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Merge branch 'collected-small-changes' into collected-post-stable-patches

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Axel Kohlmeyer
2018-12-16 20:41:02 -05:00
parent e39ba20e42 34e0c05b09
commit 980f7e3b36
10 changed files with 348 additions and 116 deletions
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6
doc/src/fix_nh.txt
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@ -626,10 +626,10 @@ over time or the atom count becomes very small.
[Default:]
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
not coupled to barostat, otherwise no.
flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd
dimension and not coupled to barostat, otherwise no.
:line

13
doc/src/region.txt
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@ -26,7 +26,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
dim = {x} or {y} or {z} = axis of cylinder
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
radius = cylinder radius (distance units)
radius can be a variable (see below)
c1,c2, and radius can be a variable (see below)
lo,hi = bounds of cylinder in dim (distance units)
{plane} args = px py pz nx ny nz
px,py,pz = point on the plane (distance units)
@ -39,7 +39,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
{sphere} args = x y z radius
x,y,z = center of sphere (distance units)
radius = radius of sphere (distance units)
radius can be a variable (see below)
x,y,z, and radius can be a variable (see below)
{union} args = N reg-ID1 reg-ID2 ...
N = # of regions to follow, must be 2 or greater
reg-ID1,reg-ID2, ... = IDs of regions to join together
@ -179,12 +179,17 @@ The {radius} value for style {sphere} and {cylinder} can be specified
as an equal-style "variable"_variable.html. If the value is a
variable, it should be specified as v_name, where name is the variable
name. In this case, the variable will be evaluated each timestep, and
its value used to determine the radius of the region.
its value used to determine the radius of the region. For style {sphere}
also the x-, y-, and z- coordinate of the center of the sphere and for
style {cylinder} the two center positions c1 and c2 for the location of
the cylinder axes can be a variable with the same kind of effect and
requirements than for the radius.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent radius.
time. Thus it is easy to specify a time-dependent radius or have
a time dependent position of the sphere or cylinder region.
See the "Howto tricilinc"_Howto_triclinic.html doc page for a
geometric description of triclinic boxes, as defined by LAMMPS, and