The bin/sphere style defines a set of spherical shells around the -origin (xorig,*yorig*,*zorig*), using nsbin shells with radii -equally spaced between srmin and srmax, for effectively a 1d +
The bin/sphere style defines a set of spherical shell bins around +the origin (xorig,*yorig*,*zorig*), using nsbin bins with radii +equally spaced between srmin and srmax. This is effectively a 1d vector of bins. For example, if srmin = 1.0 and srmax = 10.0 and nsbin = 9, then the first bin spans 1.0 < r < 2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins is the same whether the @@ -298,29 +298,30 @@ simulation box is orthogonal or triclinic; i.e. the spherical shells are not tilted or scaled differently in different dimensions to transform them into ellipsoidal shells.
The bin/cylinder style defines bins for a cylinder oriented along -the axis dim with the axis position in the other two radial +the axis dim with the axis coordinates in the other two radial dimensions at (c1,*c2*). For dim = x, c1/c2 = y/z; for dim = y, -c1/c2 = x/z; for dim = z, c1/c2 = x/y. These can be thought of as a -2d array of bins, each of which is a pie-shaped wedge (radial -dimensions) of finite height (along the cylinder axis). The bin size +c1/c2 = x/z; for dim = z, c1/c2 = x/y. This is effectively a 2d array +of bins. The first dimension is along the cylinder axis, the second +dimension is radially outward from the cylinder axis. The bin size and positions along the cylinder axis are specified by the origin and delta values, the same as for the bin/1d, bin/2d, and -bin/3d styles. There are ncbin concentric circles in the radial -direction from the cylinder axis with radii equally spaced between -crmin and crmax. For example, if crmin = 1.0 and crmax = 10.0 -and ncbin = 9, then the first bin spans 1.0 < r < 2.0, and the last -bin spans 9.0 < r 10.0. The geometry of the bins in the radial -dimensions is the same whether the simulation box is orthogonal or -triclinic; i.e. the circles are not tilted or scaled differently in -the two different dimensions to transform them into ellipses.
+bin/3d styles. There are ncbin concentric circle bins in the +radial direction from the cylinder axis with radii equally spaced +between crmin and crmax. For example, if crmin = 1.0 and +crmax = 10.0 and ncbin = 9, then the first bin spans 1.0 < r < +2.0, and the last bin spans 9.0 < r 10.0. The geometry of the bins in +the radial dimensions is the same whether the simulation box is +orthogonal or triclinic; i.e. the concetric circles are not tilted or +scaled differently in the two different dimensions to transform them +into ellipses.The created bins (and hence the chunk IDs) are numbered consecutively -from 1 to the number of bins = Nchunk. For 2d and 3d bins, the +from 1 to the number of bins = Nchunk. For bin2d and bin3d, the numbering varies most rapidly in the first dimension (which could be x, y, or z), next rapidly in the 2nd dimension, and most slowly in the -3rd dimension. For spherical 1d bins, the innermost shell is chunk 1 -and the outermost shell is chunk Nchunk = nsbin. For cylindrical -2d bins, the numbering varies most rapidly in the dimension along the -cylinder axis and most slowly in the radial direction.
+3rd dimension. For bin/sphere, the bin with smallest radii is chunk +1 and the bni with largest radii is chunk Nchunk = ncbin. For +bin/cylinder, the numbering varies most rapidly in the dimension +along the cylinder axis and most slowly in the radial direction.Each time this compute is invoked, each atom is mapped to a bin based on its current position. Note that between reneighboring timesteps, atoms can move outside the current simulation box. If the box is @@ -718,7 +719,7 @@ the restarted simulation begins.
@@ -226,7 +226,7 @@ LAMMPS output options. @@ -238,7 +238,7 @@ above. @@ -210,7 +210,7 @@ distance units. @@ -234,7 +234,7 @@ distance units. @@ -203,7 +203,7 @@ above. @@ -242,7 +242,7 @@ explained above. @@ -206,7 +206,7 @@ LAMMPS was built with that package. See the var DOCUMENTATION_OPTIONS = { URL_ROOT:'./', - VERSION:'9 Dec 2015', + VERSION:'11 Dec 2015', COLLAPSE_INDEX:false, FILE_SUFFIX:'.html', HAS_SOURCE: true diff --git a/doc/compute_dihedral_local.html b/doc/compute_dihedral_local.html index 4a3eb0c197..dbb207f371 100644 --- a/doc/compute_dihedral_local.html +++ b/doc/compute_dihedral_local.html @@ -8,7 +8,7 @@ -