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@ -137,17 +137,50 @@ LAMMPS <A HREF = "Section_tools.html">post-processing tools</A>, including
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this format.
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</P>
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<P>For post-processing purposes the <I>atom</I> and <I>custom</I> text files are
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self-describing in the following sense. The simulation box bounds are
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included in each snapshot and if the box is triclinic
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(non-orthogonal), then the tilt factors are also printed; see the
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<A HREF = "region.html">region prism</A> command for a description of tilt factors.
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For triclinic boxes the box bounds themselves (first 2 quantities on
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each line) are a true "bounding box" around the simulation domain,
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which means they include the effect of any tilt. The "ITEM: ATOMS"
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line in each snapshot also lists the meaning of each column of the
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per-atom lines that follow. For example, this would be "id type xs ys
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zs" for the default <I>atom</I> style, and it will be the atom attributes
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you specify in the dump command for the <I>custom</I> style.
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self-describing in the following sense.
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</P>
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<P>The simulation box bounds are included in each snapshot. For
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orthogonal boxes this is formatted as:
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</P>
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<PRE>ITEM: BOX BOUNDS
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xlo xhi
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ylo yhi
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zlo zhi
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</PRE>
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<P>where xlo,xhi are the bounds of the simulation box in the x-dimension,
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and similarly for y and z.
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</P>
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<P>For triclinic boxes (non-orthogonal), the tilt factors are also
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included, as a 3rd value on each line:
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</P>
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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>See the <A HREF = "region.html">region prism</A> or <A HREF = "read_data.html">read_data</A>
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commands for a description of tilt factors in LAMMPS, and their
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relationship to other nomenclatures for triclinic geometries,
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e.g. using 3 lattice constants <I>a</I>, <I>b</I>, and <I>c</I>, and 3 angles
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<I>alpha</I>, <I>beta</I> and <I>gamma</I>.
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</P>
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<P>IMPORTANT NOTE: As noted above, for triclinic simulation boxes, the 6
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box bounds (xlo,xhi,ylo,yhi,zlo,zhi) are actually written to the dump
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file as a "bounding box" around the simulation domain, which means
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they include the effect of any tilt, which is convenient for many
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visualization programs. The bounding box is calculated as follows:
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</P>
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<PRE>xlo_bound = MIN(xlo,xlo+xy,xlo+xz,xlo+xy+xz)
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xhi_bound = MAX(xhi,xhi+xy,xhi+xz,xhi+xy+xz)
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ylo_bound = MIN(ylo,ylo+yz)
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yhi_bound = MAX(yhi,yhi+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>The "ITEM: ATOMS" line in each snapshot lists column descriptors for
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the per-atom lines that follow. For example, the descriptors would be
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"id type xs ys zs" for the default <I>atom</I> style, and would be the atom
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attributes you specify in the dump command for the <I>custom</I> style.
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</P>
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<P>For style <I>atom</I>, atom coordinates are written to the file, along with
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the atom ID and atom type. By default, atom coords are written in a
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55
doc/dump.txt
55
doc/dump.txt
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@ -127,17 +127,50 @@ LAMMPS "post-processing tools"_Section_tools.html, including
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this format.
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For post-processing purposes the {atom} and {custom} text files are
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self-describing in the following sense. The simulation box bounds are
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included in each snapshot and if the box is triclinic
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(non-orthogonal), then the tilt factors are also printed; see the
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"region prism"_region.html command for a description of tilt factors.
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For triclinic boxes the box bounds themselves (first 2 quantities on
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each line) are a true "bounding box" around the simulation domain,
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which means they include the effect of any tilt. The "ITEM: ATOMS"
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line in each snapshot also lists the meaning of each column of the
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per-atom lines that follow. For example, this would be "id type xs ys
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zs" for the default {atom} style, and it will be the atom attributes
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you specify in the dump command for the {custom} style.
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self-describing in the following sense.
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The simulation box bounds are included in each snapshot. For
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orthogonal boxes this is formatted as:
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ITEM: BOX BOUNDS
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xlo xhi
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ylo yhi
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zlo zhi :pre
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where xlo,xhi are the bounds of the simulation box in the x-dimension,
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and similarly for y and z.
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For triclinic boxes (non-orthogonal), the tilt factors are also
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included, as a 3rd value on each line:
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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 :pre
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See the "region prism"_region.html or "read_data"_read_data.html
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commands for a description of tilt factors in LAMMPS, and their
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relationship to other nomenclatures for triclinic geometries,
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e.g. using 3 lattice constants {a}, {b}, and {c}, and 3 angles
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{alpha}, {beta} and {gamma}.
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IMPORTANT NOTE: As noted above, for triclinic simulation boxes, the 6
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box bounds (xlo,xhi,ylo,yhi,zlo,zhi) are actually written to the dump
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file as a "bounding box" around the simulation domain, which means
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they include the effect of any tilt, which is convenient for many
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visualization programs. The bounding box is calculated as follows:
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xlo_bound = MIN(xlo,xlo+xy,xlo+xz,xlo+xy+xz)
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xhi_bound = MAX(xhi,xhi+xy,xhi+xz,xhi+xy+xz)
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ylo_bound = MIN(ylo,ylo+yz)
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yhi_bound = MAX(yhi,yhi+yz)
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zlo_bound = zlo
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zhi_bound = zhi :pre
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The "ITEM: ATOMS" line in each snapshot lists column descriptors for
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the per-atom lines that follow. For example, the descriptors would be
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"id type xs ys zs" for the default {atom} style, and would be the atom
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attributes you specify in the dump command for the {custom} style.
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For style {atom}, atom coordinates are written to the file, along with
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the atom ID and atom type. By default, atom coords are written in a
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@ -109,8 +109,8 @@ since if the maximum tilt factor is 5 (as in this example), then
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configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
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equivalent.
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</P>
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<P>Many crystal structures are defined using three lattice constants <I>a</I>,
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<I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and <I>gamma</I>. The
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<P>Crystal structures are often defined using three lattice constants
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<I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and <I>gamma</I>. The
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relationships between these quantities and the LAMMPS box dimensions
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(lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are
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as follows:
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@ -106,8 +106,8 @@ since if the maximum tilt factor is 5 (as in this example), then
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configurations with tilt = ..., -15, -5, 5, 15, 25, ... are all
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equivalent.
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Many crystal structures are defined using three lattice constants {a},
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{b}, and {c}, and three angles {alpha}, {beta} and {gamma}. The
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Crystal structures are often defined using three lattice constants
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{a}, {b}, and {c}, and three angles {alpha}, {beta} and {gamma}. The
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relationships between these quantities and the LAMMPS box dimensions
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(lx,ly,lz) = (xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are
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as follows:
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@ -85,11 +85,13 @@ region 2 sphere 0.0 0.0 0.0 5 side out wiggle 1 1 0 10
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</P>
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<P>This command defines a geometric region of space. Various other
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commands use regions. For example, the region can be filled with
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atoms via the <A HREF = "create_atoms.html">create_atoms</A> command. Or the atoms
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in the region can be identified as a group via the <A HREF = "group.html">group</A>
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command, or deleted via the <A HREF = "delete_atoms.html">delete_atoms</A> command.
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Or the surface of the region can be used as a boundary wall via the
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<A HREF = "fix_wall_region.html">fix wall/region</A> command.
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atoms via the <A HREF = "create_atoms.html">create_atoms</A> command. Or a bounding
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box around the region, can be used to define the simulation box via
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the <A HREF = "create_box.html">create_box</A> command. Or the atoms in the region
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can be identified as a group via the <A HREF = "group.html">group</A> command, or
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deleted via the <A HREF = "delete_atoms.html">delete_atoms</A> command. Or the
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surface of the region can be used as a boundary wall via the <A HREF = "fix_wall_region.html">fix
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wall/region</A> command.
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</P>
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<P>Normally, regions in LAMMPS are "static", meaning their geometric
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extent does not change with time. If the <I>vel</I> or <I>wiggle</I> or
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@ -162,6 +164,13 @@ results in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3
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edge vectors starting from its origin given by a = (xhi-xlo,0,0); b =
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(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
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</P>
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<P>Crystal structures are often defined using three lattice constants
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<I>a</I>, <I>b</I>, and <I>c</I>, and three angles <I>alpha</I>, <I>beta</I> and <I>gamma</I>. The
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relationships between these quantities and a prism with (lx,ly,lz) =
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(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are as follows:
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</P>
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<CENTER><IMG SRC = "Eqs/box.jpg">
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</CENTER>
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<P>A prism region used with the <A HREF = "create_box.html">create_box</A> command must
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have tilt factors (xy,xz,yz) that do not skew the box more than half
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the distance of the parallel box length. For example, if xlo = 2 and
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@ -76,11 +76,13 @@ region 2 sphere 0.0 0.0 0.0 5 side out wiggle 1 1 0 10 :pre
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This command defines a geometric region of space. Various other
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commands use regions. For example, the region can be filled with
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atoms via the "create_atoms"_create_atoms.html command. Or the atoms
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in the region can be identified as a group via the "group"_group.html
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command, or deleted via the "delete_atoms"_delete_atoms.html command.
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Or the surface of the region can be used as a boundary wall via the
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"fix wall/region"_fix_wall_region.html command.
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atoms via the "create_atoms"_create_atoms.html command. Or a bounding
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box around the region, can be used to define the simulation box via
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the "create_box"_create_box.html command. Or the atoms in the region
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can be identified as a group via the "group"_group.html command, or
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deleted via the "delete_atoms"_delete_atoms.html command. Or the
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surface of the region can be used as a boundary wall via the "fix
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wall/region"_fix_wall_region.html command.
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Normally, regions in LAMMPS are "static", meaning their geometric
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extent does not change with time. If the {vel} or {wiggle} or
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@ -153,6 +155,13 @@ results in a parallelepiped whose "origin" is at (xlo,ylo,zlo) with 3
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edge vectors starting from its origin given by a = (xhi-xlo,0,0); b =
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(xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
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Crystal structures are often defined using three lattice constants
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{a}, {b}, and {c}, and three angles {alpha}, {beta} and {gamma}. The
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relationships between these quantities and a prism with (lx,ly,lz) =
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(xhi-xlo,yhi-ylo,zhi-zlo) and tilt factors (xy,xz,yz) are as follows:
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:c,image(Eqs/box.jpg)
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A prism region used with the "create_box"_create_box.html command must
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have tilt factors (xy,xz,yz) that do not skew the box more than half
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the distance of the parallel box length. For example, if xlo = 2 and
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