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Merge remote branch 'lammps-ro/master' into lammps-icms

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Resolved Conflicts:
	tools/msi2lmp/src/WriteDataFile05.c
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Axel Kohlmeyer
2013-07-02 14:20:12 +02:00
parent 331054d64f 7206633474
commit 45ede15f1e
6 changed files with 53 additions and 14 deletions
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12
doc/Section_commands.html
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@ -535,12 +535,12 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm/omp</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf/omp</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear/omp</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly/omp</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline/omp</A></TD><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/omp</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_peri.html">peri/lps/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb/omp</A></TD><TD ><A HREF = "pair_airebo.html">rebo/omp</A></TD><TD ><A HREF = "pair_resquared.html">resquared/gpu</A></TD><TD ><A HREF = "pair_resquared.html">resquared/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft/omp</A></TD><TD ><A HREF = "pair_sw.html">sw/cuda</A></TD><TD ><A HREF = "pair_sw.html">sw/omp</A></TD><TD ><A HREF = "pair_table.html">table/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/cuda</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl/omp</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj/omp</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/gpu</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/gpu</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/omp</A>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/omp</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps/omp</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb/omp</A></TD><TD ><A HREF = "pair_airebo.html">rebo/omp</A></TD><TD ><A HREF = "pair_resquared.html">resquared/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared/omp</A></TD><TD ><A HREF = "pair_soft.html">soft/omp</A></TD><TD ><A HREF = "pair_sw.html">sw/cuda</A></TD><TD ><A HREF = "pair_sw.html">sw/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table/gpu</A></TD><TD ><A HREF = "pair_table.html">table/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/cuda</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/table/omp</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl/omp</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj/omp</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa/omp</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/gpu</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/omp</A>
</TD></TR></TABLE></DIV>
<HR>

2
doc/dihedral_fourier.html
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@ -20,7 +20,7 @@
<P><B>Examples:</B>
</P>
<PRE>dihedral_style fourier
dihedral_coeff 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
</PRE>
<P><B>Description:</B>
</P>

13
doc/pair_coeff.html
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@ -96,10 +96,17 @@ directory specified by the LAMMPS_POTENTIALS environment variable.
Thus if this is set to the potentials directory in the LAMMPS distro,
then you can use those files from anywhere on your system, without
copying them into your working directory. Environment variables are
set in different ways for different shells. For example, in tcsh, you
could type the following or put it in your .cshrc file:
set in different ways for different shells. Here are example settings
for
</P>
<PRE>% setenv LAMMPS_POTENTIALS /home/users/plimpton/lammps/potentials
<PRE>csh, tcsh:
% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials
</PRE>
<PRE>bash:
% export LAMMPS_POTENTIALS=/path/to/lammps/potentials
</PRE>
<PRE>Windows:
% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials
</PRE>
<HR>

13
doc/pair_coeff.txt
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@ -93,10 +93,17 @@ directory specified by the LAMMPS_POTENTIALS environment variable.
Thus if this is set to the potentials directory in the LAMMPS distro,
then you can use those files from anywhere on your system, without
copying them into your working directory. Environment variables are
set in different ways for different shells. For example, in tcsh, you
could type the following or put it in your .cshrc file:
set in different ways for different shells. Here are example settings
for
% setenv LAMMPS_POTENTIALS /home/users/plimpton/lammps/potentials :pre
csh, tcsh:
% setenv LAMMPS_POTENTIALS /path/to/lammps/potentials :pre
bash:
% export LAMMPS_POTENTIALS=/path/to/lammps/potentials :pre
Windows:
% set LAMMPS_POTENTIALS="C:\Path to LAMMPS\Potentials :pre
:line

3
doc/pair_list.html
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@ -50,7 +50,8 @@ Morse and a harmonic potential.
<LI>empty lines will be ignored
<LI>comment text starts with a '#' character
line syntax: ID1 ID2 style coeffs cutoff
<LI>line syntax: <I>ID1 ID2 style coeffs cutoff</I>
<PRE> ID1 = atom ID of first atom
ID2 = atom ID of second atom

24
doc/pair_nb3b_harmonic.html
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@ -11,6 +11,8 @@
<H3>pair_style nb3b/harmonic command
</H3>
<H3>pair_style nb3b/harmonic/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style nb3b/harmonic
@ -89,6 +91,28 @@ simulation; LAMMPS ignores those entries.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
the same as the corresponding style without the suffix. They have
been optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>This pair style can only be used if LAMMPS was built with the