forked from lijiext/lammps
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This commit is contained in:
sjplimp
parent
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@ -144,7 +144,7 @@ listed above.
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<BR>
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4.11 <A HREF = "Section_howto.html#4_11">Visualizing LAMMPS snapshots</A>
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<BR>
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4.12 <A HREF = "Section_howto.html#4_12">Non-orthogonal simulation boxes</A>
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4.12 <A HREF = "Section_howto.html#4_12">Triclinic (non-orthogonal) simulation boxes</A>
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<BR>
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4.13 <A HREF = "Section_howto.html#4_13">NEMD simulations</A>
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<BR>
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@ -106,7 +106,7 @@ listed above.
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4.9 "SPC water model"_4_9 :b
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4.10 "Coupling LAMMPS to other codes"_4_10 :b
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4.11 "Visualizing LAMMPS snapshots"_4_11 :b
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4.12 "Non-orthogonal simulation boxes"_4_12 :b
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4.12 "Triclinic (non-orthogonal) simulation boxes"_4_12 :b
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4.13 "NEMD simulations"_4_13 :b
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4.14 "Extended spherical and aspherical particles"_4_14 :b
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4.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_4_15 :b
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@ -25,7 +25,7 @@ certain kinds of LAMMPS simulations.
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4.9 <A HREF = "#4_9">SPC water model</A><BR>
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4.10 <A HREF = "#4_10">Coupling LAMMPS to other codes</A><BR>
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4.11 <A HREF = "#4_11">Visualizing LAMMPS snapshots</A><BR>
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4.12 <A HREF = "#4_12">Non-orthogonal simulation boxes</A><BR>
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4.12 <A HREF = "#4_12">Triclinic (non-orthogonal) simulation boxes</A><BR>
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4.13 <A HREF = "#4_13">NEMD simulations</A><BR>
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4.14 <A HREF = "#4_14">Extended spherical and aspherical particles</A><BR>
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4.15 <A HREF = "#4_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
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@ -724,22 +724,60 @@ See the <A HREF = "dump.html">dump</A> command for more information on XTC files
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<HR>
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<A NAME = "4_12"></A><H4>4.12 Non-orthogonal simulation boxes
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<A NAME = "4_12"></A><H4>4.12 Triclinic (non-orthogonal) simulation boxes
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</H4>
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<P>By default, LAMMPS uses an orthogonal simulation box to encompass the
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particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
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conditions of the box (periodic, non-periodic, etc). If the box size
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is xprd by yprd by zprd then the 3 mutually orthogonal edge vectors of
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an orthogonal simulation box are a = (xprd,0,0), b = (0,yprd,0), and c
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= (0,0,zprd).
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conditions of the box (periodic, non-periodic, etc). The orthogonal
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box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
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starting from the origin given by A = (xhi-xlo,0,0); B =
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(0,yhi-ylo,0); C = (0,0,zhi-zlo). The 6 parameters
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(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simluation box
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is created, e.g. by the <A HREF = "create_box.html">create_box</A> or
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
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where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
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parameters, as well as lx,ly,lz, can be output via the <A HREF = "thermo_style.html">thermo_style
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custom</A> command.
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</P>
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<P>LAMMPS also allows non-orthogonal simulation boxes (triclinic
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symmetry) to be defined with 3 additional "tilt" parameters which
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change the edge vectors of the simulation box to be a = (xprd,0,0), b
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= (xy,yprd,0), and c = (xz,yz,zprd). The xy, xz, and yz parameters
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can be positive or negative. The simulation box must be periodic in
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both dimensions associated with a tilt factor. For example, if xz !=
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0.0, then the x and z dimensions must be periodic.
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<P>LAMMPS also allows simulations to be perfored in non-orthogonal
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simulation boxes shaped as a parallelepiped with triclinic symmetry.
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The parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by
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3 edge vectors starting from the origin given by A = (xhi-xlo,0,0); B
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= (xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or
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positive or negative values and are called "tilt factors" because they
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are the amount of displacement applied to faces of an originally
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orthogonal box to transform it into the parallelepiped. Note that in
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LAMMPS the triclinic simulation box edge vectors A,B,C cannot be
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arbitrary vectors. As indicated, A must be aligned with the x axis, B
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must be in the xy plane, and C is arbitrary. However, this is not a
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restriction since it is possible to rotate any set of 3 crystal basis
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vectors so that they meet this restriction.
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</P>
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<P>The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
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time the simluation box is created. This happens in one of 3 ways.
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If the <A HREF = "create_box.html">create_box</A> command is used with a region of
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style <I>prism</I>, then a triclinic box is setup. See the
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<A HREF = "region.html">region</A> command for details. If the
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<A HREF = "read_data.html">read_data</A> command is used to define the simulation
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box, and the header of the data file contains a line with the "xy xz
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yz" keyword, then a triclinic box is setup. See the
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<A HREF = "read_data.html">read_data</A> command for details. Finally, if the
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<A HREF = "read_restart.html">read_restart</A> command reads a restart file which
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was written from a simulation using a triclinic box, then a triclinic
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box will be setup for the restarted simulation.
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</P>
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<P>Note that you can define a triclinic box with all 3 tilt factors =
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0.0, so that it is initially orthogonal. This is necessary if the box
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will become non-orthogonal, e.g. due to the <A HREF = "fix_nh.html">fix npt</A> or
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<A HREF = "fix_deform.html">fix deform</A> commands. Alternatively, you can use the
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<A HREF = "change_box.html">change_box</A> command to convert a simulation box from
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orthogonal to triclinic and vice versa.
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</P>
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<P>As with orthogonal boxes, LAMMPS defines triclinic box size parameters
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lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
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The 9 parameters, as well as lx,ly,lz, can be output via the
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<A HREF = "thermo_style.html">thermo_style custom</A> command.
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</P>
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<P>To avoid extremely tilted boxes (which would be computationally
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inefficient), no tilt factor can skew the box more than half the
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@ -749,43 +787,62 @@ the x box length is 10 and the xy tilt factor must be between -5 and
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5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and
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+(yhi-ylo)/2. Note that this is not a limitation, since if the
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maximum tilt factor is 5 (as in this example), then configurations
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with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
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with tilt = ..., -15, -5, 5, 15, 25, ... are geometrically all
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equivalent.
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</P>
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<P>You tell LAMMPS to use a non-orthogonal box when the simulation box is
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defined. This happens in one of 3 ways. If the
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<A HREF = "create_box.html">create_box</A> command is used with a region of style
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<I>prism</I>, then a non-orthogonal domain is setup. See the
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<A HREF = "region.html">region</A> command for details. If the
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<A HREF = "read_data.html">read_data</A> command is used to define the simulation
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box, and the header of the data file contains a line with the "xy xz
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yz" keyword, then a non-orthogonal domain is setup. See the
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<A HREF = "read_data.html">read_data</A> command for details. Finally, if the
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<A HREF = "read_restart.html">read_restart</A> command reads a restart file which
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was written from a simulation using a triclinic box, then a
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non-orthogonal box will be enabled for the restarted simulation.
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<P>Triclinic crystal structures are often defined using three lattice
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constants <I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and
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<I>gamma</I>. Note that in this nomenclature, the a,b,c lattice constants
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are the scalar lengths of the 3 A,B,C edge vectors defined above. The
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relationship between these 6 quantities (a,b,c,alpha,beta,gamma) and
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the LAMMPS box sizes (lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt
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factors (xy,xz,yz) is as follows:
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</P>
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<P>Note that you can define a non-orthogonal box with all 3 tilt factors
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= 0.0, so that it is initially orthogonal. This is necessary if the
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box will become non-orthogonal. Alternatively, you can use the
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<A HREF = "change_box.html">change_box</A> command to convert a simulation box from
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orthogonal to non-orthogonal and vice versa.
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<CENTER><IMG SRC = "Eqs/box.jpg">
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</CENTER>
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<P>As discussed on the <A HREF = "dump.html">dump</A> command doc page, when the BOX
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BOUNDS for a snapshot is written to a dump file for a triclinic box,
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an orthogonal bounding box which encloses the triclinic simulation box
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is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
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box, formatted as follows:
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</P>
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<P>One use of non-orthogonal boxes is to model solid-state crystals with
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triclinic symmetry. The <A HREF = "lattice.html">lattice</A> command can be used
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with non-orthogonal basis vectors to define a lattice that will tile a
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non-orthogonal simulation box via the <A HREF = "create_atoms.html">create_atoms</A>
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command. Note that while the box edge vectors a,b,c cannot be
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arbitrary vectors (e.g. a must be aligned with the x axis), it is
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possible to rotate any crystal's basis vectors so that they meet these
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restrictions.
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<PRE>ITEM: BOX BOUNDS xy xz yz
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xlo_bound xhi_bound xy
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ylo_bound yhi_bound xz
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zlo_bound zhi_bound yz
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</PRE>
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<P>This bounding box is convenient for many visualization programs and is
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calculated from the 9 triclinic box parameters
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(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
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</P>
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<P>A second use of non-orthogonal boxes is to shear a bulk solid to study
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the response of the material. The <A HREF = "fix_deform.html">fix deform</A>
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command can be used for this purpose. It allows dynamic control of
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the xy, xz, and yz tilt factors as a simulation runs.
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<PRE>xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
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xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
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ylo_bound = ylo + MIN(0.0,yz)
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yhi_bound = yhi + MAX(0.0,yz)
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zlo_bound = zlo
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zhi_bound = zhi
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</PRE>
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<P>These formulas can be inverted if you need to convert the bounding box
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back into the triclinic box parameters, e.g. xlo = xlo_bound -
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MIN(0.0,xy,xz,xy+xz).
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</P>
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<P>Another use of non-orthogonal boxes is to perform non-equilibrium MD
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(NEMD) simulations, as discussed in the next section.
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<P>One use of triclinic simulation boxes is to model solid-state crystals
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with triclinic symmetry. The <A HREF = "lattice.html">lattice</A> command can be
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used with non-orthogonal basis vectors to define a lattice that will
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tile a triclinic simulation box via the
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<A HREF = "create_atoms.html">create_atoms</A> command.
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</P>
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<P>A second use is to run Parinello-Rahman dyanamics via the <A HREF = "fix_nh.html">fix
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npt</A> command, which will adjust the xy, xz, yz tilt
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factors to compensate for off-diagonal components of the pressure
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tensor. The analalog for an <A HREF = "minimize.html">energy minimization</A> is
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the <A HREF = "fix_box_relax.html">fix box/relax</A> command.
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</P>
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<P>A third use is to shear a bulk solid to study the response of the
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material. The <A HREF = "fix_deform.html">fix deform</A> command can be used for
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this purpose. It allows dynamic control of the xy, xz, yz tilt
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factors as a simulation runs. This is discussed in the next section
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on non-equilibrium MD (NEMD) simulations.
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</P>
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<HR>
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|
|
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@ -22,7 +22,7 @@ certain kinds of LAMMPS simulations.
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4.9 "SPC water model"_#4_9
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4.10 "Coupling LAMMPS to other codes"_#4_10
|
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4.11 "Visualizing LAMMPS snapshots"_#4_11
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4.12 "Non-orthogonal simulation boxes"_#4_12
|
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4.12 "Triclinic (non-orthogonal) simulation boxes"_#4_12
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4.13 "NEMD simulations"_#4_13
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4.14 "Extended spherical and aspherical particles"_#4_14
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4.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#4_15
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@ -716,22 +716,60 @@ See the "dump"_dump.html command for more information on XTC files.
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:line
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4.12 Non-orthogonal simulation boxes :link(4_12),h4
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4.12 Triclinic (non-orthogonal) simulation boxes :link(4_12),h4
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By default, LAMMPS uses an orthogonal simulation box to encompass the
|
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particles. The "boundary"_boundary.html command sets the boundary
|
||||
conditions of the box (periodic, non-periodic, etc). If the box size
|
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is xprd by yprd by zprd then the 3 mutually orthogonal edge vectors of
|
||||
an orthogonal simulation box are a = (xprd,0,0), b = (0,yprd,0), and c
|
||||
= (0,0,zprd).
|
||||
conditions of the box (periodic, non-periodic, etc). The orthogonal
|
||||
box has its "origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors
|
||||
starting from the origin given by A = (xhi-xlo,0,0); B =
|
||||
(0,yhi-ylo,0); C = (0,0,zhi-zlo). The 6 parameters
|
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(xlo,xhi,ylo,yhi,zlo,zhi) are defined at the time the simluation box
|
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is created, e.g. by the "create_box"_create_box.html or
|
||||
"read_data"_read_data.html or "read_restart"_read_restart.html
|
||||
commands. Additionally, LAMMPS defines box size parameters lx,ly,lz
|
||||
where lx = xhi-xlo, and similarly in the y and z dimensions. The 6
|
||||
parameters, as well as lx,ly,lz, can be output via the "thermo_style
|
||||
custom"_thermo_style.html command.
|
||||
|
||||
LAMMPS also allows non-orthogonal simulation boxes (triclinic
|
||||
symmetry) to be defined with 3 additional "tilt" parameters which
|
||||
change the edge vectors of the simulation box to be a = (xprd,0,0), b
|
||||
= (xy,yprd,0), and c = (xz,yz,zprd). The xy, xz, and yz parameters
|
||||
can be positive or negative. The simulation box must be periodic in
|
||||
both dimensions associated with a tilt factor. For example, if xz !=
|
||||
0.0, then the x and z dimensions must be periodic.
|
||||
LAMMPS also allows simulations to be perfored in non-orthogonal
|
||||
simulation boxes shaped as a parallelepiped with triclinic symmetry.
|
||||
The parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by
|
||||
3 edge vectors starting from the origin given by A = (xhi-xlo,0,0); B
|
||||
= (xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or
|
||||
positive or negative values and are called "tilt factors" because they
|
||||
are the amount of displacement applied to faces of an originally
|
||||
orthogonal box to transform it into the parallelepiped. Note that in
|
||||
LAMMPS the triclinic simulation box edge vectors A,B,C cannot be
|
||||
arbitrary vectors. As indicated, A must be aligned with the x axis, B
|
||||
must be in the xy plane, and C is arbitrary. However, this is not a
|
||||
restriction since it is possible to rotate any set of 3 crystal basis
|
||||
vectors so that they meet this restriction.
|
||||
|
||||
The 9 parameters (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) are defined at the
|
||||
time the simluation box is created. This happens in one of 3 ways.
|
||||
If the "create_box"_create_box.html command is used with a region of
|
||||
style {prism}, then a triclinic box is setup. See the
|
||||
"region"_region.html command for details. If the
|
||||
"read_data"_read_data.html command is used to define the simulation
|
||||
box, and the header of the data file contains a line with the "xy xz
|
||||
yz" keyword, then a triclinic box is setup. See the
|
||||
"read_data"_read_data.html command for details. Finally, if the
|
||||
"read_restart"_read_restart.html command reads a restart file which
|
||||
was written from a simulation using a triclinic box, then a triclinic
|
||||
box will be setup for the restarted simulation.
|
||||
|
||||
Note that you can define a triclinic box with all 3 tilt factors =
|
||||
0.0, so that it is initially orthogonal. This is necessary if the box
|
||||
will become non-orthogonal, e.g. due to the "fix npt"_fix_nh.html or
|
||||
"fix deform"_fix_deform.html commands. Alternatively, you can use the
|
||||
"change_box"_change_box.html command to convert a simulation box from
|
||||
orthogonal to triclinic and vice versa.
|
||||
|
||||
As with orthogonal boxes, LAMMPS defines triclinic box size parameters
|
||||
lx,ly,lz where lx = xhi-xlo, and similarly in the y and z dimensions.
|
||||
The 9 parameters, as well as lx,ly,lz, can be output via the
|
||||
"thermo_style custom"_thermo_style.html command.
|
||||
|
||||
To avoid extremely tilted boxes (which would be computationally
|
||||
inefficient), no tilt factor can skew the box more than half the
|
||||
|
|
@ -741,43 +779,62 @@ the x box length is 10 and the xy tilt factor must be between -5 and
|
|||
5. Similarly, both xz and yz must be between -(xhi-xlo)/2 and
|
||||
+(yhi-ylo)/2. Note that this is not a limitation, since if the
|
||||
maximum tilt factor is 5 (as in this example), then configurations
|
||||
with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
|
||||
with tilt = ..., -15, -5, 5, 15, 25, ... are geometrically all
|
||||
equivalent.
|
||||
|
||||
You tell LAMMPS to use a non-orthogonal box when the simulation box is
|
||||
defined. This happens in one of 3 ways. If the
|
||||
"create_box"_create_box.html command is used with a region of style
|
||||
{prism}, then a non-orthogonal domain is setup. See the
|
||||
"region"_region.html command for details. If the
|
||||
"read_data"_read_data.html command is used to define the simulation
|
||||
box, and the header of the data file contains a line with the "xy xz
|
||||
yz" keyword, then a non-orthogonal domain is setup. See the
|
||||
"read_data"_read_data.html command for details. Finally, if the
|
||||
"read_restart"_read_restart.html command reads a restart file which
|
||||
was written from a simulation using a triclinic box, then a
|
||||
non-orthogonal box will be enabled for the restarted simulation.
|
||||
Triclinic crystal structures are often defined using three lattice
|
||||
constants {a}, {b}, and {c}, and three angles {alpha}, {beta} and
|
||||
{gamma}. Note that in this nomenclature, the a,b,c lattice constants
|
||||
are the scalar lengths of the 3 A,B,C edge vectors defined above. The
|
||||
relationship between these 6 quantities (a,b,c,alpha,beta,gamma) and
|
||||
the LAMMPS box sizes (lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt
|
||||
factors (xy,xz,yz) is as follows:
|
||||
|
||||
Note that you can define a non-orthogonal box with all 3 tilt factors
|
||||
= 0.0, so that it is initially orthogonal. This is necessary if the
|
||||
box will become non-orthogonal. Alternatively, you can use the
|
||||
"change_box"_change_box.html command to convert a simulation box from
|
||||
orthogonal to non-orthogonal and vice versa.
|
||||
:c,image(Eqs/box.jpg)
|
||||
|
||||
One use of non-orthogonal boxes is to model solid-state crystals with
|
||||
triclinic symmetry. The "lattice"_lattice.html command can be used
|
||||
with non-orthogonal basis vectors to define a lattice that will tile a
|
||||
non-orthogonal simulation box via the "create_atoms"_create_atoms.html
|
||||
command. Note that while the box edge vectors a,b,c cannot be
|
||||
arbitrary vectors (e.g. a must be aligned with the x axis), it is
|
||||
possible to rotate any crystal's basis vectors so that they meet these
|
||||
restrictions.
|
||||
As discussed on the "dump"_dump.html command doc page, when the BOX
|
||||
BOUNDS for a snapshot is written to a dump file for a triclinic box,
|
||||
an orthogonal bounding box which encloses the triclinic simulation box
|
||||
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
|
||||
box, formatted as follows:
|
||||
|
||||
A second use of non-orthogonal boxes is to shear a bulk solid to study
|
||||
the response of the material. The "fix deform"_fix_deform.html
|
||||
command can be used for this purpose. It allows dynamic control of
|
||||
the xy, xz, and yz tilt factors as a simulation runs.
|
||||
ITEM: BOX BOUNDS xy xz yz
|
||||
xlo_bound xhi_bound xy
|
||||
ylo_bound yhi_bound xz
|
||||
zlo_bound zhi_bound yz :pre
|
||||
|
||||
Another use of non-orthogonal boxes is to perform non-equilibrium MD
|
||||
(NEMD) simulations, as discussed in the next section.
|
||||
This bounding box is convenient for many visualization programs and is
|
||||
calculated from the 9 triclinic box parameters
|
||||
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:
|
||||
|
||||
xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
|
||||
xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
|
||||
ylo_bound = ylo + MIN(0.0,yz)
|
||||
yhi_bound = yhi + MAX(0.0,yz)
|
||||
zlo_bound = zlo
|
||||
zhi_bound = zhi :pre
|
||||
|
||||
These formulas can be inverted if you need to convert the bounding box
|
||||
back into the triclinic box parameters, e.g. xlo = xlo_bound -
|
||||
MIN(0.0,xy,xz,xy+xz).
|
||||
|
||||
One use of triclinic simulation boxes is to model solid-state crystals
|
||||
with triclinic symmetry. The "lattice"_lattice.html command can be
|
||||
used with non-orthogonal basis vectors to define a lattice that will
|
||||
tile a triclinic simulation box via the
|
||||
"create_atoms"_create_atoms.html command.
|
||||
|
||||
A second use is to run Parinello-Rahman dyanamics via the "fix
|
||||
npt"_fix_nh.html command, which will adjust the xy, xz, yz tilt
|
||||
factors to compensate for off-diagonal components of the pressure
|
||||
tensor. The analalog for an "energy minimization"_minimize.html is
|
||||
the "fix box/relax"_fix_box_relax.html command.
|
||||
|
||||
A third use is to shear a bulk solid to study the response of the
|
||||
material. The "fix deform"_fix_deform.html command can be used for
|
||||
this purpose. It allows dynamic control of the xy, xz, yz tilt
|
||||
factors as a simulation runs. This is discussed in the next section
|
||||
on non-equilibrium MD (NEMD) simulations.
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
|
|
@ -32,32 +32,43 @@ geometric domain.
|
|||
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.
|
||||
(block, sphere, etc) with an axis-aligned orthogonal bounding 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).
|
||||
As defined by the <A HREF = "region.html">region prism</A> command, the
|
||||
parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3
|
||||
edge vectors starting from the origin given by A = (xhi-xlo,0,0); B =
|
||||
(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or
|
||||
positive or negative values and are called "tilt factors" because they
|
||||
are the amount of displacement applied to faces of an originally
|
||||
orthogonal box to transform it into the parallelipiped.
|
||||
</P>
|
||||
<P>A prism region used with the create_box command must have tilt factors
|
||||
(xy,xz,yz) that do not skew the box more than half the distance of the
|
||||
parallel box length. For example, if xlo = 2 and xhi = 12, then the x
|
||||
box length is 10 and the xy tilt factor must be between -5 and 5.
|
||||
Similarly, both xz and yz must be between -(xhi-xlo)/2 and
|
||||
+(yhi-ylo)/2. Note that this is not a limitation, since if the
|
||||
maximum tilt factor is 5 (as in this example), then configurations
|
||||
with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
|
||||
<P>A <I>prism</I> region used with the create_box command must have tilt
|
||||
factors (xy,xz,yz) that do not skew the box more than half the
|
||||
distance of the parallel box length. For example, if xlo = 2 and xhi
|
||||
= 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
geometrically equivalent.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_howto.html#4_12">this section</A> of the doc pages for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
how to transform these parameters into other commonly used triclinic
|
||||
representations.
|
||||
</P>
|
||||
<P>When a prism region is used, the simulation domain must be periodic in
|
||||
any dimensions with a non-zero tilt factor, as defined by the
|
||||
<A HREF = "boundary.html">boundary</A> command. I.e. if the xy tilt 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.
|
||||
be periodic if yz is non-zero. Also note that if your simulation will
|
||||
tilt the box, e.g. via the <A HREF = "fix_deform.html">fix deform</A> command, the
|
||||
simulation box must be defined as triclinic, even if the tilt factors
|
||||
are initially 0.0.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
|
||||
you should not make the lo/hi box dimensions (as defined in your
|
||||
|
|
|
|||
|
|
@ -29,32 +29,43 @@ 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.
|
||||
(block, sphere, etc) with an axis-aligned orthogonal bounding 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).
|
||||
As defined by the "region prism"_region.html command, the
|
||||
parallelepiped has its "origin" at (xlo,ylo,zlo) and is defined by 3
|
||||
edge vectors starting from the origin given by A = (xhi-xlo,0,0); B =
|
||||
(xy,yhi-ylo,0); C = (xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or
|
||||
positive or negative values and are called "tilt factors" because they
|
||||
are the amount of displacement applied to faces of an originally
|
||||
orthogonal box to transform it into the parallelipiped.
|
||||
|
||||
A prism region used with the create_box command must have tilt factors
|
||||
(xy,xz,yz) that do not skew the box more than half the distance of the
|
||||
parallel box length. For example, if xlo = 2 and xhi = 12, then the x
|
||||
box length is 10 and the xy tilt factor must be between -5 and 5.
|
||||
Similarly, both xz and yz must be between -(xhi-xlo)/2 and
|
||||
+(yhi-ylo)/2. Note that this is not a limitation, since if the
|
||||
maximum tilt factor is 5 (as in this example), then configurations
|
||||
with tilt = ..., -15, -5, 5, 15, 25, ... are all equivalent.
|
||||
A {prism} region used with the create_box command must have tilt
|
||||
factors (xy,xz,yz) that do not skew the box more than half the
|
||||
distance of the parallel box length. For example, if xlo = 2 and xhi
|
||||
= 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
geometrically equivalent.
|
||||
|
||||
See "this section"_Section_howto.html#4_12 of the doc pages for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
how to transform these parameters into other commonly used triclinic
|
||||
representations.
|
||||
|
||||
When a prism region is used, the simulation domain must be periodic in
|
||||
any dimensions with a non-zero tilt factor, as defined by the
|
||||
"boundary"_boundary.html command. I.e. if the xy tilt 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.
|
||||
be periodic if yz is non-zero. Also note that if your simulation will
|
||||
tilt the box, e.g. via the "fix deform"_fix_deform.html command, the
|
||||
simulation box must be defined as triclinic, even if the tilt factors
|
||||
are initially 0.0.
|
||||
|
||||
IMPORTANT NOTE: If the system is non-periodic (in a dimension), then
|
||||
you should not make the lo/hi box dimensions (as defined in your
|
||||
|
|
|
|||
|
|
@ -140,7 +140,7 @@ this format.
|
|||
self-describing in the following sense.
|
||||
</P>
|
||||
<P>The dimensions of the simulation box are included in each snapshot.
|
||||
For orthogonal simulation boxes this is formatted as:
|
||||
For an orthogonal simulation box this information is is formatted as:
|
||||
</P>
|
||||
<PRE>ITEM: BOX BOUNDS
|
||||
xlo xhi
|
||||
|
|
@ -150,37 +150,24 @@ zlo zhi
|
|||
<P>where xlo,xhi are the maximum extents of the simulation box in the
|
||||
x-dimension, and similarly for y and z.
|
||||
</P>
|
||||
<P>For triclinic simulation boxes (non-orthogonal), the tilt factors are
|
||||
also included, as a 3rd value on each line:
|
||||
<P>For triclinic simulation boxes (non-orthogonal), an orthogonal
|
||||
bounding box which encloses the triclinic simulation box is output,
|
||||
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
|
||||
formatted as follows:
|
||||
</P>
|
||||
<PRE>ITEM: BOX BOUNDS xy xz yz
|
||||
xlo_bound xhi_bound xy
|
||||
ylo_bound yhi_bound xz
|
||||
zlo_bound zhi_bound yz
|
||||
</PRE>
|
||||
<P>See the <A HREF = "region.html">region prism</A> or <A HREF = "read_data.html">read_data</A>
|
||||
commands for a description of tilt factors in LAMMPS, and their
|
||||
relationship to other nomenclatures for triclinic geometries,
|
||||
e.g. using 3 lattice constants <I>a</I>, <I>b</I>, and <I>c</I>, and 3 angles
|
||||
<I>alpha</I>, <I>beta</I> and <I>gamma</I>.
|
||||
<P>This bounding box is convenient for many visualization programs.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: As the notation above indicates, for triclinic
|
||||
simulation boxes, the 6 box bounds written to the dump file
|
||||
(xlo_bound,xhi_bound,ylo_bound,yhi_bound,zlo_bound,zhi_bound) are NOT
|
||||
equivalent to the 6 extents (xlo,xhi,ylo,yhi,zlo,zhi) in the
|
||||
orthogoonal case. Instead they are the extent in each dimension of
|
||||
the smallest orthogonal "bounding box" that encapsulates the entire
|
||||
tricilinc simulation box, including the effects of any tilt. This
|
||||
bounding box is convenient for many visualization programs and is
|
||||
calculated as follows:
|
||||
<P>See <A HREF = "Section_howto.html#4_12">this section</A> of the doc pages for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, simple
|
||||
formulas for how the 6 bounding box extents (xlo_bound,xhi_bound,etc)
|
||||
are calculated from the triclinic parameters, and how to transform
|
||||
those parameters into other commonly used triclinic representations.
|
||||
</P>
|
||||
<PRE>xlo_bound = MIN(xlo,xlo+xy,xlo+xz,xlo+xy+xz)
|
||||
xhi_bound = MAX(xhi,xhi+xy,xhi+xz,xhi+xy+xz)
|
||||
ylo_bound = MIN(ylo,ylo+yz)
|
||||
yhi_bound = MAX(yhi,yhi+yz)
|
||||
zlo_bound = zlo
|
||||
zhi_bound = zhi
|
||||
</PRE>
|
||||
<P>The "ITEM: ATOMS" line in each snapshot lists column descriptors for
|
||||
the per-atom lines that follow. For example, the descriptors would be
|
||||
"id type xs ys zs" for the default <I>atom</I> style, and would be the atom
|
||||
|
|
|
|||
35
doc/dump.txt
35
doc/dump.txt
|
|
@ -130,7 +130,7 @@ For post-processing purposes the {atom} and {custom} text files are
|
|||
self-describing in the following sense.
|
||||
|
||||
The dimensions of the simulation box are included in each snapshot.
|
||||
For orthogonal simulation boxes this is formatted as:
|
||||
For an orthogonal simulation box this information is is formatted as:
|
||||
|
||||
ITEM: BOX BOUNDS
|
||||
xlo xhi
|
||||
|
|
@ -140,36 +140,23 @@ zlo zhi :pre
|
|||
where xlo,xhi are the maximum extents of the simulation box in the
|
||||
x-dimension, and similarly for y and z.
|
||||
|
||||
For triclinic simulation boxes (non-orthogonal), the tilt factors are
|
||||
also included, as a 3rd value on each line:
|
||||
For triclinic simulation boxes (non-orthogonal), an orthogonal
|
||||
bounding box which encloses the triclinic simulation box is output,
|
||||
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
|
||||
formatted as follows:
|
||||
|
||||
ITEM: BOX BOUNDS xy xz yz
|
||||
xlo_bound xhi_bound xy
|
||||
ylo_bound yhi_bound xz
|
||||
zlo_bound zhi_bound yz :pre
|
||||
|
||||
See the "region prism"_region.html or "read_data"_read_data.html
|
||||
commands for a description of tilt factors in LAMMPS, and their
|
||||
relationship to other nomenclatures for triclinic geometries,
|
||||
e.g. using 3 lattice constants {a}, {b}, and {c}, and 3 angles
|
||||
{alpha}, {beta} and {gamma}.
|
||||
This bounding box is convenient for many visualization programs.
|
||||
|
||||
IMPORTANT NOTE: As the notation above indicates, for triclinic
|
||||
simulation boxes, the 6 box bounds written to the dump file
|
||||
(xlo_bound,xhi_bound,ylo_bound,yhi_bound,zlo_bound,zhi_bound) are NOT
|
||||
equivalent to the 6 extents (xlo,xhi,ylo,yhi,zlo,zhi) in the
|
||||
orthogoonal case. Instead they are the extent in each dimension of
|
||||
the smallest orthogonal "bounding box" that encapsulates the entire
|
||||
tricilinc simulation box, including the effects of any tilt. This
|
||||
bounding box is convenient for many visualization programs and is
|
||||
calculated as follows:
|
||||
|
||||
xlo_bound = MIN(xlo,xlo+xy,xlo+xz,xlo+xy+xz)
|
||||
xhi_bound = MAX(xhi,xhi+xy,xhi+xz,xhi+xy+xz)
|
||||
ylo_bound = MIN(ylo,ylo+yz)
|
||||
yhi_bound = MAX(yhi,yhi+yz)
|
||||
zlo_bound = zlo
|
||||
zhi_bound = zhi :pre
|
||||
See "this section"_Section_howto.html#4_12 of the doc pages for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, simple
|
||||
formulas for how the 6 bounding box extents (xlo_bound,xhi_bound,etc)
|
||||
are calculated from the triclinic parameters, and how to transform
|
||||
those parameters into other commonly used triclinic representations.
|
||||
|
||||
The "ITEM: ATOMS" line in each snapshot lists column descriptors for
|
||||
the per-atom lines that follow. For example, the descriptors would be
|
||||
|
|
|
|||
|
|
@ -82,7 +82,7 @@ is different than the default.
|
|||
<LI><I>xlo xhi</I> = simulation box boundaries in x dimension
|
||||
<LI><I>ylo yhi</I> = simulation box boundaries in y dimension
|
||||
<LI><I>zlo zhi</I> = simulation box boundaries in z dimension
|
||||
<LI><I>xy xz yz</I> = simulation box tilt factors for triclinic domain
|
||||
<LI><I>xy xz yz</I> = simulation box tilt factors for triclinic system
|
||||
</UL>
|
||||
<P>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
|
||||
|
|
@ -91,38 +91,37 @@ In any dimension, the system may be periodic or non-periodic; see the
|
|||
<P>If the <I>xy xz yz</I> line does not appear, 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 <A HREF = "region.html">region
|
||||
prism</A> command for a description of how the extent of the
|
||||
parallelepiped is defined. 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). Note that if
|
||||
your simulation will tilt the box, e.g. via the <A HREF = "fix_deform.html">fix
|
||||
deform</A> command, the simulation box must be triclinic,
|
||||
even if the tilt factors are initially 0.0.
|
||||
parallelepiped with triclinic symmetry. The parallelepiped has its
|
||||
"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
|
||||
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
|
||||
(xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or positive or negative values
|
||||
and are called "tilt factors" because they are the amount of
|
||||
displacement applied to faces of an originally orthogonal box to
|
||||
transform it into the parallelepiped.
|
||||
</P>
|
||||
<P>The tilt factors (xy,xz,yz) can not skew the box more than half the
|
||||
distance of the parallel box length. For example, if xlo = 2 and xhi
|
||||
= 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
equivalent.
|
||||
distance of the corresponding parallel box length. For example, if
|
||||
xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
|
||||
factor must be between -5 and 5. Similarly, both xz and yz must be
|
||||
between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
|
||||
limitation, since if the maximum tilt factor is 5 (as in this
|
||||
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
|
||||
... are all geometrically equivalent.
|
||||
</P>
|
||||
<P>Crystal structures are often defined using three lattice constants
|
||||
<I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and <I>gamma</I>. The
|
||||
relationships between these quantities and the LAMMPS box dimensions
|
||||
(lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are
|
||||
as follows:
|
||||
<P>See <A HREF = "Section_howto.html#4_12">this section</A> of the doc pages for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
how to transform these parameters into other commonly used triclinic
|
||||
representations.
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/box.jpg">
|
||||
</CENTER>
|
||||
<P>When a triclinic system is used, the simulation domain must be
|
||||
periodic in any dimensions with a non-zero tilt factor, as defined by
|
||||
the <A HREF = "boundary.html">boundary</A> command. I.e. if the xy tilt 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.
|
||||
be periodic if yz is non-zero. Also note that if your simulation will
|
||||
tilt the box, e.g. via the <A HREF = "fix_deform.html">fix deform</A> command, the
|
||||
simulation box must be defined as triclinic, even if the tilt factors
|
||||
are initially 0.0.
|
||||
</P>
|
||||
<P>For 2d simulations, the <I>zlo zhi</I> values should be set to bound the z
|
||||
coords for atoms that appear in the file; the default of -0.5 0.5 is
|
||||
|
|
|
|||
|
|
@ -79,7 +79,7 @@ is different than the default.
|
|||
{xlo xhi} = simulation box boundaries in x dimension
|
||||
{ylo yhi} = simulation box boundaries in y dimension
|
||||
{zlo zhi} = simulation box boundaries in z dimension
|
||||
{xy xz yz} = simulation box tilt factors for triclinic domain :ul
|
||||
{xy xz yz} = simulation box tilt factors for triclinic system :ul
|
||||
|
||||
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
|
||||
|
|
@ -88,38 +88,37 @@ In any dimension, the system may be periodic or non-periodic; see the
|
|||
If the {xy xz yz} line does not appear, 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"_region.html command for a description of how the extent of the
|
||||
parallelepiped is defined. 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). Note that if
|
||||
your simulation will tilt the box, e.g. via the "fix
|
||||
deform"_fix_deform.html command, the simulation box must be triclinic,
|
||||
even if the tilt factors are initially 0.0.
|
||||
parallelepiped with triclinic symmetry. The parallelepiped has its
|
||||
"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
|
||||
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
|
||||
(xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or positive or negative values
|
||||
and are called "tilt factors" because they are the amount of
|
||||
displacement applied to faces of an originally orthogonal box to
|
||||
transform it into the parallelepiped.
|
||||
|
||||
The tilt factors (xy,xz,yz) can not skew the box more than half the
|
||||
distance of the parallel box length. For example, if xlo = 2 and xhi
|
||||
= 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
equivalent.
|
||||
distance of the corresponding parallel box length. For example, if
|
||||
xlo = 2 and xhi = 12, then the x box length is 10 and the xy tilt
|
||||
factor must be between -5 and 5. Similarly, both xz and yz must be
|
||||
between -(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a
|
||||
limitation, since if the maximum tilt factor is 5 (as in this
|
||||
example), then configurations with tilt = ..., -15, -5, 5, 15, 25,
|
||||
... are all geometrically equivalent.
|
||||
|
||||
Crystal structures are often defined using three lattice constants
|
||||
{a}, {b}, and {c}, and three angles {alpha}, {beta} and {gamma}. The
|
||||
relationships between these quantities and the LAMMPS box dimensions
|
||||
(lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are
|
||||
as follows:
|
||||
|
||||
:c,image(Eqs/box.jpg)
|
||||
See "this section"_Section_howto.html#4_12 of the doc pages for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
how to transform these parameters into other commonly used triclinic
|
||||
representations.
|
||||
|
||||
When a triclinic system is used, the simulation domain must be
|
||||
periodic in any dimensions with a non-zero tilt factor, as defined by
|
||||
the "boundary"_boundary.html command. I.e. if the xy tilt 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.
|
||||
be periodic if yz is non-zero. Also note that if your simulation will
|
||||
tilt the box, e.g. via the "fix deform"_fix_deform.html command, the
|
||||
simulation box must be defined as triclinic, even if the tilt factors
|
||||
are initially 0.0.
|
||||
|
||||
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
|
||||
|
|
|
|||
|
|
@ -151,35 +151,29 @@ half-space in the direction of the normal vector; see the discussion
|
|||
of the <I>side</I> option below.
|
||||
</P>
|
||||
<P>For style <I>prism</I>, a parallelepiped is defined (it's too hard to spell
|
||||
parallelepiped in an input script!). Think of the parallelepiped 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" or "tilted"
|
||||
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 tilt. 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).
|
||||
parallelepiped in an input script!). The parallelepiped has its
|
||||
"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
|
||||
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
|
||||
(xz,yz,zhi-zlo). <I>Xy,xz,yz</I> can be 0.0 or positive or negative values
|
||||
and are called "tilt factors" because they are the amount of
|
||||
displacement applied to faces of an originally orthogonal box to
|
||||
transform it into the parallelepiped.
|
||||
</P>
|
||||
<P>Crystal structures are often defined using three lattice constants
|
||||
<I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and <I>gamma</I>. The
|
||||
relationships between these quantities and a prism with (lx,ly,lz) =
|
||||
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are as follows:
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/box.jpg">
|
||||
</CENTER>
|
||||
<P>A prism region used with the <A HREF = "create_box.html">create_box</A> command must
|
||||
have tilt factors (xy,xz,yz) that do not skew the box more than half
|
||||
the distance of the parallel box length. For example, if xlo = 2 and
|
||||
<P>A prism region that will be used with the <A HREF = "create_box.html">create_box</A>
|
||||
command to define a triclinic simulation box must have tilt factors
|
||||
(xy,xz,yz) that do not skew the box more than half the distance of
|
||||
corresponding the parallel box length. For example, if xlo = 2 and
|
||||
xhi = 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
equivalent.
|
||||
geometrically equivalent.
|
||||
</P>
|
||||
<P>See <A HREF = "Section_howto.html#4_12">this section</A> of the doc pages for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
how to transform these parameters into other commonly used triclinic
|
||||
representations.
|
||||
</P>
|
||||
<P>The <I>union</I> style creates a region consisting of the volume of all the
|
||||
listed regions combined. The <I>intersect</I> style creates a region
|
||||
|
|
|
|||
|
|
@ -142,35 +142,29 @@ half-space in the direction of the normal vector; see the discussion
|
|||
of the {side} option below.
|
||||
|
||||
For style {prism}, a parallelepiped is defined (it's too hard to spell
|
||||
parallelepiped in an input script!). Think of the parallelepiped 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" or "tilted"
|
||||
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 tilt. 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).
|
||||
parallelepiped in an input script!). The parallelepiped has its
|
||||
"origin" at (xlo,ylo,zlo) and is defined by 3 edge vectors starting
|
||||
from the origin given by A = (xhi-xlo,0,0); B = (xy,yhi-ylo,0); C =
|
||||
(xz,yz,zhi-zlo). {Xy,xz,yz} can be 0.0 or positive or negative values
|
||||
and are called "tilt factors" because they are the amount of
|
||||
displacement applied to faces of an originally orthogonal box to
|
||||
transform it into the parallelepiped.
|
||||
|
||||
Crystal structures are often defined using three lattice constants
|
||||
{a}, {b}, and {c}, and three angles {alpha}, {beta} and {gamma}. The
|
||||
relationships between these quantities and a prism with (lx,ly,lz) =
|
||||
(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are as follows:
|
||||
|
||||
:c,image(Eqs/box.jpg)
|
||||
|
||||
A prism region used with the "create_box"_create_box.html command must
|
||||
have tilt factors (xy,xz,yz) that do not skew the box more than half
|
||||
the distance of the parallel box length. For example, if xlo = 2 and
|
||||
A prism region that will be used with the "create_box"_create_box.html
|
||||
command to define a triclinic simulation box must have tilt factors
|
||||
(xy,xz,yz) that do not skew the box more than half the distance of
|
||||
corresponding the parallel box length. For example, if xlo = 2 and
|
||||
xhi = 12, then the x box length is 10 and the xy tilt factor must be
|
||||
between -5 and 5. Similarly, both xz and yz must be between
|
||||
-(xhi-xlo)/2 and +(yhi-ylo)/2. Note that this is not a limitation,
|
||||
since if the maximum tilt factor is 5 (as in this example), then
|
||||
configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
|
||||
equivalent.
|
||||
geometrically equivalent.
|
||||
|
||||
See "this section"_Section_howto.html#4_12 of the doc pages for a
|
||||
geometric description of triclinic boxes, as defined by LAMMPS, and
|
||||
how to transform these parameters into other commonly used triclinic
|
||||
representations.
|
||||
|
||||
The {union} style creates a region consisting of the volume of all the
|
||||
listed regions combined. The {intersect} style creates a region
|
||||
|
|
|
|||
Loading…
Reference in New Issue