Diffusion lammps 14e85af66bea

Merge branch 'openmp-step5' into openmp-master
14e85af66bea
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Oct 16 2011, 19:03.

Description

Merge branch 'openmp-step5' into openmp-master

Resolved Conflicts:
src/USER-OMP/pair_airebo_omp.cpp
src/USER-OMP/pair_comb_omp.h

Details

Committed

Axel Kohlmeyer <akohlmey@gmail.com>

Oct 16 2011, 19:03

Pushed

junge

Oct 6 2016, 16:49

Parents

rLAMMPS5a28241e6757: complete port of dihedral styles
rLAMMPS27c6af21d264: avoid race condition in REBO neighbor list

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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS14e85af66bea: Merge branch 'openmp-step5' into openmp-master (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Oct 16 2011, 19:03

Merged Changes

This commit merges a very large number of changes. Only the first 50 are shown.

Commit	Author	Details	Committed
5a28241e6757	Axel Kohlmeyer	complete port of dihedral styles	Oct 16 2011
c11cd8e8d233	Axel Kohlmeyer	make -suffix omp imply using package omp with default settings	Oct 16 2011
79dbd4f7c9ad	Axel Kohlmeyer	port CHARMM dihedrals to new threading	Oct 16 2011
d2c033d96362	Axel Kohlmeyer	ported first dihedral	Oct 16 2011
1ab5bcfc20c5	Axel Kohlmeyer	ported the final pair styles	Oct 16 2011
745ed99913df	Axel Kohlmeyer	bugfix for resquared potential	Oct 16 2011
b40688c17306	Axel Kohlmeyer	ported resquared	Oct 16 2011
92cd5bf435b5	Axel Kohlmeyer	fix bug in openmp neighbor list selection logic and port morse and peridynamics	Oct 16 2011
94fafdcaf965	Axel Kohlmeyer	ported final lj styles and lubricate	Oct 16 2011
56994681f764	Axel Kohlmeyer	ported a first chunk of lj pair potentials	Oct 16 2011
c0b7289780e0	Axel Kohlmeyer	use const where possible to help the compiler to do a better job	Oct 16 2011
0d37279e8539	Axel Kohlmeyer	port dreiding hbond potentials	Oct 15 2011
fbf9c8970b6d	Axel Kohlmeyer	ported granular pair styles	Oct 15 2011
4d1a17cea3df	Axel Kohlmeyer	performance optimization for gay-berne	Oct 15 2011
4d68dfabd93b	Axel Kohlmeyer	prot gauss and gay-berne	Oct 15 2011
f379e385d12a	Axel Kohlmeyer	port over eam and eim	Oct 15 2011
5547df4854e9	Axel Kohlmeyer	port pair styles using name starting with c or d	Oct 15 2011
aac322c77131	Axel Kohlmeyer	reformulate text one more time	Oct 15 2011
669b4e628ade	Axel Kohlmeyer	fix compilation issues without OpenMP active clarify message about threaded…	Oct 15 2011
80cea44a3d04	Axel Kohlmeyer	hook omp neighbor list build versions into list selection	Oct 15 2011
72c850ce8b32	Axel Kohlmeyer	reinstate non-openmp versions of the neighbor list builds	Oct 15 2011
7b7a041ff257	Axel Kohlmeyer	move OpenMP parallel neighbor list builds to separate files	Oct 15 2011
8972490ff755	Axel Kohlmeyer	reinstate special neighbors handling for local atoms	Oct 15 2011
8591189ea09b	Axel Kohlmeyer	add code to support switching neighbor list flags with package omp	Oct 15 2011
e2b5a643f766	Axel Kohlmeyer	we cannot look for special atoms when building a full neighborlist with ghosts	Oct 15 2011
ef4a84321910	Axel Kohlmeyer	coefficient shadowing bugfix	Oct 15 2011
60e04bfead26	Axel Kohlmeyer	REBO neighbor list allocation bugfix	Oct 14 2011
afab10eedbe5	Axel Kohlmeyer	fix PI vs MY_PI issue	Oct 14 2011
8fa59cc88e2f	Axel Kohlmeyer	complete support for airebo	Oct 14 2011
8ff73df6d742	Axel Kohlmeyer	remove remaining race conditions in neighbor list builds	Oct 14 2011
a055c0dfc4ac	Axel Kohlmeyer	more scripted changes to prepare for conversion	Oct 14 2011
8416aba5cf39	Axel Kohlmeyer	convert all b*/omp pair styles	Oct 14 2011
5344894becf0	Axel Kohlmeyer	change ThrOMP initializer through sed script	Oct 14 2011
9fe212d8e68e	Axel Kohlmeyer	convert two more pair styles	Oct 14 2011
06a02ca6750a	Axel Kohlmeyer	zeroing out arrays is no longer needed in eval()	Oct 14 2011
cb230b449486	Axel Kohlmeyer	convert all pair header files to new thread infrastructure	Oct 14 2011
c43abbce7f76	Axel Kohlmeyer	more cleanup and rewrites in thread support. port adp/omp.	Oct 14 2011
f4de9d0c42c0	Axel Kohlmeyer	correct calculation of memory usage	Oct 14 2011
f5424c6f3a4c	Axel Kohlmeyer	refactor argument parsing for "package omp" handle selection of OpenMP or…	Oct 13 2011
236f48fc0471	Axel Kohlmeyer	fix API for rRESPA fix methods silence warnings in loop setup helper function	Oct 13 2011
111bc088b957	Axel Kohlmeyer	rename API for more clarity	Oct 13 2011
1f21b4e693e0	Axel Kohlmeyer	whitespace cleanup	Oct 13 2011
c36e9214f346	Axel Kohlmeyer	simplified loop setup and access to force	Oct 13 2011
17ff605492f5	Axel Kohlmeyer	some more cleanups and simplifications	Oct 13 2011
d94fbfa39c21	Axel Kohlmeyer	another massive overhaul. now all stress calculations are working well. false…	Oct 13 2011
747ea7246185	Axel Kohlmeyer	force arrays and alike are cleared in parallel when the omp package command is…	Oct 13 2011
c9ca5dad3787	Axel Kohlmeyer	another step toward proper thread data handling	Oct 12 2011
e180f2168c9a	Axel Kohlmeyer	code works for "newton off"	Oct 12 2011
a1d85e42fa68	Axel Kohlmeyer	manage per thread data similar to force and torque	Oct 12 2011
a8e368e7ac06	Axel Kohlmeyer	start integrating new thread infrastructure	Oct 11 2011

Changes (186)
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				Path
	M			doc/package.txt
	M			src/ASPHERE/pair_resquared.cpp
	M			src/MANYBODY/pair_adp.cpp
	M			src/MANYBODY/pair_airebo.cpp
	M			src/PERI/compute_damage_atom.cpp
	M			src/PERI/fix_peri_neigh.h
	M			src/PERI/pair_peri_lps.cpp
	M			src/PERI/pair_peri_lps.h
	M			src/PERI/pair_peri_pmb.cpp
	M			src/PERI/pair_peri_pmb.h
	M			src/USER-CUDA/pppm_cuda.cpp
	M			src/USER-OMP/Install.sh
	M			src/USER-OMP/Package.sh
	M			src/USER-OMP/dihedral_charmm_omp.cpp
	M			src/USER-OMP/dihedral_charmm_omp.h
	M			src/USER-OMP/dihedral_class2_omp.cpp
	M			src/USER-OMP/dihedral_class2_omp.h
	M			src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
	M			src/USER-OMP/dihedral_cosine_shift_exp_omp.h
	M			src/USER-OMP/dihedral_harmonic_omp.cpp
	M			src/USER-OMP/dihedral_harmonic_omp.h
	M			src/USER-OMP/dihedral_helix_omp.cpp
	M			src/USER-OMP/dihedral_helix_omp.h
	M			src/USER-OMP/dihedral_multi_harmonic_omp.cpp
	M			src/USER-OMP/dihedral_multi_harmonic_omp.h
	M			src/USER-OMP/dihedral_opls_omp.cpp
	M			src/USER-OMP/dihedral_opls_omp.h
	A			src/USER-OMP/fix_omp.cpp
	A			src/USER-OMP/fix_omp.h
	A			src/USER-OMP/fix_peri_neigh_omp.cpp
	P			src/USER-OMP/fix_peri_neigh_omp.h Copied from src/main.cpp
	M			src/USER-OMP/pair_adp_omp.cpp
	M			src/USER-OMP/pair_adp_omp.h
	M			src/USER-OMP/pair_airebo_omp.cpp
	M			src/USER-OMP/pair_airebo_omp.h
	M			src/USER-OMP/pair_born_coul_long_omp.cpp
	M			src/USER-OMP/pair_born_coul_long_omp.h
	M			src/USER-OMP/pair_born_omp.cpp
	M			src/USER-OMP/pair_born_omp.h
	M			src/USER-OMP/pair_buck_coul_cut_omp.cpp
	M			src/USER-OMP/pair_buck_coul_cut_omp.h
	M			src/USER-OMP/pair_buck_coul_long_omp.cpp
	M			src/USER-OMP/pair_buck_coul_long_omp.h
	M			src/USER-OMP/pair_buck_coul_omp.cpp
	M			src/USER-OMP/pair_buck_coul_omp.h
	M			src/USER-OMP/pair_buck_omp.cpp
	M			src/USER-OMP/pair_buck_omp.h
	M			src/USER-OMP/pair_cdeam_omp.cpp
	M			src/USER-OMP/pair_cdeam_omp.h
	M			src/USER-OMP/pair_colloid_omp.cpp
	M			src/USER-OMP/pair_colloid_omp.h
	M			src/USER-OMP/pair_comb_omp.cpp
	M			src/USER-OMP/pair_comb_omp.h
	M			src/USER-OMP/pair_coul_cut_omp.cpp
	M			src/USER-OMP/pair_coul_cut_omp.h
	M			src/USER-OMP/pair_coul_debye_omp.cpp
	M			src/USER-OMP/pair_coul_debye_omp.h
	M			src/USER-OMP/pair_coul_long_omp.cpp
	M			src/USER-OMP/pair_coul_long_omp.h
	M			src/USER-OMP/pair_dipole_cut_omp.cpp
	M			src/USER-OMP/pair_dipole_cut_omp.h
	M			src/USER-OMP/pair_dipole_sf_omp.cpp
	M			src/USER-OMP/pair_dipole_sf_omp.h
	M			src/USER-OMP/pair_dpd_omp.cpp
	M			src/USER-OMP/pair_dpd_omp.h
	M			src/USER-OMP/pair_dpd_tstat_omp.cpp
	M			src/USER-OMP/pair_dpd_tstat_omp.h
	M			src/USER-OMP/pair_eam_omp.cpp
	M			src/USER-OMP/pair_eam_omp.h
	M			src/USER-OMP/pair_edip_omp.cpp
	M			src/USER-OMP/pair_edip_omp.h
	M			src/USER-OMP/pair_eim_omp.cpp
	M			src/USER-OMP/pair_eim_omp.h
	M			src/USER-OMP/pair_gauss_omp.cpp
	M			src/USER-OMP/pair_gauss_omp.h
	M			src/USER-OMP/pair_gayberne_omp.cpp
	M			src/USER-OMP/pair_gayberne_omp.h
	M			src/USER-OMP/pair_gran_hertz_history_omp.cpp
	M			src/USER-OMP/pair_gran_hertz_history_omp.h
	M			src/USER-OMP/pair_gran_hooke_history_omp.cpp
	M			src/USER-OMP/pair_gran_hooke_history_omp.h
	M			src/USER-OMP/pair_gran_hooke_omp.cpp
	M			src/USER-OMP/pair_gran_hooke_omp.h
	M			src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
	M			src/USER-OMP/pair_hbond_dreiding_lj_omp.h
	M			src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
	M			src/USER-OMP/pair_hbond_dreiding_morse_omp.h
	M			src/USER-OMP/pair_lj96_cut_omp.cpp
	M			src/USER-OMP/pair_lj96_cut_omp.h
	M			src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
	M			src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h
	M			src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
	M			src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h
	M			src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
	M			src/USER-OMP/pair_lj_charmm_coul_long_omp.h
	M			src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
	M			src/USER-OMP/pair_lj_class2_coul_cut_omp.h
	M			src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
	M			src/USER-OMP/pair_lj_class2_coul_long_omp.h
	M			src/USER-OMP/pair_lj_class2_omp.cpp
	M			src/USER-OMP/pair_lj_class2_omp.h
	M			src/USER-OMP/pair_lj_coul_omp.cpp
	M			src/USER-OMP/pair_lj_coul_omp.h
	M			src/USER-OMP/pair_lj_cubic_omp.cpp
	M			src/USER-OMP/pair_lj_cubic_omp.h
	M			src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
	M			src/USER-OMP/pair_lj_cut_coul_cut_omp.h
	M			src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
	M			src/USER-OMP/pair_lj_cut_coul_debye_omp.h
	M			src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
	M			src/USER-OMP/pair_lj_cut_coul_long_omp.h
	M			src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp
	M			src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h
	M			src/USER-OMP/pair_lj_cut_omp.cpp
	M			src/USER-OMP/pair_lj_cut_omp.h
	M			src/USER-OMP/pair_lj_expand_omp.cpp
	M			src/USER-OMP/pair_lj_expand_omp.h
	M			src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
	M			src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h
	M			src/USER-OMP/pair_lj_gromacs_omp.cpp
	M			src/USER-OMP/pair_lj_gromacs_omp.h
	M			src/USER-OMP/pair_lj_sf_omp.cpp
	M			src/USER-OMP/pair_lj_sf_omp.h
	M			src/USER-OMP/pair_lj_smooth_omp.cpp
	M			src/USER-OMP/pair_lj_smooth_omp.h
	M			src/USER-OMP/pair_lubricate_omp.cpp
	M			src/USER-OMP/pair_lubricate_omp.h
	M			src/USER-OMP/pair_morse_omp.cpp
	M			src/USER-OMP/pair_morse_omp.h
	M			src/USER-OMP/pair_peri_lps_omp.cpp
	M			src/USER-OMP/pair_peri_lps_omp.h
	M			src/USER-OMP/pair_peri_pmb_omp.cpp
	M			src/USER-OMP/pair_peri_pmb_omp.h
	M			src/USER-OMP/pair_resquared_omp.cpp
	M			src/USER-OMP/pair_resquared_omp.h
	M			src/USER-OMP/pair_soft_omp.cpp
	M			src/USER-OMP/pair_soft_omp.h
	M			src/USER-OMP/pair_sw_omp.cpp
	M			src/USER-OMP/pair_sw_omp.h
	M			src/USER-OMP/pair_table_omp.cpp
	M			src/USER-OMP/pair_table_omp.h
	M			src/USER-OMP/pair_tersoff_omp.cpp
	M			src/USER-OMP/pair_tersoff_omp.h
	M			src/USER-OMP/pair_yukawa_colloid_omp.cpp
	M			src/USER-OMP/pair_yukawa_colloid_omp.h
	M			src/USER-OMP/pair_yukawa_omp.cpp
	M			src/USER-OMP/pair_yukawa_omp.h
	A			src/USER-OMP/thr_data.cpp
	A			src/USER-OMP/thr_data.h
	M			src/USER-OMP/thr_omp.cpp
	M			src/USER-OMP/thr_omp.h
	M			src/angle.cpp
	M			src/bond.cpp
	M			src/dihedral.cpp
	M			src/domain.cpp
	M			src/domain.h
	M			src/improper.cpp
	M			src/input.cpp
	M			src/integrate.cpp
	M			src/integrate.h
	P			src/main.cpp Copied to src/USER-OMP/fix_peri_neigh_omp.h
	M			src/min.cpp
	M			src/min.h
	M			src/neigh_derive.cpp
	A			src/neigh_derive_omp.cpp
	P			src/neigh_full.cpp Copied to src/neigh_full_omp.cpp
	P			src/neigh_full_omp.cpp Copied from src/neigh_full.cpp
	P			src/neigh_gran.cpp Copied to src/neigh_gran_omp.cpp
	P			src/neigh_gran_omp.cpp Copied from src/neigh_gran.cpp
	P			src/neigh_half_bin.cpp Copied to src/neigh_half_bin_omp.cpp
	P			src/neigh_half_bin_omp.cpp Copied from src/neigh_half_bin.cpp
	P			src/neigh_half_multi.cpp Copied to src/neigh_half_multi_omp.cpp
	P			src/neigh_half_multi_omp.cpp Copied from src/neigh_half_multi.cpp
	P			src/neigh_half_nsq.cpp Copied to src/neigh_half_nsq_omp.cpp
	P			src/neigh_half_nsq_omp.cpp Copied from src/neigh_half_nsq.cpp
	M			src/neigh_list.cpp
	M			src/neigh_request.cpp
	M			src/neigh_request.h
	P			src/neigh_respa.cpp Copied to src/neigh_respa_omp.cpp
	P			src/neigh_respa_omp.cpp Copied from src/neigh_respa.cpp
	M			src/neighbor.cpp
	M			src/neighbor.h
	A			src/neighbor_omp.h
	M			src/pair.cpp
	M			src/respa.cpp
	M			src/verlet.cpp