diff --git a/doc/read_data.html b/doc/read_data.html index e1d897a36c..2a049868e9 100644 --- a/doc/read_data.html +++ b/doc/read_data.html @@ -60,12 +60,13 @@ valid.

These are the recognized header keywords. Header lines can come in -any order. The value(s) is read from the beginning of the line. Thus -the keyword atoms should be in a line like "1000 atoms" and the -keyword ylo yhi should be in a line like "-10.0 10.0 ylo yhi". All -these settings have a default value of 0, except the lo/hi box size -defaults are -0.5 and 0.5. A line need only appear if the value is -different than the default. +any order. The value(s) are read from the beginning of the line. +Thus the keyword atoms should be in a line like "1000 atoms"; the +keyword ylo yhi should be in a line like "-10.0 10.0 ylo yhi"; the +keyword xy xz yz should be in a line like "0.0 5.0 6.0 xy xz yz". +All these settings have a default value of 0, except the lo/hi box +size defaults are -0.5 and 0.5. A line need only appear if the value +is different than the default.

-

For 2d simulations, the zlo zhi values should be set to bound the z -coords for atoms that appear in the file; the default of -0.5 0.5 is -valid if all z coords are 0.0. -

The initial simulation box size is determined by the lo/hi settings. In any dimension, the system may be periodic or non-periodic; see the boundary command.

+

If the xy xz yz line does not appear, then LAMMPS will set up an +axis-aligned (orthogonal) simulation box. If the line does appear, +LAMMPS creates a non-orthogonal simulation domain shaped as a +parallelepiped with triclinic symmetry. See the region +prism command for a description of how the extent of the +parallelepiped is defined. Basically, the parallelepiped has its +"origin" at (xlo,ylo,zlo) and 3 edge vectors starting from the origin +given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c = (xz,yz,zhi-zlo). +

+

The skew factors (xy,xz,yz) must not skew the box more than half the +distance of its side lengths. For example, if ylo = 2 and yhi = 12, +then the y box length is 10 and the xy factor must be between -5 and +5. Similary xz must be between -(zhi-zlo)/2 and +(zhi-zlo)/2 and yz +must be between -(zhi-zlo)/2 and +(zhi-zlo)/2. +

+

When a triclinic system is used, the simulation domain must be +periodic in any dimensions with a non-zero skew factor, as defined by +the boundary command. I.e. if the xy factor is +non-zero, then both the x and y dimensions must be periodic. +Similarly, x and z must be periodic if xz is non-zero and y and z must +be periodic if yz is non-zero. +

+

For 2d simulations, the zlo zhi values should be set to bound the z +coords for atoms that appear in the file; the default of -0.5 0.5 is +valid if all z coords are 0.0. For 2d triclinic simulations, the xz +and yz skew factors must be 0.0. +

If the system is non-periodic (in a dimension), then all atoms in the data file should have coordinates (in that dimension) between the lo and hi values. Furthermore, if running in parallel, the lo/hi values @@ -543,24 +568,22 @@ script.

Velocities section:

-