From 7b5a83562eecc0d69045f81f61be93c6816fbc29 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 11 Jan 2010 20:54:59 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3643 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_move.html | 5 ++- doc/fix_move.txt | 5 ++- doc/fix_wall_region.html | 5 ++- doc/fix_wall_region.txt | 5 ++- doc/region.html | 88 ++++++++++++++++++++++++++++++++++++---- doc/region.txt | 88 ++++++++++++++++++++++++++++++++++++---- doc/reset_timestep.html | 4 ++ doc/reset_timestep.txt | 4 ++ 8 files changed, 182 insertions(+), 22 deletions(-) diff --git a/doc/fix_move.html b/doc/fix_move.html index c3f69b0a4a..4ddd6019dc 100644 --- a/doc/fix_move.html +++ b/doc/fix_move.html @@ -117,7 +117,10 @@ each atom to (omega cross Rperp) where omega is its angular velocity around the rotation axis and Rperp is a perpendicular vector from the rotation axis to the atom. If the defined atom_style assigns an angular velocity to each atom, -then each atom's angular velocity is also set to omega. +then each atom's angular velocity is also set to omega. Note that the +direction of rotation for the atoms around the rotation axis is +consistent with the right-hand rule: if the right-hand's thumb points +along R, then the fingers wrap around in the direction of rotation.

The variable style allows the position and velocity components of each atom to be set by formulas specified via the diff --git a/doc/fix_move.txt b/doc/fix_move.txt index cf589f3f16..08c2e05684 100644 --- a/doc/fix_move.txt +++ b/doc/fix_move.txt @@ -108,7 +108,10 @@ each atom to (omega cross Rperp) where omega is its angular velocity around the rotation axis and Rperp is a perpendicular vector from the rotation axis to the atom. If the defined "atom_style"_atom_style.html assigns an angular velocity to each atom, -then each atom's angular velocity is also set to omega. +then each atom's angular velocity is also set to omega. Note that the +direction of rotation for the atoms around the rotation axis is +consistent with the right-hand rule: if the right-hand's thumb points +along {R}, then the fingers wrap around in the direction of rotation. The {variable} style allows the position and velocity components of each atom to be set by formulas specified via the diff --git a/doc/fix_wall_region.html b/doc/fix_wall_region.html index cbbdabd2ef..4f6c0545fd 100644 --- a/doc/fix_wall_region.html +++ b/doc/fix_wall_region.html @@ -44,7 +44,10 @@ particles, i.e. the direction of the surface normal. Regions can either be primitive shapes (block, sphere, cylinder, etc) or combinations of primitive shapes specified via the union or intersect region styles. These latter styles can be used to -construct particle containers with complex shapes. +construct particle containers with complex shapes. Regions can also +change over time via keywords like linear, wiggle, and rotate, +which when used with this fix, have the effect of moving the region +surface in a prescribed manner.

IMPORTANT NOTE: As discussed on the region command doc page, regions in LAMMPS do not get wrapped across periodic boundaries. diff --git a/doc/fix_wall_region.txt b/doc/fix_wall_region.txt index 6ac90926c3..aff9f30a41 100644 --- a/doc/fix_wall_region.txt +++ b/doc/fix_wall_region.txt @@ -41,7 +41,10 @@ particles, i.e. the direction of the surface normal. Regions can either be primitive shapes (block, sphere, cylinder, etc) or combinations of primitive shapes specified via the {union} or {intersect} region styles. These latter styles can be used to -construct particle containers with complex shapes. +construct particle containers with complex shapes. Regions can also +change over time via keywords like {linear}, {wiggle}, and {rotate}, +which when used with this fix, have the effect of moving the region +surface in a prescribed manner. IMPORTANT NOTE: As discussed on the "region"_region.html command doc page, regions in LAMMPS do not get wrapped across periodic boundaries. diff --git a/doc/region.html b/doc/region.html index c86c614894..33f5387ac7 100644 --- a/doc/region.html +++ b/doc/region.html @@ -51,14 +51,23 @@

  • zero or more keyword/value pairs may be appended -
  • keyword = side or units +
  • keyword = side or units or vel or wiggle or rotate 
      side value = in or out
     in = the region is inside the specified geometry
     out = the region is outside the specified geometry
   units value = lattice or box
     lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units 
+    box = the geometry is defined in simulation box units
+  vel args = Vx Vy Vz
+    Vx,Vy,Vz = components of velocity vector (velocity units)
+  wiggle args = Ax Ay Az period
+    Ax,Ay,Az = components of amplitude vector (distance units)
+    period = period of oscillation (time units)
+  rotate args = Px Py Pz Rx Ry Rz period
+    Px,Py,Pz = origin point of axis of rotation (distance units)
+    Rx,Ry,Rz = axis of rotation vector
+    period = period of rotation (time units)
    @@ -68,8 +77,14 @@ region 2 sphere 0.0 0.0 0.0 5 side out region void cylinder y 2 3 5 -5.0 EDGE units box region 1 prism 0 10 0 10 0 10 2 0 0 -region outside union 4 side1 side2 side3 side4 +region outside union 4 side1 side2 side3 side4 +region 2 sphere 0.0 0.0 0.0 5 side out wiggle 1 1 0 10 +

    Note that the +direction of rotation for the atoms around the rotation axis is +consistent with the right-hand rule: if the right-hand's thumb points +along R, then the fingers wrap around in the direction of rotation. +

    Description:

    This command defines a geometric region of space. Various other @@ -80,6 +95,15 @@ command, or deleted via the delete_atoms comma Or the surface of the region can be used as a boundary wall via the fix wall/region command.

    +

    Normally, regions in LAMMPS are "static", meaning their geometric +extent does not change with time. If the vel or wiggle or +rotate keyword is used, as described below, the region becomes +"dynamic", meaning it's location or orientation changes with time. +This may be useful, for example, when thermostatting a region, via the +compute temp/region command, or when the fix wall/region command uses +a region surface as a bounding wall on particle motion, i.e. a +rotating container. +

    The lo/hi values for block or cone or cylinder or prism styles can be specified as EDGE or INF. EDGE means they extend all the way to the global simulation box boundary. Note that this is the current @@ -151,6 +175,8 @@ equivalent. listed regions combined. The intersect style creates a region consisting of the volume that is common to all the listed regions.

    +
    +

    The side keyword determines whether the region is considered to be inside or outside of the specified geometry. Using this keyword in conjunction with union and intersect regions, complex geometries @@ -162,12 +188,16 @@ both of the spheres.

    The units keyword determines the meaning of the distance units used to define the region for any argument above listed as having distance -units. A box value selects standard distance units as defined by -the units command, e.g. Angstroms for units = real or -metal. A lattice value means the distance units are in lattice -spacings. The lattice command must have been -previously used to define the lattice spacings which are used as -follows: +units. It also affects the scaling of the velocity vector specfied +with the vel keyword, the amplitude vector specified with the +wiggle keyword, and the rotation point specified with the rotate +keyword, since they each involve a distance metric. +

    +

    A box value selects standard distance units as defined by the +units command, e.g. Angstroms for units = real or metal. +A lattice value means the distance units are in lattice spacings. +The lattice command must have been previously used to +define the lattice spacings which are used as follows:

    +
    + +

    If the vel or wiggle or rotate keywords are used, the region +is "dynamic", meaning its location or orientation changes with time. +No more than one of these keywords can be used at a time. These +keywords cannot be used with a union or intersect style region. +Instead, the keywords should be used to define the individual +sub-regions of the union or intersect region. Normally, each +sub-region should be "dynamic" in the same manner (e.g. rotate around +the same point), though this is not a requirement. +

    +

    The vel style moves the region at a constant velocity, so that its +position X = (x,y,z) as a function of time is given in vector +notation as +

    +
    X(t) = X0 + V * delta 
+
    +

    where X0 = (x0,y0,z0) is its position at the time the region is +specified, V is the specified velocity vector with components +(Vx,Vy,Vz), and delta is the time elapsed since the region was +specified. +

    +

    The wiggle style moves the region in an oscillatory fashion, so that +its position X = (x,y,z) as a function of time is given in vector +notation as +

    +
    X(t) = X0 + A sin(omega*delta) 
+
    +

    where X0 = (x0,y0,z0) is its position at the time the region is +specified, A is the specified amplitude vector with components +(Ax,Ay,Az), omega is 2 PI / period, and delta is the time +elapsed since the region was specified. +

    +

    The rotate style rotates the region around a rotation axis R = +(Rx,Ry,Rz) that goes thru a point P = (Px,Py,Pz). The period of +the rotation is also specified. The direction of rotation for the +region around the rotation axis is consistent with the right-hand +rule: if your right-hand thumb points along R, then your fingers +wrap around the axis in the direction of rotation. +

    Restrictions:

    A prism cannot be of 0.0 thickness in any dimension; use a small z diff --git a/doc/region.txt b/doc/region.txt index f1cf039f68..d529ff2b8a 100644 --- a/doc/region.txt +++ b/doc/region.txt @@ -44,13 +44,22 @@ style = {block} or {cone} or {cylinder} or {plane} or {prism} or {sphere} or {un N = # of regions to follow, must be 2 or greater reg-ID1,reg-ID2, ... = IDs of regions to intersect :pre zero or more keyword/value pairs may be appended :l -keyword = {side} or {units} :l +keyword = {side} or {units} or {vel} or {wiggle} or {rotate} :l {side} value = {in} or {out} {in} = the region is inside the specified geometry {out} = the region is outside the specified geometry {units} value = {lattice} or {box} {lattice} = the geometry is defined in lattice units - {box} = the geometry is defined in simulation box units :pre + {box} = the geometry is defined in simulation box units + {vel} args = Vx Vy Vz + Vx,Vy,Vz = components of velocity vector (velocity units) + {wiggle} args = Ax Ay Az period + Ax,Ay,Az = components of amplitude vector (distance units) + period = period of oscillation (time units) + {rotate} args = Px Py Pz Rx Ry Rz period + Px,Py,Pz = origin point of axis of rotation (distance units) + Rx,Ry,Rz = axis of rotation vector + period = period of rotation (time units) :pre :ule [Examples:] @@ -59,7 +68,13 @@ region 1 block -3.0 5.0 INF 10.0 INF INF region 2 sphere 0.0 0.0 0.0 5 side out region void cylinder y 2 3 5 -5.0 EDGE units box region 1 prism 0 10 0 10 0 10 2 0 0 -region outside union 4 side1 side2 side3 side4 :pre +region outside union 4 side1 side2 side3 side4 +region 2 sphere 0.0 0.0 0.0 5 side out wiggle 1 1 0 10 :pre + +Note that the +direction of rotation for the atoms around the rotation axis is +consistent with the right-hand rule: if the right-hand's thumb points +along {R}, then the fingers wrap around in the direction of rotation. [Description:] @@ -71,6 +86,15 @@ command, or deleted via the "delete_atoms"_delete_atoms.html command. Or the surface of the region can be used as a boundary wall via the "fix wall/region"_fix_wall_region.html command. +Normally, regions in LAMMPS are "static", meaning their geometric +extent does not change with time. If the {vel} or {wiggle} or +{rotate} keyword is used, as described below, the region becomes +"dynamic", meaning it's location or orientation changes with time. +This may be useful, for example, when thermostatting a region, via the +compute temp/region command, or when the fix wall/region command uses +a region surface as a bounding wall on particle motion, i.e. a +rotating container. + The lo/hi values for {block} or {cone} or {cylinder} or {prism} styles can be specified as EDGE or INF. EDGE means they extend all the way to the global simulation box boundary. Note that this is the current @@ -142,6 +166,8 @@ The {union} style creates a region consisting of the volume of all the listed regions combined. The {intersect} style creates a region consisting of the volume that is common to all the listed regions. +:line + The {side} keyword determines whether the region is considered to be inside or outside of the specified geometry. Using this keyword in conjunction with {union} and {intersect} regions, complex geometries @@ -153,12 +179,16 @@ both of the spheres. The {units} keyword determines the meaning of the distance units used to define the region for any argument above listed as having distance -units. A {box} value selects standard distance units as defined by -the "units"_units.html command, e.g. Angstroms for units = real or -metal. A {lattice} value means the distance units are in lattice -spacings. The "lattice"_lattice.html command must have been -previously used to define the lattice spacings which are used as -follows: +units. It also affects the scaling of the velocity vector specfied +with the {vel} keyword, the amplitude vector specified with the +{wiggle} keyword, and the rotation point specified with the {rotate} +keyword, since they each involve a distance metric. + +A {box} value selects standard distance units as defined by the +"units"_units.html command, e.g. Angstroms for units = real or metal. +A {lattice} value means the distance units are in lattice spacings. +The "lattice"_lattice.html command must have been previously used to +define the lattice spacings which are used as follows: For style {block}, the lattice spacing in dimension x is applied to xlo and xhi, similarly the spacings in dimensions y,z are applied to @@ -187,6 +217,46 @@ For style {sphere}, the lattice spacing in dimensions x,y,z are applied to the sphere center x,y,z. The spacing in dimension x is applied to the sphere radius. :l,ule +:line + +If the {vel} or {wiggle} or {rotate} keywords are used, the region +is "dynamic", meaning its location or orientation changes with time. +No more than one of these keywords can be used at a time. These +keywords cannot be used with a {union} or {intersect} style region. +Instead, the keywords should be used to define the individual +sub-regions of the {union} or {intersect} region. Normally, each +sub-region should be "dynamic" in the same manner (e.g. rotate around +the same point), though this is not a requirement. + +The {vel} style moves the region at a constant velocity, so that its +position {X} = (x,y,z) as a function of time is given in vector +notation as + +X(t) = X0 + V * delta :pre + +where {X0} = (x0,y0,z0) is its position at the time the region is +specified, {V} is the specified velocity vector with components +(Vx,Vy,Vz), and {delta} is the time elapsed since the region was +specified. + +The {wiggle} style moves the region in an oscillatory fashion, so that +its position {X} = (x,y,z) as a function of time is given in vector +notation as + +X(t) = X0 + A sin(omega*delta) :pre + +where {X0} = (x0,y0,z0) is its position at the time the region is +specified, {A} is the specified amplitude vector with components +(Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time +elapsed since the region was specified. + +The {rotate} style rotates the region around a rotation axis {R} = +(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz). The {period} of +the rotation is also specified. The direction of rotation for the +region around the rotation axis is consistent with the right-hand +rule: if your right-hand thumb points along {R}, then your fingers +wrap around the axis in the direction of rotation. + [Restrictions:] A prism cannot be of 0.0 thickness in any dimension; use a small z diff --git a/doc/reset_timestep.html b/doc/reset_timestep.html index a59fb07bb1..021ee37155 100644 --- a/doc/reset_timestep.html +++ b/doc/reset_timestep.html @@ -51,6 +51,10 @@ include the "ave" fixes such as fix ave/spatial. Also fix dt/reset and fix deposit.

    +

    This command cannot be used when any dynamic regions are defined via +the region command, which have time-dependent position +and orientation. +

    There are other fixes which use the current timestep which may produce unexpected behavior, but LAMMPS allows them to be in place when resetting the timestep. For example, commands which thermostat the diff --git a/doc/reset_timestep.txt b/doc/reset_timestep.txt index c90925e4a5..db11a2f0f0 100644 --- a/doc/reset_timestep.txt +++ b/doc/reset_timestep.txt @@ -48,6 +48,10 @@ include the "ave" fixes such as "fix ave/spatial"_fix_ave_spatial.html. Also "fix dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposity.html. +This command cannot be used when any dynamic regions are defined via +the "region"_region.html command, which have time-dependent position +and orientation. + There are other fixes which use the current timestep which may produce unexpected behavior, but LAMMPS allows them to be in place when resetting the timestep. For example, commands which thermostat the