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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@452 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-04-02 14:26:01 +00:00
parent 99b1e31a4a
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13
doc/Section_start.html
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@ -428,10 +428,15 @@ mpirun -np 4 lmp_linux < in.lj.nve
</PRE>
<P>The screen output from LAMMPS is described in the next section. As it
runs, LAMMPS also writes a log.lammps file with the same information.
Note that this sequence of commands copied the LAMMPS executable
(lmp_linux) to the directory with the input files. If you don't do
this, LAMMPS may look for input files or create output files in the
directory where the executable is, rather than where you run it from.
</P>
<P>Note that this sequence of commands copies the LAMMPS executable
(lmp_linux) to the directory with the input files. This may not be
necessary, but some versions of MPI reset the working directory to
where the executable is, rather than leave it as the directory where
you launch mpirun from. If that happens, LAMMPS will look for
additional input files and write its output files to the executable
directory, rather than your working directory, which is probably not
what you want.
</P>
<P>If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING

13
doc/Section_start.txt
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@ -421,10 +421,15 @@ mpirun -np 4 lmp_linux < in.lj.nve :pre
The screen output from LAMMPS is described in the next section. As it
runs, LAMMPS also writes a log.lammps file with the same information.
Note that this sequence of commands copied the LAMMPS executable
(lmp_linux) to the directory with the input files. If you don't do
this, LAMMPS may look for input files or create output files in the
directory where the executable is, rather than where you run it from.
Note that this sequence of commands copies the LAMMPS executable
(lmp_linux) to the directory with the input files. This may not be
necessary, but some versions of MPI reset the working directory to
where the executable is, rather than leave it as the directory where
you launch mpirun from. If that happens, LAMMPS will look for
additional input files and write its output files to the executable
directory, rather than your working directory, which is probably not
what you want.
If LAMMPS encounters errors in the input script or while running a
simulation it will print an ERROR message and stop or a WARNING

24
doc/create_box.html
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@ -43,19 +43,21 @@ 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>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
opposing box length. For example, if ylo = 2 and yhi = 12, then the y
box length is 10 and the xy tilt factor must be between -5 and 5.
Similarly, both xz and yz must be between -(zhi-zlo)/2 and
+(zhi-zlo)/2. From a mechanics persepctive this is equivalent to
saying the shear strain of the system (sideways displacement divided
by perpendicular box length) must be between -0.5 and 0.5.
</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.
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.
</P>
<P><B>Restrictions:</B>
</P>

24
doc/create_box.txt
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@ -40,19 +40,21 @@ 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.
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
opposing box length. For example, if ylo = 2 and yhi = 12, then the y
box length is 10 and the xy tilt factor must be between -5 and 5.
Similarly, both xz and yz must be between -(zhi-zlo)/2 and
+(zhi-zlo)/2. From a mechanics persepctive this is equivalent to
saying the shear strain of the system (sideways displacement divided
by perpendicular box length) must be between -0.5 and 0.5.
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.
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.
[Restrictions:]

4
doc/fix_recenter.html
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@ -88,8 +88,8 @@ warn you if your fixes are not ordered this way.
shift in the system on the 1st timestep, due to the requested COM
being very different from the initial COM. This could cause atoms to
be lost,especially in parallel. Instead, use the
<A HREF = "displace_atoms.html">displace_atoms</A> command, which can be used
several times in succession to move atoms a large distance.
<A HREF = "displace_atoms.html">displace_atoms</A> command, which can be used to
move atoms a large distance.
</P>
<P><B>Related commands:</B>
</P>

4
doc/fix_recenter.txt
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@ -80,8 +80,8 @@ This fix should not be used with an x,y,z setting that causes a large
shift in the system on the 1st timestep, due to the requested COM
being very different from the initial COM. This could cause atoms to
be lost,especially in parallel. Instead, use the
"displace_atoms"_displace_atoms.html command, which can be used
several times in succession to move atoms a large distance.
"displace_atoms"_displace_atoms.html command, which can be used to
move atoms a large distance.
[Related commands:]

3
doc/fix_volume_rescale.html
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@ -41,7 +41,8 @@ box dimensions is controlled separately. Any dimension being varied
by this command must be periodic - see the <A HREF = "boundary.html">boundary</A>
command. Dimensions not varied by this command can be periodic or
non-periodic. The volume associated with an unspecified dimension can
also be controlled by a <A HREF = "fix_npt.html">fix npt</A> command.
also be controlled by a <A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix
nph</A> command.
</P>
<P>The initial simulation box boundaries at the beginning of a run are
specified by the <A HREF = "create_box.html">create_box</A> or

7
doc/fix_volume_rescale.txt
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@ -32,7 +32,8 @@ box dimensions is controlled separately. Any dimension being varied
by this command must be periodic - see the "boundary"_boundary.html
command. Dimensions not varied by this command can be periodic or
non-periodic. The volume associated with an unspecified dimension can
also be controlled by a "fix npt"_fix_npt.html command.
also be controlled by a "fix npt"_fix_npt.html or "fix
nph"_fix_nph.html command.
The initial simulation box boundaries at the beginning of a run are
specified by the "create_box"_create_box.html or
@ -55,7 +56,3 @@ Any dimension being varied by this fix must be periodic.
[Related commands:] none
[Default:] none

25
doc/read_data.html
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@ -92,19 +92,22 @@ 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).
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).
</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>The tilt factors (xy,xz,yz) must not skew the box more than half the
distance of the opposing box length. For example, if ylo = 2 and yhi
= 12, then the y box length is 10 and the xy tilt factor must be
between -5 and 5. Similarly, both xz and yz must be between
-(zhi-zlo)/2 and +(zhi-zlo)/2. From a mechanics persepctive this is
equivalent to saying the shear strain of the system (sideways
displacement divided by perpendicular box length) must be between -0.5
and 0.5.
</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
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.
@ -112,7 +115,7 @@ be periodic if yz is non-zero.
<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.
and yz tilt 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

25
doc/read_data.txt
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@ -87,19 +87,22 @@ 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).
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).
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.
The tilt factors (xy,xz,yz) must not skew the box more than half the
distance of the opposing box length. For example, if ylo = 2 and yhi
= 12, then the y box length is 10 and the xy tilt factor must be
between -5 and 5. Similarly, both xz and yz must be between
-(zhi-zlo)/2 and +(zhi-zlo)/2. From a mechanics persepctive this is
equivalent to saying the shear strain of the system (sideways
displacement divided by perpendicular box length) must be between -0.5
and 0.5.
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
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.
@ -107,7 +110,7 @@ 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.
and yz tilt 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

22
doc/region.html
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@ -29,9 +29,9 @@
lo,hi = bounds of cylinder in dim (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)
xy = distance to tilt y in x direction (distance units)
xz = distance to tilt z in x direction (distance units)
yz = distance to tilt 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)
@ -91,14 +91,14 @@ parallelepiped in an input script!). A prism region is used by the
(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 =
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).
</P>
<P>The <I>union</I> style creates a region consisting of the volume of all the

22
doc/region.txt
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@ -24,9 +24,9 @@ style = {block} or {cylinder} or {prism} or {sphere} or {union} or {intersect} :
lo,hi = bounds of cylinder in dim (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)
xy = distance to tilt y in x direction (distance units)
xz = distance to tilt z in x direction (distance units)
yz = distance to tilt 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)
@ -82,14 +82,14 @@ parallelepiped in an input script!). A prism region is used by the
(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 =
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).
The {union} style creates a region consisting of the volume of all the

7
doc/run.html
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@ -70,9 +70,10 @@ performed and you want a <A HREF = "fix.html">fix</A> command that ramps some va
of runs and not just a single run. Fixes in this category include
<A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_langevin.html">fix
langevin</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>,
<A HREF = "fix_volume_rescale.html">fix volume/rescale</A>, and <A HREF = "fix_indent.html">fix
indent</A>. The <A HREF = "pair_style.html">pair_style soft</A>
potential also ramps its coefficients in a similar way.
<A HREF = "fix_volume_rescale.html">fix volume/rescale</A>, <A HREF = "fix_deform.html">fix
deform</A>, and <A HREF = "fix_indent.html">fix indent</A>. The
<A HREF = "pair_style.html">pair_style soft</A> potential also ramps its
coefficients in a similar way.
</P>
<P>For example, consider this fix followed by 10 run commands:
</P>

7
doc/run.txt
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@ -63,9 +63,10 @@ performed and you want a "fix"_fix.html command that ramps some value
of runs and not just a single run. Fixes in this category include
"fix nvt"_fix_nvt.html, "fix npt"_fix_npt.html, "fix
langevin"_fix_langevin.html, "fix temp/rescale"_fix_temp_rescale.html,
"fix volume/rescale"_fix_volume_rescale.html, and "fix
indent"_fix_indent.html. The "pair_style soft"_pair_style.html
potential also ramps its coefficients in a similar way.
"fix volume/rescale"_fix_volume_rescale.html, "fix
deform"_fix_deform.html, and "fix indent"_fix_indent.html. The
"pair_style soft"_pair_style.html potential also ramps its
coefficients in a similar way.
For example, consider this fix followed by 10 run commands: