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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@362 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2007-03-06 15:13:57 +00:00
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commit ed114fb152
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73
doc/read_data.html
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@ -60,12 +60,13 @@ valid.
<HR>
<P>These are the recognized header keywords. Header lines can come in
any order. The value(s) is read from the beginning of the line. Thus
the keyword <I>atoms</I> should be in a line like "1000 atoms" and the
keyword <I>ylo yhi</I> should be in a line like "-10.0 10.0 ylo yhi". All
these settings have a default value of 0, except the lo/hi box size
defaults are -0.5 and 0.5. A line need only appear if the value is
different than the default.
any order. The value(s) are read from the beginning of the line.
Thus the keyword <I>atoms</I> should be in a line like "1000 atoms"; the
keyword <I>ylo yhi</I> should be in a line like "-10.0 10.0 ylo yhi"; the
keyword <I>xy xz yz</I> should be in a line like "0.0 5.0 6.0 xy xz yz".
All these settings have a default value of 0, except the lo/hi box
size defaults are -0.5 and 0.5. A line need only appear if the value
is different than the default.
</P>
<UL><LI><I>atoms</I> = # of atoms in system
<LI><I>bonds</I> = # of bonds in system
@ -79,16 +80,40 @@ different than the default.
<LI><I>improper types</I> = # of improper types in system
<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>zlo zhi</I> = simulation box boundaries in z dimension
<LI><I>xy xz yz</I> = simulation box tilt factors for triclinic domain
</UL>
<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
valid if all z coords are 0.0.
</P>
<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
<A HREF = "boundary.html">boundary</A> command.
</P>
<P>If the <I>xy xz yz</I> line does not appear, then LAMMPS will set up an
axis-aligned (orthogonal) simulation box. If the line does appear,
LAMMPS creates a non-orthogonal simulation domain shaped as a
parallelepiped with triclinic symmetry. See the <A HREF = "region.html">region
prism</A> command for a description of how the extent of the
parallelepiped is defined. Basically, the parallelepiped has its
"origin" at (xlo,ylo,zlo) and 3 edge vectors starting from the origin
given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
</P>
<P>The skew factors (xy,xz,yz) must not skew the box more than half the
distance of its side lengths. For example, if ylo = 2 and yhi = 12,
then the y box length is 10 and the xy factor must be between -5 and
5. Similary xz must be between -(zhi-zlo)/2 and +(zhi-zlo)/2 and yz
must be between -(zhi-zlo)/2 and +(zhi-zlo)/2.
</P>
<P>When a triclinic system is used, the simulation domain must be
periodic in any dimensions with a non-zero skew factor, as defined by
the <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>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
valid if all z coords are 0.0. For 2d triclinic simulations, the xz
and yz skew factors must be 0.0.
</P>
<P>If the system is non-periodic (in a dimension), then all atoms in the
data file should have coordinates (in that dimension) between the lo
and hi values. Furthermore, if running in parallel, the lo/hi values
@ -543,24 +568,22 @@ script.
<P><I>Velocities</I> section:
</P>
<UL>one line per atom
<LI>line syntax: atom-ID vx vy vz
<PRE> atom-ID = integer ID of atom to assign velocity to
vx,vy,vz = components of velocity of the atom
</PRE>
<LI>example:
<PRE> 45 -3.4 0.05 1.25
</PRE>
<UL><LI>one line per atom
<LI>line syntax: depends on atom style
</UL>
<DIV ALIGN=center><TABLE WIDTH="0%" BORDER=1 >
<TR><TD >all styles except granular</TD><TD > atom-ID vx vy vz</TD></TR>
<TR><TD >granular</TD><TD > atom-ID vx vy vz phix phiy phiz
</TD></TR></TABLE></DIV>
<P>The velocity lines can appear in any order. This section can only be
used after an <I>Atoms</I> section. The <I>Atoms</I> section must have assigned
a unique atom ID to each atom so that velocities can be assigned in
this way. Velocities can also be set by the <A HREF = "velocity.html">velocity</A>
command in the input script.
this way. Vx,vy,vz are in <A HREF = "units.html">units</A> of velocity.
Phix,phiy,phiz are in units of angular velocity (radians/time).
</P>
<P>Translational velocities can also be set by the
<A HREF = "velocity.html">velocity</A> command in the input script.
</P>
<HR>

66
doc/read_data.txt
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@ -55,12 +55,13 @@ valid.
:line
These are the recognized header keywords. Header lines can come in
any order. The value(s) is read from the beginning of the line. Thus
the keyword {atoms} should be in a line like "1000 atoms" and the
keyword {ylo yhi} should be in a line like "-10.0 10.0 ylo yhi". All
these settings have a default value of 0, except the lo/hi box size
defaults are -0.5 and 0.5. A line need only appear if the value is
different than the default.
any order. The value(s) are read from the beginning of the line.
Thus the keyword {atoms} should be in a line like "1000 atoms"; the
keyword {ylo yhi} should be in a line like "-10.0 10.0 ylo yhi"; the
keyword {xy xz yz} should be in a line like "0.0 5.0 6.0 xy xz yz".
All these settings have a default value of 0, except the lo/hi box
size defaults are -0.5 and 0.5. A line need only appear if the value
is different than the default.
{atoms} = # of atoms in system
{bonds} = # of bonds in system
@ -74,16 +75,40 @@ different than the default.
{improper types} = # of improper types in system
{xlo xhi} = simulation box boundaries in x dimension
{ylo yhi} = simulation box boundaries in y dimension
{zlo zhi} = simulation box boundaries in z dimension :ul
For 2d simulations, the {zlo zhi} values should be set to bound the z
coords for atoms that appear in the file; the default of -0.5 0.5 is
valid if all z coords are 0.0.
{zlo zhi} = simulation box boundaries in z dimension
{xy xz yz} = simulation box tilt factors for triclinic domain :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
"boundary"_boundary.html command.
If the {xy xz yz} line does not appear, then LAMMPS will set up an
axis-aligned (orthogonal) simulation box. If the line does appear,
LAMMPS creates a non-orthogonal simulation domain shaped as a
parallelepiped with triclinic symmetry. See the "region
prism"_region.html command for a description of how the extent of the
parallelepiped is defined. Basically, the parallelepiped has its
"origin" at (xlo,ylo,zlo) and 3 edge vectors starting from the origin
given by a = (xhi-xlo,0,0); b = (xy,yhi-ylo,0); c = (xz,yz,zhi-zlo).
The skew factors (xy,xz,yz) must not skew the box more than half the
distance of its side lengths. For example, if ylo = 2 and yhi = 12,
then the y box length is 10 and the xy factor must be between -5 and
5. Similary xz must be between -(zhi-zlo)/2 and +(zhi-zlo)/2 and yz
must be between -(zhi-zlo)/2 and +(zhi-zlo)/2.
When a triclinic system is used, the simulation domain must be
periodic in any dimensions with a non-zero skew factor, as defined by
the "boundary"_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.
For 2d simulations, the {zlo zhi} values should be set to bound the z
coords for atoms that appear in the file; the default of -0.5 0.5 is
valid if all z coords are 0.0. For 2d triclinic simulations, the xz
and yz skew factors must be 0.0.
If the system is non-periodic (in a dimension), then all atoms in the
data file should have coordinates (in that dimension) between the lo
and hi values. Furthermore, if running in parallel, the lo/hi values
@ -460,19 +485,20 @@ script.
{Velocities} section:
one line per atom :ulb
line syntax: atom-ID vx vy vz :l
atom-ID = integer ID of atom to assign velocity to
vx,vy,vz = components of velocity of the atom :pre
example: :l
45 -3.4 0.05 1.25 :pre
:ule
one line per atom
line syntax: depends on atom style :ul
all styles except granular: atom-ID vx vy vz
granular: atom-ID vx vy vz phix phiy phiz :tb(s=:)
The velocity lines can appear in any order. This section can only be
used after an {Atoms} section. The {Atoms} section must have assigned
a unique atom ID to each atom so that velocities can be assigned in
this way. Velocities can also be set by the "velocity"_velocity.html
command in the input script.
this way. Vx,vy,vz are in "units"_units.html of velocity.
Phix,phiy,phiz are in units of angular velocity (radians/time).
Translational velocities can also be set by the
"velocity"_velocity.html command in the input script.
:line