Merge pull request #533 from lammps/user-intel
b5300724bb8b
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Authored by sjplimp <sjplimp@sandia.gov> on Jun 20 2017, 15:44.

Description

Merge pull request #533 from lammps/user-intel

Updates for USER-INTEL package and NEB command flags/docs updates and issues

Details

Committed

GitHub <noreply@github.com>

Jun 20 2017, 15:44

Pushed

junge

Oct 19 2017, 09:53

Parents

rLAMMPS8c54fcd1b6c9: cleanup from aidan for fix reax/c/species and its KOKKOS version
rLAMMPSe129f18e6f19: Merge pull request #530 from akohlmey/no_static_sort_in_dump

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GitHub <noreply@github.com> committed rLAMMPSb5300724bb8b: Merge pull request #533 from lammps/user-intel (authored by sjplimp <sjplimp@sandia.gov>).Jun 20 2017, 15:44

Merged Changes

Commit	Author	Details	Committed
8c54fcd1b6c9	Axel Kohlmeyer	cleanup from aidan for fix reax/c/species and its KOKKOS version	Jun 19 2017
f5047ac3c7f9	Axel Kohlmeyer	augment fix shardlow check for ordering fixes to be KOKKOS compatible	Jun 19 2017
3c329d170791	Axel Kohlmeyer	massive whitespace cleanup in USER-INTEL	Jun 19 2017
b687d16177fe	Axel Kohlmeyer	insert C++ file format indicator comments	Jun 19 2017
9d3e34e4922c	Axel Kohlmeyer	add missing reference for lj/smooth/linear	Jun 19 2017
8988b692a392	Emile Maras	modified the documentation, first and last freeend can have different spring…	Jun 19 2017
c97415aefab7	Emile Maras	corrected the initial free end	Jun 19 2017
cd88b31450c3	Steve Plimpton	same PR, also has cosmetic changes to new fix neb options	Jun 17 2017
9b9f6d6fe2f4	Steve Plimpton	USER-INTEL upgrade from M Brown	Jun 17 2017

Changes (120)
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				Path
	M			doc/src/JPG/user_intel.png
	M			doc/src/Section_commands.txt
	M			doc/src/accelerate_intel.txt
	M			doc/src/fix_neb.txt
	M			doc/src/kspace_modify.txt
	M			doc/src/kspace_style.txt
	M			doc/src/pair_lj_long.txt
	M			doc/src/pair_lj_smooth_linear.txt
	M			examples/neb/README
	M			examples/neb/in.neb.hop1
	V			examples/neb/{in.neb.hop1.end ← in.neb.hop1freeend}
	V			examples/neb/{in.neb.hop1freeend → in.neb.hop1.end}
	M			examples/neb/in.neb.hop2
	V			examples/neb/{initial.hop1.end ← initial.hop1freeend}
	V			examples/neb/{initial.hop1freeend → initial.hop1.end}
	A			examples/neb/log.19June17.neb.hop1.end.g++.4
	A			examples/neb/log.19June17.neb.hop1.end.g++.8
	V			examples/neb/{log.19June17.neb.hop1.g++.4 ← log.5Oct16.neb.hop1.g++.4}
	V			examples/neb/{log.19June17.neb.hop1.g++.8 ← log.5Oct16.neb.hop1.g++.8}
	A			examples/neb/log.19June17.neb.hop2.g++.4
	A			examples/neb/log.19June17.neb.hop2.g++.8
	A			examples/neb/log.19June17.neb.sivac.g++.4
	A			examples/neb/log.19June17.neb.sivac.g++.8
	V			examples/neb/{log.5Oct16.neb.hop1.g++.4 → log.19June17.neb.hop1.g++.4}
	V			examples/neb/{log.5Oct16.neb.hop1.g++.8 → log.19June17.neb.hop1.g++.8}
	D			examples/neb/log.5Oct16.neb.hop2.g++.4
	D			examples/neb/log.5Oct16.neb.hop2.g++.8
	D			examples/neb/log.5Oct16.neb.sivac.g++.3
	D			examples/neb/log.5Oct16.neb.sivac.g++.6
	D			examples/neb/log.5Oct16.neb.sivac.g++.9
	M			src/KOKKOS/fix_reaxc_species_kokkos.cpp
	M			src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi
	M			src/MAKE/OPTIONS/Makefile.intel_knl_coprocessor
	M			src/MAKE/OPTIONS/Makefile.knl
	M			src/REPLICA/fix_neb.cpp
	M			src/REPLICA/fix_neb.h
	M			src/USER-DPD/fix_shardlow.cpp
	M			src/USER-INTEL/README
	M			src/USER-INTEL/TEST/README
	M			src/USER-INTEL/TEST/in.intel.eam
	M			src/USER-INTEL/TEST/in.intel.lc
	M			src/USER-INTEL/TEST/in.intel.lj
	M			src/USER-INTEL/TEST/in.intel.rhodo
	M			src/USER-INTEL/TEST/in.intel.sw
	M			src/USER-INTEL/TEST/in.intel.tersoff
	M			src/USER-INTEL/TEST/in.intel.water
	M			src/USER-INTEL/TEST/in.lc_generate_restart
	A			src/USER-INTEL/TEST/run_benchmarks.sh
	M			src/USER-INTEL/angle_charmm_intel.cpp
	M			src/USER-INTEL/angle_charmm_intel.h
	M			src/USER-INTEL/angle_harmonic_intel.cpp
	M			src/USER-INTEL/angle_harmonic_intel.h
	M			src/USER-INTEL/bond_fene_intel.cpp
	M			src/USER-INTEL/bond_fene_intel.h
	M			src/USER-INTEL/bond_harmonic_intel.cpp
	M			src/USER-INTEL/bond_harmonic_intel.h
	M			src/USER-INTEL/dihedral_charmm_intel.cpp
	M			src/USER-INTEL/dihedral_charmm_intel.h
	M			src/USER-INTEL/dihedral_harmonic_intel.cpp
	M			src/USER-INTEL/dihedral_harmonic_intel.h
	M			src/USER-INTEL/dihedral_opls_intel.cpp
	M			src/USER-INTEL/dihedral_opls_intel.h
	M			src/USER-INTEL/fix_intel.cpp
	M			src/USER-INTEL/fix_intel.h
	M			src/USER-INTEL/fix_nh_intel.cpp
	M			src/USER-INTEL/fix_nh_intel.h
	M			src/USER-INTEL/fix_nve_asphere_intel.cpp
	M			src/USER-INTEL/fix_nve_intel.cpp
	M			src/USER-INTEL/improper_cvff_intel.cpp
	M			src/USER-INTEL/improper_cvff_intel.h
	M			src/USER-INTEL/improper_harmonic_intel.cpp
	M			src/USER-INTEL/improper_harmonic_intel.h
	M			src/USER-INTEL/intel_buffers.cpp
	M			src/USER-INTEL/intel_buffers.h
	M			src/USER-INTEL/intel_intrinsics.h
	M			src/USER-INTEL/intel_preprocess.h
	M			src/USER-INTEL/intel_simd.h
	M			src/USER-INTEL/math_extra_intel.h
	M			src/USER-INTEL/nbin_intel.cpp
	M			src/USER-INTEL/npair_full_bin_intel.cpp
	M			src/USER-INTEL/npair_full_bin_intel.h
	D			src/USER-INTEL/npair_half_bin_newtoff_intel.cpp
	D			src/USER-INTEL/npair_half_bin_newtoff_intel.h
	M			src/USER-INTEL/npair_half_bin_newton_intel.cpp
	M			src/USER-INTEL/npair_half_bin_newton_intel.h
	M			src/USER-INTEL/npair_half_bin_newton_tri_intel.cpp
	M			src/USER-INTEL/npair_half_bin_newton_tri_intel.h
	M			src/USER-INTEL/npair_intel.cpp
	M			src/USER-INTEL/npair_intel.h
	M			src/USER-INTEL/pair_buck_coul_cut_intel.cpp
	M			src/USER-INTEL/pair_buck_coul_cut_intel.h
	M			src/USER-INTEL/pair_buck_coul_long_intel.cpp
	M			src/USER-INTEL/pair_buck_coul_long_intel.h
	M			src/USER-INTEL/pair_buck_intel.cpp
	M			src/USER-INTEL/pair_buck_intel.h
	M			src/USER-INTEL/pair_eam_intel.cpp
	M			src/USER-INTEL/pair_eam_intel.h
	M			src/USER-INTEL/pair_gayberne_intel.cpp
	M			src/USER-INTEL/pair_gayberne_intel.h
	M			src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp
	M			src/USER-INTEL/pair_lj_charmm_coul_long_intel.h
	M			src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp
	M			src/USER-INTEL/pair_lj_cut_coul_long_intel.h
	M			src/USER-INTEL/pair_lj_cut_intel.cpp
	M			src/USER-INTEL/pair_lj_cut_intel.h
	A			src/USER-INTEL/pair_lj_long_coul_long_intel.cpp
	A			src/USER-INTEL/pair_lj_long_coul_long_intel.h
	M			src/USER-INTEL/pair_sw_intel.cpp
	M			src/USER-INTEL/pair_sw_intel.h
	M			src/USER-INTEL/pair_tersoff_intel.cpp
	M			src/USER-INTEL/pair_tersoff_intel.h
	A			src/USER-INTEL/pppm_disp_intel.cpp
	A			src/USER-INTEL/pppm_disp_intel.h
	M			src/USER-INTEL/pppm_intel.cpp
	M			src/USER-INTEL/pppm_intel.h
	M			src/USER-INTEL/verlet_lrt_intel.cpp
	M			src/USER-INTEL/verlet_lrt_intel.h
	M			src/USER-REAXC/fix_reaxc_species.cpp
	M			src/USER-REAXC/fix_reaxc_species.h
	M			src/atom.cpp