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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@618 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-06-20 12:56:25 +00:00
parent a7ab72af62
commit e922a38bb8
6 changed files with 25 additions and 28 deletions
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4
doc/Section_commands.html
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@ -322,8 +322,8 @@ description:
<TR ALIGN="center"><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_msd.html">msd</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_nph.html">nph</A></TD><TD ><A HREF = "fix_npt.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_dipole.html">nve/dipole</A></TD><TD ><A HREF = "fix_nve_gran.html">nve/gran</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD><TD ><A HREF = "fix_nvt.html">nvt</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_rdf.html">rdf</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_uniaxial.html">uniaxial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_volume_rescale.html">volume/rescale</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
<TR ALIGN="center"><TD ><A HREF = "fix_setforce.html">setforce</A></TD><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall_lj93.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_lj126.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wiggle.html">wiggle</A>
</TD></TR></TABLE></DIV>
<HR>

7
doc/boundary.html
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@ -43,10 +43,9 @@ commands.
<P>The style <I>p</I> means the box is periodic, so that particles interact
across the boundary, and they can exit one end of the box and re-enter
the other end. A periodic dimension can change in size due to
constant pressure boundary conditions or volume rescaling (see the
<A HREF = "fix_npt.html">fix npt</A> and <A HREF = "fix_volume_rescale.html">fix volume/rescale</A>
commands). The <I>p</I> style must be applied to both faces of a
dimension.
constant pressure boundary conditions or box deformation (see the <A HREF = "fix_npt.html">fix
npt</A> and <A HREF = "fix_deform.html">fix deform</A> commands). The <I>p</I>
style must be applied to both faces of a dimension.
</P>
<P>The styles <I>f</I>, <I>s</I>, and <I>m</I> mean the box is non-periodic, so that
particles do not interact across the boundary and do not move from one

2
doc/fix.html
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@ -103,9 +103,7 @@ made to the old fix via the <A HREF = "fix_modify.html">fix_modify</A> command.
<LI><A HREF = "fix_spring_self.html">fix spring/self</A> - spring from each atom to its origin
<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A> - temperature control by velocity rescaling
<LI><A HREF = "fix_tmd.html">fix tmd</A> - guide a group of atoms to a new configuration
<LI><A HREF = "fix_uniaxial.html">fix uniaxial</A> - uniaxial straining of system while preserving total volume
<LI><A HREF = "fix_viscous.html">fix viscous</A> - viscous damping for granular simulations
<LI><A HREF = "fix_volume_rescale.html">fix volume/rescale</A> - density control by volume rescaling
<LI><A HREF = "fix_wall_gran.html">fix wall/gran</A> - frictional wall(s) for granular simulations
<LI><A HREF = "fix_wall_lj93.html">fix wall/lj93</A> - Lennard-Jones 9-3 wall
<LI><A HREF = "fix_wall_lj126.html">fix wall/lj126</A> - Lennard-Jones 12-6 wall

18
doc/pair_gayberne.html
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@ -68,12 +68,12 @@ commands:
</P>
<UL><LI>epsilon = well depth (energy units)
<LI>sigma = minimum effective particle radii (distance units)
<LI>a = ellipsoid radius in x dimension (distance units)
<LI>b = ellipsoid radius in y dimension (distance units)
<LI>c = ellipsoid radius in z dimension (distance units)
<LI>epsilon_a = relative well depth for side-to-side interactions
<LI>epsilon_b = relative well depth for face-to-face interactions
<LI>epsilon_c = relative well depth for end-to-end interactions
<LI>epsilon_i_a = relative well depth of I for side-to-side interactions
<LI>epsilon_i_b = relative well depth of I for face-to-face interactions
<LI>epsilon_i_c = relative well depth of I for end-to-end interactions
<LI>epsilon_j_a = relative well depth of J for side-to-side interactions
<LI>epsilon_j_b = relative well depth of J for face-to-face interactions
<LI>epsilon_j_c = relative well depth of J for end-to-end interactions
<LI>cutoff (distance units)
</UL>
<P>The last coefficient is optional. If not specified, the global
@ -94,9 +94,9 @@ above. The "shift yes" option currently cannot be used with this
potential to shift energies to 0 at the cutoff due to the anisotropic
dependence of the interaction. Angular velocities are all set to zero
initially. The Gay-Berne potential does not become isotropic as r
increases <A HREF = "#Everaers">(Everaers)</A>. The distance of closest approach
approximation becomes less accurate as the shape of ellipsoids becomes
more dissimilar (high aspect ratio particles).
increases <A HREF = "#Everaers">(Everaers)</A>. The distance-of-closest-approach
approximation used by the code becomes less accurate as the shape of
ellipsoids becomes more dissimilar (high-aspect-ratio particles).
</P>
<P><B>Related commands:</B>
</P>

3
doc/run.html
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@ -70,8 +70,7 @@ 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>, <A HREF = "fix_deform.html">fix
deform</A>, and <A HREF = "fix_indent.html">fix indent</A>. The
<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>

19
doc/shape.html
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@ -48,14 +48,15 @@ longer in x than in y or z and with a circular cross-section in yz.
Ellipsoids that are spherical can be defined by setting all 3 shape
components the same.
</P>
<P>I can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterik can be
used to set the mass for multiple atom types. This takes the form "*"
or "*n" or "n*" or "m*n". If N = the number of atom types, then an
asterik with no numeric values means all types from 1 to N. A leading
asterik means all types from 1 to n (inclusive). A trailing asterik
means all types from n to N (inclusive). A middle asterik means all
types from m to n (inclusive).
<P>The I index can be specified in one of two ways. An explicit numeric
value can be used, as in the 1st example above. Or a wild-card
asterik can be used to set the mass for multiple atom types. This
takes the form "*" or "*n" or "n*" or "m*n". If N = the number of
atom types, then an asterik with no numeric values means all types
from 1 to N. A leading asterik means all types from 1 to n
(inclusive). A trailing asterik means all types from n to N
(inclusive). A middle asterik means all types from m to n
(inclusive).
</P>
<P>A line in a data file that specifies shape uses the same format as the
arguments of the shape command in an input script, except that no
@ -63,7 +64,7 @@ wild-card asterik can be used. For example, under the "Shapes"
section of a data file, the line that corresponds to the 1st example
above would be listed as
</P>
<PRE>1 1.0
<PRE>1 1.0 1.0 1.0
</PRE>
<P><B>Restrictions:</B>
</P>