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update docs and references for name changes in USER-MOP package, remove obsoleted files

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Axel Kohlmeyer
2018-09-04 08:42:32 -04:00
parent a797a0d193
commit cb4ffaf95c
14 changed files with 12 additions and 1634 deletions
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10
doc/src/Packages_details.txt
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@ -1577,11 +1577,11 @@ USER-MOP package :link(PKG-USER-MOP),h4
[Contents:]
This package contains two compute styles: compute mop and compute mop/profile.
This package contains two compute styles: compute stress/mop and compute stress/mop/profile.
compute mop calculates components of the local stress tensor using the method of planes, applied on one plane.
compute stress/mop calculates components of the local stress tensor using the method of planes, applied on one plane.
compute mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
compute stress/mop/profile calculates profiles of components of the local stress tensor using the method of planes, applied on an array of regularly spaced planes.
[Author:] Laurent Joly (University of Lyon 1)
Romain Vermorel at (University of Pau and Pays de l'Adour)
@ -1590,8 +1590,8 @@ Romain Vermorel at (University of Pau and Pays de l'Adour)
src/USER-MOP: filenames -> commands
src/USER-MOP/README
"compute mop"_compute_mop.html
"compute mop/profile"_compute_mop.html
"compute stress/mop"_compute_stress_mop.html
"compute stress/mop/profile"_compute_stress_mop.html
examples/USER/mop :ul
:line

2
doc/src/Packages_user.txt
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@ -57,7 +57,7 @@ Package, Description, Doc page, Example, Library
"USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
"USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
"USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style mop"_compute_mop.html, USER/mop, no
"USER-MOP"_Packages_details.html#PKG-USER-MOP, compute stress via method-of-planes, "compute_style stress/mop"_compute_stress_mop.html, USER/mop, no
"USER-MOFFF"_Packages_details.html#PKG-USER-MOFFF, styles for "MOF-FF"_MOFplus force field, "pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html, USER/mofff, no
"USER-MOLFILE"_Packages_details.html#PKG-USER-MOLFILE, "VMD"_https://www.ks.uiuc.edu/Research/vmd/ molfile plug-ins,"dump molfile"_dump_molfile.html, n/a, ext
"USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext

111
doc/src/compute_mop.txt
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@ -1,111 +0,0 @@
"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 mop command :h3
compute 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 = {mop} or {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
{mop} args = pos
pos = {lower} or {center} or {upper} or coordinate value (distance units) is the position of the plane
{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 mop x lower total
compute 1 liquid 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 mop/profile x lower 0.1 total
compute 1 liquid 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 {mop} and compute {mop/profile} define computations that
calculate components of the local stress tensor using the method of
planes "(Todd)"_#mop-todd. Specifically in compute {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 {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 {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 {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:]
This style is part of the USER-MOP package. It is 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).

2
doc/src/computes.txt
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@ -55,7 +55,6 @@ Computes :h1
compute_meso_e_atom
compute_meso_rho_atom
compute_meso_t_atom
compute_mop
compute_msd
compute_msd_chunk
compute_msd_nongauss
@ -99,6 +98,7 @@ Computes :h1
compute_sna_atom
compute_spin
compute_stress_atom
compute_stress_mop
compute_tally
compute_tdpd_cc_atom
compute_temp

2
doc/src/lammps.book
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@ -446,7 +446,6 @@ compute_ke_rigid.html
compute_meso_e_atom.html
compute_meso_rho_atom.html
compute_meso_t_atom.html
compute_mop.html
compute_msd.html
compute_msd_chunk.html
compute_msd_nongauss.html
@ -490,6 +489,7 @@ compute_smd_vol.html
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