diff --git a/doc/Manual.html b/doc/Manual.html index f6b15095f8..373018c8bf 100644 --- a/doc/Manual.html +++ b/doc/Manual.html @@ -134,8 +134,8 @@

LAMMPS-ICMS Documentation

-
-

24 Dec 2015 version

+
+

11 Jan 2016 version

Version info:

diff --git a/doc/Manual.txt b/doc/Manual.txt index 43cab3909e..a3ff300d04 100644 --- a/doc/Manual.txt +++ b/doc/Manual.txt @@ -1,7 +1,7 @@ LAMMPS-ICMS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS-ICMS Documentation :c,h3 -24 Dec 2015 version :c,h4 +11 Jan 2016 version :c,h4 Version info: :h4 diff --git a/doc/compute_chunk_atom.html b/doc/compute_chunk_atom.html index ac158cc46a..70b562a06c 100644 --- a/doc/compute_chunk_atom.html +++ b/doc/compute_chunk_atom.html @@ -171,7 +171,7 @@ style = bin/1d or bin/2d or bin/3d or bin/sphere<
  • zero or more keyword/values pairs may be appended
    • -
  • keyword = region or nchunk or static or compress or bound or discard or units
    • +
  • keyword = region or nchunk or static or compress or bound or discard or pbc or units
 region value = region-ID
@@ -198,6 +198,8 @@ style = bin/1d or bin/2d or bin/3d or bin/sphere<
   x/y/z = x or y or z to bound sptial bins in this dimension
   lo = lower or coordinate value (distance units)
   hi = upper or coordinate value (distance units)
+pbc value = no or yes
+  yes = use periodic distance for bin/sphere and bin/cylinder styles
 units value = box or lattice or reduced
@@ -616,6 +618,19 @@ value, which is assumed to be inside (or at least near) the simulation box boundaries, though LAMMPS does not check for this. Note that using the bound keyword typically reduces the total number of bins and thus the number of chunks Nchunk.

+

The pbc keyword only applies to the bin/sphere and bin/cylinder +styles. If set to yes, the distance an atom is from the sphere +origin or cylinder axis is calculated in a minimum image sense with +respect to periodic dimensions, when determining which bin the atom is +in. I.e. if x is a periodic dimension and the distance between the +atom and the sphere center in the x dimension is greater than 0.5 * +simulation box length in x, then a box length is subtracted to give a +distance < 0.5 * simulation box length. This allosws the sphere or +cylinder center to be near a box edge, and atoms on the other side of +the periodic box will still be close to the center point/axis. Note +that with a setting of yes, the outer sphere or cylinder radius must +also be <= 0.5 * simulation box length in any periodic dimension +except for the cylinder axis dimension, or an error is generated.

The units keyword only applies to the binning styles; otherwise it is ignored. For the bin/1d, bin/2d, bin/3d styles, it determines the meaning of the distance units used for the bin sizes @@ -683,6 +698,7 @@ the restarted simulation begins.

  • discard = yes, for all styles except binning
  • discard = mixed, for binning styles
  • bound = lower and upper in all dimensions
    • +
  • pbc = no
  • units = lattice
    • diff --git a/doc/compute_chunk_atom.txt b/doc/compute_chunk_atom.txt index bef333a4b8..9b56c264c9 100644 --- a/doc/compute_chunk_atom.txt +++ b/doc/compute_chunk_atom.txt @@ -48,7 +48,7 @@ style = {bin/1d} or {bin/2d} or {bin/3d} or {bin/sphere} or {type} or {molecule} v_name = per-atom vector calculated by an atom-style variable with name :pre zero or more keyword/values pairs may be appended :l -keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard} or {units} :l +keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard} or {pbc} or {units} :l {region} value = region-ID region-ID = ID of region atoms must be in to be part of a chunk {nchunk} value = {once} or {every} @@ -73,6 +73,8 @@ keyword = {region} or {nchunk} or {static} or {compress} or {bound} or {discard} x/y/z = {x} or {y} or {z} to bound sptial bins in this dimension lo = {lower} or coordinate value (distance units) hi = {upper} or coordinate value (distance units) + {pbc} value = {no} or {yes} + yes = use periodic distance for bin/sphere and bin/cylinder styles {units} value = {box} or {lattice} or {reduced} :pre :ule @@ -570,6 +572,20 @@ box boundaries, though LAMMPS does not check for this. Note that using the {bound} keyword typically reduces the total number of bins and thus the number of chunks {Nchunk}. +The {pbc} keyword only applies to the {bin/sphere} and {bin/cylinder} +styles. If set to {yes}, the distance an atom is from the sphere +origin or cylinder axis is calculated in a minimum image sense with +respect to periodic dimensions, when determining which bin the atom is +in. I.e. if x is a periodic dimension and the distance between the +atom and the sphere center in the x dimension is greater than 0.5 * +simulation box length in x, then a box length is subtracted to give a +distance < 0.5 * simulation box length. This allosws the sphere or +cylinder center to be near a box edge, and atoms on the other side of +the periodic box will still be close to the center point/axis. Note +that with a setting of {yes}, the outer sphere or cylinder radius must +also be <= 0.5 * simulation box length in any periodic dimension +except for the cylinder axis dimension, or an error is generated. + The {units} keyword only applies to the {binning} styles; otherwise it is ignored. For the {bin/1d}, {bin/2d}, {bin/3d} styles, it determines the meaning of the distance units used for the bin sizes @@ -645,4 +661,5 @@ compress = no discard = yes, for all styles except binning discard = mixed, for binning styles bound = lower and upper in all dimensions +pbc = no units = lattice :ul diff --git a/doc/compute_saed.html b/doc/compute_saed.html index e035fe1612..86241dd067 100644 --- a/doc/compute_saed.html +++ b/doc/compute_saed.html @@ -169,7 +169,7 @@ fix saed/vtk 1 1 1 c_2 file Ni_000.saed

    Description

    Define a computation that calculates electron diffraction intensity as -described in (Coleman) on a mesh of reciprocal lattice nodes +described in (Coleman) on a mesh of reciprocal lattice nodes defined by the entire simulation domain (or manually) using simulated radiation of wavelength lambda.

    The electron diffraction intensity I at each reciprocal lattice point @@ -212,13 +212,14 @@ the Kmax, Zone, and dR_Ewald parameters. The rectili created about the origin of reciprocal space is terminated at the boundary of a sphere of radius Kmax centered at the origin. If Zone parameters z1=z2=z3=0 are used, diffraction intensities are -computed throughout the entire spherical volume - note this can greatly -increase the cost of computation. Otherwise, Zone parameters will -denote the z1=h, z2=k, and z3=l (in a global since) zone axis of an -intersecting Ewald sphere. Diffraction intensities will only be -computed at the intersection of the reciprocal lattice mesh and a -dR_Ewald thick surface of the Ewald sphere. See the example 3D -intestiety data and the intersection of a [010] zone axis in the below image.

    +computed throughout the entire spherical volume - note this can +greatly increase the cost of computation. Otherwise, Zone +parameters will denote the z1=h, z2=k, and z3=l (in a global since) +zone axis of an intersecting Ewald sphere. Diffraction intensities +will only be computed at the intersection of the reciprocal lattice +mesh and a dR_Ewald thick surface of the Ewald sphere. See the +example 3D intestiety data and the intersection of a [010] zone axis +in the below image.

    Restrictions

    +

    This compute is part of the USER-DIFFRACTION package. It is only +enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

    The compute_saed command does not work for triclinic cells.