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Diffusion lammps 31dc359e82f6

Merge branch 'master' into openmp-step6
31dc359e82f6
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Authored by Axel Kohlmeyer <akohlmey@gmail.com> on Oct 21 2011, 21:50.

Description

Merge branch 'master' into openmp-step6

Resolved Conflicts:
src/GPU/pppm_gpu.cpp
src/KSPACE/ewald.h
src/MANYBODY/pair_airebo.cpp
src/MANYBODY/pair_comb.cpp
src/MANYBODY/pair_comb.h
src/MANYBODY/pair_tersoff.h
src/MOLECULE/pair_hbond_dreiding_lj.cpp
src/MOLECULE/pair_hbond_dreiding_morse.cpp
src/USER-CUDA/pppm_cuda.cpp
src/USER-OMP/Install.sh
src/USER-OMP/Package.sh
src/USER-OMP/dihedral_charmm_omp.cpp
src/USER-OMP/dihedral_charmm_omp.h
src/USER-OMP/dihedral_class2_omp.cpp
src/USER-OMP/dihedral_class2_omp.h
src/USER-OMP/dihedral_cosine_shift_exp_omp.cpp
src/USER-OMP/dihedral_cosine_shift_exp_omp.h
src/USER-OMP/dihedral_harmonic_omp.cpp
src/USER-OMP/dihedral_harmonic_omp.h
src/USER-OMP/dihedral_helix_omp.cpp
src/USER-OMP/dihedral_helix_omp.h
src/USER-OMP/dihedral_multi_harmonic_omp.cpp
src/USER-OMP/dihedral_multi_harmonic_omp.h
src/USER-OMP/dihedral_opls_omp.cpp
src/USER-OMP/dihedral_opls_omp.h
src/USER-OMP/fix_nve_sphere_omp.cpp
src/USER-OMP/pair_adp_omp.cpp
src/USER-OMP/pair_adp_omp.h
src/USER-OMP/pair_born_coul_long_omp.cpp
src/USER-OMP/pair_born_coul_long_omp.h
src/USER-OMP/pair_born_omp.cpp
src/USER-OMP/pair_born_omp.h
src/USER-OMP/pair_buck_coul_cut_omp.cpp
src/USER-OMP/pair_buck_coul_cut_omp.h
src/USER-OMP/pair_buck_coul_long_omp.cpp
src/USER-OMP/pair_buck_coul_long_omp.h
src/USER-OMP/pair_buck_coul_omp.cpp
src/USER-OMP/pair_buck_coul_omp.h
src/USER-OMP/pair_buck_omp.cpp
src/USER-OMP/pair_buck_omp.h
src/USER-OMP/pair_cdeam_omp.cpp
src/USER-OMP/pair_cdeam_omp.h
src/USER-OMP/pair_colloid_omp.cpp
src/USER-OMP/pair_colloid_omp.h
src/USER-OMP/pair_coul_cut_omp.cpp
src/USER-OMP/pair_coul_cut_omp.h
src/USER-OMP/pair_coul_debye_omp.cpp
src/USER-OMP/pair_coul_debye_omp.h
src/USER-OMP/pair_coul_long_omp.cpp
src/USER-OMP/pair_coul_long_omp.h
src/USER-OMP/pair_dipole_cut_omp.cpp
src/USER-OMP/pair_dipole_cut_omp.h
src/USER-OMP/pair_dipole_sf_omp.cpp
src/USER-OMP/pair_dipole_sf_omp.h
src/USER-OMP/pair_dpd_omp.cpp
src/USER-OMP/pair_dpd_omp.h
src/USER-OMP/pair_dpd_tstat_omp.cpp
src/USER-OMP/pair_dpd_tstat_omp.h
src/USER-OMP/pair_eam_omp.cpp
src/USER-OMP/pair_eam_omp.h
src/USER-OMP/pair_edip_omp.cpp
src/USER-OMP/pair_edip_omp.h
src/USER-OMP/pair_eim_omp.cpp
src/USER-OMP/pair_eim_omp.h
src/USER-OMP/pair_gauss_omp.cpp
src/USER-OMP/pair_gauss_omp.h
src/USER-OMP/pair_gayberne_omp.cpp
src/USER-OMP/pair_gayberne_omp.h
src/USER-OMP/pair_gran_hertz_history_omp.cpp
src/USER-OMP/pair_gran_hertz_history_omp.h
src/USER-OMP/pair_gran_hooke_history_omp.cpp
src/USER-OMP/pair_gran_hooke_history_omp.h
src/USER-OMP/pair_gran_hooke_omp.cpp
src/USER-OMP/pair_gran_hooke_omp.h
src/USER-OMP/pair_hbond_dreiding_lj_omp.cpp
src/USER-OMP/pair_hbond_dreiding_lj_omp.h
src/USER-OMP/pair_hbond_dreiding_morse_omp.cpp
src/USER-OMP/pair_hbond_dreiding_morse_omp.h
src/USER-OMP/pair_lj96_cut_omp.cpp
src/USER-OMP/pair_lj96_cut_omp.h
src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.cpp
src/USER-OMP/pair_lj_charmm_coul_charmm_implicit_omp.h
src/USER-OMP/pair_lj_charmm_coul_charmm_omp.cpp
src/USER-OMP/pair_lj_charmm_coul_charmm_omp.h
src/USER-OMP/pair_lj_charmm_coul_long_omp.cpp
src/USER-OMP/pair_lj_charmm_coul_long_omp.h
src/USER-OMP/pair_lj_class2_coul_cut_omp.cpp
src/USER-OMP/pair_lj_class2_coul_cut_omp.h
src/USER-OMP/pair_lj_class2_coul_long_omp.cpp
src/USER-OMP/pair_lj_class2_coul_long_omp.h
src/USER-OMP/pair_lj_class2_omp.cpp
src/USER-OMP/pair_lj_class2_omp.h
src/USER-OMP/pair_lj_coul_omp.cpp
src/USER-OMP/pair_lj_coul_omp.h
src/USER-OMP/pair_lj_cubic_omp.cpp
src/USER-OMP/pair_lj_cubic_omp.h
src/USER-OMP/pair_lj_cut_coul_cut_omp.cpp
src/USER-OMP/pair_lj_cut_coul_cut_omp.h
src/USER-OMP/pair_lj_cut_coul_debye_omp.cpp
src/USER-OMP/pair_lj_cut_coul_debye_omp.h
src/USER-OMP/pair_lj_cut_coul_long_omp.cpp
src/USER-OMP/pair_lj_cut_coul_long_omp.h
src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.cpp
src/USER-OMP/pair_lj_cut_coul_long_tip4p_omp.h
src/USER-OMP/pair_lj_cut_omp.cpp
src/USER-OMP/pair_lj_expand_omp.cpp
src/USER-OMP/pair_lj_expand_omp.h
src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp
src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.h
src/USER-OMP/pair_lj_gromacs_omp.cpp
src/USER-OMP/pair_lj_gromacs_omp.h
src/USER-OMP/pair_lj_sf_omp.cpp
src/USER-OMP/pair_lj_sf_omp.h
src/USER-OMP/pair_lj_smooth_omp.cpp
src/USER-OMP/pair_lj_smooth_omp.h
src/USER-OMP/pair_lubricate_omp.cpp
src/USER-OMP/pair_lubricate_omp.h
src/USER-OMP/pair_morse_omp.cpp
src/USER-OMP/pair_morse_omp.h
src/USER-OMP/pair_peri_lps_omp.cpp
src/USER-OMP/pair_peri_lps_omp.h
src/USER-OMP/pair_peri_pmb_omp.cpp
src/USER-OMP/pair_peri_pmb_omp.h
src/USER-OMP/pair_resquared_omp.cpp
src/USER-OMP/pair_resquared_omp.h
src/USER-OMP/pair_soft_omp.cpp
src/USER-OMP/pair_soft_omp.h
src/USER-OMP/pair_sw_omp.cpp
src/USER-OMP/pair_sw_omp.h
src/USER-OMP/pair_table_omp.cpp
src/USER-OMP/pair_table_omp.h
src/USER-OMP/pair_tersoff_omp.cpp
src/USER-OMP/pair_tersoff_omp.h
src/USER-OMP/pair_yukawa_colloid_omp.cpp
src/USER-OMP/pair_yukawa_colloid_omp.h
src/USER-OMP/pair_yukawa_omp.cpp
src/USER-OMP/pair_yukawa_omp.h
src/USER-OMP/thr_omp.cpp
src/USER-OMP/thr_omp.h
src/read_data.cpp

Details

Committed
Axel Kohlmeyer <akohlmey@gmail.com>Oct 21 2011, 21:50
Pushed
jungeOct 6 2016, 16:49
Parents
rLAMMPSb1492a195bb8: fix race conditions and omissions in ewald/omp
rLAMMPSfa80bceb30d0: git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7163 f3b2605a-c512-4ea7…
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Axel Kohlmeyer <akohlmey@gmail.com> committed rLAMMPS31dc359e82f6: Merge branch 'master' into openmp-step6 (authored by Axel Kohlmeyer <akohlmey@gmail.com>).Oct 21 2011, 21:50

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Changes (200)
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This commit is very large. Load each file individually.
Path
Mdoc/Section_commands.html
Mdoc/Section_commands.txt
Mdoc/Section_intro.html
Mdoc/Section_intro.txt
Mdoc/Section_modify.html
Mdoc/Section_modify.txt
Mdoc/Section_start.html
Mdoc/Section_start.txt
Mdoc/atom_style.html
Mdoc/atom_style.txt
Mdoc/compute_erotate_asphere.html
Mdoc/compute_erotate_asphere.txt
Mdoc/compute_property_atom.html
Mdoc/compute_property_atom.txt
Mdoc/fix.html
Mdoc/fix.txt
Adoc/fix_nve_line.html
Adoc/fix_nve_line.txt
Adoc/fix_nve_tri.html
Adoc/fix_nve_tri.txt
Mdoc/fix_rigid.html
Mdoc/fix_rigid.txt
Mdoc/fix_srd.html
Mdoc/fix_srd.txt
Mdoc/pair_coeff.html
Mdoc/pair_coeff.txt
Adoc/pair_line_lj.html
Adoc/pair_line_lj.txt
Mdoc/pair_style.html
Mdoc/pair_style.txt
Mdoc/pair_sw.html
Mdoc/pair_sw.txt
Mdoc/pair_tersoff.html
Mdoc/pair_tersoff.txt
Adoc/pair_tri_lj.html
Adoc/pair_tri_lj.txt
Mdoc/read_data.html
Mdoc/read_data.txt
Mdoc/set.html
Mdoc/set.txt
Mexamples/README
A(dir)examples/dreiding/
Aexamples/dreiding/README
Aexamples/dreiding/ch3oh.box.dreiding.bgf
Aexamples/dreiding/ch3oh.box.dreiding.cerius2.eng.dat
Aexamples/dreiding/data.dreiding
Aexamples/dreiding/in.dreiding
Aexamples/dreiding/log.dreiding.11Oct11.linux.1
Aexamples/dreiding/log.dreiding.11Oct11.linux.4
Mlib/cuda/Makefile.defaults
Mlib/cuda/Makefile.lammps
V{lib/cuda ← src/USER-CUDA}/cuda_common.h
Mlib/cuda/cuda_pair.cu
Mlib/cuda/cuda_pair_kernel.cu
Mlib/cuda/cuda_pair_virial_kernel_nc.cu
Mlib/cuda/cuda_precision.h
Mlib/cuda/cuda_shared.h
Mlib/cuda/neighbor.cu
Mlib/cuda/neighbor_kernel.cu
Alib/cuda/pair_manybody_const.h
Alib/cuda/pair_sw_cuda.cu
Alib/cuda/pair_sw_cuda_cu.h
Alib/cuda/pair_sw_cuda_kernel_nc.cu
Alib/cuda/pair_tersoff_cuda.cu
Alib/cuda/pair_tersoff_cuda_cu.h
Alib/cuda/pair_tersoff_cuda_kernel_nc.cu
Mlib/gpu/Makefile.linux
Msrc/ASPHERE/Install.sh
Msrc/ASPHERE/compute_erotate_asphere.cpp
Psrc/ASPHERE/compute_erotate_asphere.h
Copied to multiple locations:
src/ASPHERE/fix_nve_line.h
src/ASPHERE/fix_nve_tri.h
Asrc/ASPHERE/fix_nve_line.cpp
Psrc/ASPHERE/fix_nve_line.h
Copied from src/ASPHERE/compute_erotate_asphere.h
Asrc/ASPHERE/fix_nve_tri.cpp
Psrc/ASPHERE/fix_nve_tri.h
Copied from src/ASPHERE/compute_erotate_asphere.h
Asrc/ASPHERE/pair_line_lj.cpp
Psrc/ASPHERE/pair_line_lj.h
Copied from src/pair_soft.h
Asrc/ASPHERE/pair_tri_lj.cpp
Psrc/ASPHERE/pair_tri_lj.h
Copied from src/pair_soft.h
Msrc/CLASS2/angle_class2.cpp
Msrc/CLASS2/dihedral_class2.cpp
Msrc/CLASS2/dihedral_class2.h
Msrc/CLASS2/improper_class2.cpp
Msrc/CLASS2/improper_class2.h
Msrc/CLASS2/pair_lj_class2.cpp
Msrc/CLASS2/pair_lj_class2_coul_cut.cpp
Msrc/CLASS2/pair_lj_class2_coul_long.cpp
Msrc/COLLOID/pair_lubricate.cpp
Msrc/GPU/pppm_gpu.cpp
Msrc/GRANULAR/fix_pour.cpp
Msrc/GRANULAR/fix_pour.h
Msrc/GRANULAR/fix_wall_gran.cpp
Msrc/KSPACE/ewald.cpp
Msrc/KSPACE/ewald.h
Msrc/KSPACE/pair_born_coul_long.cpp
Msrc/KSPACE/pair_buck_coul_long.cpp
Msrc/KSPACE/pair_lj_cut_coul_long.cpp
Msrc/MAKE/Makefile.g++
Msrc/MAKE/Makefile.serial
Msrc/MANYBODY/pair_airebo.cpp
Msrc/MANYBODY/pair_comb.cpp
Msrc/MANYBODY/pair_comb.h
Msrc/MANYBODY/pair_tersoff.h
Msrc/MC/fix_gcmc.cpp
Msrc/MOLECULE/angle_charmm.cpp
Msrc/MOLECULE/angle_cosine.cpp
Msrc/MOLECULE/angle_cosine_periodic.cpp
Msrc/MOLECULE/angle_cosine_squared.cpp
Msrc/MOLECULE/angle_harmonic.cpp
Msrc/MOLECULE/angle_table.cpp
Msrc/MOLECULE/dihedral_charmm.cpp
Msrc/MOLECULE/dihedral_helix.cpp
Msrc/MOLECULE/improper_harmonic.cpp
Msrc/MOLECULE/improper_umbrella.cpp
Msrc/MOLECULE/pair_hbond_dreiding_lj.cpp
Msrc/MOLECULE/pair_hbond_dreiding_lj.h
Msrc/MOLECULE/pair_hbond_dreiding_morse.cpp
Msrc/SHOCK/fix_append_atoms.cpp
Msrc/SRD/fix_srd.cpp
Msrc/SRD/fix_srd.h
Msrc/USER-CG-CMM/angle_cg_cmm.cpp
Msrc/USER-CG-CMM/pair_cmm_common.cpp
Msrc/USER-CUDA/Install.sh
Msrc/USER-CUDA/comm_cuda.cpp
Msrc/USER-CUDA/cuda.cpp
V{src/USER-CUDA → lib/cuda}/cuda_common.h
Dsrc/USER-CUDA/cuda_precision.h
Dsrc/USER-CUDA/cuda_shared.h
Msrc/USER-CUDA/fix_gravity_cuda.cpp
Msrc/USER-CUDA/fix_shake_cuda.cpp
Msrc/USER-CUDA/fix_shake_cuda.h
Msrc/USER-CUDA/neighbor_cuda.cpp
Asrc/USER-CUDA/pair_sw_cuda.cpp
Asrc/USER-CUDA/pair_sw_cuda.h
Asrc/USER-CUDA/pair_tersoff_cuda.cpp
Asrc/USER-CUDA/pair_tersoff_cuda.h
Asrc/USER-CUDA/pair_tersoff_zbl_cuda.cpp
Asrc/USER-CUDA/pair_tersoff_zbl_cuda.h
Msrc/USER-CUDA/pppm_cuda.cpp
Msrc/USER-CUDA/verlet_cuda.cpp
Msrc/USER-EFF/atom_vec_electron.h
Msrc/USER-OMP/Install.sh
Msrc/USER-OMP/Package.sh
Asrc/USER-OMP/README
Msrc/USER-OMP/dihedral_helix_omp.cpp
Msrc/USER-OMP/dihedral_multi_harmonic_omp.cpp
Msrc/angle.cpp
Msrc/angle.h
Msrc/atom.cpp
Msrc/atom.h
Psrc/atom_vec_ellipsoid.cpp
Copied to multiple locations:
src/atom_vec_line.cpp
src/atom_vec_tri.cpp
Psrc/atom_vec_ellipsoid.h
Copied to multiple locations:
src/atom_vec_line.h
src/atom_vec_tri.h
Psrc/atom_vec_line.cpp
Copied from src/atom_vec_ellipsoid.cpp
Psrc/atom_vec_line.h
Copied from src/atom_vec_ellipsoid.h
Msrc/atom_vec_sphere.cpp
Msrc/atom_vec_sphere.h
Psrc/atom_vec_tri.cpp
Copied from src/atom_vec_ellipsoid.cpp
Psrc/atom_vec_tri.h
Copied from src/atom_vec_ellipsoid.h
Msrc/compute_angle_local.cpp
Msrc/compute_dihedral_local.cpp
Msrc/compute_improper_local.cpp
Msrc/compute_property_atom.cpp
Msrc/compute_property_atom.h
Msrc/compute_rdf.cpp
Msrc/dihedral.cpp
Msrc/dihedral.h
Msrc/dump_image.cpp
Msrc/dump_image.h
Msrc/fix_adapt.cpp
Msrc/fix_addforce.cpp
Msrc/fix_deform.cpp
Msrc/fix_gravity.cpp
Msrc/fix_move.cpp
Msrc/fix_orient_fcc.cpp
Msrc/fix_orient_fcc.h
Msrc/fix_restrain.cpp
Msrc/fix_rigid.cpp
Msrc/fix_rigid.h
Msrc/fix_shake.cpp
Msrc/fix_shake.h
Msrc/improper.cpp
Msrc/improper.h
Msrc/input.cpp
Msrc/lammps.cpp
Msrc/pair_born.cpp
Msrc/pair_buck.cpp
Msrc/pair_buck_coul_cut.cpp
Msrc/pair_hybrid.cpp
Msrc/pair_lj96_cut.cpp
Msrc/pair_lj_cut.cpp
Msrc/pair_lj_cut_coul_cut.cpp
Msrc/pair_lj_expand.cpp
Msrc/pair_soft.cpp
Psrc/pair_soft.h
Copied to multiple locations:
src/ASPHERE/pair_line_lj.h
src/ASPHERE/pair_tri_lj.h
Msrc/read_data.cpp
Msrc/read_data.h
Msrc/set.cpp
Msrc/set.h
Msrc/thermo.cpp
Msrc/version.h
Mtools/amber2lmp/amber2lammps.py

rLAMMPS31dc359e82f6

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examples/README

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examples/dreiding/README

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examples/dreiding/ch3oh.box.dreiding.bgf

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examples/dreiding/ch3oh.box.dreiding.cerius2.eng.dat

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examples/dreiding/data.dreiding

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examples/dreiding/log.dreiding.11Oct11.linux.1

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lib/cuda/Makefile.lammps

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lib/cuda/cuda_pair.cu

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lib/cuda/cuda_pair_kernel.cu

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lib/cuda/cuda_pair_virial_kernel_nc.cu

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lib/cuda/neighbor.cu

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lib/cuda/neighbor_kernel.cu

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lib/cuda/pair_manybody_const.h

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lib/cuda/pair_sw_cuda.cu

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lib/cuda/pair_sw_cuda_cu.h

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lib/cuda/pair_sw_cuda_kernel_nc.cu

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lib/cuda/pair_tersoff_cuda.cu

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lib/cuda/pair_tersoff_cuda_cu.h

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lib/cuda/pair_tersoff_cuda_kernel_nc.cu

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lib/gpu/Makefile.linux

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src/ASPHERE/Install.sh

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src/ASPHERE/compute_erotate_asphere.cpp

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src/ASPHERE/compute_erotate_asphere.h

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src/ASPHERE/fix_nve_line.cpp

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src/ASPHERE/fix_nve_line.h

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src/ASPHERE/fix_nve_tri.cpp

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src/ASPHERE/fix_nve_tri.h

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src/ASPHERE/pair_line_lj.cpp

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src/CLASS2/angle_class2.cpp

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src/CLASS2/pair_lj_class2_coul_long.cpp

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src/COLLOID/pair_lubricate.cpp

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src/GPU/pppm_gpu.cpp

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src/GRANULAR/fix_pour.cpp

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src/GRANULAR/fix_pour.h

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src/GRANULAR/fix_wall_gran.cpp

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src/KSPACE/ewald.cpp

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src/KSPACE/ewald.h

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src/KSPACE/pair_born_coul_long.cpp

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src/KSPACE/pair_buck_coul_long.cpp

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src/KSPACE/pair_lj_cut_coul_long.cpp

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src/MAKE/Makefile.g++

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src/MAKE/Makefile.serial

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src/MANYBODY/pair_airebo.cpp

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src/MANYBODY/pair_comb.cpp

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src/MANYBODY/pair_comb.h

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src/MANYBODY/pair_tersoff.h

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src/MC/fix_gcmc.cpp

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src/MOLECULE/angle_charmm.cpp

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src/MOLECULE/angle_cosine.cpp

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src/MOLECULE/angle_cosine_periodic.cpp

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src/MOLECULE/angle_cosine_squared.cpp

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src/MOLECULE/angle_harmonic.cpp

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src/MOLECULE/angle_table.cpp

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src/MOLECULE/dihedral_helix.cpp

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src/MOLECULE/improper_harmonic.cpp

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src/MOLECULE/improper_umbrella.cpp

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src/MOLECULE/pair_hbond_dreiding_lj.cpp

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src/MOLECULE/pair_hbond_dreiding_lj.h

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src/MOLECULE/pair_hbond_dreiding_morse.cpp

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src/SHOCK/fix_append_atoms.cpp

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src/SRD/fix_srd.cpp

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src/SRD/fix_srd.h

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src/USER-CG-CMM/angle_cg_cmm.cpp

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src/USER-CG-CMM/pair_cmm_common.cpp

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src/USER-CUDA/Install.sh

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src/USER-CUDA/comm_cuda.cpp

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src/USER-CUDA/cuda.cpp

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src/USER-CUDA/cuda_common.h

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src/USER-CUDA/cuda_shared.h

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src/USER-CUDA/fix_shake_cuda.h

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src/USER-CUDA/neighbor_cuda.cpp

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src/USER-CUDA/pair_sw_cuda.cpp

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src/USER-CUDA/pair_tersoff_cuda.h

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src/USER-CUDA/pair_tersoff_zbl_cuda.cpp

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src/USER-CUDA/pair_tersoff_zbl_cuda.h

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src/USER-CUDA/pppm_cuda.cpp

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src/USER-CUDA/verlet_cuda.cpp

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src/USER-EFF/atom_vec_electron.h

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src/USER-OMP/Install.sh

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src/USER-OMP/README

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src/USER-OMP/dihedral_helix_omp.cpp

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src/USER-OMP/dihedral_multi_harmonic_omp.cpp

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src/atom_vec_ellipsoid.cpp

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src/atom_vec_ellipsoid.h

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src/atom_vec_line.cpp

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src/atom_vec_line.h

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src/atom_vec_sphere.h

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src/compute_angle_local.cpp

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src/compute_property_atom.h

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src/dihedral.cpp

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src/fix_shake.h

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src/improper.cpp

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src/pair_born.cpp

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src/pair_buck.cpp

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src/pair_buck_coul_cut.cpp

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src/pair_hybrid.cpp

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src/pair_lj_cut.cpp

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src/pair_lj_expand.cpp

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src/pair_soft.cpp

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src/pair_soft.h

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src/read_data.cpp

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src/thermo.cpp

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tools/amber2lmp/amber2lammps.py

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