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

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	doc/Manual.html
	doc/Manual.txt
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Axel Kohlmeyer
2015-03-07 14:41:45 +01:00
parent dfbdc3d57a 08e77a79b3
commit d6d368f447
32 changed files with 3590 additions and 76 deletions
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\documentstyle[12pt]{article}
\begin{document}
$$
E = \frac{C q_i q_j}{\epsilon (r + r_{min})} \qquad r \rightarrow 0
$$
\end{document}

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doc/Manual.html
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@ -1,7 +1,7 @@
<HTML>
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="5 Mar 2015 version">
<META NAME="docnumber" CONTENT="6 Mar 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -22,7 +22,7 @@
<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
<CENTER><H4>5 Mar 2015 version
<CENTER><H4>6 Mar 2015 version
</H4></CENTER>
<H4>Version info:
</H4>

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doc/Manual.txt
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@ -1,7 +1,7 @@
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="5 Mar 2015 version">
<META NAME="docnumber" CONTENT="6 Mar 2015 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -19,7 +19,7 @@
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
5 Mar 2015 version :c,h4
6 Mar 2015 version :c,h4
Version info: :h4

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doc/Section_commands.html
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@ -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

3
doc/Section_commands.txt
View File

@ -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,

193
doc/Section_howto.html
View File

@ -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>

192
doc/Section_howto.txt
View File

@ -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).

21
doc/Section_packages.html
View File

@ -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 (Technical U of Munich)</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>

21
doc/Section_packages.txt
View File

@ -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 (Technical U of Munich), "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

117
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@ -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>

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@ -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).

5
doc/fix_shake.html
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@ -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>

5
doc/fix_shake.txt
View File

@ -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).

91
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<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>

83
doc/pair_cs.txt Normal file
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@ -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).

13
doc/pair_hybrid.html
View File

@ -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

13
doc/pair_hybrid.txt
View File

@ -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

3
examples/README
View File

@ -58,10 +58,11 @@ section of the LAMMPS WWW Site.
These are the sample problems and their output in the various
sub-directories:
accelerate: use of all the various accelerator packages
accelerate: use of all the various accelerator packages
balance: dynamic load balancing, 2d system
body: body particles, 2d system
colloid: big colloid particles in a small particle solvent, 2d system
coreshell: adiabatic core/shell model
comb: models using the COMB potential
crack: crack propagation in a 2d solid
deposit: deposition of atoms and molecules onto a 3d substrate

1114
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File diff suppressed because it is too large Load Diff

72
examples/coreshell/in.coreshell Normal file
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@ -0,0 +1,72 @@
# Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
group cores type 1 2
group shells type 3 4
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
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
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press &
epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#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
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000

188
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@ -0,0 +1,188 @@
LAMMPS (5 Mar 2015)
# Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 1 by 1 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
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
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#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
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Ewald initialization ...
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 22
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
Ewald initialization ...
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 6.86279 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -628.35255 -668.0717 39.719144 1427 -20608.918 -668.0717 1.6320365 1025.8481 -1695.5518 0 3.4602128e-14 4.1910919e-15 13990.5
50 -632.83924 -664.88103 32.041787 1151.1736 -4098.5062 -668.28414 37.966205 988.74855 -1694.9989 3.4031081 25.060198 9.2894103 13990.5
100 -630.51517 -660.52949 30.014321 1078.3323 -3202.2416 -664.01378 39.505874 991.23277 -1694.7524 3.4842892 26.36833 10.674509 13990.5
150 -628.58401 -661.59121 33.007195 1185.8581 106.75378 -665.3449 46.400029 982.93422 -1694.6791 3.7536882 27.270427 10.826035 13990.5
200 -627.39592 -662.45902 35.063102 1259.7212 -1672.1319 -665.61583 41.658839 987.14579 -1694.4205 3.1568106 23.525213 6.58382 13990.5
250 -625.74143 -660.30023 34.558805 1241.6032 -1596.9927 -664.13159 42.148927 988.19127 -1694.4718 3.8313604 27.156726 8.5397995 13990.5
300 -625.07332 -659.68738 34.614061 1243.5884 -1525.4995 -663.38119 42.077062 989.22231 -1694.6806 3.6938081 26.233327 9.2896507 13990.5
350 -623.86869 -663.20518 39.336492 1413.2524 -1932.3573 -667.15923 40.519069 986.96395 -1694.6422 3.9540529 30.551213 14.69189 13990.5
400 -623.55169 -660.39199 36.840301 1323.5711 -1747.3638 -664.07907 41.004982 989.66515 -1694.7492 3.6870716 27.463501 11.288658 13990.5
450 -623.03498 -658.41209 35.377106 1271.0025 1243.4895 -662.14754 48.097573 984.42115 -1694.6663 3.735455 24.531264 6.5614635 13990.5
500 -622.34231 -660.50992 38.167608 1371.2576 -1301.9479 -664.26607 41.813817 988.57955 -1694.6594 3.7561473 23.595051 5.844275 13990.5
Loop time of 8.51483 on 1 procs for 500 steps with 432 atoms
Pair time (%) = 7.73226 (90.8093)
Bond time (%) = 0.00232315 (0.0272836)
Kspce time (%) = 0.518208 (6.08594)
Neigh time (%) = 0.17925 (2.10514)
Comm time (%) = 0.0653358 (0.767317)
Outpt time (%) = 0.000309229 (0.00363165)
Other time (%) = 0.0171449 (0.201354)
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9307 ave 9307 max 9307 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297357 ave 297357 max 297357 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297357
Ave neighs/atom = 688.326
Ave special neighs/atom = 1
Neighbor list builds = 21
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Ewald initialization ...
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 6.86279 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -622.34231 -660.50992 38.167608 1371.2576 -1301.9479 -664.26607 41.813817 988.57955 -1694.6594 3.7561473 23.595051 5.844275 13990.5
550 -622.53283 -661.59223 39.059403 1403.2973 -385.2836 -664.93615 43.738024 985.8195 -1694.4937 3.3439143 21.675844 3.5834691 13990.5
600 -622.20391 -659.47921 37.275306 1339.1996 473.13042 -663.45898 46.093667 985.15793 -1694.7106 3.9797724 25.783443 9.4059533 13990.5
650 -622.3473 -660.85461 38.507306 1383.462 -1021.6262 -664.41457 42.581674 987.48335 -1694.4796 3.5599548 24.069859 6.9189396 13990.5
700 -621.9195 -660.92044 39.000937 1401.1968 71.427836 -664.81486 44.86887 985.26444 -1694.9482 3.894424 28.397753 9.3904596 13990.5
750 -622.28852 -658.93918 36.650662 1316.7579 -1249.2306 -662.31101 41.915549 990.48822 -1694.7148 3.3718339 24.259772 4.9454879 13990.5
800 -622.31982 -657.72021 35.400389 1271.839 254.0237 -661.60518 45.506498 987.48185 -1694.5935 3.8849638 24.386892 7.4962982 13990.5
850 -622.31623 -661.4936 39.177375 1407.5357 37.74414 -665.02673 44.380924 985.14989 -1694.5575 3.5331239 23.316952 5.5622744 13990.5
900 -621.83183 -660.10965 38.277816 1375.2171 1738.9676 -664.10328 48.428909 981.86752 -1694.3997 3.9936342 28.519154 11.384782 13990.5
950 -622.03652 -659.97862 37.942096 1363.1555 -49.888312 -663.91816 44.582637 986.15057 -1694.6514 3.9395363 27.011672 8.4915326 13990.5
1000 -621.71637 -660.69133 38.97496 1400.2635 -46.518055 -665.12412 44.669238 984.85534 -1694.6487 4.432789 29.799247 9.5235093 13990.5
1050 -621.90579 -658.42698 36.521187 1312.1062 27.913475 -662.80273 44.953547 986.65365 -1694.4099 4.3757505 28.035827 8.4898226 13990.5
1100 -621.92929 -661.57742 39.648126 1424.4485 820.11499 -665.35048 46.491843 982.84734 -1694.6897 3.7730563 27.803982 8.4955015 13990.5
1150 -622.36518 -659.3383 36.973112 1328.3426 -799.63876 -662.87451 43.109263 988.96432 -1694.9481 3.5362185 23.473216 4.2340288 13990.5
1200 -621.80278 -659.38996 37.587182 1350.4045 173.56518 -663.76385 45.4017 985.49478 -1694.6603 4.3738897 29.25765 11.540749 13990.5
1250 -621.89233 -658.13657 36.244239 1302.1562 -194.31216 -662.25387 44.600608 987.50208 -1694.3566 4.1173041 27.781148 11.737589 13990.5
1300 -622.01575 -659.4502 37.43445 1344.9172 419.91066 -663.67863 46.041458 984.96293 -1694.683 4.2284307 27.725967 9.666138 13990.5
1350 -621.64918 -658.52586 36.876681 1324.8781 -1542.8395 -662.92795 41.627963 989.87571 -1694.4316 4.4020823 30.153096 11.999079 13990.5
1400 -621.65713 -657.77765 36.120515 1297.7112 -2133.9795 -662.63382 40.620287 991.32101 -1694.5751 4.8561686 30.546416 11.476013 13990.5
1450 -621.92858 -659.45137 37.522795 1348.0912 217.78723 -663.34796 45.334127 985.96702 -1694.6491 3.8965883 27.625033 7.3805255 13990.5
1500 -621.9432 -657.57884 35.635634 1280.2907 632.02267 -661.89128 46.527064 986.00347 -1694.4218 4.3124408 28.010625 8.740067 13990.5
Loop time of 17.041 on 1 procs for 1000 steps with 432 atoms
Pair time (%) = 15.4577 (90.7085)
Bond time (%) = 0.00465488 (0.0273157)
Kspce time (%) = 1.03763 (6.08902)
Neigh time (%) = 0.390329 (2.29052)
Comm time (%) = 0.131336 (0.770706)
Outpt time (%) = 0.000611782 (0.00359005)
Other time (%) = 0.0188062 (0.110358)
Nlocal: 432 ave 432 max 432 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9406 ave 9406 max 9406 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 297120 ave 297120 max 297120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 297120
Ave neighs/atom = 687.778
Ave special neighs/atom = 1
Neighbor list builds = 46
Dangerous builds = 0

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@ -0,0 +1,188 @@
LAMMPS (5 Mar 2015)
# Testsystem for core-shell model compared to Mitchel and Finchham
# Hendrik Heenen, June 2014
# ------------------------ INITIALIZATION ----------------------------
units metal
dimension 3
boundary p p p
atom_style full
# ----------------------- ATOM DEFINITION ----------------------------
fix csinfo all property/atom i_CSID
read_data data.coreshell fix csinfo NULL CS-Info
orthogonal box = (0 0 0) to (24.096 24.096 24.096)
1 by 2 by 2 MPI processor grid
reading atoms ...
432 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
216 bonds
1 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
group cores type 1 2
216 atoms in group cores
group shells type 3 4
216 atoms in group shells
neighbor 2.0 bin
comm_modify vel yes
# ------------------------ FORCE FIELDS ------------------------------
kspace_style ewald 1.0e-6
pair_style born/coul/long/cs 20.0 20.0 # A, rho, sigma=0, C, D
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
bond_style harmonic
bond_coeff 1 63.014 0.0
bond_coeff 2 25.724 0.0
# ------------------------ Equilibration Run -------------------------------
reset_timestep 0
thermo 50
thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol
compute CSequ all temp/cs cores shells
# output via chunk method
#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
#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector
thermo_modify temp CSequ
# velocity bias option
velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
Ewald initialization ...
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 10 steps, check yes
master list distance cutoff = 22
velocity all scale 1427 temp CSequ
fix thermoberendsen all temp/berendsen 1427 1427 0.4
fix nve all nve
fix_modify thermoberendsen temp CSequ
# 2 fmsec timestep
timestep 0.002
run 500
Ewald initialization ...
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 6.15182 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
0 -628.35255 -668.0717 39.719144 1427 -20608.918 -668.0717 1.6320365 1025.8481 -1695.5518 0 3.6635741e-14 5.3290705e-15 13990.5
50 -632.86102 -664.881 32.019982 1150.3902 -4100.2367 -668.28423 37.966091 988.74858 -1694.9989 3.403224 25.060809 9.2893842 13990.5
100 -630.51552 -660.52959 30.014075 1078.3235 -3202.4205 -664.01411 39.505563 991.23276 -1694.7524 3.4845198 26.369799 10.674421 13990.5
150 -628.58443 -661.59141 33.006978 1185.8503 106.65351 -665.34508 46.399848 982.93423 -1694.6792 3.7536698 27.270648 10.826129 13990.5
200 -627.39641 -662.45927 35.062861 1259.7125 -1672.2627 -665.61606 41.658596 987.1458 -1694.4205 3.1567877 23.525464 6.5838195 13990.5
250 -625.74093 -660.30053 34.559597 1241.6316 -1597.1305 -664.13208 42.148526 988.19121 -1694.4718 3.831555 27.157597 8.5399516 13990.5
300 -625.07349 -659.68703 34.613535 1243.5695 -1525.6663 -663.38085 42.076798 989.22292 -1694.6806 3.6938245 26.233967 9.2898941 13990.5
350 -623.86899 -663.20625 39.337263 1413.2801 -1933.067 -667.16008 40.51735 986.96485 -1694.6423 3.9538285 30.550701 14.691984 13990.5
400 -623.55154 -660.39034 36.838804 1323.5173 -1746.896 -664.07771 41.006288 989.66515 -1694.7492 3.687369 27.463762 11.289238 13990.5
450 -623.03522 -658.41494 35.37972 1271.0964 1245.1415 -662.15059 48.1009 984.41515 -1694.6666 3.7356529 24.533936 6.5615795 13990.5
500 -622.34349 -660.51826 38.174772 1371.515 -1306.7035 -664.27406 41.802611 988.58329 -1694.66 3.7557939 23.595131 5.801075 13990.5
Loop time of 2.53127 on 4 procs for 500 steps with 432 atoms
Pair time (%) = 1.94114 (76.6863)
Bond time (%) = 0.000725508 (0.0286618)
Kspce time (%) = 0.353945 (13.9829)
Neigh time (%) = 0.0488738 (1.9308)
Comm time (%) = 0.17332 (6.84714)
Outpt time (%) = 0.000516713 (0.0204132)
Other time (%) = 0.012753 (0.503818)
Nlocal: 108 ave 132 max 90 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 6500 ave 6530 max 6448 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 74339.8 ave 91261 max 61188 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 297359
Ave neighs/atom = 688.331
Ave special neighs/atom = 1
Neighbor list builds = 21
Dangerous builds = 0
unfix thermoberendsen
# ------------------------ Dynamic Run -------------------------------
run 1000
Ewald initialization ...
G vector (1/distance) = 0.175257
estimated absolute RMS force accuracy = 1.49563e-05
estimated relative force accuracy = 1.03866e-06
KSpace vectors: actual max1d max3d = 257 5 665
kxmax kymax kzmax = 5 5 5
Memory usage per processor = 6.15373 Mbytes
Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
500 -622.34349 -660.51826 38.174772 1371.515 -1306.7035 -664.27406 41.802611 988.58329 -1694.66 3.7557939 23.595131 5.801075 13990.5
550 -622.53431 -661.60445 39.070141 1403.6831 -388.25413 -664.94784 43.727803 985.81836 -1694.494 3.3433892 21.667306 3.5808033 13990.5
600 -622.20561 -659.56223 37.356624 1342.1211 428.9464 -663.53655 45.982645 985.19136 -1694.7106 3.974322 25.725869 9.3871295 13990.5
650 -622.35823 -660.82051 38.462275 1381.8442 -1009.0888 -664.38771 42.618521 987.47881 -1694.485 3.5671985 24.149905 7.00428 13990.5
700 -621.97407 -660.92034 38.946267 1399.2327 142.95891 -664.75916 45.033131 985.16618 -1694.9585 3.8388194 27.934663 8.7392159 13990.5
750 -622.29209 -658.81919 36.527095 1312.3185 -952.526 -662.17886 42.618062 989.9262 -1694.7231 3.3596669 24.324239 4.9087128 13990.5
800 -622.33521 -658.14785 35.812637 1286.6499 135.34005 -661.96381 45.178323 987.39314 -1694.5353 3.815955 24.107767 7.0978979 13990.5
850 -622.37957 -660.474 38.094424 1368.6283 857.3439 -663.9925 46.509627 984.19258 -1694.6947 3.5185004 23.581763 5.0835354 13990.5
900 -622.29844 -660.66771 38.369271 1378.5028 2861.462 -664.35013 50.97682 979.13332 -1694.4603 3.6824207 24.493416 6.3661215 13990.5
950 -622.35097 -659.43438 37.083412 1332.3054 705.55718 -663.24413 46.294781 984.74433 -1694.2832 3.8097517 24.11493 4.1360943 13990.5
1000 -622.08622 -658.28773 36.201516 1300.6213 421.181 -662.27058 45.865645 986.51483 -1694.6511 3.98285 26.774991 7.4172909 13990.5
1050 -622.10558 -657.21399 35.108408 1261.3489 -464.31761 -661.46995 44.291275 988.69737 -1694.4586 4.2559609 25.983762 5.4926993 13990.5
1100 -622.29369 -658.21246 35.918767 1290.4629 123.81951 -662.20344 45.651482 986.92119 -1694.7761 3.990985 25.85199 5.2327524 13990.5
1150 -621.98418 -658.28218 36.297998 1304.0876 546.02432 -662.38868 46.194374 985.7826 -1694.3657 4.1065008 27.128736 6.901853 13990.5
1200 -621.76032 -658.36996 36.60964 1315.2841 198.92215 -662.79546 45.536182 986.45023 -1694.7819 4.4255014 30.59935 9.4790152 13990.5
1250 -621.77583 -657.79539 36.019569 1294.0844 521.16569 -662.12132 46.16971 986.26128 -1694.5523 4.3259289 29.294668 9.6073346 13990.5
1300 -622.0461 -659.54559 37.499494 1347.2541 -854.68333 -663.33538 42.882224 988.27569 -1694.4933 3.7897892 26.707354 8.861147 13990.5
1350 -621.7984 -657.10932 35.310914 1268.6244 -1010.1044 -661.35487 42.90716 990.41696 -1694.679 4.2455538 29.623565 10.702495 13990.5
1400 -622.2597 -660.89426 38.634556 1388.0337 2292.235 -664.36487 49.907981 980.3269 -1694.5997 3.4706065 25.34727 6.8458703 13990.5
1450 -622.36952 -660.43856 38.069033 1367.716 199.44207 -664.44407 45.483438 984.89046 -1694.818 4.0055092 24.149259 3.9431126 13990.5
1500 -621.84913 -659.73606 37.886922 1361.1733 -1274.5089 -663.96475 42.049386 988.31676 -1694.3309 4.2286938 28.927291 10.527466 13990.5
Loop time of 5.06693 on 4 procs for 1000 steps with 432 atoms
Pair time (%) = 3.90916 (77.1504)
Bond time (%) = 0.00148368 (0.0292816)
Kspce time (%) = 0.657798 (12.9822)
Neigh time (%) = 0.108943 (2.15008)
Comm time (%) = 0.373417 (7.36968)
Outpt time (%) = 0.00109911 (0.0216918)
Other time (%) = 0.0150309 (0.296647)
Nlocal: 108 ave 113 max 100 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 6461 ave 6519 max 6372 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 74316.8 ave 77778 max 69869 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Total # of neighbors = 297267
Ave neighs/atom = 688.118
Ave special neighs/atom = 1
Neighbor list builds = 46
Dangerous builds = 0

503
src/CORESHELL/compute_temp_cs.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Hendrik Heenen (Technical University of Munich)
(hendrik.heenen at mytum.com)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "math.h"
#include "compute_temp_cs.h"
#include "atom.h"
#include "atom_vec.h"
#include "domain.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "fix_store.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 5) error->all(FLERR,"Illegal compute temp/cs command");
if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Compute temp/cs used when bonds are not allowed");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
extarray = 0;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// find and define groupbits for core and shell groups
cgroup = group->find(arg[3]);
if (cgroup == -1)
error->all(FLERR,"Could not find specified group ID for core particles");
groupbit_c = group->bitmask[cgroup];
sgroup = group->find(arg[4]);
if (sgroup == -1)
error->all(FLERR,"Could not find specified group ID for shell particles");
groupbit_s = group->bitmask[sgroup];
// create a new fix STORE style
// id = compute-ID + COMPUTE_STORE, fix group = compute group
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
id_fix = new char[n];
strcpy(id_fix,id);
strcat(id_fix,"_COMPUTE_STORE");
char **newarg = new char*[5];
newarg[0] = id_fix;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "0";
newarg[4] = (char *) "1";
modify->add_fix(5,newarg);
fix = (FixStore *) modify->fix[modify->nfix-1];
delete [] newarg;
// set fix store values = 0 for now
// fill them in via setup() once Comm::borders() has been called
// skip if resetting from restart file
if (fix->restart_reset) {
fix->restart_reset = 0;
firstflag = 0;
} else {
double *partner = fix->vstore;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) partner[i] = ubuf(0).d;
firstflag = 1;
}
// allocate memory
vector = new double[6];
maxatom = 0;
vint = NULL;
// set comm size needed by this Compute
comm_reverse = 1;
}
/* ---------------------------------------------------------------------- */
ComputeTempCS::~ComputeTempCS()
{
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
delete [] vector;
memory->destroy(vint);
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::init()
{
if (comm->ghost_velocity == 0)
error->all(FLERR,"Compute temp/cs requires ghost atoms store velocity");
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::setup()
{
if (firstflag) {
firstflag = 0;
// insure # of core atoms = # of shell atoms
int ncores = group->count(cgroup);
nshells = group->count(sgroup);
if (ncores != nshells)
error->all(FLERR,"Number of core atoms != number of shell atoms");
// for each C/S pair:
// set partner IDs of both atoms if this atom stores bond between them
// will set partner IDs for ghost atoms if needed by another proc
// nall loop insures all ghost atom partner IDs are set before reverse comm
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
tagint *tag = atom->tag;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *partner = fix->vstore;
tagint partnerID;
int nall = nlocal + atom->nghost;
for (int i = nlocal; i < nall; i++) partner[i] = ubuf(0).d;
int i,j,m,match;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
for (m = 0; m < num_bond[i]; m++) {
partnerID = bond_atom[i][m];
j = atom->map(partnerID);
if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
match = 0;
if (mask[i] & groupbit_c && mask[j] & groupbit_s) match = 1;
if (mask[i] & groupbit_s && mask[j] & groupbit_c) match = 1;
if (match) {
partner[i] = ubuf(partnerID).d;
partner[j] = ubuf(tag[i]).d;
}
}
}
}
// reverse comm to acquire unknown partner IDs from ghost atoms
// only needed if newton_bond = on
if (force->newton_bond) comm->reverse_comm_compute(this);
// check that all C/S partners were found
int flag = 0;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
partnerID = (tagint) ubuf(partner[i]).i;
if (partnerID == 0) flag = 1;
}
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all(FLERR,"Core/shell partners were not all found");
}
// calculate DOF for temperature
fix_dof = -1;
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::dof_compute()
{
if (fix_dof) adjust_dof_fix();
int nper = domain->dimension;
double natoms = group->count(igroup);
dof = nper * natoms;
dof -= nper * nshells;
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempCS::compute_scalar()
{
int i;
double vthermal[3];
invoked_scalar = update->ntimestep;
vcm_pairs();
// calculate thermal scalar in respect to atom velocities as center-of-mass
// velocities of its according core/shell pairs
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double t = 0.0;
for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit) {
vthermal[0] = v[i][0] - vint[i][0];
vthermal[1] = v[i][1] - vint[i][1];
vthermal[2] = v[i][2] - vint[i][2];
if (rmass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
}
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::compute_vector()
{
double vthermal[3];
invoked_vector = update->ntimestep;
vcm_pairs();
// calculate thermal vector in respect to atom velocities as center-of-mass
// velocities of its according C/S pairs
double **v = atom->v;
int *mask = atom->mask;
tagint *molecule = atom->molecule;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double massone;
double t[6];
for (int i = 0; i < 6; i++) t[i] = 0.0;
for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit) {
vthermal[0] = v[i][0] - vint[i][0];
vthermal[1] = v[i][1] - vint[i][1];
vthermal[2] = v[i][2] - vint[i][2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
t[0] += massone * vthermal[0]*vthermal[0];
t[1] += massone * vthermal[1]*vthermal[1];
t[2] += massone * vthermal[2]*vthermal[2];
t[3] += massone * vthermal[0]*vthermal[1];
t[4] += massone * vthermal[0]*vthermal[2];
t[5] += massone * vthermal[1]*vthermal[2];
}
}
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::vcm_pairs()
{
int i,j;
double massone,masstwo;
double vcm[3];
// reallocate vint if necessary
int nlocal = atom->nlocal;
if (nlocal > maxatom) {
memory->destroy(vint);
maxatom = atom->nmax;
memory->create(vint,maxatom,3,"temp/cs:vint");
}
// vcm = COM velocity of each CS pair
// vint = internal velocity of each C/S atom, used as bias
double **v = atom->v;
int *mask = atom->mask;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
double *partner = fix->vstore;
tagint partnerID;
for (int i = 0; i < nlocal; i++) {
if ((mask[i] & groupbit) &&
(mask[i] & groupbit_c || mask[i] & groupbit_s)) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
vcm[0] = v[i][0]*massone;
vcm[1] = v[i][1]*massone;
vcm[2] = v[i][2]*massone;
partnerID = (tagint) ubuf(partner[i]).i;
j = atom->map(partnerID);
if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
if (rmass) masstwo = rmass[j];
else masstwo = mass[type[j]];
vcm[0] += v[j][0]*masstwo;
vcm[1] += v[j][1]*masstwo;
vcm[2] += v[j][2]*masstwo;
vcm[0] /= (massone + masstwo);
vcm[1] /= (massone + masstwo);
vcm[2] /= (massone + masstwo);
vint[i][0] = v[i][0] - vcm[0];
vint[i][1] = v[i][1] - vcm[1];
vint[i][2] = v[i][2] - vcm[2];
} else vint[i][0] = vint[i][1] = vint[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
thermal velocity in this case is COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::remove_bias(int i, double *v)
{
v[0] -= vint[i][0];
v[1] -= vint[i][1];
v[2] -= vint[i][2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
thermal velocity in this case is COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::remove_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vint[i][0];
v[i][1] -= vint[i][1];
v[i][2] -= vint[i][2];
}
}
/* ----------------------------------------------------------------------
reset thermal velocity of all atoms to be consistent with bias
called from velocity command after it creates thermal velocities
this resets each atom's velocity to COM velocity of C/S pair
------------------------------------------------------------------------- */
void ComputeTempCS::reapply_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// recalculate current COM velocities
vcm_pairs();
// zero vint after using ti so that Velocity call to restore_bias_all()
// will not further alter the velocities within a C/S pair
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vint[i][0];
v[i][1] -= vint[i][1];
v[i][2] -= vint[i][2];
vint[i][0] = 0.0;
vint[i][1] = 0.0;
vint[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempCS::restore_bias(int i, double *v)
{
v[0] += vint[i][0];
v[1] += vint[i][1];
v[2] += vint[i][2];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempCS::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vint[i][0];
v[i][1] += vint[i][1];
v[i][2] += vint[i][2];
}
}
/* ---------------------------------------------------------------------- */
int ComputeTempCS::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
double *partner = fix->vstore;
m = 0;
last = first + n;
for (i = first; i < last; i++) buf[m++] = partner[i];
return m;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCS::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
double *partner = fix->vstore;
tagint partnerID;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
partnerID = (tagint) ubuf(buf[m++]).i;
if (partnerID) partner[j] = ubuf(partnerID).d;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeTempCS::memory_usage()
{
double bytes = (bigint) maxatom * 3 * sizeof(double);
return bytes;
}

120
src/CORESHELL/compute_temp_cs.h Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(temp/cs,ComputeTempCS)
#else
#ifndef LMP_COMPUTE_TEMP_CS_H
#define LMP_COMPUTE_TEMP_CS_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeTempCS : public Compute {
public:
ComputeTempCS(class LAMMPS *, int, char **);
~ComputeTempCS();
void init();
void setup();
double compute_scalar();
void compute_vector();
double memory_usage();
void remove_bias(int, double *);
void remove_bias_all();
void reapply_bias_all();
void restore_bias(int, double *);
void restore_bias_all();
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
private:
int groupbit_c,groupbit_s;
int nshells;
int firstflag;
int maxatom;
int cgroup,sgroup;
int fix_dof;
double tfactor;
double **vint;
char *id_fix;
class FixStore *fix;
void dof_compute();
void vcm_pairs();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Option mol of compute temp/vcm requires molecular atom style
Self-explanatory.
E: Option prop of compute temp/vcm requires one set of parameters
added by the property/atom fix
Self-explanatory.
E: Fix property/atom vector must contain only intergers to assign
sub-ID property
Self-explanatory.
E: Specified sub-ID property does not exist or has not been created
by the property/atom fix
Self-explanatory. Usually this means that the specified fix
property/atom ID does not match the ID stated in the compute temp/vcm.
E: Molecule count changed in compute com/temp/molecule
Number of molecules must remain constant over time.
E: Sub-ID count changed in compute vcm/temp
Number of Sub-ID groups must remain constant over time.
W: Atom with sub-ID = 0 included in compute group
Self-explanatory. A sub-ID with value 0 will be counted as a normal sub-ID
and not left out of by the compute treatment. Therefore a sub-ID of 0 is to
be avoided.
E: Too many sub-ID groups for compute
Self-explanatory.
W: More than 2 atoms specified with the same sub-ID, in the case
of a core-shell model simulation only core and shell should share the same ID
Self-explanatory.
*/

199
src/CORESHELL/pair_born_coul_long_cs.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_born_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
#define EPSILON 1.0e-20
#define EPS_EWALD 1.0e-6
#define EPS_EWALD_SQR 1.0e-12
/* ---------------------------------------------------------------------- */
PairBornCoulLongCS::PairBornCoulLongCS(LAMMPS *lmp) : PairBornCoulLong(lmp)
{
ewaldflag = pppmflag = 1;
ftable = NULL;
writedata = 1;
}
/* ---------------------------------------------------------------------- */
void PairBornCoulLongCS::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itable,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double r,rexp;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j];
if (factor_coul < 1.0) {
// When bonded parts are being calculated a minimal distance (EPS_EWALD)
// has to be added to the prefactor and erfc in order to make the
// used approximation functions valid
grij = g_ewald * (r+EPS_EWALD);
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor /= (r+EPS_EWALD);
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - (1.0-factor_coul));
// Additionally r2inv needs to be accordingly modified since the later
// scaling of the overall force shall be consistent
r2inv = 1.0/(rsq + EPS_EWALD_SQR);
} else {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor /= r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r = sqrt(rsq);
r6inv = r2inv*r2inv*r2inv;
rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
+ born3[itype][jtype]*r2inv*r6inv;
} else forceborn = 0.0;
fpair = (forcecoul + factor_lj*forceborn) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
+ d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}

67
src/CORESHELL/pair_born_coul_long_cs.h Normal file
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@ -0,0 +1,67 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.com)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(born/coul/long/cs,PairBornCoulLongCS)
#else
#ifndef LMP_PAIR_BORN_COUL_LONG_CS_H
#define LMP_PAIR_BORN_COUL_LONG_CS_H
#include "pair_born_coul_long.h"
namespace LAMMPS_NS {
class PairBornCoulLongCS : public PairBornCoulLong {
public:
PairBornCoulLongCS(class LAMMPS *);
virtual void compute(int, int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Pair style born/coul/long requires atom attribute q
An atom style that defines this attribute must be used.
E: Pair style requires a KSpace style
No kspace style is defined.
*/

197
src/CORESHELL/pair_buck_coul_long_cs.cpp Normal file
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@ -0,0 +1,197 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.de)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_buck_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
#define EPSILON 1.0e-20
#define EPS_EWALD 1.0e-6
#define EPS_EWALD_SQR 1.0e-12
/* ---------------------------------------------------------------------- */
PairBuckCoulLongCS::PairBuckCoulLongCS(LAMMPS *lmp) : PairBuckCoulLong(lmp)
{
ewaldflag = pppmflag = 1;
writedata = 1;
ftable = NULL;
}
/* ---------------------------------------------------------------------- */
void PairBuckCoulLongCS::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itable,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double fraction,table;
double rsq,r2inv,r6inv,forcecoul,forcebuck,factor_coul,factor_lj;
double grij,expm2,prefactor,t,erfc;
double r,rexp;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qtmp = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
rsq += EPSILON; // Add Epsilon for case: r = 0; Interaction must be removed by special bond;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) {
r = sqrt(rsq);
prefactor = qqrd2e * qtmp*q[j];
if (factor_coul < 1.0) {
// When bonded parts are being calculated a minimal distance (EPS_EWALD)
// has to be added to the prefactor and erfc in order to make the
// used approximation functions for the Ewald correction valid
grij = g_ewald * (r+EPS_EWALD);
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor /= (r+EPS_EWALD);
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2 - (1.0-factor_coul));
// Additionally r2inv needs to be accordingly modified since the later
// scaling of the overall force shall be consistent
r2inv = 1.0/(rsq + EPS_EWALD_SQR);
} else {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
prefactor /= r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
}
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r = sqrt(rsq);
r6inv = r2inv*r2inv*r2inv;
rexp = exp(-r*rhoinv[itype][jtype]);
forcebuck = buck1[itype][jtype]*r*rexp - buck2[itype][jtype]*r6inv;
} else forcebuck = 0.0;
fpair = (forcecoul + factor_lj*forcebuck) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}

67
src/CORESHELL/pair_buck_coul_long_cs.h Normal file
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@ -0,0 +1,67 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Hendrik Heenen (hendrik.heenen@mytum.com)
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(buck/coul/long/cs,PairBuckCoulLongCS)
#else
#ifndef LMP_PAIR_BUCK_COUL_LONG_CS_H
#define LMP_PAIR_BUCK_COUL_LONG_CS_H
#include "pair_buck_coul_long.h"
namespace LAMMPS_NS {
class PairBuckCoulLongCS : public PairBuckCoulLong {
public:
PairBuckCoulLongCS(class LAMMPS *);
virtual void compute(int, int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Pair style buck/coul/long requires atom attribute q
The atom style defined does not have these attributes.
E: Pair style requires a KSpace style
No kspace style is defined.
*/

2
src/Makefile
View File

@ -13,7 +13,7 @@ OBJ = $(SRC:.cpp=.o)
# Package variables
PACKAGE = asphere body class2 colloid dipole fld gpu granular kim \
PACKAGE = asphere body class2 colloid coreshell dipole fld gpu granular kim \
kokkos kspace manybody mc meam misc molecule mpiio opt peri poems \
qeq reax replica rigid shock snap srd voronoi xtc

4
src/velocity.cpp
View File

@ -99,15 +99,15 @@ void Velocity::command(int narg, char **arg)
else if (style == ZERO) options(narg-3,&arg[3]);
// special cases where full init and border communication must be done first
// for CREATE/SET if compute temp/cs is used
// for ZERO if fix rigid/small is used
// for CREATE/SET if compute temp/cs is used
// b/c methods invoked in the compute/fix perform forward/reverse comm
int initcomm = 0;
if (style == ZERO && rfix >= 0 &&
strcmp(modify->fix[rfix]->style,"rigid/small") == 0) initcomm = 1;
if ((style == CREATE || style == SET) && temperature &&
strcmp(temperature->style,"temp/cs2") == 0) initcomm = 1;
strcmp(temperature->style,"temp/cs") == 0) initcomm = 1;
if (initcomm) {
lmp->init();

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "5 Mar 2015"
#define LAMMPS_VERSION "6 Mar 2015"