From f06c0d5f85d18cde23a708c47a9ad32ec9d8a6f9 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 3 Jul 2007 18:39:09 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@729 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/lattice.html | 57 ++++++++++++++++++++++++++++-------------------- doc/lattice.txt | 57 ++++++++++++++++++++++++++++-------------------- 2 files changed, 66 insertions(+), 48 deletions(-) diff --git a/doc/lattice.html b/doc/lattice.html index 129012bede..5921fc3d6e 100644 --- a/doc/lattice.html +++ b/doc/lattice.html @@ -66,8 +66,9 @@ points inside the simulation box. Note that the create_atoms command allows different atom types to be assigned to different basis atoms of the lattice. Second, the lattice spacing in the x,y,z dimensions implied by the lattice, can be -used by other commands as distance units (e.g. region -and velocity), which are often convenient when the +used by other commands as distance units +(e.g. create_box, region and +velocity), which are often convenient to use when the underlying problem geometry is atoms on a lattice.

The lattice style must be consistent with the dimension of the @@ -105,9 +106,9 @@ corner and one at the center of the square. A hex style is also a and a2 = 0.0 sqrt(3.0) 0.0. It has 2 basis atoms, one at the corner and one at the center of the rectangle.

-

A lattice of style custom allows you to specify a1, a2, a3, and a list -of basis atoms to put in the unit cell. By default, a1,a2,a3 are 3 -orthogonal unit vectors (edges of a unit cube). But you can specify +

A lattice of style custom allows you to specify a1, a2, a3, and a +list of basis atoms to put in the unit cell. By default, a1,a2,a3 are +3 orthogonal unit vectors (edges of a unit cube). But you can specify them to be of any length and non-orthogonal to each other, so that they describe a tilted parallelepiped. Via the basis keyword you add atoms, one at a time, to the unit cell. Its arguments are @@ -156,7 +157,12 @@ along that axis, specified as integers. E.g. "orient x 2 1 0" means the x-axis in the simulation box will be the [210] lattice direction. The 3 lattice directions you specify must be mutually orthogonal and obey the right-hand rule, i.e. (X cross Y) points in -the Z direction. +the Z direction. Note that this description is really only valid for +orthogonal lattices. if you are using the more general lattice style +custom with non-orthogonal a1,a2,a3 vectors, then think of the 3 +orient options as creating a 3x3 rotation matrix which is applied to +a1,a2,a3 to rotate the original unit cell to a new orientation in the +simulation box.

@@ -171,7 +177,7 @@ are multiplied by the multiplicative factor described above that is associated with the scale factor. Thus a spacing of 1.0 means one unit cell independent of the scale factor. This option can be useful if the spacings LAMMPS computes are inconvenient to use in subsequent -commands, which can be the case for non-orthogonal or rotated/scaled +commands, which can be the case for non-orthogonal or rotated lattices.

If the spacing option is not specified, the lattice spacings are @@ -180,20 +186,30 @@ is mapped into the simulation box (scaled, shifted, rotated), so that it now has (perhaps) a modified shape and orientation. The lattice spacing in X is defined as the difference between the min/max extent of the x coordinates of the 8 corner points of the modified unit cell. -Similarly, the Y and Z lattice spacings are defined as the min/max of -the y and z coordinates. +Similarly, the Y and Z lattice spacings are defined as the difference +in the min/max of the y and z coordinates.

-

Note that if the unit cell has axis-aligned edges (a1,a2,a3) and is -not rotated (via the orient keyword), then the lattice spacings in -each dimension are simply the scale factor (descibed above) multiplied -by the length of a1,a2,a3. Thus a hex style lattice with a scale +

Note that if the unit cell is orthogonal with axis-aligned edges (not +rotated via the orient keyword), then the lattice spacings in each +dimension are simply the scale factor (descibed above) multiplied by +the length of a1,a2,a3. Thus a hex style lattice with a scale factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and 3*sqrt(3.0) in y.

-

For unit cells with a more general shape or when a rotation is -applied, the lattice spacing is less intuitive. But regardless, the -values of the lattice spacings LAMMPS will use are printed out, so -their effect in commands that use the spacings should be decipherable. +

IMPORTANT NOTE: For non-orthogonal unit cells and/or when a rotation +is applied via the orient keyword, then the lattice spacings may be +less intuitive. In particular, in these cases, there is no guarantee +that the lattice spacing is an integer multiple of the periodicity of +the lattice in that direction. Thus, if you create an orthogonal +periodic simulation box whose size in a dimension is a multiple of the +lattice spacing, and then fill it with atoms via the +create_atoms command, you will NOT necessarily +create a periodic system. I.e. atoms may overlap incorrectly at the +faces of the simulation box. +

+

Regardless of these issues, the values of the lattice spacings LAMMPS +calculates are printed out, so their effect in commands that use the +spacings should be decipherable.

@@ -209,13 +225,6 @@ then generate an error. No additional arguments need be used with

The a1,a2,a3,basis keywords can only be used with style custom.

-

For lattices oriented at an angle or with a non-orthognal unit cell, -care must be taken when using the region and -create_atoms commands to create a periodic system. -If the box size is not chosen appropriately, the system may not -actually be periodic, and atoms may overlap incorrectly at the faces -of the simulation box. -

Related commands:

dimension, create_atoms, diff --git a/doc/lattice.txt b/doc/lattice.txt index 2c740c8c32..531161d954 100644 --- a/doc/lattice.txt +++ b/doc/lattice.txt @@ -58,8 +58,9 @@ points inside the simulation box. Note that the "create_atoms"_create_atoms.html command allows different atom types to be assigned to different basis atoms of the lattice. Second, the lattice spacing in the x,y,z dimensions implied by the lattice, can be -used by other commands as distance units (e.g. "region"_region.html -and "velocity"_velocity.html), which are often convenient when the +used by other commands as distance units +(e.g. "create_box"_create_box.html, "region"_region.html and +"velocity"_velocity.html), which are often convenient to use when the underlying problem geometry is atoms on a lattice. The lattice style must be consistent with the dimension of the @@ -97,9 +98,9 @@ corner and one at the center of the square. A {hex} style is also a and a2 = 0.0 sqrt(3.0) 0.0. It has 2 basis atoms, one at the corner and one at the center of the rectangle. -A lattice of style {custom} allows you to specify a1, a2, a3, and a list -of basis atoms to put in the unit cell. By default, a1,a2,a3 are 3 -orthogonal unit vectors (edges of a unit cube). But you can specify +A lattice of style {custom} allows you to specify a1, a2, a3, and a +list of basis atoms to put in the unit cell. By default, a1,a2,a3 are +3 orthogonal unit vectors (edges of a unit cube). But you can specify them to be of any length and non-orthogonal to each other, so that they describe a tilted parallelepiped. Via the {basis} keyword you add atoms, one at a time, to the unit cell. Its arguments are @@ -148,7 +149,12 @@ along that axis, specified as integers. E.g. "orient x 2 1 0" means the x-axis in the simulation box will be the \[210\] lattice direction. The 3 lattice directions you specify must be mutually orthogonal and obey the right-hand rule, i.e. (X cross Y) points in -the Z direction. +the Z direction. Note that this description is really only valid for +orthogonal lattices. if you are using the more general lattice style +{custom} with non-orthogonal a1,a2,a3 vectors, then think of the 3 +{orient} options as creating a 3x3 rotation matrix which is applied to +a1,a2,a3 to rotate the original unit cell to a new orientation in the +simulation box. :line @@ -163,7 +169,7 @@ are multiplied by the multiplicative factor described above that is associated with the scale factor. Thus a spacing of 1.0 means one unit cell independent of the scale factor. This option can be useful if the spacings LAMMPS computes are inconvenient to use in subsequent -commands, which can be the case for non-orthogonal or rotated/scaled +commands, which can be the case for non-orthogonal or rotated lattices. If the {spacing} option is not specified, the lattice spacings are @@ -172,20 +178,30 @@ is mapped into the simulation box (scaled, shifted, rotated), so that it now has (perhaps) a modified shape and orientation. The lattice spacing in X is defined as the difference between the min/max extent of the x coordinates of the 8 corner points of the modified unit cell. -Similarly, the Y and Z lattice spacings are defined as the min/max of -the y and z coordinates. +Similarly, the Y and Z lattice spacings are defined as the difference +in the min/max of the y and z coordinates. -Note that if the unit cell has axis-aligned edges (a1,a2,a3) and is -not rotated (via the {orient} keyword), then the lattice spacings in -each dimension are simply the scale factor (descibed above) multiplied -by the length of a1,a2,a3. Thus a {hex} style lattice with a scale +Note that if the unit cell is orthogonal with axis-aligned edges (not +rotated via the {orient} keyword), then the lattice spacings in each +dimension are simply the scale factor (descibed above) multiplied by +the length of a1,a2,a3. Thus a {hex} style lattice with a scale factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and 3*sqrt(3.0) in y. -For unit cells with a more general shape or when a rotation is -applied, the lattice spacing is less intuitive. But regardless, the -values of the lattice spacings LAMMPS will use are printed out, so -their effect in commands that use the spacings should be decipherable. +IMPORTANT NOTE: For non-orthogonal unit cells and/or when a rotation +is applied via the {orient} keyword, then the lattice spacings may be +less intuitive. In particular, in these cases, there is no guarantee +that the lattice spacing is an integer multiple of the periodicity of +the lattice in that direction. Thus, if you create an orthogonal +periodic simulation box whose size in a dimension is a multiple of the +lattice spacing, and then fill it with atoms via the +"create_atoms"_create_atoms.html command, you will NOT necessarily +create a periodic system. I.e. atoms may overlap incorrectly at the +faces of the simulation box. + +Regardless of these issues, the values of the lattice spacings LAMMPS +calculates are printed out, so their effect in commands that use the +spacings should be decipherable. :line @@ -201,13 +217,6 @@ then generate an error. No additional arguments need be used with The {a1,a2,a3,basis} keywords can only be used with style {custom}. -For lattices oriented at an angle or with a non-orthognal unit cell, -care must be taken when using the "region"_region.html and -"create_atoms"_create_atoms.html commands to create a periodic system. -If the box size is not chosen appropriately, the system may not -actually be periodic, and atoms may overlap incorrectly at the faces -of the simulation box. - [Related commands:] "dimension"_dimension.html, "create_atoms"_create_atoms.html,