Diffusion lammps 2a099bfedb48

Merge branch 'master' into lammps-icms
2a099bfedb48
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Jun 30 2012, 17:23.

Description

Merge branch 'master' into lammps-icms

Resolve Conflicts:
src/region.cpp

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Jun 30 2012, 17:23

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS71f4cdf3f117: Adding a method for estimating coulomb table precision and factoring that into…
rLAMMPSe163a2f089c9: update colvars module with the latest version

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS2a099bfedb48: Merge branch 'master' into lammps-icms (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Jun 30 2012, 17:23

Merged Changes

Commit	Author	Details	Committed
71f4cdf3f117	pscrozi	Adding a method for estimating coulomb table precision and factoring that into…	Jun 30 2012
0c9ab4551ea9	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8452 f3b2605a-c512-4ea7…	Jun 30 2012
b667ae086c82	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8450 f3b2605a-c512-4ea7…	Jun 30 2012
540c1dbc0668	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8449 f3b2605a-c512-4ea7…	Jun 30 2012
4323d1522a22	pscrozi	Making initial estimate for g_ewald more robust and better documented.	Jun 30 2012
a8338a0263ee	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8446 f3b2605a-c512-4ea7…	Jun 29 2012
3ae7999dab74	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8445 f3b2605a-c512-4ea7…	Jun 29 2012
1171c44e5e23	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8444 f3b2605a-c512-4ea7…	Jun 29 2012
271b40ea9cbb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8443 f3b2605a-c512-4ea7…	Jun 29 2012
5f46ef4e804e	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8442 f3b2605a-c512-4ea7…	Jun 29 2012
e83510effad8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8441 f3b2605a-c512-4ea7…	Jun 29 2012
4ad514f97b2c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8440 f3b2605a-c512-4ea7…	Jun 29 2012
5dbe265bbc8c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8439 f3b2605a-c512-4ea7…	Jun 29 2012
06d12cd6ec20	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8438 f3b2605a-c512-4ea7…	Jun 29 2012
4fb3d545587a	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8435 f3b2605a-c512-4ea7…	Jun 29 2012
945fc5a36a65	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8434 f3b2605a-c512-4ea7…	Jun 29 2012
fee52f2fac2b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8433 f3b2605a-c512-4ea7…	Jun 29 2012
6795f0f3afad	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8432 f3b2605a-c512-4ea7…	Jun 29 2012
0746aaeb799b	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8431 f3b2605a-c512-4ea7…	Jun 29 2012
3c1f57ce6dcb	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8430 f3b2605a-c512-4ea7…	Jun 29 2012
ab5264cbdcde	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8429 f3b2605a-c512-4ea7…	Jun 29 2012
7d32a328db94	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8428 f3b2605a-c512-4ea7…	Jun 29 2012
1b02e7be5ecd	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8427 f3b2605a-c512-4ea7…	Jun 29 2012
1624264bc847	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8426 f3b2605a-c512-4ea7…	Jun 29 2012
96f101c787ce	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8425 f3b2605a-c512-4ea7…	Jun 29 2012
76b5e67319c8	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8423 f3b2605a-c512-4ea7…	Jun 28 2012
85c6376af25f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8422 f3b2605a-c512-4ea7…	Jun 28 2012
9db45bcb9269	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8419 f3b2605a-c512-4ea7…	Jun 28 2012
6ee328d0fc65	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8413 f3b2605a-c512-4ea7…	Jun 27 2012
7a77a0a69be5	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8412 f3b2605a-c512-4ea7…	Jun 27 2012
3d3dd0d50b27	pscrozi	Bug fix to prevent segfault when deallocate_groups is called even though groups…	Jun 27 2012
f6de5943ed93	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8409 f3b2605a-c512-4ea7…	Jun 27 2012
ad9d69168597	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8408 f3b2605a-c512-4ea7…	Jun 27 2012
bd0a01b5ba1c	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8407 f3b2605a-c512-4ea7…	Jun 27 2012
4d428c59d769	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8406 f3b2605a-c512-4ea7…	Jun 26 2012
ae666be85e69	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8405 f3b2605a-c512-4ea7…	Jun 26 2012
b6303a1e837f	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8403 f3b2605a-c512-4ea7…	Jun 26 2012
9bdeeadfd8e3	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8402 f3b2605a-c512-4ea7…	Jun 26 2012
5a78b33db740	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8401 f3b2605a-c512-4ea7…	Jun 26 2012
231647f0f550	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8400 f3b2605a-c512-4ea7…	Jun 26 2012
0d3734ead467	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8399 f3b2605a-c512-4ea7…	Jun 26 2012
dfb51e6b00d4	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8398 f3b2605a-c512-4ea7…	Jun 26 2012
83784f8381ff	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8397 f3b2605a-c512-4ea7…	Jun 26 2012
05e044abf48d	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8396 f3b2605a-c512-4ea7…	Jun 26 2012
66c5617afbe6	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8395 f3b2605a-c512-4ea7…	Jun 26 2012
8f6a8d13d594	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8393 f3b2605a-c512-4ea7…	Jun 25 2012
da1c864eab79	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8392 f3b2605a-c512-4ea7…	Jun 25 2012
e8ff810ee770	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8391 f3b2605a-c512-4ea7…	Jun 25 2012
bee842bed7c0	sjplimp	git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8390 f3b2605a-c512-4ea7…	Jun 25 2012

Changes (241)
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				Path
	A			doc/Eqs/pair_bop.jpg
	A			doc/Eqs/pair_bop.tex
	M			doc/Eqs/pair_meam_spline.jpg
	M			doc/Manual.pdf
	M			doc/Section_commands.html
	M			doc/Section_commands.txt
	M			doc/Section_errors.html
	M			doc/Section_errors.txt
	M			doc/Section_packages.html
	M			doc/Section_packages.txt
	M			doc/Section_start.html
	M			doc/Section_start.txt
	M			doc/fix_rigid.html
	M			doc/fix_rigid.txt
	M			doc/min_modify.html
	M			doc/min_modify.txt
	M			doc/pair_airebo.html
	M			doc/pair_airebo.txt
	M			doc/pair_coeff.html
	M			doc/pair_coeff.txt
	M			doc/pair_style.html
	M			doc/pair_style.txt
	M			lib/cuda/Makefile.defaults
	A			potentials/AlSiMgCuFe.meam
	A			potentials/CdTe.bop
	A			potentials/CdTe.bop.table
	A			potentials/GaAs.bop
	A			potentials/GaAs.bop.table
	M			potentials/README
	M			potentials/library.meam
	M			src/CLASS2/angle_class2.cpp
	M			src/CLASS2/bond_class2.cpp
	M			src/CLASS2/dihedral_class2.cpp
	M			src/CLASS2/improper_class2.cpp
	M			src/DIPOLE/atom_vec_dipole.cpp
	M			src/DIPOLE/atom_vec_dipole.h
	M			src/Depend.sh
	M			src/FLD/pair_brownian.h
	M			src/FLD/pair_lubricate.h
	M			src/FLD/pair_lubricateU.h
	M			src/FLD/pair_lubricateU_poly.h
	M			src/FLD/pair_lubricate_poly.cpp
	M			src/FLD/pair_lubricate_poly.h
	M			src/GPU/pair_eam_gpu.cpp
	M			src/GPU/pair_eam_gpu.h
	M			src/KSPACE/ewald.cpp
	M			src/KSPACE/ewald.h
	M			src/KSPACE/pair_lj_cut_coul_long_tip4p.h
	M			src/KSPACE/pppm.cpp
	M			src/KSPACE/pppm.h
	M			src/MAKE/Makefile.serial
	M			src/MANYBODY/Install.sh
	A			src/MANYBODY/pair_bop.cpp
	A			src/MANYBODY/pair_bop.h
	M			src/MC/fix_bond_break.cpp
	M			src/MOLECULE/angle_charmm.cpp
	M			src/MOLECULE/angle_cosine.cpp
	M			src/MOLECULE/angle_cosine_delta.cpp
	M			src/MOLECULE/angle_cosine_periodic.cpp
	M			src/MOLECULE/angle_cosine_squared.cpp
	M			src/MOLECULE/angle_harmonic.cpp
	M			src/MOLECULE/angle_table.cpp
	M			src/MOLECULE/atom_vec_angle.cpp
	M			src/MOLECULE/atom_vec_angle.h
	M			src/MOLECULE/atom_vec_bond.cpp
	M			src/MOLECULE/atom_vec_bond.h
	M			src/MOLECULE/atom_vec_full.cpp
	M			src/MOLECULE/atom_vec_full.h
	M			src/MOLECULE/atom_vec_molecular.cpp
	M			src/MOLECULE/atom_vec_molecular.h
	M			src/MOLECULE/bond_fene.cpp
	M			src/MOLECULE/bond_fene_expand.cpp
	M			src/MOLECULE/bond_harmonic.cpp
	M			src/MOLECULE/bond_morse.cpp
	M			src/MOLECULE/bond_nonlinear.cpp
	M			src/MOLECULE/bond_quartic.cpp
	M			src/MOLECULE/bond_table.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/MOLECULE/improper_umbrella.cpp
	M			src/OPT/pair_lj_cut_coul_long_tip4p_opt.h
	M			src/PERI/atom_vec_peri.cpp
	M			src/PERI/atom_vec_peri.h
	M			src/POEMS/fix_poems.cpp
	M			src/REPLICA/compute_event_displace.cpp
	M			src/REPLICA/fix_event.cpp
	M			src/REPLICA/tad.cpp
	M			src/USER-AWPMD/atom_vec_wavepacket.cpp
	M			src/USER-AWPMD/atom_vec_wavepacket.h
	M			src/USER-CG-CMM/angle_cg_cmm.cpp
	M			src/USER-CG-CMM/angle_sdk.cpp
	M			src/USER-EFF/atom_vec_electron.cpp
	M			src/USER-EFF/atom_vec_electron.h
	M			src/USER-MISC/Install.sh
	M			src/USER-MISC/angle_cosine_shift.cpp
	M			src/USER-MISC/angle_cosine_shift_exp.cpp
	M			src/USER-MISC/angle_dipole.cpp
	M			src/USER-MISC/bond_harmonic_shift.cpp
	M			src/USER-MISC/bond_harmonic_shift_cut.cpp
	M			src/USER-MISC/compute_temp_rotate.cpp
	M			src/USER-MISC/dihedral_cosine_shift_exp.cpp
	M			src/USER-MISC/fix_addtorque.cpp
	M			src/USER-MISC/fix_imd.cpp
	M			src/USER-MISC/improper_cossq.cpp
	M			src/USER-MISC/improper_ring.cpp
	M			src/USER-MOLFILE/dump_molfile.cpp
	M			src/USER-OMP/angle_charmm_omp.cpp
	M			src/USER-OMP/angle_class2_omp.cpp
	M			src/USER-OMP/angle_cosine_delta_omp.cpp
	M			src/USER-OMP/angle_cosine_omp.cpp
	M			src/USER-OMP/angle_cosine_periodic_omp.cpp
	M			src/USER-OMP/angle_cosine_shift_exp_omp.cpp
	M			src/USER-OMP/angle_cosine_shift_omp.cpp
	M			src/USER-OMP/angle_cosine_squared_omp.cpp
	M			src/USER-OMP/angle_dipole_omp.cpp
	M			src/USER-OMP/angle_harmonic_omp.cpp
	M			src/USER-OMP/angle_sdk_omp.cpp
	M			src/USER-OMP/angle_table_omp.cpp
	M			src/USER-OMP/bond_class2_omp.cpp
	M			src/USER-OMP/bond_fene_expand_omp.cpp
	M			src/USER-OMP/bond_fene_omp.cpp
	M			src/USER-OMP/bond_harmonic_omp.cpp
	M			src/USER-OMP/bond_harmonic_shift_cut_omp.cpp
	M			src/USER-OMP/bond_harmonic_shift_omp.cpp
	M			src/USER-OMP/bond_morse_omp.cpp
	M			src/USER-OMP/bond_nonlinear_omp.cpp
	M			src/USER-OMP/bond_quartic_omp.cpp
	M			src/USER-OMP/bond_table_omp.cpp
	M			src/USER-OMP/dihedral_charmm_omp.cpp
	M			src/USER-OMP/dihedral_class2_omp.cpp
	M			src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
	M			src/USER-OMP/dihedral_harmonic_omp.cpp
	M			src/USER-OMP/dihedral_helix_omp.cpp
	M			src/USER-OMP/dihedral_multi_harmonic_omp.cpp
	M			src/USER-OMP/dihedral_opls_omp.cpp
	M			src/USER-OMP/improper_class2_omp.cpp
	M			src/USER-OMP/improper_cossq_omp.cpp
	M			src/USER-OMP/improper_cvff_omp.cpp
	M			src/USER-OMP/improper_harmonic_omp.cpp
	M			src/USER-OMP/improper_ring_omp.cpp
	M			src/USER-OMP/improper_umbrella_omp.cpp
	M			src/USER-SPH/atom_vec_meso.cpp
	M			src/USER-SPH/atom_vec_meso.h
	M			src/XTC/dump_xtc.cpp
	M			src/atom.cpp
	M			src/atom.h
	A			src/atom_map.cpp
	M			src/atom_vec.h
	M			src/atom_vec_atomic.cpp
	M			src/atom_vec_atomic.h
	M			src/atom_vec_charge.cpp
	M			src/atom_vec_charge.h
	M			src/atom_vec_ellipsoid.cpp
	M			src/atom_vec_ellipsoid.h
	M			src/atom_vec_hybrid.cpp
	M			src/atom_vec_hybrid.h
	M			src/atom_vec_line.cpp
	M			src/atom_vec_line.h
	M			src/atom_vec_sphere.cpp
	M			src/atom_vec_sphere.h
	M			src/atom_vec_tri.cpp
	M			src/atom_vec_tri.h
	M			src/balance.h
	M			src/change_box.cpp
	M			src/compute_com_molecule.cpp
	M			src/compute_displace_atom.cpp
	M			src/compute_group_group.h
	M			src/compute_gyration.cpp
	M			src/compute_gyration_molecule.cpp
	M			src/compute_msd.cpp
	M			src/compute_msd_molecule.cpp
	M			src/compute_property_atom.cpp
	M			src/compute_stress_atom.cpp
	M			src/create_atoms.cpp
	M			src/create_atoms.h
	M			src/displace_atoms.cpp
	M			src/domain.cpp
	M			src/domain.h
	M			src/dump_atom.cpp
	M			src/dump_custom.cpp
	M			src/dump_dcd.cpp
	M			src/fix.cpp
	M			src/fix_addforce.cpp
	M			src/fix_ave_atom.h
	M			src/fix_ave_correlate.h
	M			src/fix_ave_histo.h
	M			src/fix_ave_spatial.h
	M			src/fix_ave_time.h
	M			src/fix_aveforce.cpp
	M			src/fix_balance.h
	M			src/fix_deform.cpp
	M			src/fix_gravity.h
	M			src/fix_momentum.cpp
	M			src/fix_move.cpp
	M			src/fix_nh.cpp
	M			src/fix_nh.h
	M			src/fix_orient_fcc.cpp
	M			src/fix_restrain.h
	M			src/fix_rigid.cpp
	M			src/fix_rigid.h
	M			src/fix_rigid_nve.cpp
	M			src/fix_rigid_nvt.cpp
	M			src/fix_shake.cpp
	M			src/fix_spring_rg.cpp
	M			src/fix_spring_self.cpp
	M			src/fix_store_state.cpp
	M			src/fix_temp_berendsen.h
	M			src/fix_temp_rescale.h
	M			src/fix_tmd.cpp
	M			src/group.cpp
	M			src/kspace.cpp
	M			src/kspace.h
	M			src/lmptype.h
	M			src/modify.h
	M			src/neigh_bond.cpp
	M			src/neigh_bond.h
	M			src/neighbor.h
	M			src/output.cpp
	M			src/output.h
	M			src/pair.h
	M			src/read_data.cpp
	M			src/read_data.h
	M			src/read_dump.cpp
	M			src/read_dump.h
	M			src/reader.h
	M			src/reader_native.h
	M			src/reader_xyz.h
	M			src/region.cpp
	M			src/replicate.cpp
	M			src/rerun.h
	M			src/respa.h
	M			src/set.cpp
	M			src/update.cpp
	M			src/update.h
	M			src/velocity.cpp
	M			src/version.h