lammps/doc/compute_stress_atom.txt

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compute stress/atom command :h3

[Syntax:]

compute ID group-ID stress/atom keyword ... :pre

ID, group-ID are documented in "compute"_compute.html command
stress/atom = style name of this compute command
zero or more keywords may be appended
keyword = {ke} or {pair} or {bond} or {angle} or {dihedral} or {improper} or {fix} or {virial} :ul

[Examples:]

compute 1 mobile stress/atom
compute 1 all stress/atom pair bond :pre

[Description:]

Define a computation that computes the symmetric per-atom stress
tensor for each atom in a group.  The tensor for each atom has 6
components: xx, yy, zz, xy, xz, yz.  See the "compute
pressure"_compute_pressure.html command if you want the stress tensor
(pressure) of the entire system.  The 6 components can be accessed by
indices 1-6 by any command that uses per-atom computes as input,
e.g. the "dump custom"_dump.html command or "fix
ave/spatial"_fix_ave_spatial.html command or "fix
ave/atom"_fix_ave_atom.html command.  See "this
section"_Section_howto.html#4_15 for an overview.

The stress tensor for atom {I} is given by the following formula,
where {a} and {b} take on values x,y,z to generate the 6 components of
the symmetric tensor:

:c,image(Eqs/stress_tensor.jpg)

The first term is a kinetic energy contribution for atom {I}.  The
second term is a pairwise energy contribution where {n} loops over the
{Np} neighbors of atom {I}, {r1} and {r2} are the positions of the 2
atoms in the pairwise interaction, and {F1} and {F2} are the forces on
the 2 atoms resulting from the pairwise interaction.  The third term
is a bond contribution of similar form for the {Nb} bonds which atom
{I} is part of.  There are similar terms for the {Na} angle, {Nd}
dihedral, and {Ni} improper interactions atom {I} is part of.
Finally, there is a term for the {Nf} "fixes"_fix.html that apply
internal constraint forces to atom {I}.  Currently, only the "fix
shake"_fix_shake.html and "fix rigid"_fix_rigid.html commands
contribute to this term.

As the coefficients in the formula imply, a virial contribution
produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
atoms in a Tersoff 3-body interaction) is assigned in equal portions
to each atom in the set.  E.g. 1/4 of the dihedral virial to each of
the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
to atoms in a a water molecule via the "fix shake"_fix_shake.html
command.

If no extra keywords are listed, all of the terms in this formula are
included in the per-atom stress tensor.  If any extra keywords are
listed, only those terms are summed to compute the tensor.  The
{virial} keyword means include all terms except the kinetic energy
{ke}.

Note that the stress for each atom is due to its interaction with all
other atoms in the simulation, not just with other atoms in the group.

The "dihedral_style charmm"_dihedral_charmm.html style calculates
pairwise interactions between 1-4 atoms.  The virial contribution of
these terms is included in the pair virial, not the dihedral virial.

Note that as defined in the formula, per-atom stress is the negative
of the per-atom pressure tensor.  It is also really a stress-volume
formulation, meaning the computed quantity is in units of
pressure-volume.  It would need to be divided by a per-atom volume to
have units of stress (pressure), but an individual atom's volume is
not easy to compute in a deformed solid or a liquid.  Thus, if the
diagonal components of the per-atom stress tensor are summed for all
atoms in the system and the sum is divided by dV, where d = dimension
and V is the volume of the system, the result should be -P, where P is
the total pressure of the system.

These lines in an input script for a 3d system should yield that
result.  I.e. the last 2 columns of thermo output will be the same:

compute		peratom all stress/atom
compute		p all reduce sum c_peratom\[1\] c_peratom\[2\] c_peratom\[3\]
variable	press equal -(c_p\[1\]+c_p\[2\]+c_p\[3\])/(3*vol)
thermo_style	custom step temp etotal press v_press :pre

IMPORTANT NOTE: The per-atom stress does NOT include contributions due
to long-range Coulombic interactions (via the
"kspace_style"_kspace_style.html command).  It's not clear this
contribution can easily be computed.

[Output info:]

This compute calculates a vector of length 6 for each atom, which can
be accessed by indices 1-6 by any command that uses per-atom computes
as input.  See "this section"_Section_howto.html#4_15 for an overview
of LAMMPS output options.  The 6 components of the vector are ordered
xx, yy, zz, xy, xz, yz.

[Restrictions:] none

[Related commands:]

"compute pe"_compute_pe.html, "compute pressure"_compute_pressure.html

[Default:] none