ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9614 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2013-03-07 21:22:06 +00:00
parent 4fd5028c19
commit bfa67dbdf8
16 changed files with 165 additions and 83 deletions
Download Patch File Download Diff File Expand all files Collapse all files

42
doc/Section_commands.html
View File

@ -456,14 +456,14 @@ potentials. Click on the style itself for a full description:
<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_mie.html">mie/cut</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam.html">meam</A></TD><TD ><A HREF = "pair_mie.html">mie/cut</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if
@ -509,19 +509,19 @@ package</A>.
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/opt</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/omp</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/opt</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm/omp</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear/omp</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_lubricate.html">lubricate/omp</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_peri.html">peri/pmb/omp</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_soft.html">soft/omp</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_table.html">table/omp</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl/omp</A></TD></TR>
<TR ALIGN="center"><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><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/omp</A>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/omp</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/omp</A></TD></TR>
<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>
</TD></TR></TABLE></DIV>
<HR>

6
doc/Section_commands.txt
View File

@ -729,12 +729,13 @@ potentials. Click on the style itself for a full description:
"lj/cut/coul/dsf"_pair_lj.html,
"lj/cut/coul/long"_pair_lj.html,
"lj/cut/coul/msm"_pair_lj.html,
"lj/long/coul/long"_pair_lj_long.html,
"lj/cut/tip4p/cut"_pair_lj.html,
"lj/cut/tip4p/long"_pair_lj.html,
"lj/long/tip4p/long"_pair_lj_long.html,
"lj/expand"_pair_lj_expand.html,
"lj/gromacs"_pair_gromacs.html,
"lj/gromacs/coul/gromacs"_pair_gromacs.html,
"lj/long/coul/long"_pair_lj_long.html,
"lj/long/tip4p/long"_pair_lj_long.html,
"lj/smooth"_pair_lj_smooth.html,
"lj/smooth/linear"_pair_lj_smooth_linear.html,
"lj96/cut"_pair_lj96.html,
@ -890,6 +891,7 @@ package"_Section_accelerate.html.
"lj/cut/gpu"_pair_lj.html,
"lj/cut/omp"_pair_lj.html,
"lj/cut/opt"_pair_lj.html,
"lj/cut/tip4p/cut/omp"_pair_lj.html,
"lj/cut/tip4p/long/omp"_pair_lj.html,
"lj/cut/tip4p/long/opt"_pair_lj.html,
"lj/expand/cuda"_pair_lj_expand.html,

8
doc/Section_errors.html
View File

@ -6398,16 +6398,16 @@ then a kspace style must also be used.
<DD>The atom style defined does not have this attribute.
<DT><I>Pair style lj/cut/coul/long/tip4p requires atom IDs</I>
<DT><I>Pair style lj/cut/tip4p/long requires atom IDs</I>
<DD>There are no atom IDs defined in the system and the TIP4P potential
requires them to find O,H atoms with a water molecule.
<DT><I>Pair style lj/cut/coul/long/tip4p requires atom attribute q</I>
<DT><I>Pair style lj/cut/tip4p/long requires atom attribute q</I>
<DD>The atom style defined does not have these attributes.
<DT><I>Pair style lj/cut/coul/long/tip4p requires newton pair on</I>
<DT><I>Pair style lj/cut/tip4p/long requires newton pair on</I>
<DD>This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors.
@ -8020,7 +8020,7 @@ variable doc page for ideas on how to make this work.
<DD>Self-explanatory.
<DT><I>Water H epsilon must be 0.0 for pair style lj/cut/coul/long/tip4p</I>
<DT><I>Water H epsilon must be 0.0 for pair style lj/cut/tip4p/long</I>
<DD>This is because LAMMPS does not compute the Lennard-Jones interactions
with these particles for efficiency reasons.

8
doc/Section_errors.txt
View File

@ -6394,16 +6394,16 @@ The atom style defined does not have this attribute. :dd
The atom style defined does not have this attribute. :dd
{Pair style lj/cut/coul/long/tip4p requires atom IDs} :dt
{Pair style lj/cut/tip4p/long requires atom IDs} :dt
There are no atom IDs defined in the system and the TIP4P potential
requires them to find O,H atoms with a water molecule. :dd
{Pair style lj/cut/coul/long/tip4p requires atom attribute q} :dt
{Pair style lj/cut/tip4p/long requires atom attribute q} :dt
The atom style defined does not have these attributes. :dd
{Pair style lj/cut/coul/long/tip4p requires newton pair on} :dt
{Pair style lj/cut/tip4p/long requires newton pair on} :dt
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors. :dd
@ -8016,7 +8016,7 @@ Self-explanatory. :dd
Self-explanatory. :dd
{Water H epsilon must be 0.0 for pair style lj/cut/coul/long/tip4p} :dt
{Water H epsilon must be 0.0 for pair style lj/cut/tip4p/long} :dt
This is because LAMMPS does not compute the Lennard-Jones interactions
with these particles for efficiency reasons. :dd

4
doc/Section_howto.html
View File

@ -498,7 +498,7 @@ angle style of <I>harmonic</I> or <I>charmm</I> should also be used.
</P>
<P>A TIP4P model is run with LAMMPS using two commands:
</P>
<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long/tip4p</A>
<UL><LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/long</A>
<LI><A HREF = "kspace_style.html">kspace_style pppm/tip4p</A>
</UL>
<P>Note that only a TIP4P model with long-range Coulombics is currently
@ -554,7 +554,7 @@ cutoff + 2*(OM distance), to shrink the size of the neighbor list.
This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the <A HREF = "pair_lj.html">pair_style
lj/cut/coul/long/tip4p</A> command.
lj/cut/tip4p/long</A> command.
</P>
<P>Wikipedia also has a nice article on <A HREF = "http://en.wikipedia.org/wiki/Water_model">water
models</A>.

4
doc/Section_howto.txt
View File

@ -493,7 +493,7 @@ angle style of {harmonic} or {charmm} should also be used.
A TIP4P model is run with LAMMPS using two commands:
"pair_style lj/cut/coul/long/tip4p"_pair_lj.html
"pair_style lj/cut/tip4p/long"_pair_lj.html
"kspace_style pppm/tip4p"_kspace_style.html :ul
Note that only a TIP4P model with long-range Coulombics is currently
@ -549,7 +549,7 @@ cutoff + 2*(OM distance), to shrink the size of the neighbor list.
This leads to slightly larger cost for the long-range calculation, so
you can test the trade-off for your model. The OM distance and the LJ
and Coulombic cutoffs are set in the "pair_style
lj/cut/coul/long/tip4p"_pair_lj.html command.
lj/cut/tip4p/long"_pair_lj.html command.
Wikipedia also has a nice article on "water
models"_http://en.wikipedia.org/wiki/Water_model.

2
doc/Section_python.html
View File

@ -165,7 +165,7 @@ which Python is invoked by root.
</P>
<P>Note that if you want Python to be able to load different versions of
the LAMMPS shared library (see <A HREF = "#py_5">this section</A> below), you will
need to manually copy files like lmplammps_g++.so into the appropriate
need to manually copy files like liblammps_g++.so into the appropriate
system directory. This is not needed if you set the LD_LIBRARY_PATH
environment variable as described above.
</P>

2
doc/Section_python.txt
View File

@ -161,7 +161,7 @@ which Python is invoked by root.
Note that if you want Python to be able to load different versions of
the LAMMPS shared library (see "this section"_#py_5 below), you will
need to manually copy files like lmplammps_g++.so into the appropriate
need to manually copy files like liblammps_g++.so into the appropriate
system directory. This is not needed if you set the LD_LIBRARY_PATH
environment variable as described above.

2
doc/kspace_style.html
View File

@ -127,7 +127,7 @@ or not. Its default value is 1.0e-5.
<P>The <I>pppm/tip4p</I> style is identical to the <I>pppm</I> style except that it
adds a charge at the massless 4th site in each TIP4P water molecule.
It should be used with <A HREF = "pair_style.html">pair styles</A> with a
<I>long/tip4p</I> in their style name.
<I>tip4p/long</I> in their style name.
</P>
<HR>

2
doc/kspace_style.txt
View File

@ -120,7 +120,7 @@ or not. Its default value is 1.0e-5.
The {pppm/tip4p} style is identical to the {pppm} style except that it
adds a charge at the massless 4th site in each TIP4P water molecule.
It should be used with "pair styles"_pair_style.html with a
{long/tip4p} in their style name.
{tip4p/long} in their style name.
:line

25
doc/pair_coeff.html
View File

@ -99,21 +99,27 @@ section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
</UL>
<UL><LI><A HREF = "pair_adp.html">pair_style adp</A> - angular dependent potential (ADP) of Mishin
<LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AIREBO potential of Stuart
<LI><A HREF = "pair_beck.html">pair_style beck</A> - Beck potential
<LI><A HREF = "pair_body.html">pair_style body</A> - interactions between body particles
<LI><A HREF = "pair_bop.html">pair_style bop</A> - BOP potential of Pettifor
<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulombics
<LI><A HREF = "pair_born.html">pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
<LI><A HREF = "pair_born.html<A HREF = "pair_born.html">>pair_style born/coul/msm</A> - Born-Mayer-Huggins with long-range MSM Coulombics
<LI>pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
<LI><A HREF = "pair_brownian.html">pair_style brownian</A> - Brownian potential for Fast Lubrication Dynamics
<LI><A HREF = "pair_brownian.html">pair_style brownian/poly</A> - Brownian potential for Fast Lubrication Dynamics with polydispersity
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckingham with cutoff Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulombics
<LI><A HREF = "pair_buck.html">pair_style buck/coul/msm</A> - Buckingham long-range MSM Coulombics
<LI><A HREF = "pair_buck.html">pair_style buck/long/coul/long</A> - long-range Buckingham with long-range Coulombics
<LI><A HREF = "pair_colloid.html">pair_style colloid</A> - integrated colloidal potential
<LI><A HREF = "pair_comb.html">pair_style comb</A> - charge-optimized many-body (COMB) potential
<LI><A HREF = "pair_coul.html">pair_style coul/cut</A> - cutoff Coulombic potential
<LI><A HREF = "pair_coul.html">pair_style coul/debye</A> - cutoff Coulombic potential with Debye screening
<LI><A HREF = "pair_coul.html">pair_style coul/dsf</A> - Coulombics via damped shifted forces
<LI><A HREF = "pair_coul.html">pair_style coul/long</A> - long-range Coulombic potential
<LI><A HREF = "pair_coul.html">pair_style coul/msm</A> - long-range MSM Coulombics
<LI><A HREF = "pair_coul.html">pair_style coul/wolf</A> - Coulombics via Wolf potential
<LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A> - point dipoles with cutoff
<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
@ -130,36 +136,43 @@ section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
<LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/lj</A> - DREIDING hydrogen bonding LJ potential
<LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/morse</A> - DREIDING hydrogen bonding Morse potential
<LI><A HREF = "pair_kim.html">pair_style kim</A> - interface to potentials provided by KIM project
<LI><A HREF = "pair_lcbop.html">pair_style lcbop</A> - long-range bond-order potential (LCBOP)
<LI><A HREF = "pair_line_lj.html">pair_style line/lj</A> - LJ potential between line segments
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/msm</A> - CHARMM with long-range MSM Coulombics
<LI><A HREF = "pair_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/long</A> - COMPASS with long-range Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut</A> - cutoff Lennard-Jones potential with no Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye screening added to Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long/tip4p</A> - LJ with long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/dsf</A> - LJ with Coulombics via damped shifted forces
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulombics
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/msm</A> - LJ with long-range MSM Coulombics
<LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/cut</A> - LJ with cutoff Coulomb for TIP4P water
<LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/long</A> - LJ with long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
<LI><A HREF = "pair_lj_long.html">pair_style lj/long/coul/long</A> - long-range LJ and long-range Coulombics
<LI><A HREF = "pair_lj_long.html">pair_style lj/long/tip4p/long</A> - long-range LJ and long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj_smooth_linear.html">pair_style lj/smooth/linear</A> - linear smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj96.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential
<LI><A HREF = "pair_lubricate.html">pair_style lubricate</A> - hydrodynamic lubrication forces
<LI><A HREF = "pair_lubricate.html">pair_style lubricate/poly</A> - hydrodynamic lubrication forces with polydispersity
<LI><A HREF = "pair_lubricateU.html">pair_style lubricateU</A> - hydrodynamic lubrication forces for Fast Lubrication Dynamics
<LI><A HREF = "pair_lubricateU.html">pair_style lubricateU/poly</A> - hydrodynamic lubrication forces for Fast Lubrication Dynamics with polydispersity
<LI><A HREF = "pair_lubricateU.html">pair_style lubricateU/poly</A> - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
<LI><A HREF = "pair_meam.html">pair_style meam</A> - modified embedded atom method (MEAM)
<LI><A HREF = "pair_mie.html">pair_style mie/cut</A> - Mie potential
<LI><A HREF = "pair_morse.html">pair_style morse</A> - Morse potential
<LI><A HREF = "pair_peri.html">pair_style peri/lps</A> - peridynamic LPS potential
<LI><A HREF = "pair_peri.html">pair_style peri/pmb</A> - peridynamic PMB potential
<LI><A HREF = "pair_reax.html">pair_style reax</A> - ReaxFF potential
<LI><A HREF = "pair_airebo.html">pair_style rebo</A> - 2nd-generation REBO potential of Brenner
<LI><A HREF = "pair_airebo.html">pair_style rebo</A> - 2nd generation REBO potential of Brenner
<LI><A HREF = "pair_resquared.html">pair_style resquared</A> - Everaers RE-Squared ellipsoidal potential
<LI><A HREF = "pair_soft.html">pair_style soft</A> - Soft (cosine) potential
<LI><A HREF = "pair_sw.html">pair_style sw</A> - Stillinger-Weber 3-body potential

25
doc/pair_coeff.txt
View File

@ -96,21 +96,27 @@ section of "this page"_Section_commands.html#cmd_5.
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
"pair_style beck"_pair_beck.html - Beck potential
"pair_style body"_pair_body.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics
"pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential
"pair_style born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics
pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential
"pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics
"pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics
"pair_style buck/coul/msm"_pair_buck.html - Buckingham long-range MSM Coulombics
"pair_style buck/long/coul/long"_pair_buck.html - long-range Buckingham with long-range Coulombics
"pair_style colloid"_pair_colloid.html - integrated colloidal potential
"pair_style comb"_pair_comb.html - charge-optimized many-body (COMB) potential
"pair_style coul/cut"_pair_coul.html - cutoff Coulombic potential
"pair_style coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
"pair_style coul/dsf"_pair_coul.html - Coulombics via damped shifted forces
"pair_style coul/long"_pair_coul.html - long-range Coulombic potential
"pair_style coul/msm"_pair_coul.html - long-range MSM Coulombics
"pair_style coul/wolf"_pair_coul.html - Coulombics via Wolf potential
"pair_style dipole/cut"_pair_dipole.html - point dipoles with cutoff
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
@ -127,36 +133,43 @@ section of "this page"_Section_commands.html#cmd_5.
"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential
"pair_style hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential
"pair_style kim"_pair_kim.html - interface to potentials provided by KIM project
"pair_style lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
"pair_style line/lj"_pair_line_lj.html - LJ potential between line segments
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
"pair_style lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics
"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
"pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
"pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
"pair_style lj/cut/coul/long/tip4p"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
"pair_style lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
"pair_style lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
"pair_style lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water
"pair_style lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
"pair_style lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
"pair_style lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics
"pair_style lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential
"pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
"pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
"pair_style lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
"pair_style lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics
"pair_style lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics with polydispersity
"pair_style lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
"pair_style mie/cut"_pair_mie.html - Mie potential
"pair_style morse"_pair_morse.html - Morse potential
"pair_style peri/lps"_pair_peri.html - peridynamic LPS potential
"pair_style peri/pmb"_pair_peri.html - peridynamic PMB potential
"pair_style reax"_pair_reax.html - ReaxFF potential
"pair_style rebo"_pair_airebo.html - 2nd-generation REBO potential of Brenner
"pair_style rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
"pair_style resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
"pair_style soft"_pair_soft.html - Soft (cosine) potential
"pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential

39
doc/pair_lj.html
View File

@ -55,6 +55,10 @@
</H3>
<H3>pair_style lj/cut/coul/msm/omp command
</H3>
<H3>pair_style lj/cut/tip4p/cut command
</H3>
<H3>pair_style lj/cut/tip4p/cut/omp command
</H3>
<H3>pair_style lj/cut/tip4p/long command
</H3>
<H3>pair_style lj/cut/tip4p/long/omp command
@ -87,6 +91,12 @@
<I>lj/cut/coul/msm</I> args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/tip4p/cut</I> args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
<I>lj/cut/tip4p/long</I> args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
@ -190,7 +200,9 @@ computed in reciprocal space.
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond
and angle types for OH and HOH interactions, and the distance to the
massless charge site are specified as pair_style arguments.
massless charge site are specified as pair_style arguments. Style
<I>lj/cut/tip4p/cut</I> is similar to <I>lj/cut/tip4p/long</I>, only it uses a
cutoff for Coulomb interactions.
</P>
<P>IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
IDs for the O and 2 H atoms must be consecutive, with the O atom
@ -208,11 +220,12 @@ LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the
neighbor list. This leads to slightly larger cost for the long-range
calculation, so you can test the trade-off for your model.
</P>
<P>The following coefficients must be defined for each pair of atoms
types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
above, or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below:
<P>For all of the <I>lj/cut</I> pair styles, the following coefficients must
be defined for each pair of atoms types via the
<A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above, or in
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
or <A HREF = "read_restart.html">read_restart</A> commands, or by mixing as
described below:
</P>
<UL><LI>epsilon (energy units)
<LI>sigma (distance units)
@ -267,7 +280,7 @@ and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is <I>geometric</I>. See the "pair_modify" command
for details.
</P>
<P>All of the lj/cut pair styles support the
<P>All of the <I>lj/cut</I> pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> shift option for the energy of the
Lennard-Jones portion of the pair interaction.
</P>
@ -275,16 +288,16 @@ Lennard-Jones portion of the pair interaction.
<A HREF = "pair_modify.html">pair_modify</A> table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
</P>
<P>All of the lj/cut pair styles support the
<P>All of the <I>lj/cut</I> pair styles support the
<A HREF = "pair_modify.html">pair_modify</A> tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.
</P>
<P>All of the lj/cut pair styles write their information to <A HREF = "restart.html">binary
<P>All of the <I>lj/cut</I> pair styles write their information to <A HREF = "restart.html">binary
restart files</A>, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
</P>
<P>The lj/cut and lj/cut/coul/long pair styles support the use of the
<P>The <I>lj/cut</I> and <I>lj/cut/coul/long</I> pair styles support the use of the
<I>inner</I>, <I>middle</I>, and <I>outer</I> keywords of the <A HREF = "run_style.html">run_style
respa</A> command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
@ -296,9 +309,11 @@ See the <A HREF = "run_style.html">run_style</A> command for details.
<P><B>Restrictions:</B>
</P>
<P>The <I>lj/cut/coul/long</I> and <I>lj/cut/tip4p/long</I> styles are part of the
KSPACE package. They are only enabled if LAMMPS was built with those
KSPACE package. The <I>lj/cut/tip4p/cut</I> style is part of the MOLECULE
package. These styles 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. Note that the KSPACE package is installed by default.
for more info. Note that the KSPACE and MOLECULE packages are
installed by default.
</P>
<P><B>Related commands:</B>
</P>

37
doc/pair_lj.txt
View File

@ -29,6 +29,8 @@ pair_style lj/cut/coul/long/opt command :h3
pair_style lj/cut/coul/long/omp command :h3
pair_style lj/cut/coul/msm command :h3
pair_style lj/cut/coul/msm/omp command :h3
pair_style lj/cut/tip4p/cut command :h3
pair_style lj/cut/tip4p/cut/omp command :h3
pair_style lj/cut/tip4p/long command :h3
pair_style lj/cut/tip4p/long/omp command :h3
pair_style lj/cut/tip4p/long/opt command :h3
@ -58,6 +60,12 @@ args = list of arguments for a particular style :ul
{lj/cut/coul/msm} args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/tip4p/cut} args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
qdist = distance from O atom to massless charge (distance units)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
{lj/cut/tip4p/long} args = otype htype btype atype qdist cutoff (cutoff2)
otype,htype = atom types for TIP4P O and H
btype,atype = bond and angle types for TIP4P waters
@ -161,7 +169,9 @@ Style {lj/cut/tip4p/long} implements the TIP4P water model of
short distance away from the oxygen atom along the bisector of the HOH
angle. The atomic types of the oxygen and hydrogen atoms, the bond
and angle types for OH and HOH interactions, and the distance to the
massless charge site are specified as pair_style arguments.
massless charge site are specified as pair_style arguments. Style
{lj/cut/tip4p/cut} is similar to {lj/cut/tip4p/long}, only it uses a
cutoff for Coulomb interactions.
IMPORTANT NOTE: For each TIP4P water molecule in your system, the atom
IDs for the O and 2 H atoms must be consecutive, with the O atom
@ -179,11 +189,12 @@ LJ cutoff >= Coulomb cutoff + 2*qdist, to shrink the size of the
neighbor list. This leads to slightly larger cost for the long-range
calculation, so you can test the trade-off for your model.
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below:
For all of the {lj/cut} pair styles, the following coefficients must
be defined for each pair of atoms types via the
"pair_coeff"_pair_coeff.html command as in the examples above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands, or by mixing as
described below:
epsilon (energy units)
sigma (distance units)
@ -238,7 +249,7 @@ and cutoff distance for all of the lj/cut pair styles can be mixed.
The default mix value is {geometric}. See the "pair_modify" command
for details.
All of the lj/cut pair styles support the
All of the {lj/cut} pair styles support the
"pair_modify"_pair_modify.html shift option for the energy of the
Lennard-Jones portion of the pair interaction.
@ -246,16 +257,16 @@ The {lj/cut/coul/long} and {lj/cut/tip4p/long} pair styles support the
"pair_modify"_pair_modify.html table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
All of the lj/cut pair styles support the
All of the {lj/cut} pair styles support the
"pair_modify"_pair_modify.html tail option for adding a long-range
tail correction to the energy and pressure for the Lennard-Jones
portion of the pair interaction.
All of the lj/cut pair styles write their information to "binary
All of the {lj/cut} pair styles write their information to "binary
restart files"_restart.html, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/cut and lj/cut/coul/long pair styles support the use of the
The {lj/cut} and {lj/cut/coul/long} pair styles support the use of the
{inner}, {middle}, and {outer} keywords of the "run_style
respa"_run_style.html command, meaning the pairwise forces can be
partitioned by distance at different levels of the rRESPA hierarchy.
@ -267,9 +278,11 @@ See the "run_style"_run_style.html command for details.
[Restrictions:]
The {lj/cut/coul/long} and {lj/cut/tip4p/long} styles are part of the
KSPACE package. They are only enabled if LAMMPS was built with those
KSPACE package. The {lj/cut/tip4p/cut} style is part of the MOLECULE
package. These styles are only enabled if LAMMPS was built with those
packages. See the "Making LAMMPS"_Section_start.html#start_3 section
for more info. Note that the KSPACE package is installed by default.
for more info. Note that the KSPACE and MOLECULE packages are
installed by default.
[Related commands:]

21
doc/pair_style.html
View File

@ -101,21 +101,27 @@ section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
</UL>
<UL><LI><A HREF = "pair_adp.html">pair_style adp</A> - angular dependent potential (ADP) of Mishin
<LI><A HREF = "pair_airebo.html">pair_style airebo</A> - AIREBO potential of Stuart
<LI><A HREF = "pair_beck.html">pair_style beck</A> - Beck potential
<LI><A HREF = "pair_body.html">pair_style body</A> - interactions between body particles
<LI><A HREF = "pair_bop.html">pair_style bop</A> - BOP potential of Pettifor
<LI><A HREF = "pair_born.html">pair_style born</A> - Born-Mayer-Huggins potential
<LI><A HREF = "pair_born.html">pair_style born/coul/long</A> - Born-Mayer-Huggins with long-range Coulombics
<LI><A HREF = "pair_born.html">pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
<LI><A HREF = "pair_born.html<A HREF = "pair_born.html">>pair_style born/coul/msm</A> - Born-Mayer-Huggins with long-range MSM Coulombics
<LI>pair_style born/coul/wolf</A> - Born-Mayer-Huggins with Coulombics via Wolf potential
<LI><A HREF = "pair_brownian.html">pair_style brownian</A> - Brownian potential for Fast Lubrication Dynamics
<LI><A HREF = "pair_brownian.html">pair_style brownian/poly</A> - Brownian potential for Fast Lubrication Dynamics with polydispersity
<LI><A HREF = "pair_buck.html">pair_style buck</A> - Buckingham potential
<LI><A HREF = "pair_buck.html">pair_style buck/coul/cut</A> - Buckingham with cutoff Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulomb
<LI><A HREF = "pair_buck.html">pair_style buck/coul/long</A> - Buckingham with long-range Coulombics
<LI><A HREF = "pair_buck.html">pair_style buck/coul/msm</A> - Buckingham long-range MSM Coulombics
<LI><A HREF = "pair_buck.html">pair_style buck/long/coul/long</A> - long-range Buckingham with long-range Coulombics
<LI><A HREF = "pair_colloid.html">pair_style colloid</A> - integrated colloidal potential
<LI><A HREF = "pair_comb.html">pair_style comb</A> - charge-optimized many-body (COMB) potential
<LI><A HREF = "pair_coul.html">pair_style coul/cut</A> - cutoff Coulombic potential
<LI><A HREF = "pair_coul.html">pair_style coul/debye</A> - cutoff Coulombic potential with Debye screening
<LI><A HREF = "pair_coul.html">pair_style coul/dsf</A> - Coulombics via damped shifted forces
<LI><A HREF = "pair_coul.html">pair_style coul/long</A> - long-range Coulombic potential
<LI><A HREF = "pair_coul.html">pair_style coul/msm</A> - long-range MSM Coulombics
<LI><A HREF = "pair_coul.html">pair_style coul/wolf</A> - Coulombics via Wolf potential
<LI><A HREF = "pair_dipole.html">pair_style dipole/cut</A> - point dipoles with cutoff
<LI><A HREF = "pair_dpd.html">pair_style dpd</A> - dissipative particle dynamics (DPD)
@ -132,22 +138,29 @@ section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
<LI><A HREF = "pair_gran.html">pair_style gran/hooke/history</A> - granular potential without history effects
<LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/lj</A> - DREIDING hydrogen bonding LJ potential
<LI><A HREF = "pair_hbond_dreiding.html">pair_style hbond/dreiding/morse</A> - DREIDING hydrogen bonding Morse potential
<LI><A HREF = "pair_kim.html">pair_style kim</A> - interface to potentials provided by KIM project
<LI><A HREF = "pair_lcbop.html">pair_style lcbop</A> - long-range bond-order potential (LCBOP)
<LI><A HREF = "pair_line_lj.html">pair_style line/lj</A> - LJ potential between line segments
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm</A> - CHARMM potential with cutoff Coulomb
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/charmm/implicit</A> - CHARMM for implicit solvent
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A> - CHARMM with long-range Coulomb
<LI><A HREF = "pair_charmm.html">pair_style lj/charmm/coul/msm</A> - CHARMM with long-range MSM Coulombics
<LI><A HREF = "pair_class2.html">pair_style lj/class2</A> - COMPASS (class 2) force field with no Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/cut</A> - COMPASS with cutoff Coulomb
<LI><A HREF = "pair_class2.html">pair_style lj/class2/coul/long</A> - COMPASS with long-range Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut</A> - cutoff Lennard-Jones potential with no Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/cut</A> - LJ with cutoff Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/debye</A> - LJ with Debye screening added to Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulomb
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long/tip4p</A> - LJ with long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/dsf</A> - LJ with Coulombics via damped shifted forces
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/long</A> - LJ with long-range Coulombics
<LI><A HREF = "pair_lj.html">pair_style lj/cut/coul/msm</A> - LJ with long-range MSM Coulombics
<LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/cut</A> - LJ with cutoff Coulomb for TIP4P water
<LI><A HREF = "pair_lj.html">pair_style lj/cut/tip4p/long</A> - LJ with long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj_expand.html">pair_style lj/expand</A> - Lennard-Jones for variable size particles
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs</A> - GROMACS-style Lennard-Jones potential
<LI><A HREF = "pair_gromacs.html">pair_style lj/gromacs/coul/gromacs</A> - GROMACS-style LJ and Coulombic potential
<LI><A HREF = "pair_lj_long.html">pair_style lj/long/coul/long</A> - long-range LJ and long-range Coulombics
<LI><A HREF = "pair_lj_long.html">pair_style lj/long/tip4p/long</A> - long-range LJ and long-range Coulomb for TIP4P water
<LI><A HREF = "pair_lj_smooth.html">pair_style lj/smooth</A> - smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj_smooth_linear.html">pair_style lj/smooth/linear</A> - linear smoothed Lennard-Jones potential
<LI><A HREF = "pair_lj96.html">pair_style lj96/cut</A> - Lennard-Jones 9/6 potential

21
doc/pair_style.txt
View File

@ -98,21 +98,27 @@ section of "this page"_Section_commands.html#cmd_5.
"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
"pair_style beck"_pair_beck.html - Beck potential
"pair_style body"_pair_body.html - interactions between body particles
"pair_style bop"_pair_bop.html - BOP potential of Pettifor
"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics
"pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential
"pair_style born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics
pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential
"pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics
"pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity
"pair_style buck"_pair_buck.html - Buckingham potential
"pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulomb
"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics
"pair_style buck/coul/msm"_pair_buck.html - Buckingham long-range MSM Coulombics
"pair_style buck/long/coul/long"_pair_buck.html - long-range Buckingham with long-range Coulombics
"pair_style colloid"_pair_colloid.html - integrated colloidal potential
"pair_style comb"_pair_comb.html - charge-optimized many-body (COMB) potential
"pair_style coul/cut"_pair_coul.html - cutoff Coulombic potential
"pair_style coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
"pair_style coul/dsf"_pair_coul.html - Coulombics via damped shifted forces
"pair_style coul/long"_pair_coul.html - long-range Coulombic potential
"pair_style coul/msm"_pair_coul.html - long-range MSM Coulombics
"pair_style coul/wolf"_pair_coul.html - Coulombics via Wolf potential
"pair_style dipole/cut"_pair_dipole.html - point dipoles with cutoff
"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
@ -129,22 +135,29 @@ section of "this page"_Section_commands.html#cmd_5.
"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential
"pair_style hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential
"pair_style kim"_pair_kim.html - interface to potentials provided by KIM project
"pair_style lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
"pair_style line/lj"_pair_line_lj.html - LJ potential between line segments
"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
"pair_style lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics
"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
"pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
"pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulomb
"pair_style lj/cut/coul/long/tip4p"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
"pair_style lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
"pair_style lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
"pair_style lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water
"pair_style lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
"pair_style lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
"pair_style lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics
"pair_style lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water
"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
"pair_style lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential
"pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential