forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@373 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
1c94474954
commit
ff12c6b9b7
|
|
@ -24,14 +24,39 @@
|
|||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>This command creates a simulation box that encloses the specified
|
||||
region. Thus a <A HREF = "region.html">region</A> command must first be used to
|
||||
define a geometric domain. If the region is not of style <I>block</I>,
|
||||
LAMMPS encloses it with a rectangular simulation box.
|
||||
<P>This command creates a simulation box based on the specified region.
|
||||
Thus a <A HREF = "region.html">region</A> command must first be used to define a
|
||||
geometric domain.
|
||||
</P>
|
||||
<P>The argument N is the number of atom types that will be used in the
|
||||
simulation.
|
||||
</P>
|
||||
<P>If the region is not of style <I>prism</I>, then LAMMPS encloses the region
|
||||
(block, sphere, etc) with an axis-aligned (orthogonal) box which
|
||||
becomes the simulation domain.
|
||||
</P>
|
||||
<P>If the region is of style <I>prism</I>, LAMMPS creates a non-orthogonal
|
||||
simulation domain shaped as a parallelepiped with triclinic symmetry.
|
||||
See the <A HREF = "region.html">region prism</A> command for a description of how
|
||||
the shape of the parallelepiped is defined. The parallelepiped has
|
||||
its "origin" at (xlo,ylo,zlo) and 3 edge vectors starting from its
|
||||
origin given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c =
|
||||
(xz,yz,zhi-zlo).
|
||||
</P>
|
||||
<P>A prism region used with the create_box command must have skew factors
|
||||
(xy,xz,yz) that do 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.
|
||||
</P>
|
||||
<P>When a prism region is used, the simulation domain must be periodic in
|
||||
any dimensions with a non-zero skew factor, as defined by the
|
||||
<A HREF = "boundary.html">boundary</A> 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.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>An <A HREF = "atom_style.html">atom_style</A> and <A HREF = "region.html">region</A> must have
|
||||
|
|
|
|||
|
|
@ -21,14 +21,39 @@ create_atoms 2 mybox :pre
|
|||
|
||||
[Description:]
|
||||
|
||||
This command creates a simulation box that encloses the specified
|
||||
region. Thus a "region"_region.html command must first be used to
|
||||
define a geometric domain. If the region is not of style {block},
|
||||
LAMMPS encloses it with a rectangular simulation box.
|
||||
This command creates a simulation box based on the specified region.
|
||||
Thus a "region"_region.html command must first be used to define a
|
||||
geometric domain.
|
||||
|
||||
The argument N is the number of atom types that will be used in the
|
||||
simulation.
|
||||
|
||||
If the region is not of style {prism}, then LAMMPS encloses the region
|
||||
(block, sphere, etc) with an axis-aligned (orthogonal) box which
|
||||
becomes the simulation domain.
|
||||
|
||||
If the region is of style {prism}, LAMMPS creates a non-orthogonal
|
||||
simulation domain shaped as a parallelepiped with triclinic symmetry.
|
||||
See the "region prism"_region.html command for a description of how
|
||||
the shape of the parallelepiped is defined. The parallelepiped has
|
||||
its "origin" at (xlo,ylo,zlo) and 3 edge vectors starting from its
|
||||
origin given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c =
|
||||
(xz,yz,zhi-zlo).
|
||||
|
||||
A prism region used with the create_box command must have skew factors
|
||||
(xy,xz,yz) that do 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 prism region is used, the simulation domain must be periodic in
|
||||
any dimensions with a non-zero skew factor, as defined by the
|
||||
"boundary"_boundary.html 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.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
An "atom_style"_atom_style.html and "region"_region.html must have
|
||||
|
|
|
|||
|
|
@ -281,6 +281,13 @@ could then be output with these keywords.
|
|||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>Scaled coordinates cannot be writted to dump files when the simulation
|
||||
box is triclinic (non-orthogonal). Note that this is the default for
|
||||
dump style <I>atom</I>; the <A HREF = "dump_modify.html">dump_modify command</A> must be
|
||||
used to change it. The exception is DCD files which store the tilt
|
||||
factors for subsequent visualization by programs like
|
||||
<A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A>.
|
||||
</P>
|
||||
<P>To write gzipped dump files, you must compile LAMMPS with the -DGZIP
|
||||
option - see the <A HREF = "Section_start.html#2_2">Making LAMMPS</A> section of the
|
||||
documentation.
|
||||
|
|
|
|||
|
|
@ -271,6 +271,13 @@ could then be output with these keywords.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
Scaled coordinates cannot be writted to dump files when the simulation
|
||||
box is triclinic (non-orthogonal). Note that this is the default for
|
||||
dump style {atom}; the "dump_modify command"_dump_modify.html must be
|
||||
used to change it. The exception is DCD files which store the tilt
|
||||
factors for subsequent visualization by programs like
|
||||
"VMD"_http://www.ks.uiuc.edu/Research/vmd.
|
||||
|
||||
To write gzipped dump files, you must compile LAMMPS with the -DGZIP
|
||||
option - see the "Making LAMMPS"_Section_start.html#2_2 section of the
|
||||
documentation.
|
||||
|
|
|
|||
|
|
@ -79,9 +79,11 @@ also set to the derivative of this expression.
|
|||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>Can only be used if LAMMPS was built with the "granular" package. A
|
||||
zcylinder wall can only be oscillated in the z dimension. This fix
|
||||
can only be used with atom_style granular.
|
||||
<P>Any dimension (xyz) that has a granular wall must be non-periodic.
|
||||
</P>
|
||||
<P>This fix can only be used if LAMMPS was built with the "granular"
|
||||
package and with atom_style granular. A zcylinder wall can only be
|
||||
oscillated in the z dimension.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -69,9 +69,11 @@ also set to the derivative of this expression.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
Can only be used if LAMMPS was built with the "granular" package. A
|
||||
zcylinder wall can only be oscillated in the z dimension. This fix
|
||||
can only be used with atom_style granular.
|
||||
Any dimension (xyz) that has a granular wall must be non-periodic.
|
||||
|
||||
This fix can only be used if LAMMPS was built with the "granular"
|
||||
package and with atom_style granular. A zcylinder wall can only be
|
||||
oscillated in the z dimension.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -56,7 +56,9 @@ want that energy to be included in the total potential energy of the
|
|||
system (the quantity being minimized), you must enable the
|
||||
<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>Any dimension (xyz) that has a LJ 12/6 wall must be non-periodic.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -53,7 +53,9 @@ want that energy to be included in the total potential energy of the
|
|||
system (the quantity being minimized), you must enable the
|
||||
"fix_modify"_fix_modify.html {energy} option for this fix.
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
Any dimension (xyz) that has a LJ 12/6 wall must be non-periodic.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -57,7 +57,9 @@ want that energy to be included in the total potential energy of the
|
|||
system (the quantity being minimized), you must enable the
|
||||
<A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option for this fix.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>Any dimension (xyz) that has a LJ 9/3 wall must be non-periodic.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -54,7 +54,9 @@ want that energy to be included in the total potential energy of the
|
|||
system (the quantity being minimized), you must enable the
|
||||
"fix_modify"_fix_modify.html {energy} option for this fix.
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
Any dimension (xyz) that has a LJ 9/3 wall must be non-periodic.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -28,10 +28,7 @@ fix walls all wall/reflect xlo ylo zlo xhi yhi zhi
|
|||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Bound the simulation with one or more walls which reflect particles
|
||||
when they attempt to move thru them. Normally, the simulation domain
|
||||
should be set non-periodic via the <A HREF = "boundary.html">boundary</A> command in
|
||||
any dimension that has such a wall, but LAMMPS does not check for this
|
||||
condition.
|
||||
when they attempt to move thru them.
|
||||
</P>
|
||||
<P>Reflection means that if an atom moves outside the box on a timestep
|
||||
by a distance delta (e.g. due to <A HREF = "fix_nve.html">fix nve</A>), then it is
|
||||
|
|
@ -46,7 +43,9 @@ in the input script, since the adjustments it makes to atom
|
|||
coordinates should come after the changes made by time integration.
|
||||
LAMMPS will warn you if your fixes are not ordered this way.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>Any dimension (xyz) that has a reflecting wall must be non-periodic.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -25,10 +25,7 @@ fix walls all wall/reflect xlo ylo zlo xhi yhi zhi :pre
|
|||
[Description:]
|
||||
|
||||
Bound the simulation with one or more walls which reflect particles
|
||||
when they attempt to move thru them. Normally, the simulation domain
|
||||
should be set non-periodic via the "boundary"_boundary.html command in
|
||||
any dimension that has such a wall, but LAMMPS does not check for this
|
||||
condition.
|
||||
when they attempt to move thru them.
|
||||
|
||||
Reflection means that if an atom moves outside the box on a timestep
|
||||
by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is
|
||||
|
|
@ -43,7 +40,9 @@ in the input script, since the adjustments it makes to atom
|
|||
coordinates should come after the changes made by time integration.
|
||||
LAMMPS will warn you if your fixes are not ordered this way.
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
Any dimension (xyz) that has a reflecting wall must be non-periodic.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -15,7 +15,7 @@
|
|||
</P>
|
||||
<PRE>lattice style scale keyword values ...
|
||||
</PRE>
|
||||
<UL><LI>style = <I>none</I> or <I>sc</I> or <I>bcc</I> or <I>fcc</I> or <I>diamond</I> or <I>sq</I> or <I>sq2</I> or <I>hex</I> or <I>user</I>
|
||||
<UL><LI>style = <I>none</I> or <I>sc</I> or <I>bcc</I> or <I>fcc</I> or <I>diamond</I> or <I>sq</I> or <I>sq2</I> or <I>hex</I> or <I>custom</I>
|
||||
|
||||
<LI>scale = scale factor between lattice and simulation box
|
||||
|
||||
|
|
@ -27,13 +27,15 @@
|
|||
</PRE>
|
||||
<LI>zero or more keyword/value pairs may be appended
|
||||
|
||||
<LI>keyword = <I>origin</I> or <I>orient</I> or <I>a1</I> or <I>a2</I> or <I>a3</I> or <I>basis</I>
|
||||
<LI>keyword = <I>origin</I> or <I>orient</I> or <I>spacings</I> or <I>a1</I> or <I>a2</I> or <I>a3</I> or <I>basis</I>
|
||||
|
||||
<PRE> <I>origin</I> values = x y z
|
||||
x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
|
||||
<I>orient</I> values = dim i j k
|
||||
dim = <I>x</I> or <I>y</I> or <I>z</I>
|
||||
i,j,k = integer lattice directions
|
||||
<I>spacing</I> values = dx dy dz
|
||||
dx,dy,dz = lattice spacings in the x,y,z box directions
|
||||
<I>a1</I>,<I>a2</I>,<I>a3</I> values = x y z
|
||||
x,y,z = primitive vector components that define unit cell
|
||||
<I>basis</I> values = x y z
|
||||
|
|
@ -46,8 +48,8 @@
|
|||
<PRE>lattice fcc 3.52
|
||||
lattice hex 0.85
|
||||
lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
|
||||
lattice user 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
|
||||
basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
|
||||
basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
lattice none
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
|
|
@ -71,7 +73,7 @@ underlying problem geometry is atoms on a lattice.
|
|||
<P>The lattice style must be consistent with the dimension of the
|
||||
simulation - see the <A HREF = "dimension.html">dimension</A> command. Styles <I>sc</I>
|
||||
or <I>bcc</I> or <I>fcc</I> or <I>diamond</I> are for 3d problems. Styles <I>sq</I> or
|
||||
<I>sq2</I> or <I>hex</I> are for 2d problems. Style <I>user</I> can be used for
|
||||
<I>sq2</I> or <I>hex</I> are for 2d problems. Style <I>custom</I> can be used for
|
||||
either 2d or 3d problems.
|
||||
</P>
|
||||
<P>A lattice consists of a unit cell, a set of basis atoms within that
|
||||
|
|
@ -103,7 +105,7 @@ corner and one at the center of the square. A <I>hex</I> 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.
|
||||
</P>
|
||||
<P>A lattice of style <I>user</I> allows you to specify a1, a2, a3, and a list
|
||||
<P>A lattice of style <I>custom</I> 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
|
||||
|
|
@ -116,7 +118,7 @@ means a position half-way across the unit cell in that dimension.
|
|||
|
||||
<P>This sub-section discusses the arguments that determine how the
|
||||
idealized unit cell is transformed into a lattice of points within the
|
||||
simulation box with desired spacings.
|
||||
simulation box.
|
||||
</P>
|
||||
<P>The <I>scale</I> argument determines how the size of the unit cell will be
|
||||
scaled when mapping it into the simulation box. I.e. it determines a
|
||||
|
|
@ -159,17 +161,27 @@ the Z direction.
|
|||
<HR>
|
||||
|
||||
<P>Several LAMMPS commands have the option to use distance units that are
|
||||
inferred from "lattice spacings" in the x,y,z directions. E.g. the
|
||||
<A HREF = "region.html">region</A> command can create a block of size 10x20x20,
|
||||
where 10 means 10 lattice spacings in the x direction.
|
||||
inferred from "lattice spacings" in the x,y,z box directions.
|
||||
E.g. the <A HREF = "region.html">region</A> command can create a block of size
|
||||
10x20x20, where 10 means 10 lattice spacings in the x direction.
|
||||
</P>
|
||||
<P>These lattice spacings are computed by LAMMPS in the following way. A
|
||||
unit cell of the lattice 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.
|
||||
<P>The <I>spacing</I> option sets the 3 lattice spacings directly. All must
|
||||
be non-zero (use 1.0 for dz in a 2d simulation). The specified values
|
||||
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
|
||||
lattices.
|
||||
</P>
|
||||
<P>If the <I>spacing</I> option is not specified, the lattice spacings are
|
||||
computed by LAMMPS in the following way. A unit cell of the lattice
|
||||
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.
|
||||
</P>
|
||||
<P>Note that if the unit cell has axis-aligned edges (a1,a2,a3) and is
|
||||
not rotated (via the <I>orient</I> keyword), then the lattice spacings in
|
||||
|
|
@ -180,7 +192,7 @@ factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
|
|||
</P>
|
||||
<P>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 computed lattice spacings are printed by LAMMPS, so
|
||||
values of the lattice spacings LAMMPS will use are printed out, so
|
||||
their effect in commands that use the spacings should be decipherable.
|
||||
</P>
|
||||
<HR>
|
||||
|
|
@ -195,14 +207,14 @@ then generate an error. No additional arguments need be used with
|
|||
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The <I>a1,a2,a3,basis</I> keywords can only be used with style <I>user</I>.
|
||||
<P>The <I>a1,a2,a3,basis</I> keywords can only be used with style <I>custom</I>.
|
||||
</P>
|
||||
<P>For lattices oriented at an angle or with a non-orthognal unit cell,
|
||||
care must be taken when using the <A HREF = "region.html">region</A> and
|
||||
<A HREF = "create_atoms.html">create_atoms</A> 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 incorretly at the faces of
|
||||
the simulation box.
|
||||
actually be periodic, and atoms may overlap incorrectly at the faces
|
||||
of the simulation box.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ lattice command :h3
|
|||
lattice style scale keyword values ... :pre
|
||||
|
||||
style = {none} or {sc} or {bcc} or {fcc} or {diamond} or \
|
||||
{sq} or {sq2} or {hex} or {user} :ulb,l
|
||||
{sq} or {sq2} or {hex} or {custom} :ulb,l
|
||||
scale = scale factor between lattice and simulation box :l
|
||||
for style {none}:
|
||||
scale is not specified (nor any optional args)
|
||||
|
|
@ -21,12 +21,14 @@ scale = scale factor between lattice and simulation box :l
|
|||
scale = reduced density rho* (for LJ units)
|
||||
scale = lattice constant in Angstroms (for real or metal units) :pre
|
||||
zero or more keyword/value pairs may be appended :l
|
||||
keyword = {origin} or {orient} or {a1} or {a2} or {a3} or {basis} :l
|
||||
keyword = {origin} or {orient} or {spacings} or {a1} or {a2} or {a3} or {basis} :l
|
||||
{origin} values = x y z
|
||||
x,y,z = fractions of a unit cell (0 <= x,y,z < 1)
|
||||
{orient} values = dim i j k
|
||||
dim = {x} or {y} or {z}
|
||||
i,j,k = integer lattice directions
|
||||
{spacing} values = dx dy dz
|
||||
dx,dy,dz = lattice spacings in the x,y,z box directions
|
||||
{a1},{a2},{a3} values = x y z
|
||||
x,y,z = primitive vector components that define unit cell
|
||||
{basis} values = x y z
|
||||
|
|
@ -38,8 +40,8 @@ keyword = {origin} or {orient} or {a1} or {a2} or {a3} or {basis} :l
|
|||
lattice fcc 3.52
|
||||
lattice hex 0.85
|
||||
lattice sq 0.8 origin 0.0 0.5 0.0 orient x 1 1 0 orient y -1 1 0
|
||||
lattice user 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
|
||||
basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
lattice custom 3.52 a1 1.0 0.0 0.0 a2 0.5 1.0 0.0 a3 0.0 0.0 0.5 &
|
||||
basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
lattice none :pre
|
||||
|
||||
[Description:]
|
||||
|
|
@ -63,7 +65,7 @@ underlying problem geometry is atoms on a lattice.
|
|||
The lattice style must be consistent with the dimension of the
|
||||
simulation - see the "dimension"_dimension.html command. Styles {sc}
|
||||
or {bcc} or {fcc} or {diamond} are for 3d problems. Styles {sq} or
|
||||
{sq2} or {hex} are for 2d problems. Style {user} can be used for
|
||||
{sq2} or {hex} are for 2d problems. Style {custom} can be used for
|
||||
either 2d or 3d problems.
|
||||
|
||||
A lattice consists of a unit cell, a set of basis atoms within that
|
||||
|
|
@ -95,7 +97,7 @@ 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 {user} allows you to specify a1, a2, a3, and a list
|
||||
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
|
||||
|
|
@ -108,7 +110,7 @@ means a position half-way across the unit cell in that dimension.
|
|||
|
||||
This sub-section discusses the arguments that determine how the
|
||||
idealized unit cell is transformed into a lattice of points within the
|
||||
simulation box with desired spacings.
|
||||
simulation box.
|
||||
|
||||
The {scale} argument determines how the size of the unit cell will be
|
||||
scaled when mapping it into the simulation box. I.e. it determines a
|
||||
|
|
@ -151,17 +153,27 @@ the Z direction.
|
|||
:line
|
||||
|
||||
Several LAMMPS commands have the option to use distance units that are
|
||||
inferred from "lattice spacings" in the x,y,z directions. E.g. the
|
||||
"region"_region.html command can create a block of size 10x20x20,
|
||||
where 10 means 10 lattice spacings in the x direction.
|
||||
inferred from "lattice spacings" in the x,y,z box directions.
|
||||
E.g. the "region"_region.html command can create a block of size
|
||||
10x20x20, where 10 means 10 lattice spacings in the x direction.
|
||||
|
||||
These lattice spacings are computed by LAMMPS in the following way. A
|
||||
unit cell of the lattice 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.
|
||||
The {spacing} option sets the 3 lattice spacings directly. All must
|
||||
be non-zero (use 1.0 for dz in a 2d simulation). The specified values
|
||||
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
|
||||
lattices.
|
||||
|
||||
If the {spacing} option is not specified, the lattice spacings are
|
||||
computed by LAMMPS in the following way. A unit cell of the lattice
|
||||
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.
|
||||
|
||||
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
|
||||
|
|
@ -172,7 +184,7 @@ factor of 3.0 Angstroms, would have a lattice spacing of 3.0 in x and
|
|||
|
||||
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 computed lattice spacings are printed by LAMMPS, so
|
||||
values of the lattice spacings LAMMPS will use are printed out, so
|
||||
their effect in commands that use the spacings should be decipherable.
|
||||
|
||||
:line
|
||||
|
|
@ -187,14 +199,14 @@ then generate an error. No additional arguments need be used with
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
The {a1,a2,a3,basis} keywords can only be used with style {user}.
|
||||
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 incorretly at the faces of
|
||||
the simulation box.
|
||||
actually be periodic, and atoms may overlap incorrectly at the faces
|
||||
of the simulation box.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -76,7 +76,7 @@ the DYNAMO <I>funcfl</I> format. Either single element or alloy systems
|
|||
can be modeled using multiple <I>funcfl</I> files and style <I>eam</I>. For the
|
||||
alloy case LAMMPS mixes the single-element potentials to produce alloy
|
||||
potentials, the same way that DYNAMO does. Alternatively, a single
|
||||
DYNAMO <I>setfl</I> file of Finnis/Sinclair EAM file can be used by LAMMPS
|
||||
DYNAMO <I>setfl</I> file or Finnis/Sinclair EAM file can be used by LAMMPS
|
||||
to model alloy systems by invoking the <I>eam/alloy</I> or <I>eam/fs</I> styles
|
||||
as described below. These files require no mixing since they specify
|
||||
alloy interactions explicitly.
|
||||
|
|
|
|||
|
|
@ -68,7 +68,7 @@ the DYNAMO {funcfl} format. Either single element or alloy systems
|
|||
can be modeled using multiple {funcfl} files and style {eam}. For the
|
||||
alloy case LAMMPS mixes the single-element potentials to produce alloy
|
||||
potentials, the same way that DYNAMO does. Alternatively, a single
|
||||
DYNAMO {setfl} file of Finnis/Sinclair EAM file can be used by LAMMPS
|
||||
DYNAMO {setfl} file or Finnis/Sinclair EAM file can be used by LAMMPS
|
||||
to model alloy systems by invoking the {eam/alloy} or {eam/fs} styles
|
||||
as described below. These files require no mixing since they specify
|
||||
alloy interactions explicitly.
|
||||
|
|
|
|||
|
|
@ -77,9 +77,11 @@ and three-body coefficients in the formula above:
|
|||
<LI>p
|
||||
<LI>q
|
||||
</UL>
|
||||
<P>The epsilon, sigma, a, A, B, p, and q parameters are for two-body
|
||||
interactions. The lambda, gamma, and costheta0 parameters are for
|
||||
three-body interactions. The non-annotated parameters are unitless.
|
||||
<P>The A, B, p, and q parameters are used only for two-body
|
||||
interactions. The lambda, gamma, and costheta0 parameters are used only for
|
||||
three-body interactions. The epsilon, sigma and a parameters are used
|
||||
for both two-body and three-body interactions.
|
||||
The non-annotated parameters are unitless.
|
||||
</P>
|
||||
<P>The Stillinger-Weber potential file must contain entries for all the
|
||||
elements listed in the pair_coeff command. It can also contain
|
||||
|
|
@ -96,13 +98,17 @@ entries would be required, etc.
|
|||
<P>As annotated above, the first element in the entry is the center atom
|
||||
in a three-body interaction. Thus an entry for SiCC means a Si atom
|
||||
with 2 C atoms as neighbors. By symmetry, three-body parameters for
|
||||
SiCSi and SiSiC entries should be the same. Two-body parameters for
|
||||
an interaction come from the entry where the 2nd element is repeated.
|
||||
Thus the two-body parameters for Si interacting with C, comes from the
|
||||
SiCC entry. Again by symmetry, the two-body parameters in the SiCC
|
||||
and CSiSi entries should thus be the same. Two-body parameters in
|
||||
entries whose 2nd and 3rd element are different (e.g. SiCSi) are
|
||||
ignored.
|
||||
SiCSi and SiSiC entries should be the same. The parameters used for
|
||||
the two-body interaction come
|
||||
from the entry where the 2nd element is repeated. Thus the two-body
|
||||
parameters for Si interacting with C, comes from the SiCC entry.
|
||||
Again by symmetry, the two-body parameters in the SiCC
|
||||
and CSiSi entries should thus be the same.
|
||||
The parameters used for a particular three-body
|
||||
interaction come from the entry with the corresponding three elements.
|
||||
The parameters used only for two-body interactions (A, B, p, and q)
|
||||
in entries whose 2nd and 3rd element are different (e.g. SiCSi)
|
||||
are not used for anything and can be set to 0.0 if desired.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -79,10 +79,11 @@ above:
|
|||
<LI>lambda1 (1/distance units)
|
||||
<LI>A (energy units)
|
||||
</UL>
|
||||
<P>The n, beta, lambda2, B, R, D, lambda1, and A parameters are for
|
||||
<P>The n, beta, lambda2, B, lambda1, and A parameters are only used for
|
||||
two-body interactions. The lambda3, c, d, and costheta0 parameters
|
||||
are for three-body interactions. The non-annotated parameters are
|
||||
unitless.
|
||||
are only used for three-body interactions. The R and D parameters
|
||||
are used for both two-body and three-body interactions. The
|
||||
non-annotated parameters are unitless.
|
||||
</P>
|
||||
<P>The Tersoff potential file must contain entries for all the elements
|
||||
listed in the pair_coeff command. It can also contain entries for
|
||||
|
|
@ -101,12 +102,16 @@ in a three-body interaction and it is bonded to the 2nd atom and the
|
|||
bond is influenced by the 3rd atom. Thus an entry for SiCC means Si
|
||||
bonded to a C with another C atom influencing the bond. Thus
|
||||
three-body parameters for SiCSi and SiSiC entries will not, in
|
||||
general, be the same. Two-body parameters for an interaction come
|
||||
general, be the same. The parameters used for the two-body interaction come
|
||||
from the entry where the 2nd element is repeated. Thus the two-body
|
||||
parameters for Si interacting with C, comes from the SiCC entry. By
|
||||
symmetry, the two-body parameters in the SiCC and CSiSi entries should
|
||||
thus be the same. Two-body parameters in entries whose 2nd and 3rd
|
||||
element are different (e.g. SiCSi) are ignored.
|
||||
symmetry, the twobody parameters in the SiCC and CSiSi entries should
|
||||
thus be the same. The parameters used for a particular three-body
|
||||
interaction come from the entry with the corresponding three elements.
|
||||
The parameters used only for two-body interactions
|
||||
(n, beta, lambda2, B, lambda1, and A)
|
||||
in entries whose 2nd and 3rd element are different (e.g. SiCSi)
|
||||
are not used for anything and can be set to 0.0 if desired.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -47,8 +47,8 @@ behavior is wrong.
|
|||
</P>
|
||||
<P>Because restart files are binary, they may not be portable to other
|
||||
machines. They can be converted to ASCII data files using the
|
||||
restart2data tool in the tools sub-directory of the LAMMPS
|
||||
distribution.
|
||||
<A HREF = "Section_tools.html#restart">restart2data tool</A> in the tools
|
||||
sub-directory of the LAMMPS distribution.
|
||||
</P>
|
||||
<P>Similar to how restart files are written (see the
|
||||
<A HREF = "write_restart.html">write_restart</A> and <A HREF = "restart.html">restart</A>
|
||||
|
|
@ -78,12 +78,14 @@ current LAMMPS simulation.
|
|||
<HR>
|
||||
|
||||
<P>A restart file stores the units and atom style, simulation box
|
||||
attibutes, individual atoms and their attributes including molecular
|
||||
topology, force field styles and coefficients,
|
||||
<A HREF = "special_bonds.html">special_bonds</A> settings, and atom group
|
||||
definitions. This means that commands for these quantities do not
|
||||
need to be specified in your input script that reads the restart file.
|
||||
The exceptions to this are listed below in the Restrictions section.
|
||||
attibutes (including whether it is an orthogonal box or a
|
||||
non-orthogonal parallelepiped with triclinic symmetry), individual
|
||||
atoms and their attributes including molecular topology, force field
|
||||
styles and coefficients, <A HREF = "special_bonds.html">special_bonds</A> settings,
|
||||
and atom group definitions. This means that commands for these
|
||||
quantities do not need to be specified in your input script that reads
|
||||
the restart file. The exceptions to this are listed below in the
|
||||
Restrictions section.
|
||||
</P>
|
||||
<P>Information about the <A HREF = "kspace_style.html">kspace_style</A> settings are
|
||||
not stored in the restart file. Hence if you wish to invoke an Ewald
|
||||
|
|
@ -120,11 +122,11 @@ bonds will still be broken when the restart file is read.
|
|||
</P>
|
||||
<P>The <A HREF = "pair_style.html">pair_style</A> <I>eam</I>, <I>table</I>, and <I>hybrid</I> styles
|
||||
do not store coefficient data for individual atom type pairs in the
|
||||
restart file. Nor does the <A HREF = "bond_style.html">bond_style</A> <I>hybrid</I>
|
||||
style. Thus you must use new <A HREF = "pair_coeff.html">pair_coeff</A> and
|
||||
<A HREF = "bond_coeff.html">bond_coeff</A> commands to read the appropriate
|
||||
tabulated files or reset the coefficients after the restart file is
|
||||
read.
|
||||
restart file. Nor does the <A HREF = "bond_style.html">bond_style hybrid</A> style
|
||||
(angle, dihedral hybrid, etc). Thus for these styles you must use new
|
||||
<A HREF = "pair_coeff.html">pair_coeff</A> and <A HREF = "bond_coeff.html">bond_coeff</A> (angle,
|
||||
dihedral, etc) commands to read the appropriate tabulated files or
|
||||
reset the coefficients after the restart file is read.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -44,8 +44,8 @@ behavior is wrong.
|
|||
|
||||
Because restart files are binary, they may not be portable to other
|
||||
machines. They can be converted to ASCII data files using the
|
||||
restart2data tool in the tools sub-directory of the LAMMPS
|
||||
distribution.
|
||||
"restart2data tool"_Section_tools.html#restart in the tools
|
||||
sub-directory of the LAMMPS distribution.
|
||||
|
||||
Similar to how restart files are written (see the
|
||||
"write_restart"_write_restart.html and "restart"_restart.html
|
||||
|
|
@ -75,12 +75,14 @@ current LAMMPS simulation.
|
|||
:line
|
||||
|
||||
A restart file stores the units and atom style, simulation box
|
||||
attibutes, individual atoms and their attributes including molecular
|
||||
topology, force field styles and coefficients,
|
||||
"special_bonds"_special_bonds.html settings, and atom group
|
||||
definitions. This means that commands for these quantities do not
|
||||
need to be specified in your input script that reads the restart file.
|
||||
The exceptions to this are listed below in the Restrictions section.
|
||||
attibutes (including whether it is an orthogonal box or a
|
||||
non-orthogonal parallelepiped with triclinic symmetry), individual
|
||||
atoms and their attributes including molecular topology, force field
|
||||
styles and coefficients, "special_bonds"_special_bonds.html settings,
|
||||
and atom group definitions. This means that commands for these
|
||||
quantities do not need to be specified in your input script that reads
|
||||
the restart file. The exceptions to this are listed below in the
|
||||
Restrictions section.
|
||||
|
||||
Information about the "kspace_style"_kspace_style.html settings are
|
||||
not stored in the restart file. Hence if you wish to invoke an Ewald
|
||||
|
|
@ -117,11 +119,11 @@ bonds will still be broken when the restart file is read.
|
|||
|
||||
The "pair_style"_pair_style.html {eam}, {table}, and {hybrid} styles
|
||||
do not store coefficient data for individual atom type pairs in the
|
||||
restart file. Nor does the "bond_style"_bond_style.html {hybrid}
|
||||
style. Thus you must use new "pair_coeff"_pair_coeff.html and
|
||||
"bond_coeff"_bond_coeff.html commands to read the appropriate
|
||||
tabulated files or reset the coefficients after the restart file is
|
||||
read.
|
||||
restart file. Nor does the "bond_style hybrid"_bond_style.html style
|
||||
(angle, dihedral hybrid, etc). Thus for these styles you must use new
|
||||
"pair_coeff"_pair_coeff.html and "bond_coeff"_bond_coeff.html (angle,
|
||||
dihedral, etc) commands to read the appropriate tabulated files or
|
||||
reset the coefficients after the restart file is read.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -27,12 +27,11 @@
|
|||
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
|
||||
radius = cylinder radius (distance units)
|
||||
lo,hi = bounds of cylinder in dim (distance units)
|
||||
<I>prism</I> args = xlo xhi ylo yhi zlo zhi yxtilt zxtilt zytilt
|
||||
xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism in all
|
||||
dimensions (distance units)
|
||||
yxtilt = distance to shift upper y in x direction (distance units)
|
||||
zxtilt = distance to shift upper z in x direction (distance units)
|
||||
zytilt = distance to shift upper z in y direction (distance units)
|
||||
<I>prism</I> args = xlo xhi ylo yhi zlo zhi xy xz yz
|
||||
xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
|
||||
xy = distance to skew y in x direction (distance units)
|
||||
xz = distance to skew z in x direction (distance units)
|
||||
yz = distance to skew z in y direction (distance units)
|
||||
<I>sphere</I> args = x y z radius
|
||||
x,y,z = center of sphere (distance units)
|
||||
radius = radius of sphere (distance units)
|
||||
|
|
@ -86,18 +85,21 @@ third example above specifes a cylinder with its axis in the
|
|||
y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
|
||||
extending in the y-direction from -5.0 to the upper box boundary.
|
||||
</P>
|
||||
<P>For style <I>prism</I>, a tilted block is defined. The bounds of the
|
||||
untilted axis-aligned block are specified in the same way as for the
|
||||
<I>block</I> style. A tilt factor for each dimension with respect to
|
||||
another dimension is also specified. If the lower xy face of the
|
||||
prism is initially a rectangle (untilted), then the yxtilt factor
|
||||
specifies how far the upper y edge of that face is shifted in the x
|
||||
direction (skewing that face, keeping the xy face a parallelogram). A
|
||||
plus or minus value can be chosen; 0.0 would be no tilt. Similarly,
|
||||
zxtilt and zytilt describe how far the upper xy face of the prism is
|
||||
translated in the x and y directions to further tilt the prism. The
|
||||
final prism shape remains a parallelipiped, with opposing pairs of the
|
||||
6 faces remaining parallel to each other.
|
||||
<P>For style <I>prism</I>, a parallelepiped is defined (it's too hard to spell
|
||||
parallelepiped in an input script!). A prism region is used by the
|
||||
<A HREF = "create_box.html">create_box</A> command to define a triclinic
|
||||
(non-orthogonal) simulation domain. Think of the parallelepided as
|
||||
initially an axis-aligned orthogonal box with the same xyz lo/hi
|
||||
parameters as region style <I>block</I> would define. Then, while holding
|
||||
the (xlo,ylo,zlo) corner point fixed, the box is "skewed" in 3
|
||||
directions. First, for the lower xy face of the box, the <I>xy</I> factor
|
||||
is how far the upper y edge is shifted in the x direction. The lower
|
||||
xy face is now a parallelogram. A plus or minus value for <I>xy</I> can be
|
||||
specified; 0.0 means no skew. Then, the upper xy face of the box is
|
||||
translated in the x and y directions by <I>xz</I> and <I>yz</I>. This results
|
||||
in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3 edge
|
||||
vectors starting from its origin given by a = (xhi-xlo,0,0); b =
|
||||
(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
|
||||
</P>
|
||||
<P>The <I>union</I> style creates a region consisting of the volume of all the
|
||||
listed regions combined. The <I>intesect</I> style creates a region
|
||||
|
|
@ -122,8 +124,8 @@ previously used to define the lattice spacing.
|
|||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P>A prism cannot be of 0.0 thickness in any dimension; use a small z
|
||||
thickness for 2d simulations. For 2d simulations, the zxtilt and
|
||||
zytilt parameters must be 0.0.
|
||||
thickness for 2d simulations. For 2d simulations, the xz and yz
|
||||
parameters must be 0.0.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
|
|
|
|||
|
|
@ -22,12 +22,11 @@ style = {block} or {cylinder} or {prism} or {sphere} or {union} or {intersect} :
|
|||
c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
|
||||
radius = cylinder radius (distance units)
|
||||
lo,hi = bounds of cylinder in dim (distance units)
|
||||
{prism} args = xlo xhi ylo yhi zlo zhi yxtilt zxtilt zytilt
|
||||
xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism in all
|
||||
dimensions (distance units)
|
||||
yxtilt = distance to shift upper y in x direction (distance units)
|
||||
zxtilt = distance to shift upper z in x direction (distance units)
|
||||
zytilt = distance to shift upper z in y direction (distance units)
|
||||
{prism} args = xlo xhi ylo yhi zlo zhi xy xz yz
|
||||
xlo,xhi,ylo,yhi,zlo,zhi = bounds of untilted prism (distance units)
|
||||
xy = distance to skew y in x direction (distance units)
|
||||
xz = distance to skew z in x direction (distance units)
|
||||
yz = distance to skew z in y direction (distance units)
|
||||
{sphere} args = x y z radius
|
||||
x,y,z = center of sphere (distance units)
|
||||
radius = radius of sphere (distance units)
|
||||
|
|
@ -77,18 +76,21 @@ third example above specifes a cylinder with its axis in the
|
|||
y-direction located at x = 2.0 and z = 3.0, with a radius of 5.0, and
|
||||
extending in the y-direction from -5.0 to the upper box boundary.
|
||||
|
||||
For style {prism}, a tilted block is defined. The bounds of the
|
||||
untilted axis-aligned block are specified in the same way as for the
|
||||
{block} style. A tilt factor for each dimension with respect to
|
||||
another dimension is also specified. If the lower xy face of the
|
||||
prism is initially a rectangle (untilted), then the yxtilt factor
|
||||
specifies how far the upper y edge of that face is shifted in the x
|
||||
direction (skewing that face, keeping the xy face a parallelogram). A
|
||||
plus or minus value can be chosen; 0.0 would be no tilt. Similarly,
|
||||
zxtilt and zytilt describe how far the upper xy face of the prism is
|
||||
translated in the x and y directions to further tilt the prism. The
|
||||
final prism shape remains a parallelipiped, with opposing pairs of the
|
||||
6 faces remaining parallel to each other.
|
||||
For style {prism}, a parallelepiped is defined (it's too hard to spell
|
||||
parallelepiped in an input script!). A prism region is used by the
|
||||
"create_box"_create_box.html command to define a triclinic
|
||||
(non-orthogonal) simulation domain. Think of the parallelepided as
|
||||
initially an axis-aligned orthogonal box with the same xyz lo/hi
|
||||
parameters as region style {block} would define. Then, while holding
|
||||
the (xlo,ylo,zlo) corner point fixed, the box is "skewed" in 3
|
||||
directions. First, for the lower xy face of the box, the {xy} factor
|
||||
is how far the upper y edge is shifted in the x direction. The lower
|
||||
xy face is now a parallelogram. A plus or minus value for {xy} can be
|
||||
specified; 0.0 means no skew. Then, the upper xy face of the box is
|
||||
translated in the x and y directions by {xz} and {yz}. This results
|
||||
in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3 edge
|
||||
vectors starting from its origin given by a = (xhi-xlo,0,0); b =
|
||||
(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
|
||||
|
||||
The {union} style creates a region consisting of the volume of all the
|
||||
listed regions combined. The {intesect} style creates a region
|
||||
|
|
@ -113,8 +115,8 @@ previously used to define the lattice spacing.
|
|||
[Restrictions:] none
|
||||
|
||||
A prism cannot be of 0.0 thickness in any dimension; use a small z
|
||||
thickness for 2d simulations. For 2d simulations, the zxtilt and
|
||||
zytilt parameters must be 0.0.
|
||||
thickness for 2d simulations. For 2d simulations, the xz and yz
|
||||
parameters must be 0.0.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -43,7 +43,7 @@
|
|||
enthalpy = enthalpy (pe + press*vol)
|
||||
evdwl = VanderWaal pairwise energy
|
||||
ecoul = Coulombic pairwise energy
|
||||
epair = pairwise energy (evdwl + ecoul)
|
||||
epair = pairwise energy (evdwl + ecoul + elong + etail)
|
||||
ebond = bond energy
|
||||
eangle = angle energy
|
||||
edihed = dihedral energy
|
||||
|
|
|
|||
|
|
@ -38,7 +38,7 @@ args = list of arguments for a particular style :l
|
|||
enthalpy = enthalpy (pe + press*vol)
|
||||
evdwl = VanderWaal pairwise energy
|
||||
ecoul = Coulombic pairwise energy
|
||||
epair = pairwise energy (evdwl + ecoul)
|
||||
epair = pairwise energy (evdwl + ecoul + elong + etail)
|
||||
ebond = bond energy
|
||||
eangle = angle energy
|
||||
edihed = dihedral energy
|
||||
|
|
|
|||
Loading…
Reference in New Issue