forked from lijiext/lammps
121 lines
4.9 KiB
Plaintext
121 lines
4.9 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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compute stress/atom command :h3
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[Syntax:]
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compute ID group-ID stress/atom keyword ... :pre
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ID, group-ID are documented in "compute"_compute.html command
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stress/atom = style name of this compute command
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zero or more keywords may be appended
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keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {fix} :ul
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[Examples:]
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compute 1 mobile stress/atom :pre
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compute 1 all stress/atom pair bond :pre
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[Description:]
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Define a computation that computes the symmetric per-atom stress
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tensor for each atom in a group. The tensor for each atom has 6
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components: xx, yy, zz, xy, xz, yz. See the "compute
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pressure"_compute_pressure.html command if you want the stress tensor
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(pressure) of the entire system. The 6 components can be accessed by
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indices 1-6 by any command that uses per-atom computes as input,
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e.g. the "dump custom"_dump.html command or "fix
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ave/spatial"_fix_ave_spatial.html command or "fix
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ave/atom"_fix_ave_atom.html command. See "this
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section"_Section_howto.html#4_15 for an overview.
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The stress tensor for atom {I} is given by the following formula,
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where {a} and {b} take on values x,y,z to generate the 6 components of
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the symmetric tensor:
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:c,image(Eqs/stress_tensor.jpg)
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The first term is a kinetic energy contribution for atom {I}. The
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second term is a pairwise energy contribution where {n} loops over the
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{Np} neighbors of atom {I}, {r1} and {r2} are the positions of the 2
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atoms in the pairwise interaction, and {F1} and {F2} are the forces on
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the 2 atoms resulting from the pairwise interaction. The third term
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is a bond contribution of similar form for the {Nb} bonds which atom
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{I} is part of. There are similar terms for the {Na} angle, {Nd}
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dihedral, and {Ni} improper interactions atom {I} is part of.
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Finally, there is a term for the {Nf} "fixes"_fix.html that apply
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internal constraint forces to atom {I}. Currently, only the "fix
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shake"_fix_shake.html and "fix rigid"_fix_rigid.html commands
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contribute to this term.
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As the coefficients in the formula imply, a virial contribution
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produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
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atoms in a Tersoff 3-body interaction) is assigned in equal portions
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to each atom in the set. E.g. 1/4 of the dihedral virial to each of
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the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
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to atoms in a a water molecule via the "fix shake"_fix_shake.html
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command.
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If no extra keywords are listed, all of the terms in this formula are
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included in the per-atom stress tensor. If any extra keywords are
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listed, only those terms are summed to compute the tensor.
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Note that the stress for each atom is due to its interaction with all
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other atoms in the simulation, not just with other atoms in the group.
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The "dihedral_style charmm"_dihedral_charmm.html style calculates
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pairwise interactions between 1-4 atoms. The virial contribution of
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these terms is included in the pair virial, not the dihedral virial.
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Note that as defined in the formula, per-atom stress is the negative
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of the per-atom pressure tensor. It is also really a stress-volume
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formulation. It would need to be divided by a per-atom volume to have
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units of stress, but an individual atom's volume is not easy to
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compute in a deformed solid or a liquid. Thus, if the diagonal
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components of the per-atom stress tensor are summed for all atoms in
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the system and the sum is divided by 3V, where V is the volume of the
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system, the result should be -P, where P is the total pressure of the
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system.
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These lines in an input script should yield that result. I.e. the
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last 2 columns of thermo output will be the same:
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compute peratom all stress/atom
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compute p all sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
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variable press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
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thermo_style custom step temp etotal press v_press :pre
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IMPORTANT NOTE: The per-atom stress does NOT include contributions due
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to long-range Coulombic interactions (via the
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"kspace_style"_kspace_style.html command). It's not clear this
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contribution can easily be computed. There are also a few pair styles
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for manybody potentials that are not yet instrumented to yield
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per-atom stress. See the Restrictions below.
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[Output info:]
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This compute calculates a vector of length 6 for each atom, which can
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be accessed by indices 1-6 by any command that uses per-atom computes
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as input. See "this section"_Section_howto.html#4_15 for an overview
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of LAMMPS output options. The 6 components of the vector are ordered
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xx, yy, zz, xy, xz, yz.
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[Restrictions:]
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These pair styles do not yet tabulate per-atom virials to allow them
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to work with this compute: "airebo"_pair_airebo.html,
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"meam"_pair_meam.html, and "TIP4P"_pair_lj.html.
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[Related commands:]
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"compute pe"_compute_pe.html, "compute
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stress/atom"_compute_stress_atom.html
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[Default:] none
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