forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13198 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
42adc21fe0
commit
3c499e7896
Binary file not shown.
|
After Width: | Height: | Size: 3.4 KiB |
|
|
@ -0,0 +1,9 @@
|
|||
\documentstyle[12pt]{article}
|
||||
|
||||
\begin{document}
|
||||
|
||||
$$
|
||||
E = \frac{C q_i q_j}{\epsilon (r + r_{min})} \qquad r \rightarrow 0
|
||||
$$
|
||||
|
||||
\end{document}
|
||||
|
|
@ -449,9 +449,9 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
<TR ALIGN="center"><TD ><A HREF = "compute_msd_chunk.html">msd/chunk</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe (c)</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure (c)</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_chunk.html">property/chunk</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_sna.html">sna/atom</A></TD><TD ><A HREF = "compute_sna.html">snad/atom</A></TD><TD ><A HREF = "compute_sna.html">snav/atom</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (c)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp (c)</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_chunk.html">temp/chunk</A></TD><TD ><A HREF = "compute_temp_cs.html">temp/cs</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial (c)</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_torque_chunk.html">torque/chunk</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_vcm_chunk.html">vcm/chunk</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>These are additional compute styles in USER packages, which can be
|
||||
|
|
@ -478,30 +478,31 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo (o)</A></TD><TD ><A HREF = "pair_beck.html">beck (go)</A></TD><TD ><A HREF = "pair_body.html">body</A></TD><TD ><A HREF = "pair_bop.html">bop</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born (go)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long (cgo)</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm (o)</A></TD><TD ><A HREF = "pair_born.html">born/coul/wolf (go)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_brownian.html">brownian (o)</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly (o)</A></TD><TD ><A HREF = "pair_buck.html">buck (cgko)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut (cgo)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long (cgo)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/msm (o)</A></TD><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long (o)</A></TD><TD ><A HREF = "pair_colloid.html">colloid (go)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_comb.html">comb (o)</A></TD><TD ><A HREF = "pair_comb.html">comb3</A></TD><TD ><A HREF = "pair_coul.html">coul/cut (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/debye (go)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/dsf (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/long (go)</A></TD><TD ><A HREF = "pair_coul.html">coul/msm</A></TD><TD ><A HREF = "pair_coul.html">coul/streitz</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/wolf (ko)</A></TD><TD ><A HREF = "pair_dpd.html">dpd (o)</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat (o)</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam (cgkot)</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy (cgot)</A></TD><TD ><A HREF = "pair_eam.html">eam/fs (cgot)</A></TD><TD ><A HREF = "pair_eim.html">eim (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gauss.html">gauss (go)</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne (gio)</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history (o)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke (co)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke/history (o)</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj (o)</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse (o)</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lcbop.html">lcbop</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj (o)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm (co)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit (co)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long (cgio)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2 (cgo)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut (co)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long (cgo)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgo)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (go)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgo)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgo)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (co)</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD><TD ><A HREF = "pair_dipole.html">lj/long/dipole/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 (co)</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</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 (o)</A></TD><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/eps</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD><TD ><A HREF = "pair_snap.html">snap</A></TD><TD ><A HREF = "pair_soft.html">soft (go)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw (cgio)</A></TD><TD ><A HREF = "pair_table.html">table (gko)</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff (co)</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (o)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD><TD ><A HREF = "pair_zbl.html">zbl (o)</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born (go)</A></TD><TD ><A HREF = "pair_born.html">born/coul/long (cgo)</A></TD><TD ><A HREF = "pair_cs.html">born/coul/long/cs</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/wolf (go)</A></TD><TD ><A HREF = "pair_brownian.html">brownian (o)</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly (o)</A></TD><TD ><A HREF = "pair_buck.html">buck (cgko)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut (cgo)</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long (cgo)</A></TD><TD ><A HREF = "pair_cs.html">buck/coul/long/cs</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/msm (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long (o)</A></TD><TD ><A HREF = "pair_colloid.html">colloid (go)</A></TD><TD ><A HREF = "pair_comb.html">comb (o)</A></TD><TD ><A HREF = "pair_comb.html">comb3</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/debye (go)</A></TD><TD ><A HREF = "pair_coul.html">coul/dsf (gko)</A></TD><TD ><A HREF = "pair_coul.html">coul/long (go)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/msm</A></TD><TD ><A HREF = "pair_coul.html">coul/streitz</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf (ko)</A></TD><TD ><A HREF = "pair_dpd.html">dpd (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd/tstat (o)</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam (cgkot)</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy (cgot)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs (cgot)</A></TD><TD ><A HREF = "pair_eim.html">eim (o)</A></TD><TD ><A HREF = "pair_gauss.html">gauss (go)</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne (gio)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hertz/history (o)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke (co)</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history (o)</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse (o)</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD><TD ><A HREF = "pair_lcbop.html">lcbop</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm (co)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit (co)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long (cgio)</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2 (cgo)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut (co)</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long (cgo)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut (cgikot)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut (cgko)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye (cgo)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf (go)</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long (cgikot)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut (go)</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long (ot)</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand (cgo)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs (cgo)</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs (co)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long (o)</A></TD><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth (co)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear (o)</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut (cgo)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate (o)</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><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 (o)</A></TD><TD ><A HREF = "pair_mie.html">mie/cut (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse (cgot)</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut (o)</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/coul/long (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/eps</A></TD><TD ><A HREF = "pair_peri.html">peri/lps (o)</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo (o)</A></TD><TD ><A HREF = "pair_resquared.html">resquared (go)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_snap.html">snap</A></TD><TD ><A HREF = "pair_soft.html">soft (go)</A></TD><TD ><A HREF = "pair_sw.html">sw (cgio)</A></TD><TD ><A HREF = "pair_table.html">table (gko)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff (co)</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod (o)</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl (o)</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut (o)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/long (o)</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj (o)</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa (go)</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid (go)</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_zbl.html">zbl (o)</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<P>These are additional pair styles in USER packages, which can be used
|
||||
|
|
|
|||
|
|
@ -681,6 +681,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
"temp/asphere"_compute_temp_asphere.html,
|
||||
"temp/com"_compute_temp_com.html,
|
||||
"temp/chunk"_compute_temp_chunk.html,
|
||||
"temp/cs"_compute_temp_cs.html,
|
||||
"temp/deform"_compute_temp_deform.html,
|
||||
"temp/partial (c)"_compute_temp_partial.html,
|
||||
"temp/profile"_compute_temp_profile.html,
|
||||
|
|
@ -732,6 +733,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
"bop"_pair_bop.html,
|
||||
"born (go)"_pair_born.html,
|
||||
"born/coul/long (cgo)"_pair_born.html,
|
||||
"born/coul/long/cs"_pair_cs.html,
|
||||
"born/coul/msm (o)"_pair_born.html,
|
||||
"born/coul/wolf (go)"_pair_born.html,
|
||||
"brownian (o)"_pair_brownian.html,
|
||||
|
|
@ -739,6 +741,7 @@ KOKKOS, o = USER-OMP, t = OPT.
|
|||
"buck (cgko)"_pair_buck.html,
|
||||
"buck/coul/cut (cgo)"_pair_buck.html,
|
||||
"buck/coul/long (cgo)"_pair_buck.html,
|
||||
"buck/coul/long/cs"_pair_cs.html,
|
||||
"buck/coul/msm (o)"_pair_buck.html,
|
||||
"buck/long/coul/long (o)"_pair_buck_long.html,
|
||||
"colloid (go)"_pair_colloid.html,
|
||||
|
|
|
|||
|
|
@ -36,7 +36,8 @@
|
|||
6.21 <A HREF = "#howto_21">Calculating viscosity</A><BR>
|
||||
6.22 <A HREF = "#howto_22">Calculating a diffusion coefficient</A><BR>
|
||||
6.23 <A HREF = "#howto_23">Using chunks to calculate system properties</A><BR>
|
||||
6.24 <A HREF = "#howto_24">Setting parameters for the kspace_style pppm/disp command</A> <BR>
|
||||
6.24 <A HREF = "#howto_24">Setting parameters for the kspace_style pppm/disp command</A><BR>
|
||||
6.25 <A HREF = "#howto_25">Adiabatic core/shell model</A> <BR>
|
||||
|
||||
<P>The example input scripts included in the LAMMPS distribution and
|
||||
highlighted in <A HREF = "Section_example.html">Section_example</A> also show how to
|
||||
|
|
@ -2418,6 +2419,191 @@ to specify this command explicitly.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "howto_25"></A><H4>6.25 Adiabatic core/shell model
|
||||
</H4>
|
||||
<P>The adiabatic core-shell model by <A HREF = "#MitchellFinchham">Mitchell and
|
||||
Finchham</A> is a simple method for adding
|
||||
polarizability to a system. In order to mimic the electron shell of
|
||||
an ion, a ghost atom is attached to it. This way the ions are split
|
||||
into a core and a shell where the latter is meant to react to the
|
||||
electrostatic environment inducing polarizability.
|
||||
</P>
|
||||
<P>Technically, shells are attached to the cores by a spring force f =
|
||||
k*r where k is a parametrized spring constant and r is the distance
|
||||
between the core and the shell. The charges of the core and the shell
|
||||
add up to the ion charge, thus q(ion) = q(core) + q(shell). In a
|
||||
similar fashion the mass of the ion is distributed on the core and the
|
||||
shell with the core having the larger mass.
|
||||
</P>
|
||||
<P>To run this model in LAMMPS, <A HREF = "atom_style.html">atom_style</A> <I>full</I> can
|
||||
be used since atom charge and bonds are needed. Each kind of
|
||||
core/shell pair requires two atom types and a bond type. The core and
|
||||
shell of a core/shell pair should be bonded to each other with a
|
||||
harmonic bond that provides the spring force. For example, a data file
|
||||
for NaCl, as found in examples/coreshell, has this format:
|
||||
</P>
|
||||
<PRE>432 atoms # core and shell atoms
|
||||
216 bonds # number of core/shell springs
|
||||
</PRE>
|
||||
<PRE>4 atom types # 2 cores and 2 shells for Na and Cl
|
||||
2 bond types
|
||||
</PRE>
|
||||
<PRE>0.0 24.09597 xlo xhi
|
||||
0.0 24.09597 ylo yhi
|
||||
0.0 24.09597 zlo zhi
|
||||
</PRE>
|
||||
<PRE>Masses # core/shell mass ratio = 0.1
|
||||
</PRE>
|
||||
<PRE>1 20.690784 # Na core
|
||||
2 31.90500 # Cl core
|
||||
3 2.298976 # Na shell
|
||||
4 3.54500 # Cl shell
|
||||
</PRE>
|
||||
<PRE>Atoms
|
||||
</PRE>
|
||||
<PRE>1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
|
||||
2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
|
||||
3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
|
||||
4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
|
||||
(...)
|
||||
</PRE>
|
||||
<PRE>Bonds # Bond topology for spring forces
|
||||
</PRE>
|
||||
<PRE>1 2 1 2 # spring for core/shell pair 1
|
||||
2 2 3 4 # spring for core/shell pair 2
|
||||
(...)
|
||||
</PRE>
|
||||
<P>Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
|
||||
defined between the shells. Coulombic interactions are defined
|
||||
between all cores and shells. If desired, additional bonds can be
|
||||
specified between cores.
|
||||
</P>
|
||||
<P>The <A HREF = "special_bonds.html">special_bonds</A> command should be used to
|
||||
turn-off the Coulombic interaction within core/shell pairs, since that
|
||||
interaction is set by the bond spring. This is done using the
|
||||
<A HREF = "special_bonds.html">special_bonds</A> command with a 1-2 weight = 0.0,
|
||||
which is the default value.
|
||||
</P>
|
||||
<P>Since the core/shell model permits distances of r = 0.0 between the
|
||||
core and shell, a pair style with a "cs" suffix needs to be used to
|
||||
implement a valid long-range Coulombic correction. Several such pair
|
||||
styles are provided in the CORESHELL package. See <A HREF = "pair_cs.html">this doc
|
||||
page</A> for details. All of the core/shell enabled pair
|
||||
styles require the use of a long-range Coulombic solver, as specified
|
||||
by the <A HREF = "kspace_style.html">kspace_style</A> command. Either the PPPM or
|
||||
Ewald solvers can be used.
|
||||
</P>
|
||||
<P>For the NaCL example problem, these pair style and bond style settings
|
||||
are used:
|
||||
</P>
|
||||
<PRE>pair_style born/coul/long/cs 20.0 20.0
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
|
||||
</PRE>
|
||||
<PRE>bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0
|
||||
</PRE>
|
||||
<P>When running dynamics with the adiabatic core/shell model, the
|
||||
following issues should be considered. Since the relative motion of
|
||||
the core and shell particles corresponds to the polarization, typical
|
||||
thermostats can alter the polarization behaviour, meaining the shell
|
||||
will not react freely to its electrostatic environment. Therefore
|
||||
it's typically desirable to decouple the relative motion of the
|
||||
core/shell pair, which is an imaginary degree of freedom, from the
|
||||
real physical system. To do that, the <A HREF = "compute_temp_cs.html">compute
|
||||
temp/cs</A> command can be used, in conjunction with
|
||||
any of the thermostat fixes, such as <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin">fix
|
||||
langevin</A>. This compute uses the center-of-mass velocity
|
||||
of the core/shell pairs to calculate a temperature, and insures that
|
||||
velocity is what is rescaled for thermostatting purposes. The
|
||||
<A HREF = "compute_temp_cs.html">compute temp/cs</A> command requires input of two
|
||||
groups, one for the core atoms, another for the shell atoms. These
|
||||
can be defined using the <A HREF = "group.html">group <I>type</I></A> command. Note that
|
||||
to perform thermostatting using this definition of temperature, the
|
||||
<A HREF = "fix_modify.html">fix modify temp</A> command should be used to assign the
|
||||
comptue to the thermostat fix. Likewise the <A HREF = "thermo_modify.html">thermo_modify
|
||||
temp</A> command can be used to make this temperature
|
||||
be output for the overall system.
|
||||
</P>
|
||||
<P>For the NaCl example, this can be done as follows:
|
||||
</P>
|
||||
<PRE>group cores type 1 2
|
||||
group shells type 3 4
|
||||
compute CSequ all temp/cs cores shells
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
|
||||
fix thermostatequ all nve # integrator as needed for the berendsen thermostat
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
thermo_modify temp CSequ # output of center-of-mass derived temperature
|
||||
</PRE>
|
||||
<P>When intializing the velocities of a system with core/shell pairs, it
|
||||
is also desirable to not introduce energy into the relative motion of
|
||||
the core/shell particles, but only assign a center-of-mass velocity to
|
||||
the pairs. This can be done by using the <I>bias</I> keyword of the
|
||||
<A HREF = "velocity.html">velocity create</A> command and assigning the <A HREF = "compute_temp_cs.html">compute
|
||||
temp/cs</A> command to the <I>temp</I> keyword of the
|
||||
<A HREF = "velocity.html">velocity</A> commmand, e.g.
|
||||
</P>
|
||||
<PRE>velocity all create 1427 134 bias yes temp CSequ
|
||||
velocity all scale 1427 temp CSequ
|
||||
</PRE>
|
||||
<P>It is important to note that the polarizability of the core/shell
|
||||
pairs is based on their relative motion. Therefore the choice of
|
||||
spring force and mass ratio need to ensure much faster relative motion
|
||||
of the 2 atoms within the core/shell pair than their center-of-mass
|
||||
velocity. This allow the shells to effectively react instantaneously
|
||||
to the electrostatic environment. This fast movement also limits the
|
||||
timestep size that can be used.
|
||||
</P>
|
||||
<P>Additionally, the mass mismatch of the core and shell particles means
|
||||
that only a small amount of energy is transfered to the decoupled
|
||||
imaginary degrees of freedom. However, this transfer will typically
|
||||
lead to a a small drift in total energy over time. This internal
|
||||
energy can be monitored using the <A HREF = "compute_chunk_atom.html">compute
|
||||
chunk/atom</A> and <A HREF = "compute_temp_chunk.html">compute
|
||||
temp/chunk</A> commands. The internal kinetic
|
||||
energies of each core/shell pair can then be summed using the sum()
|
||||
special functino of the <A HREF = "variable.html">variable</A> command. Or they can
|
||||
be time/averaged and output using the <A HREF = "fix_ave_time.html">fix ave/time</A>
|
||||
command. To use these commands, each core/shell pair must be defined
|
||||
as a "chunk". If each core/shell pair is defined as its own molecule,
|
||||
the molecule ID can be used to define the chunks. If cores are bonded
|
||||
to each other to form larger molecules, then another way to define the
|
||||
chunks is to use the <A HREF = "fix_property_atom.html">fix property/atom</A> to
|
||||
assign a core/shell ID to each atom via a special field in the data
|
||||
file read by the <A HREF = "read_data.html">read_data</A> command. This field can
|
||||
then be accessed by the <A HREF = "compute_property_atom.html">compute
|
||||
property/atom</A> command, to use as input to
|
||||
the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command to define the
|
||||
core/shell pairs as chunks.
|
||||
</P>
|
||||
<P>For example,
|
||||
</P>
|
||||
<PRE>fix csinfo all property/atom i_CSID # property/atom command
|
||||
read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
|
||||
compute prop all property/atom i_CSID
|
||||
compute cs_chunk all chunk/atom c_prop
|
||||
compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
|
||||
fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
|
||||
</PRE>
|
||||
<P>The additional section in the date file would be formatted like this:
|
||||
</P>
|
||||
<PRE>CS-Info # header of additional section
|
||||
</PRE>
|
||||
<PRE>1 1 # column 1 = atom ID, column 2 = core/shell ID
|
||||
2 1
|
||||
3 2
|
||||
4 2
|
||||
5 3
|
||||
6 3
|
||||
7 4
|
||||
8 4
|
||||
(...)
|
||||
</PRE>
|
||||
<HR>
|
||||
|
||||
<HR>
|
||||
|
||||
<A NAME = "Berendsen"></A>
|
||||
|
|
@ -2463,4 +2649,9 @@ Phys, 79, 926 (1983).
|
|||
|
||||
<P><B>(Shinoda)</B> Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
||||
</P>
|
||||
<A NAME = "MitchellFinchham"></A>
|
||||
|
||||
<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
|
||||
5, 1031-1038 (1993).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -33,7 +33,8 @@ This section describes how to perform common tasks using LAMMPS.
|
|||
6.21 "Calculating viscosity"_#howto_21
|
||||
6.22 "Calculating a diffusion coefficient"_#howto_22
|
||||
6.23 "Using chunks to calculate system properties"_#howto_23
|
||||
6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24 :all(b)
|
||||
6.24 "Setting parameters for the kspace_style pppm/disp command"_#howto_24
|
||||
6.25 "Adiabatic core/shell model"_#howto_25 :all(b)
|
||||
|
||||
The example input scripts included in the LAMMPS distribution and
|
||||
highlighted in "Section_example"_Section_example.html also show how to
|
||||
|
|
@ -2401,6 +2402,191 @@ Note that the code does not check automatically whether any mixing
|
|||
rule is fulfilled. If mixing rules do not apply, the user will have
|
||||
to specify this command explicitly.
|
||||
|
||||
:line
|
||||
|
||||
6.25 Adiabatic core/shell model :link(howto_25),h4
|
||||
|
||||
The adiabatic core-shell model by "Mitchell and
|
||||
Finchham"_#MitchellFinchham is a simple method for adding
|
||||
polarizability to a system. In order to mimic the electron shell of
|
||||
an ion, a ghost atom is attached to it. This way the ions are split
|
||||
into a core and a shell where the latter is meant to react to the
|
||||
electrostatic environment inducing polarizability.
|
||||
|
||||
Technically, shells are attached to the cores by a spring force f =
|
||||
k*r where k is a parametrized spring constant and r is the distance
|
||||
between the core and the shell. The charges of the core and the shell
|
||||
add up to the ion charge, thus q(ion) = q(core) + q(shell). In a
|
||||
similar fashion the mass of the ion is distributed on the core and the
|
||||
shell with the core having the larger mass.
|
||||
|
||||
To run this model in LAMMPS, "atom_style"_atom_style.html {full} can
|
||||
be used since atom charge and bonds are needed. Each kind of
|
||||
core/shell pair requires two atom types and a bond type. The core and
|
||||
shell of a core/shell pair should be bonded to each other with a
|
||||
harmonic bond that provides the spring force. For example, a data file
|
||||
for NaCl, as found in examples/coreshell, has this format:
|
||||
|
||||
432 atoms # core and shell atoms
|
||||
216 bonds # number of core/shell springs :pre
|
||||
|
||||
4 atom types # 2 cores and 2 shells for Na and Cl
|
||||
2 bond types :pre
|
||||
|
||||
0.0 24.09597 xlo xhi
|
||||
0.0 24.09597 ylo yhi
|
||||
0.0 24.09597 zlo zhi :pre
|
||||
|
||||
Masses # core/shell mass ratio = 0.1 :pre
|
||||
|
||||
1 20.690784 # Na core
|
||||
2 31.90500 # Cl core
|
||||
3 2.298976 # Na shell
|
||||
4 3.54500 # Cl shell :pre
|
||||
|
||||
Atoms :pre
|
||||
|
||||
1 1 2 1.5005 0.00000000 0.00000000 0.00000000 # core of core/shell pair 1
|
||||
2 1 4 -2.5005 0.00000000 0.00000000 0.00000000 # shell of core/shell pair 1
|
||||
3 2 1 1.5056 4.01599500 4.01599500 4.01599500 # core of core/shell pair 2
|
||||
4 2 3 -0.5056 4.01599500 4.01599500 4.01599500 # shell of core/shell pair 2
|
||||
(...) :pre
|
||||
|
||||
Bonds # Bond topology for spring forces :pre
|
||||
|
||||
1 2 1 2 # spring for core/shell pair 1
|
||||
2 2 3 4 # spring for core/shell pair 2
|
||||
(...) :pre
|
||||
|
||||
Non-Coulombic (e.g. Lennard-Jones) pairwise interactions are only
|
||||
defined between the shells. Coulombic interactions are defined
|
||||
between all cores and shells. If desired, additional bonds can be
|
||||
specified between cores.
|
||||
|
||||
The "special_bonds"_special_bonds.html command should be used to
|
||||
turn-off the Coulombic interaction within core/shell pairs, since that
|
||||
interaction is set by the bond spring. This is done using the
|
||||
"special_bonds"_special_bonds.html command with a 1-2 weight = 0.0,
|
||||
which is the default value.
|
||||
|
||||
Since the core/shell model permits distances of r = 0.0 between the
|
||||
core and shell, a pair style with a "cs" suffix needs to be used to
|
||||
implement a valid long-range Coulombic correction. Several such pair
|
||||
styles are provided in the CORESHELL package. See "this doc
|
||||
page"_pair_cs.html for details. All of the core/shell enabled pair
|
||||
styles require the use of a long-range Coulombic solver, as specified
|
||||
by the "kspace_style"_kspace_style.html command. Either the PPPM or
|
||||
Ewald solvers can be used.
|
||||
|
||||
For the NaCL example problem, these pair style and bond style settings
|
||||
are used:
|
||||
|
||||
pair_style born/coul/long/cs 20.0 20.0
|
||||
pair_coeff * * 0.0 1.000 0.00 0.00 0.00
|
||||
pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
|
||||
pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
|
||||
pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl :pre
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 63.014 0.0
|
||||
bond_coeff 2 25.724 0.0 :pre
|
||||
|
||||
When running dynamics with the adiabatic core/shell model, the
|
||||
following issues should be considered. Since the relative motion of
|
||||
the core and shell particles corresponds to the polarization, typical
|
||||
thermostats can alter the polarization behaviour, meaining the shell
|
||||
will not react freely to its electrostatic environment. Therefore
|
||||
it's typically desirable to decouple the relative motion of the
|
||||
core/shell pair, which is an imaginary degree of freedom, from the
|
||||
real physical system. To do that, the "compute
|
||||
temp/cs"_compute_temp_cs.html command can be used, in conjunction with
|
||||
any of the thermostat fixes, such as "fix nvt"_fix_nh.html or "fix
|
||||
langevin"_fix_langevin. This compute uses the center-of-mass velocity
|
||||
of the core/shell pairs to calculate a temperature, and insures that
|
||||
velocity is what is rescaled for thermostatting purposes. The
|
||||
"compute temp/cs"_compute_temp_cs.html command requires input of two
|
||||
groups, one for the core atoms, another for the shell atoms. These
|
||||
can be defined using the "group {type}"_group.html command. Note that
|
||||
to perform thermostatting using this definition of temperature, the
|
||||
"fix modify temp"_fix_modify.html command should be used to assign the
|
||||
comptue to the thermostat fix. Likewise the "thermo_modify
|
||||
temp"_thermo_modify.html command can be used to make this temperature
|
||||
be output for the overall system.
|
||||
|
||||
For the NaCl example, this can be done as follows:
|
||||
|
||||
group cores type 1 2
|
||||
group shells type 3 4
|
||||
compute CSequ all temp/cs cores shells
|
||||
fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
|
||||
fix thermostatequ all nve # integrator as needed for the berendsen thermostat
|
||||
fix_modify thermoberendsen temp CSequ
|
||||
thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
|
||||
|
||||
When intializing the velocities of a system with core/shell pairs, it
|
||||
is also desirable to not introduce energy into the relative motion of
|
||||
the core/shell particles, but only assign a center-of-mass velocity to
|
||||
the pairs. This can be done by using the {bias} keyword of the
|
||||
"velocity create"_velocity.html command and assigning the "compute
|
||||
temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
|
||||
"velocity"_velocity.html commmand, e.g.
|
||||
|
||||
velocity all create 1427 134 bias yes temp CSequ
|
||||
velocity all scale 1427 temp CSequ :pre
|
||||
|
||||
It is important to note that the polarizability of the core/shell
|
||||
pairs is based on their relative motion. Therefore the choice of
|
||||
spring force and mass ratio need to ensure much faster relative motion
|
||||
of the 2 atoms within the core/shell pair than their center-of-mass
|
||||
velocity. This allow the shells to effectively react instantaneously
|
||||
to the electrostatic environment. This fast movement also limits the
|
||||
timestep size that can be used.
|
||||
|
||||
Additionally, the mass mismatch of the core and shell particles means
|
||||
that only a small amount of energy is transfered to the decoupled
|
||||
imaginary degrees of freedom. However, this transfer will typically
|
||||
lead to a a small drift in total energy over time. This internal
|
||||
energy can be monitored using the "compute
|
||||
chunk/atom"_compute_chunk_atom.html and "compute
|
||||
temp/chunk"_compute_temp_chunk.html commands. The internal kinetic
|
||||
energies of each core/shell pair can then be summed using the sum()
|
||||
special functino of the "variable"_variable.html command. Or they can
|
||||
be time/averaged and output using the "fix ave/time"_fix_ave_time.html
|
||||
command. To use these commands, each core/shell pair must be defined
|
||||
as a "chunk". If each core/shell pair is defined as its own molecule,
|
||||
the molecule ID can be used to define the chunks. If cores are bonded
|
||||
to each other to form larger molecules, then another way to define the
|
||||
chunks is to use the "fix property/atom"_fix_property_atom.html to
|
||||
assign a core/shell ID to each atom via a special field in the data
|
||||
file read by the "read_data"_read_data.html command. This field can
|
||||
then be accessed by the "compute
|
||||
property/atom"_compute_property_atom.html command, to use as input to
|
||||
the "compute chunk/atom"_compute_chunk_atom.html command to define the
|
||||
core/shell pairs as chunks.
|
||||
|
||||
For example,
|
||||
|
||||
fix csinfo all property/atom i_CSID # property/atom command
|
||||
read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
|
||||
compute prop all property/atom i_CSID
|
||||
compute cs_chunk all chunk/atom c_prop
|
||||
compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
|
||||
fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector :pre
|
||||
|
||||
The additional section in the date file would be formatted like this:
|
||||
|
||||
CS-Info # header of additional section :pre
|
||||
|
||||
1 1 # column 1 = atom ID, column 2 = core/shell ID
|
||||
2 1
|
||||
3 2
|
||||
4 2
|
||||
5 3
|
||||
6 3
|
||||
7 4
|
||||
8 4
|
||||
(...) :pre
|
||||
|
||||
:line
|
||||
:line
|
||||
|
||||
|
|
@ -2437,3 +2623,7 @@ Phys, 79, 926 (1983).
|
|||
|
||||
:link(Shinoda)
|
||||
[(Shinoda)] Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
|
||||
|
||||
:link(MitchellFinchham)
|
||||
[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
|
||||
5, 1031-1038 (1993).
|
||||
|
|
|
|||
|
|
@ -44,26 +44,27 @@ packages, more details are provided.
|
|||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR>
|
||||
<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">Section_howto</A></TD><TD > ellipse</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">Section_howto 6.14</A></TD><TD > ellipse</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >BODY</TD><TD > body-style particles</TD><TD > -</TD><TD > <A HREF = "body.html">body</A></TD><TD > body</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >CORESHELL</TD><TD > adiabatic core/shell model</TD><TD > Hendrik Heenen</TD><TD > <A HREF = "Section_howto.html#howto_25">Section_howto 6.25</A></TD><TD > coreshell</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled styles</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "Section_accelerate.html#acc_6">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
|
||||
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">Section_howto</A></TD><TD > pour</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled styles</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "accelerate_gpu.html">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR>
|
||||
<TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">Section_howto 6.6</A></TD><TD > pour</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > KIM</TD></TR>
|
||||
<TR ALIGN="center"><TD >KOKKOS</TD><TD > Kokkos-enabled styles</TD><TD > Trott & Edwards (4)</TD><TD > <A HREF = "Section_accelerate.html#acc_8">Section_accelerate</A></TD><TD > kokkos</TD><TD > lib/kokkos</TD></TR>
|
||||
<TR ALIGN="center"><TD >KOKKOS</TD><TD > Kokkos-enabled styles</TD><TD > Trott & Edwards (4)</TD><TD > <A HREF = "accelerate_kokkos.html">Section_accelerate</A></TD><TD > kokkos</TD><TD > lib/kokkos</TD></TR>
|
||||
<TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR>
|
||||
<TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">Section_howto</A></TD><TD > peptide</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair styles</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "Section_accelerate.html#acc_4">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">Section_howto 6.3</A></TD><TD > peptide</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >OPT</TD><TD > optimized pair styles</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "accelerate_opt.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR>
|
||||
<TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD > lib/reax</TD></TR>
|
||||
<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">Section_howto</A></TD><TD > tad</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">Section_howto 6.5</A></TD><TD > tad</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >RIGID</TD><TD > rigid bodies</TD><TD > -</TD><TD > <A HREF = "fix_rigid.html">fix rigid</A></TD><TD > rigid</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >SNAP</TD><TD > quantum-fit potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_snap.html">pair snap</A></TD><TD > snap</TD><TD > -</TD></TR>
|
||||
|
|
@ -123,14 +124,14 @@ on how to build LAMMPS with both kinds of auxiliary libraries.
|
|||
<TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (3)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "Section_accelerate.html#acc_7">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "accelerate_cuda.html">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "fix_adapt.html">fix adapt/fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "Section_accelerate.html#acc_9">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > VMD-MOLFILE</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "Section_accelerate.html#acc_5">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "accelerate_omp.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-PHONON</TD><TD > phonon dynamical matrix</TD><TD > Ling-Ti Kong (Shanghai Jiao Tong U)</TD><TD > <A HREF = "fix_phonon.html">fix phonon</A></TD><TD > USER/phonon</TD><TD > -</TD><TD > -</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-QMMM</TD><TD > QM/MM coupling</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "fix_qmmm.html">fix qmmm</A></TD><TD > USER/qmmm</TD><TD > -</TD><TD > lib/qmmm</TD></TR>
|
||||
<TR ALIGN="center"><TD >USER-QUIP</TD><TD > QM/MM coupling</TD><TD > Albert Bartok-Partay (U Cambridge)</TD><TD > <A HREF = "fix_quip.html">fix quip</A></TD><TD > USER/quip</TD><TD > -</TD><TD > lib/quip</TD></TR>
|
||||
|
|
|
|||
|
|
@ -39,26 +39,27 @@ packages, more details are provided.
|
|||
The current list of standard packages is as follows:
|
||||
|
||||
Package, Description, Author(s), Doc page, Example, Library
|
||||
ASPHERE, aspherical particles, -, "Section_howto"_Section_howto.html#howto_14, ellipse, -
|
||||
ASPHERE, aspherical particles, -, "Section_howto 6.14"_Section_howto.html#howto_14, ellipse, -
|
||||
BODY, body-style particles, -, "body"_body.html, body, -
|
||||
CLASS2, class 2 force fields, -, "pair_style lj/class2"_pair_class2.html, -, -
|
||||
COLLOID, colloidal particles, -, "atom_style colloid"_atom_style.html, colloid, -
|
||||
CORESHELL, adiabatic core/shell model, Hendrik Heenen, "Section_howto 6.25"_Section_howto.html#howto_25, coreshell, -
|
||||
DIPOLE, point dipole particles, -, "pair_style dipole/cut"_pair_dipole.html, dipole, -
|
||||
FLD, Fast Lubrication Dynamics, Kumar & Bybee & Higdon (1), "pair_style lubricateU"_pair_lubricateU.html, -, -
|
||||
GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_Section_accelerate.html#acc_6, gpu, lib/gpu
|
||||
GRANULAR, granular systems, -, "Section_howto"_Section_howto.html#howto_6, pour, -
|
||||
GPU, GPU-enabled styles, Mike Brown (ORNL), "Section accelerate"_accelerate_gpu.html, gpu, lib/gpu
|
||||
GRANULAR, granular systems, -, "Section_howto 6.6"_Section_howto.html#howto_6, pour, -
|
||||
KIM, openKIM potentials, Smirichinski & Elliot & Tadmor (3), "pair_style kim"_pair_kim.html, kim, KIM
|
||||
KOKKOS, Kokkos-enabled styles, Trott & Edwards (4), "Section_accelerate"_Section_accelerate.html#acc_8, kokkos, lib/kokkos
|
||||
KOKKOS, Kokkos-enabled styles, Trott & Edwards (4), "Section_accelerate"_accelerate_kokkos.html, kokkos, lib/kokkos
|
||||
KSPACE, long-range Coulombic solvers, -, "kspace_style"_kspace_style.html, peptide, -
|
||||
MANYBODY, many-body potentials, -, "pair_style tersoff"_pair_tersoff.html, shear, -
|
||||
MEAM, modified EAM potential, Greg Wagner (Sandia), "pair_style meam"_pair_meam.html, meam, lib/meam
|
||||
MC, Monte Carlo options, -, "fix gcmc"_fix_gcmc.html, -, -
|
||||
MOLECULE, molecular system force fields, -, "Section_howto"_Section_howto.html#howto_3, peptide, -
|
||||
OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_Section_accelerate.html#acc_4, -, -
|
||||
MOLECULE, molecular system force fields, -, "Section_howto 6.3"_Section_howto.html#howto_3, peptide, -
|
||||
OPT, optimized pair styles, Fischer & Richie & Natoli (2), "Section accelerate"_accelerate_opt.html, -, -
|
||||
PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
|
||||
POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
|
||||
REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
|
||||
REPLICA, multi-replica methods, -, "Section_howto"_Section_howto.html#howto_5, tad, -
|
||||
REPLICA, multi-replica methods, -, "Section_howto 6.5"_Section_howto.html#howto_5, tad, -
|
||||
RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
|
||||
SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
|
||||
SNAP, quantum-fit potential, Aidan Thompson (Sandia), "pair snap"_pair_snap.html, snap, -
|
||||
|
|
@ -115,14 +116,14 @@ USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (2), "fix at
|
|||
USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
|
||||
USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
|
||||
USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (3), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
|
||||
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_Section_accelerate.html#acc_7, USER/cuda, -, lib/cuda
|
||||
USER-CUDA, NVIDIA GPU styles, Christian Trott (U Tech Ilmenau), "Section accelerate"_accelerate_cuda.html, USER/cuda, -, lib/cuda
|
||||
USER-EFF, electron force field, Andres Jaramillo-Botero (Caltech), "pair_style eff/cut"_pair_eff.html, USER/eff, "eff"_eff, -
|
||||
USER-FEP, free energy perturbation, Agilio Padua (U Blaise Pascal Clermont-Ferrand), "fix adapt/fep"_fix_adapt.html, USER/fep, -, -
|
||||
USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_Section_accelerate.html#acc_9, examples/intel, -, -
|
||||
USER-INTEL, Vectorized CPU and Intel(R) coprocessor styles, W. Michael Brown (Intel), "Section accelerate"_accelerate_intel.html, examples/intel, -, -
|
||||
USER-LB, Lattice Boltzmann fluid, Colin Denniston (U Western Ontario), "fix lb/fluid"_fix_lb_fluid.html, USER/lb, -, -
|
||||
USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
|
||||
USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
|
||||
USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_Section_accelerate.html#acc_5, -, -, -
|
||||
USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section accelerate"_accelerate_omp.html, -, -, -
|
||||
USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
|
||||
USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
|
||||
USER-QUIP, QM/MM coupling, Albert Bartok-Partay (U Cambridge), "fix quip"_fix_quip.html, USER/quip, -, lib/quip
|
||||
|
|
|
|||
|
|
@ -0,0 +1,117 @@
|
|||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>compute temp/cs command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<P>compute ID group-ID temp/cs group1 group2 pre
|
||||
</P>
|
||||
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
|
||||
<LI>temp/cs = style name of this compute command
|
||||
<LI>group1 = group-ID of either cores or shells
|
||||
<LI>group2 = group-ID of either shells or cores
|
||||
</UL>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>compute oxygen_c-s all temp/cs O_core O_shell
|
||||
compute core_shells all temp/cs cores shells
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Define a computation that calculates the temperature of a system based
|
||||
on the center-of-mass velocity of atom pairs that are bonded to each
|
||||
other. This compute is designed to be used with the adiabatic
|
||||
core/shell model of <A HREF = "#MitchellFinchham">(Mitchell and Finchham)</A>. See
|
||||
<A HREF = "Section_howto.html#howto_25">Section_howto 25</A> of the manual for an
|
||||
overview of the model as implemented in LAMMPS. Specifically, this
|
||||
compute enables correct temperature calculation and thermostatting of
|
||||
core/shell pairs where it is desirable for the internal degrees of
|
||||
freedom of the core/shell pairs to not be influenced by a thermostat.
|
||||
A compute of this style can be used by any command that computes a
|
||||
temperature via <A HREF = "fix_modify.html">fix_modify</A> e.g. <A HREF = "fix_temp_rescale.html">fix
|
||||
temp/rescale</A>, <A HREF = "fix_nh.html">fix npt</A>, etc.
|
||||
</P>
|
||||
<P>For this compute, core and shell particles are specified by two
|
||||
respective group IDs, which can be defined using the
|
||||
<A HREF = "group.html">group</A> command. The number of atoms in the two groups
|
||||
must be the same and there should be one bond defined between a pair
|
||||
of atoms in the two groups.
|
||||
</P>
|
||||
<P>The temperature is calculated by the formula KE = dim/2 N k T, where
|
||||
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
||||
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
|
||||
in the group, k = Boltzmann constant, and T = temperature. Note that
|
||||
the velocity of each core or shell atom used in the KE calculation is
|
||||
the velocity of the center-of-mass (COM) of the core/shell pair the
|
||||
atom is part of.
|
||||
</P>
|
||||
<P>A kinetic energy tensor, stored as a 6-element vector, is also
|
||||
calculated by this compute for use in the computation of a pressure
|
||||
tensor. The formula for the components of the tensor is the same as
|
||||
the above formula, except that v^2 is replaced by vx*vy for the xy
|
||||
component, etc. The 6 components of the vector are ordered xx, yy,
|
||||
zz, xy, xz, yz. Again, the velocity of each core or shell atom is its
|
||||
COM velocity.
|
||||
</P>
|
||||
<P>The change this fix makes to core/shell atom velocities is essentially
|
||||
computing the temperature after a "bias" has been removed from the
|
||||
velocity of the atoms. This "bias" is the velocity of the atom
|
||||
relative to the COM velocity of the core/shell pair. If this compute
|
||||
is used with a fix command that performs thermostatting then this bias
|
||||
will be subtracted from each atom, thermostatting of the remaining COM
|
||||
velocity will be performed, and the bias will be added back in. This
|
||||
means the thermostating will effectively be performed on the
|
||||
core/shell pairs, instead of on the individual core and shell atoms.
|
||||
Thermostatting fixes that work in this way include <A HREF = "fix_nh.html">fix
|
||||
nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_temp_berendsen.html">fix
|
||||
temp/berendsen</A>, and <A HREF = "fix_langevin.html">fix
|
||||
langevin</A>.
|
||||
</P>
|
||||
<P>The internal energy of core/shell pairs can be calculated by the
|
||||
<A HREF = "compute_temp_chunk.html">compute temp/chunk</A> command, if chunks are
|
||||
defined as core/shell pairs. See <A HREF = "Section_howto.html#howto_25">Section_howto
|
||||
25</A> for more discussion on how to do this.
|
||||
</P>
|
||||
<P><B>Output info:</B>
|
||||
</P>
|
||||
<P>This compute calculates a global scalar (the temperature) and a global
|
||||
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
|
||||
These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input.
|
||||
</P>
|
||||
<P>The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
</P>
|
||||
<P>The scalar value will be in temperature <A HREF = "units.html">units</A>. The
|
||||
vector values will be in energy <A HREF = "units.html">units</A>.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>The number of core/shell pairs contributing to the temperature is
|
||||
assumed to be constant for the duration of the run. No fixes should
|
||||
be used which generate new molecules or atoms during a simulation.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "compute_temp.html">compute temp</A>, <A HREF = "compute_temp_chunk.html">compute
|
||||
temp/chunk</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "MitchellFinchham"></A>
|
||||
|
||||
<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
|
||||
5, 1031-1038 (1993).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,111 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
compute temp/cs command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
compute ID group-ID temp/cs group1 group2 pre
|
||||
|
||||
ID, group-ID are documented in "compute"_compute.html command
|
||||
temp/cs = style name of this compute command
|
||||
group1 = group-ID of either cores or shells
|
||||
group2 = group-ID of either shells or cores :ul
|
||||
|
||||
[Examples:]
|
||||
|
||||
compute oxygen_c-s all temp/cs O_core O_shell
|
||||
compute core_shells all temp/cs cores shells :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Define a computation that calculates the temperature of a system based
|
||||
on the center-of-mass velocity of atom pairs that are bonded to each
|
||||
other. This compute is designed to be used with the adiabatic
|
||||
core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See
|
||||
"Section_howto 25"_Section_howto.html#howto_25 of the manual for an
|
||||
overview of the model as implemented in LAMMPS. Specifically, this
|
||||
compute enables correct temperature calculation and thermostatting of
|
||||
core/shell pairs where it is desirable for the internal degrees of
|
||||
freedom of the core/shell pairs to not be influenced by a thermostat.
|
||||
A compute of this style can be used by any command that computes a
|
||||
temperature via "fix_modify"_fix_modify.html e.g. "fix
|
||||
temp/rescale"_fix_temp_rescale.html, "fix npt"_fix_nh.html, etc.
|
||||
|
||||
For this compute, core and shell particles are specified by two
|
||||
respective group IDs, which can be defined using the
|
||||
"group"_group.html command. The number of atoms in the two groups
|
||||
must be the same and there should be one bond defined between a pair
|
||||
of atoms in the two groups.
|
||||
|
||||
The temperature is calculated by the formula KE = dim/2 N k T, where
|
||||
KE = total kinetic energy of the group of atoms (sum of 1/2 m v^2),
|
||||
dim = 2 or 3 = dimensionality of the simulation, N = number of atoms
|
||||
in the group, k = Boltzmann constant, and T = temperature. Note that
|
||||
the velocity of each core or shell atom used in the KE calculation is
|
||||
the velocity of the center-of-mass (COM) of the core/shell pair the
|
||||
atom is part of.
|
||||
|
||||
A kinetic energy tensor, stored as a 6-element vector, is also
|
||||
calculated by this compute for use in the computation of a pressure
|
||||
tensor. The formula for the components of the tensor is the same as
|
||||
the above formula, except that v^2 is replaced by vx*vy for the xy
|
||||
component, etc. The 6 components of the vector are ordered xx, yy,
|
||||
zz, xy, xz, yz. Again, the velocity of each core or shell atom is its
|
||||
COM velocity.
|
||||
|
||||
The change this fix makes to core/shell atom velocities is essentially
|
||||
computing the temperature after a "bias" has been removed from the
|
||||
velocity of the atoms. This "bias" is the velocity of the atom
|
||||
relative to the COM velocity of the core/shell pair. If this compute
|
||||
is used with a fix command that performs thermostatting then this bias
|
||||
will be subtracted from each atom, thermostatting of the remaining COM
|
||||
velocity will be performed, and the bias will be added back in. This
|
||||
means the thermostating will effectively be performed on the
|
||||
core/shell pairs, instead of on the individual core and shell atoms.
|
||||
Thermostatting fixes that work in this way include "fix
|
||||
nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
|
||||
temp/berendsen"_fix_temp_berendsen.html, and "fix
|
||||
langevin"_fix_langevin.html.
|
||||
|
||||
The internal energy of core/shell pairs can be calculated by the
|
||||
"compute temp/chunk"_compute_temp_chunk.html command, if chunks are
|
||||
defined as core/shell pairs. See "Section_howto
|
||||
25"_Section_howto.html#howto_25 for more discussion on how to do this.
|
||||
|
||||
[Output info:]
|
||||
|
||||
This compute calculates a global scalar (the temperature) and a global
|
||||
vector of length 6 (KE tensor), which can be accessed by indices 1-6.
|
||||
These values can be used by any command that uses global scalar or
|
||||
vector values from a compute as input.
|
||||
|
||||
The scalar value calculated by this compute is "intensive". The
|
||||
vector values are "extensive".
|
||||
|
||||
The scalar value will be in temperature "units"_units.html. The
|
||||
vector values will be in energy "units"_units.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
The number of core/shell pairs contributing to the temperature is
|
||||
assumed to be constant for the duration of the run. No fixes should
|
||||
be used which generate new molecules or atoms during a simulation.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute temp"_compute_temp.html, "compute
|
||||
temp/chunk"_compute_temp_chunk.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(MitchellFinchham)
|
||||
[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
|
||||
5, 1031-1038 (1993).
|
||||
|
|
@ -235,11 +235,10 @@ of SHAKE parameters and monitoring the energy versus time.
|
|||
<A NAME = "Ryckaert"></A>
|
||||
|
||||
<P><B>(Ryckaert)</B> J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen,
|
||||
Journal of Computational Physics, 23, 327–341 (1977).
|
||||
J of Comp Phys, 23, 327-341 (1977).
|
||||
</P>
|
||||
<A NAME = "Andersen"></A>
|
||||
|
||||
<P><B>(Andersen)</B> H. Andersen,
|
||||
Journal of Computational Physics, 52, 24-34 (1983).
|
||||
<P><B>(Andersen)</B> H. Andersen, J of Comp Phys, 52, 24-34 (1983).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
|
|||
|
|
@ -218,8 +218,7 @@ of SHAKE parameters and monitoring the energy versus time.
|
|||
|
||||
:link(Ryckaert)
|
||||
[(Ryckaert)] J.-P. Ryckaert, G. Ciccotti and H. J. C. Berendsen,
|
||||
Journal of Computational Physics, 23, 327–341 (1977).
|
||||
J of Comp Phys, 23, 327-341 (1977).
|
||||
|
||||
:link(Andersen)
|
||||
[(Andersen)] H. Andersen,
|
||||
Journal of Computational Physics, 52, 24-34 (1983).
|
||||
[(Andersen)] H. Andersen, J of Comp Phys, 52, 24-34 (1983).
|
||||
|
|
|
|||
|
|
@ -0,0 +1,91 @@
|
|||
<HTML>
|
||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
||||
</CENTER>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<HR>
|
||||
|
||||
<H3>pair_style born/coul/long/cs command
|
||||
</H3>
|
||||
<H3>pair_style buck/coul/long/cs command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>pair_style style args
|
||||
</PRE>
|
||||
<UL><LI>style = <I>born/coul/long/cs</I> or <I>buck/coul/long/cs</I>
|
||||
<LI>args = list of arguments for a particular style
|
||||
</UL>
|
||||
<PRE> <I>born/coul/long/cs</I> args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
<I>buck/coul/long/cs</I> args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
</PRE>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>pair_style born/coul/long/cs 10.0 8.0
|
||||
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51
|
||||
</PRE>
|
||||
<PRE>pair_style buck/coul/long/cs 10.0
|
||||
pair_style buck/coul/long/cs 10.0 8.0
|
||||
pair_coeff * * 100.0 1.5 200.0
|
||||
pair_coeff 1 1 100.0 1.5 200.0 9.0
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>These pair styles are designed to be used with the adiabatic
|
||||
core/shell model of <A HREF = "#MitchellFinchham">(Mitchell and Finchham)</A>. See
|
||||
<A HREF = "Section_howto.html#howto_25">Section_howto 25</A> of the manual for an
|
||||
overview of the model as implemented in LAMMPS.
|
||||
</P>
|
||||
<P>These pair styles are identical to the <A HREF = "pair_born.html">pair_style
|
||||
born/coul/long</A> and <A HREF = "pair_buck.html">pair_style
|
||||
buck/coul/long</A> styles, except they correctly treat the
|
||||
special case where the distance between two charged core and shell
|
||||
atoms in the same core/shell pair approach r = 0.0. This needs
|
||||
special treatment when a long-range solver for Coulombic interactions
|
||||
is also used, i.e. via the <A HREF = "kspace_style.html">kspace_style</A> command.
|
||||
</P>
|
||||
<P>More specifically, the short-range Coulomb interaction between a core
|
||||
and its shell should be turned off using the
|
||||
<A HREF = "special_bonds.html">special_bonds</A> command by setting the 1-2 weight
|
||||
to 0.0, which works because the core and shell atoms are bonded to
|
||||
each other. This induces a long-range correction approximation which
|
||||
fails at small distances (~< 10e-8). Therefore, the Coulomb term which
|
||||
is used to calculate the correction factor is extended by a minimal
|
||||
distance (r_min = 1.0-6) when the interaction between a core/shell
|
||||
pair is treated, as follows
|
||||
</P>
|
||||
<CENTER><IMG SRC = "Eqs/pair_cs.jpg">
|
||||
</CENTER>
|
||||
<P>where C is an energy-conversion constant, Qi and Qj are the charges on
|
||||
the core and shell, epsilon is the dielectric constant and r_min is the
|
||||
minimal distance.
|
||||
</P>
|
||||
<P><B>Restrictions:</B>
|
||||
</P>
|
||||
<P>These pair styles are part of the CORESHELL package. They are only
|
||||
enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
|
||||
LAMMPS</A> section for more info.
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
</P>
|
||||
<P><A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_born.html">pair_style born</A>,
|
||||
<A HREF = "pair_buck.html">pair_style buck</A>
|
||||
</P>
|
||||
<P><B>Default:</B> none
|
||||
</P>
|
||||
<HR>
|
||||
|
||||
<A NAME = "MitchellFinchham"></A>
|
||||
|
||||
<P><B>(Mitchell and Finchham)</B> Mitchell, Finchham, J Phys Condensed Matter,
|
||||
5, 1031-1038 (1993).
|
||||
</P>
|
||||
</HTML>
|
||||
|
|
@ -0,0 +1,83 @@
|
|||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
pair_style born/coul/long/cs command :h3
|
||||
pair_style buck/coul/long/cs command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
pair_style style args :pre
|
||||
|
||||
style = {born/coul/long/cs} or {buck/coul/long/cs}
|
||||
args = list of arguments for a particular style :ul
|
||||
{born/coul/long/cs} args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units)
|
||||
{buck/coul/long/cs} args = cutoff (cutoff2)
|
||||
cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
|
||||
cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
|
||||
|
||||
[Examples:]
|
||||
|
||||
pair_style born/coul/long/cs 10.0 8.0
|
||||
pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
|
||||
|
||||
pair_style buck/coul/long/cs 10.0
|
||||
pair_style buck/coul/long/cs 10.0 8.0
|
||||
pair_coeff * * 100.0 1.5 200.0
|
||||
pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
These pair styles are designed to be used with the adiabatic
|
||||
core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See
|
||||
"Section_howto 25"_Section_howto.html#howto_25 of the manual for an
|
||||
overview of the model as implemented in LAMMPS.
|
||||
|
||||
These pair styles are identical to the "pair_style
|
||||
born/coul/long"_pair_born.html and "pair_style
|
||||
buck/coul/long"_pair_buck.html styles, except they correctly treat the
|
||||
special case where the distance between two charged core and shell
|
||||
atoms in the same core/shell pair approach r = 0.0. This needs
|
||||
special treatment when a long-range solver for Coulombic interactions
|
||||
is also used, i.e. via the "kspace_style"_kspace_style.html command.
|
||||
|
||||
More specifically, the short-range Coulomb interaction between a core
|
||||
and its shell should be turned off using the
|
||||
"special_bonds"_special_bonds.html command by setting the 1-2 weight
|
||||
to 0.0, which works because the core and shell atoms are bonded to
|
||||
each other. This induces a long-range correction approximation which
|
||||
fails at small distances (~< 10e-8). Therefore, the Coulomb term which
|
||||
is used to calculate the correction factor is extended by a minimal
|
||||
distance (r_min = 1.0-6) when the interaction between a core/shell
|
||||
pair is treated, as follows
|
||||
|
||||
:c,image(Eqs/pair_cs.jpg)
|
||||
|
||||
where C is an energy-conversion constant, Qi and Qj are the charges on
|
||||
the core and shell, epsilon is the dielectric constant and r_min is the
|
||||
minimal distance.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
These pair styles are part of the CORESHELL package. They are only
|
||||
enabled if LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"pair_coeff"_pair_coeff.html, "pair_style born"_pair_born.html,
|
||||
"pair_style buck"_pair_buck.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
:line
|
||||
|
||||
:link(MitchellFinchham)
|
||||
[(Mitchell and Finchham)] Mitchell, Finchham, J Phys Condensed Matter,
|
||||
5, 1031-1038 (1993).
|
||||
|
|
@ -302,12 +302,13 @@ sub-styles of the hybrid potential.
|
|||
and J,J is the same, and if the sub-style allows for mixing, then the
|
||||
coefficients for I,J can be mixed. This means you do not have to
|
||||
specify a pair_coeff command for I,J since the I,J type pair will be
|
||||
assigned automatically to the I,I sub-style and its coefficients
|
||||
generated by the mixing rule used by that sub-style. For the
|
||||
<I>hybrid/overlay</I> style, there is an additional requirement that both
|
||||
the I,I and J,J pairs are assigned to a single sub-style. See the
|
||||
"pair_modify" command for details of mixing rules. See the See the
|
||||
doc page for the sub-style to see if allows for mixing.
|
||||
assigned automatically to the sub-style defined for both I,I and J,J
|
||||
and its coefficients generated by the mixing rule used by that
|
||||
sub-style. For the <I>hybrid/overlay</I> style, there is an additional
|
||||
requirement that both the I,I and J,J pairs are assigned to a single
|
||||
sub-style. See the "pair_modify" command for details of mixing rules.
|
||||
See the See the doc page for the sub-style to see if allows for
|
||||
mixing.
|
||||
</P>
|
||||
<P>The hybrid pair styles supports the <A HREF = "pair_modify.html">pair_modify</A>
|
||||
shift, table, and tail options for an I,J pair interaction, if the
|
||||
|
|
|
|||
|
|
@ -296,12 +296,13 @@ For atom type pairs I,J and I != J, if the sub-style assigned to I,I
|
|||
and J,J is the same, and if the sub-style allows for mixing, then the
|
||||
coefficients for I,J can be mixed. This means you do not have to
|
||||
specify a pair_coeff command for I,J since the I,J type pair will be
|
||||
assigned automatically to the I,I sub-style and its coefficients
|
||||
generated by the mixing rule used by that sub-style. For the
|
||||
{hybrid/overlay} style, there is an additional requirement that both
|
||||
the I,I and J,J pairs are assigned to a single sub-style. See the
|
||||
"pair_modify" command for details of mixing rules. See the See the
|
||||
doc page for the sub-style to see if allows for mixing.
|
||||
assigned automatically to the sub-style defined for both I,I and J,J
|
||||
and its coefficients generated by the mixing rule used by that
|
||||
sub-style. For the {hybrid/overlay} style, there is an additional
|
||||
requirement that both the I,I and J,J pairs are assigned to a single
|
||||
sub-style. See the "pair_modify" command for details of mixing rules.
|
||||
See the See the doc page for the sub-style to see if allows for
|
||||
mixing.
|
||||
|
||||
The hybrid pair styles supports the "pair_modify"_pair_modify.html
|
||||
shift, table, and tail options for an I,J pair interaction, if the
|
||||
|
|
|
|||
Loading…
Reference in New Issue