mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12153 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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@ -534,43 +534,44 @@ package</A>.
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<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/gpu</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/msm/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/cuda</A></TD><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/omp</A></TD><TD ><A HREF = "pair_colloid.html">colloid/gpu</A></TD><TD ><A HREF = "pair_colloid.html">colloid/omp</A></TD><TD ><A HREF = "pair_comb.html">comb/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut/omp</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/cut/soft/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/debye/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/dsf/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/dsf/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/long/gpu</A></TD><TD ><A HREF = "pair_coul.html">coul/long/omp</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/long/soft/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/msm/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf</A></TD><TD ><A HREF = "pair_dpd.html">dpd/omp</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/cd/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_edip.html">edip/omp</A></TD><TD ><A HREF = "pair_eim.html">eim/omp</A></TD><TD ><A HREF = "pair_gauss.html">gauss/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gauss.html">gauss/omp</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/omp</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse/omp</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/omp</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/charmm/coul/long/soft</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/charmm/coul/long/soft/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/msm/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm/opt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/kk</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut/omp</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf/gpu</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/opt</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/gpu</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/opt</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm/omp</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf/omp</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/omp</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear/omp</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly/omp</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_mie.html">mie/cut/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic/omp</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/omp</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_peri.html">peri/lps/omp</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb/omp</A></TD><TD ><A HREF = "pair_airebo.html">rebo/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared/gpu</A></TD><TD ><A HREF = "pair_resquared.html">resquared/omp</A></TD><TD ><A HREF = "pair_soft.html">soft/gpu</A></TD><TD ><A HREF = "pair_soft.html">soft/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw/cuda</A></TD><TD ><A HREF = "pair_sw.html">sw/gpu</A></TD><TD ><A HREF = "pair_sw.html">sw/omp</A></TD><TD ><A HREF = "pair_table.html">table/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table/kk</A></TD><TD ><A HREF = "pair_table.html">table/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/cuda</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table/omp</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl/omp</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/long/omp</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft/omp</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj/omp</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_yukawa.html">yukawa/omp</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/gpu</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/omp</A></TD><TD ><A HREF = "pair_zbl.html">zbl/omp</A>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut/gpu</A></TD><TD ><A HREF = "pair_coul.html">coul/cut/omp</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/cut/soft/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/debye/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/debye/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/dsf/gpu</A></TD><TD ><A HREF = "pair_coul.html">coul/dsf/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/long/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/long/omp</A></TD><TD ><A HREF = "pair_lj_soft.html">coul/long/soft/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/msm/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd/omp</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/cd/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_edip.html">edip/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_eim.html">eim/omp</A></TD><TD ><A HREF = "pair_gauss.html">gauss/gpu</A></TD><TD ><A HREF = "pair_gauss.html">gauss/omp</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke/omp</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj/omp</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse/omp</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/omp</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/charmm/coul/long/soft</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj_soft.html">lj/charmm/coul/long/soft/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/msm/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/omp</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/omp</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/cut/soft/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/opt</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm/opt</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/coul/long/soft/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/kk</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut/gpu</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut/omp</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf/gpu</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/soft/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/omp</A></TD></TR>
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<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/opt</A></TD><TD ><A HREF = "pair_lj_soft.html">lj/cut/tip4p/long/soft/omp</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/gpu</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/omp</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/opt</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj_sf.html">lj/sf/omp</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/omp</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/poly/omp</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline/omp</A></TD><TD ><A HREF = "pair_mie.html">mie/cut/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/omp</A></TD><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/omp</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut/omp</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_peri.html">peri/lps/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb/omp</A></TD><TD ><A HREF = "pair_airebo.html">rebo/omp</A></TD><TD ><A HREF = "pair_resquared.html">resquared/gpu</A></TD><TD ><A HREF = "pair_resquared.html">resquared/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft/gpu</A></TD><TD ><A HREF = "pair_soft.html">soft/omp</A></TD><TD ><A HREF = "pair_sw.html">sw/cuda</A></TD><TD ><A HREF = "pair_sw.html">sw/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw/omp</A></TD><TD ><A HREF = "pair_table.html">table/gpu</A></TD><TD ><A HREF = "pair_table.html">table/kk</A></TD><TD ><A HREF = "pair_table.html">table/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/cuda</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/omp</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl/omp</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut/omp</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long/omp</A></TD><TD ><A HREF = "pair_lj_soft.html">tip4p/long/soft/omp</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_tri_lj.html">tri/lj/omp</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/gpu</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/omp</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/gpu</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/omp</A></TD><TD ><A HREF = "pair_zbl.html">zbl/omp</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<HR>
|
||||
|
|
|
|||
|
|
@ -905,8 +905,10 @@ package"_Section_accelerate.html.
|
|||
"colloid/gpu"_pair_colloid.html,
|
||||
"colloid/omp"_pair_colloid.html,
|
||||
"comb/omp"_pair_comb.html,
|
||||
"coul/cut/gpu"_pair_coul.html,
|
||||
"coul/cut/omp"_pair_coul.html,
|
||||
"coul/cut/soft/omp"_pair_lj_soft.html,
|
||||
"coul/debye/gpu"_pair_coul.html,
|
||||
"coul/debye/omp"_pair_coul.html,
|
||||
"coul/dsf/gpu"_pair_coul.html,
|
||||
"coul/dsf/omp"_pair_coul.html,
|
||||
|
|
|
|||
|
|
@ -11,10 +11,14 @@
|
|||
|
||||
<H3>pair_style coul/cut command
|
||||
</H3>
|
||||
<H3>pair_style coul/cut/gpu command
|
||||
</H3>
|
||||
<H3>pair_style coul/cut/omp command
|
||||
</H3>
|
||||
<H3>pair_style coul/debye command
|
||||
</H3>
|
||||
<H3>pair_style coul/debye/gpu command
|
||||
</H3>
|
||||
<H3>pair_style coul/debye/omp command
|
||||
</H3>
|
||||
<H3>pair_style coul/dsf command
|
||||
|
|
|
|||
|
|
@ -7,8 +7,10 @@
|
|||
:line
|
||||
|
||||
pair_style coul/cut command :h3
|
||||
pair_style coul/cut/gpu command :h3
|
||||
pair_style coul/cut/omp command :h3
|
||||
pair_style coul/debye command :h3
|
||||
pair_style coul/debye/gpu command :h3
|
||||
pair_style coul/debye/omp command :h3
|
||||
pair_style coul/dsf command :h3
|
||||
pair_style coul/dsf/gpu command :h3
|
||||
|
|
|
|||
|
|
@ -25,7 +25,7 @@ pair_coeff * * Ar Ar
|
|||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>This pair style is a wrapper on the <A HREF = "http://openkim.org">Knowledge Base for Interatomic
|
||||
<P>This pair style is a wrapper on the <A HREF = "https://openkim.org">Knowledge Base for Interatomic
|
||||
Models (KIM)</A> repository of interatomic potentials,
|
||||
so that they can be used by LAMMPS scripts.
|
||||
</P>
|
||||
|
|
@ -36,8 +36,8 @@ cutoffs.
|
|||
</P>
|
||||
<P>The argument <I>virialmode</I> determines how the global virial is
|
||||
calculated. If <I>KIMvirial</I> is specified, the KIM model performs the
|
||||
global virial calculation. If <I>LAMMPSvirial</I> is specified, LAMMPS
|
||||
computes the global virial using its fdotr mechanism.
|
||||
global virial calculation (if it knows how). If <I>LAMMPSvirial</I> is
|
||||
specified, LAMMPS computes the global virial using its fdotr mechanism.
|
||||
</P>
|
||||
<P>The argument <I>model</I> is the name of the KIM model for a specific
|
||||
potential as KIM defines it. In principle, LAMMPS can invoke any KIM
|
||||
|
|
@ -76,174 +76,118 @@ directory where LAMMPS is running.
|
|||
</P>
|
||||
<HR>
|
||||
|
||||
<P>Here is information on how to build KIM for use with LAMMPS. There is
|
||||
a directory src/KIM/ with an important file in it: Makefile.lammps.
|
||||
When you do 'make yes-kim' LAMMPS will use the settings in
|
||||
src/KIM/Makefile.lammps to find KIM header files and the KIM library
|
||||
itself for linking purposes. Thus, you should ensure Makefile.lammps
|
||||
has the correct settings for your system and your build of KIM.
|
||||
<P>Here is information on how to build KIM for use with LAMMPS.
|
||||
</P>
|
||||
<P>Consult the KIM documentation for further details on KIM specifics.
|
||||
</P>
|
||||
<P>OpenKIM is available for download from <A HREF = "http://openkim.org">this site</A>,
|
||||
namely http://openkim.org. The tarball you download is
|
||||
"openkim-api-vX.X.X.tgz", which can be unpacked via
|
||||
<P>The KIM API is available for download from <A HREF = "https://openkim.org">this
|
||||
site</A>, namely https://openkim.org. The tarball
|
||||
you download is "openkim-api-vX.X.X.tgz", which can be unpacked via
|
||||
</P>
|
||||
<PRE>tar xvfz openkim*tgz
|
||||
</PRE>
|
||||
<P>The openkim-api-vX.X.X/DOCS directory has further documentation. For
|
||||
more information on installing KIM and troubleshooting refer to
|
||||
openkim/INSTALL.
|
||||
<P>The openkim-api-vX.X.X/DOCS/ directory has further documentation. In
|
||||
order to compile and install the KIM API follow the instructions found
|
||||
in the file openkim-api-vX.X.X/INSTALL. (Don't forget to download and
|
||||
compile any Model Drivers and Models that you want to use.)
|
||||
</P>
|
||||
<P>Here is a brief summary of how to build KIM:
|
||||
<P>Once you have successfully compiled and installed the KIM API, you
|
||||
need to set up LAMMPS to use your KIM API system. In the LAMMPS
|
||||
package there is a directory src/KIM/ with an important file in it:
|
||||
Makefile.lammps. When you do 'make yes-kim' LAMMPS will use the
|
||||
settings in src/KIM/Makefile.lammps to find the KIM API header files
|
||||
and the KIM API library itself for linking purposes. Thus, you should
|
||||
edit src/KIM/Makefile.lammps to ensure it has the correct settings for
|
||||
your system and your build of KIM.
|
||||
</P>
|
||||
<OL><LI>If you have previously used the openkim-api package (versions 1.1.1 or
|
||||
below), it is recommended that you remove all associated environment
|
||||
variables from your environment. (These include, KIM_DIR, KIM_INTEL,
|
||||
KIM_SYSTEM32, KIM_DYNAMIC, KIM_API_DIR, KIM_TESTS_DIR,
|
||||
KIM_MODEL_DRIVERS_DIR, and KIM_MODELS_DIR.) All setting are now
|
||||
specified in the Makefile.KIM_Config file.
|
||||
<P>The following is an example of how to download, compile, and run
|
||||
LAMMPS with the KIM API:
|
||||
</P>
|
||||
<pre>
|
||||
mkdir lammps-kim
|
||||
cd lammps-kim
|
||||
|
||||
<LI>Set up the Makefile.KIM_Config file
|
||||
#
|
||||
# download lammps and the KIM API
|
||||
#
|
||||
|
||||
<PRE> (a) Copy the file Makefile.KIM_Config.example to Makefile.KIM_Config
|
||||
For example, if you untarred the `openkim-api-vX.X.X.tgz' tarball in
|
||||
your home directory, you would do:
|
||||
</PRE>
|
||||
<PRE> % cd $HOME/openkim-api-vX.X.X
|
||||
% cp Makefile.KIM_Config.example Makefile.KIM_Config
|
||||
</PRE>
|
||||
<PRE> The `%' symbol represents the bash sell prompt and should not be typed.
|
||||
wget http://lammps.sandia.gov/tars/lammps-DDMMMYY.tar.gz # replace DDMMMYY as appropriate here and below
|
||||
wget http://s3.openkim.org/openkim-api/openkim-api-vX.X.X.tgz # replace X.X.X as appropriate here and below
|
||||
tar zxvf openkim-api-vX.X.X.tgz
|
||||
|
||||
</PRE>
|
||||
<PRE> (Above `vX.X.X' represents the current release number.)
|
||||
</PRE>
|
||||
<PRE> (b) Edit the file Makefile.KIM_Config and set the appropriate value for the
|
||||
KIM_DIR variable. This must expand to an absolute path. Using the same
|
||||
assumptions as above, this would be
|
||||
</PRE>
|
||||
<PRE> KIM_DIR = $(HOME)/openkim-api-vX.X.X
|
||||
</PRE>
|
||||
<PRE> (c) If appropriate, set explicit values for the remaining three
|
||||
directories
|
||||
</PRE>
|
||||
<PRE> KIM_MODEL_DRIVERS_DIR =
|
||||
KIM_MODELS_DIR =
|
||||
KIM_TESTS_DIR =
|
||||
</PRE>
|
||||
<PRE> If these lines are commented out, defaults will be provided by the
|
||||
openkim-api make system.
|
||||
</PRE>
|
||||
<PRE> (d) Set the value of KIM_COMPILERSUITE. Possible values are `GCC' and
|
||||
`INTEL'.
|
||||
</PRE>
|
||||
<PRE> KIM_COMPILERSUITE = GCC
|
||||
</PRE>
|
||||
<PRE> (e) Set the value of KIM_SYSTEMLINKER. Possible values are `linux',
|
||||
`freebsd', and `darwin'.
|
||||
</PRE>
|
||||
<PRE> KIM_SYSTEMLINKER = linux
|
||||
</PRE>
|
||||
<PRE> (f) Set the value of KIM_SYSTEMARCH. Possible values are `32bit' and
|
||||
`64bit'.
|
||||
</PRE>
|
||||
<PRE> KIM_SYSTEMARCH = 64bit
|
||||
</PRE>
|
||||
<PRE> (g) Set the value of KIM_LINK. Possible values are `dynamic-load',
|
||||
`dynamic-link', and `static-link'.
|
||||
</PRE>
|
||||
<PRE> KIM_LINK = dynamic-load
|
||||
</PRE>
|
||||
<PRE> `dynamic-load' is the preferred option. (Unless performance or
|
||||
other issues require it, you should use dynamic-load.)
|
||||
`dynamic-link' is like `dynamic-load' but does not use the dl.h
|
||||
library. This option requires a more complicated Makefile
|
||||
process, but may improve computation time in some instances.
|
||||
`static-link' only works with ONE Model and AT MOST ONE Model
|
||||
Driver (in order to avoid the possibility of symbol
|
||||
clashes).
|
||||
</PRE>
|
||||
<PRE> (h) Set override values for other variables, if necessary, by
|
||||
adding the desired variable name (after the "# overwrite
|
||||
default variable values here" line) and filling in appropriate
|
||||
values.
|
||||
</PRE>
|
||||
<PRE> # overwrite default variable values here
|
||||
</PRE>
|
||||
<PRE> # overwrite default compiler options
|
||||
</PRE>
|
||||
<PRE> CC =
|
||||
CXX =
|
||||
FC =
|
||||
</PRE>
|
||||
<PRE> # overwrite default compiler option flag lists
|
||||
FFLAGS =
|
||||
CCFLAGS =
|
||||
CXXFLAGS =
|
||||
LDFLAGS =
|
||||
</PRE>
|
||||
<PRE> # overwrite default linker options
|
||||
LDSHAREDFLAG =
|
||||
LINKSONAME =
|
||||
LDWHOLEARCHIVESTARTFLAG =
|
||||
LDWHOLEARCHIVEENDFLAG =
|
||||
</PRE>
|
||||
<PRE> # overwrite default install directories
|
||||
package_name =
|
||||
prefix =
|
||||
libdir =
|
||||
</PRE>
|
||||
<LI>In the remainder of the documentation we will use the string $KD to
|
||||
represent the location of the openkim-api source package (the value of
|
||||
the KIM_DIR variable discussed above). If you wish to, type the below
|
||||
commands exactly as written to set the shell variable KD to the
|
||||
appropriate value:
|
||||
#
|
||||
# Get OpenKIM models, setup and compile
|
||||
#
|
||||
|
||||
<PRE> bash:
|
||||
% export KD=$HOME/openkim-api-vX.X.X
|
||||
</PRE>
|
||||
<LI>To compile the package, including the provided examples, change to the
|
||||
$KD directory and execute `make examples' and then `make':
|
||||
cd openkim-api-vX.X.X
|
||||
cp Makefile.KIM_Config.example Makefile.KIM_Config
|
||||
vi Makefile.KIM_Config # edit file as appropriate following the instructions given in the INSTALL file
|
||||
cd MODEL_DRIVERS
|
||||
wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo__MD_120291908751_000&compression=gz'
|
||||
tar zxvf EAM_Dynamo__MD_120291908751_000.tgz
|
||||
cd ../MODELS
|
||||
wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000&compression=gz'
|
||||
tar zxvf EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000.tgz
|
||||
cd ../
|
||||
make
|
||||
cd ../
|
||||
|
||||
<PRE> % cd $KD
|
||||
% make examples
|
||||
% make
|
||||
</PRE>
|
||||
<PRE> This builds all Model Drivers, Models, Tests, and the openkim-api service
|
||||
routine library. The targets defined by the Makefile in this directory
|
||||
include:
|
||||
</PRE>
|
||||
<PRE> `make' -- compiles the API and all Models and Tests
|
||||
`make all' -- same as `make'
|
||||
`make clean' -- will remove appropriate .o, .mod, .a, .so and
|
||||
executable files
|
||||
`make install' -- install files to `/usr/local/lib' by default
|
||||
`make uninstall' -- delete files installed by `make install'
|
||||
`make openkim-api' -- compiles only the API
|
||||
`make examples' -- copies examples into the appropriate
|
||||
directories (no overwrite)
|
||||
`make examples-force' -- copies examples into the appropriate
|
||||
directories (overwrite)
|
||||
`make examples-clean' -- remove all examples from the MODEL_DRIVERS,
|
||||
MODELS, and TESTS directories.
|
||||
</PRE>
|
||||
<LI>Verify that the compilation was successful by running a Test.
|
||||
#
|
||||
# setup and compile lammps
|
||||
#
|
||||
|
||||
tar zxvf lammps-DDMMMYY.tar.gz
|
||||
cd lammps-DDMMMYY/src/KIM
|
||||
vi Makefile.lammps # edit the three lines to look like below:
|
||||
# kim_SYSINC = -I../../../openkim-api-vX.X.X/KIM_API
|
||||
# kim_SYSLIB = -lkim
|
||||
# kim_SYSPATH = -L../../../openkim-api-vX.X.X/KIM_API
|
||||
cd ../
|
||||
make yes-kim
|
||||
cd STUBS
|
||||
make
|
||||
cd ../
|
||||
make serial
|
||||
|
||||
#
|
||||
# run simple example with KIM model
|
||||
#
|
||||
|
||||
cd ../../
|
||||
vi al-input # create file with the following content
|
||||
#----------------------------------------------------------------------------------------
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 4.0500
|
||||
region box block 0.0 ${xx} 0.0 ${yy} 0.0 ${zz}
|
||||
create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style kim KIMvirial EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000
|
||||
pair_coeff * * Al
|
||||
|
||||
mass 1 26.98
|
||||
velocity all create 200.0 232345 loop geom
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 100
|
||||
#----------------------------------------------------------------------------------------
|
||||
|
||||
./lammps-DDMMYY/src/lmp_serial < al-input
|
||||
|
||||
</pre>
|
||||
|
||||
<PRE> The provided example Tests read in the name of a Model (or Models)
|
||||
which they use to perform their calculations. For most Tests the
|
||||
name of the Model can be piped in using an `echo' command. For
|
||||
example, the following Fortran 90 Test reads in one Model:
|
||||
</PRE>
|
||||
<PRE> % cd $KD/TESTs/test_Ar_free_cluster_CLUSTER_F90
|
||||
% echo "model_Ar_P_MLJ_CLUSTER_C" | ./test_Ar_free_cluster_CLUSTER_F90
|
||||
</PRE>
|
||||
<PRE> (See the README files in the Test directories for an explanation of what
|
||||
the Tests do.)
|
||||
</PRE>
|
||||
<LI>Each Test (and Model) has its own make file for compiling and linking.
|
||||
If changes are made to the code, re-compile (from the $KD
|
||||
directory).
|
||||
</OL>
|
||||
<HR>
|
||||
|
||||
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
|
||||
|
|
|
|||
234
doc/pair_kim.txt
234
doc/pair_kim.txt
|
|
@ -23,7 +23,7 @@ pair_coeff * * Ar Ar :pre
|
|||
[Description:]
|
||||
|
||||
This pair style is a wrapper on the "Knowledge Base for Interatomic
|
||||
Models (KIM)"_http://openkim.org repository of interatomic potentials,
|
||||
Models (KIM)"_https://openkim.org repository of interatomic potentials,
|
||||
so that they can be used by LAMMPS scripts.
|
||||
|
||||
In KIM lingo, a potential is a "model" and a model contains both the
|
||||
|
|
@ -33,8 +33,8 @@ cutoffs.
|
|||
|
||||
The argument {virialmode} determines how the global virial is
|
||||
calculated. If {KIMvirial} is specified, the KIM model performs the
|
||||
global virial calculation. If {LAMMPSvirial} is specified, LAMMPS
|
||||
computes the global virial using its fdotr mechanism.
|
||||
global virial calculation (if it knows how). If {LAMMPSvirial} is
|
||||
specified, LAMMPS computes the global virial using its fdotr mechanism.
|
||||
|
||||
The argument {model} is the name of the KIM model for a specific
|
||||
potential as KIM defines it. In principle, LAMMPS can invoke any KIM
|
||||
|
|
@ -73,172 +73,116 @@ directory where LAMMPS is running.
|
|||
|
||||
:line
|
||||
|
||||
Here is information on how to build KIM for use with LAMMPS. There is
|
||||
a directory src/KIM/ with an important file in it: Makefile.lammps.
|
||||
When you do 'make yes-kim' LAMMPS will use the settings in
|
||||
src/KIM/Makefile.lammps to find KIM header files and the KIM library
|
||||
itself for linking purposes. Thus, you should ensure Makefile.lammps
|
||||
has the correct settings for your system and your build of KIM.
|
||||
Here is information on how to build KIM for use with LAMMPS.
|
||||
|
||||
Consult the KIM documentation for further details on KIM specifics.
|
||||
|
||||
OpenKIM is available for download from "this site"_http://openkim.org,
|
||||
namely http://openkim.org. The tarball you download is
|
||||
"openkim-api-vX.X.X.tgz", which can be unpacked via
|
||||
The KIM API is available for download from "this
|
||||
site"_https://openkim.org, namely https://openkim.org. The tarball
|
||||
you download is "openkim-api-vX.X.X.tgz", which can be unpacked via
|
||||
|
||||
tar xvfz openkim*tgz :pre
|
||||
|
||||
The openkim-api-vX.X.X/DOCS directory has further documentation. For
|
||||
more information on installing KIM and troubleshooting refer to
|
||||
openkim/INSTALL.
|
||||
The openkim-api-vX.X.X/DOCS/ directory has further documentation. In
|
||||
order to compile and install the KIM API follow the instructions found
|
||||
in the file openkim-api-vX.X.X/INSTALL. (Don't forget to download and
|
||||
compile any Model Drivers and Models that you want to use.)
|
||||
|
||||
Here is a brief summary of how to build KIM:
|
||||
Once you have successfully compiled and installed the KIM API, you
|
||||
need to set up LAMMPS to use your KIM API system. In the LAMMPS
|
||||
package there is a directory src/KIM/ with an important file in it:
|
||||
Makefile.lammps. When you do 'make yes-kim' LAMMPS will use the
|
||||
settings in src/KIM/Makefile.lammps to find the KIM API header files
|
||||
and the KIM API library itself for linking purposes. Thus, you should
|
||||
edit src/KIM/Makefile.lammps to ensure it has the correct settings for
|
||||
your system and your build of KIM.
|
||||
|
||||
If you have previously used the openkim-api package (versions 1.1.1 or
|
||||
below), it is recommended that you remove all associated environment
|
||||
variables from your environment. (These include, KIM_DIR, KIM_INTEL,
|
||||
KIM_SYSTEM32, KIM_DYNAMIC, KIM_API_DIR, KIM_TESTS_DIR,
|
||||
KIM_MODEL_DRIVERS_DIR, and KIM_MODELS_DIR.) All setting are now
|
||||
specified in the Makefile.KIM_Config file. :olb,l
|
||||
The following is an example of how to download, compile, and run
|
||||
LAMMPS with the KIM API:
|
||||
|
||||
Set up the Makefile.KIM_Config file :l
|
||||
<pre>
|
||||
mkdir lammps-kim
|
||||
cd lammps-kim :
|
||||
|
||||
(a) Copy the file Makefile.KIM_Config.example to Makefile.KIM_Config
|
||||
For example, if you untarred the `openkim-api-vX.X.X.tgz' tarball in
|
||||
your home directory, you would do: :pre
|
||||
#
|
||||
# download lammps and the KIM API
|
||||
# :
|
||||
|
||||
% cd $HOME/openkim-api-vX.X.X
|
||||
% cp Makefile.KIM_Config.example Makefile.KIM_Config :pre
|
||||
wget http://lammps.sandia.gov/tars/lammps-DDMMMYY.tar.gz # replace DDMMMYY as appropriate here and below
|
||||
wget http://s3.openkim.org/openkim-api/openkim-api-vX.X.X.tgz # replace X.X.X as appropriate here and below
|
||||
tar zxvf openkim-api-vX.X.X.tgz :
|
||||
|
||||
The `%' symbol represents the bash sell prompt and should not be typed.
|
||||
:pre
|
||||
#
|
||||
# Get OpenKIM models, setup and compile
|
||||
# :
|
||||
|
||||
(Above `vX.X.X' represents the current release number.) :pre
|
||||
cd openkim-api-vX.X.X
|
||||
cp Makefile.KIM_Config.example Makefile.KIM_Config
|
||||
vi Makefile.KIM_Config # edit file as appropriate following the instructions given in the INSTALL file
|
||||
cd MODEL_DRIVERS
|
||||
wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo__MD_120291908751_000&compression=gz'
|
||||
tar zxvf EAM_Dynamo__MD_120291908751_000.tgz
|
||||
cd ../MODELS
|
||||
wget --content-disposition 'https://kim-items.openkim.org/archive?kimid=EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000&compression=gz'
|
||||
tar zxvf EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000.tgz
|
||||
cd ../
|
||||
make
|
||||
cd ../ :
|
||||
|
||||
(b) Edit the file Makefile.KIM_Config and set the appropriate value for the
|
||||
KIM_DIR variable. This must expand to an absolute path. Using the same
|
||||
assumptions as above, this would be :pre
|
||||
#
|
||||
# setup and compile lammps
|
||||
# :
|
||||
|
||||
KIM_DIR = $(HOME)/openkim-api-vX.X.X :pre
|
||||
tar zxvf lammps-DDMMMYY.tar.gz
|
||||
cd lammps-DDMMMYY/src/KIM
|
||||
vi Makefile.lammps # edit the three lines to look like below:
|
||||
# kim_SYSINC = -I../../../openkim-api-vX.X.X/KIM_API
|
||||
# kim_SYSLIB = -lkim
|
||||
# kim_SYSPATH = -L../../../openkim-api-vX.X.X/KIM_API
|
||||
cd ../
|
||||
make yes-kim
|
||||
cd STUBS
|
||||
make
|
||||
cd ../
|
||||
make serial :
|
||||
|
||||
(c) If appropriate, set explicit values for the remaining three
|
||||
directories :pre
|
||||
#
|
||||
# run simple example with KIM model
|
||||
# :
|
||||
|
||||
KIM_MODEL_DRIVERS_DIR =
|
||||
KIM_MODELS_DIR =
|
||||
KIM_TESTS_DIR = :pre
|
||||
cd ../../
|
||||
vi al-input # create file with the following content
|
||||
#----------------------------------------------------------------------------------------
|
||||
variable x index 1
|
||||
variable y index 1
|
||||
variable z index 1 :
|
||||
|
||||
If these lines are commented out, defaults will be provided by the
|
||||
openkim-api make system. :pre
|
||||
variable xx equal 20*$x
|
||||
variable yy equal 20*$y
|
||||
variable zz equal 20*$z :
|
||||
|
||||
(d) Set the value of KIM_COMPILERSUITE. Possible values are `GCC' and
|
||||
`INTEL'. :pre
|
||||
units metal
|
||||
atom_style atomic :
|
||||
|
||||
KIM_COMPILERSUITE = GCC :pre
|
||||
lattice fcc 4.0500
|
||||
region box block 0.0 $\{xx\} 0.0 $\{yy\} 0.0 $\{zz\}
|
||||
create_box 1 box
|
||||
create_atoms 1 box :
|
||||
|
||||
(e) Set the value of KIM_SYSTEMLINKER. Possible values are `linux',
|
||||
`freebsd', and `darwin'. :pre
|
||||
pair_style kim KIMvirial EAM_Dynamo_Angelo_Moody_NiAlH__MO_418978237058_000
|
||||
pair_coeff * * Al :
|
||||
|
||||
KIM_SYSTEMLINKER = linux :pre
|
||||
mass 1 26.98
|
||||
velocity all create 200.0 232345 loop geom :
|
||||
|
||||
(f) Set the value of KIM_SYSTEMARCH. Possible values are `32bit' and
|
||||
`64bit'. :pre
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes :
|
||||
|
||||
KIM_SYSTEMARCH = 64bit :pre
|
||||
fix 1 all nve :
|
||||
|
||||
(g) Set the value of KIM_LINK. Possible values are `dynamic-load',
|
||||
`dynamic-link', and `static-link'. :pre
|
||||
run 100
|
||||
#---------------------------------------------------------------------------------------- :
|
||||
|
||||
KIM_LINK = dynamic-load :pre
|
||||
|
||||
`dynamic-load' is the preferred option. (Unless performance or
|
||||
other issues require it, you should use dynamic-load.)
|
||||
`dynamic-link' is like `dynamic-load' but does not use the dl.h
|
||||
library. This option requires a more complicated Makefile
|
||||
process, but may improve computation time in some instances.
|
||||
`static-link' only works with ONE Model and AT MOST ONE Model
|
||||
Driver (in order to avoid the possibility of symbol
|
||||
clashes). :pre
|
||||
|
||||
(h) Set override values for other variables, if necessary, by
|
||||
adding the desired variable name (after the "# overwrite
|
||||
default variable values here" line) and filling in appropriate
|
||||
values. :pre
|
||||
|
||||
# overwrite default variable values here :pre
|
||||
|
||||
# overwrite default compiler options :pre
|
||||
CC =
|
||||
CXX =
|
||||
FC = :pre
|
||||
|
||||
# overwrite default compiler option flag lists
|
||||
FFLAGS =
|
||||
CCFLAGS =
|
||||
CXXFLAGS =
|
||||
LDFLAGS = :pre
|
||||
|
||||
# overwrite default linker options
|
||||
LDSHAREDFLAG =
|
||||
LINKSONAME =
|
||||
LDWHOLEARCHIVESTARTFLAG =
|
||||
LDWHOLEARCHIVEENDFLAG = :pre
|
||||
|
||||
# overwrite default install directories
|
||||
package_name =
|
||||
prefix =
|
||||
libdir = :pre
|
||||
|
||||
In the remainder of the documentation we will use the string $KD to
|
||||
represent the location of the openkim-api source package (the value of
|
||||
the KIM_DIR variable discussed above). If you wish to, type the below
|
||||
commands exactly as written to set the shell variable KD to the
|
||||
appropriate value: :l
|
||||
|
||||
bash:
|
||||
% export KD=$HOME/openkim-api-vX.X.X :pre
|
||||
|
||||
To compile the package, including the provided examples, change to the
|
||||
$KD directory and execute `make examples' and then `make': :l
|
||||
|
||||
% cd $KD
|
||||
% make examples
|
||||
% make :pre
|
||||
|
||||
This builds all Model Drivers, Models, Tests, and the openkim-api service
|
||||
routine library. The targets defined by the Makefile in this directory
|
||||
include: :pre
|
||||
|
||||
`make' -- compiles the API and all Models and Tests
|
||||
`make all' -- same as `make'
|
||||
`make clean' -- will remove appropriate .o, .mod, .a, .so and
|
||||
executable files
|
||||
`make install' -- install files to `/usr/local/lib' by default
|
||||
`make uninstall' -- delete files installed by `make install'
|
||||
`make openkim-api' -- compiles only the API
|
||||
`make examples' -- copies examples into the appropriate
|
||||
directories (no overwrite)
|
||||
`make examples-force' -- copies examples into the appropriate
|
||||
directories (overwrite)
|
||||
`make examples-clean' -- remove all examples from the MODEL_DRIVERS,
|
||||
MODELS, and TESTS directories. :pre
|
||||
|
||||
Verify that the compilation was successful by running a Test. :l
|
||||
|
||||
The provided example Tests read in the name of a Model (or Models)
|
||||
which they use to perform their calculations. For most Tests the
|
||||
name of the Model can be piped in using an `echo' command. For
|
||||
example, the following Fortran 90 Test reads in one Model: :pre
|
||||
|
||||
% cd $KD/TESTs/test_Ar_free_cluster_CLUSTER_F90
|
||||
% echo "model_Ar_P_MLJ_CLUSTER_C" | ./test_Ar_free_cluster_CLUSTER_F90 :pre
|
||||
|
||||
(See the README files in the Test directories for an explanation of what
|
||||
the Tests do.) :pre
|
||||
|
||||
Each Test (and Model) has its own make file for compiling and linking.
|
||||
If changes are made to the code, re-compile (from the $KD
|
||||
directory). :l,ole
|
||||
./lammps-DDMMYY/src/lmp_serial < al-input :
|
||||
</pre>
|
||||
|
||||
:line
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue