions
|
||||
int opposite_sides(double* n, double* x0, double* a, double* b);
|
||||
void project_pt_plane(const double* q, const double* p,
|
||||
const double* n, double* q_proj, double &d);
|
||||
void project_pt_plane(const double* q, const double* x1, const double* x2,
|
||||
const double* x3, double* q_proj, double &d, int& inside);
|
||||
void project_pt_line(const double* q, const double* xi1, const double* xi2,
|
||||
double* h, double& d, double& t);
|
||||
void inside_polygon(int ibody, int face_index, double* xmi,
|
||||
const double* q1, const double* q2, int& inside1, int& inside2);
|
||||
|
||||
void distance_bt_edges(const double* x1, const double* x2,
|
||||
const double* x3, const double* x4,
|
||||
double* h1, double* h2, double& t1, double& t2, double& r);
|
||||
void total_velocity(double* p, double *xcm, double* vcm, double *angmom,
|
||||
double *inertia, double *quat, double* vi);
|
||||
void sanity_check();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair body/rounded/polyhedron requires atom style body rounded/polyhedron
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Pair body requires body style rounded/polyhedron
|
||||
|
||||
This pair style is specific to the rounded/polyhedron body style.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue