Merge pull request #1092 from RomainVermorel/master

"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

compute stress/mop command :h3

compute stress/mop/profile command :h3

[Syntax:]

compute ID group-ID style dir args keywords ... :pre

ID, group-ID are documented in "compute"_compute.html command

style = {stress/mop} or {stress/mop/profile}

dir = {x} or {y} or {z} is the direction normal to the plane

args = argument specific to the compute style

keywords = {kin} or {conf} or {total} (one of more can be specified) :ul

  {stress/mop} args = pos

    pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane

  {stress/mop/profile} args = origin delta

    origin = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the first plane

    delta = value (distance units) is the distance between planes :pre

compute 1 all stress/mop x lower total

compute 1 liquid stress/mop z 0.0 kin conf

fix 1 all ave/time 10 1000 10000 c_1\[*\] file mop.time

fix 1 all ave/time 10 1000 10000 c_1\[2\] file mop.time :pre

compute 1 all stress/mop/profile x lower 0.1 total

compute 1 liquid stress/mop/profile z 0.0 0.25 kin conf

fix 1 all ave/time 500 20 10000 c_1\[*\] ave running overwrite file mopp.time mode vector :pre

[Description:]

Compute {stress/mop} and compute {stress/mop/profile} define computations that

calculate components of the local stress tensor using the method of

planes "(Todd)"_#mop-todd.  Specifically in compute {stress/mop} calculates 3

components are computed in directions {dir},{x}; {dir},{y}; and

{dir},{z}; where {dir} is the direction normal to the plane, while

in compute {stress/mop/profile} the profile of the stress is computed.

Contrary to methods based on histograms of atomic stress (i.e. using

"compute stress/atom"_compute_stress_atom.html), the method of planes is

compatible with mechanical balance in heterogeneous systems and at

interfaces "(Todd)"_#mop-todd.

The stress tensor is the sum of a kinetic term and a configurational

term, which are given respectively by Eq. (21) and Eq. (16) in

"(Todd)"_#mop-todd. For the kinetic part, the algorithm considers that

atoms have crossed the plane if their positions at times t-dt and t are

one on either side of the plane, and uses the velocity at time t-dt/2

given by the velocity-Verlet algorithm.

Between one and three keywords can be used to indicate which

contributions to the stress must be computed: kinetic stress (kin),

configurational stress (conf), and/or total stress (total).

NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID. 

NOTE 2: The local stress does not include any Lennard-Jones tail

corrections to the pressure added by the "pair_modify tail

yes"_pair_modify.html command, since those are contributions to the global system pressure.

[Output info:]

Compute {stress/mop} calculates a global vector (indices starting at 1), with 3

values for each declared keyword (in the order the keywords have been

declared). For each keyword, the stress tensor components are ordered as

follows: stress_dir,x, stress_dir,y, and stress_dir,z.

Compute {stress/mop/profile} instead calculates a global array, with 1 column

giving the position of the planes where the stress tensor was computed,

and with 3 columns of values for each declared keyword (in the order the

keywords have been declared). For each keyword, the profiles of stress

tensor components are ordered as follows: stress_dir,x; stress_dir,y;

and stress_dir,z.

The values are in pressure "units"_units.html. 

The values produced by this compute can be accessed by various "output commands"_Howto_output.html. For instance, the results can be written to a file using the "fix ave/time"_fix_ave_time.html command. Please see the example in the examples/USER/mop folder.

[Restrictions:] 

These styles are part of the USER-MISC package. They are only enabled if

LAMMPS is built with that package. See the "Build package"_Build_package.html

doc page on for more info.

The method is only implemented for 3d orthogonal simulation boxes whose

size does not change in time, and axis-aligned planes.

The method only works with two-body pair interactions, because it

requires the class method pair->single() to be implemented. In

particular, it does not work with more than two-body pair interactions,

intra-molecular interactions, and long range (kspace) interactions.

[Related commands:]

"compute stress/atom"_compute_stress_atom.html

[Default:] none

:line

:link(mop-todd)

[(Todd)] B. D. Todd, Denis J. Evans, and Peter J. Daivis: "Pressure tensor for inhomogeneous fluids", 

Phys. Rev. E 52, 1627 (1995).

   compute_sna_atom

   compute_spin

   compute_stress_atom

   compute_stress_mop

   compute_tally

   compute_tdpd_cc_atom

   compute_temp

compute_sna_atom.html

compute_spin.html

compute_stress_atom.html

compute_stress_mop.html

compute_tally.html

compute_tdpd_cc_atom.html

compute_temp.html

variable T equal 0.8

variable p_solid equal 0.05

read_data data.mop

pair_style lj/cut 2.5

pair_coeff * * 1.0 1.0

pair_coeff 1 2 0.5 1.0 

pair_coeff 2 2 0.0 0.0

neigh_modify delay 0

group liquid type 1

group solid type 2

region bottom block INF INF INF INF INF 7.0

group bottom region bottom

group solid_bottom intersect solid bottom

group solid_up subtract solid solid_bottom

variable faSolid equal ${p_solid}*lx*ly/count(solid_up)

fix piston_up solid_up aveforce NULL NULL -${faSolid} 

fix freeze_up solid_up setforce 0.0 0.0 NULL 

fix freeze_bottom solid_bottom setforce 0.0 0.0 0.0

fix nvesol solid nve

compute Tliq liquid temp

fix nvtliq liquid nvt temp $T $T 0.5

fix_modify nvtliq temp Tliq

thermo 1000

thermo_modify flush yes temp Tliq

fix fxbal all balance 1000 1.05 shift z 10 1.05

compute mopz0 all stress/mop z center kin conf

fix mopz0t all ave/time 1 1 1 c_mopz0[*] file mopz0.time

compute moppz liquid stress/mop/profile z 0.0 0.1 kin conf

fix moppzt all ave/time 1 1 1 c_moppz[*] ave running overwrite file moppz.time mode vector

run 0