Diffusion lammps eac710420df6

Merge branch 'master' into lammps-icms
eac710420df6
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Feb 23 2011, 16:58.

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Merge branch 'master' into lammps-icms

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Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Feb 23 2011, 16:58

Pushed

junge

Oct 6 2016, 16:49

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rLAMMPS2fd2543d88bb: git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5721 f3b2605a-c512-4ea7…
rLAMMPS2ef82ccd2b4a: adjustments for compiling REAX and MEAM.

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPSeac710420df6: Merge branch 'master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Feb 23 2011, 16:58

Merged Changes

Commit	Author	Details	Committed
2fd2543d88bb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5721 f3b2605a-c512-4ea7…	Feb 22 2011
fc3dca692a68	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5720 f3b2605a-c512-4ea7…	Feb 22 2011
2204858474ba	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5719 f3b2605a-c512-4ea7…	Feb 22 2011
2bd4074d8c8f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5718 f3b2605a-c512-4ea7…	Feb 22 2011
a21e59fa7ec9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5717 f3b2605a-c512-4ea7…	Feb 22 2011
691894ab343c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5716 f3b2605a-c512-4ea7…	Feb 22 2011
1d4a6440d108	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5715 f3b2605a-c512-4ea7…	Feb 22 2011
f50885fd4625	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5714 f3b2605a-c512-4ea7…	Feb 22 2011
faf9b4f21b84	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5713 f3b2605a-c512-4ea7…	Feb 22 2011
49b72ac36e14	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5712 f3b2605a-c512-4ea7…	Feb 22 2011
46104f158832	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5711 f3b2605a-c512-4ea7…	Feb 22 2011
38cf9047ea8b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5709 f3b2605a-c512-4ea7…	Feb 22 2011
49f5603f7fb0	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5708 f3b2605a-c512-4ea7…	Feb 22 2011
d7ce656741a1	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5706 f3b2605a-c512-4ea7…	Feb 22 2011
d51c47d9ab02	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5705 f3b2605a-c512-4ea7…	Feb 22 2011
e9f22f70d0d4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5703 f3b2605a-c512-4ea7…	Feb 22 2011
bf7d42342369	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5702 f3b2605a-c512-4ea7…	Feb 22 2011
81b600132e72	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5701 f3b2605a-c512-4ea7…	Feb 22 2011
eae0731cae5b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5700 f3b2605a-c512-4ea7…	Feb 22 2011
b41824a13738	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5698 f3b2605a-c512-4ea7…	Feb 22 2011
1d0bef316fdf	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5697 f3b2605a-c512-4ea7…	Feb 22 2011
8d2dd0f6ab2f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5696 f3b2605a-c512-4ea7…	Feb 22 2011
f1a718234533	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5694 f3b2605a-c512-4ea7…	Feb 22 2011
658d4c20ff76	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5693 f3b2605a-c512-4ea7…	Feb 22 2011
6d6d45f25e6c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5692 f3b2605a-c512-4ea7…	Feb 22 2011

Changes (203)

		Path
M		doc/pair_eff.html
M		doc/pair_eff.txt
M		doc/pair_meam.html
M		doc/pair_meam.txt
M		doc/read_data.html
M		doc/read_data.txt
A		examples/USER/eff/CH4/in.ch4.min
A	(dir)	examples/USER/eff/ECP/
A		examples/USER/eff/ECP/README
A	(dir)	examples/USER/eff/ECP/Si2H6/
A		examples/USER/eff/ECP/Si2H6/data.Si2H6
A		examples/USER/eff/ECP/Si2H6/data.Si2H6.ang
A		examples/USER/eff/ECP/Si2H6/in.Si2H6
A		examples/USER/eff/ECP/Si2H6/in.Si2H6.ang
A	(dir)	examples/USER/eff/ECP/SiH4/
A		examples/USER/eff/ECP/SiH4/data.SiH4
A		examples/USER/eff/ECP/SiH4/data.SiH4.ang
A		examples/USER/eff/ECP/SiH4/in.SiH4
A		examples/USER/eff/ECP/SiH4/in.SiH4.ang
V		examples/USER/eff/H/{data.h_atom → data.h_atom.bohr}
A		examples/USER/eff/H/data.h_atom.ang
V		examples/USER/eff/H/{data.h_atom.bohr ← data.h_atom}
D		examples/USER/eff/H/in.h_atom.min
D		examples/USER/eff/H/in.h_atom.spe
A		examples/USER/eff/H/in.h_atom.spe.ang
A		examples/USER/eff/H/in.h_atom.spe.bohr
M		examples/USER/eff/H_plasma/data.h2bulk
A		examples/USER/eff/H_plasma/data.h2bulk.ang
A		examples/USER/eff/H_plasma/in.h2bulk.nve.ang
V		examples/USER/eff/Li-solid/{data.Li → data.Li.bohr}
A		examples/USER/eff/Li-solid/data.Li.ang
V		examples/USER/eff/Li-solid/{data.Li.bohr ← data.Li}
D		examples/USER/eff/Li-solid/in.Li
A		examples/USER/eff/Li-solid/in.Li.ang
A		examples/USER/eff/Li-solid/in.Li.bohr
A	(dir)	examples/USER/eff/fixed-core/
A	(dir)	examples/USER/eff/fixed-core/C2H6/
A		examples/USER/eff/fixed-core/C2H6/data.C2H6fc.ang
A		examples/USER/eff/fixed-core/C2H6/data.C2H6fc.bohr
A		examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang
A		examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr
A	(dir)	examples/USER/eff/fixed-core/CH4/
A		examples/USER/eff/fixed-core/CH4/data.CH4fc.ang
A		examples/USER/eff/fixed-core/CH4/data.CH4fc.bohr
A		examples/USER/eff/fixed-core/CH4/in.CH4fc.ang
A		examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr
A		examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang
A		examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr
A		examples/USER/eff/fixed-core/README
M		lib/meam/meam_data.F
M		lib/meam/meam_dens_final.F
M		lib/meam/meam_dens_init.F
M		lib/meam/meam_force.F
M		lib/meam/meam_setup_done.F
M		lib/meam/meam_setup_global.F
M		lib/meam/meam_setup_param.F
M		potentials/ffield.comb
M		src/ASPHERE/atom_vec_ellipsoid.cpp
M		src/CLASS2/dihedral_class2.cpp
M		src/CLASS2/improper_class2.cpp
M		src/COLLOID/atom_vec_colloid.cpp
M		src/DIPOLE/atom_vec_dipole.cpp
M		src/GPU/pair_cg_cmm_coul_long_gpu.cpp
M		src/GPU/pair_cg_cmm_gpu.cpp
M		src/GPU/pair_gayberne_gpu.cpp
M		src/GPU/pair_lj96_cut_gpu.cpp
M		src/GPU/pair_lj_charmm_coul_long_gpu.cpp
M		src/GPU/pair_lj_cut_coul_cut_gpu.cpp
M		src/GPU/pair_lj_cut_coul_long_gpu.cpp
M		src/GPU/pair_lj_cut_gpu.cpp
M		src/GRANULAR/atom_vec_granular.cpp
M		src/KSPACE/pppm.cpp
M		src/KSPACE/pppm.h
M		src/MANYBODY/fix_qeq_comb.cpp
M		src/MANYBODY/fix_qeq_comb.h
M		src/MANYBODY/pair_comb.cpp
M		src/MEAM/pair_meam.cpp
M		src/MOLECULE/atom_vec_angle.cpp
M		src/MOLECULE/atom_vec_bond.cpp
M		src/MOLECULE/atom_vec_full.cpp
M		src/MOLECULE/atom_vec_molecular.cpp
M		src/MOLECULE/bond_fene.cpp
M		src/MOLECULE/bond_fene_expand.cpp
M		src/MOLECULE/dihedral_charmm.cpp
M		src/MOLECULE/dihedral_harmonic.cpp
M		src/MOLECULE/dihedral_helix.cpp
M		src/MOLECULE/dihedral_multi_harmonic.cpp
M		src/MOLECULE/dihedral_opls.cpp
M		src/MOLECULE/improper_cvff.cpp
M		src/MOLECULE/improper_harmonic.cpp
M		src/PERI/atom_vec_peri.cpp
M		src/PERI/fix_peri_neigh.cpp
M		src/PERI/fix_peri_neigh.h
M		src/PERI/pair_peri_lps.cpp
M		src/PERI/pair_peri_pmb.cpp
M		src/REAX/fix_reax_bonds.cpp
M		src/REAX/fix_reax_bonds.h
M		src/REPLICA/fix_event_prd.cpp
M		src/REPLICA/fix_event_prd.h
M		src/REPLICA/fix_event_tad.cpp
M		src/REPLICA/fix_event_tad.h
M		src/REPLICA/neb.cpp
M		src/REPLICA/prd.cpp
M		src/REPLICA/temper.cpp
M		src/SRD/fix_wall_srd.h
M		src/USER-EFF/Install.sh
M		src/USER-EFF/README
M		src/USER-EFF/atom_vec_electron.cpp
M		src/USER-EFF/compute_ke_atom_eff.cpp
M		src/USER-EFF/compute_ke_eff.cpp
M		src/USER-EFF/compute_temp_deform_eff.cpp
M		src/USER-EFF/compute_temp_deform_eff.h
M		src/USER-EFF/compute_temp_eff.cpp
M		src/USER-EFF/compute_temp_eff.h
M		src/USER-EFF/compute_temp_region_eff.cpp
M		src/USER-EFF/compute_temp_region_eff.h
M		src/USER-EFF/fix_langevin_eff.cpp
M		src/USER-EFF/fix_nh_eff.cpp
M		src/USER-EFF/fix_nph_eff.h
M		src/USER-EFF/fix_npt_eff.cpp
M		src/USER-EFF/fix_nve_eff.cpp
M		src/USER-EFF/fix_nve_eff.h
M		src/USER-EFF/fix_nvt_eff.h
M		src/USER-EFF/fix_nvt_sllod_eff.cpp
M		src/USER-EFF/fix_nvt_sllod_eff.h
M		src/USER-EFF/fix_temp_rescale_eff.cpp
M		src/USER-EFF/fix_temp_rescale_eff.h
M		src/USER-EFF/pair_eff_cut.cpp
M		src/USER-EFF/pair_eff_cut.h
M		src/USER-EFF/pair_eff_inline.h
M		src/USER-REAXC/reaxc_types.h
M		src/USER-REAXC/reaxc_valence_angles.cpp
M		src/atom.h
M		src/atom_vec_atomic.cpp
M		src/atom_vec_charge.cpp
M		src/atom_vec_hybrid.cpp
M		src/compute.cpp
M		src/compute.h
M		src/compute_reduce.cpp
M		src/compute_reduce.h
M		src/compute_reduce_region.h
M		src/create_atoms.cpp
M		src/delete_atoms.cpp
M		src/displace_atoms.cpp
M		src/displace_box.cpp
M		src/dump.cpp
M		src/dump.h
M		src/dump_dcd.cpp
M		src/fix.h
M		src/fix_ave_atom.cpp
M		src/fix_ave_atom.h
M		src/fix_ave_correlate.cpp
M		src/fix_ave_correlate.h
M		src/fix_ave_histo.cpp
M		src/fix_ave_histo.h
M		src/fix_ave_spatial.cpp
M		src/fix_ave_spatial.h
M		src/fix_ave_time.cpp
M		src/fix_ave_time.h
M		src/fix_dt_reset.h
M		src/fix_shake.cpp
M		src/fix_shake.h
M		src/fix_tmd.cpp
M		src/fix_ttm.cpp
M		src/group.cpp
M		src/group.h
M		src/integrate.cpp
M		src/integrate.h
M		src/library.cpp
M		src/lmptype.h
M		src/memory.cpp
M		src/min.cpp
M		src/min.h
M		src/min_cg.cpp
M		src/min_quickmin.cpp
M		src/modify.h
M		src/neigh_bond.cpp
M		src/neighbor.cpp
M		src/output.h
M		src/read_data.cpp
M		src/read_restart.cpp
M		src/read_restart.h
M		src/region.h
M		src/replicate.cpp
M		src/run.cpp
M		src/thermo.h
M		src/update.cpp
M		src/update.h
M		src/velocity.cpp
M		src/version.h
M		src/write_restart.cpp
M		src/write_restart.h
M		tools/eff/README
M		tools/eff/VMD-input.py
A		tools/eff/bohr2ang.py
M		tools/eff/cfg2lammps.py
M		tools/eff/lmp2radii.py
M		tools/eff/lmp2radii.pyx
M		tools/eff/lmp2radii_col.py
M		tools/eff/lmp2xyz.py
M		tools/eff/radii.vmd
A		tools/eff/restart2data-pEFF.cpp
A		tools/eff/structure_generators/Li-solid-angstrom.pl